bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inferring population history withDIY ABC: a user-friendly approach to approximate Bayesian computation
Authors: Cornuet Jean-Marie , Santos Filipe , Beaumont Mark A. , Robert Christian P. , Marin Jean-Michel , Balding David J. , Guillemaud Thomas , Estoup Arnaud 
Published: October 2008

AbstractSummary: Genetic data obtained on population samples convey information about their evolutionary history. Inference methods can extract part of this information but they require sophisticated statistical techniques that have been made available to the biologist community (through computer programs) only for simple and standard situations typically involving a small number of samples. We propose here a computer program (DIY ABC) for inference based on approximate Bayesian computation (ABC), in which scenarios can be customized by the user to fit many complex situations involving any number of populations and samples. Such scenarios involve any combination of population divergences, admixtures and population size changes. DIY ABC can be used to compare competing scenarios, estimate parameters for one or more scenarios and compute bias and precision measures for a given scenario and known values of parameters (the current version applies to unlinked microsatellite data). This article describes key methods used in the program and provides its main features. The analysis of one simulated and one real dataset, both with complex evolutionary scenarios, illustrates the main possibilities of DIY ABC.Availability: The software DIY ABC is freely available at http://www.montpellier.inra.fr/CBGP/diyabc.Contact: j.cornuet@imperial.ac.ukSupplementary information: Supplementary data are also available at http://www.montpellier.inra.fr/CBGP/diyabc
GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus
Authors: Zhu Yuelin , Davis Sean , Stephens Robert , Meltzer Paul S. , Chen Yidong 
Published: October 2008

Abstract
The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data in GEO can be challenging. We have developed GEOmetadb in an attempt to make querying the GEO metadata both easier and more powerful. All GEO metadata records as well as the relationships between them are parsed and stored in a local MySQL database. A powerful, flexible web search interface with several convenient utilities provides query capabilities not available via NCBI tools. In addition, a Bioconductor package, GEOmetadb that utilizes a SQLite export of the entire GEOmetadb database is also available, rendering the entire GEO database accessible with full power of SQL-based queries from within R.
Availability: The web interface and SQLite databases available at http://gbnci.abcc.ncifcrf.gov/geo/. The Bioconductor package is available via the Bioconductor project. The corresponding MATLAB implementation is also available at the same website.
Contact: yidong@mail.nih.gov
A flexible forward simulator for populations subject to selection and