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Australian Bureau of Statistics
Celebrating the International Year of Statistics 2013
ABS Home > Statistics > By Release Date
1304.5 - Stats Talk WA, Mar 2010
Previous ISSUE Released at 11:30 AM (CANBERRA TIME) 30/03/2010
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Statistical News
Developments In ABS Statistics
Australians Are Using Less Water But More Energy
Australia’s Environment: Issues and Trends presents a snapshot of environmental issues affecting Australia. The 2010 edition also includes a feature article on the issue of climate change, and what it means for Australia.
This edition highlights that water use by agriculture has fallen by almost half in two years, with the biggest reductions occurring in New South Wales and Victoria, while the proportion of households using water saving devices has doubled between 1994 and 2007.
While water consumption fell, energy use rose. Australia’s heavy reliance on fossil fuels, especially for power generation, has seen greenhouse gas emissions in the energy sector rise by almost one-half since 1990, however emissions per head of population fell by 12% over the same period.
The Northern Territory and Western Australia lead other states in solar hot water use (54% and 21%, respectively), but overall, less than 10% of Australian homes were using solar hot water in 2008.
Australians are also living in larger homes with fewer people; this is increasing greenhouse emissions from the electricity and gas used to build and run them.
Further details can be found in Australia’s Environment: Issues and Trends January 2010 (cat. no. 4613.0).
Record Numbers Enter And Leave Australia
The total number of international arrivals and departures reached a record high last year.
There were 12.4 million overseas arrivals and 12.3 million departures in 2009, making a record of 24.7 million international movements across Australia’s borders. This is an increase in overseas movements of nearly 60% since 1999.
In 2009, short-term movements accounted for 96% of the total 24.7 million movements. Short-term movements are travellers who have an intended stay in, or absence from, Australia of less than one year.
Short-term visitors arriving in Australia remained steady at 5.6 million. New Zealand, the UK, and the USA were the three top source countries, accounting for 40% of all short-term visitor arrivals.
For more information see Overseas Arrivals and Departures, Australia, December 2009 (cat. no. 3401.0).
Australian Social Trends
The ABS released the latest edition of Australian Social Trends (cat. no. 4102.0) on 16 March 2010. The publication draws together a wide range of statistics from the ABS and other official sources to provide a picture of Australian society and how it is changing over time.
Increasing education participation and improving transition to work outcomes for young Australians are key objectives of the Council of Australian Governments 2009 National Partnership Agreement on Youth Attainment. This looks at the levels of engagement of young people in study and work including the transitions of recent school leavers.
In Western Australia, around 18% of young people aged 15-24 years were not fully engaged (in either study or work). This was just under the national average of 19%.
In the justice area, the imprisonment rate has increased steadily over the last decade. Australian Social Trends looks at prisoners who have been released from prison and then reimprisoned within 10 years of their release.
Within 10 years of release, 38% of prisoners in Western Australia were reimprisoned, compared with the national average of 39%.
© Commonwealth of Australia 2013
Unless otherwise noted, content on this website is licensed under a Creative Commons Attribution 2.5 Australia Licence together with any terms, conditions and exclusions as set out in the website Copyright notice. For permission to do anything beyond the scope of this licence and copyright terms contact us.
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Australian Bureau of Statistics
Celebrating the International Year of Statistics 2013
ABS Home > Statistics > By Release Date
8731.0 - Building Approvals, Australia, Nov 2004
Previous ISSUE Released at 11:30 AM (CANBERRA TIME) 07/01/2005
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ABOUT THIS RELEASE
Provides the number and value of dwelling units approved by sector (public/private) and by state, number and value of new other residential dwelling units approved by type of building, and the number and value of non-residential building jobs approved by type of building (i.e. by function such as 'retail and wholesale trade', 'offices') and value ranges. State data includes the number of private sector houses approved; number and value of new other residential dwellings by type of building such as flats, units or apartments in a building of one or two storeys; number and value of non-residential building jobs by type of building and sector; and for Capital City Statistical Divisions, the total number of dwelling units approved broken down by Houses, Other Dwellings and Total Dwelling Units. Seasonally adjusted and trend estimates by state are included for the number of dwelling units and value of building approved. The quarterly value of building approved is shown in chain volume measure terms.
© Commonwealth of Australia 2013
Unless otherwise noted, content on this website is licensed under a Creative Commons Attribution 2.5 Australia Licence together with any terms, conditions and exclusions as set out in the website Copyright notice. For permission to do anything beyond the scope of this licence and copyright terms contact us.
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Australian Bureau of Statistics
Celebrating the International Year of Statistics 2013
ABS Home > Statistics > By Release Date
1376.0 - Local Government and ABS (Newsletter), Jun 2004
Previous ISSUE Released at 11:30 AM (CANBERRA TIME) 07/07/2004
© Commonwealth of Australia 2013
Unless otherwise noted, content on this website is licensed under a Creative Commons Attribution 2.5 Australia Licence together with any terms, conditions and exclusions as set out in the website Copyright notice. For permission to do anything beyond the scope of this licence and copyright terms contact us.
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Research article
Stages of development and injury: An epidemiological survey of young children presenting to an emergency department
Kirsty MacInnes and David H Stone*
Author Affiliations
Faculty of Medicine, University of Glasgow, Glasgow, UK
For all author emails, please log on.
BMC Public Health 2008, 8:120 doi:10.1186/1471-2458-8-120
The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2458/8/120
Received:1 February 2008
Accepted:14 April 2008
Published:14 April 2008
© 2008 MacInnes and Stone; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract
Background
The aim of our study was to use a local (Glasgow, west of Scotland) version of a Canadian injury surveillance programme (CHIRPP) to investigate the relationship between the developmental stage of young (pre-school) children, using age as a proxy, and the occurrence (incidence, nature, mechanism and location) of injuries presenting to a Scottish hospital emergency department, in an attempt to replicate the findings of a recent study in Kingston, Canada.
Methods
We used the Glasgow CHIRPP data to perform two types of analyses. First, we calculated injury rates for that part of the hospital catchment area for which reasonably accurate population denominators were available. Second, we examined detailed injury patterns, in terms of the circumstances, mechanisms, location and types of injury. We compared our findings with those of the Kingston researchers.
Results
A total of 17,793 injury records for children aged up to 7 years were identified over the period 1997–99. For 1997–2001, 6,188 were used to calculate rates in the west of the city only. Average annual age specific rates per 1000 children were highest in both males and females aged 12–35 months. Apart from the higher rates in Glasgow, the pattern of injuries, in terms of breakdown factors, mechanism, location, context, and nature of injury, were similar in Glasgow and Kingston.
Conclusion
We replicated in Glasgow, UK, the findings of a Canadian study demonstrating a correlation between the pattern of childhood injuries and developmental stage. Future research should take account of the need to enhance statistical power and explore the interaction between age and potential confounding variables such as socio-economic deprivation. Our findings highlight the importance of designing injury prevention interventions that are appropriate for specific stages of development in children.
Background
The close relationship between the stage of child development and the risk of injury is well recognised [1]. With each new stage of physical, cognitive and social development, new injury hazards emerge. Epidemiologically, this changing level of risk is reflected by the varying pattern of causes of injury across the age groups.
Although several formal health programmes aim to prevent injury in the early years, few population-based studies investigating the changing pattern of injury by developmental stage have been performed. By looking at patient demographics and details on the nature of injuries within small age groupings representative of developmental stage, it may be possible to identify population subgroups that could be at greater risk for injury. These insights are important for planning preventive strategies. One study carried out in Canada using the Kingston CHIRPP (Canadian Hospitals Injury Reporting and Prevention Programme) set out to address this gap in the literature [2]. They described changing mechanisms of injury according to developmental stage and used these findings to identify preventive priorities.
The aim of our study was to use a local version of CHIRPP [3] to investigate the relationship between the developmental stage of young (pre-school) children, using age as a proxy, and the occurrence (incidence, nature, mechanism and location) of injury, in an attempt to replicate the Kingston study and compare our findings with those of the Canadian researchers.
Methods
Glasgow CHIRPP
CHIRPP ran in the Royal Hospital for Sick Children (Yorkhill), Glasgow, from the mid-1990s to 2006. It was designed to capture information on all injuries presenting to the emergency department (ED) in order to generate data to assist injury prevention initiatives. A CHIRPP form was supposed to be completed for every injured child presenting at the ED. The first part was completed by the accompanying adult (or older child) and contained information on where the child was, what he/she was doing and what went wrong to cause the injury. The second part was completed by a clinician who provided details on the nature of the injury, the body parts involved and any treatment received. Once the CHIRPP form was completed the data were coded, entered and stored on a computer.
Analyses of injury rates and patterns
We used the CHIRPP data to perform two types of analyses. First, we calculated injury rates for that part of the hospital catchment area for which reasonably accurate population denominators were available. Second, we examined detailed injury patterns, in terms of the circumstances, mechanisms, location and types of injury. Computerised data analysis was performed using SPSS v. 14 and Microsoft Excel 2007.
To calculate injury rates, we analysed the data for a period of five complete calendar years (1997 – 2001). In common with many other hospitals in Scotland, there was no rigidly enforced boundary for the Yorkhill catchment area. Cases from the west of Glasgow only were used in order to establish a clear denominator as it was assumed that most children injured in the west of the city would present to the Yorkhill ED, since they lived closest to the hospital. We adopted a denominator-based approach to the analysis as a previous study using the Glasgow CHIRPP showed that this method generated more reliable findings than a frequency based analysis [4].
Overall age and sex specific rates (per 1000 population) of injury and associated 95% confidence intervals were calculated for each of the five years of the study period. Ages were then re-coded allowing the data to be analysed in the four specified age categories. These were 0–11, 12–35, 36–59 and 60–83 months – the same categories used by the Kingston study [2] permitting comparison of the two sets of findings. The population at risk was considered to be all children under the age of seven years living in a west Glasgow postcode sector. Denominators were derived from 2001 census data that gave an estimated number of children living in each postcode sector in one-year age groupings.
To investigate injury patterns, we analysed the data for a period of three complete years (1997 – 1999). Later years were excluded from this part of the analysis as the CHIRPP collection forms were modified in 2000 to include tick boxes with the result that much of the detail surrounding the injury event was lost. All postcode sectors were included to increase the number of injury events available for analysis. The CHIRPP categories included "breakdown", "mechanism", "context" and "location". The categories describing the consequences of injury include "severest injury", "most severely injured body part" and "disposition". Multiple response tables and frequencies were formulated using SPSS to characterise injury patterns within and across age groups.
Results
Injury rates by age and sex categories
A total of 6,188 injury records of children under seven years, living in West Glasgow postcode sectors, were identified over the five-year study period. An average of 1,238 attended the Yorkhill ED each year, giving an average injury rate of 144/1000/year (95% CI 115 – 180). Average annual age specific rates per 1000 children were highest in both males and females aged 12–35 months (Table 1). Apart from the higher rates in Glasgow, the pattern followed a similar trend to that found in the Kingston study (Figure 1). Boys appeared at higher risk than girls in every age group though this was not statistically significant as the 95% confidence intervals consistently overlapped.
Table 1. Trends in injury presentations to Yorkhill ED by age category (rates per 1000 population, calculated as an annual average over a 5 year period 1997–2001). CHIRPP data from west Glasgow postcode sectors only.
Figure 1. Trends in injury presentations to Yorkhill and Kingston by age. (Rates per 1000 population, calculated as an annual average over a 5 year period 1997–2001). CHIRPP data from west Glasgow postcode sectors only.
Pattern of Injury Analysis
We identified, through CHIRPP, a total of 17,793 children aged up to seven years, living in all Glasgow postcode sectors, who attended the emergency department of the hospital with an injury or ingestion over the study period (1997–1999).
"Breakdown" and "mechanism" factors
The details of what went wrong ("breakdown") to cause the injury and what actually inflicted the injury ("mechanism") can be seen in Tables 2 and 3 respectively. Falls were responsible for 41% of all injuries. Drops and falls were highest in the 0–11 month category where they accounted for 55% of all injuries in this age group. They declined to 39% in the 12–35 month age group and then levelled off. Other relatively frequent types of injury were ingestions (61% of which were in toddlers aged 12–35 months), strains, grazes/lacerations (that became progressively more frequent with increasing age), and foreign body injuries (that peaked in frequency at 36–59 months).
Table 2. Trends in breakdown factors (what went wrong) resulting in the injury at presentation to Yorkhill ED by age category. (Frequencies are an annual average of injury types in each age group over a 3 year period 1997–1999).
Table 3. Trends in mechanism (how the injury was inflicted) by which the injury was inflicted at presentation to Yorkhill ED by age. (Frequencies are an annual average of injury types in each age group over a 3 year period 1997–1999).
Location of injury occurrence
Over two-thirds (68%) of injuries occurred in home locations. The number of injuries occurring in the home decreased with advancing age, from 85% in the 0–11 month age group to only 45% in the 60–83 month group. Injuries in educational facilities, footpaths, playgrounds and sports facilities became more frequent with increasing age (Table 4).
Table 4. Trends in location (where injury happened) where the injury occurred at presentation to Yorkhill ED by age. (Frequencies are an annual average of injury type in each age group over a 3 year period 1997–1999).
Context of injury
Almost two-thirds (62%) of injuries happened when the child was engaged in play. This proportion was lowest in the 0–11 month age category (37%), was almost double (64) % in the 12–35 month category and thereafter levelled off.
Around 17% of injuries took place when the child was on the move (walking, running or crawling). This proportion was lowest in the 0–11 month age category (10%) and almost doubled (19%) in the 12–35 month category where it reached a plateau and thereafter remained steady (Table 5).
Table 5. Trends in context (what child was doing at time of injury) surrounding the injury at presentation to Yorkhill ED by age. (Frequencies are an annual average of injury type in each age group over a 3 year period 1997–1999).
Anatomical site of injury
There were substantial variations in the most frequent types of injury by age group. The head was involved in 52% of injuries in the 0–11 month age group but this declined with age and comprised only 44% of all injuries in the 60–83 month age group. Injuries affecting the extremities showed the opposite trend with those affecting the upper extremity steadily increasing from 10% in the 0–11 month age group to 20% in the 60–83 month age group. Injuries affecting the lower extremities also rose, from 8% in the 0–11 month age group to 21% in the 60–83 month group.
Nature of injury
Open wounds and fractures increased progressively with age, with open wounds rising from 10% of all injuries in the 0–11 month age group to 27% in the 60–83 month group. Fractures increased from 6% of all injuries in the youngest group to 17% in the eldest group.
Discussion
Remarkably little epidemiological research has focused on the changing risk of injury in young children according to developmental stage. To our knowledge, our study is the first to investigate this issue using a population-based approach in a high-risk area of the UK. Moreover, we were able to compare our experience in the West of Scotland with that of Canadian colleagues, thanks to the operation in both locations of a virtually identical injury surveillance system.
Injury Rates by Age Category
The pattern of injury rates at Yorkhill displayed a similar pattern across the age groups to the Kingston data. This consistency offers generalisable evidence of a relationship between stage of development and injury risk. The finding is a plausible one. Once mobility is established, exploration of their surroundings is a crucial part of childhood development but it is a behaviour that, combined with their lack of understanding of – and physiological incapacity to negotiate – many environmental hazards, places them at particular risk of injury [2].
The average annual injury rate in Yorkhill was higher than that of Kingston though the difference was not quite statistically significant. A higher rate at Yorkhill may reflect different degrees of socio-economic deprivation in the two populations and injury risk is correlated with poverty. Even within the UK, Scotland exhibits significantly higher rates of injury than in England and Wales [5], probably for that reason.
As in Kingston, the average annual rate at Yorkhill was higher for boys than for girls, though this did not reach statistical significance. A number of factors may contribute to the male excess in injury mortality, including differences in exposure to hazards, behaviour and socialisation as well as possible differences in parental attitudes to boys and girls.
Patterns of Injury
The observed injury patterns reflect the exposure of young children to a range of hazards, with varying and continuously changing vulnerabilities over time that are influenced by physical, cognitive and social characteristics at different stages of development.
Mechanisms of injury
The finding that drops and falls were the most common causes of injury and peaked in the first year was consistent with the Kingston study. This is unsurprising as during this time children become mobile and increasingly curious about their environment. Ingestions and foreign body injuries were also fairly common cause of injury and most numerous in the 12–35 month age category (61%). This was similar to the Canadian data and may be explained by the developmental progress that occurs during this period of a child's life.
Location of injury occurrence
The home was the most common place for an injury to occur in all age groups, particularly in the first year. This result too is unsurprising and reflects the amount of time a young child spends in the home, usually in the presence of a carer. Injuries outside of the home in places such as playgrounds, footpaths, sports and educational facilities all increased with age. This may be attributable to the gradual emergence of the child from the home and a growing attempt to achieve independence from adult carers.
Nature of injury
The most common type of injury was a blow to the head and this was highest in the 0–11 month group (52%). This was also reported in the Kingston study and may be due to two factors: the minimal control that babies are able to exert over head position and movements, and their relatively inability to take avoiding or protective action during a fall or when confronted with an external hazard. Injuries affecting the upper limb displayed the second highest frequency and peaked in the 60–83 month group. This is probably because older children tend to throw up their hands to protect their head when they fall, thus placing their arms at increased risk of injury.
Strengths and weaknesses of the study
The main disadvantage of using Yorkhill as a setting for an ED based surveillance system was the lack of a clear denominator. As with other hospitals in Glasgow, there is no clearly delineated catchment area. By including only cases from the West of the city, we are reasonably confident of their representative nature for the purpose calculating rates. At the same time, we inevitably sacrificed a larger potential sample size and therefore statistical power.
As the injury rates calculated were limited to ED encounters, they are likely to underestimate the actual burden of paediatric injury in the population. In effect, we examined only the tip of the injury iceberg because a proportion (perhaps as many as two-thirds) of all injuries present to primary care [6]. Furthermore, CHIRPP relied on self-reports, the reliability of which is a matter for speculation.
One area of concern about the Yorkhill data was the frequent lack distinction drawn between the data coded in the 'mechanism' and 'breakdown' variables. Another related to the field for intent as this was often left incomplete, possibly due to staff reservations about possible medico-legal consequences.
Ideally, an injury surveillance system should capture information on the severity of injury, or at least include only those cases that exceed a predetermined severity threshold [7]. At Yorkhill, as at other CHIRPP sites, such information was not included.
Data collection rates varied depending on the time of day and the day of the week. By confining the study period to the selected years, we attempted to minimise the impact of such varying data quality; in the period 1997 to 2001, the capture and completion rates were known to be consistently high (over 90%).
Despite its limitations, our study employed a population-based approach using an evaluated injury surveillance system [8] to investigate a large number of injuries to children residing in a busy emergency department located in a relatively high risk urban area. We believe that our findings are therefore scientifically robust and have generated important insights into the link between the development of young children and their risk of injury. These insights should prove as valuable to those responsible for planning and implementing preventive measures in Glasgow as they have in Kingston. The key developmentally-sensitive preventive priorities identified by the Kingston group – careful supervision and risk anticipation, limiting access to hazards, and fall avoidance through safe play behaviour and environments – are all equally applicable in Glasgow and, most probably, elsewhere.
Conclusion
We replicated the key findings of the Kingston study that there is a clear correlation between the developmental stage of children and the injuries they sustain, thereby reinforcing the pertinence of the preventive messages offered by our Canadian colleagues. Future research should take account of the need to enhance statistical power and explore the interaction between age and potential confounding variables such as socio-economic deprivation. Our findings highlight the importance of designing injury prevention interventions that are appropriate for specific stages of development in children.
Competing interests
The author(s) declare that they have no competing interests.
DS conceived the study, advised on its design, supervised the analysis and assisted with the writing of the paper. KM conducted the study, undertook the analysis and was the main contributor to the writing of the paper.
Acknowledgements
We are indebted to Mr NV Doraiswamy and staff of the ED of the Royal Hospital for Sick Children, Yorkhill, Glasgow, the clinical effectiveness staff and senior management of that hospital, the Public Health Agency of Canada for technical support, Dr Deborah Shipton for methodological advice and support, and the parents and children who provided the data.
References
1. Warrington SA, Wright CM, ALSPACS Team: Accidents and resulting injuries in premobile infants: data from the ALSPAC study.
Arch Dis Child 2001, 85:104-7. PubMed Abstract | Publisher Full Text | PubMed Central Full Text
2. Flavin MP, Dostaler SM, Simpson K, Brison RJ, Pickett W: Stages of development and injury patterns in the early years: a population-based analysis.
BMC Pub Health 2006, 6:187. BioMed Central Full Text
3. Morrison A, Stone DH, Doraiswamy N, Ramsay L: Injury surveillance in an accident and emergency department: a year in the life of CHIRPP.
Arch Dis Child 1999, 80(6):533-536. PubMed Abstract | Publisher Full Text | PubMed Central Full Text
4. Brown CE, Chishti P, Stone DH: Measuring socio-economic inequalities in the presentation of injuries to a paediatric A&E department: the importance of an epidemiological approach.
J Public Health 2005, 119:721-5. Publisher Full Text
5. BMA Board of Science and Education: Injury Prevention. London, British Medical Association; 2001.
6. Hambidge SJ, Davidson AJ, Gonzales R, Steiner JF: Epidemiology of pediatric injury-related primary care office visits in the United States.
Pediatrics 2002, 109:559-565. PubMed Abstract | Publisher Full Text
7. Cryer C, Langley JD, Stephenson SC, Jarvis SN, Edwards P: Measure for measure: the quest for valid indicators of non-fatal injury incidence.
Public Health 2002, 116(5):257-62. PubMed Abstract
8. Macarthur C, Pless IB: Evaluation of the quality of an injury surveillance system.
Am J Epidemiol 1999, 149(6):586-592. PubMed Abstract | Publisher Full Text
Pre-publication history
The pre-publication history for this paper can be accessed here:
http://www.biomedcentral.com/1471-2458/8/120/prepub
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Category:Archives and Libraries in KentEdit This Page
From FamilySearch Wiki
The main article for this category is Kent Archives and Libraries.
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"warc_url": "http://www.familysearch.org/learn/wiki/en/index.php?title=Special:RecentChangesLinked&hideliu=1&target=Help%3ADiscussion_Pages_(Talk_Pages)"
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Changes related to "Help:Discussion Pages (Talk Pages)"
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"uncompressed_offset": 499866661,
"url": "www.grandtheftwiki.com/Category:Areas_in_Vice_City",
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Category:Areas in Vice City
From Grand Theft Wiki
Jump to: navigation, search
This category lists all areas in Vice City. Locations can only be considered into the category only if the game displays the locations name on the heads-up display. Little Havana is considered an area but Fort Baxter Air Base, which is within Escobar International, is not considered an area. Any locations not considered an area are in Category:Places in Vice City.
Pages in category ‘Areas in Vice City’
The following 12 pages are in this category, out of 12 total.
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Medicine » Oncology
Treatment of Metastatic Melanoma
Edited by Rachael Morton, ISBN 978-953-307-574-7, Hard cover, 348 pages, Publisher: InTech, Chapters published October 05, 2011 under CC BY 3.0 license
DOI: 10.5772/1034
Surgery continues to be the mainstay treatment for melanoma localized to the primary tumor and/or lymph nodes. Results from randomized controlled trials indicate that sentinel node biopsy for the treatment of cutaneous melanoma of intermediate thickness has a beneficial effect on recurrence rates, and adjuvant radiotherapy to regional lymph node fields following surgical resection reduces loco-regional recurrence in patients at high risk of relapse. Isolated limb perfusion, electrochemotherapy, and photodynamic therapy continue to be evaluated for treatment of stage IV disease. However, the greatest excitement in new treatment has been with targeted therapies for genetic mutations. In particular, the promising results of partial and complete tumor response in stage IV disease from early phase trials of the B-RAF kinase inhibitors. This book provides a contemporary insight into the therapeutic treatment options for patients with metastatic melanoma and is relevant to clinicians and researchers worldwide. In addition, an update on current clinical trials for melanoma treatment has been included, and two chapters have been reserved to discuss the treatment of oral and uveal melanoma.
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Bibliography: The Best of Philip Jose Farmer
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Title: The Best of Philip Jose Farmer
Author: Philip José Farmer
Year: 2006
Type: COLLECTION
Language: English
ISFDB Record Number: 179326
User Rating: This title has fewer than 5 votes. VOTE
Current Tags: None Add Tags
Publications:
Reviews:
Copyright (c) 1995-2011 Al von Ruff.
ISFDB Engine - Version 4.00 (04/24/06)
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Brown BIOL1220:Notebook/SynBio in Theory and Practice
From OpenWetWare
Jump to: navigation, search
Search this Project
Customize your entry pages
Project Description/Abstract
• Place short description of project or notes regarding this project
People
Instructor
TAs
• Kate
• Rima
Students
Meleha, Will, Steph, John, War War, Annie Rose, Margaret, Abe, Ahmad, Indu, Katrina, Eli, Minoo, Michael, Ashley
Notebooks
Useful Links
Notes
• Place some notes here for visitors
• Example: This project is currently on hold until further notice.
Media:bacteria.ppt
Recent changes
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"warc_url": "http://www.openwetware.org/index.php?title=Endy:Contact&oldid=282464"
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Endy:Contact
From OpenWetWare
Revision as of 22:22, 3 February 2009 by Endy (Talk | contribs)
Jump to: navigation, search
Add to My Links
Home Lab Members Research Notebooks Publications Internal Contact
Contents
Office Address
Drew Endy, Stanford Bioengineering
Y2E2-269B, MC4200
473 Via Ortega
Stanford, CA 94305
Administrative
Jean Cookinham, Stanford Bioengineering
Y2E2-269B, MC4200
473 Via Ortega
Stanford, CA 94305 jcookinh@stanford.edu
Laboratory / Shipping Address
<Insert Name> c/o Endy Lab
Y2E2-B007, MC4200
473 Via Ortega
Stanford, CA 94305
(650) 721-6373
Laboratory Phone & Fax
Lab. (650) 721-5886
Fax. n/a
Location on Campus, Parking
Red star = Y2E2 building; Green stars = parking, if needed; click for larger
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Kafatos:Kafatos/Christophides Lab
From OpenWetWare
Revision as of 09:57, 25 November 2009 by Mpovelones (Talk | contribs)
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Contact
Laboratory of Immunogenomics
Imperial College
Division of Cell & Molecular Biology
SAF building
South Kensington Campus
London, SW7 2AZ
UK
Malaria & Innate Immunity in the mosquito Anopheles gambiae
dewikify
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STEM Facility
From OpenWetWare
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Line 34: Line 34:
Per Grid* – non-proprietary…………………………..$391.02**
Per Grid* – non-proprietary…………………………..$391.02**
-
*See attached for description, minimum of 3 grids per specimen
+
*See attachment, Minimum of 3 grids per specimen
Revision as of 15:55, 10 July 2008
THE STEM (Scanning Transmission Electron Microscope) FACILITY
at Brookhaven National Laboratory
The STEM used to be an NIH Research Resource and as such was available to outside users with appropriate projects free of charge. We have lost this support, but continue to operate half-time as a User Facility on a Fee-For-Service basis.
We are updating our web page.
See it (reload or refresh) http://www.biology.bnl.gov/stem/stem.html for details.
PURPOSE OF THIS PAGE
Our web page (link given above) has essentially all the useful information about the facility and its use.
We will try to use this page for transient information, such as announcements and "news".
A NEW POSTING
The microscope is now running with our new computer system. STEM Users who have been using the STEM PCMass programs for analyses and viewing, should be using the most recent version of PCMass. It reflects the new data acquisition system, is much more user-friendly, and has more tutorials. A new, complete, PCMass program will soon be on our ftp site.
FEE-FOR-SERVICE
Details on our web page include: Services Provided, Guarantee, Description of Service
SAMPLE CHARGE
Biology’s Scanning Transmission Electron Microscope (STEM)
Per Grid* – non-proprietary…………………………..$391.02**
• See attachment, Minimum of 3 grids per specimen
USERS
Most users mail (ON Express) their samples. Frozen samples, in a well-insulated package with lots of dry ice, will stay frozen for many days -- long enough to clear customs if they are from abroad. A sample package is shown below (held by Joe and Beth):
Retrieved from "http://www.openwetware.org/wiki/Image:--Package-file.jpg--"
ANNUAL EM WORKSHOP
No annual STEM/EM Workshop was held in 2008 at the end of the RapiData Crystallography course.
A GOLD-LABELING WORKSHOP
Was held Sept. 11-13, 2007. It was organized by Dr. James Hainfeld.
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Talk:CH391L/S12/Pattern Formation
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• Jeffrey E. Barrick 10:29, 6 April 2012 (EDT):Images need citations. Chili peppers are tiny?
• Jared Ellefson 18:17, 7 April 2012 (EDT):Fixed the chili problem. But it's not letting me add text to the figures? I'll keep working on it
• Jeffrey E. Barrick 10:29, 6 April 2012 (EDT):There's a nice presentation posted many places online, including here, which seems to contain unpublished computational modeling of more complex circuits and pattern formation, but without any wet lab work.
• Jared Ellefson 18:10, 7 April 2012 (EDT):I think this brings up an interesting topic. How much weight should a non-tested biological model hold? Biological models sometimes don't work due to idiosyncrasies. But that said, I'd be curious to see how that circuit would work, it has a very BZ reaction feel which is cool (http://www.youtube.com/watch?v=3JAqrRnKFHo).
• Jeffrey E. Barrick 10:29, 6 April 2012 (EDT):Your references aren't working correctly: the syntax for the end of the line is pmid=12219076
• Jeffrey E. Barrick 10:44, 6 April 2012 (EDT): Spelling: "achieved". First sentence of "Synthetic pattern formation..." needs help.
• Jeffrey E. Barrick 10:44, 6 April 2012 (EDT):Has anything "useful" ever been done with synthetic pattern formation? Do you think it would be possible to get noncircular colony growth for E. coli (or noncircular spreading in soft agar) by putting one of these circuits in that would "sector" the colony and change how it spread or something like that?
• Jared Ellefson 18:10, 7 April 2012 (EDT):Depends on the definition of useful. I certainly foresee this being an enabling technology. But I'm not sure how useful it will be in E.coli. The real biomedical applications might start to take place once systems like this are imported into mammalian cell culture. In terms of non-circular colony growth, yeah I bet this is possible. My guess is tricky though, if you're dealing with cell survival. I'm not sure the exact parameters you are thinking of (autonomous vs non-autonomous), but I bet you could do some fun stuff with light controlling cell growth.
• Jared Ellefson 11:54, 9 April 2012 (EDT):This paper[1] is pretty cool. They use DNA to form extracellular matrix-like scaffolds. In which cells can do things based on the structural characteristics of the scaffold. And this is fully programmable because it is made of DNA.
• Jeffrey E. Barrick 13:57, 9 April 2012 (EDT): I was thinking autonomous. Like, can you engineer a cell that forms dumbbell shaped colonies.
• Ben Slater 20:27, 8 April 2012 (EDT): Think it's possible to design a color bacterial photo system? As in, color output, not just input?
• Jared Ellefson 11:07, 9 April 2012 (EDT):YES! Definitely. For instance the multicolor system has two lacZ genes, one that is turned "ON" by Green and the other turned "ON" by RED. I think simply just changing the LacZ genes to GFP and mCherry for instance could give you an exact color copy of the image you display. It would be fun to just see how complicated you can build these light circuits.
• Adam Meyer 11:21, 9 April 2012 (EDT):It seems as though in all the cases listed, the pattern is specified by the investigator. Are there systems in which the investigator sets up conditions and the organisms form an optimal pattern that fits those conditions? In other words, the pattern is not known a priori but answers some question.
• Jared Ellefson 11:54, 9 April 2012 (EDT):This paper[2] describes pattern formation where the program is natural to the organism, but the parameters are synthetic. In the paper, a mold is grown on a plate with strategically placed food sources that resemble the Tokyo rail system. The mold then creates the most efficient pathing between the food nodes. It is really surprising that the biological map created from this highly resembles the actual engineered routes.
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Katherine Gruner
From OpenWetWare
(Redirected from User:Katherine Gruner)
Jump to: navigation, search
Katherine Gruner
Department of Pathology
303 E. Chicago Ave.
Ward Building, 7-011
Chicago, IL 60611
Your e-mail..
Hello, I am .... in the Tourtellotte Lab at Northwestern University.
Research Interests
• research 1
• research 2
Education
M.Sc, University of xxx
My undergrad degree was in...
Publications
My publication In this journal... in 2004...
// or you could use biblio if your publication is in pubmed: e.g
1. John Smith. The art of saying nothing. Verbose Editions 1999. [somebook]
2. Ministerial Meeting on Population of the Non-Aligned Movement (1993: Bali). . pmid:12345678. PubMed HubMed [coolpmid]
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President Davis to the Marvland Commissioners.
--The subjoined admirable reply of President Davis to the Maryland Commissioners, is published in the Baltimore papers:
Monthomert, 25 May, 1861.
Gentlemen — I receive with sincere pleasure the assurance that the State of Maryland sympathizes with the people of these States in their determined vindication of the right of self government, and that the people of Maryland ‘"are culisted with their whole hearts on the side of reconciliation and peace."’
The people of these Confederate States, not withstanding their separation from their late sister, have not ceased to feel a deep solicitude in her welfare, and to hope that, at no distant day, a State whose people, habits and institutions are so closely related and assimilated with theirs, will seek to unite her fate and fortunes with those of this Confederacy.
The Government of the Confederate States receive with respect the suggestion of the State of Maryland ‘"that there should be a general cessation of hostilities now impending until the meeting of Congress in July next, in order that said body may, if possible, arrange for an adjustment of existing troubles, by means of negotiation rather than the sword,"’ but is at a loss how to reply without a repetition of the language it has used on every possible occasion that has presented itself since the establishment of its independence.
In deference to the State of Maryland, however, I again assert, in the most emphaticterms, that its sincere and earnest desire is peace; that whilst the Government would readily entertain any proposition from the Government of the United States tending to a peaceful solution of the pending difficulties the recent attempts of this Government to enter into negotiations with that of the United States were attended with results which forbid any renewal of proposals from it to that Government.
If any further assurance of the desire of this Government for peace were necessary, it would be sufficient to observe that, being formed of a confederation of sovereign States, each acting and deciding for itself, the right of every other sovereign State to the same self-action and self-government is necessarily acknowledged. Hence conquests of other States are wholly inconsistent with the fundamental principles, and subversive of the very origination of this Government. Its policy cannot but be peace — peace with all nations and people. Very respectfully,
Jeff. Davis.
Messrs. McLaig, Yellott and Harding, Committee of Maryland Legislature.
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The 1000th Post - What I Have Learned In 1000th Posts On A SEO Forum
Oct 19, 2005 • 11:37 am | (0) by | Filed Under SEO & SEM Forum News
One of the things that I have liked over the years as being a moderator at SEO Chat Forums is the tradition of members going to great lengths to do really incredible 1000th posts on the forum. Many wait for the day for which they can contribute in some meaningful way to the forum by posting the knowledge they have learned and gleamed during their time as a forum junkie. Some of these 1000th's posts are long dissertations on what they have learned in SEO and then there are the quick highlighted lists of essentials you must know in order to survive in this crazy internet world successfully. The posts are badges of honor and a final thesis for many into the world of SEO/SEM. They are usually quite great to read and good information to refer too. At some point most involved members on SEOchat will do a 1000th or 500th post, there are even 2000th and 3000th posts. Sometimes people make planned exits from boards on the date of their big post (dramatics seems to heighten the effect these posts can have). I once did a 500th post and used my 1000th to welcome a new moderator on the board. In order to honor these fun and useful posts I am highlighting some of the great ones from SEOchat. If you have one you would like to add please leave a comment and I will add them.
Previous story: Impact of Tables On Search Engine Optimization
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Poll Results On How Google Views SEOs (Innocent or Guilty)
Jun 19, 2009 • 7:07 am | (0) by | Filed Under Search Engine Industry News
A week ago, we asked our readers to vote on their thoughts on if Google sees SEOs as criminals. If you remember, this is based on the double-standard that some bloggers feel Google is placing on some groups over another group.
With just under a 150 responses, I wanted to share how we (SEOs) perceive how Google sees us.
Question: Does Google See SEOs as Criminals?
:: Only Some Groups of SEOs said 77 respondents or 52% :: Yes said 43 respondents or 29% :: No said 25 respondents or 17% :: Other answer... said 3 respondents or 2%
It is very interesting looking at how SEOs perceive how Google sees SEOs. Kind of a circular statement there, but you know what I mean.
Forum discussion continued at Sphinn (Lisa), Sphinn (Michael) and Sphinn (Susan).
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Place:Pforzheim, Baden, Germany
Watchers
NamePforzheim
Alt namesPorta Hercyniaesource: Canby, Historic Places (1984) II, 732
TypeIndependent City
Coordinates48.892°N 8.706°E
Located inBaden, Germany
Also located inEnzkreis, Karlsruhe, Baden-Württemberg, Germany
Contained Places
Inhabited place
Mühlhausen
Unknown
Dietlingen
Neuhausen
Weiler
source: Getty Thesaurus of Geographic Names
source: Family History Library Catalog
the text in this section is copied from an article in Wikipedia
is a town of nearly 120,000 inhabitants in the state of Baden-Württemberg, southwest Germany at the gate to the Black Forest. It is well-known -for its jewelry and watch-making industry. Until 1565 it was the home to the Margraves of Baden. Because of that it gained the nickname "Goldstadt" or Golden City. It has an area of 98 km² and is situated between the cities of Stuttgart and Karlsruhe at the confluence of three rivers (Enz, Nagold and Würm) and marks the frontier between Baden and Württemberg, being located on Baden territory. Pforzheim is located on the Bertha Benz Memorial Route.
The City of Pforzheim does not belong to any administrative district (Kreis), although it hosts the administrative offices of the Enz district which surrounds the town.
During World War II, Pforzheim was bombed a number of times. The largest raid, and one of the most devastating area bombardments of World War II, was carried out by the Royal Air Force (RAF) on the evening of 23 February 1945. About one quarter of the town's population, over 17,000 people, were killed in the air raid, and about 83% of the town's buildings were destroyed. The town was thought by the Allies to be producing precision instruments for use in the German war effort and to be a transport centre for the movement of German troops. The story of the bombardment is dramatically recounted in the 2011 history book by Giles Milton, entitled .
After the war, the rubble from the destruction was heaped into a large pile on mount Wallberg and into the Brötzinger Tal valley on the outskirts of the town, resulting in a volcano-ish look of the mountain and the disappearance of the valley. Similar efforts were undertaken in other destroyed cities such as Stuttgart and Munich. In the twenty years following the end of the war, Pforzheim was gradually rebuilt, giving the town a quite modern look and making it home to some landmark buildings of the 1950s.
Contents
History
the text in this section is copied from an article in Wikipedia
Since 90: A settlement was established by Roman citizens at the Enz river near the modern Altstädter Brücke (old town bridge). Archeological surveys have unearthed several items from that period which are kept and displayed in the Kappelhof Museum. The settlement was located where the Roman military road connecting the military camp Argentoratum (nowadays Strasbourg in France) and the military camp at Cannstatt (now a suburb of Stuttgart) at the Upper Germanic Limes border line of the Roman Empire crossed the Enz river. This place was known as Portus (river crossing, harbor), which is believed to be the origin of the first part of the city's name "Pforzheim". A Roman milestone (the so-called 'Leugenstein') from the year 245 and later excavated at nowadays Friolzheim shows the exact distance to 'Portus'; it is the first document about the settlement.
259/260: The Roman settlement 'Portus' was destroyed completely, as the Frank and Alemanni tribes overrun the Upper Germanic Limes border line of the Roman Empire and conquered the Roman administrated area west of the Rhine river. From then on, over an extended period of time historical records about the settlement are not available.
6th/7th century: Graves from this period indicate that the settlement had been continued.
1067: The settlement of Pforzheim was mentioned for the first time in a document by Henry IV, Holy Roman Emperor as "Phorzheim". Visits to Pforzheim by Heinrich IV in 1067 and 1074 are documented.
Before 1080: The "old town" of Pforzheim was awarded market rights (Marktrecht). At that time Pforzheim belonged to the estate of Hirsau Monastery, according to monastery documents.
From 1150: Establishment of the "new town" west of the "old town" at the foot of the Schlossberg (palais hill) under Margrave Hermann V.
1200: The town charter of the "new town" was mentioned for the first time in a document. The "old town" continued to exist as a legally independent entity.
1220: The Margraves of Baden selected Pforzheim as their residence. The "new town" became prominent.
1240: A mayor of Pforzheim was mentioned in a document for the first time.
13th/14th century: Pforzheim enjoyed its first period of flourishment. A group of influential patricians emerged. They developed extensive activities on the financial markets of those days. The town drew its income from the wood trade, timber rafting, the tannery trade, textile manufacturing and other crafts. Documents mention mayor, judge, council and citizens. The town walls surrounding the new town were completed at about 1290. During this era three catholic orders established their convents in town (the Franciscan order established their domicile within the town wall at nowadays Barfuesserkirche (the choir of which remains), the Dominican nun order established their domicile outside of the walls of the old town near Auer bridge, and the Prediger cloister was located east of the Schlossberg, probably inside the town walls). Outside of the town wall across the Enz river, the suburb Flösser Quarters (the home of the timber floating trade) was established. Next to the western town wall, the suburb of Brötzingen gradually developed. The Margraves of Baden considered Pforzheim as their most important power base up to the first half of the 14th century. Under Margrave Bernard I (Bernhard I) Pforzheim became one of the administrative centers of the margraviate.
1322: Holy Ghost Hospital was founded at Tränk Street (nowadays Deimling Street).
15th century: Various fraternities among people working in the same trade were established: The fraternity of tailors in 1410, the fraternity of bakers on May 14, 1422, the fraternity of the weavers in 1469, the fraternity of the wine-growers in 1491, the fraternity of the skippers and timber raftsmen in 1501, and the fraternity of the carters in 1512. Members of the same fraternity assisted each other in various ways, for example with funerals and in cases of sickness. In a sense, the fraternities were early forms of health and life insurance.
August 8/9, 1418: Sigismund, Holy Roman Emperor visits Margrave Bernard I (Bernhard I) in Pforzheim. On this occasion the mint of the Margraves of Baden in Pforzheim was mentioned. Mint master was Jakob Broeglin between 1414–1431. The emperor appointed the master of the Pforzheim mint, Jakob Bröglin, and Bois von der Winterbach for five years as Royal Mint Masters of the mints of Frankfurt and Nördlingen. The Margrave was appointed as their patron.
1447: The wedding of Margrave Charles I (Karl I) of Baden with Katharina of Austria, the sister of Frederick III, Holy Roman Emperor (Friedrich III), was celebrated in Pforzheim with great pomp (including tournaments and dances).
1455: Johannes Reuchlin, the great German humanist, was born in Pforzheim on January 29 (he died in Stuttgart on June 30, 1522). He attended the Latin School section of the monastery school run by the Dominican order of Pforzheim in the late 1460s. Later, partly due to Reuchlin's efforts, the Latin School of Pforzheim developed into one of the most prominent schools in southwestern Germany, named Reuchlin-Gymnasium. The school's teachers and pupils played an outstanding role in the dissemination of the ideas of humanism and the protestant reformation movement. The most famous pupils included Reuchlin himself, Reuchlin's nephew Philipp Melanchthon, and Simon Grynaeus.
1460: Margrave Charles I established a kind of monastery (Kollegialstift) at the site of Schlosskirche St. Michael, turning the church into a collegiate church. There were also plans to establish a university in Pforzheim, but this plan had to be abandoned because Margrave Charles I lost the Battle of Seckenheim.
1463: Margrave Charles I was forced to transfer the palace and the town of Pforzheim as a fiefdom to the Elector Palatine after losing the Battle of Seckenheim. He then began to build a new palace in modern Baden-Baden. Margrave Christoph I finally moved the residence of the margraves to Baden-Baden. This gradually ended the first period of Pforzheim's flourishment. The rich merchants gradually left the town, which declined to the status of a country town of mostly small traders.
1486: The Weavers Ordinance (Wollweberordnung) for the towns Pforzheim und Ettlingen was approved by Margrave Christoph I. This was a contract concerning the town privileges of Pforzheim. This regulation of the weaving trade did not allow the formation of a regular guild (Zunft).
1491: A contract between Margrave Christoph I and the citizens of Pforzheim was concluded, granting the town of Pforzheim several privileges concerning taxes and business.
1496: Foundation of the first printer's shop by Thomas Anshelm. During the first half of the 16th century Pforzheim's printers contributed significantly to the establishment of this (in those days) new medium.
1501: Margrave Christoph I of Baden enacted the "Ordinance on the timber rafting profession in Pforzheim". The single timber logs that were floated from the deeper Black Forest areas down the Enz, Nagold and Wuerm rivers were bound together in the Au area to form larger timber rafts. Those rafts were then floated down the lower Enz, Neckar and Rhine rivers. The timber rafting stations of Weissenstein, Dillstein and Pforzheim were well known in the profession.
1501 was also the year for which an outbreak of the plague (probably the bubonic plague) is recorded in the Swabian chronicle Annalium Suevicorum by Eberhard Karls University of Tübingen professor Martin Grusius, published 1596. It is not known how many of Pforzheim's citizens died in that year, but there are reports of 500 deceased in the close-by city of Calw and about 4000 in Stuttgart, which accounted for approximately one quarter to one half of the populations of those towns. Outbreaks of the disease were reported for many places in southwestern Germany, Bohemia, the Alsace region in nowadays France, Switzerland, and Italy. Common graves with massive numbers of human bones at the cemetery of St. Michael Church and the cemetery on the estate of the Dominican order near nowadays Waisenhausplatz found during the last century may indicate that hundreds of citizens became the victims of the plague. There are indications that a fraternity for taking care of the sick and removing the bodies of the deceased from houses was formed in 1501, whose members later on stayed together and became known as the choral society Singergesellschaft, which is still active today as the Loebliche Singergesellschaft of 1501. (They are probably one of the oldest clubs in Europe).
1520s: The ideas of the protestant religious movement advanced by Martin Luther spread rapidly in Pforzheim. Its most prominent promoters were Johannes Schwebel, a preacher at Holy Ghost church (Heiliggeistkirche), and Johannes Unger, the principal of the Dominican Latin school.
1535–1565: Due to the heritage division of the clan of the Margraves of Baden, Margrave Ernst of Baden made Pforzheim the residential town of his family line. He decided to use the Schlosskirche St. Michael as the entombment site for his family line.
1549: A large fire caused severe damage to the town.
1556: After the conclusion of the Peace of Augsburg in 1555, Margrave Karl II introduced Lutherism (protestantism) as the state religion in the district Baden-Durlach, which included Pforzheim. The (Catholic) monasteries were gradually shut down.
1565: Margrave Karl II chooses Durlach as the new residential town. Pforzheim stayed one of the administrative centers of Baden.
1618: At the beginning of the Thirty Years' War, the number of inhabitants of Pforzheim is estimated to have been between 2500 and 3000. This was the largest town among all towns in Baden, even though at that time it had already declined somewhat.
1645: Toward the end of the Thirty Years' War the "old town" was burned down by Bavarian (i.e. Catholic) troops. It was rebuilt, but without the former fortifications, which gave it the status of a village-like settlement. It soon vanished from historical records. The "new town" had survived.
1688–1697: The "War of the Palatinian Succession" (also called the Nine Years War) caused tremendous destruction in Southwestern Germany. The French "sun king" Louis XIV's efforts to expand the territory of France up to the Upper Rhine river and to put the Elector Palatine under pressure to severe its ties with the League of Augsburg included the Brûlez le Palatinat! tactics of destroying major towns on both sides of the Rhine river. These tactics seem to have been mainly the idea of the French war minister, François Michel le Tellier, Marquis de Louvois.
Pforzheim was occupied by French troops on October 10, 1688. Commanding officer is said to have been Joseph de Montclar. The town was forced to accommodate a large number of soldiers and had to pay a large amount of "contributions" to the French. When the army unit was about to depart early in the morning of January 21, 1689 (obviously because an army of the Holy Roman Empire had been approaching), they set many major buildings on fire, including the palais, the city hall, and vicarages. About 70 houses (i.e. one quarter of all houses) and part of the town's fortifications were reportedly destroyed.
Between August 2 and August 4, the French army under the general command of Marshal Jacques Henri de Durfort de Duras again crossed the Rhine river and began the destruction of major towns in Baden. On August 10, 1689, a French army unit under the command of General Ezéchiel du Mas, Comte de Mélac appeared in front of Pforzheims town gates, but this time the town refused to surrender. In response, the French army began shelling the town with cannons from the Rod hill located southwest of the town, and the several hundred soldiers of the German imperial command, who were defending the town, were forced to surrender. After a short period of looting, the French troops set the inner town area on fire on August 15, which made that area uninhabitable for several weeks. Then the French moved on.
During the following two years French troops stayed away from Pforzheim, but the economic situation of the town was miserable. In addition to this, the reconstruction of the town and the repairs of the fortifications under the supervision of Johann Matthaeus Faulhaber, the chief construction officer of the Margraviate Baden, required a lot of efforts. The accommodation of an imperial garrison under the command of (then) colonel Count Palfy also was a heavy burden.
In 1691 Louvois instructed his marshals to destroy those towns which were to serve as winter quarters for imperial troops, explicitly including Pforzheim, and then continue to Wuerttemberg for further destructions. After the French troops had crossed the Rhine river under the command of Marshal Guy Aldonce de Durfort de Lorges at Philippsburg on August 3, 1691, they assaulted the Margraves' residential town of Durlach and 1,200 cavalry men, 300 dragoons and 1,200 infantry men advanced toward Pforzheim where they arrived in the morning on August 9 and surrounded the town. When the approximately 200 imperial soldiers under the command of Captain Zickwolf and other men in the town refused to surrender, the siege began. After shelling the town during the day and the following night, the resistance of the town broke down and on August 10 in the morning the French forced the town gates open, occupied and looted it (although with little success, as there was not much left to be taken away). On August 12, the French moved on, this time refraining from setting houses on fire. The fortification had again been damaged, though (the White Tower, the Auer Bridge Gate, the Upper Mill and the Nonnen Mill were burnt down). The French also stole all church bells, except for one minor one.
On September 20, 1692, again crossed the Rhine river under the general command of Marshal Guy Aldonce de Durfort de Lorges, and advanced toward Durlach and Pforzheim. On September 24, 2,000 cavalry soldiers and 1,200 infantry and artillery troops under the command of Marshal Noël Bouton de Chamilly, moved to Pforzheim, where the town and 600 soldiers of the imperial German army in town surrendered without any military engagements. The rest of the French army arrived on September 27 under the command of Marshal de Lorges. On the same day, the French army moved on to Oetisheim near Mühlacker and attacked an imperial army unit of 4,000 cavalry men under the command of Duke Frederick Charles of Württemberg-Winnental in their camp. As they were taken by surprise, they withdrew hastily and lost several hundred men, either killed or captured by the French. (The Duke himself was among the French prisoners.) On September 28, the French army returned to Pforzheim and established a camp. It was reported that the entire Enz valley between the village of Eutingen east of Pforzheim and the village of Birkenfeld west of Pforzheim was occupied by the 30,000 French soldiers' camps. From their base in Pforzheim, French army units obviously under the leadership of Marshal de Chamilly advanced along the river valleys of Nagold and Wuerm and looted and destroyed the villages and towns of Huchenfeld, Calw, Hirsau, Liebenzell and Zavelstein. They also destroyed Liebeneck castle about 10 kilometers from Pforzheim towering above the Wuerm valley, where part of the Pforzheim town archives were hidden. The archive was burned. Another part of the town archive as well as documents of Baden administrative office had been brought to Calw, were they went up in flames, too.
When the French troops left after about one week of occupation, they again looted Pforzheim and put it on fire. This time, all houses which had survived the two previous fires, were destroyed. In the Au suburb, only three houses survived. The Au bridge was heavily damaged. Only four houses survived in the Broetzingen suburb. The town church St. Stephan and a large part of the Dominican monastery complex were also destroyed. The Castle Church (Schlosskirche) St. Michael was heavily damaged, and the family tombs of the Baden Margraves in the church were ravaged by the soldiers. The last remaining church bell and the churches' clockworks were stolen as well. The town wall was damaged again, including the town gates. After the one-week presence of 30,000 soldiers in a town of only a few thousand citizens, all food was gone, including the seeds saved for next spring's sowing season. Every tree and grapevine on the valley slopes had been used up as firewood. The French army reached their camp in Philippsburg on October 5, 1692.
1718: Inauguration of the "institution for orphans, the mad, the sick, for discipline and work" in a building of the former Dominican order Convent by the Enz river. Fifty years later this institution was to become the incubator of Pforzheim's jewellery and watchmaking industries.
1715–1730: During this period there was a prolonged dispute between Pforzheim's citizens and the Margrave of Baden concerning the privileges granted to the town in 1491, which the Margrave considered obsolete and therefore demanded significantly higher tax payments from Pforzheim citizens. The issue was taken all the way to the Imperial Court of Justice, where the town's motion was defeated.
1767: Establishment of a watch and jewellery factory in the orphanage. This led to Pforzheim's jewellery industries. Watchmaking was given up later on.
1805/06: Typhus epidemic in Pforzheim.
1809: The Administrative District Pforzheim of Baden was split into a Municipal District Administration Pforzheim and two Rural Districts.
1813: The two Rural Districts were combined to form the Rural District Administration Pforzheim.
1819: Municipal District Pforzheim and Rural District Pforzheim are merged to form the Higher District Administration Pforzheim.
1836: Ferdinand Öchsle in Pforzheim invented a device for measuring the sugar content in freshly pressed grape juice for assessing the future quality of wine (Mostwaage). It is still in use in the winery business.
1861/62: Pforzheim was connected to the German railway network with the completion of a section of the Karlsruhe–Mühlacker line between Wilferdingen and Pforzheim.
1863: The railway section between Pforzheim and Mühlacker was completed, thus establishing railway traffic between the capital of Baden, Karlsruhe, and the capital of Württemberg, Stuttgart.
1864: The Higher District Administration Pforzheim was made the Regional Administration Pforzheim.
1868: The Enz Valley Railway between Pforzheim and Wildbad was completed.
1869: Establishment of the first worker's union in Pforzheim, the "Pforzheim Gold(-metal) Craftsmen's Union".
1874: The section of the Nagold Valley Railway between Pforzheim and Calw was completed.
1877: Inauguration of the Arts and Crafts School (Kunstgewerbeschule; now incorporated into Hochschule (University) Pforzheim).
1888: Bertha Benz and her two sons arrived in Pforzheim on the first "long-distance" drive in the history of the automobile in a car manufactured by her husband Carl Benz in order to visit relatives. She had started her drive in Mannheim, which is located about 106 km (more than sixty miles) from Pforzheim. The very first gasoline-powered, automobile with an internal combustion engine of the inventor had hit the roads only two years earlier after a patent for this new technology had been granted to Karl Benz on January 29, 1886. She bought the gasoline necessary for her trip back home in a "pharmacy" in Pforzheim. During the trip Bertha Benz had to make repairs with a hairpin to open a blocked fuel line, and after returning home, suggested to her husband that another gear be provided in his automobile for climbing hills. To commemorate this first long-distance journey by automobile the Bertha Benz Memorial Route was officially approved as a route of industrial heritage of mankind in 2008. Now everybody can follow the 194 km of signposted route from Mannheim via Heidelberg to Pforzheim and back.
1893: Inauguration of the Pforzheim Synagogue.
The company Wellendorff, a family-owned jewellery producting until now, is founded by Ernst Alexander Wellendorff. The enterprise sells many kinds of jewelry at the highest level worldwide.
From 1900: Revival of the Pforzheim watchmaking industry.
1906: The 1st FC Pforzheim Football (soccer) Club was defeated by VfB Leipzig with a score of 1:2 in the final game of the German soccer championship.
1914–1918: Pforzheim was not a battlefield in World War I, but 1600 men from Pforzheim lost their lives as soldiers on the battlefields.
1920s: The Pforzheim watchmaking industry thrived due to the new popularity of wrist-watches.
1927: Pforzheim-born (1877) Professor of Munich University Heinrich Otto Wieland received the Nobel prize in chemistry.
From 1933: Along with the installation of the Nazi government in Germany the local subsidiaries of all political parties, groups and organizations other than the NSDAP were gradually disbanded in town. Public life as well as individual affairs were increasingly affected by Nazi influences. Persecution of Jewish fellow citizens occurred in Pforzheim, too, with boycotts of Jewish shops and companies.
1938: Establishment of the municipal Jewellery Museum.
1938: On November 9, the so-called Kristallnacht, the Pforzheim Synagogue (see WWW-site) of the Jewish community was so badly damaged by Nazi activists that it had to be demolished later on.
1939: Regional Administration Pforzheim (Bezirksamt) was converted to the Rural District Pforzheim (Landkreis) with Pforzheim city as its administrative site. However, the town itself became a district-less administrative body.
1940: Deportation of Jewish citizens of Pforzheim to the concentration camp in Gurs (France). Only 55 of the 195 deported persons escaped from the holocaust.
1944: Many factories were converted to produce weaponry such as anti-aircraft shells, fuzes for bombs, and allegedly even parts for the V1 and V2 rockets.
1945: On 23 February, Pforzheim was bombed in one of the most devastating area bombardments of World War II. It was carried out by the Royal Air Force (RAF) on the evening of February 23, 1945. About one quarter of the town's population, over 17,000 people, were killed in the air raid, and about 83% of the town's buildings were destroyed. The mission order to bomb Pforzheim issued by RAF Bomber Command states as the intention of the raid on Pforzheim "to destroy built up area and associated industries and rail facilities". The bombardment was carried out as part of the British carpet bombing campaign. The town was put on the target list for bombardments in November 1944 because it was thought by the Allies to be producing precision instruments for use in the German war effort and as transport centre for the movement of German troops. (Additional details are given in Bombing of Pforzheim in World War II.)
There were also several minor raids in 1944 and 1945.
After the main attack, about 30,000 people had to be fed by makeshift public kitchens because their housing had been destroyed. Almost 90% of the buildings in the core city area had been destroyed. Many Pforzheim citizens were buried in mass graves at Pforzheim's main cemetery because they could not be identified. There are also many graves of complete families. Among the dead were several hundred foreigners who had been in Pforzheim as forced labor workers. The inner-city districts were severely depopulated. According to the State Statistics Bureau (Statistisches Landesamt), in the Market Square area (Marktplatzviertel) in 1939 there were 4,112 registered inhabitants, in 1945 none (0). In the Old Town area (Altstadtviertel) in 1939 there were 5,109 inhabitants, in 1945 only 2 persons were still living there. In the Leopold Square area, in 1939 there were 4,416 inhabitants, in 1945 only 13.
The German Army Report of February 24, 1945 devoted only two lines to reporting the bombardment: "In the early evening hours of February 23, a forceful British attack was directed at Pforzheim." RAF Bomber Command later assessed the bombing raid as the one with "probably the greatest proportion (of destroyed built-up area) (of any target) in one raid during the war".
In early April as the allied forces and notably the French Army advanced toward Pforzheim, the local German military commander gave orders to destroy the electric power generating plant and those gas and water supply lines that were still working, but citizens succeeded in persuading the staff sergeant in charge of the operation to refrain from this absurd endeavor in the face of the imminent and inevitable surrender of the German military. Likewise, orders were issued for the destruction of those bridges that had remained unscathed (some of the bridges had been destroyed by air strikes even before and after February 23), and this could not be prevented. Only the Iron (Railway) Bridge in Weißenstein ward was saved by stout-hearted citizens who, during an unguarded moment, pulled off the fuze wiring from the explosive devices, which had already been installed, and dropped it into Nagold river. Soon after that on April 8, French troops (an armored vehicle unit) moved into Pforzheim from the northwest and were able to occupy the area north of Enz river, but the area south of the Enz river was defended by a German infantry unit using artillery. Fighting was especially fierce in Broetzingen. The French army units (including an Algerian and Moroccan unit) suffered heavy losses; among the dead was the commander of the army unit, Capitaine Dorance. The advance of the French army came to a halt temporarily, but with the support of fighterbomber aircraft and due to the bad condition of the defenders (which included many old men and young boys who had been drafted in a last desperate war effort) the French troops finally succeeded and on April 18 took possession of the vast rubble field which once was the proud residential town of the Baden Margraves.
The three months of French occupation were reportedly marked by hostile attitudes on both the French army side and the Pforzheim population side; incidences of rape and looting, mainly by Moroccan soldiers, were also reported. Au Bridge (Auerbruecke) and Wuerm Bridge received makeshift repairs by the French military. The US Army, which replaced the French troops on July 8, 1945, helped repair Goethe Bridge, Benckiser Bridge, Old Town Bridge (Altstädterbrücke) and Horse Bridge (Roßbrücke) in 1945 and the following year. The relationship between the population and the US military was reportedly more relaxed than had been the case with the French army.
1945–1965: Pforzheim was gradually rebuilt, giving Pforzheim a quite modern look. In September 1951 the Northern Town Bridge (Nordstadtbrücke) was inaugurated (the ceremony was attended by then Federal President Prof. Dr. Theodor Heuss). Jahn Bridge followed in December 1951, Werder Bridge in May 1952, the rebuilt Goethe Bridge in October 1952, and the rebuilt Old Town Bridge was inaugurated in 1954.
1955: On the occasion of the 500th birthday anniversary of Johannes Reuchlin, the city of Pforzheim established the Reuchlin Prize and awarded it for the first time in the presence of then President of the Federal Republic of Germany (West-Germany), Prof. Dr. Theodor Heuss.
1961: Inauguration of the culture center "Reuchlinhaus", which from then on housed the Jewellery Museum, the Arts and Crafts Association, the City Library, the Homeland Museum (Heimatmuseum), and the City Archives.
1968: On July 10 shortly before 22:00, Pforzheim and its surrounding areas were hit by a rare tornado. It had strength F4 on the Fujita scale. Two persons died and more than 200 were injured, and 1750 buildings were damaged. Across the town between Buechenbronn ward and the village of Wurmberg the storm caused severe damage to forest areas (i.e. most trees fell to the ground). During the first night and the following days the soldiers of the French 3rd Husar Regiment and the US Army Unit, which were still stationed at the Buckenberg Barracks, helped clear the streets of a lot of fallen trees (especially in the Buckenberg/Haidach area). It took about four weeks to carry out the most necessary repairs on buildings. The overhead electric contact wires for the electric trolley buses then still operating in town and the streetcar transport system to the village of Ittersbach were never repaired; those transport systems were retired.
1971–1975: The townships of Würm, Hohenwart, Buechenbronn, Huchenfeld and Eutingen were incorporated into the city administration.
1973: Inauguration of the new Pforzheim City Hall.
1973 As part of the reform of administrative districts, the rural district of Pforzheim was incorporated into the newly established Enz rural district, which has its administration in Pforzheim. But the city of Pforzheim itself remains a district-less city. In addition, Pforzheim became the administrative center of the newly formed Northern Black Forest Region.
1975 On January 1, the population exceeded 100.000 and Pforzheim gained the status of a "large city" (Grossstadt).
1979: Inauguration of the Pforzheim City Museum.
1983: Inauguration of the "Technical Museum of the Jewellery and Watchmaking Industry" and the "Citizens Museum".
1987: Inauguration of the City Convention Center.
1987/1990: Inauguration of the City Theater at the Waisenhausplatz.
1989: Sister City agreement with the City of Gernika, Spain.
1990: Sister City agreement with the City of Saint-Maur-des-Fosses, France.
1991: Sister City agreement with the City of Vicenza, Italy.
1992: State Gardening Expo in Pforzheim. Enzauenpark was created and part of the Enz river was re-naturalized.
1994: Inauguration of the cultural institution "Kulturhaus Osterfeld".
1994: Merger of the Pforzheim Business School and the Pforzheim School of Design to form the Pforzheim University of Applied Sciences in Design, Technology and Business.
1995: Inauguration of the Archeological Site Kappelhof.
2000: Inauguration of the Pforzheim Gallery.
2002: In November, during excavation works for a new shopping center right in the center of the city, a power shovel hit a 250 kg bomb which had not gone off during the bombardment of 1945. On a Sunday, about 5000 citizens had to temporarily leave their homes as a precautionary measure while specialists were defusing and disposing of the (so far) last of a large number of unexploded explosive devices found in Pforzheim's grounds since 1945.
See also History of Baden.
Administrative unions
Formerly independent communities and districts which were incorporated into the City of Pforzheim.
Year Community Increase in km²
January 1, 1905 Broetzingen 13.01
January 1, 1913 Dillweissenstein 4.612
April 1, 1924 Parts of Haidach district 0.76
October 1, 1929 Parts of Hagenschiess district 16.23
September 1, 1971 Würm 8.22
April 1, 1972 Hohenwart 4.92
January 1, 1974 Büchenbronn 11.14
January 1, 1975 Huchenfeld 9.47
September 20, 1975 Eutingen on the Enz 8.45
Population growth
The table below shows the number of inhabitants for the past 500 years. Until 1789 the numbers represent estimates, after that they represent census results (¹) or official recordings by the Statistics Offices or the city administration.
Year Population figures
1500 c. 800
1689 c. 1,000
1789 4,311
1810 5,572
1830 6,284
1855 10,711
1849 12,377
December 1, 1871¹ 19,803
December 1, 1890 ¹ 29,988
December 1, 1900 ¹ 43,373
December 1, 1910 ¹ 69,082
June 16, 1925 ¹ 78,859
June 16, 1933 ¹ 79,816
May 17, 1939 ¹ 79,011
1946 46,752
September 13, 1950 ¹ 54,143
June 6, 1961 ¹ 82,524
May 27, 1970 ¹ 90,338
June 30, 1975 108,635
June 30, 1980 106,500
June 30, 1985 104,100
May 27, 1987 ¹ 106,530
December 31, 1990 112,944
June 30, 1997 118,300
December 31, 2000 117,156
June 30, 2003 115,777
¹ Result of census
The population growth diagrams show that the largest growth rates were recorded between about 1830 and 1925, which was the period following the political reorganisation of Europe agreed upon at the Vienna Congress of 1815 after the violent period that was so much dominated by Napoleon Bonaparte of France. This high population growth period coincided with the period of intensive industrialisation of Germany. Population growth weakened due to the effects of World War I and World War II. The population declined sharply due to the destruction on February 23, 1945, and increased sharply in the post-WWII era due to high economic growth levels in West-Germany and the rapid rebuilding efforts in Pforzheim. Earlier setbacks were recorded during the Thirty Years' War period in the 17th century.
Religions
After margrave Karl II of Baden in 1556 installed the Protestant Reformation in the Margraviate of Baden, of which Pforzheim was the capital in those days, Pforzheim continued to be a Protestant town for several centuries. The congregations in Pforzheim were affiliated with the deanery (Dekanat) of Pforzheim of the Protestant National Church of Baden, unless they were members of one of the independent churches (Freikirche).
Since the 19th century at the latest Catholics settled in Pforzheim again. They are affiliated with the deanery of Pforzheim which belongs to Archdiocese of Freiburg.
Other denominations and religious sects in Pforzheim are:
Research Tips
This page uses content from the English Wikipedia. The original content was at Pforzheim. The list of authors can be seen in the page history. As with WeRelate, the content of Wikipedia is available under the Creative Commons Attribution/Share-Alike License.
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Place:Westover, Clearfield, Pennsylvania, United States
Watchers
NameWestover
TypeBorough
Coordinates40.751°N 78.672°W
Located inClearfield, Pennsylvania, United States
Also located inChest, Clearfield, Pennsylvania, United States
source: Getty Thesaurus of Geographic Names
the text in this section is copied from an article in Wikipedia
Westover is a borough in Clearfield County, Pennsylvania, United States. The population was 390 at the 2010 census.
Research Tips
This page uses content from the English Wikipedia. The original content was at Westover, Pennsylvania. The list of authors can be seen in the page history. As with WeRelate, the content of Wikipedia is available under the Creative Commons Attribution/Share-Alike License.
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Place:Westwood, Lassen, California, United States
Watchers
NameWestwood
TypeCensus-designated place
Coordinates40.305°N 121.003°W
Located inLassen, California, United States
source: Getty Thesaurus of Geographic Names
source: Family History Library Catalog
the text in this section is copied from an article in Wikipedia
Westwood is a census-designated place (CDP) in Lassen County, California, United States. Westwood is located west-southwest of Susanville, at an elevation of 5128 feet (1563 m).[1] The population was 1,647 at the 2010 census, down from 1,998 at the 2000 census.
The BNSF Railway (BNSF) has a Maintenance of Way station and a siding that is used to store BNSF snow fighting equipment.
Research Tips
This page uses content from the English Wikipedia. The original content was at Westwood, California. The list of authors can be seen in the page history. As with WeRelate, the content of Wikipedia is available under the Creative Commons Attribution/Share-Alike License.
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Source:Lewis, George Harlan. Edmund Lewis of Lynn, Massachusetts : And Some of His Descendants
Watchers
Source Edmund Lewis of Lynn, Massachusetts : and some of his descendants
Author Lewis, George Harlan
Coverage
Surname Davis, Gordon, Ingalls, Lewis, Newhall, Phillips, Stone
Subject History
Publication information
Type Miscellaneous
Publisher Genealogical Society of Utah
Date issued 1977
Place issued Salt Lake City, Utah
Citation
Lewis, George Harlan. Edmund Lewis of Lynn, Massachusetts : and some of his descendants. (Salt Lake City, Utah: Genealogical Society of Utah, 1977).
Repositories
Family History Centerhttp://www.familysearch.org/eng/library/fhlcatal..Family history center
Usage Tips
May be ordered through the nearest Family History Center.
FHL film numbers
• 1016921 Item 10
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Australian Bureau of Statistics
Celebrating the International Year of Statistics 2013
ABS Home > Statistics > By Catalogue Number
4159.0 - General Social Survey: Summary Results, Australia, 2010
Latest ISSUE Released at 11:30 AM (CANBERRA TIME) 30/09/2011
Page tools: RSS Search this Product
Presents results of the 2010 General Social Survey, which brings together a wide range of information to enable it to be linked across areas of social concern. The focus is on the relationships between characteristics from different areas, rather than in depth information about a particular field. Topics include health, housing, education, work, income, financial stress and resilience, broad assets and liabilities, transport, social capital, voluntary work, family and community, and crime. Provides an overview through summary tables for different population groups and selected themes. More detailed cross classified tables also cover selected themes.
This product is produced in Printed publication format on a Irregular basis.
Issue Details
Latest Issue: 2010
Price on Application
© Commonwealth of Australia 2013
Unless otherwise noted, content on this website is licensed under a Creative Commons Attribution 2.5 Australia Licence together with any terms, conditions and exclusions as set out in the website Copyright notice. For permission to do anything beyond the scope of this licence and copyright terms contact us.
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104 reputation
6
bio website lavinski.tumblr.com
location Brisbane, Australia
age 23
visits member for 1 year, 3 months
seen Apr 20 at 4:03
stats profile views 8
C# .Net and Games Developer
Read more at
Twitter: http://twitter.com/lavinski
Blog: http://lavinski.tumblr.com
Facebook: http://www.facebook.com/Lavinski
May
25
asked What are the typical duties of an accountant for a software startup?
May
24
asked Becomming an app developer
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Wikia
SRD:Hat of Disguise
Talk0
9,502pages on
this wiki
Revision as of 06:37, August 11, 2009 by Surgo (Talk | contribs)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
This material is published under the OGL
Hat of Disguise: This apparently normal hat allows its wearer to alter her appearance as with a disguise self spell. As part of the disguise, the hat can be changed to appear as a comb, ribbon, headband, cap, coif, hood, helmet, and so on.
Faint illusion; CL 1st; Craft Wondrous Item, disguise self; Price 1,800 gp.
Back to Main PageSystem Reference DocumentMagic Items
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CT-PC89E
From eLinux.org
Revision as of 15:03, 4 March 2010 by Lkcl (Talk | contribs)
Jump to: navigation, search
Chitech CT-PC89E
The CT-PC89E is a low-cost netbook with an 8.9in 1024x600 screen, weighing only 720 grammes (0.72kg). In size it's approximately 23.5 x 16.5 x 2.5 cm (9.25 x 6.5 x 1 in). Its 667mhz Samsung S3C6410 embedded ARM CPU is on a factory-upgradeable SO-DIMM which also has, in the standard low-cost option, 256mb of RAM and 2gb of NAND Flash. The rest of the features are pretty much "standard" fare for a low-cost netbook: 2x USB2, stereo speakers, microphone, SD-Card slot, headphone and microphone sockets, and 802.11 WIFI. A built-in Webcam is available as an option. To further save on cost, there is a micro VGA output, but by default the IC to enable it is again optional. Also, the design has two internal USB2-capable (only) PCI-express slots, which can take 50x30mm PCI-e cards. One is occupied with the RALink RT2070 WIFI, whilst the other is designed to take a 3G or an EDGE modem: there is even a slot for a SIM card (next to the SD card slot).
As this machine is very new, only a few brave Debian-ARM souls have bought it so far, direct from the factory in China, in order to evaluate it and help re-engineer it. We're aware that one other U.S. customer has ordered a batch of them, thus guaranteeing its production over the next few months (as of Feb 2010). The nice surprise is that far from being truly dreadful, the embedded OS on the device, from http://mid-fun.com is actually pretty good: it's called MOS and the web site is here: http://mid-linux.org. As of yet, we've been unable to reach Mid-Fun to get them to provide the root password and the GPL source code of the OS, but that's okay because we've discovered three security flaws in two days, each of which gives full root access to the machine. (24feb2010: by running "john" on the DES64/64 root passwd entry, we've established that the root password is mos2010)
So, at this early stage, for more information please contact mailto:lkcl@lkcl.net, mailto:luke.leighton@gmail.com or Asia Sourcing http://www.asiasourcing.net/ and as soon as we find or hear from a retail outlet or a distributor brave enough to sell these systems we'll let you know.
Also worth noting: we're currently asking the factory for a price on engineering an SO-DIMM with 512mb of DDR2 RAM and an 833mhz Samsung ARM Cortex A8: the S5PC100, which is the same CPU as used in the iPhone 3G. This would ironically not only reduce the price of the system, because DDR1 RAM is actually more expensive than DDR2, but also give it a huge performance jump, without increasing power consumption (the S5PC100 is a 45nm part).
The mailing list is presently being kindly hosted by Alain Williams, at http://lists.phcomp.co.uk/mailman/listinfo/arm-netbook
There is a description of the system, and photos (internal and external), here: http://lkcl.net/arm_systems/CT-PC89E
Info Pages
Technical Info
This section contains technical info needed to configure a linux kernel. Taken from kern.log
• LCD Type is: N10116 (innolux?)
• DM9000 is at f7600300,f7600304 IRQ74
• fb0 map video memory: ff200000:0012c000 dma=5e200000
• fb1 map video memory: ff32d000:0012c000 dma=5e400000
• fb0 map video memory: ff45a000:0012c000 dma=5e600000
• mmc0 (NAND flash) address 9535
• mmc1 (SDcard) address a95c
• audio: WM9713/WM9714
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Italy, Napoli, Serrara Fontana, Civil Registration (FamilySearch Historical Records)Edit This Page
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Modify
Opened 3 years ago
Closed 3 years ago
Last modified 3 years ago
#4538 closed defect (fixed)
Orthogonalization refuses to work on some almost-orthogonal shapes
Reported by: bilbo Owned by: bastiK
Priority: normal Component: Core
Version: Keywords:
Cc:
Description
Seem the orthogonalization refuses to do anything and just spit error message when even one tiny segment of way have angle about 45 degrees in relation to rest of the segments.
In attachment there is example of such way.
This error message is thrown even when I explicitly select two nodes on the way to specify the orthogonalization direction.
While it may be useful for newbies so they won't accidentally orthogonalize something that should not be orthogonalized, I think the orthogonalization action should be a bit less picky about what to orthogonalize and not and it should never fail when I explicitly pick two points. (there is an undo function after all .... )
Attachments (1)
noorto.osm (1.1 KB) - added by bilbo 3 years ago.
Example of unorthogonalizable building
Download all attachments as: .zip
Change History (4)
Changed 3 years ago by bilbo
comment:1 Changed 3 years ago by bastiK
• Owner changed from team to bastiK
comment:2 Changed 3 years ago by bastiK
• Resolution set to fixed
• Status changed from new to closed
comment:3 Changed 3 years ago by bastiK
Modify Ticket
Change Properties
<Author field>
Action
as closed .
as The resolution will be set. Next status will be 'closed'.
The resolution will be deleted. Next status will be 'reopened'.
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E-mail address and user name can be saved in the Preferences.
Note: See TracTickets for help on using tickets.
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TOPOGRAPHY-INDUCED FOCUSING OF RANDOM WAVES
Pieter Bart Smit, T. T. Janssen, T. H. C. Herbers
Abstract
Refraction of narrow-band surface waves in coastal areas can result in wave-focal zones where due to interference, wave statistics vary rapidly and on similar length scales as those of individual waves. However such interference patterns, or wave coherence, are not accounted for in conventional stochastic wave models that are based on the energy balance equation or radiative transfer equation. In this work we present a quasi-coherent theory, which is an extension of the radiative transfer equation and quasi-homogeneous theory. We show that this new stochastic modelling approach can resolve rapid variations in wave statistics that occur in the vicinity of a wave caustic. The results compare favourably to those obtained from ensemble averages calculated with a deterministic phase resolving model (SWASH) and, in a focal zone, constitute a significant improvement over those obtained with a conventional stochastic wave model based on an energy balance equation (SWAN).
Keywords
wave focusing; random waves; stochastic wave model
References
Mandel, L. & Wolf, E. 1995 Optical coherence and Quantum Optics. Cambridge, Cambridge Univ. Press. 595 pp.
Mase, H. 2001, Multi-Directional Random Wave Transformation Model Based On Energy Balance Equation, Coastal Engineering, 43, 317-337http://dx.doi.org/10.1142/S0578563401000396
McWilliams, J. C. & Restrepo, J. M. 1999 The wave-driven ocean circulation. Oceanogr. 29, 2523–2540.
O'Reilly, W. C. & Guza, R. T. 1991 Comparison of spectral refraction and refraction-diffraction wave models. J. Wat, Port Coast. Ocean Eng. 117, 199–215.
Resio, D.T., 1988. A steady-state wave model for coastal applications. Proceedings of 21 st Conference on Coastal Engineering, ASCE, 929 – 940.
Stamnes, J.J. 1986 Waves in focal regions: propagation, diffraction, and focusing of light, sound, and water waves. Boston, A. Hilger.
PMid:3810572
Penney, W. G. & Price, A. T. 1952 Part i. the diffraction theory of sea waves and the shelter afforded by breakwaters. Proc. R. Soc. London 244 (882), 236–253.
Smit, P.B. & Janssen, T.T. 2011, Coherent interference and diffraction in random waves, presented at the 12th International Workshop on Wave Hindcasting and Forecasting. Kohala Coast, Hawaii
Smit, P.B. & Janssen, T.T. 2012 Coherent structures in random waves. Manuscript in preparation for J. Phys. Ocean.
Stiassnie, M., Regev, A. & Agnon, Y. 2008 Recurrent solutions of alber's equation for random water wavefields. J. Fluid Mech. 598, 245–266.http://dx.doi.org/10.1017/S0022112007009998
The WAMDI Group 1988 The wam model - a third generation ocean wave prediction model. J. Phys. Ocean. 18, 1775–1810.
Thomson, J., Elgar, S., Herbers, T. H. C., Raubenheimer, B. & Guza, R. T. 2007 Refraction and reflection of infragravity waves near submarine canyons. J. Geophys. Res. 112, C10009http://dx.doi.org/10.1029/2007JC004227
Tolman, H. L. 1991 A third-generation model for wind waves on slowly varying, unsteady, and inhomogeneous depths and currents. J. Phys. Ocean. 21, 782–797.http://dx.doi.org/10.1175/1520-0485(1991)021<0782:ATGMFW>2.0.CO;2
Wise Group 2007 Wave modelling - the state of the art. Progr. In Oceanogr. 75, 603–674.http://dx.doi.org/10.1016/j.pocean.2007.05.005
Zijlema M., Stelling G., and Smit. P.B., 2011, SWASH: An operational public domain code for simulating wave fields and rapidly varied flows in coastal waters. Coastal Engineering, 58, 992–1012.http://dx.doi.org/10.1016/j.coastaleng.2011.05.015
Full Text: PDF
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A time for action: One student's commitment to free and open access
Image credits: opensource.com
(8 votes)
Information is power. But like all power, there are those who want to keep it for themselves.—Aaron Swartz
I have been a PhD student for less than two years. On the other hand, for six years, I have been a member of the free culture movement, which emphasizes the importance of access to and openness of technology and information.
Recently, I’ve been frustrated... sad... angry. Just over a year ago, a friend and fellow member of the free culture community, Ilya Zhitomirskiy, committed suicide. He was 22. A few weeks ago, an acquaintance, a friend of many close friends, and—really—a role model, just one year older than myself and networked with many institutions and individuals I have come to work with and/or admire (such as MIT, the Berkman Center, the EFF, Creative Commons; frankly, there are too many individual people to list) committed suicide. Aaron Swartz was admired for his bravery to stand up for his ideals, and the work he put into the world demonstrated no less than exactly those ideals. I followed his actions with awe and complete understanding.
When I look at the goals that Aaron pursued, I feel disappointed in myself for not also working harder toward similar aspirations. But I want that to change. Though Aaron frequently called for more extreme forms of activism, such as through his Guerilla Open Access Manifesto, I want to begin with what is an easy solution that has been solvable for years, which I do not even think deserves to be called activism. It’s merely what should be.
So I have decided that I will further my ideals by refusing to restrict the knowledge I create in outdated publishing models that retain and maintain a detrimental status quo within the academic community. I know that Aaron detested the absurdity of contemporary academic establishments and norms; in many regards, I agree with his sentiments wholeheartedly.
But even though I still commit to furthering my career as a pursuer and producer of knowledge, I recognize that things just have to change already. We need to fix this.
Accessible by default
The easiest thing... is simply not volunteering our labor to lock academic writing away from the public.—Nick Montfort
While I’ve supported and campaigned for open access in the past as a member of Students for Free Culture, I can no longer support the outdated, profit-driven models of modern academic publishing companies. I feel it is finally time to stand up and challenge the status quo, in which academics send knowledge to journals whose sole purpose of existing is to disseminate that knowledge to others. By blocking access to and charging fees for that knowledge, I believe that journals have failed in the primary purpose for the education system as a whole: to teach and share knowledge with others.
There’s an inherent flaw in modern academia: scholars are expected to publish in "high ranking" journals, foundational compilations of academic articles that—over time—have become engrained in the institutional social fabric of knowledge production within the academy. They are, however, closed to the public. But these kinds of journals do nothing for someone like me, a young, digitally networked, curious researcher. Unlike scholars of the past, I no longer wait for journals to appear on my doorstep to gain access to the latest scholarship; the internet, search engines, and personal homepages are my distributors and discovery mechanisms.
It angers me that scholars think that the solution to this status quo is to post copies of their articles online. Some academics, in reality, must publish in closed journals and thus decide to free their own writing individually. But in my opinion, that is not enough. By continuing to publish in and thereby support closed journals, we continue to maintain and uphold an outdated mode of knowledge circulation. Scholars need to realize that the base act of publishing in a closed journal continues its existence: even if you make your own knowledge available, others’ may not be.
I’m no longer afraid of the threat that publishing in certain closed journals might affect my career. My future depends on my work being relevant and widely read. And I will never support nor desire an institution that would punish me for pursuing those goals.
I am boycotting locked-down journals and I'd like to ask other academics to do the same.—Danah Boyd
What I must do
I have come to the conclusion that my knowledge should and will be accessible. Therefore, I will only publish openly.
I will only publish in open access journals.
I will only review for open access publications.
I will only sign book and chapter contracts that share copies of the text online (whether licensed through Creative Commons or made available in some other, free form).
I will only attend conferences that make any related publications accessible for free.
I will also only contribute to open access publications that do not charge authors inordinate costs for publishing.
The academic community is only hurting itself, and its long term public support, by keeping its knowledge behind high subscription walls.—Andrew Carr
What you (and we) can do
Change begins when we as a community move forward together. However, absolute change can only come about with absolute decisions.
If you are a graduate student:
• Adopt the same stance: only publish in open access academic venues; refuse all others.
• Encourage your cohort, classmates, friends, colleagues, teachers, and advisors to do the same.
If you are a senior scholar:
• Help young scholars like me establish a variety of new and current open venues for publication.
• Refuse to review for closed journals; volunteer to review for open access publications.
• Cite scholarly works from open access venues when research is worthy of it.
• Recognize junior faculty’s efforts in the tenure process for pursuing open access ideals.
• Petition closed journals to shift their policies to open access.
• Help spread the word that closed publications are no longer acceptable.
Open Access benefits literally everyone, for the same reasons that research itself benefits literally everyone.—Peter Suber
The movement toward open access as a norm within academia has been and will likely be a slow and ongoing process, and many better people than myself have contributed to changing the status quo in substantial ways. But I feel that individual decisions like the one made on this page can contribute to that shift and ultimately change this situation. If you are ready to take the same step, I encourage you to promote your thoughts on your own webpage and spread the word. There’s no image to share, no petition to sign, no badge to display: at this critical and crucial point, there is only action.
Originally posted on Alex Leavitt's website. Reposted under Creative Commons.
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The danger of transparency: A lesson from Slovakia
Image by opensource.com
(7 votes)
A week ago I wrote an article about the winners of the Open Data Challenge. The winner of the application category was ZNasichDani.sk ("From Our Taxes" in Slovak), which provides an interface for users to find the people standing behind companies and enterprises that are linked to government contracts. It empowers citizens to review those connections, including contract prices and commissions.
However, it appears some people might not be very comfortable with the additional transparency this application provides. Apparently, one of the relevant company’s managers found herself in the database and took the case to the court. The court in Bratislava requested immediate censorship of some information, including prices in the application, even though all data displayed in the application comes from publicly-available sources. This injunction has been issued before any final verdict in the case. Zuzana Wienk, director at Fair-Play Alliance - the owner of the application, considers this court action to be a violation of Slovakia’s constitution .
As Irish politician Gerry Adams once said, one man's transparency is another's humiliation. That's why open data, which can make publicly-available information even more accessible and transparent, sometimes doesn't come easy.
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Tigerfly's bookmarks
"Remember tonight.. for it is the beginning of always."
Unknown, Source on beginning
6 fans of this quote
"Nothing separates the generations more than music. By the time a child is eight or nine, he has developed a passion for his own music that is even stronger than his passions for procrastination and weird clothes."
Cosby, Bill on music
5 fans of this quote
"The most important thing that parents can teach their children is how to get along without them."
Clark, Frank A. on parents and parenting
5 fans of this quote
Cindy's quote collection
I'm female and made my book on 25th March 2011.
My book as a pdf
My feed
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Quotation added by staff
Why not add this quote to your bookmarks?
The fickleness of the women I love is only equaled by the infernal constancy of the women who love me. Shaw, George Bernard
This quote is about love · Search on Google Books to find all references and sources for this quotation.
A bit about Shaw, George Bernard ...
George Bernard Shaw (July 26, 1856 November 2, 1950) was an Irish playwright and winner of the Nobel Prize for Literature in 1925.
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Quotation added by staff
Why not add this quote to your bookmarks?
From things that have happened and from things as they exist and from all things that you know and all those you cannot know, you make something through your invention that is not a representation but a whole new thing truer than anything true and alive, and you make it alive, and if you make it well enough, you give it immortality. That is why you write and for no other reason that you know of. But what about all the reasons that no one knows? Hemingway, Ernest
This quote is about creativity · Search on Google Books to find all references and sources for this quotation.
A bit about Hemingway, Ernest ...
Ernest Miller Hemingway (July 21, 1899 July 2, 1961) was an American novelist and short story writer whose works, drawn from his wide range of experiences in World War I, the Spanish Civil War, and World War II, are characterized by terse minimalism and understatement; they exerted a significant influence on the development of twentieth century fiction. Hemingway's protagonists are typically stoic male individuals, often interpreted as projections of his own character, who must master "grace under pressure". Many of his works, like The Sun Also Rises, A Farewell to Arms and The Old Man and the Sea, are now considered classics in the canon of American literature.
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It's easy! Just pick the product you like and click-through to buy it from trusted partners of Quotations Book. We hope you like these personalized gifts as much as we do.
Make and then buy your OWN fantastic personalized gift from this quote
One out of four people in this country is mentally imbalanced. Think of your three closest friends. If they seem okay, then you're the one. Landers, Ann
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212 - The Extra Degree
The one extra degree makes the difference. This simple analogy reflects the ultimate definition of excellence. Because it's the one extra degree of effort, in business and life, that can separate the good from the great. This powerful book by S.L. Parker and Mac Anderson gives great examples, great quotes and great stories to illustrate the 212° concept. A warning - once you read it, it will be hard to forget. Your company will have a target for everything you do ... 212°
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It's easy! Just pick the product you like and click-through to buy it from trusted partners of Quotations Book. We hope you like these personalized gifts as much as we do.
Make and then buy your OWN fantastic personalized gift from this quote
Beauty is only skin deep, but it's a valuable asset if you're poor or haven't any sense. Hubbard, Kin
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212 - The Extra Degree
The one extra degree makes the difference. This simple analogy reflects the ultimate definition of excellence. Because it's the one extra degree of effort, in business and life, that can separate the good from the great. This powerful book by S.L. Parker and Mac Anderson gives great examples, great quotes and great stories to illustrate the 212° concept. A warning - once you read it, it will be hard to forget. Your company will have a target for everything you do ... 212°
Click here to buy this »
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Game 7 Motivation: Part 5
RedsArmyAdmin June 17, 2010 Uncategorized 4 Comments
It ain't about how hard you're hit… it's about how hard you can get hit and keep moving forward… how much you can take and keep moving forward. That's how winning is done.
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Daily Archives: May 13, 2013
Foreign Born Celtic – Michael Olowokandi
It's possible you've erased this fact from your memory, but Michael Olowokandi did play a couple of seasons in Boston. Olowokandi was born on April 3, 1975 in Lagos, Nigeria. His father was a diplomat who eventually moved to London. Michael was an athlete in cricket and rugby among other random sports not called basketball. [...]
August 12, 2011 Jnoble Celtics Uncategorized 1
Celtics Sneaker Madness: Round 2
The hottest release of 2011 thus far, Ray Allen’s AJ XIII, are the first pair to move on to Round 3. They were victorius over his Evolution 85 home version, earning 60% of your votes. Now on to the next match-up: #2 Ray Allen Air Jordan XI white/green/gold I would be scared of what would happen if [...]
August 12, 2011 KWAPT Uncategorized 4
Casting call for Celtics fans in DC/Baltimore
I just received this email from a production company that wishes to remain anonymous: The show is for a network in which we are looking for fans who have knowledge of Boston sports, preferably Celtics. We are looking for them to debate topics about the Celtics (IE: Who is better Russell or Bird and so [...]
August 12, 2011 Chuck - Red's Army Uncategorized 2
Ultimate 1-on-1: Reggie Lewis vs. Bill Russell
Kevin McHale made short work of his former point guard yesterday. Almost 90% of you think McHale would win a 1-on-1 against Dennis Johnson. He moves on to face the winner of the Rajon Rondo, John Havlicek matchup. That's a few days away. Today, we've got Reggie Lewis matching up against Bill Russell. (5) [...]
August 12, 2011 RedsArmyAdmin Uncategorized Comments Off
Shaq wants to fight Danny Ainge
Ok, not really. He was doing a little thing on an MMA show where he was listing NBA guys he would fight. The first four guys were some tough SOB's. Then he said "I'm gonna throw a white guy in there… who's a tough little white guy?" before adding Danny Ainge as the last name [...]
August 12, 2011 RedsArmyAdmin Uncategorized 1
Class is in session..
Our boy Rajon Rondo is back in the 2nd year of Foot Locker's "The Educators" promotion. "Mr. Rondo", the drama teacher joins Stat, (The Principal) Larry Fitzgerald, (Science) Blake Griffin (Detention) and Anna Pierce. (Math) You can "enroll" in the Foot Locker Advantage Academy and complete a full-set of interactive courses-which consist of short video-clips. [...]
August 12, 2011 KWAPT Uncategorized Comments Off
Your Morning Dump… Is the commish on vacation?
Every morning, we compile the links of the day and dump them here… highlighting the big storyline. Because there's nothing quite as satisfying as a good morning dump. Players Association officials disputed NBA commissioner David Stern’s contention that the union canceled a scheduled negotiating session Wednesday with the league. Union sources said the players didn’t [...]
August 12, 2011 Chuck - Red's Army Uncategorized 1
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Australian Bureau of Statistics
Celebrating the International Year of Statistics 2013
ABS Home > Statistics > By Release Date
4914.0.55.001 - Newsletter: Age Matters, Mar 2007
Previous ISSUE Released at 11:30 AM (CANBERRA TIME) 30/03/2007
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Age Matters is a bi-monthly newsletter about age related statistics. It includes topical articles and reviews of relevant ABS publications. Age Matters highlights developments in statistics on the ageing population, and other information of likely interest to ageing researchers and policy makers. Interested readers are also invited to visit the Ageing theme page on the ABS website for links to ageing-relevant ABS datasets and other web sites.
© Commonwealth of Australia 2013
Unless otherwise noted, content on this website is licensed under a Creative Commons Attribution 2.5 Australia Licence together with any terms, conditions and exclusions as set out in the website Copyright notice. For permission to do anything beyond the scope of this licence and copyright terms contact us.
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Australian Bureau of Statistics
Celebrating the International Year of Statistics 2013
ABS Home > Statistics > By Release Date
6291.0.55.001 - Labour Force, Australia, Detailed - Electronic Delivery, Aug 2006
Previous ISSUE Released at 11:30 AM (CANBERRA TIME) 14/09/2006
Page tools: Print Page Print All RSS Search this Product
A range of Excel spreadsheets and SuperTABLE datacubes. The monthly and quarterly spreadsheets contain broad level data covering all the major items of the Labour Force Survey in time series format, including seasonally adjusted and trend estimates. The monthly, quarterly and annual datacubes contain more detailed and cross classified original data than the spreadsheets.
© Commonwealth of Australia 2013
Unless otherwise noted, content on this website is licensed under a Creative Commons Attribution 2.5 Australia Licence together with any terms, conditions and exclusions as set out in the website Copyright notice. For permission to do anything beyond the scope of this licence and copyright terms contact us.
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Australian Bureau of Statistics
Celebrating the International Year of Statistics 2013
ABS Home > Statistics > By Catalogue Number
1352.0.55.019 - Research Paper: Modelling Detailed Business Operating Expenses from ABS Economic Collections (Methodology Advisory Committee), Nov 1998
Latest ISSUE Released at 11:30 AM (CANBERRA TIME) 05/11/1998 First Issue
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BACKGROUND MATERIAL
The background material for this session comprises excerpts from a working paper of the same title, which is currently being written.
Chapter 1 contains an overview of the working paper, and is included to give some perspective on the current state of this research.
Chapter 2 (incomplete) contains some relevant background information on ABS economic collections.
Chapter 3 contains the core of the material which is to be presented in the session. It introduces the motivation for using model-based estimation techniques, develops the theory underlying a number of simple models designed to capture the essential elements of the survey data, and provides a strategy for selecting the best model from the alternatives.
Some material on the issues of model prediction and the extension of the models to provide economy-wide estimates of detailed operating expenses will be presented in the session, but are not specifically addressed in the background papers.
AUTHORS NOTE
The approach to model-based estimation presented in this paper evolved during the course of an empirical review into a range of modelling approaches proposed by other ABS researchers. The models are essentially exploratory in nature, and are not put forward with the intention of supplanting the efforts of those who have the more onerous task of actually producing the official estimates. (Indeed it is unlikely that the more complex models could be made operational within a production environment.) The primary objectives of this research are to gain greater insight into the characteristics of the data, and to provide guidance to those responsible for collecting, processing and interpreting the data. I would strongly welcome any suggestions from the Committee which may assist in re-directing this research to better meet these objectives.
ISSUES SUBMITTED FOR CONSIDERATION BY THE COMMITTEE
A number of issues which have been raised by this research are presented below, under three broad category headings. Each issue is accompanied by a number of supplementary questions and discussion points.
A. Policy issues
A.1 What are the potential advantages and disadvantages of model-based estimation (especially the use of auxiliary information) for ABS respondents and clients? How should ABS assess the net impact and determine whether to proceed?
• Will model-based estimation always result in "superior" estimates?
• What if the auxiliary data are of poor quality?
• Should more auxiliary data items be collected?
• What if the size of the survey is reduced?
• If "size" is shown to be a significant factor in determining the allocation of expenditures (as economic theory would suggest), how should the ABS deal with the representation of small, medium and large businesses in its collections?
• By "pooling" data collected in successive surveys, it may be possible to form better estimates of expenditure patterns, and possibly reduce sample sizes. What are the problems associated with this approach ? [eg. price effects, overlap of respondents, weighting.]
• Does model-based estimation compromise the usefulness of the estimates for subsequent economic analysis? For example, is it possible that the estimation procedure will "build-in" or strengthen relationships between some economic variables, while concurrently destroying other linkages?
B. Technical Issues - General
B.1 Are Committee members aware of any precedents and/or alternatives to the treatment of "missing" data put forward in this research ?
• The proposed modification of the multinomial model to accommodate "missing" data is a conceptually simple idea (although somewhat more complex to implement). It is likely that similar models have been fitted by other researchers ¾ although none have so far come to light.
• Is there is an easier way of accounting for "missing" data ?
B.2 The ABS is required to produce high quality, objective statistics. The use of model-based estimation methods has the potential to impose subjective assumptions upon the data. Conversely, the quality of the estimates may be queried if the ABS uses modelling techniques which appear to contradict established economic theory. Is it possible to meet both criteria ?
• The multinomial model (and variants) imply rather strong assumptions about the nature of expenditure patterns. Is this a problem ? Are there ways of minimising the problem (eg. grouping) ? Are there simple modifications which can be made to the models ?
• What diagnostic tests might be employed to check the distributional assumptions of the models ?
• Can the use of auxiliary variables be made atheoretic ?
B.3 How can the problem of identifying "missing" data be addressed ?
• The main economic surveys currently collect aggregate "other operating expenses" as a single item. Respondents are not required to indicate which of the 25 component items they have included in their total.
• The accuracy of the prediction process could be improved considerably if respondents were required to indicate which expenditure items they have included in "other operating expenses".
• Alternatively, the catch-all category "other operating expenses" could be split, so that additional broad categories of expenditure (eg. Taxes & charges, Repairs & maintenance) can be more satisfactorily identified.
• Some expenditure items are reported by only a small proportion of businesses. When present, these items sometimes account for a significant share of total expenditure. It might be preferable to collect data on such items separately (or not at all).
• There would appear to be advantages in defining "other operating expenditure" to include only those expense items which are incurred regularly by the majority of businesses.
C. Technical Issues - Specific
Comments on any of the following specific topics would be welcome. Please don't restrict your comments to the accompanying dot points.
C.1 "Probability of selection" weights
• "Probability of selection" weights are clearly required at the prediction stage to produce economy-wide estimates. They have also been used throughout the modelling stage to combine contributions to the log-likelihood function. The basic idea is that the model should fit more closely those respondents which represent the largest number of businesses.
• The weights do not necessarily indicate that the response of any individual business is more characteristic of the wider population. This criticism may apply particularly where "missing" data are involved. There is perhaps a case for fitting unweighted models.
C.2 Post-stratification
• Stratification variables are generally determined by reconciling client needs with considerations of sampling efficiency. Model-based estimation, however, cannot be applied at the usual level of detail of such sampling schemes ¾ which may result in only one or two respondents per cell. That is, the model-based estimation approach must assume some degree of homogeneity across sample strata.
• Post-stratification can be implemented by either fitting the model separately to defined subsets of respondents, or (equivalently) by employing categorical explanatory variables. Serious problems of interpretation arise when such categorical variables are combined with auxiliary variables which are not specifically restricted to strata.
• Where post-strata have an inherent ordering (eg. "small" and "large") care will be required to maintain the continuity of fitted functional relationships across strata boundaries.
• The results from modelling may provide useful feedback to survey designers on similarities and dissimilarities between strata and on the need to adjust sample sizes.
C.3 Logit transformation
• The logit transformation will fit a curvilinear relationship between expenditure shares and the explanatory variables. This relationship tends to become more linear and monotonic as the number of categories increases. Is the logit transformation likely to be flexible enough to capture the expected functional relationships ? Are there potential problems at the extremes of the data (or asymptotically) ?
• By fitting the model to hierarchical groups of expense categories, it may be possible to achieve greater functional flexibility.
C.4 Grouping categories
• Modelling expenditure shares within hierarchical groups can undoubtedly lead to substantial computational efficiencies. However, the process of grouping data imposes additional restrictions on the model.
• It is possible that clients may be specifically interested in particular subsets of the model, and it may be advantageous to be able to detach parts of the model.
• Grouping may provide a means of containing problems with infrequently reported data items.
C.5 Imputation
• Imputed data cannot be used for model-based estimation, as the assumptions underlying the imputation process will almost certainly contradict the assumptions of the model.
• How could the model itself be used for imputation ?
C.6 Non-response
• Is it sensible to model the rate of non-response (a component of "missing" data) if the respondents to the detailed survey are subjected to more intensive follow-up than those in the main survey ?
• Should predictions be adjusted for probable non-response ?
C.7 Standard errors on predictions
• This topic has not yet been explored. Any comments or suggestions would be welcomed.
© Commonwealth of Australia 2013
Unless otherwise noted, content on this website is licensed under a Creative Commons Attribution 2.5 Australia Licence together with any terms, conditions and exclusions as set out in the website Copyright notice. For permission to do anything beyond the scope of this licence and copyright terms contact us.
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Australian Bureau of Statistics
Celebrating the International Year of Statistics 2013
ABS Home > Statistics > By Release Date
6321.0 - Industrial Disputes, Australia, Mar 2003
Previous ISSUE Released at 11:30 AM (CANBERRA TIME) 19/06/2003
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• About this Release
ABOUT THIS RELEASE
Continued by 6321.0.55.001
The March 2004 edition will be the first quarterly publication and first electronic publication.
Number of disputes, employees involved, working days lost and working days lost per 1,000 employees in industrial disputes involving stoppages of work of 10 working days or more, classified by State, industry, duration, cause and method of settlement.
More detailed data are released on request.
© Commonwealth of Australia 2013
Unless otherwise noted, content on this website is licensed under a Creative Commons Attribution 2.5 Australia Licence together with any terms, conditions and exclusions as set out in the website Copyright notice. For permission to do anything beyond the scope of this licence and copyright terms contact us.
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Marvel, 1944 Series
< Previous Issue |
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Volume:
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Indicia Publisher:
U.S.A. Comic Magazine Corp.
Format:
Standard U.S. Golden Age; Color; Glossy Cover; Newsprint Interior; Saddle-Stitched
Editing
Table of Contents
This issue was most recently modified by:
• Henry Andrews
Issues in this series have been indexed by:
• Mike Nielsen
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Schibsted, 2003 Series
Series Timeline
See series details by issue (displays one row per issue with no gaps, by the regular issue sort order)
This page attempts to show how the issues in this series were published over time by laying them out in a timeline with alternately gray or white rows roughly corresponding to months. The correspondence is less accurate for bi-monthly, quarterly or annual books. Weekly or other more-frequent-than-monthly issues are simply grouped into the same color row by month.
The timeline feature depends on the key date field to order issues into a timeline. Please note that if the key dates are not filled out to correspond to the publication months of the issues, then the timeline will not be accurate.
Key Date Pub. Date On-sale date Number Indicia Publisher Brand Pages Price ISBN Barcode
2004-00-00 2004 2003-11 [nn] Chr. Schibsteds Forlag AS S Schibsted Forlag 136 [98,00 NOK] 82-516-2101-1 9788251621014
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You are here: Home / About EEA / Documents / Administrative documents / EEA Annual Accounts for the year 2007
EEA Annual Accounts for the year 2007
Note: new versions are available!
Annual accounts for the European Environment Agency, financial year 2007
Published by
• EEA (European Environment Agency)
• Published: May 22, 2008
Content
European Environment Agency (EEA)
Kongens Nytorv 6
1050 Copenhagen K
Denmark
Phone: +45 3336 7100
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Cyprus
Country profile - Distinguishing factors (Cyprus)
Cyprus is the third largest island in the Mediterranean, situated at its north-eastern corner. Being at the intersection of important transport and communication routes it links Europe to the Middle East and Asia. The history of the island, being one of the oldest recorded in the world, was largely influenced by its geographic location. Its strategic position at the crossroads of three continents, as well as its considerable supplies of copper and timber in the past, combined to make it a highly desirable territorial acquisition. Over the centuries, Cyprus was conquered by various nations but managed to retain intact its Greek identity, language and culture. Its geographic position, the country’s island character, its isolation over the centuries from the mainland and its climatic conditions have all led to the creation of a great biological diversity and a significant number of native species.
Biodiversity
Being an island, Cyprus is sufficiently isolated to have allowed the evolution of a strong endemic element. At the same time, being surrounded by big continents, it incorporates elements of the neighbouring land masses. About 7% of the indigenous plants of the island – 140 different species and subspecies – are endemic to Cyprus.
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Barnsley St George, YorkshireEdit This Page
From FamilySearch Wiki
England Yorkshire Yorkshire Parishes West Riding Barnsley St George
Contents
Parish History
BARNSLEY, a township comprised of three chapelries, including St George (1831), St Mary (1568), and St John (1844) in the parish of Silkstone, West Yorkshire. The township includes the hamlets of Old Barnsley, Measborough, Kinston-place, and Old Mill. Other places of worship include Society of Friends, Independents, Primitive Methodists, Methodists of the New Connexion, and Wesleyans; and a Roman Catholic chapel.[1]
Resources
Civil Registration
Birth, marriages and deaths were kept by the government, from July 1837 to the present day. The civil registration article tells more about these records. There are several Internet sites with name lists or indexes. A popular site is FreeBMD.
Church records
Online Records
Online data content from chapelry registers of Barnsley St George exists at some of the following websites and for the specified ranges of years:
AO = Archive.org
FS = FamilySearch.org
FMP = FindMyPast.co.uk (£)
JMI = JoinerMarriageIndex.co.uk
BARNSLEY ST GEORGE Chapelry (1832) Online Records
Baptisms
Marriages
Burials
Indexes Images Indexes Images Indexes Images
FS None
1840
None
JMI None
1832-1837
None
FMP (£) None
None
None
HATH None
None
None
AO None
None
None
To find the names of the neighbouring parishes, use England Jurisdictions 1851. In this site, search for the name of the parish, click on the location "pin", click Options and click List contiguous parishes.
This ancient parish (AP) was created before 1813. Church of England records began in date.
Contributor: Include here information for parish registers, Bishop’s Transcripts, nonconformist and other types of church records, such as parish chest records. Add the contact information for the office holding the original records. Add links to the Family History Library Catalog showing the film numbers in their collection.
Census records
a. Census records from 1841-1891 are available on film through a Family History Center or at the Family History Library. The first film number is 464275. To view these census images online, they are available through the following websites for a fee ($) or free:
• FamilySearch has some of the British Censuses available.
• FindMyPast ($) has all available census records including images, and is free at Family History Centers and the Family History Library and some public and academic libraries.
• Ancestry.co.uk ($) has now all available census records but free at Family History Centers and the Family History Library and at numerous public and academic libraries. The library versions are known as AncestryInstitution.com.
• The Genealogist.co.uk ($) has all available censuses and is free at Family History Centers and the Family History Library and various other libraries.
• FreeCen is a UK census searches. It is not complete and individuals are always asked to consider helping out with transcriptions.
Probate records
Records of wills, administrations, inventories, indexes, etc. were filed by the court with jurisdiction over this parish. Go to Yorkshire Probate Records to find the name of the court having primary jurisdiction. Scroll down in the article to the section Court Jurisdictions by Parish.
Maps and Gazetteers
Maps are a visual look at the locations in England. Gazetteers contain brief summaries about a place.
Web sites
References
1. Wilson, John M., Imperial Gazetteer of England & Wales, publ. London & Edinburgh: 1870. Adapted.
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• This page was last modified on 8 February 2013, at 20:17.
• This page has been accessed 338 times.
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Main Page/NewsEdit This Page
From FamilySearch Wiki
The Southern California Genealogical Society's 39th Annual Genealogy Jamboree will be held Friday through Sunday, June 27 through 29. The ethnic focus is German, Eastern European and Jewish ancestry.
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• This page was last modified on 2 January 2011, at 20:45.
• This page has been accessed 223 times.
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Sachsen (Saxony)Königreich (kingdom) Probate RecordsEdit This Page
From FamilySearch Wiki
Germany Kingdom of Saxony Probate Records
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• This page was last modified on 1 December 2012, at 03:38.
• This page has been accessed 168 times.
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Changes related to "Calcasieu Parish, Louisiana"
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Box Elder County, UtahEdit This Page
From FamilySearch Wiki
Revision as of 22:53, 6 February 2013 by ElizabethSnow (Talk | contribs)
United States Utah Box Elder County
The Box Elder County, Utah genealogy guide to find parents, birth, marriage, death, and more since 1856, when the county was formed. This page lists online, published, and original resources, such as cemeteries, censuses, church, court, land, probate, and obituaries.
Dates for major county records[1]
Birth
Marriage
Death
Census
Land
Probate
1898-present 1888-present 1898-present 1856, 1860... 1856-present 1856-present
For earlier dates, try Church | Obituaries | Cemeteries | Parent counties
Utah
Online Records
Box Elder County, Utah
Map
Location in the state of Utah
Location of Utah in the U.S.
Facts
Founded January 5, 1856
County Seat Brigham City
Courthouse
Address County Courthouse<br>1 South Main St.<br>Brigham City, UT 84302
Website: www.boxeldercounty.org
Named for: the many box elder trees in the area, Latin: Acer_negundo
Cite error: Invalid <ref> tag; refs with no name must have contentList of counties in Utah
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Contents
Helpful Facts
County Court House
Box Elder County Courthouse
1 South Main Street
Brigham City, Utah 84302
Phone: 435:734-3388
County Clerk has birth and death records 1898-1905, marriage records from 1887, divorce, probate, court and land records from 1856.[2]
Parent Counties
Box Elder County, Utah was created January 5, 1856 from: Unorganized territory | Weber and Green River (old)
Boundary Changes
• Boundary changes timeline for Box Elder County, Utah from "UT: Index of Counties," Newberry Library's Utah Atlas of Historical County Boundaries.
Neighboring Counties
Box Elder County, Utah is surrounded by: Tooele | Davis | Weber | Cache | Idaho counties: Cassia | Oneida; Nevada county: Elko
Resources
Bible Records
Biography
• History of Box Elder County [3]
• Box Elder County, Utah newspaper card index historical, biographical, vital records
Newspaper card index to births, deaths, divorces, marriages, and subject index, 1890-1915 [4]
Newspaper card index, locality index [5]
Newspaper card index, biographies [6]
Newspaper card index, subject and vital record index - Corinne newspapers, 1869-1875 [7]
Business Records and Commerce
Cemeteries
Cemetery records often reveal birth, death, relationship, military, and religious information. The spouse and children who died young are frequently buried nearby.
More than tombstone inscriptions, cemetery records include sextons (caretakers) records and interment (burial) records, each with slightly different information. See Utah Cemeteries.
State and national resources for Box Elder County, Utah cemeteries
Online Grave Transcripts
or Images
Published Grave
Transcripts
Lists of Cemeteries
in the County
FindAGrave
Interment.net
Utah Cemeteries & Burial Database
Utah Gravestones
Billion Graves
Linkpendium
Veterans to 1966
FamilySearch Library
Early Church Info File
WorldCat
Utah Periodicals
FindAGrave
USGenWeb Tombstone Project
UTGenWeb Cemeteries
Epodunk
Utah Hometown Locator Cemeteries
Utah Cemeteries Search
Genealogy Trails
See Utah Cemeteries for details about each site.
Additional information on Box Elder County cemeteries
• List of Box Elder County, Utah Cemeteries that exist or in some cases no longer exist.
• The Garland, Utah Interment & Disinterment Registers are part of the FamilySearch Historical Record Collection: Utah, State Archives Records, 1848-2001.
• This register appears to have been started in 1908; but includes references to burials prior to 1908 that presumably came from tombstones standing in 1908.
• USGenWeb Archives Box Elder County, Utah provides names in Plymouth Cemetery and Woodmen of the World of Box Elder County.
____________________
Census
The 1860, 1870, 1880, 1900, 1910, 1920, and 1930 U.S. federal population schedules of Box Elder County are available online. For tips on accessing census records online, see Utah Census. If you're having trouble finding your ancestors in national indexes, try checking local indexes. Created by experts familiar with the area's families, these indexes are often transcribed more accurately than nationwide indexes. See Utah Population Schedule Indexes: Fiche, Film, or Book for more information about statewide printed indexes.
Churches and Religious Groups
The Church of Jesus Christ of Latter-day Saints (the Mormons)
Historically, most people in Utah were Mormons. Their records are, therefore, very important for early Utah research. For additional information, see Tracing LDS Ancestors and Utah Church Records.
Click a church unit name in the chart below for its history, boundaries, and availability of records, which are often in microfilm format
(Section In process. Want to help?)
Box Elder County, Utah guide to history and records of LDS wards and branches
Stakes and the areas they cover:
Places: Beaverdam · Bothwell · Brigham City · Cedar Creek · Corinne · Deweyville · Elwood · Fielding · Garland · Honeyville · Howell · Mantua · Park Valley · Perry · Plymouth · Promontory · Snowville · Tremonton · Washakie · Willard · Yost
Church units without place names:
Beaver Ward, see Beaverdam · Penrose Ward (in a rural area of Box Elder County, Utah) · Thatcher ·
____________________
Court Records
Directories
Ethnic and Other Groups
Funeral Homes
Gillies Funeral Chapel and Crematory[8]
634 East 200 South
Brigham City, UT 84302
Phone: 435-723-5236
Toll Free Phone: 888-723-5236
Fax: 435-723-6905
Myers Mortuary[9]
205 South 100 East
Brigham City, UT 84302
Phone: 435-723-8484
Fax: 435-723-7170
Rogers and Taylor Funeral Home[10]
111 North 1st East
Tremonton, UT 84337
Phone:435-257-3424
Fax: 435-257-7384
Gazetteers
Genealogy
A FamilySearch Community Tree is available for this place.
History
History Timeline
• Boundary changes timeline for Box Elder County, Utah from "UT: Index of Counties," Newberry Library's Utah Atlas of Historical County Boundaries.
NOTE: Unless otherwise mentioned, the events below were gleaned from Wikipedia for Box Elder County.
• 1800’s- The Bear River Valley was originally inhabited by the Fremont and Shoshoni Indians. Then French-Canadian trappers entered the valley.
• 1851. First permanent homes in county at site of present Brigham City. Early name was Box Elder.
• 1851. Willard settled by Mormon settlers.
• 1852. Perry was settled by Orrin Porter Rockwell. Early name was Three Mile Creek.
• 1853. Lorenzo Snow created first self-sufficient city (present-day Brigham City).
• 1856. Box Elder County formed.
• 1861. Honeyville settled. Agricultural community.
• 1863. Mantua settled by Danish families called by authorities of L.D.S. Church to settle in valley.
• 1864. Deweyville settled by William Empey.
• 1868. Elwood settled by homesteaders and families with "squatter rights."
• 1869 May. Golden spike driven at Promontory Summit to connect Union Pacific and Central Pacific railroads.
• 1869. Plymouth founded. Named for imagined resemblance of nearby large rock to the Plymouth Rock.
• 1869. Corinne laid out by Union Pacific and settled by people of different religions.
• 1871. Snowville settled at direction of Brigham Young. Named after Mormon Apostle Lorenzo Snow.
• 1886. Bear River City incorporated.
• 1890. Penrose named for Mormon Apostle Charles W. Penrose.
• 1892. Town of Fielding erected. Named after Mary Fielding Smith.
• 1929. Elwood established. Early name was Manila Ward.
• 1940’s. Economic boost during WWII, with creation of Bushnell General Hospital[11]
• 1950-1960’s. Major growth in county, with Thiokol plant built in 1957.
Land
Wiki articles describing online collection are found at:
Maps
For historical maps of Utah and Box Elder County, see:
Migration
Early migration routes to and from Box Elder County, Utah for emigrant settlers included: :
Military
Naturalization and Citizenship
Newspapers
Small town newspapers contain obituaries, birth or death notices, community news (such as the visit of someone's relatives), legal notices and provide historical content. See Utah newspapers for tips, resources, and details. Resources include:
Obituaries
Obituaries may mention birth, marriage, spouse, parents, and living family members. See Utah Obituaries for state level compendiums and United States Obituaries for tips and insights regarding this record type.
Obituaries for residents may be found in:
Officials and Employees
Periodicals
Poorhouses, Poor Law, etc.
In Utah, such records may be difficult to find. Try records of the church they may have attended. Realize, however, that such records may have not been preserved, and would not be in the typical records of membership.
It is possible there were records kept by civilian authorities. Ask town or county officials and local librarians and the State Archives. Also try National Union Catalog of Manuscript Collections (online).
Probate
Public Records
Resource Repositories
Courthouses
Wikipedia has more about this subject: Box Elder County, Utah
Address: 1 South Main St, Brigham City, UT 84302
Phone (Brigham City): 435-734-3300
Phone (Tremonton): 435-257-5810
Hours: 8am - 5pm Monday - Friday
Box Elder County Home Page History of the Box Elder County Courthouse
County seat: Brigham City
Family History Centers
Libraries
Societies
Brigham City Museum
24 North 300 West
Brigham City, UT 84302
(435) 226-1439
The de facto historical society for Box Elder County. Collections include historical artifacts, photographs, and other archival materials from areas throughout the county. Online collections (partial holdings only)
Bear River City DUP Museum
4600 West 5900 North (in the park)
Bear River, UT 84301
Open on request; free admission
435-279-8350
Brigham City DUP (Restored Log Cabin)
200 North 300 West (Pioneer Park)
Brigham City, UT 84302
Open by appointment; free admission
Taxation
Vital Records
Birth
Below are the best sources to find birth information (dates and places of birth and names of parents) for Box Elder County, Utah. Also available: How to Find Birth Information in Utah.
Follow the suggestions under the year span that matches when your ancestor was born:
Before 1856
Box Elder County, Utah was formed 5 January 1856.
If your records show the person was born here before the county was formed,
search parent counties
1856 - 1897
No birth records were created for Box Elder County, Utah by either by county or state civil authorities in this time period.
Follow these suggestions to find birth information for this time period:
1898-present
County clerks became responsible for recording births beginning in 1898.[17] In 1905, the State Department of Health assumed responsibility and required the counties to forward copies of the records to them.
Records open to the public
Birth records created more than 100 years ago[18] are open to the public.
• 1898-1905 Series #84098 at Utah State Archives. Not online, no online index. Copies available through FamilySearch Library copy: FSL film 480875 . There are no names of children in the records. (Census or church records will help.)
• 1906-1910 online images for Box Elder County, Utah at the State Archives. Browse the "not yet indexed" area by year and county. Most entries do have names of children.
• Online Utah, Births and Christenings, 1892-1941, a FamilySearch Historical Records Collection. (Index only, free). Created from the old IGI, this is a mix of some extracted records and submissions by patrons. Please realize it is not complete.
Restricted records
Access to official birth records within 100 years is restricted to those who meet certain requirements. Order copies:
• Office of Vital Records and Statistics, 288 North 1460 West, Salt Lake City, Utah, Phone: (801) 538-6105. How to order online, by mail, or in person.
____________________
Marriage
Wiki articles describing marriage a collection is found at:
Utah, Box Elder County Records (FamilySearch Historical Records)
Divorce
Death
• Utah Death Certificates 1904 - 1956 -A free internet access to the 1904-1956 death certificates can be viewed at https://www.familysearch.org/ . Utah requires a death certificate before a burial is completed. A death certificate may contain information as to the name of the deceased, date of death, and place of death, as well as the age, birthdate, parents, gender, marital status, spouse and place of residence.
• Utah State Burial Index for death before 1904
• Utah State Vital Records :Utah Department of Health Office of Vital Records & Statistics :P.O. Box 141010 :Salt Lake City, Utah 84114-1010 :Phone: (801) 538-6101
• Box Elder County Utah Vital Records :Box Elder County Clerk :1 S Main Street :Brigham City, UT 84302 :Phone: (435) 734-3388
• First District Court (Divorce Records) :43 North Main :P.O. Box 873 :Brigham City, UT 84302-0873 :Phone: (435) 734-4600 Fax: (435) 734-4610
• Vital records. of Box Elder County, Utah are listed in the FamilySearch Library. To obtain closer-to-home access to resources, see. public libraries.
• USGenWeb Archives Box Elder County, Utah provides the Death Certificates of 1903-1908
Death Record Substitutes
• 1870 - U.S. Federal Census Mortality Schedules, 1850-1885 at Ancestry ($). Includes 1870 Box Elder County, Utah mortality schedule.
Voting Registers
Towns and Communities
References
1. Alice Eichholz, Red Book: American State, County and Town Sources, 3rd ed. (Salt Lake City: Ancestry Pub., 2004), 676-677. At various libraries (WorldCat); FHL Book 973 D27rb 2004.
2. Handybook for Genealogists: United States of America, 10th ed. (Draper, Utah: Everton Pub., 2002), Box Elder County, Utah Page 686 At various libraries (WorldCat); FHL Book 973 D27e 2002.
3. Forsgren, Lydia Walker History of Box Elder County WorldCat 10418828
4. Film [[FHL|1145491
5. FHL 1145492 Item 1
6. FHL 1145492 Item 2
7. FHL 1145492 Item 3
8. Funeral Home and Cemetery Directory.(Youngstown, OH: Nomis Publications, Inc., c2009,937.
9. Funeral Home and Cemetery Directory.(Youngstown, OH: Nomis Publications, Inc., c2009,937.
10. Funeral Home and Cemetery Directory.(Youngstown, OH: Nomis Publications, Inc., c2009,941.
11. Kathleen Bradford, Bushnell General Hospital Utah History Encyclopedia (Accessed 4 September 2012)
12. National Park Service, "California Trail" (map) in California National Historic Trail at http://www.nps.gov/cali/planyourvisit/upload/CALImap1-web.pdf (accessed 2 August 2011).
13. "The Pioneer Story: The Mormon Pioneer Trail" in The Church of Jesus Christ of Latter-day Saints at http://lds.org/gospellibrary/pioneer/pioneerstory.htm (accessed 2 August 2011).
14. Wikipedia contributors, "First Transcontinental Railroad" in Wikipedia: the Free Encyclopedia at http://en.wikipedia.org/wiki/First_Transcontinental_Railroad (accessed 2 August 2011).
15. “Box Elder County, Utah Certificates of Citizenship Record Books, 1868-1869” Ancestry.com ( search.ancestry.com/search/db.aspx?dbid=7056 : accessed 24 Oct 2012), “Source Information”.
16. “Box Elder County, Utah Certificates of Citizenship Record Books, 1868-1869” Ancestry.com ( earch.ancestry.com/search/db.aspx?dbid=7056 : accessed 24 Oct 2012), “About Box Elder County, Utah Certificates of Citizenship Record Books, 1868-1869”.
17. Utah State Archives, Birth Records guide, accessed 28 July 2012.)
18. State Department of Health Birth, Marriage, and Death Certificates page. Accessed 7/31/2012
19. "Box Elder County, Utah: Family History and Genealogy, Census, Birth, Marriage, Death Vital Records and More," Linkpendium, http://www.linkpendium.com/genealogy/USA/UT/Box_Elder/, accessed 1 February 2012.
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Community Wiki Support Meeting 17 April 2012Edit This Page
From FamilySearch Wiki
Revision as of 22:26, 11 May 2012 by Ldrew (Talk | contribs)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
MeetingPlace ID: 3232; Join the meeting; Dial-in number: 877-453-7266 9:00 am. Mountain time on Tuesdays
• You can join up to 10 minutes early. If you try to join the meeting at any other time, you will get an error that the meeting doesn't exist.
• Prior to joining the meeting for the first time, run the MeetingPlace Test to verify that you can participate in a web meeting.
Purpose of the meeting
Improve the Wiki
• Forge solutions with other community contributors.
• Share best practices, ideas, and content.
• Discuss current issues, community matters, and strategies.
• Move issues to decision.
Contents
Meeting Agenda
Introduce new members
• Blake Reneau
• Jana Stokes - helping with Utah content
Kudos go to ...
Updates and follow up
• Maintenance status - Good progress, but pages with Unresolved Issues need attention. Do we need a committee to work on these, or make assignments to specific people? Should this topic be better in Content, rather than Administrative?
Business/Announcements
Maintenance Report - Sandra
• Uncategorized pages are down to about 800. Most of the rest are indexing pages that we can't control.
• Many of the other categories are at zero and progress is being made.
• Unresolved pages - some may not be able to be resolved.
• What is the process for handling Unresolved pages?
• Our team may not be able to address some of these issues. We can bring them into the open to get more discussion on them.
• We might make simple changes if there is a consensus on the page.
• We can build consensus by posting on the Talk page or in Forums - or post to several other user talk pages for opinions
• Ask someone else to take a look at it and get opinions - especially for older posts.
• Some pages may need to be addressed in our 1:00 meetings.
• Ken will deal with the England unresolved pages
• Family History Centers - Lee has been contacting some about their pages and Talk pages.
Improve the Wiki
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England
From FamilySearch Wiki
(Difference between revisions)
(added link)
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*[[England Manors|Manor Records]]
*[[England Manors|Manor Records]]
*[[England Maps|Maps]]
*[[England Maps|Maps]]
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*[[England Medical Records|Medical Records]]
*[[British Merchant Marine|Merchant Marine]]
*[[British Merchant Marine|Merchant Marine]]
*[[England Military Records|Military Records]]
*[[England Military Records|Military Records]]
Revision as of 17:48, 1 August 2012
News and Events
More news items... More events...
Topics
Key Topics to get Started:
Other Topics:
The Research Forums have been closed. For a limited time the England Research Forums will be available in read-only mode.
Genealogy courses: Learn how to research from an expert in England courses.
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England is a one of the four constituent countries of the United Kingdom. It has a history that goes back over a thousand years.
In 1707, the Kingdom of England joined the Kingdom of Scotland in union to become the Kingdom of Great Britain.
Beginner's Corner
The Beginner’s Corner links to information that will help you get started researching your English ancestors. Choose from one of the following:
These articles may also help you as you begin researching your English ancestors:
See also English Ancestry in the FamilySearch Learning Center
Featured Resources
Counties
Click on a county to go to that county's page:
Or click on a link below:
Research tools
Research Strategies in England Records
Follow these principles as you search the records for your ancestor:
Always search for one generation at a time
Prove ancestry one generation at a time; always allow the evidence to lead where it takes you under all circumstances. Never jump to conclusions seeking specifically with the intent to connect into families of nobility or Royalty.
Always search for an ancestor's entire family
Each person in a family is precious. Records for each person may include clues for identifying other family members. In most families, children were born at regular intervals (every two to three years). Where gaps appear for a longer period between some children (four to five years), re-examine the birth-christening and the death-burial records for a child who may have been overlooked. Consider looking at parish chest and other records and in other places to find a missing family member, i.e. first-born children are often christened in the parish of the bride (mother).
Search each source thoroughly
The information you need to find a person or trace the family further may be a minor detail of the record you are searching; especially ancestors with more common surnames. So always note identifying factors such as the occupation of your ancestor, become familiar with his/her signature, a street address, place of abode, age, note a middle name, given-names usage, names of witnesses, godparents (in Catholic registers), neighbors, relatives, guardians, children's birth order in a family, and others.
Search a broad time period
Dates obtained from some sources may not be accurate. Look several years before and after the date you think an event, such as a birth, occurred.
Search indexes
Many records are indexed, including especially census, civil registrations of births, marriages and deaths (post-1837), and probate records; and to a lesser extent, church records. Most indexes are incomplete, even if just a little. Often indexes include only the name of the specific person the record is about, excluding most pieces of evidence shown in the original documents. Always be aware that those recording original information may have misheard and thus miss-recorded the names of people and places; moreover, at the indexing-stage, indexers may have have omitted, miss-spelled given, surnames and places as well.
Search for emigrant's origins in records of country of settlement
Information about an England emigrant ancestor's place of birth or residence is vital to successful research. In pre-1700 England many people in England especially used a small variety of names, knowing the place of residence or birth is critical before you can research in England's records for further generations. Identifying the correct ancestor (example: Richard Taylor from other Richard Taylor), requires extensive research in all available records in the country of settlement--to the fullest extent possible such as noting neighbors, others possessing the same surname in the same or nearby township[s], given-naming patterns and searching for the same matching given-name usage in England via searching in the largest available online databases, including (but not limited to) 1) FamilySearch, 2) FindMyPast, 3) Ancestry.co.uk, 4) FreeReg, 5) county OPC projects (Online Parish Clerk), 6) TNA (National Archives), 7) BritishOriginsNetwork, FHLFavorites, and others.
Searching Parish records: Always include a search in the chapelry registers also
Difficult ancestral trails often 'disappear' when an area is dotted with a mixture of chapels among the parishes, such as in especially Lancashire and Middlesex, and to a lesser extent in Cheshire, Yorkshire, Northumberland, northeast Surrey and in England's large cities, such as Bristol, Norwich and others. Aways search all chapels that exist and lay within an ancient parish. Check the following outstanding online resources and aids to help you to more accurately identify all chapels lying within an ancient parish boundary. Thorough research critically depends upon this endeavor:
Watch for spelling variations
Look for the many ways a person or place name could have been spelled. Spelling was not standardized when most early records were made. You may find a name spelled differently than it is today, as well as several different spelling variations in the original records.
Record Your Searches and Findings
Copy the information you find and keep detailed notes about each record you search. These notes should include the author, title, location, call numbers, description, and results of your search. Most researchers use a research log for this purpose.
FamilySearch Historical Records
Wiki articles describing England-related online collections that can be found at FamilySearch.org
Main article: England FamilySearch Historical Records
Ideas for Finding Compiled Information on English Ancestry
Here's an article entitled "A Checklist of Compiled Sources and Where to Find Them" that's specifically focused to aiding researchers--beginners to professional--who want to learn of compiled genealogical data on (i.e. immigrant) ancestry from England and Great Britain in general.
This article shares numerous resources such as gateway websites which provide access to ultimately billions of names that researchers worldwide have gathered and shared online or in major archives on British ancestry.
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Difference between pages "Live-Forensics" and "User:Secure.india.css"
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(Live-Forensics is a site dedicated to Windows live incident response and live forensics.)
m (Creating user page with biography of new user.)
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Live-Forensics is a site dedicated to Windows live incident response and live forensics. It has several free tools that can be added to incident response scripts as well as just used to analyze information.
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Myspace layouts website, feedback needed
Newbie Member
18Nov2008,09:52 #1
Hi guys, this is my personal myspace layouts site : acelayouts.com, i want to relook it, could i please have feedback, critics and
suggestions, i think it badly needs a new look!
thanks!
Go4Expert Founder
18Nov2008,10:00 #2
You can ask for review after you review 3 other sites. Thread closed.
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"Modern Metrology Concerns", book edited by Luigi Cocco, ISBN 978-953-51-0584-8, Published: May 16, 2012 under CC BY 3.0 license
Chapter 10
Optical Measurements: Polarization and Coherence of Light Fields
By O. V. Angelsky, P. V. Polyanskii, I. I. Mokhun, C. Yu. Zenkova, H. V. Bogatyryova, Ch. V. Felde, V. T. Bachinskiy, T. M. Boichuk and A. G. Ushenko
DOI: 10.5772/36553
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L. Raymond Jones - Summary Bibliography
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Other views: Awards Alphabetical Chronological
Cover Art Interior Art
Copyright (c) 1995-2011 Al von Ruff.
ISFDB Engine - Version 4.00 (04/24/06)
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Caravan of Dump Trucks On 9/11 Rolls Into Downtown NYC
January 17, 2013
By
One more piece of evidence suggesting a contrived plot.
In the video below, you’ll see a massive caravan of privately owned dump trucks rolling into the disaster site on the afternoon of 9/11. I find it hard to believe that the city had organized a clean up effort with a private company while the buildings were still collapsing, as that would constitute hauling evidence away from a crime scene.
This video was shot 10 minutes after the collapse of WTC7. People were still trapped in the debris field at that time.
“New York City Office of Emergency Management was the agency responsible for coordination of the City’s response to the attacks. Headed by then-Director Richard Sheirer, the agency was forced to vacate its headquarters, located in 7 World Trade Center, within hours of the attack. The building later collapsed due to fire. OEM reestablished operations temporarily at the police academy, where Mayor Giuliani gave many press conferences throughout the afternoon and evening of September 11. By Friday, rescue and reliefs were organized and administered from Pier 92 on the Hudson River.[29]”
While all that was going on, I’m sure someone had the foresight to contract a multi-million dollar clean up deal that entailed the use of hundreds of dump trucks, and then actually have those dump trucks get to the site 10 minutes after the collapse of the last building.
for the doubters:
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The free office suite
Download LibreOffice
LibreOffice Linux - rpm (x86_64), version 3.6.5, Kinyarwanda. Not the version you wanted? Change System, Version or Language
You need to download and install these files in order:
• Source code
LibreOffice is an open source project and you can therefore download the source code to build your own installer.
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Molecules 2010, 15(2), 1082-1088; doi:10.3390/molecules15021082
Communication
Remarkable Iodine-Catalyzed Synthesis of Novel Pyrrole- Bearing N-Polyaromatic β-Lactams
Department of Chemistry, The University of Texas-Pan American, 1201 West University Drive, Edinburg, TX 78541, USA
* Author to whom correspondence should be addressed.
Received: 22 December 2009; in revised form: 8 February 2010 / Accepted: 20 February 2010 / Published: 23 February 2010
(This article belongs to the Special Issue Organic Iodine Chemistry)
Download PDF Full-Text [165 KB, uploaded 23 February 2010 15:40 CET]
Abstract: Because of their interesting biological properties various methods for the synthesis of substituted pyrroles are described in the literature. However, synthesis of pyrroles fused with a β-lactam ring has not been reported. Our group has demonstrated synthesis and biological evaluation of various β-lactams as anticancer agents. The anticancer activities of these compounds have prompted us to study the synthesis of pyrroles bound to the β-lactams. We have identified an expeditious synthetic method for the preparation of pyrroles fused with β-lactams by reacting 3-amino β-lactams with acetonylacetone in the presence of catalytic amounts (5 mol%) of molecular iodine at room temperature. It has also been discovered that the reaction gives products under domestic and automated microwave oven irradiation. To our knowledge, there are no other prior reports that describe the synthesis of pyrrole-substituted β-lactams.
Keywords: iodine; catalysis; β-lactams; pyrroles
Article Statistics
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Cite This Article
MDPI and ACS Style
Bandyopadhyay, D.; Rivera, G.; Salinas, I.; Aguilar, H.; Banik, B.K. Remarkable Iodine-Catalyzed Synthesis of Novel Pyrrole- Bearing N-Polyaromatic β-Lactams. Molecules 2010, 15, 1082-1088.
AMA Style
Bandyopadhyay D, Rivera G, Salinas I, Aguilar H, Banik BK. Remarkable Iodine-Catalyzed Synthesis of Novel Pyrrole- Bearing N-Polyaromatic β-Lactams. Molecules. 2010; 15(2):1082-1088.
Chicago/Turabian Style
Bandyopadhyay, Debasish; Rivera, Gildardo; Salinas, Isabel; Aguilar, Hector; Banik, Bimal K. 2010. "Remarkable Iodine-Catalyzed Synthesis of Novel Pyrrole- Bearing N-Polyaromatic β-Lactams." Molecules 15, no. 2: 1082-1088.
Molecules EISSN 1420-3049 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
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Int. J. Mol. Sci. 2013, 14(2), 2717-2738; doi:10.3390/ijms14022717
Article
Identification and Dynamic Regulation of microRNAs Involved in Salt Stress Responses in Functional Soybean Nodules by High-Throughput Sequencing
1 Key State Laboratory of Plant Cell & Chromosome Engineering, Center of Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, Hebei, China 2 Graduate School of Chinese Academy of Sciences, 19A Yuquanlu Shijingshanqu, Beijing 100049, China 3 Shijiazhuang Academy of Agriculture and Forestry Sciences, Shijiazhuang 050041, Hebei, China 4 National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China 5 Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
* Author to whom correspondence should be addressed.
Received: 10 November 2012; in revised form: 9 January 2013 / Accepted: 15 January 2013 / Published: 28 January 2013
(This article belongs to the Special Issue Non-Coding RNAs 2012)
Download PDF Full-Text [759 KB, Updated Version, uploaded 30 January 2013 09:55 CET]
The original version is still available [726 KB, uploaded 28 January 2013 11:44 CET]
Abstract: Both symbiosis between legumes and rhizobia and nitrogen fixation in functional nodules are dramatically affected by salt stress. Better understanding of the molecular mechanisms that regulate the salt tolerance of functional nodules is essential for genetic improvement of nitrogen fixation efficiency. microRNAs (miRNAs) have been implicated in stress responses in many plants and in symbiotic nitrogen fixation (SNF) in soybean. However, the dynamic regulation of miRNAs in functioning nodules during salt stress response remains unknown. We performed deep sequencing of miRNAs to understand the miRNA expression profile in normal or salt stressed-soybean mature nodules. We identified 110 known miRNAs belonging to 61 miRNA families and 128 novel miRNAs belonging to 64 miRNA families. Among them, 104 miRNAs were dramatically differentially expressed (>2-fold or detected only in one library) during salt stress. qRT-PCR analysis of eight miRNAs confirmed that these miRNAs were dynamically regulated in response to salt stress in functional soybean nodules. These data significantly increase the number of miRNAs known to be expressed in soybean nodules, and revealed for the first time a dynamic regulation of miRNAs during salt stress in functional nodules. The findings suggest great potential for miRNAs in functional soybean nodules during salt stress.
Keywords: functional nodules; miRNA; nitrogen fixation; salt stress; soybean
Supplementary Files
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Cite This Article
MDPI and ACS Style
Dong, Z.; Shi, L.; Wang, Y.; Chen, L.; Cai, Z.; Wang, Y.; Jin, J.; Li, X. Identification and Dynamic Regulation of microRNAs Involved in Salt Stress Responses in Functional Soybean Nodules by High-Throughput Sequencing. Int. J. Mol. Sci. 2013, 14, 2717-2738.
AMA Style
Dong Z, Shi L, Wang Y, Chen L, Cai Z, Wang Y, Jin J, Li X. Identification and Dynamic Regulation of microRNAs Involved in Salt Stress Responses in Functional Soybean Nodules by High-Throughput Sequencing. International Journal of Molecular Sciences. 2013; 14(2):2717-2738.
Chicago/Turabian Style
Dong, Zhanghui; Shi, Lei; Wang, Yanwei; Chen, Liang; Cai, Zhaoming; Wang, Youning; Jin, Jingbo; Li, Xia. 2013. "Identification and Dynamic Regulation of microRNAs Involved in Salt Stress Responses in Functional Soybean Nodules by High-Throughput Sequencing." Int. J. Mol. Sci. 14, no. 2: 2717-2738.
Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
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Once when Cyrus was holding a general review1 and parade of all his men under arms, a messenger came from Cyaxares saying that an embassy had arrived from India. “He therefore bids you come as soon as possible. Moreover,” said the messenger, “I am bringing you a very beautiful robe from Cyaxares; for he expressed the wish that you appear as brilliant and splendid as possible when you come, for the Indians will see how you approach him.”
1 An embassy from India
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Google's Supplemental Index Showing More Than the Title Tag as the Title?
Jun 21, 2006 • 11:20 am | (1) by | Filed Under Google Search Engine Optimization
I have been watching a WebmasterWorld thread named Loads of Supplemental and the titles are all corrupt. It is true, there are many examples of pages in Google's supplemental index that have inaccurate titles. It appears that Google is listing the title plus some of the first piece of content at the top of the page.
I have an example, but the site owner asked I keep the URL and any revealing information hidden. Take a look at this search result;
The part after the blank area in the clickable title is actually from the content at the top of the page that shows the day and date. This result is also obviously in the supplemental index, as you can see in the green font on the right side of the image.
This is a very interesting observation. Google isn't always doing this, it may depend on the query at hand. Is this a sign that Google may be producing dynamic titles based on queries? I know Google sometimes opts for DMOZ titles, but this is way different than that.
But by taking the top text, which is normally standard header text, in our case date information, but in many cases text such as "home," "about us," etc. this can make for a poor search experience.
Big hat tip to Tyson and also over SEO4Fun.
Forum discussion at WebmasterWorld.
Previous story: Are Google Advertisers Opting Out of Content Network: Dropping AdSense
blog comments powered by Disqus
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{
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Place:Easthampstead, Berkshire, England
Watchers
NameEasthampstead
Alt namesLachenestedesource: Domesday Book (1985) p 36
TypeVillage
Coordinates51.4°N 0.767°W
Located inBerkshire, England
source: Getty Thesaurus of Geographic Names
source: Family History Library Catalog
the text in this section is copied from an article in Wikipedia
Easthampstead is today a southern suburb of the town of Bracknell in the English county of Berkshire, although the old village can still be easily identified around the Church of St Michael and St Mary Magdalene. This beautiful building houses some of the finest stained glass works of Sir Edward Burne-Jones.
Research Tips
This page uses content from the English Wikipedia. The original content was at Easthampstead. The list of authors can be seen in the page history. As with WeRelate, the content of Wikipedia is available under the Creative Commons Attribution/Share-Alike License.
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User:Kristyspillane
Browse
Family Trees
Kristy's Family Tree (view) (launch FTE)
people: 2564
Users Researching
Watson
Legg
Jones
Whitney
Hello, my name is Kristy Spillane. I have just started working on Family History. It is fun to see where my ancestors came from. I have a long way to go but I really enjoy it.
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Tell me more ×
Answers OnStartups is a question and answer site for entrepreneurs looking to start or run a new business. It's 100% free, no registration required.
I've been working for a company as a contractor for several months. While working for this company, I created some seriously sensitive IP. This is IP that is nigh on patentable.
My employment with this company is based on a handshake deal. There was no employment contract, NDA, or even invoices for the paychecks I've received. I had even suggested signing an NDA when I started working, but the owner refused. The IP is software that I haven't even been released to the company (it's SaaS that I both author and run).
I've become disillusioned with the CEO of the company who is obviously making terrible choices for the company, while underpaying and overworking employees to an extreme and also treating customers poorly and overcharging.
I believe I can do a better job running the company, so I've decided to quit and start my own version. I am already well into the black, but I've used the old company's IP (only IP I've generated) and sales leads (picking up their lost, frustrated clients).
I have no intentions to deny the company access to this IP, but I do intend to use it fully.
Are there any implications to this, both ethical and legal? Assuming I've had no written interactions via e-mail saying that I've been paid to develop IP for this company.
share|improve this question
4 Answers
He takes you to court, you lose your business.
This is VERY dark and as you portray him he has some funds AND the character to take you to court, while you haven't even consulted a lawyer.
You will lose, especially if you are in the US, the moment he starts hitting you with court orders.
share|improve this answer
I think that there are quite a few negative ethical implications to this, and it sounds like you aren't entirely comfortable with those.
A "handshake" deal can still be legally binding, although it's naturally very hard to prove what it was exactly that you originally agreed. Posting this online could be used as evidence, however.
It's the cliche advice, but consult a lawyer. You'll need one at some point regardless and this one of those big-deal kinds of questions that only a lawyer should be advising you on.
share|improve this answer
Why do say it is the company's IP? This website has some helpful information about copyright ownership:
If a work is created by an independent contractor (that is, someone who is not an employee), the work may still be a work for hire, but the definition is much harder to meet. In order for the work of an independent contractor to be a work made for hire, the following facts must exist:
• the work must be specially ordered or commissioned;
• the work must come within one of the nine categories of works listed in the definition above; and
• there must be a written agreement between the parties specifying that the work is a work made for hire.
It looks like this applies to you since you are an independent contractor and not an employee. It also looks like you own the copyright to the code you have written since there is not a written agreement saying this was a work for hire.
I don't know whether ethics is on your side but the law seems to be (get a lawyer to find out for sure). The CEO who hired you is incompetent in that he should have had a written agreement saying it is a work for hire.
Looks like you are free to continue to providing services to this company and use the code you wrote for other purposes as you see fit.
One final note, you mention that the code may be patentable, but it is not clear who the inventor of the invention is. If you implemented someone else's invention, then the owner of the invention is the inventor and not the implementor.
share|improve this answer
Seems to me the Law is on the side of who files the lawsuite first and not who is right. I'd file a lawsuite first. But on a serious note, if you have an ethical background and you know for a fact that he hired you to write this code then it was "code for hire" and you don't own the rights to it. But it sounds like you got dis-illusioned with the CEO and wanted to get back at him. What you should have done was to make him an offer and worked out some deal where he'd get some royalties and such.
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Tell me more ×
Answers OnStartups is a question and answer site for entrepreneurs looking to start or run a new business. It's 100% free, no registration required.
I'm thinking to build an android and iPhone app, with short jokes, phrases from movies. The length of the jokes is 2-3 seconds maximum.
I don't plan to make any money from this app(by advertising or any other method), but i think I'm not allowed to use parts of movies.
Is there any way of using parts(sounds/voices) from movies but to not have troubles. The thing is that are some movies(friends, big bang theory, seinfeld, 2.5 men), which i like to listen their jokes when i'm in subway or something. I'm software engineer an I'm capable to build such an app.
share|improve this question
2 Answers
up vote -1 down vote accepted
There are no rules or limitation about how someone or a company can go about protecting their copyrights so it is a very shaky ground to stand on. But, you can protect yourself somewhat by: 1. keep the clips short, not longer than 30 seconds. Long time ago there was something about fair use of materials if clips are 30 sec. or shorter but that might be old now, anyway keep them as short as possible. 2. create a way for general public to upload their content. This way you become and aggregator of the content, kinda like youtube. Ideally you would not get involved in filtering of the content because then you take on responsibility for anything that slips through the cracks. 3. Have a clear DMCA policy and respond quickly to any DMCA notices.
share|improve this answer
Probably not. While fair use allows people to use other people's copyrighted material, it is only under certain conditions (parody, news, etc). Check out this from the Copyright Office. Taking someone else's materials for no other reason than to share how funny it is probably doesn't meet any of the fair use exceptions. The length of the clips would probably not matter in this case.
Also, allowing others to upload the content and trying to use the DMCA safe harbor provisions may not protect you either. If you are asking people to upload infringing content, you would probably not be protected (See the Limewire lawsuit).
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Source link: http://archive.mises.org/8375/how-much-money/
How Much Money?
August 5, 2008 by
How Much Money Does an Economy Need? is an outstanding guide to the essentials of monetary theory. Not content to expound his own views, Lewis carefully explains conflicting standpoints as well. Lewis does not disguise his own strong commitment to Austrian economics, but the reader of this book will understand not only this position, but its chief competitors as well. If the literate public absorbs its lessons, the book cannot fail to have a salutary effect on current economic policy. Hunter Lewis deserves congratulations for his notable achievement. FULL ARTICLE
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Tuesday, July 13, 2010
From Slime Mold to Neurons
I wasn't going to write much about clouds, being focused on my new area of research but I could hardly let James' post go unchallenged.
Before I critique the post, I need to go through some basic genetics for those of you who are new to that subject.
DNA is the accepted means of providing genetic instructions used in the development and functioning of all known living organisms. There are exclusions, such as RNA Viruses (which are considered not to be living organisms) and forms of non DNA based inheritance.
DNA doesn't operate in isolation, for example the same DNA sequence in a human produces a multitude of specialised cells. It instead acts in combination with both the environment it exists within and the environments it has existed within. Hence it is more correct to say that DNA contains genetic information that influences the phenotype (characteristics) of an organism.
To keep things simple, I'll ignore the multitude of RNA types (from messenger to transport), the issues of expression, the terminology of genes and 3D geometry and take a few chunky liberties in the description of how DNA works.
In principle, DNA consists of a long double helix sequence of four basic nucleotides (the base pairs) known as C,G,A,T. Different sections of this sequence (referred to as genes) are transcribed and translated into protein structures which affect the operation of the cell. Each three letter word (a codon) of the genetic sequence (i.e. CGT or GAT, giving 64 possible combinations) is translated to an amino acid (of which there are 22 standard).
The entire complexity of life is built upon such simple subsystems which in turn are part of ever more complex systems. Without this component structure, the level of complexity in living organisms would not have been feasible. It's worth noting that the agility of complex structures to evolve is dependent upon the organisation of their subsystems.
So, what has this to do with cloud?
Well, if you take an example such as Amazon's Web Services, the complexity of the many systems that users have developed with cloud services is based upon the provision of simple, standard subsystems for storage, compute resources and networks.
There is some limited variability in the type of subsystems (for example the size of Amazon instances) and the introduction of a new Cluster Compute Instance but these are the genetic analogy to amino acids which are then used to build more complex protein structures. Your deployment scripts (whether you use a system such as RightScale or another) are your DNA which is then transcribed and translated into the deployment of basic instances to create the complex structures you require.
So, back to James' post. My objection to the post is that whilst you, as a user, can create a slime mould or a neuron or a million other cellular anologies with these basic components, the key is how YOU combine these common and well defined (i.e. commodity-like) components.
James' however infers in his post that we need to see alternative cloud models, not just the "slime mold model cloud" but "more complex topologies" with the "emergence of more topologically calibrated and therefore feature rich clouds". In principle he is arguing for more configuration of these basic subsystems.
Whilst I agree that some additional basic subsystems (e.g. the cluster computer instance) are needed, I'd argue against the principle of wide ranging configuration in the subsystems.
Whilst such a richness of diversity in the underlying subsystems does create benefits for technology vendors - which company hasn't fallen for the "competitive advantage of customizing a CRM system" gag - it will not create the "wealth" and diversity in user created systems. Instead, it's more likely to create further lock-in issues, move us away from competitive marketplaces and end up with users spending vastly more time building and configuring stuff which really doesn't matter.
There are always edge cases, however in general the range of subsystems we require are fairly limited and it's from these we can build all the different type of systems (or cells) we want.
If there is anything that should be learned from biological analogies, it is from such "modest entities", such simple subsystems that complexity and diversity is created. We've learned this lesson throughout time, from the electronic to the industrial revolution to the works of Vitruvius.
Unfortunately, as the old adage goes - "the one thing you learn from history, is we never learn from history".
One final note: analogies between cloud computing and biological systems are generally weak at best - my above example is no exception. I use it purely to continue in the same spirit as the original discussion and to try and highlight the core issue of diversity in the subsystems vs diversity in what is built with stable subsystems. I don't recommend comparing cloud computing to biology, unless you want endless arguments.
One very final note: computer models are based on simple arithmetic and hence are bound to Goedel's law of incompleteness, neither being being both complete and certain. As activities provided through software tend towards being ubiquitous and well defined, they will tend towards being a good enough component like a defined brick with standardised interfaces. The components themselves will have some inherent non-linear qualities (i.e. the halting problem) which is why the design for failure paradigm is so important.
Biological components are also only linear at a superficial level and on an individual level they are highly non-linear and cannot be described by simple arithmetic means nor modeled with certainty by a computer. I suspect, this is why virtual worlds tend to only seem "real" when populated by real people. The interface might be standardised and the avatars can be seen as having a set limit of linear capabilities but the actual component (i.e. the person) is highly non-linear.
For these reasons, biological system have evolved highly complex regulatory systems (such as the human immune system) which even today we barely understand. However, we're acutely aware that a major function of it is to control rogue cells. This level of complexity is far beyond the capabilities of modern computing and also filled with numerous information barriers (the uncertainty principle is only one of many) which prevent us from anything more than approximation. For these reasons, I find some useful concepts in biological systems (Red Queen, Ecosystems, Co-evolution etc) along with certain derived concepts, such as design for failure, but direct comparison is filled with danger.
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Friday, July 11, 2008
Loose Feathers #157
Green-winged Teal / Photo by Dave Menke (USFWS)
Bird news
• Birds that migrate at night tend to do so in loose flocks. This was the conclusion of a radar study that tracked pairs of migrating birds simultaneously and compared their flight paths and speed. Some pairs of birds were as much as 200 meters apart. (Apparently biologists can track migrating birds with a sousaphone.)
• In Washington state, the timber industry and conservationists have formed a working group to preserve spotted owl habitat on private lands.
• The mid-continent breeding duck population has declined 9% from 2007 to 2008. The steepest decline was among canvasback. Possible reasons include loss of habitat and drought. On a positive note, both redheads and green-winged teal have increased their numbers from last year and are above their long-term average.
• Unfortunately, it seems that the USDA will lift penalties for taking land out of the Conservation Reserve Program.
• Biologists at Plum Island are conducting a breeding study of saltmarsh sharp-tailed sparrows to track the effect of mercury contamination on the wetlands there. Typically the mercury levels in the sparrows' bloodstream rises during the summers at Plum Island and falls while the birds winter elsewhere. (via Plover Warden Diaries)
• Neurons that control singing in songbirds are programmed to die back at the end of each breeding season.
• A conservation worker in New Zealand accidentally killed a rare takahe while shooting at a flock of the more common pukeko. The latter species was being culled to protect other endangered birds.
• The Everglades snail kite is rapidly disappearing from the Everglades; the current population is one-third what it was in 200. Their decline stems from a crash in the apple snail population.
• Ornithologists in Britain have recorded some very long-lived birds, some living and some recently deceased, due to the recovery of banded birds. They include a 41-year-old razorbill, a 13-year-old barn owl, a 31-year-old curlew, a 20-year-old turnstone, a 27-year-old black-headed gull, a 27-year-old Canada goose, and a 27-year-old knot.
Birds in the blogosphere
Environmental news
Carnivals and newsletters
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Information for "Data Read In Place"
Jump to: navigation, search
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SHIP MOTION STUDY FOR THE 2010 AND 2020 PLAN IN THE SAN PEDRO BAY, CALIFORNIA
A.F. Yuen, M.G. Burke, T.C. Leung
Abstract
The Port of Long Beach, in cooperation with the Port of Los Angeles and the Corps of Engineers, has been working on the development of a Master Plan for the San Pedro Bay area. This Master Plan, nicknamed the "2020 Plan", is intended to project the Port's land and channel requirements through the year 2020. Any landfill expansion program would be implemented in phases throughout the life of the Master Plan. The initial phases of such a plan would greatly limit the ability of the Port to revise the future configuration of landfill phases, making it important for the Port to determine a final landfill configuration before implementing the early phases. In developing the 2020 Plan, the Port projected a need for approximately 2,600 acres of additional land. In attempting to turn this 2,600 acre figure into a landfill scheme, the controlling agencies had to take a number of factors into consideration, including (1) water quality and tidal circulation; (2) potential ship motion problems; (3) additional berths required for future development; (4) land and waterside transportation corridors required; (5) availability of dredge material for creating the land; (6) available areas for creating landfills; (7) efficiency of land usage in various configurations; (8) types of ships anticipated to use the new landfills; (9) types of terminals anticipated to be located on the new landfills. The Port of Long Beach developed two basic schemes which addressed the requirements listed above. In either case, the landfill configuration for the Port of Los Angeles remained the same. The first scheme (called the island scheme, Figure 1) had the advantage of more closely matching the proposed Port of Los Angeles development. Water quality and tidal circulation would be improved with this scheme. The second scheme (called the horseshoe scheme, Figure 2) created a channel on the Long Beach side which did not match the orientation of the channel on the Los Angeles side. This channel was better protected from wave forces than the island scheme, where ships would have to be berthed along the exposed southerly boundary.
Keywords
San Pedro Bay; ship motion; 2010 Plan; 2020 Plan
Full Text: PDF
This work is licensed under a Creative Commons Attribution 3.0 License.
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Tuesday, February 23, 2010
The Death of Cursive…
The first assignment after the winter break was a rainy half day in a 5th grade class. The lesson plan had a typical work load including a practice spelling test.
Plan instruction: “After the test, have them self correct with handout and practice writing each word 5x.”
Easy peasy lemon squeezy…until the end of the test when I handed out the spelling work sheet (see below) for self correction purposes.
The first hands started to appear: “Do we have to write the words five times in cursive?”
Since this is a spelling test and the emphasis should be correct spelling over the method; I allowed those who wanted, to “print” instead of “writing” the words to do so.
That satisfied most but not all; “But, I can’t read cursive!” was the next complaint.
Sure enough, there was a note on the lesson plan that stated I might have to “print” the spelling words on the whiteboard for those who can’t read cursive. Amazingly, I was not surprised that today’s 5th graders can’t write cursive longhand. I was surprised that I expected them to be able to read it! Why would I expect them to read longhand when they don’t write?
Personally, my penmanship is so bad it’s illegible. Other than my signature, I almost never write cursive because I never had to use it. The introduction of the typewriter and subsequently the computer keyboard had pretty much made “fancy writing” obsolete by the time I left school. Fortunately for me, a 30 year career in software development never once required writing documentation longhand.
While there are some who might be nostalgic about loss of beautiful penmanship, I can’t see the point other than as artistic exercise. Try Googling “death of cursive” and you can see the handwriting on the wall, so to speak.
(I was going to post this using a cursive font, but the Blogger editor doesn't provide one!)
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Fotolog Of The Week: DJ Felipe Lira
Considering a weekend full of parties is coming up soon for New Year's, I thought DJ Felipe Lira would be the perfect choice for fotolog this week. The 25-year-old DJ has only been playing in São Paulo for a year, but seems destined to become a big name in the country.
Party pictures and more of Felipe Lira after the jump.
And a fresh one from this past Sunday at The Week's Pool Party:
If you are in Rio for New Year's, Felipe will be spinning alongside Jeff Valle and Robix at Baby Day party right after Alegria, on December 30.
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The Thresher (Houston, Tex.), Vol. 40, No. 35, Ed. 1 Friday, April 17, 1953
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Item Metadata
dc.coverage.spatial United States - Texas - Harris County - Houston
dc.coverage.temporal Into Modern Times, 1939-Present
dc.date.accessioned 2012-11-07T03:00:51Z
dc.date.available 2012-11-07T03:00:51Z
dc.date.issued 1953-04-17
dc.identifier.uri http://hdl.handle.net/1911/66057
dc.description eight pages : ill. ; page 21 x 15 in.
dc.description.abstract A weekly student newspaper from the Rice Institute in Houston, Texas that includes campus news and commentaries along with advertising.
dc.language eng
dc.publisher Rice University
dc.relation.ispartof This digitized newspaper is also presented online at the Portal to Texas History, at http://texashistory.unt.edu/ark:/67531/metapth230939/
dc.relation.ispartofseries This Issue appears in Vol. 40 of the Rice Thresher.
dc.rights Rights to this material belong to Rice University. This digital version is licensed under a Creative Commons Attribution 3.0 Unported license.
dc.rights.uri http://creativecommons.org/licenses/by/3.0/
dc.subject.lcsh Harris County (Tex.) -- Newspapers
Houston (Tex.) -- Newspapers
Houston (Tex.) -- Periodicals
Student publications -- Texas -- Houston
College student newspapers and periodicals -- Texas -- Houston
dc.title The Thresher (Houston, Tex.), Vol. 40, No. 35, Ed. 1 Friday, April 17, 1953
dc.digitization.specifications Page images were scanned by the UNT Portal to Texas History from microfilm as 8-bit grayscale at 400 dpi and saved as TIF masters, with OCR'd PDF access copies.
dc.source.collection Rice Thresher, Fondren Library, Rice University, Houston, Tex.
dc.citation.volumeNumber 40
dc.citation.issueNumber 35
dc.identifier.digital thr19530417
dc.contributor.publisher Rice Institute
dc.type.genre Newspaper
dc.type.dcmi Text
dc.identifier.citation (1953). "The Thresher (Houston, Tex.), Vol. 40, No. 35, Ed. 1 Friday, April 17, 1953." vol. 40. no. 35,
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Genes and Society: Cloning via Infographics
My favourite data visualization blog just published a nice infographic about the difference between research cloning and reproductive cloning. Click on the image for full version.
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Showing results 1 to 3 of 3 @ 0.03 seconds. Search: Posts Made By: Kwljunky
Forum: Nokia N900 03-25-2010, 07:32 PM
Replies: 186
Views: 45,624
Posted By Kwljunky
Re: porn vids made on your n900...
im pretty sure we dont want to see your A>S>S dude.
Forum: Maemo 5 / Fremantle 01-18-2010, 08:01 AM
Replies: 70
Views: 15,164
Posted By Kwljunky
Re: NDS emu request
thats wat i thought too but the ds runs on
CPUs: Two ARM processors, an ARM946E-S main CPU and ARM7TDMI coprocessor at clock speeds of 67 MHz and 33 MHz respectively. The ARM946E-S CPU processes...
Forum: General 01-13-2010, 08:48 AM
Replies: 97
Views: 12,896
Posted By Kwljunky
Re: N900 on vodaphone issues*
Sucess !
I LIKE !
Anyone else with vodaphone branded 205 im going to be helpful and i suggest doing this (Just so theres a tutorial in this thread/ dont have to go searching and stuff):
First...
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Australian Bureau of Statistics
Celebrating the International Year of Statistics 2013
ABS Home > Statistics > By Release Date
4715.0 - National Health Survey: Aboriginal and Torres Strait Islander Results, Australia, 2001
Previous ISSUE Released at 11:30 AM (CANBERRA TIME) 20/11/2002
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INTRODUCTION
1 This publication presents selected summary information about the health of Indigenous Australians from the 2001 National Health Survey (NHS). Estimates for the non-Indigenous population from the 2001 NHS are included for comparison purposes. While the publication has a focus on results for 2001, it also includes data from the 1995 NHS to allow comparisons over time to be made. Some data are presented separately for remote and non-remote areas at a national level. However, State and Territory estimates for Indigenous Australians are not available due to the limited sample size for Indigenous Australians. Results from the NHS for the total Australian population are published in National Health Survey: Summary of Results, 2001 (cat. no. 4364.0).
SCOPE
2 A total of 3,198 Aboriginal and Torres Strait Islander adults and children from across Australia were included in a supplementary Indigenous sample to the 2001 NHS which was conducted throughout Australia from June to November 2001. In addition, 483 Indigenous Australians were enumerated in the 2001 NHS sample of 26,863 people. The Indigenous results included in this publication are based on the total sample (known as the NHS(I)) of 3,681 Indigenous Australians comprising 1,853 adults and 1,828 children. The NHS(I) included respondents from both remote and non-remote areas of Australia.
3 The NHS sample covered usual residents of private dwellings only. Usual residents of 'special' dwellings such as hotels, motels, hostels and hospitals were not included in the survey.
The following groups of people were also excluded from the survey:
• certain diplomatic personnel of overseas governments, customarily excluded from the Census and estimated resident population figures
• persons whose usual place of residence was outside Australia
• members of non-Australian defence forces (and their dependants) stationed in Australia
• visitors to private dwellings.
4 Non-Indigenous people were not eligible for selection in the supplementary Indigenous sample unless they were the parent or guardian of an Indigenous child and acted as spokesperson for the child (see below for further details).
SAMPLE DESIGN
5 The NHS(I) was designed to produce reliable estimates at the national level for persons in scope of the survey. The sample design was based on a broad dissection of Australia into non-sparsely settled and sparsely settled areas. The samples for non-sparsely settled areas and sparsely settled areas were designed separately with each involving a multistage sampling process. The 2001 NHS was designed to cover only non-sparsely settled areas. Therefore the Indigenous supplement provided both additional selections in these areas as well as the total Indigenous sample in sparsely settled areas.
6 Dwellings in non-sparsely settled areas were selected using a stratified multistage area sample. A number of Census collection districts (CDs) were randomly selected based on the number of dwellings containing Indigenous persons in the area as at the 1996 Census of Population and Housing. A random selection of dwellings within selected CDs were then screened to assess their usual residents' Indigenous status. Where a dwelling contained one or more Indigenous usual residents aged 18 years or more, one Indigenous adult (18 years of age or more) and up to two Indigenous children (0 to 17 years of age) were randomly selected to participate in the survey.
7 In sparsely settled areas, the sample was obtained from a random selection of discrete Indigenous communities and outstations across Australia using information collected in the 1999 Community Housing and Infrastructure Needs Survey (CHINS). Within selected communities and outstations a random selection of dwellings was made. Within selected dwellings, one Indigenous adult (18 years of age or more) and up to one Indigenous child (0 to 17 years of age) were randomly selected to participate in the survey.
8 For the non-sparsely settled area component of the supplementary survey, approximately 91% of households identified with in-scope Indigenous residents responded to the survey. This response rate does not take into account the 6.5% of households in the screened component of the sample that were unable to be contacted to establish the Indigenous status of the occupants. For the sparsely settled area component, approximately 87% of in-scope households responded to the survey.
DATA COLLECTION
9 Data collection was undertaken by ABS interviewers. Persons aged 18 years or more were interviewed personally, with the exception of persons who were too sick or otherwise unable to respond personally. Persons aged 15 to 17 years were interviewed with the consent of a parent or guardian; otherwise a parent or guardian was interviewed on their behalf. For persons aged less than 15 years, information was obtained from a person responsible for the child.
10 There were, however, a number of differences in the data collection methods in sparse and non-sparse areas. In non-sparsely settled areas, adult females were invited to complete a small additional questionnaire covering specific supplementary women's health topics. This additional questionnaire was voluntary and self-enumerated. Of the women invited to complete the supplementary questionnaire in non-sparsely settled areas, 91% responded.
11 In sparsely settled areas, standard household survey approaches were modified to take account of language and cultural issues. In addition, interviewers worked in teams of two, one male and one female, to collect the survey information. Male interviewers collected personal information from male respondents, and female interviewers collected personal information from female respondents. The interviewers were accompanied, wherever possible, by local Indigenous facilitators, preferably one male and one female, who assisted in the conduct and completion of the interviews. The Indigenous facilitators explained the purpose of the survey to respondents, introduced the interviewers, assisted in identifying the usual residents of a household and in locating residents who were not at home, and assisted respondent understanding of the questions where necessary.
12 In addition, the survey content in sparsely settled areas was limited to those topics for which data of acceptable quality could be collected. Some questions were reworded to assist respondents in understanding the concepts. Of the supplementary women's health topics that were collected with a self enumerated questionnaire in non-sparsely settled areas, in sparsely settled areas a subset was collected through personal interview with adult female respondents who were informed of the potential sensitivity and voluntary nature of these additional questions.
SURVEY CONTENT
13 The NHS Indigenous supplementary sample was designed to obtain data on a wide range of health issues and to enable comparisons between the Indigenous and non-Indigenous populations.
The survey collected information about:
• health status, including long-term medical conditions and recent injuries
• use of health services such as consultations with health practitioners and visits to hospitals, and other health-related actions
• health-related aspects lifestyle, such as smoking, diet, exercise and alcohol consumption
• demographic and socio-economic characteristics.
14 Specific topics included in the survey were:
• self-assessed health status
• long-term medical conditions (e.g. asthma, injuries, diabetes, cancer, cardiovascular conditions, hearing and sight problems)
• admissions to hospitals
• visits to casualty/outpatient facilities
• visits to hospital day clinics
• doctor consultations
• dental consultations
• consultations with other health professionals
• days away from work/school due to illness
• other days of reduced activity due to illness
• use of medications
• smoking
• alcohol consumption
• exercise
• body mass
• dietary behaviours
• adult immunisation
• child immunisation
• child breastfeeding status
• supplementary women's health issues (e.g. mammograms, pap smear tests, hysterectomy, breastfeeding history and use of contraceptives).
15 The survey content for the Indigenous supplement to the NHS in non-sparsely settled areas is the same as the content included in the 2001 NHS, with the exception of mental health information which was not collected from the supplementary Indigenous sample. The Kessler Psychological Distress Scale 10 (K-10) module of questions used in the 2001 NHS was not considered to be culturally appropriate for the Indigenous population.
16 The content for the Indigenous supplement to the NHS in sparsely settled areas is a subset (approximately 50%) of the content collected in non-sparsely settled areas. The sparsely settled content was confined to those items for which acceptable data quality levels could be achieved.
17 For a full list of data items collected in non-sparsely settled and sparsely settled areas, refer to the National Health Survey: Users Guide, 2001 which will be available on the ABS web site in December 2002.
RELIABILITY OF ESTIMATES
18 The estimates in this publication are subject to sampling and non-sampling error.
Sampling error
19 Sampling error is the difference between the published estimates, derived from a sample of persons, and the value that would have been produced if all persons in scope of the survey had been included.
20 In this publication, estimates with a relative standard error of 25% to 50% are preceded by an asterisk (e.g. *3.4) to indicate that the estimate should be used with caution. Estimates with a relative standard error over 50% are indicated by a double asterisk (e.g. **0.6) and should be considered unreliable for most purposes. For more information on sampling error and its impact on interpreting results in this publication refer to the Technical Notes.
Non-sampling error
21 Non-sampling error may occur in any data collection, whether it is based on a sample or a full count such as a Census. Sources of non-sampling error include non-response, errors in reporting by respondents or recording of answers by interviewers, and errors in coding and processing data.
22 Non-response occurs when people cannot or will not cooperate, or cannot be contacted. Non-response can affect the reliability of results and can introduce a bias. The magnitude of any bias depends upon the rate of non-response and the extent of the difference between the characteristics of those people who responded to the survey and those who did not.
23 The following methods were adopted to reduce the level and impact of non-response:
• face-to-face interviews with respondents
• the use of Indigenous facilitators to assist with survey interviews
• follow-up of respondents if there was initially no response
• weighting to population benchmarks to reduce non-response bias.
24 For details about the steps taken to minimise other non-sampling error, see paragraph 9 of the Technical Notes. For more details about non-sampling error see paragraphs 25 to 35 of these Explanatory Notes.
INTERPRETATION OF RESULTS
25 Information recorded in this survey is essentially 'as reported' by respondents, and hence may differ from information available from other sources or collected using different methodologies.
26 Reported information on long-term medical conditions was not medically verified, and was not necessarily based on diagnosis by a medical practitioner. Conditions which have a considerable effect on well-being or lifestyle are expected to be better reported than those which have little effect. Some people may be unaware of minor conditions, and occasionally may have serious conditions which have not been diagnosed.
27 There may be some instances of under-reporting as a consequence of respondents being unwilling to talk about a particular condition at an interview. Results of previous health surveys conducted by the ABS also suggest a tendency for respondents in the general population to under-report alcohol and tobacco consumption levels, underestimate their weight, and to over-estimate their height.
28 Information in this publication is presented by the Australian Standard Geographical Classification (ASGC) Remoteness Structure. Non-remote area estimates have been derived from data collected in non-sparsely settled areas by excluding a small component of non-sparse areas which are defined as remote in the ASGC Remoteness Structure. Similarly, estimates from remote areas have been derived from data collected in sparsely settled areas together with the small component of non-sparsely settled areas which are defined as remote.
29 As the content collected in sparsely settled areas was a subset of that collected in non-sparsely settled areas, not all data items are available for the total Indigenous population. In addition, no 1995 NHS data are available for remote areas restricting comparisons between Indigenous estimates for 1995 and 2001 to non-remote areas.
30 In both 1995 and 2001, all children of Aboriginal and/or Torres Strait Islander origin living in households in non-sparsely settled areas had a random chance of selection in the main NHS. Similarly, all such Indigenous children had a chance of selection in the Indigenous supplement to the 1995 NHS, as selected households in non-sparsely settled areas identified to have at least one usual resident of Aboriginal and/or Torres Strait Islander origin were enumerated.
31 However, in the 2001 Indigenous supplement to the NHS, selected households were screened to identify only those households where at least one adult (18 years or over) of Aboriginal and/or Torres Strait Islander origin was usually resident. Therefore, Indigenous children living in households in non-remote areas where there was no Indigenous adult usually resident (up to one quarter of all Indigenous children in non-remote areas reside in such households) did not have a chance of selection in the supplement.
32 Responses from the main sample and from the Indigenous supplement are weighted and then benchmarked to Indigenous population estimates (for age, sex, and area of usual residence) so that final survey estimates will be representative of the age and sex characteristics of the Indigenous population in different areas. However, it is possible that the health characteristics of Indigenous children living in households where there are no Indigenous adults may be different to those of Indigenous children of the same age and sex living in the same non-remote areas, but in households where Indigenous adults are resident. If such differences exist, it may mean that the survey results for Indigenous children under-represent these differences. However, in context of the relative standard errors for the estimates from the Indigenous component of the 2001 NHS, any differences due to such under-representation could in some cases affect the interpretation of results.
33 In the 2004-05 Indigenous Health Survey, field procedures will be changed to provide for adequate representation of Indigenous children in households with no resident Indigenous adult.
34 Other issues to be aware of when interpreting results from the NHS(I) include:
• Respondents were asked to refer to children's immunisation records and to medication packets/bottles when answering related questions. However, reference was not possible in all cases which may have reduced the reliability of the information reported.
• Different data items were collected for different timeframes, e.g. health-related actions taken in the 2 weeks prior to interview; whether a person was injured in the 4 weeks prior to interview; or whether a person was immunised in the 5 years prior to interview. The reliability and accuracy of data related to timeframes is dependent upon the respondent's ability to recall the timing of events.
• The reliability of data on fruit and vegetable intake may be affected by the respondent's understanding of what constitutes a usual serving size.
35 Many results presented in this publication have been adjusted for differences in the age structure between the Indigenous, non-Indigenous and total Australian populations to take account of the younger age profile of the Indigenous population. This age-standardisation has been undertaken using the direct method (see Technical Notes). Data which have been tabulated according to broad age groupings have not been age-standardised and hence the rates apply to the Indigenous and non-Indigenous populations without adjustments to account for the differing age structures. These rates, together with the total estimates presented in Appendix 1, can be used to calculate the actual population estimate for an item of interest. The ABS considers that comparisons of unadjusted rates within the broad age groups presented in this publication and would be little different if standardised within the age ranges.
36 Further information on the interpretation of results is contained in the National Health Survey: Users Guide, 2001, which will be available on the ABS web site in December 2002.
37 Major classifications used for items shown in this publication are:
• The broad geographical regions defined as remote and non-remote are based on the ASGC Remoteness Structure.
• All reported long-term medical conditions were coded to a list of approximately 1,000 condition categories which were prepared for this survey. Information about medical conditions classified at this level of detail is not available for output from the survey. However, the detailed classification categories can be regrouped in various ways for output. The standard output developed by the ABS for this survey and which are included in this publication are:
• A classification based on the International Classification of Diseases, 10th revision (ICD-10). See Glossary for definitions of ICD-10 based output categories used in this publication.
• A classification based on the International Classification of Diseases, 9th revision (ICD-9), which is similar to the classification of conditions used in the 1995 NHS, and has been retained to assist data users in comparing 2001 and 1995 results.
38 Further information about these classifications is contained in the National Health Survey: Users Guide, 2001 which will be available on the ABS web site in December 2002.
COMPARABILITY WITH 1995 NATIONAL HEALTH SURVEY
39 This publication contains selected results from the Indigenous component of the 1995 NHS. These results are limited to topics where a reasonable level of comparability between the 1995 and 2001 data is expected. While the 2001 NHS is similar to the 1995 survey in many ways, there are important differences in sample design and coverage, survey methodology and content, definitions, etc. which affect the degree to which data are directly comparable between the surveys.
40 The main differences between the 1995 and 2001 collections, apart from the differences in field procedures discussed in paragraphs 30 to 32 above, which may affect the comparability of data presented in this publication are outlined below.
• Data relating to asthma, cancer and cardiovascular conditions were collected in detailed topic-specific question modules in 2001 whereas in 1995 the topics were covered in the context of general long-term conditions. There is expected to be a greater tendency among respondents to report conditions in response to the direct questions used in 2001 rather than in response to the more general questions used in 1995.
• Data relating to asthma, cancer, cardiovascular conditions and diabetes/high sugar levels were primarily collected in 2001 through questions which screened out conditions which had not been medically diagnosed. This was not the case in the 1995 survey. Although the data are therefore conceptually different between surveys, the nature of the conditions involved is such that most cases reported in the 1995 survey are expected to have been medically diagnosed and therefore effects on the comparability of data are expected to be relatively small.
• The coding systems and used for long-term conditions and alcohol consumption differed between the surveys.
• Care should be taken in interpreting apparent changes over time in the prevalence of certain long-term conditions. Some movements between 1995 and 2001 estimates can, at least in part, be attributed to conceptual, methodological and/or classification differences. However, there are some instances where other factors may be contributing to the movements; for example changes in community awareness or attitudes to certain conditions, changes in common terminology for conditions, improvements in diagnosis, etc. The degree of change attributable to all these factors relative to actual change in the prevalence of conditions cannot be determined from information collected in this survey.
• The types of other health professionals (OHP) covered by the survey have expanded. Types introduced in the 2001 collection were Aboriginal health worker, accredited counsellor and alcohol and drug worker. As a result, data for OHP at the aggregate level are not directly comparable.
• Alcohol consumption was collected for a sub-sample of non-Indigenous adult respondents in 1995, but for all adults in 2001.
41 Due to the small size of the supplementary Indigenous samples in the 1995 and 2001 NHS, the Indigenous results from these surveys are not available below the national level and have a larger associated sampling error than results from many other ABS surveys. For this reason, differences in reported rates for 1995 and 2001 may or may not be statistically significant. Significance testing has been undertaken on selected Indigenous and non-Indigenous comparisons (table 1) and time series data (table 2) presented in the publication to assist readers with understanding the level of significance that should be attributed to apparent differences in rates. For further information about significance testing, please see the Technical Notes section of this publication.
42 Time series information for 1995 and 2001 presented in this publication is based on data for non-remote areas only due to concerns about the quality of remote area data collected in the 1995 survey. After an extensive investigation into Indigenous results from the 1995 collection, responses from people living in remote areas were excluded.
43 For further information about comparability between the 1995 and 2001 NHS see the National Health Survey, Users Guide, 2001 which will be available on the ABS web site in December 2002.
© Commonwealth of Australia 2013
Unless otherwise noted, content on this website is licensed under a Creative Commons Attribution 2.5 Australia Licence together with any terms, conditions and exclusions as set out in the website Copyright notice. For permission to do anything beyond the scope of this licence and copyright terms contact us.
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Australian Bureau of Statistics
Celebrating the International Year of Statistics 2013
ABS Home > Statistics > By Release Date
1345.4 - SA Stats, Aug 2009
Previous ISSUE Released at 11:30 AM (CANBERRA TIME) 25/08/2009
Page tools: Print Page Print All RSS Search this Product
CONTENTS
Feature Articles
Heating and Cooling
Demography
Includes: Estimated resident population, Components of population change
South Australia's population increased by 18,500 during the year ended 30 December 2008.
Labour Force
Includes: Contents, Employed persons, Unemployment, Participation rate
Trend unemployment rate for South Australia lower than the national rate.
Incomes
Includes: Average weekly earnings
In the year ended May 2009 average weekly full time earnings in South Australia grew by 6.9% compared to 5.9% nationally.
State Accounts
Includes: State accounts, Household final consumption expenditure (HFCE)
South Australia the only state with increased State Final Demand in the March quarter 2009.
Consumption
Includes: Retail trade, New motor vehicle sales
South Australian spending on clothes and soft goods increased 24% in the June quarter 2009.
Investment
Includes: Private new capital expenditure, Mineral and petroleum exploration expenditure
South Australia's Private New Capital Expenditure decreased by 2.3% to $1,201m in the March 2009 quarter.
Construction
Includes: Building approvals, Construction work done
For the year ended June 2009, dwelling unit approvals in the South East Statistical Division rose 37.5%.
Price Indexes
Includes: Contents, Consumer price index, Wage price index, House price index
Adelaide's house price index rises for the first time since March 2008.
Housing Finance
Includes: Housing finance commitments
Average home loan size in South Australia significantly lower than the national average.
International Merchandise Trade
Includes: Exports and Imports
The value of South Australia's merchandise exports falls to $634m in June 2009
Water
Includes: Rainfall, Reservoir levels
Wettest July since 1996 sees water storage in Adelaide's reservoirs rise to 73% of capacity.
© Commonwealth of Australia 2013
Unless otherwise noted, content on this website is licensed under a Creative Commons Attribution 2.5 Australia Licence together with any terms, conditions and exclusions as set out in the website Copyright notice. For permission to do anything beyond the scope of this licence and copyright terms contact us.
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Australian Bureau of Statistics
Celebrating the International Year of Statistics 2013
ABS Home > Statistics > By Release Date
1307.4 - South Australian Economic Indicators, Feb 2001
Previous ISSUE Released at 11:30 AM (CANBERRA TIME) 02/01/2001
Past Releases
First Release
• First Issue: Apr 1993
© Commonwealth of Australia 2013
Unless otherwise noted, content on this website is licensed under a Creative Commons Attribution 2.5 Australia Licence together with any terms, conditions and exclusions as set out in the website Copyright notice. For permission to do anything beyond the scope of this licence and copyright terms contact us.
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Australian Bureau of Statistics
Celebrating the International Year of Statistics 2013
ABS Home > Statistics > By Catalogue Number
4819.0.55.001 - Asthma in Australia: A Snapshot, 2004-05
Latest ISSUE Released at 11:30 AM (CANBERRA TIME) 13/10/2006
Past Releases
© Commonwealth of Australia 2013
Unless otherwise noted, content on this website is licensed under a Creative Commons Attribution 2.5 Australia Licence together with any terms, conditions and exclusions as set out in the website Copyright notice. For permission to do anything beyond the scope of this licence and copyright terms contact us.
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Australian Bureau of Statistics
Celebrating the International Year of Statistics 2013
ABS Home > Statistics > By Release Date
7215.0 - Livestock Products, Australia, Sep 2001
Previous ISSUE Released at 11:30 AM (CANBERRA TIME) 13/11/2001
Future Releases
• Next Issue: Jun 2013 expected for release on 12/08/2013
Past Releases
© Commonwealth of Australia 2013
Unless otherwise noted, content on this website is licensed under a Creative Commons Attribution 2.5 Australia Licence together with any terms, conditions and exclusions as set out in the website Copyright notice. For permission to do anything beyond the scope of this licence and copyright terms contact us.
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Research article
Machine learning methods can replace 3D profile method in classification of amyloidogenic hexapeptides
Jerzy Stanislawski1, Malgorzata Kotulska2* and Olgierd Unold1*
Author Affiliations
1 Institute of Computer Engineering, Control and Robotics, Wroclaw University of Technology, 50-370, Wroclaw, Poland
2 Institute of Biomedical Engineering and Instrumentation, Wroclaw University of Technology, 50-370, Wroclaw, Poland
For all author emails, please log on.
BMC Bioinformatics 2013, 14:21 doi:10.1186/1471-2105-14-21
The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2105/14/21
Received:22 May 2012
Accepted:19 December 2012
Published:17 January 2013
© 2013 Stanislawski et al.; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract
Background
Amyloids are proteins capable of forming fibrils. Many of them underlie serious diseases, like Alzheimer disease. The number of amyloid-associated diseases is constantly increasing. Recent studies indicate that amyloidogenic properties can be associated with short segments of aminoacids, which transform the structure when exposed. A few hundreds of such peptides have been experimentally found. Experimental testing of all possible aminoacid combinations is currently not feasible. Instead, they can be predicted by computational methods. 3D profile is a physicochemical-based method that has generated the most numerous dataset - ZipperDB. However, it is computationally very demanding. Here, we show that dataset generation can be accelerated. Two methods to increase the classification efficiency of amyloidogenic candidates are presented and tested: simplified 3D profile generation and machine learning methods.
Results
We generated a new dataset of hexapeptides, using more economical 3D profile algorithm, which showed very good classification overlap with ZipperDB (93.5%). The new part of our dataset contains 1779 segments, with 204 classified as amyloidogenic. The dataset of 6-residue sequences with their binary classification, based on the energy of the segment, was applied for training machine learning methods. A separate set of sequences from ZipperDB was used as a test set. The most effective methods were Alternating Decision Tree and Multilayer Perceptron. Both methods obtained area under ROC curve of 0.96, accuracy 91%, true positive rate ca. 78%, and true negative rate 95%. A few other machine learning methods also achieved a good performance. The computational time was reduced from 18-20 CPU-hours (full 3D profile) to 0.5 CPU-hours (simplified 3D profile) to seconds (machine learning).
Conclusions
We showed that the simplified profile generation method does not introduce an error with regard to the original method, while increasing the computational efficiency. Our new dataset proved representative enough to use simple statistical methods for testing the amylogenicity based only on six letter sequences. Statistical machine learning methods such as Alternating Decision Tree and Multilayer Perceptron can replace the energy based classifier, with advantage of very significantly reduced computational time and simplicity to perform the analysis. Additionally, a decision tree provides a set of very easily interpretable rules.
Keywords:
Amyloid; 3D profile; WEKA; Alternating decision tree; Neural network
Background
Amyloids are proteins that can form fibrils - highly ordered aggregates of a characteristic zipper structure [1-4]. Majority of these proteins natively have a completely different functional structure in their physiological state, although functional amyloids also exist [5,6]. A hypothesis holds that in vivo amyloidogenic regions are usually capped by gatekeeper aminoacids, like prolines and glycines, which prevent aggregation, and may have a high affinity to chaperone proteins [7]. Very often amyloids lead to serious diseases, like Alzheimer disease (amyloid-β, tau), Parkinson disease (α-synuclein), type 2 diabetes (amylin), Creutzfeldt-Jakob disease (prion protein), Huntington disease (huntington), amyotrophic lateral sclerosis (SOD1), etc. (for a review see e.g. [5]). The number of diseases that turn out amyloid-associated is constantly increasing. It is believed that their toxicity is related to insertion of non-mature aggregates into plasma membranes as non-selective ion channels.
Recently, it was discovered that amyloidogenic properties can be due to short segments of aminoacids in a protein sequence (hot spots), which can transform the structure when non-burried [8]. It was proposed that hexapeptides can sufficiently represent such hot-spots, although they may vary between 4–10 aminoacids. A few hundreds of such peptides have been experimentally found, however testing all combinations is not possible. Instead, they can be predicted by computational methods.
Several physico-chemical methods have been proposed to predict amylogenicity of a peptide, e.g. Tango [9], ZipperDB [10,11], Pasta [12], AggreScan [13], PreAmyl [14], Zyggregator [15], CamFold [16], NetCSSP [17], FoldAmyloid [18], AmyloidMutant [19,20], BetaScan [21], and consensus AmylPred [22]. The majority of these methods predict probability of a sequence to form β-aggregates. As it turned out, such an approach was not always successful. Although β-aggregation is related to amyloidosis, structural and biophysical properties are different [7,9]. β-aggregation is quite common in highly concentrated proteins, which do not form fibers. On the other hand, certain amyloids, like prions, are poorly predicted by tools dedicated to β-aggregates.
Methods like 3D profile, applied in ZipperDB or AmyloidMutant, which take into account more specific structural features of amyloids - resembling a steric zipper [4] - work better in such cases. Also statistical elements seem to help in the classification, as shown in Waltz [23] using Position Specific Scoring Matrices (PSSM), or Bayesian classifier and weighted decision tree applied to long sequences of bacterial antibodies [24].
Experimental datasets, upon which new classification methods could be built, are still very limited. Those sequences that show amyloid propensity are rarely well characterized. For the majority of them, it is not known which segment is responsible for their amylogenicity and few of them have an experimental structure of high resolution [4]. The biggest database of potential hexapeptides, generated with the 3D profile method, comes from the ZipperDB. The classical 3D profile method applies over 2.5 thousand scaffolds resembling a steric zipper structure, on which tested hexapeptides are threaded, and their minimal energy is calculated. If the minimal energy of one chain is below a threshold value, which could be obtained from experimental dataset of hexapeptides, then the hexapeptide is classified as amyloidogenic. The method is reasonable and quite accurate - the authors of Waltz tested it on the independent dataset from prion protein sup35, which was experimentally derived. They reported that the 3D profile method showed accuracy of 0.8, with sensitivity of 0.67 and specificity of 0.84 [23]. The database in ZipperDB, which is freely available on-line [25], is constantly growing. Currently it covers all ORFs from 3 genomes: H. sapiens, S. cervisiae, and E. coli, with 50% redundancy. Interestingly, the database shows hot spots in a majority of proteins. It does not mean that they can easily turn into amyloids in the physiological conditions but it shows new interesting aspects of this topic. Unfortunately, the 3D profile method is very computationally expensive and not very simple to use.
In this paper, we propose two methods to extend the ZipperDB dataset, classifying hexapeptide candidates at lower computational cost. One of the methods is closely related to the original idea of ZipperDB, only reducing the number of profiles. The other one, which introduces the main increase of the efficiency, uses a completely different statistical approach - machine learning. Both methods are tested versus original ZipperDB database classification.
Results and discussion
Dataset
We generated a new dataset of 4481 hexapeptdes, which was later used for training machine learning methods (see Additional file 1, trainset(+) and trainset(-)), using our version of 3D profile method with very significantly reduced number of profiles (see Methods - Dataset), and the method of exact energy calculation proposed in ZipperDB 2006 [10]. The dataset contains 825 positively and 3656 negatively classified segments. Part of our dataset (2702 hexapeptides, see Additional file 1) is also available in ZipperDB 2010 (as of February 2012), which uses the simplified "triplet" method of calculating the energy and fuzzy logic. Energies of these hexapeptides, obtained from our study and from ZipperDB, were compared. Based on the energy criterion, 93.5% of the segments were identically classified with regard to their amyloid properties (Additional file 1). In this set, 622 (23%) hexapeptides were classified by our energy value as amyloidogenic; ZipperDB classified 612 (22.6%) as amyloidogenic. Differently classified hexapeptides often had energies close to the classification threshold of −23 kcal/mol. The mean absolute value of the energy difference, between these two sources, was 1 kcal/mol; 90% of the difference was below 1.4 kcal/mol. Energy values could differ because of limited number of threading profiles, as well as randomization element in Rosetta Design. Moreover, computationally faster but simplified triplet method, used in ZipperDB 2010, also affected the results. As stated by the ZipperDB authors, who tested it on segments of E. coli ORFs, an average error introduced by the triplet method was of 4 kcal/mol (90% of the difference) with the tendency to overestimate amylogenicity [11].
Additional file 1. Dataset of hexapeptides with calculated energies and amylogenic classification.
Format: XLSX Size: 295KB Download file
Our study shows that the results from our threading method are very comparable with those from ZipperDB 2010. In the new part of our dataset (1779 segments), 204 (11%) of the hexapeptides were classified as amyloidogenic (Additional file 1). Also position dependant frequencies of each aminoacid are similar in our set and the set from ZipperDB (see Methods – Dataset and Additional file 2).
Additional file 2. Position specific aminoacid frequencies of the training and test datasets.
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This file can be viewed with: Adobe Acrobat Reader
Machine learning methods
Our dataset, with a binary classification of sequence amyloid propensities based on their calculated energies, was applied for training machine learning methods [26], provided by WEKA [27]. Our objective was testing a potential for sequence based machine learning methods, which could be very significantly faster than threading and energy calculation. From a hundred of different machine learning methods, pre-selection was carried out (see Methods). Special consideration was given to methods with the highest potential for biochemical interpretation. From the preliminary tests, using cross-validation on the training set and selected efficiency measures, ten methods gave promising results: Alternating Decision Tree (ADTree) [28], Best-First Tree (BFTree) [29], Functional Tree (FT) [30], a clone of the Repeated Incremental Pruning to Produce Error Reduction (JRip) [31], a PART decision list (PART) [32], Ripple Down Rule (Ridor) [33], Support Vector Machine (SVM) method, implemented in WEKA with Sequential Minimal Optimization (SMO) algorithm for training a support vector classifier using polynomial or RBF kernels [34], MultiLayer Perceptron (MLP) [35], Naive Bayes [36], and Random Forest (RF) [37].
The final results of these 10 methods, using a separate test set (see Methods – Database) are shown in Table 1. The parameters of the methods (True Positive Rate - TPR, where amyloidogenic is regarded as “positive”, True Negative Rate - TNR, Area Under ROC Curve - AUC) were optimized. Top methods were selected according to their AUC ROC (Figure 1).
Table 1. Machine learning performance
Figure 1. A plot of ROC curves of all methods. A plot of ROC curve for all the methods. Among all methods, MultiLayer Perceptron and Alternating Decision Tree with 250 boosting iterations cover the maximum area under the curve (i.e. 0.96), closely followed by Naive Bayes (AUC of 0.95) and Alternating Decision Tree with 50 boosting iterations (AUC of 0.94). In Table 1 all the corresponding AUC values are reported.
The tests showed that some of the standard WEKA methods can be very successfully used for classification of amyloidogenic segments, compatible with 3D profile method. In the best methods, Acc was typically close to 90%. The most effective methods from WEKA were MLP, ADTree, and Naive Bayes (results in Table 1, model details in Additional file 3).
Additional file 3. Detailed results of the best machine learning methods trained on the full and reduced training sets.
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The best ADTree, with 250 rules, achieved AUC=0.96, which is close to maximum AUC=1, characteristic of an ideal classifier, TPR=0.78, TNR= 0.95, and Acc= 0.91. Identical results were achieved with MLP classifier. We have also tested if removal of hexapaptides that overlap experimental datasets and introduce a bias in sequences, coming from the highly redundant AmylHex dataset, influence the result of our classifiers. The ADTree 250 trained on the reduced training set, deprived of hexapeptides overlapping AmylHex and Waltz, showed higher efficiency – it obtained AUC=0.98, TPR=0.81, TNR=0.96, and Acc=0.94. The rules (trained on the full set) concerning each hexapeptide position are presented and compared in Additional file 4. There are some differences between trees built on the full and reduced training sets. For example, the tree from the full training set favored valine at position 3 (rule 14 with factor 0.6, Additional file 4), overrepresented in AmylHex, while the tree built on the reduced dataset shows valine only in rule 47 (less significant), and with factor 0.45. The trees with a lower number of rules, which are easier for interpretation, are also good classifiers (see ADTree with 50 rules in Figure 2). The top rules for this tree are fairly compatible with the PSSM underlying Waltz method reported in [23], and they indicate, for example, that isoleucine (I) is highly expected at position 4 (see ADTree with 50 rules in Figure 2, rule 1: AA4=I with the factor of 0.926), while proline (P) and arginine (R) are not welcome (Figure 2, ADTree with 50 rules, rule 12: AA4=P with the factor of −2.077, and rule 13:AA4=R with the factor of −1.636, respectively).
Additional file 4. Rules of ADTree 250 methods for full and reduced training sets. Columns contain the rules corresponding to each position in amyloidogenic hexapeptides in decreasing order of their importance. Yellow cells denote positive rules, purple – negative rules.
Format: XLSX Size: 16KB Download file
Figure 2. ADTree with 50 rules. In notation of the rules, n: AA j, n indicates the rule number (ordered by their significance), j denotes the aminoacid position. Below the rule label, the aminoacid occurrence (or absence marked by “!”) are valued by numbers. Negative numbers denote low aminoacid occurrence. A detailed explanation on how to read the Alternating Decision Tree is given in the main text.
Efficiency of the MLP method was not sensitive to the presence of the redundant hexapeptides in the training set (results in Additional file 3). Naive Bayes improved its efficiency when trained on the reduced set (AUC=0.97, TPR=0.54, TNR=0.99, Acc=0.91).
A representative estimate of WEKA methods performance, which was independent of class distribution and the specifics of the training data set (see Methods) is presented in Table 2, showing the number of wins, draws and losses when all methods are compared to each other for AUC. The corrected paired t-test showed that ADTree and MLP had statistically significantly higher AUCs than other methods, at the 5% of the significance level.
Table 2. Statistical evaluation
Compatibility of the energy based classification with FoldAmyloid and Waltz
To test to what extent the 3D profile method overlaps with other state of the art methods, i.e. how universal its extended datasets could be, we performed the amylogenicity prediction with other tools: FoldAmyloid and Waltz, using different classification methods. FoldAmyloid is based on the packing density [23] and Waltz is based on PSSMs primarily derived from a dataset classified by physicochemical modeling [9]. The whole set of 4481 hexapeptides was tested, using all FoldAmyloid options and Waltz optimizations for overall performance and sensitivity (Additional file 5). The results are summarized in Table 3.
Additional file 5. Amylogenic classification of our dataset obtained with reduced 3D profile (additional file 1: trainset(+) and trainset(-)) with different methods: 3D profile, FoldAmyloid and Waltz. The file includes the spreadsheets labeled according to the name of the external method.
Format: XLSX Size: 1.7MB Download file
Table 3. ZipperDB versus other methods
The overall classification overlap was similar in all methods; typically 80% of the hexapeptides were classified identically, using 3D profile and FoldAmyloid or Waltz. On the other hand, 84-88% of hexapeptides, classified by 3D profile as non-amyloidogenic, were also negatively classified by FoldAmyloid; Waltz overlap of negatives was 91-97%. However, classification of the positive hexapeptides was less compatible - ranging from 11% in Waltz best performance method to 43% in FoldAmyloid triple hybrid method. This result shows that classification of positive instances is more challenging and should become the target. Less numerous positive datasets of experimental data, on which all classification methods were previously trained, could contribute to this situation. Also in our dataset, only 18.4% of hexapeptides were regarded as positive. Importantly, recognition of non-amyloid segments in the optimal method overlapped in 84%. This means that negative peptides can be eliminated efficiently and consistently between different methods. We have also tested the consensus between 3D profile, FoldAmyloid triple hybrid and Waltz high sensitivity. It turned out that the overlap was 69%, in which positive rate was 21% and negative 65%.
Conclusions
Extending of the hexapeptide dataset, with computationally effective methods, could help in predicting amyloidogenic regions without laboratory experiments, which are currently not possible on all sequence combinations. We proposed an optimization to the classical 3D profile method, and using only 54 arbitrarily selected profiles we generated the new dataset of hexapeptides classified with regard to their amylogenicity. Energies of our segments showed very good overlap with the segments currently available in ZipperDB, which used the simplified Triplet method to calculate the energy. The new part of our dataset contains 1779 segments that have not been previously considered, with 204 segments classified by energy value as amyloidogenic.
We also performed the amylogenicity prediction on our dataset, using different classification methods - FoldAmyloid and Waltz. The best result was obtained with FoldAmyloid triple hybrid method, which overlapped the 3D profile classification in 77% (total), 43% (amyloidogenic), and 84% (non-amyloidogenic). It showed that different methods are quite compatible in the elimination process, and in this respect datasets generated with the 3D profile methods are universal.
To test whether statistical approach, trained on our dataset, could replace the energy based classifier, we used machine learning methods implemented in WEKA. Our dataset of 6-residue sequences, with a binary classification of their amyloidogenic propensities based on the calculated energy, was applied for training. From all available WEKA methods, we selected those giving the best results and tested with a separate test set, obtained from ZipperDB. Our study showed that some of the methods could be very successfully used for classification of amyloidogenic segments, compatible to the 3D profile method. The most effective methods in WEKA, in terms of AUC ROC, were Alternating Decision Tree and a Neural Network of a Multilayer Perceptron architecture, both with AUC=0.96. The ADTree efficiency could be increased to AUC=0.98 when highly redundant set of experimental hexapeptides was removed from the training set. The performance was then very close to an ideal classifier, for which AUC=1. A great advantage of ADTree method is a set of very easily interpretable rules. Part of the rules were fairly compatible with the PSSM underlying another classification method -Waltz, which was based on different data All those methods could classify almost 80% of positive and 95% of negative hexapeptides identically as the 3D profile method.
Such a good result of classification, based only on aminoacid sequence and its binary classification, is very interesting. It shows a good correlation between classification with the laborious 3D profile method using the minimal chain energy from numerous putative structures, and purely statistical machine learning methods - using just 6 letters and the binary classification. This is possible only if a strong statistical pattern exists in the amyloid sequences recognized by 3D profile. Our results also prove that our new dataset is representative enough for training machine learning methods, in order to obtain amylogenicity of new segments only based on their six letter sequences, with no need to carry out threading procedure and energy evaluation.
The main advantage of the machine learning approach, presented in this paper, is very significantly reduced computational time. Instead of 18–20 CPU-hours with the full 3D profile method or 0.5 CPU-hours with the simplified 3D profile, the classification can take below 1 CPU-minute with a very good overlap of the results. Such a reduction of the computational time is crucial when large amount of hexapeptides should be classified. Additionally, the machine learning enhances the simplicity to perform the analysis.
Methods
Database
As a reference dataset of 6-residue sequences, also applied to test our machine learning results, we used the first set published in ZipperDB as of 2010 (Additional file 1: testset(+) and testset(−)) [11].
The set used for training machine learning methods was obtained from non-redundant protein sequences of UniProt [38], cut into 6-residue windows by shifting of 1 position along the full sequence. The hexapeptides were then divided into amylo-positive and amylo-negative candidates with our simplified 3D profile method. To increase chances of finding amyloid segments, UniProt entries containing the keyword “amyloid” and proteins from AmyPDB database [39,40] were selected for the procedure (both accessed in September 2010). The sequences were first cut into strings not exceeding 80 aminoacids each, and excessive redundancy was reduced at the level of 90%, with CD-HIT (Cluster Database at High Identity with Tolerance) [41,42]. Next, the remaining sequences were cut into hexapeptides with a window of length 6, shifted of 1 position in each move. The set was finally enlarged with 266 hexapeptides studied experimentally: AmylHex dataset [10] and Waltz [23].
The full dataset do not show position dependence of aminoacids, with statistics close to the frequencies of aminoacids in all UniProt [43]. Even closer statistics were obtained for the dataset not enriched with the hexapeptides from AmylHex and Waltz. The statistics of the test set is also close to the same characteristics, although some numbers slightly differ (e.g. prolines are excluded in the test set). Standard deviations are negligible in both datasets. The statistics of datasets, in the form of tables and logos (prepared with WebLogo [44]), are presented in Additional file 2.
Threading and energy calculation
First, all cysteines were replaced by serines to avoid disulfide bridges as in [10]. Similarly to 3D profile method [10], a fibril-forming peptide NNQQNY, from sup35 prion protein of Saccharomyces, was used as a scaffold in the threading method. Each hexapeptide from the set was threaded on the scaffold; 5 identical copies of the hexapeptide formed one of two identical β-sheets. In the final structure, one of the β-sheets was shifted relative to the other one. In our implementation, which differs from 3D profile method, the movement was exercised in two planes: along the chains of 0-8 Å with the step of 1 Å, and across the sheets fixing the distance between them to 6–11 Å with the step of 1 Å. We did not use the third direction, which was implemented in [10]. Finally, we obtained 54 profiles, instead of 2,511 in full method [10]; no fuzzy logic was used to reduce the number of profiles as in [10]. Then, the energies of 54 profiles were calculated. For each segment from the dataset the energy was obtained with Rosetta Design program [45,46], which added the side chains to the backbones, applied a random component of the simulated annealing to relax the structure, and calculated the energy of infinite periodic system (for more details of the energy calculation procedure see [45]). As an optimal configuration, for each hexapeptide a structure with minimal energy was selected from the set of profiles. Similarly as in [10], the threshold of −23 kcal/mol was assumed to classify amylogenicity of a segment. Positive instances contained at least one chain whose energy was not greater than the threshold.
The full original 3D profile method, evaluating a single 6-residue segment, required 18–20 CPU-hours (2.5 GHz AMD Opteron, Phenom or Intel Xeon CPU), while 2–2.5 CPU hours were needed with the triplet method and fuzzy logic selecting 80–100 templates [11], supplement. Our method applies the original method, only reducing the number of templates 46 times (from 2 500 to 54). The energy calculation would take 0.5 CPU-hour for each hexapeptide, with the same computer.
Machine learning
The classifiers were trained on all 4481 hexapeptides from our dataset obtained by simplified 3D profile method (Additional file 1). Prediction methods were provided by WEKA 3.6.6 (Waikato Environment for Knowledge Analysis) [27],which includes a hundred of different classifiers. Pre-selection, to find the most effective methods, was carried out with default WEKA sets of parameters and 10-fold cross-validation on the training set. Next, we chose 10 most promising methods from WEKA suite. Finally, we used the following methods with the optimized parameters:
ADTree (numOfBoostingInterations=250 or 50, randomSeed=1),
BFTree (minNumObj=4, numFoldsPruning=4, seed=2, pruningStrategy=un-pruned),
FT (minNumInstances=26, numBoostingIterations=86),
RF (maxDepth=unlimited, numFeatures=log2(7)+1, numTrees=200, seed=1),
JRip (folds=4, minNo=1, optimizations=7, seed=4),
MLP (hiddenLayers=1 with 60 nodes, learningRate=0.1, Momentum=0.2, seed=0, trainingTime=500),
PART (confidenceFactor=0.3, mniNumObj=1, numFold=3, seed=1),
Ridor (folds=3, minNo=6, seed=1, shuffle=7),
SVM (c=2.0, kernel=linear)
Naive Bayes (no parameters).
Parameters not specified have their values set to default.
Out of the above mentioned methods, ADTree algorithm has several advantages over other machine learning methods, such as MLP or SVM, including easy interpretation of the results. An alternating decision tree is in fact a graphical representation of a collection of user interpretable rules. Each tree consists of decision and prediction nodes. The prediction node contains a single number, whereas decision node defines a predicate conditions. To classify an instance, the ADTree follows all paths for which all decision nodes are true. The final classification score is gained by summing all the prediction nodes through which the instance it passes.
Prediction accuracy assessment
The binary test set included 346 positive and 1240 negative hexapeptides from ZipperDB, as of May 2010 (Additional file 1). The classification results were evaluated based on typical measures: Sensitivity (called True Positive Rate - TPR), Specificity (True Negative Rate - TNR), Accuracy (Acc). These criteria widely used to evaluate the performance of prediction models, and defined as below:
where TP, FP, FN and TN represent the numbers of true positives, false positives, false negatives and true negatives respectively. The overall quality of a classifier can be evaluated with area under ROC curve (AUC) [47]. The value of the AUC score ranges from zero to one, with a score of 0.5 corresponding to random guess and a score of 1.0 indicating perfect separation. This estimator evaluates the method in separating amyloids from non-amyloids. In particular, The AUC is well received in the imbalanced dataset community and it is becoming the standard evaluation method.
Statistical validation
In order to obtain a representative estimate of WEKA methods performance, which is independent of class distribution and the specifics of the training data set, we performed an experiment with 10 train and test runs. The data used for training and testing - a dataset of 4481 hexapeptides - was randomly divided into 66% and 34%, respectively. The results were analysed statistically using a corrected paired samples t-test [46] where we computed p-values at the 5% significance level, comparing every method with every other method for their AUC. This is a parametric procedure used to determine whether there is a significant difference between the average values of the same performance measure for two different methods. The test assumes that the paired differences are independent and identically normally distributed. Although the measurements themselves may not be normally distributed, the pair wise differences often are.
Validation with other classification methods
Two different state of the art methods were used to test the inter-compatibility of the energy based method: FoldAmyloid [18,48] and Waltz [23,49] (as of March 2012). We performed the analysis on the whole set of 4481 hexapeptides, using our scripts in Python programming language and spynner - open source web browsing module for communication with both services. All standard FoldAmyloid methods were applied: contacts, bone-bone donors, bone-bone acceptors, hybrid (contacts + donors), and triple hybrid (contacts + donors + acceptors). Waltz was run with its standard optimizations for overall performance and sensitivity.
Competing interests
The authors declare that they have no competing interests.
Authors’ contributions
JS proposed the simplified 3D profile method, generated the dataset and did preliminary tests on the machine learning methods. MK validated the dataset with ZipperDB, ran and analyzed machine learning, FoldAmyloid and Waltz methods, and drafted the manuscript. OU ran and analyzed machine learning methods, performed the statistical analysis, and participated in writing the manuscript. MK and OU designed and supervised the study. All authors read and approved the final manuscript.
Acknowledgements
This work was in part supported by the grant N N519 643540 from National Science Center of Poland. Wroclaw Centre for Networking and Supercomputing at Wroclaw University of Technology is greatly acknowledged.
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Methodology article
De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley
Burkhard Steuernagel1, Stefan Taudien2, Heidrun Gundlach3, Michael Seidel3, Ruvini Ariyadasa1, Daniela Schulte1, Andreas Petzold2, Marius Felder2, Andreas Graner1, Uwe Scholz1, Klaus FX Mayer3, Matthias Platzer2 and Nils Stein1*
Author affiliations
1 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correnstr. 3, D-06466 Gatersleben, Germany
2 Leibniz Institute for Age Research, Fritz Lipmann Institute (FLI), Beutenbergstr. 11, D-07745 Jena, Germany
3 MIPS/IBIS, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, D-85764 Neuherberg, Germany
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Citation and License
BMC Genomics 2009, 10:547 doi:10.1186/1471-2164-10-547
Published: 20 November 2009
Abstract
Background
De novo sequencing the entire genome of a large complex plant genome like the one of barley (Hordeum vulgare L.) is a major challenge both in terms of experimental feasibility and costs. The emergence and breathtaking progress of next generation sequencing technologies has put this goal into focus and a clone based strategy combined with the 454/Roche technology is conceivable.
Results
To test the feasibility, we sequenced 91 barcoded, pooled, gene containing barley BACs using the GS FLX platform and assembled the sequences under iterative change of parameters. The BAC assemblies were characterized by N50 of ~50 kb (N80 ~31 kb, N90 ~21 kb) and a Q40 of 94%. For ~80% of the clones, the best assemblies consisted of less than 10 contigs at 24-fold mean sequence coverage. Moreover we show that gene containing regions seem to assemble completely and uninterrupted thus making the approach suitable for detecting complete and positionally anchored genes.
By comparing the assemblies of four clones to their complete reference sequences generated by the Sanger method, we evaluated the distribution, quality and representativeness of the 454 sequences as well as the consistency and reliability of the assemblies.
Conclusion
The described multiplex 454 sequencing of barcoded BACs leads to sequence consensi highly representative for the clones. Assemblies are correct for the majority of contigs. Though the resolution of complex repetitive structures requires additional experimental efforts, our approach paves the way for a clone based strategy of sequencing the barley genome.
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Research article
LEA (Late Embryogenesis Abundant) proteins and their encoding genes in Arabidopsis thaliana
Michaela Hundertmark and Dirk K Hincha*
Author Affiliations
Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam, Germany
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BMC Genomics 2008, 9:118 doi:10.1186/1471-2164-9-118
The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2164/9/118
Received:1 October 2007
Accepted:4 March 2008
Published:4 March 2008
© 2008 Hundertmark and Hincha; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract
Background
LEA (late embryogenesis abundant) proteins have first been described about 25 years ago as accumulating late in plant seed development. They were later found in vegetative plant tissues following environmental stress and also in desiccation tolerant bacteria and invertebrates. Although they are widely assumed to play crucial roles in cellular dehydration tolerance, their physiological and biochemical functions are largely unknown.
Results
We present a genome-wide analysis of LEA proteins and their encoding genes in Arabidopsis thaliana. We identified 51 LEA protein encoding genes in the Arabidopsis genome that could be classified into nine distinct groups. Expression studies were performed on all genes at different developmental stages, in different plant organs and under different stress and hormone treatments using quantitative RT-PCR. We found evidence of expression for all 51 genes. There was only little overlap between genes expressed in vegetative tissues and in seeds and expression levels were generally higher in seeds. Most genes encoding LEA proteins had abscisic acid response (ABRE) and/or low temperature response (LTRE) elements in their promoters and many genes containing the respective promoter elements were induced by abscisic acid, cold or drought. We also found that 33% of all Arabidopsis LEA protein encoding genes are arranged in tandem repeats and that 43% are part of homeologous pairs. The majority of LEA proteins were predicted to be highly hydrophilic and natively unstructured, but some were predicted to be folded.
Conclusion
The analyses indicate a wide range of sequence diversity, intracellular localizations, and expression patterns. The high fraction of retained duplicate genes and the inferred functional diversification indicate that they confer an evolutionary advantage for an organism under varying stressful environmental conditions. This comprehensive analysis will be an important starting point for future efforts to elucidate the functional role of these enigmatic proteins.
Background
Late embryogenesis abundant proteins (LEA proteins) were first found in cotton (Gossypium hirsutum) seeds, accumulating late in embryogenesis [1]. They were subsequently found in the seeds of many other plants, but also in vegetative organs, especially under stress conditions such as cold, drought, or high salinity (see [2,3] for reviews). According to the appearance of different sequence motifs/patterns or biased amino acid composition, plant LEA proteins have been separated into different groups [4-7]. However, the grouping of proteins and the nomenclature of the groups have not been consistent in the literature (see [8] for a recent review).
LEA proteins are not plant specific. They have also been found in other organisms, such as the bacteria Deinococcus radiodurans [9] and Bacillus subtilis [10], the chironomid Polypedilum vanderplanki [11], the brine shrimp Artemia [12], different species of nematodes [13-15], rotifers [16,17] and cyanobacteria [18]. The presence of LEA proteins has been associated with cellular tolerance to dehydration, which may be induced by freezing, saline conditions, or drying. In extreme cases, organisms can even survive a complete loss of water (anhydrobiosis; see [19] for review). Sugars, especially the disaccharides sucrose and trehalose, are thought to play important roles in cellular desiccation tolerance [19], but it is clear that additional substances are necessary for a cell to attain anhydrobiosis [20,21]. Desiccation-tolerant rotifers can even survive complete desiccation without accumulating sugars [22], but they show enhanced expression of genes encoding LEA proteins during drying [16,17]. Likewise, a strong induction of LEA gene expression has been found in the desiccation tolerant resurrection plant Craterostigma plantagineum during slow drying [23]. These and many other examples in the literature suggest that LEA proteins may indeed be important determinants of cellular dehydration tolerance in a variety of organisms from bacteria to plants and lower animals.
A common feature of LEA proteins is a biased amino acid composition that leads to high hydrophilicity [24] and heat stability in solution. This is similar to the recently developed concept of "hydrophilins" [25] and indeed many LEA proteins were classified as hydrophilins by these authors. However, since a distinguishing feature of hydrophilins is a high glycine content, not all LEA proteins were classified as hydrophilins and instead other non-LEA proteins were included. The functional significance of membership in either or both of these groups is unclear. The resolution of this and many other questions concerning LEA proteins is severely hampered by the fact that, although these proteins have been known for 25 years, only limited functional information is available.
The overexpression of genes encoding LEA proteins can improve the stress tolerance of transgenic plants. Expression of the barley gene HVA1 in wheat and rice conferred increased drought tolerance to plants [26,27] and expression of the wheat genes PMA80 and PMA1959 increased the dehydration tolerance of transgenic rice [28]. The cold tolerance of transgenic tobacco was increased by the expression of a citrus gene encoding a LEA protein (CuCOR19; [29]). Likewise, the freezing tolerance of Arabidopsis was increased by the ectopic expression of the wheat gene WCS19 [30], the Arabidopsis gene COR15A [31], and the co-expression of the genes RAB18 and COR47, and XERO2 and ERD10 [32]. The freezing tolerance of strawberry leaves was enhanced by expression of the wheat dehydrin gene WCOR410 [33]. Mutant analysis showed that the EM6 protein is required for normal seed development in Arabidopsis [34]. On the other hand, the expression of two cold-induced LEA proteins from spinach [35] and three desiccation-induced LEA proteins from C. plantagineum [36] in tobacco did not induce any significant changes in the freezing or drought tolerance of the respective transgenic plants. This may indicate either that not all LEA proteins make a significant contribution to plant stress tolerance, or that they need a particular background to function in, as suggested for transgenic strawberry plants [33].
An alternative approach for in vivo functional studies is the expression of LEA proteins in yeast or bacteria. Such studies have shown that a wheat LEA protein conferred tolerance against hyperosmotic stress to Saccharomyces cerevisiae cells [37], while LEA proteins from Chlorella, tomato and barley protected yeast cells against high salt concentrations and freezing [38-40]. Likewise, a LEA protein from soybean increased the salt tolerance, but not the tolerance against hyperosmotic stress, when expressed in Escherichia coli [41].
Parallel efforts have concentrated on determining biochemical and biophysical activities of these proteins. A stabilization of lactate dehydrogenase and malate dehydrogenase during freezing and/or drying has been shown for LEA proteins from citrus [42,43], Chlorella [44], barley [45], Arabidopsis, and C. plantagineum [46,47]. Fumarase and rhodanese could be stabilized during drying by the addition of a pea seed LEA protein [48], catalase by a citrus LEA protein [42], and citrate synthase by LEA proteins from wheat, the nematode Aphelenchus avenae [49] and the rotifer Adineta ricciae [16]. These data indicate that several LEA proteins have the ability to stabilize labile enzymes under stress conditions. However, since no systematic studies, including negative results, across different groups of LEA proteins have been reported, it can not be judged whether this is a general property of LEA proteins or whether specific structural requirements exist.
Only a few papers have investigated other functional properties of LEA proteins. The Arabidopsis dehydrin ERD10 binds more water during drying than non-LEA control proteins [50,51] and this and other dehydrins bind calcium, iron and other divalent cations in a phosphorylation-dependent manner [52-54]. Radical scavenging by a citrus LEA protein [29] and the stabilization of dry sugar glasses by LEA proteins from Typha latifolia [55] and soybean [56] have also been reported.
These data indicate that LEA proteins have interesting functional properties related to their presumed role as cellular stabilizers under stress conditions. Unfortunately, the available data are too fragmented between species, structural groups, and methodologies to draw any general conclusions about structure-function relationships and physiological roles of LEA proteins. Such knowledge is not only of great basic scientific interest, but would also help to lead transgenic approaches and the technical use of LEA proteins as biostabilizers beyond mere trial and error. To obtain such knowledge, systematic biochemical, functional and physiological studies are required. Before such studies can be undertaken, genome-wide approaches are necessary to describe and classify the entire LEA complement of model organisms. We present such an analysis of LEA proteins and their respective genes in Arabidopsis thaliana. We correct previous annotation errors and annotate new genes, resulting in the identification of 51 genes in Arabidopsis that encode LEA proteins. Gene expression data, together with in silico analyses of promoter elements, and of the structure, localization and biochemical properties provide a comprehensive view of this enigmatic group of proteins.
Results and Discussion
LEA protein encoding genes in the Arabidopsis genome
Existing annotation and BLAST searches of well-characterized LEA genes from cotton (Gossypium hirsutum) identified 64 genes in the Arabidopsis genome that encode LEA proteins. To characterize and classify the genes, Pfam family domains were searched in the protein sequences (Table 1). Previously, LEA proteins have been separated into different groups [4-7], but the classification varies between different authors. For a better overview and tracking of proteins, we use the Pfam nomenclature, as this is uniquely related to sequence motifs. To allow easy reference to LEA proteins described in earlier publications, Table 2 compares the Pfam nomenclature with the two most frequently used systems proposed by Dure [5,6] and Bray [4].
Table 1. Characteristics of genes encoding LEA proteins in Arabidopsis thaliana
Table 2. The nomenclature of the different LEA protein groups in the Pfam database and according to Bray [4] and Dure [6].
The applied Pfam gathering threshold ensured that reliable results were retrieved from matching Pfam domains to the queried protein sequences. Thirteen genes were removed from the set of 64 (Additional file 1) because they had no significant LEA Pfam domain. It is striking that three of the removed genes contain a "root cap" Pfam domain. They were annotated as related to a LEA protein from Picea glauca, the EMB7 protein, which occurs late in embryogenesis. This LEA protein carries a root cap family domain, which, however, is not a signature domain of LEA proteins. Of the 13 Arabidopsis genes that were erroneously annotated (Additional file 1), 12 show similarities to Picea glauca genes which are expressed late in embryogenesis and therefore named LEA despite the fact that they have different structural domains.
Additional file 1. Wrongly annotated LEA genes in Arabidopsis. Compilation of all genes that have been annotated as LEA genes in the Arabidopsis genome, but that we found not to be members of any LEA group.
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We have classified two proteins (COR15A and COR15B) into LEA_4 that had previously been annotated as LEA proteins, although they do not contain a characteristic Pfam domain (Table 1, #23 and #24) above the Pfam gathering threshold. The two encoding genes form a tandem repeat and while COR15B contains a LEA_4 Pfam domain with a significant p-value of 0.046, the alignment for COR15A is not significant. However, we chose to include both genes in our list and in the following studies because they are structurally and functionally closely related and cluster together with other LEA_4 proteins (Fig. 1). We also included two novel LEA groups in our studies that do not have Pfam entries yet, the two AtM genes [57] and three genes homologous to the LEA18 gene from Phaseolus vulgaris [58]. These groups were included in our studies because of the similarity to known LEA proteins, namely high hydrophilicity, high expression levels during late embryogenesis and/or under abiotic stress conditions and lack of homology with other protein families. This led to the final annotation of 51 genes in the Arabidopsis genome that encode LEA proteins and these are listed in Table 1 with a numbering according to their position in the Arabidopsis genome, starting at the top of chromosome 1. This simplified numbering is used in the remainder of the paper to identify the corresponding genes and proteins. In the TIGR5 Arabidopsis thaliana database, nine of these 51 genes were not annotated as LEA, dehydrin or seed maturation protein, while seven were annotated as LEA but lacked significant Pfam domains and had high similarity to non-LEA protein families (Additional file 1).
Figure 1. Unrooted dendrogram of all Arabidopsis LEA genes. Sequence alignments were performed unsing the ClustalW algorithm and an unrooted dendrogram was drawn subsequently. The different LEA groups are indicated by different colors, COR15A and COR15B are highlighted in the LEA_4 group.
To see whether such a large number of genes encoding LEA proteins is specific to Arabidopsis, we also searched the well-annotated rice genome using the same strategy as outlined above. In addition, the draft genomic sequences of grapevine (Vitis vinifera), poplar (Populus trichocarpa) und Chlamydomonas reinhardtii are also available and we extended our search to these species as well. We applied BLAST searches (expect-value cutoff 1e-5) with the LEA genes from Gossipium hirsutum and Arabidopsis to identify matching sequences. Since in these cases the BLAST search only returns positions on the scaffolds without any gene model information, this data should be considered as preliminary. The analyses revealed the presence of 35 LEA genes in rice, 36 in grapevine, 33 in poplar and only ten in Chlamydomonas, where only regions homologous to LEA_4 genes could be detected (Fig. 2). This may indicate that all other LEA groups evolved later in higher plants. This is consistent with the finding that the only LEA genes that can be detected in lower animals belong to the LEA_4 group [8]. In the rice genome, all genes have been previously annotated as encoding LEA, dehydrin or seed maturation proteins by the TIGR Community and an approach similar to ours identified 34 LEA genes in the rice genome [59]. If the number of genes in the different groups is compared between the investigated species (Fig. 2), the main differences occur in the dehydrin, LEA_4 and LEA_5 groups. The abundance of LEA_4 genes is lowest in rice, while especially Arabidopsis and grapevine have a large LEA_4 group. On the other hand, Arabidopsis and rice have about three times as many dehydrin genes as poplar and grapevine, but poplar has many more LEA_5 genes than all other species. There are also minor variations in the other groups, but except for the AtM there is at least one member of each group found in the investigated higher plant genomes. Interestingly, a BLAST search found the AtM genes to occur only in Brassicaceae species. Whether these differences between species have any functional significance is currently unknown and awaits functional characterization of the proteins.
Figure 2. Comparison of the sizes of the different LEA gene groups in Arabidopsis, rice (Oryza), poplar (Populus), grapevine (Vitis) and Chlamydomonas.
Characteristics of the encoded LEA proteins
We performed a ClustalW alignment of all 51 LEA proteins in Arabidopsis and the resulting unrooted dendrogram shows that the identified LEA groups are quite distinct from each other (Fig. 1). This result is not unexpected since the historical annotation as LEA is due to the expression pattern and to sequence homology within groups, but not between groups.
For a better overview of the characteristic features of the different LEA groups in Arabidopsis, we have compiled group-specific characteristics in Table 3. In the Arabidopsis genome, LEA_4 group (also known as group 3 or D-7) is the most dominant containing 18 members. This group is very heterogeneous and the gene products differ greatly in size and GRAVY (Grand Average of Hydropathy) index. They also lack high sequence similarity (data not shown) and no determinant motif could be found by the PRATT algorithm. In the majority of the protein sequences, the classical proposed motif (TAQAAKEKAXE; [6]) could not be found. Although the LEA proteins in G. hirsutum show this conserved motif, it seems to be quite variable in LEA_4 group genes from other species. However, the LEA_4 group proteins contain the characteristic Pfam domain which we used as the determinant criterion. We also found LEA_4 domains in homologues of the D-29 proteins that make up LEA group 5 [4,6]. Because the LEA_4 domain was present in proteins from both groups, we combined these groups under their Pfam name (Table 2).
Table 3. Group-specific values for the different calculated traits
The second biggest group is the dehydrin group (also called group 2 or D-11) which includes ten genes. This is similar to the number found in rice (eight (Fig. 2); [59]) and in barley (13; [60]), but much more than in poplar and grapevine (Fig. 2). The Arabidopsis dehydrins show high sequence similarity at least in some parts and two common motifs are available in the Prosite database [5,61,62]. They have also been subdivided into an acidic group containing COR47 (#4), ERD10 (#5), ERD14 (#10), #14, #44, and #45, and a basic/neutral group containing #8, XERO2 (#33), XERO1 (#34), and RAB18 (#51) [53]. Figure 3 shows an alignment of all Arabidopsis dehydrin sequences. The characteristic K, Y, S, and Lys-rich segments are highlighted [63]. The KYS classification for all dehydrin proteins is given in Additional file 2. It can be seen from Figure 3 that only the K segment is present at least once in all dehydrins, making it the distinguishing feature of this group. The S segment, on the other hand, is present in eight, the Lys-rich segment in five, and the Y segment only in three of the ten proteins. Interestingly, the Lys-rich segment is only present in those LEA proteins that were highly expressed exclusively in vegetative tissues. The presence of any of the other segments was not indicative of one of the three possible expression patterns (seed, non-seed, seed+non-seed; compare Table 1).
Additional file 2. Appearance of segments in Arabidopsis dehydrins. Classification of the dehydrins found in Arabidopsis according to the KYS and Lys-rich segment system.
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Figure 3. Alignment of the dehydrin protein sequences of Arabidopsis thaliana. Amino acid sequences were aligned using the ClustalW algorithm. Dashes indicate gaps introduced for optimal alignment. The typical dehydrin sequence elements are highlighted: K segment – red; Y segment – yellow; S segment – green; Lys-rich segment – grey. The genes forming homeologous pairs and tandem repeats in the genome (compare Fig. 6, Table 6 and 7) are indicated by arrows on the right and left side of the gene identifier, respectively. The complete sequences can also be found in Additional file 5.
Only the functional significance of the S-segment is known. It is phosphorylated, leading to calcium binding activity in some, but not all, investigated dehydrins [53]. The role of phosphorylation in those proteins that do not bind calcium is unclear, as is the physiological significance of the calcium binding activity.
The SMP group (seed maturation protein, D-34 or group 6; Table 2) has six members, while the remaining groups consist only of two to four members. Apart from the original six groups, we included some unusual groups in our study. The LEA_3 group (D-95 or LEA5; Table 2) is also characterized by a Pfam entry. Along with this group, the LEA_2 genes (LEA14 or D-74; Table 2) have been identified in cotton [64]. They encode 'atypical' LEA proteins because of their more hydrophobic character. The three PvLEA18 proteins belong to a small family of hydrophilic proteins that are related to a LEA protein in Phaseolus vulgaris that was reported to be induced upon dehydration [58]. The two AtM LEA proteins [57] are also hydrophilic and are expressed late in embryo development.
Expression analysis of all Arabidopsis genes encoding LEA proteins
For the 51 LEA genes identified in the Arabidopsis genome, expression analysis was performed on samples from different organs and in leaves under various, mainly abiotic, stress conditions. A detailed compilation of all LEA gene expression data is provided in Additional file 3. Figure 4A shows the expression of the genes in various organs, with the exception of seeds, which are shown in Figure 4D. In total, 22 of the 51 genes (43%) showed high expression levels (relative expression >10) in the non-seed organs in the absence of a stress or hormone treatment. Due to the high sensitivity of the Real-Time PCR measurements, expression at lower levels was detectable for all genes at least in some non-seed tissues. Transcript levels for most of these genes were highest in seedlings. The expression of LEA genes in green siliques was low compared to the other organ samples, indicating that the onset of the expression of seed-specific LEA genes had not yet been reached. It has been shown before that LEA transcripts accumulate immediately before maturation drying and remain stable in the desiccated seeds [1,65].
Additional file 3. Expression data of all Arabidopsis LEA genes. Quantitative Real-Time RT-PCR data for the expression of LEA genes in diverse Arabidopsis organs and under stress conditions and hormone treatments.
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Figure 4. Expression analysis of all 51 LEA genes in A. thaliana. Expression was measured by quantitative RT-PCR in different organs (A), in mature leaves under different stress conditions (B), in axenic cultures under hormone induction (C) and in mature seeds (D). The color coding represents relative gene expression from 0 (yellow) to 100% (red), with 100% representing the highest expression within a given panel (compare e.g. the same leaf data as represented in A and D). See Additional file 3 for the complete data set. The numbers on the sides refer to the different LEA genes that are listed in Table 1.
Of the 22 genes highly expressed in non-seed tissues, 12 were induced more than 3-fold by different stresses (the transcripts for #10 and #26 were induced less than 3-fold; the transcripts for #11, #28, #40, #45 and #47 were undetectable in leaves and the transcripts #12, #17 and #27 were lowly expressed in leaves under control and all stress conditions; Additional file 3). The expression of LEA genes was enhanced mainly by cold, drought and salt treatment (Fig. 4B, Table 4). Under cold conditions, besides the well-known cold-regulated genes [3]COR47 (#4), ERD10 (or LTI45, #5) COR15A (#24), COR15B (#23), and XERO2 (#33), several other genes were induced (#1, #38, #41, #46, #51). Under salinity stress, the expression differed in some cases from the expression under cold stress. In addition to the genes #33 (XERO2), #38 (SAG21), #41 (AtDI21) and #51 (RAB18) that were upregulated under both conditions, the genes #7, #16 and #20 (EM6) were salt-induced. COR15A (#24) and COR15B (#23) were highly upregulated under cold stress (more than 80-fold), whereas salinity and drought stress enhanced the expression about 2-fold (COR15A) or even decreased the expression (COR15B). Cold induction had been described for these genes before [66]. Drought treatment only enhanced the expression of four genes, #7, #41 (AtDI21), #46 and #51 (RAB18), in our experiments. The induction of the genes under drought conditions seems to be high (up to 55-fold), however, the expression levels of the genes are very low in unstressed leaves and still low in drought-stressed leaves compared to other stress treatments. Expression of RAB18 (#51) was enhanced more strongly under drought stress than under cold and high salinity conditions in accordance with earlier reports [67]. High light treatment had only small effects on LEA gene expression, with five genes (#7, #23, #24, #41 and #51) induced over 3-fold. The upregulation of LEA gene expression under high light conditions has been described previously [68,69]. Infection with powdery mildew enhanced the expression of eight genes, however, mostly to a smaller extent than abiotic stress, while heat shock treatment only increased the expression of RAB18 (#51) more than 3-fold.
Table 4. Stress induced expression of LEA genes. Highly expressed LEA genes that are induced at least 3-fold in stress-treated leaf tissue. The numbering is according to Table 1. The relative expression in the different samples is shown under Expression. The first three columns show the unstressed controls ("hydroponics" for salt stress, "heat control" for heat stress, "leaf" for the other conditions). The gene expression after stress treatment compared to the appropriate controls is shown under Induction. Bold-face numbers highlight induction of genes by more than 3-fold.
SAG (senescence-associated gene) 21 (#38) is induced during natural [70] and ozone-induced senescence [71] and under drought stress [70]. Here we show its additional induction under cold and salt stress conditions. This is in agreement with the earlier hypothesis that SAG21 is not directly involved in senescence, but is rather a marker for the stresses associated with senescence and cellular degradation [70]. Among the 14 genes that were induced more than 3-fold under any stress condition (Table 4), five belong to the dehydrin group. Also, three LEA_4 genes, two LEA_3 genes, one LEA_2 gene, one gene each of the PvLEA18, the LEA_1 and the LEA_5 group were stress induced, while no members of the SMP and the AtM groups were induced under any of the tested stress conditions in leaves.
Treatment of axenic cultures with abscisic acid (ABA) resulted in high expression of 27 genes, whereas only 12 genes were highly expressed in soil-grown seedlings and 10 genes in the untreated axenic control (Fig. 4C, Table 5). Treatment with gibberellic acid (GA3) resulted in high expression of 10 genes, similar to the untreated control (Additional file 3), indicating that GA3 is not a major regulator of LEA gene expression. Of the 27 genes highly expressed in the ABA-treated cultures, 21 were induced more than 3-fold (Table 5). At least one member of each group, except for SMP and AtM was induced by ABA-treatment. The induction of most genes was high compared to the very low levels of expression in the untreated plants. For many of the induced genes, ABA induction has been previously reported, such as COR47 (#4), ERD10 (#5), ERD14 (#10), COR15A and COR15B (#24 and #23), XERO2/LTI30 (#33) and RAB18 (#51) [66,67,72]. We also found that EM6 (#20), one of the two members of the LEA_5 group, was expressed in non-seed organs and could be induced by ABA-treatment, but the homologous gene EM1 (#35), which was seed-specific, was not induced by ABA. Comparison of gene expression under stress conditions and ABA treatment showed the expected substantial overlap (compare Fig. 4A and 4C).
Table 5. ABA-induced LEA gene expression
The expression pattern of LEA genes in seeds was drastically different from the pattern in all other tissues (Fig. 4D). Only ten genes were found to be highly expressed in both seeds and in non-seed tissues under any conditions (LEA14 (#1), #7, #16, EM6 (#20), #27, #28, XERO2 (#33), SAG21 (#38), AtDI21 (#41), and #45). The overall level of expression of LEA genes in seeds was much higher compared to the expression in vegetative tissues. In addition, more LEA genes (33; 65% of all LEA genes) were highly expressed in seeds than in non-seed organs (22; 43%). We also investigated LEA gene expression in seeds of five additional Arabidopsis accessions (Landsberg erecta, C24, Niederzens, Rschew, Columbia-2). The content of LEA transcripts was similar in all accessions (Fig. 4D, Additional file 3), but some striking differences (e.g. #6, #20) were also detected. It is unclear whether these differences have any influence on seed desiccation tolerance or longevity. Comparison of the expression of LEA genes after ABA treatment of vegetative plants and in seeds showed only a limited overlap (compare Fig. 4C and 4D), indicating different signal transduction pathways in the different tissues.
We detected transcripts of every gene in at least one sample (Additional file 3). We compared our expression data with the AtGenExpress Affymetrix array data [73] and found a significant correlation (p = 1.456e-44, R = 0.5578) between the data sets. This correlation strongly confirms the reliability of our measurements, considering the different growth conditions that were used to generate the two data sets. In addition, our experiments provide expression data on three LEA genes (#3, #49, #50) that are not represented on the Affymetrix ATH1 array.
ABRE and LTRE cis-acting regulatory elements in the promoters of Arabidopsis genes encoding LEA proteins
Genes encoding LEA proteins are highly expressed during abiotic stress and in seeds (Fig. 4). The ABRE (ABA responsive element; [74]) plays a key role in ABA signalling during seed development and under abiotic stresses (see [75,76] for recent reviews), while the second prominent cis-element in relation to the expression of stress regulated genes in general and LEA genes in particular is the DRE/CRT/LTRE (drought responsive/C-repeat/low temperature response) element, which binds the CBF/DREB1 transcription factors (see [3,76] for reviews). We queried the PLACE database [77] for these elements in the -2000 nt promoter sequences of the genes and compared the occurrence in the LEA gene promoters with the occurrence in all promoters in the genome using the Fisher exact statistical test. This analysis showed that the ABRE core motif was overrepresented in the LEA gene promoters with a p-value of 2.7E-04 and the LTRE core motif with a p-value of 3.7E-05.
Closer analysis showed that 82% of all LEA genes contain the ABRE core motif in their -2000 nt promotor regions (compared to 58% of total genes in Arabidopsis), while 69% (compared to 40% of total genes) contain the LTRE core motif (Additional file 4). The majority of LEA genes (32 out of 42) containing an ABRE motif were highly inducible (> 3-fold) by ABA, but only 12 out of the 35 genes that have an LTRE element in their -2000 nt region were highly inducible by either cold or drought in our experiments. Conversely, only three genes that were highly ABA inducible did not contain an ABRE motif, while only one gene that was highly cold induced contained no LTRE motif. This indicates the importance of the CBF/DREB1 signal transduction pathway for the cold and drought regulation of LEA genes in the vegetative tissues of Arabidopsis. However, only three of the cold or drought induced genes were not induced by ABA, indicating also a possible substantial crosstalk between these signal transduction pathways.
Additional file 4. ABRE and LTRE cis-elements in LEA gene promoters. The table shows the number of the two core motifs found in the -2000 nt promoter regions of all 51 LEA genes.
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Interestingly, there were only two LEA gene promoters that contained neither an ABRE nor an LTRE motif (SAG21 and #39). Of these genes, only SAG21 (#38) was strongly upregulated by ABA, salt and cold treatment and by powdery mildew infection (Table 4). SAG21 may therefore be an interesting candidate as a reporter gene for the detection of novel stress and ABA-regulated signal transduction pathways.
Structure and subcellular localization of LEA proteins
The LEA groups show differences in structural features of their members. The mean values for the molecular mass of the proteins show that, in general, LEA proteins are relatively small, with most falling in a range from 10 to 30 kDa (Table 3). There are a few very small LEA proteins (<10 kDa), especially the members of the PvLEA18 group. In addition, also some larger (~65 kDa) LEA proteins can be found in the LEA_4 group. The most striking differences can be seen in the GRAVY values (Table 3), with the LEA_2 group the most hydrophobic and LEA_5 the most hydrophilic. The larger dehydrin and LEA_4 groups show a wide range of GRAVY values but are altogether quite hydrophilic. Characteristics and sequences of all proteins are given in Additional file 5.
Additional file 5. Details of the characteristics of all Arabidopsis LEA proteins. Information on sequences and some predicted features of the 51 LEA genes.
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The secondary structures of 17 plant LEA proteins, one LEA protein from a nematode and two from a rotifer have been experimentally determined. Four of these proteins belong to LEA_5 group [78-81]. They were all shown to be in random coil conformation in solution. For two of these proteins, partial structuring in the presence of trifluoroethanol (TFE) or during drying has been reported [79,80].
The dehydrin group is the best investigated group with eight analyzed proteins. Four of those come from Arabidopsis thaliana (COR47 (#5), LTI29/LTI45 (#6), LTI30/XERO2 (#35), RAB18 (#53); [82]). The others were from soybean (Glycine max; [83]), maize (Zea mays; [84]), cowpea (Vigna unguiculata; [85], and a resurrection plant (Craterostigma plantagineum; [86]). All showed random coil structure in solution.
Secondary structure content of LEA_4 group proteins was determined by Fourier-transform infrared spectroscopy (FTIR) for the D-7 protein from Typha latifolia [55], the GmPM16 protein from soybean [56], the LEAM protein from pea [87], and the Aav-LEA1 protein from the nematode Aphelenchus avenae [88]. FTIR enables measurements with proteins in solution and in the dry state. Since the proteins are present in desiccation tolerant tissues (T. latifolia pollen, soybean and pea seeds, and dry, viable nematodes) their response to desiccation is of particular interest. All three proteins have a random coil structure in solution, but adopt a largely α-helical structure during drying. Surprisingly, it was recently shown by circular dichroism (CD) spectroscopy that of two highly similar LEA_4 proteins from a rotifer, one (ArLEA1A) showed random coil structure in the hydrated state and high α-helix content after drying, while the other (ArLEA1B) was largely α-helical (84–87%) in both the hydrated and dry state [16]. We conclude from these data that LEA_4 group proteins have properties that allow them to adopt an α-helical structure and that this structure may be related to their cellular function in desiccation tolerance. Interestingly, these structural properties and cellular functions seem to be conserved between plants and animals.
The only protein from the SMP group to have its secondary structure determined is MtPM25 from M. truncatula [80]. It showed increased content of α-helices and β-sheets during drying. The only LEA protein demonstrated to have a defined secondary and tertiary structure in solution is the LEA_2 group protein LEA14 (#1) from Arabidopsis [89]. It contains one α-helix and seven antiparallel β-strands, as shown by x-ray diffraction on the crystallized protein. Currently, there is no structural information available for the other groups of LEA proteins.
The structural data indicate that most LEA proteins are "natively unfolded" or "intrinsically unstructured" in solution. Such proteins have been recognized in all investigated organisms, both by computational prediction and by experimental determination of secondary structure (see [90] for a recent review). In general, a combination of low hydrophobicity and large net charge are characteristic features of these proteins [91]. It has been estimated that as many as 30% of all proteins are either completely or partially disordered [92].
This indicates that unstructured proteins play important roles in cells, despite their apparent lack of a defined three-dimensional structure. Most of these proteins, however, are not completely devoid of structure, but contain residual, flexible structural elements [93], such as polyproline II (PII) helices [94]. It has been reported that such structural flexibility enhances the ability of proteins to bind to interaction partners, such as DNA, RNA, or other proteins [93,95,96]. Binding is often accompanied by a folding transition. It has been argued that such a "fly-casting" mechanism [97] has a much higher efficiency in the search for binding partners than the simple diffusion of a compact, folded protein. Potential binding partners of LEA proteins, however, remain to be identified, but could include other proteins, nucleic acids, or membranes that might be stabilized under stress conditions through such interactions.
In general, the available data on the secondary structure of LEA proteins do not allow conclusions on the structural characteristics of the different groups, because too few members have been investigated, and they were not all investigated under the same set of conditions. Therefore, more systematic structural and functional characterization will be necessary to define structure-function relationships in LEA proteins.
As a first step towards this goal, we have used a simple computational prediction of the propensity of Arabidopsis LEA proteins to be natively unfolded. Figure 5 shows a plot of the mean net charge as a function of mean hydrophobicity of all investigated Arabidopsis proteins. The line marks the empirical border of natively unstructured and folded proteins [91]. This plot indicates that most of the LEA proteins are unstructured, whereas those proteins we annotated as not being LEAs (Additional file 1) together with seed storage proteins from Arabidopsis are mostly predicted to be folded. It is striking that all members of the LEA_2 group are predicted by this analysis to be folded. This is in agreement with the crystal structure determined from LEA14 [89], indicating that this is a general feature of LEA_2 group proteins. Also, the SMP group proteins are exclusively predicted to be folded, as are the AtM LEA proteins and a few members of the LEA_4 group. However, the LEA_4 group and AtM proteins contain putative targeting sequences which are known to be hydrophobic. When the targeting sequences were removed, all proteins shifted to a position indicating a lack of structure (Fig. 5, inset). This raises the question whether the folded proteins should really be called LEA proteins sensu strictu, or whether an unfolded structure in solution is a defining property of LEA proteins. A final answer to this question will have to await information about the functional significance of this property.
Figure 5. Plot of mean net charge versus mean hydrophobicity of LEA and selected other proteins. "No LEA" refers to proteins originally annotated as LEA proteins but re-annotated in our study (Additional file 1). Arabidopsis seed storage proteins were included in the analysis, because they are a group of seed proteins that have clearly no sequence similarities to LEA proteins. The line marks the border between natively unstructured (left) and folded (right) proteins [91]. The inset documents the shift of five proteins when the putative targeting sequence is removed.
Computational prediction of the subcellular distribution of the LEA proteins using targetP indicates further differences between the LEA groups. Whereas the members of most groups are localized in the cytosol ("other" in Table 1 indicates that no signal peptide was detected), LEA_4 proteins are predicted to be present in all cellular compartments, the LEA_3 proteins are exclusively targeted to chloroplasts and mitochondria and the two AtM proteins are predicted to enter the secretory pathway. In the SMP group, one member (#49) is probably targeted to chloroplasts.
Experimental evidence for the subcellular localization of approximately 15 different LEA proteins has been published so far. Of the Arabidopsis LEA proteins, the cold induced LEA_4 group protein COR15A (#24) is localized in the chloroplast stroma [98], as is most likely the highly homologous COR15B (#23). In addition, the SMP group protein RAB28 (#31) is localized in the nucleus and it is likely that AtEPC31 (#32) has the same localization, because it contains the same targeting sequence [99]. No other data for Arabidopsis LEA proteins are available. The general conclusion from both prediction and published experimental evidence is that LEA proteins can be present in all subcellular compartments. Whether they have different functions in different compartments and what these functions are remains to be determined.
Genomic organization of the Arabidopsis genes encoding LEA proteins
A plot of the LEA genes on the Arabidopsis genome shows that LEA loci can be found on every chromosome (Fig. 6). However, the density of these loci is very high on the lower arm of chromosome 2, which contains 29% of all LEA genes. The lower arm of chromosome 3 also contains a region with a number of LEA loci as well as the upper arm of chromosome 1. Seventeen LEA genes (33%) are found in tandem repeats resulting from local duplications of small parts of a chromosome (Table 6). These include the previously reported cases of COR47 (#4) and ERD10 (#5) [67], COR15B (#23) and COR15A (#24) [66], AtM17 (#21) and AtM10 (#22) [57], RAB28 (#31) and AtEPC31 (#32) [100], and XERO2 (#33) and XERO1 (#34) [101], in addition to the uncharacterized gene pairs #11 and #12, #15 and #16, as well as #49 and #50. Gene #7 is part of a tandem repeat with a gene that has no corresponding LEA domain.
Figure 6. Localization of the 51 identified LEA genes on the Arabidopsis chromosomes. Genes related by endo-reduplication events during genome evolution (homeologous genes) are connected by lines and highlighted. Genes present as tandem repeats in the genome are boxed in.
Table 6. Tandem repeats of LEA genes in the Arabidopsis genome
It is widely accepted that the Arabidopsis genome is the result of ancient genome duplication events and a following loss of genes from the tetraploid genome that resulted in the current diploid genome (see [102,103] for recent reviews). Ten pairs of such homeologous LEA genes could be identified on different chromosomes using the Arabidopsis Syntenic Pairs/Annotation Viewer [104]. In addition, two pairs were identified that contain one LEA gene and one gene that was not classified as a LEA gene (Fig. 6, Table 7). This means that 22 of the 51 LEA genes (43%) are parts of homeologous pairs. It has been estimated that approximately 26% of all genes in the Arabidopsis genome belong to such pairs [105,106], indicating that the number of duplicated LEA genes retained in the genome is above average.
Table 7. Duplications of LEA genes in the Arabidopsis genome
After a polyploidy event, redundant duplicated genes will be lost from the genome due to random mutation and loss of function. The same can be assumed for genes duplicated in tandem repeats. It has been suggested that duplicated genes are mainly saved from removal through functional diversification, because of positive gene dosage effects, or because they are indispensible parts of a protein network, e.g. as subunits in an enzyme or signalling complex [102,106-110]. The latter factor can be largely excluded for LEA proteins, as no indication of any enzymatic function has ever been reported and they lack any domains that might link them to enzymatic or signalling complexes.
In most of the homeologous pairs and tandem repeats evidence for functional diversification could be found from either gene expression patterns, sequence divergence, or the predicted subcellular localization (compare Table 1). For the tandem repeats, COR15B (#23), for instance, was upregulated under cold and salinity stress, while COR15A (#24) was also induced by drought, as reported before [66]. Gene #15 and XERO1 (#34) transcripts were only detected in seeds, while transcripts from their respective partner genes #16 and XERO2 (#33) could be detected in seeds and in vegetative tissues before and after stress induction. The tandem gene of gene #7 contains no recognizable LEA_4 domain, indicating sequence divergence. In one case, the protein encoded by one gene in a tandem pair (#49) was predicted to be targeted to the chloroplasts, while the other (#50) showed no targeting signal. This prediction, however, obviously needs to be experimentally tested before any definite conclusions can be drawn.
In the homeologous pairs, the three that contain one LEA gene and one gene that does not belong to any LEA gene family (Table 7) are obvious examples of changes in the protein sequence after duplication. In the dehydrin group, eight out of ten genes are linked by duplication, either as tandem repeats or homeologous pairs. These eight genes fall into three sequence groups, containing COR47/ERD10/ERD14, XERO1/XERO2/RAB18, and #16/#47 (Fig. 3). A similar grouping has also been obtained from an unrooted phylogenetic tree ([53]; compare also Fig. 1), however, without any reference to the underlying gene duplication events. The three proteins in the first group show an almost identical segmental structure, with little indication of functional diversification. The three genes in the second group and the two in the third show a high degree of variability in their segmental content (Fig. 3), indicating possible functional divergence. Unfortunately, there is no information available about the functional consequences of these changes in amino acid sequence, but the present analysis clearly identifies interesting targets for future study.
A difference in the predicted subcellular localization of members of homeologous pairs (Table 7) was found in three cases (#42 and #48; #13 and #43; ERD10 (#5) and #10). However, none of these have been experimentally verified. To further test for diversification in expression patterns on a broader basis [105,107,109,110], we have used the "gene correlator" function on the Genevestigator [111] website, which compares expression patterns from publicly available expression profiling data (Table 6 and 7). This analysis shows that for both tandem repeats and homeologous pairs the correlation coefficient varies between r2 = 0.014 and 0.945. Diversification of the expression pattern is especially striking in the pairs #2 and # 38 (SAG21), #28 and At5g15960 (KIN1; no LEA), and #1 (LEA14) and #27, with r2 = 0.014, 0.043, and 0.018, respectively. Interestingly, while #28 and KIN1 show a very low level of correlation in expression, the other pair between a LEA and a non-LEA gene (#9 and At1g22600) shows a high correlation (r2 = 0.908). Also the tandem repeat between a LEA and a non-LEA gene (#7 and At1g52680) shows a high diversification in expression (r2 = 0). This suggests that changes in the coding sequence, as indicated by the LEA/non-LEA classification, and in the promoter sequence that determines the expression pattern may be independent of each other.
In summary, we have identified 12 homeologous pairs and nine tandem repeats among the 51 LEA genes in Arabidopsis. Ten of the 12 homeologous pairs and six of the nine tandem repeats showed clear evidence for functional diversification at the levels of coding sequence, subcellular localization, or expression pattern. For those genes that did not show diversification in our analysis, a final conclusion has to await the identification of the physiological and biochemical function of the proteins, as only this would enable us to judge whether small differences in the coding sequence may have effects on the functional properties of the proteins. This has recently been demonstrated for two highly similar LEA proteins from the rotifer Adineta ricciae, where one protein protects enzymes during drying, while the other shows membrane association in the dry state [16]. In addition, it remains possible that duplication of such genes leads to a larger or more rapid accumulation of functionally redundant proteins and that this may be a selective advantage for the organism under some environmental stress conditions.
Conclusion
LEA proteins have been found in phylogenetically distant organisms and have always been related to abiotic stress tolerance, especially desiccation tolerance. However, no unifying concept for their physiological role(s) and modes of action has been attained so far. This is in part due to the fact that research has been fragmented between different species, different groups of LEA proteins and different experimental approaches. In this paper, we have presented a genome-wide survey of LEA proteins and genes in Arabidopsis. The experimental and in silico analyses indicate a wide range of sequence diversity, intracellular localizations, and expression patterns. The high fraction of retained duplicate genes and the inferred functional diversification indicate that they confer an evolutionary advantage for an organism under varying stressful environmental conditions. The future elucidation of the physiological roles of these proteins and the relationship of their structures, and especially their large structural flexibility, with their modes of action should greatly benefit from the presented comprehensive analysis.
Methods
Plant material and growth conditions
Arabidopsis thaliana (accession Col-0) was grown in soil in a greenhouse at 16 h day length with light supplementation to reach 200 μE m-2 s-1 and a temperature of 20°C during the day and 18°C during the night, as described before [112]. Six-week-old plants were sampled for adult rosette leaves and roots. Seedling samples were taken 14 days after sowing. Bud, flower and stem samples were taken from plants with a fully grown inflorescence (nine weeks after sowing), and green siliques were harvested as they appeared. Plants for seed production (accessions Col-0, Col-2, Ler, C24, Nd, Rsch) were grown as described above. The mature seeds were harvested and stored for one year (12°C, 30% RH). For stress treatments, five to six-week-old plants were subjected to mild drought (no watering under the growth conditions described above, harvest one day after the first signs of wilting (relative water content of treated plants approximately 97% of control plants), high light (~400 μE m-2 s-1 for seven days) and cold (4°C for 14 days at 90 μE m-2 s-1). Leaves infected with powdery mildew (Erysiphe cichoracearum) were harvested six weeks after sowing [113]. Salt stress was applied in hydroponic culture on modified Hoagland medium (1.5 mM CaNO3, 1.26 mM KNO3, 0.75 mM MgSO4, 0.5 mM KH2PO4, 100 μM H3BO3, 100 μM Na2SiO3, 70 μM Fe-EDTA, 50 μM KCl, 10 μM MnSO4, 2 μM ZnSO4, 1.5 μM CuSO4, 75 nM Na2MoO4; K. Köhl, unpublished). The medium was changed every week and after six weeks, 100 mM NaCl was added to the medium. Leaves were harvested after an additional seven days. Control samples were taken from plants grown under the same conditions, but without additional NaCl. Heat shock was applied to detached leaves for 2 h at 37°C as described previously [114].
Axenic cultures were grown in full-nutrition medium [115] for 7 d after imbibing sterilized seeds for 3 d at 4°C. Abscisic acid (ABA) or giberellic acid (GA3) were added to a final concentration of 10 mM. Cultures were harvested after 6 h of induction.
Quantitative RT-PCR (qRT-PCR)
For the isolation of total RNA, tissue samples from 15 plants or axenic cultures from five different flasks were pooled and homogenized under liquid nitrogen. Total RNA was isolated either by the "hot borate" method [116] or using TRIZOL reagent (Invitrogen). Approximately 30 μg total RNA were treated with RNase-free DNase (Roche). The absence of genomic DNA in the samples was verified by qPCR using intron-specific primers (Additional file 6), the RNA concentration and quality were assessed by photometric measurement (Biophotometer, Eppendorf) and gel electrophoresis (2001 Bioanalyzer, RNA 6000 Nano Chip Kit, Agilent Technologies). Approximately 3 μg total RNA was utilized to synthesize single-stranded cDNA using reverse transcriptase (SuperscriptIII, Invitrogen) and oligo-dT18 primers, according to the manufacturer's instructions. The cDNA was diluted 20- to 40-fold.
Additional file 6. Sequences of all primers used in the quantitative RT-PCR experiments. List of all primers used in the present study and their nucleotide sequences.
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QRT-PCR primers were designed using the PrimerExpress 2.0 software (Applied Biosystems), with an amplicon length range from 61 to 161 bp, yielding primers of 19 to 24 bp with a melting temperature of 58–62°C (see Additional file 6 for all primer sequences). PCR reactions were performed in optical 384-well plates using the ABI PRISM 7900 HT Sequence Detection System (Applied Biosystems, USA). The SYBR Green fluorescent dye was used to detect the synthesized dsDNA. A total reaction volume of 10 μl contained 5 μl 2× SYBR Green Master Mix Reagent (Applied Biosystems), 1 μl of diluted cDNA and 200 nM of each gene-specific primer. PCR conditions were those described in detail recently [117] and data were expressed as the cycle number necessary to reach a threshold fluorescence value (CT). The reported values are the means of two technical replica from one biological experiment.
Data were normalized to the mean CT of three reference genes (At4g27960, At5g46630, and At4g34270) that were found to be stably expressed across various tissues and conditions [118]. The mean PCR efficiency (E) for every primer pair was calculated using the linregPCR software [119]. The average CT values of two technical replica for each LEA gene and each reference gene was calculated and set to the power of the respective PCR efficiency (ΔCT). If the difference in the CT values between the two technical replica was above 1.5, the values were removed from the dataset. In addition, samples that had multiple peaks in the dissociation graph were dismissed because this indicates that the PCR reaction was unspecific. Relative gene expression values (compiled in Additional file 3) were calculated from these data as:
In silico analysis of LEA genes
LEA genes in A. thaliana were identified by keyword search in Genbank, accessed through NCBI [120]. In addition, tblastn [121] searches were performed on the translated Arabidopsis genome with the protein sequences of the well-characterized LEA genes from Gossypium hirsutum.
The Pfam database of protein families and HMMs [122] was applied to characterize the proteins on the basis of their sequence homology to the stored Pfam domains [123]. In the Prosite [124,125] database, two patterns defining dehydrins are present. For most of the other groups, we were able to create patterns with the PRATT [126,127] tool. The PATTINPROT [128,129] tool was used to verify the stringency of the retrieved patterns by querying the UniProt [130,131] database. To get more information about the nature of the gene products, the GRAVY (grand average of hydropathy), the molecular weight and the pI were predicted by the PROTPARAM [132,133] tool. The signal peptide analysis was done by the TargetP [134,135] algorithm. The gene loci were plotted on the Arabidopsis chromosomes with the Chromosome Map Tool on the TAIR webpage [136]. Duplications were retrieved by the Arabidopsis Syntenic Pairs/Annotation Viewer [104]. The tandem repeats and homeologous pairs were aligned with the BLAST 2 SEQUENCES [137] tool on the NCBI webpage [120]. Multiple sequence alignments were performed using the ClustalW [138,139] algorithm and the unrooted dendrogram was drawn based on ClustaW alignments [140].
ABRE and LTRE cis-acting elements in the -2000 nt promoter region of the LEA genes were found by the plantPAG tool [141] querying the PLACE [77,142] database.
Authors' contributions
MH carried out the experimental work and the in silico analyses, participated in the design of the study and in the data analysis and helped to draft the manuscript. DKH designed the study, participated in the data analysis and drafted the manuscript. Both authors read and approved the final manuscript.
Acknowledgements
We thank Dr. Matthew A. Hannah for helpful discussions, Dr. Renate Schmidt for advice on Arabidopsis genome structure and Felix Lippold for his help with axenic cultures. M. H. gratefully acknowledges financial support through a PhD fellowship from the University of Potsdam.
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130. Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donnovan C, Redaschi N, Yeh L-SL: The universal protein resource (UniProt).
Nucleic Acids Res 2005, 33:D154-D159. PubMed Abstract | Publisher Full Text | PubMed Central Full Text
131. UniProt [http://www.expasy.uniprot.org/] webcite
132. Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A: Protein identification and analysis tools on the ExPASy server. In The Proteomics Protocols Handbook. Edited by Walker JM. Totowa, N.J.: Humana Press; 2005.
133. PROTPARAM [http://www.expasy.org/tools/protparam.html] webcite
134. Emanuelsson O, Nielsen H, Brunak S, von Heijne G: Predicting subcellular localization of proteins based on their N-terminal amino acid sequence.
J Mol Biol 2000, 300:1005-1016. PubMed Abstract | Publisher Full Text
135. TargetP [http://www.cbs.dtu.dk/services/TargetP/] webcite
136. TAIR [http://www.arabidopsis.org] webcite
137. Tatsunova TA, Madden TL: Blast 2 sequences – a new tool for comparing protein and nucleotide sequences.
FEMS Microbiol Lett 1999, 174:247-250. PubMed Abstract | Publisher Full Text
138. Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
Nucleic Acids Res 1994, 22:4673-4680. PubMed Abstract | Publisher Full Text | PubMed Central Full Text
139. ClustalW [http://www.ebi.ac.uk/clustaw/] webcite
140. Unrooted dendrogram [http://align.genome.jp/] webcite
141. plantPAG [http://plantpag.mpimp-golm.mpg.de] webcite
142. PLACE [http://www.dna.affrc.go.jp/PLACE/] webcite
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Rate This News
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America's Climate Choices
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NEWS: America's Climate Choices
This news article has been reviewed by the following Topic Editor: Sidney Draggan Ph.D.
America's Climate Choices
A report released May 12, 2011, from the National Research Council reiterates the pressing need for substantial action to limit the magnitude of climate change and to prepare to adapt to its impacts.
America's Climate Choices, which builds on the four previous America's Climate Choices panel reports, reaffirms that the preponderance of scientific evidence points to human activities as the most likely cause for most of the global warming that has occurred during the last several decades. Furthermore, the risk of dangerous climate change impacts is growing with every ton of greenhouse gases emitted into the atmosphere.
America's Climate Choices
makes the case for implementing strong federal policies that establish coherent national goals and incentives, and that promote strong U.S. engagement in international-level response efforts.
This title is part of the America's Climate Choices project, the National Research Council's most comprehensive study of climate change to date.
Follow the links below for related titles from the America's Climate Change study.
Citation
National Research Council (Content Source);Sidney Draggan Ph.D. (Topic Editor) "America's Climate Choices". In: Encyclopedia of Earth. Eds. Cutler J. Cleveland (Washington, D.C.: Environmental Information Coalition, National Council for Science and the Environment). [First published in the Encyclopedia of Earth May 12, 2011; Last revised Date March 15, 2012; Retrieved May 18, 2013 <http://www.eoearth.org/news/view/166149/?topic=54310>
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Mercer County, IllinoisEdit This Page
From FamilySearch Wiki
Revision as of 16:56, 4 August 2011 by Dianekay (Talk | contribs)
Mercer County, Illinois
Map
Location of Illinois in the U.S.
Facts
Founded: January 13, 1825
County Seat Aledo
Courthouse
Address P.O. Box 66
Aledo, IL 61231
309-582-7021
Website: www.mercercountyil.org
Named for: Hugh Mercer
United States Illinois Mercer County
Contents
Mercer County Organization
Beginning Dates for Mercer County Records
Birth Marriage Death Census Land Probate
1877
1835
1877
1830
1834
1837
County records are most often kept at the County Courthouse or another local repository. For further information about where the records for Mercer County are kept, see the Mercer County Courthouse page.
Historical Facts
Parent County
• 1825--Mercer County was created 13 January 1825 from unorganized territory and Pike County. County seat: Aledo [1]
Boundary Changes
Record Loss
Places / Localities
Populated Places
Neighboring Counties
Records and Resources
Biography
Cemeteries
Illinois cemetery records often identify birth, death, relationship, and military information, as well as religious affiliation.
• Find A Grave can be searched by the name of a person or family to find where a person is buried. Usually gives birth and death dates often with a picture of the tombstone. May give obituaries, names of family members and links to their information in Find A Grave.
Census
Historical populations
Census Pop.
190020,945
191019,723−5.8%
192018,800−4.7%
193016,641−11.5%
194017,7016.4%
195017,374−1.8%
196017,149−1.3%
197017,2940.8%
198019,28611.5%
199017,290−10.3%
200016,957−1.9%
201016,434−3.1%
IL Counties 1900-1990
1840 Pensioners
• A Census of Pensioners for Revolutionary or Military Services: With their Names, Ages, and Places of Residence, as Returned by the Marshalls of the Several Judicial Districts, Under the Act for Taking the Sixth Census. Washington, D.C., 1841. FHL 973 X2pc 1840; FHL 2321; digital version at Google Books. [See Illinois, Mercer County on page 187.]
Church Records
Court Records
Ethnic Research
African American
The following have information concerning African American research.
Genealogy
History
Local Histories
• History of Mercer and Henderson Counties Together with Biographical Matter, Statistics, Etc. Chicago, Illinois: H.H. Hill and Company, 1882. FHL fiche 6071026; digital versions at Ancestry ($), and Internet Archive (free)
• Historical Encyclopedia of Illinois and History of Mercer County. Chicago: Munsell Pub. Co., 1903. Digital version at Ancestry ($).
Land and Property
Maps
Military
• Civil War
Civil War service men from Mercer County served in various regiments. Men often joined a company (within a regiment) that originated in their county. Listed below are companies or regiments that were formed from men of Mercer County.
- 30th Regiment, Illinois Infantry, Companies A and G.
- 37th Regiment, Illinois Infantry, Company A.
- 45th Regiment, Illinois Infantry, Company I.
- 65th Regiment, Illinois Infantry (Scotch Regiment), Company B.
- 83rd Regiment, Illinois Infantry, Company D.
- 84th Regiment, Illinois Infantry, Company H.
Naturalization
Newspapers and Obituaries
Poorhouse
Mercer County Almshouse Registers Index, 1859-1948, courtesy: Illinois State Archives
Probate Records
Repositories
County Courthouse
County records are most often kept at the County Courthouse or another local repository. For further information about where the records for Mercer County are kept, see the Mercer County Courthouse page.
Family History Library
Illinois Regional Archives Depository (IRAD)
Public Libraries
Social Groups Online
Societies
The Essley-Noble Museum located at 1406 SE 2nd Ave. in Aledo Illinois is a friendly and well staffed genealogy resource for those researching Mercer County.
They specialize in having an INDEXED cross-referenced obituary collection going back to the early publication dates for the local papers. They also have microfilms available for these papers. They just completed (2010) a project for all the cemeteries in the county which contains GPS locations, which is particularly useful when trying to locate the small and hidden cemeteries in the townships.
Their current project is collecting civil war veteran photos, biographies, histories from Illinois, specifically in Mercer County.
Although the genealogy section is in a corner of the Museum it is well worth the visit. The majority of the building is devoted to collections of period attire, house wares and other antiques.
Visit their web site at mcmuseum@frontier.com for current hours (the volunteers currently staff the facility three days a week) and other details. The mailing address is PO Box 269 Aledo, IL 81231,
Taxation
Vital Records
Web Sites
References
1. The Handybook for Genealogists: United States of America, 10th ed. (Draper, UT: Everton Publishers, 2002), 196. (FHL Collection Ref Book 973 D27e 2002). WorldCat entry.
Need additional research help? Contact our research help specialists.
Need wiki, indexing, or website help? Contact our product teams.
Did you find this article helpful?
You're invited to explain your rating on the discussion page (you must be signed in).
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Pages that link to "Template talk:Helpbox"
From FamilySearch Wiki
What links here
Filters Hide transclusions | Hide links | Hide redirects
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In the FamilySearch Research Wiki, you can learn how to do genealogical research or share your knowledge with others.
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Error
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2 revisions of this difference (13629 and 13643) were not found.
This is usually caused by following an outdated diff link to a page that has been deleted. Details can be found in the deletion log.
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Recovering Overwritten Data
From Forensics Wiki
Jump to: navigation, search
Can data be recovered from a hard drive after that data has been written by 35 passes of random information? How about a single pass of zeros?
Whether or not such data can be recovered has been a question of debate for decades. Unfortunately, there have been few hard facts published.
Contents
Prior Work
The Gutmann Paper 1996
The most widely known paper in this area is Peter Gutmann's 1996 classic, Secure Deletion of Data from Magnetic and Solid-State Memory, Proceedings of the Sixth Usenix Security Symposium [1]. An extended version of the paper appears on Peter Gutmann's website [2].
In this paper, Gutmann discusses techniques using an electron microscope that might work for recovering overwritten data. He then proposes a series of erasure patterns that can be used to overwrite data from hard drives that use different kinds of encoding schemes. A total of 35 patterns are proposed, although, as Gutmann notes, there is no reason to ever use all 35 patterns (because the patterns are designed for use on different kinds of magnetic recording technology).
It's important to realize that this paper, written in 1996, discusses a magnetic recording technology that is no longer widely available. In 1998 Gutmann added the Epilogue to Gutmann's 1996 paper. The gist of that epilogue is that two passes of random data should be enough for today's disk drives.
ActionFront's Drive Independent Data Recovery 2005
In August 2005 ActionFront Data Recovery Labs presented a detailed paper at the IEEE 16th Annual Magnetic Recording Conference in which they discussed the current state-of-the-art of recovering information from hard drives without using the drive's own read/write heads [3].
One of the key points that the paper makes is that there is a high degree of variability between individual modern hard drives. Manufacturers exploit this variability to increase drive densities. Unfortunately, this variability makes it dramatically harder to perform drive independent data recovery — that is, a single recovery approach that will work on multiple drives.
Current Work
Paper: Overwriting Hard Drive Data: The Great Wiping Controversy
In December 2008 Craig Wright, Dave Kleiman, and Shyaam Sundhar R.S. presented a paper at ICISS2008, which purpose was "a categorical settlement to the controversy surrounding the misconceptions involving the belief that data can be recovered following a wipe procedure" [4].
See also
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Infraction for seoblogcentral01: Links in posts
Go4Expert Founder
11May2009,12:58 #1
Post: Improving Your Search Engine Ranking
User: seoblogcentral01
Infraction: Links in posts
Points: 2
Administrative Note:
Quote:
Confine links to signatures only
Message to User:
Quote:
Avoid Links in posts and use signatures for links to your site.
Thanks
Admin
Original Post:
Quote:
Friends!,..
If you want to improve your Search Engine Ranking you must use vbulletin .We should not need to hack vBulletin to search engine optimise it, we should only have to work on the onpage words, but yes, php mods and template changes are needed for search engine optimizations of vBulletin forums.
Thanks
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About this Journal Submit a Manuscript Table of Contents
Abstract and Applied Analysis
Volume 2012 (2012), Article ID 941063, 11 pages
doi:10.1155/2012/941063
Research Article
Exponential Convergence for Cellular Neural Networks with Time-Varying Delays in the Leakage Terms
1School of Science, Hunan University of Technology, Hunan, Zhuzhou 412000, China
2College of Mathematics, Physics and Information Engineering, Jiaxing University, Zhejiang, Jiaxing 314001, China
Received 18 August 2012; Accepted 3 October 2012
Academic Editor: Narcisa C. Apreutesei
Copyright © 2012 Zhibin Chen and Junxia Meng. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract
We consider a class of cellular neural networks with time-varying delays in the leakage terms. By applying Lyapunov functional method and differential inequality techniques, we establish new results to ensure that all solutions of the networks converge exponentially to zero point.
1. Introduction
It is well known that the delayed cellular neural networks (CNNs) have been successfully applied to signal and image processing, pattern recognition, and optimization (see [1]). Hence, they have been the object of intensive analysis by numerous authors in the past decades. In particular, extensive results on the problem of the existence and stability of the equilibrium point for CNNs are given out in many works in the literature. We refer the reader to [26] and the references cited therein. Recently, to consider CNNs with the incorporation of time delays in the leakage terms, Gopalsamy [7] and Wang et al. [8] investigated a class of CNNS described by in which corresponds to the number of units in a neural network, corresponds to the state vector of the th unit at the time , and represents the rate with which the th unit will reset its potential to the resting state in isolation when disconnected from the network and external inputs at the time . and are the connection weights at the time , and denote the leakage delay and transmission delay, respectively, denotes the external bias on the th unit at the time , and are activation functions of signal transmission, and .
Suppose that the following conditions and are constants, where , for each , there exists a nonnegative constant such that are satisfied. Avoiding the continuously distributed delay terms, the authors of [7, 8] obtained that all solutions of system (1.1) converge to the equilibrium point or the periodic solution. However, to the best of our knowledge, few authors have considered the convergence behavior for all solutions of system (1.1) without the assumptions and . Thus, it is worthwhile to continue to investigate the convergence behavior of system (1.1) in this case.
The main purpose of this paper is to give the new criteria for the convergence behavior for all solutions of system (1.1). By applying Lyapunov functional method and differential inequality techniques, without assuming and , we derive some new sufficient conditions ensuring that all solutions of system (1.1) converge exponentially to zero point. Moreover, an example is also provided to illustrate the effectiveness of our results.
Throughout this paper, for , it will be assumed that and are continuous functions, and there exist constants and such that We also assume that the following conditions , , and hold: for each , there exist nonnegative constants and such that for all and , there exist constants and such that .
The initial conditions associated with system (1.1) are of the form where denotes real-valued-bounded continuous function defined on .
2. Main Results
Theorem 2.1. Let , , and hold. Then, for every solution of system (1.1) with any initial value , there exists a positive constant such that
Proof. Let be a solution of system (1.1) with any initial value ,and let In view of (1.1), we have Let From (1.3), , and , we can choose a positive constant such that Then, it is easy to see that We now claim thatIf this is not valid, then, one of the following two cases must occur:(1)there exist and such that (2)there exist and such that Now, we consider two cases.
Case i. If (2.8) holds. Then, from (2.3), (2.5), and ()−(), we have This contradiction implies that (2.8) does not hold.
Case ii. If (2.9) holds. Then, from (2.3), (2.5), and ()−(), we get which is a contradiction and yields that (2.9) does not hold.
Consequently, we can obtain that (2.7) is true. Thus, This implies that the proof of Theorem 2.1 is now completed.
3. An Example
Example 3.1. Consider the following CNNs with time-varying delays in the leakage terms: where .
Noting that Define a continuous function by setting Then, we obtain Therefore, which, together with the continuity of , implies that we can choose positive constants and such that for all , there holds This yields that system (3.1) satisfied , , and . Hence, from Theorem 2.1, all solutions of system (3.1) converge exponentially to the zero point .
Remark 3.2. Since , and CNNs (3.1) are a very simple form of CNNs with time-varying delays in the leakage terms, it is clear that the conditions and are not satisfied. Therefore, all the results in [79] and the references therein cannot be applicable to prove that all solutions of system (3.1) converge exponentially to the zero point.
Acknowledgments
The authors would like to express their sincere appreciation to the reviewers for their helpful comments in improving the presentation and quality of the paper; this work was supported by the National Natural Science Foundation of China (Grant no. 11201184), the Hunan Provincial National Natural Science Foundation of China (12JJ3007), the Natural Scientific Research Fund of Zhejiang Provincial of China (Grants nos. Y6110436, LY2A01018), and the Natural Scientific Research Fund of Zhejiang Provincial Education Department of China (Grant no. Z201122436).
References
1. L. O. Chua and T. Roska, “Cellular neural networks with nonlinear and delay-type template elements,” in Proceedings of IEEE International Workshop on Cellular Neural Networks and Their Applications, pp. 12–25, 1990.
2. H. J. Cho and J. H. Park, “Novel delay-dependent robust stability criterion of delayed cellular neural networks,” Chaos, Solitons and Fractals, vol. 32, no. 3, pp. 1194–1200, 2007. View at Publisher · View at Google Scholar · View at Zentralblatt MATH
3. C. Ou, “Almost periodic solutions for shunting inhibitory cellular neural networks,” Nonlinear Analysis. Real World Applications, vol. 10, no. 5, pp. 2652–2658, 2009. View at Publisher · View at Google Scholar · View at Zentralblatt MATH
4. B. Liu and L. Huang, “Global exponential stability of BAM neural networks with recent-history distributed delays and impulses,” Neurocomputing, vol. 69, no. 16-18, pp. 2090–2096, 2006. View at Publisher · View at Google Scholar · View at Scopus
5. B. Liu, “Exponential convergence for a class of delayed cellular neural networks with time-varying coefficients,” Physics Letters A, vol. 372, no. 4, pp. 424–428, 2008. View at Publisher · View at Google Scholar · View at Zentralblatt MATH · View at Scopus
6. H. Zhang, W. Wang, and B. Xiao, “Exponential convergence for high-order recurrent neural networks with a class of general activation functions,” Applied Mathematical Modelling, vol. 35, no. 1, pp. 123–129, 2011. View at Publisher · View at Google Scholar · View at Zentralblatt MATH
7. K. Gopalsamy, “Leakage delays in BAM,” Journal of Mathematical Analysis and Applications, vol. 325, no. 2, pp. 1117–1132, 2007. View at Publisher · View at Google Scholar · View at Zentralblatt MATH
8. H. Wang, C. Li, and H. Xu, “Existence and global exponential stability of periodic solution of cellular neural networks with impulses and leakage delay,” International Journal of Bifurcation and Chaos in Applied Sciences and Engineering, vol. 19, no. 3, pp. 831–842, 2009. View at Publisher · View at Google Scholar · View at Zentralblatt MATH
9. B. Liu, “Global exponential stability for BAM neural networks with time-varying delays in the leakage terms,” Nonlinear Analysis. Real World Applications, vol. 14, no. 1, pp. 559–566, 2013. View at Publisher · View at Google Scholar
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About this Journal Submit a Manuscript Table of Contents
Advances in Optical Technologies
Volume 2013 (2013), Article ID 794728, 6 pages
http://dx.doi.org/10.1155/2013/794728
Research Article
Nonlocal Mean Image Denoising Using Anisotropic Structure Tensor
1Department of Electronic Engineering, Chengdu University of Information Technology, 24 Xuefu Road, Chengdu, Sichuan 610225, China
2College of Computer Science, Sichuan University, 12 Yihuan Road, Chengdu, Sichuan 610065, China
Received 24 September 2012; Accepted 3 January 2013
Academic Editor: Augusto Belendez
Copyright © 2013 Xi Wu et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract
We present a novel nonlocal mean (NLM) algorithm using an anisotropic structure tensor to achieve higher accuracy of imaging denoising and better preservation of fine image details. Instead of using the intensity to identify the pixel, the proposed algorithm uses the structure tensor to characterize the boundary information around the pixel more comprehensively. Meanwhile, similarity of the structure tensor is computed in a Riemannian space for more rigorous comparison, and the similarity weight of the pixel (or patch) is determined by the intensity and structure tensor simultaneously. The proposed algorithm is compared with the original NLM algorithm and a modified NLM algorithm that is based on the principle component analysis. Quantitative and qualitative comparisons of the three NLM algorithms are presented as well.
1. Introduction
Image denoising is a key preprocessing step for higher level of processes such as image segmentation and pattern recognition. The most straightforward denoising approach is the direct application of spatial coherence which assumes noisy samples in a local area of a given pixel follow the same distribution of that pixel [1]. Although many efforts have been done dedicatedly to overcome it such as anisotropic filtering [2] and total variation minimization [3], this kind of algorithms comes with a common drawback of image blurring due to smoothing effect in both homogeneous regions and at object boundaries. Besides denoising methods in spatial domain, removing noise in transformation domain is also well developed, such as DCT transform [4] and wavelet [5].
In contrast to spatial coherence based image smoothing, nonlocal means (NLM) denoising algorithms have been recently proposed, which average pixel intensities weighted by the similarity of pixel gray level in a certain neighborhood [6]. This kind of pixel selection scheme makes NLM significantly outperform traditional denoising methods such as anisotropic filtering [2], total variation [3], and bilateral filtering [7], which has enabled it to be used in various applications such as computer vision and statistical nonparametric regression [8, 9]. Extension of the original approach including scale and rotation invariance for the data patches used to define the weights is well studied [1013].
However, as proposed in local denoising methods before [14], the pixel intensity itself cannot fully characterize the information contained in the image. Besides this, this kind of pointwise mean will cause large flat zones and spurious contours which are called “staircasing” effects. To overcome this, higher order information, which is derived from image gradients and can provide better description of image structure, is involved in NLM for more robust or sensitive measures of pixel similarity. For instance, Buades et al. [15, 16] employ a nonlocal polynomial model to attenuate the “staircasing” effect. Chatterjee and Milanfar [17] resort to a similar higher order NLM where the polynomial approximations up to a second order are used. Other traditional techniques such as singular value decomposition [18] and principle component analysis [1921] have also been used to characterize high-order information and project image neighborhood vectors to a lower dimensional subspace. One of these methods which are referred to as principal neighborhood dictionary (PND) NLM results in a significant computational saving together with increased estimation accuracy [21].
In this paper, a novel NLM denoising algorithm based on the concept of anisotropic structure tensor is proposed. Inferred from the anisotropic filter [22], the structure tensor encapsulates structure information of the pixel (or patch), which is used in conjunction with image intensity to compute similarity weights in this work. Moreover, current algorithms (such as PND) commonly treat a patch as a vector whose components correspond to the pixel intensities in it and define the similarity weight as a mean Euclidean distance between the individual components. In the proposed algorithm, we improve upon the simplistic weighting scheme by computing the similarity distance between structure tensors in a Riemannian space and comparing the structure information of the pixel as an ensemble. It is anticipated that this new method will effectively increase the accuracy of similarity comparisons and thus will significantly enhance the performance of image denoising.
The structure of the letter is as follows. Section 2 describes the proposed algorithm in detail. Section 3 provides denoising experiments using the proposed algorithm, the PND, and the original NLM. Section 4 concludes some key contributions of this work.
2. Method
The original NLM image denoising algorithm introduced by Buades et al. [6] smoothes images according to a weighted mean with the weights defined by the intensity similarity in a predetermined neighborhood. Specifically, for a position , a filtered intensity is computed as follows: where , are the positions of image pixels, is the noised image, and is a neighborhood of with a reasonable size. The parameter is a weighting factor computed as where is an Euclidean distance between vectors whose elements are the gray levels of neighboring pixels centered around and with a fixed size, controls the rate of decay of the exponential function, and is a normalizing factor as follows
According to the equations above, the estimated value of is a weighted average of pixels in the neighborhood , and the pixels with a more similar gray level will be assigned larger weights. However, as pointed out earlier, using gray level alone does not fully capture the structure information contained in a neighborhood of pixels.
To capture the structure information, the concept of structure tensor can be used. The structure tensor encapsulates the predominant direction of the intensity gradient in a given neighborhood and the degree to which those directions are spatially coherent [22]. The 2D structure tensor can be written as a matrix as follows where is a summation index ranging over a finite set (the “window,” typically for a constant ), is a fixed weight depending on , such that the sum of all weights is 1, and is a matrix-valued array as follows: where and are mean derivatives with respect to and coordinates.
As seen in (4) and (5), the structure tensor characterizes intensity variations of the pixels in a neighborhood, so comparisons between structure tensors at different pixel locations can provide more structure information which can be used to enhance the weighting scheme of NLM.
Similar to the Euclidean distance of intensities between pixels and , the similarity of structure tensor and can be defined using Euclidean distance of individual element of the tensor. However, since the structure tensor resides in a non-Euclidean space, this Euclidean type of operation is quite problematic due to the widely recognized swelling effect which tends to blend the orientation and diffusivity feature [23]. To circumvent this issue, affine-invariant Riemannian metrics have been proposed as more rigorous and general frameworks for tensor comparisons [2426]. In this paper, a Riemannian metric called Log-Euclidean metric is used for its nice theoretical properties along with simple and fast computations [26]. According to this framework, the similarity between structure tensors and is computed as follows:
As alluded to before, comparing pixels in terms of distances in both gray level and its derivatives simultaneously provides more accurate estimation of similarity in the local image structure. Therefore, we redefine the weighting factor in (2) to include both the gray level similarity and structure similarity below: where the weighting parameter regulates a trade-off between the image intensity and structure tensor. This weighting scheme reduces to the original NLM scheme when is assigned to 0. The corresponding normalizing factor is re-defined accordingly as
3. Results
In this section, we first present experimental findings on the effects of the weighting parameter on the performance of the proposed algorithm and then quantitatively and qualitatively compare the performance of the proposed algorithm with that of the PND algorithm [21] and the original NLM algorithm [6]. It should be pointed out that selections of other parameters including the smoothing kernel , the subspace dimensionality, and search-window size are not the primary concern of this work. Therefore these parameters are defined according to literature reports [6, 21]. As suggested in [6], the parameter is used according to the noise level (), and the subspace dimensionality and the search-window size are and , respectively, which have been discussed in [21] as a relatively optimal selection.
The weighting parameter in (7) controls relative contributions of gray level similarity and structure tensor similarity. To examine the effects of , experiments using four different images (House, Coins, Lena, and Cameraman) corrupted by additive Gaussian noise with standard deviation were conduct. Figure 1 shows variations of the peak signal-to-noise ratio (PSNR) with the value of this parameter. It can be seen that, in general, the PSNR in all four images increases as the parameter increases from 0 to 20, beyond which the PSNR oscillates irregularly and tends to decline as approaches 50. Based on the observations in Figure 1, the trend of these curves implicates different roles of the gray level similarity and structure tensor similarity. Briefly, when there is a large intensity difference between the pixels under comparison, the overall similarity is mainly given by the intensity difference. On the other hand, when the difference in the intensity between two pixels is small, the structure tensor similarity will have a dominant role. Given these and the observations from Figure 1, the parameter is set to 20 in all the following experiments.
Figure 1: Variations of PSNR (dB) as a function of the parameter for the four images.
To compare the performance of the proposed algorithm with that of the PND and the NLM, the same four test images corrupted by additive Gaussian noise but with different standard deviation (, 25, and 50) were used, each of which was denoised with the three denoising algorithms above. Comparisons were made with three criteria that included: visual assessment, PSNR, and mean structure similarity index map (MSSIM) [27], with each measuring a specific aspect of the denoising effect. Among them, visual assessment (Figure 2) qualitatively demonstrates how well the denoised images can be visually interpreted, the weighting distribution of pixel similarity is demonstrated in Figure 3, the PSNR (Table 1) quantitatively measures the extent to which noise has been suppressed, and the MSSIM (Table 2) gauges the clarity of detail and boundary definition after denoising.
Table 1: PSNR values for images denoised with the proposed algorithm, the PND, and the NLM. For each image, the three rows correspond to noise levels , 25, and 50. Boldfaced numbers denote the highest values.
Table 2: MSSIM values for images denoised with the proposed algorithm, the PND, and the NLM. For each image, the three rows correspond to noise levels , 25, and 50. Boldfaced numbers denote the highest values.
Figure 2: Visual assessment of the denoising effects using the proposed algorithm, the PND, and the NLM. Top to bottom rows: House, Coins, Lena, and Cameraman.
Figure 3: Comparison of weighting distribution between NLM and the proposed algorithm: (a) uncorrupted image; (b) weighting distribution of NLM in uncorrupted image; (c) weighting distribution of the proposed algorithm in uncorrupted image; (d) noised image (); (e) weighting distribution of NLM in noised image. (f) weighting distribution of proposed algorithm in noised image.
Figure 2 presents the denoised images using the proposed algorithm, the PND, and the NLM. Among different noise levels, only the images with the highest noise standard deviation () are demonstrated in order to emphasize the differences among the algorithms. It can be seen that even in this relatively high noise standard, the denoising effects of the three algorithms are quite reasonable, except for a little blurring in the output of the NLM (the last column). Careful observations of the denoised images by the proposed algorithm (the second column) and the PND algorithm (the third column) reveal that denoised images by the proposed algorithm appear clearer (e.g., the declaration of the hat in Lena) and boundaries are much better defined (e.g., the upper edge of the roof in House). This phenomenon is reasonable because the proposed algorithm incorporates full structure information into the weighting scheme, and the comparisons are made in a Riemannian space, which provides more accurate evaluation of the tensor.
Figure 3 compares the weighting distribution between NLM and the proposed algorithm. It can be seen that the weighting distributions of both algorithms are approximately same in uncorrupted image. In noised image (Figure 3(d)), NLM lost a great number of pixels with high similarity because of the gray intensity variation caused by noise (Figure 3(e)). On the other hand, the proposed algorithm uses both gray level and structure tensor to weight the similarity and keep most of the high similarity pixels (Figure 3(f)) thus will be a great benefit for the further denoising process.
To quantitatively evaluate the denoising effects, PSNR and MSSIM of the four images corrupted by zero mean Gaussian noise with different levels and then denoised by the three algorithms are calculated, with results shown in Tables 1 and 2, respectively. In general, the proposed algorithm and the PND outperform the original NLM, though the denoising effects of the three algorithms are almost identical when the noise level is low (). And compared with the PND, the PSNR is comparable for the two algorithms (each with 6 better measures than the other), but the MSSIM is superior for the proposed algorithm (with 8 better measures). Similar to the qualitative assessment, the performance gained by the proposed algorithm is attributable to the new similarity measure defined and tensor computation in the Riemannian space.
Computational efficiency of the proposed algorithm mainly depends on the size of image. Under the parameter setting in this letter and on a notebook computer with an Intel Core i7 CPU and 4 GB RAM, the proposed algorithm uses approximately 12 seconds to denoise a image compared with 9 seconds of NLM and 5 seconds of PND.
4. Conclusions
In this paper, a novel NLM denoising algorithm simultaneously using intensity and structure information was proposed. Following the concept of anisotropic filtering, structure information around an image pixel is characterized by structure tensor more comprehensively. Moreover, similarity of the structure tensor is compared in a Riemannian space with a Log-Euclidean metrics. This method evaluates the structure tensor as an ensemble, which is anticipated to yield better comparison. The weighting scheme of the proposed method represents a reasonable trade-off between pixel intensity and structure tensor: when the pixels under comparison have a large difference in the intensity, the weight is mainly determined by the gray level; when the pixels have similar gray level, the structure information characterized by the structure tensor will dominate the weight. In sum, the proposed method fully utilizes the intensity and its derivative information to weight the compared pixels (or patches). This improvement can increase the accuracy of pixel comparisons and weighting significantly, thus enhancing the performance of NLM denoising both qualitatively and quantitatively.
Acknowledgment
This study was supported by National Natural Science Foundation of China (NSFC) Grant 81201158 and 61271330.
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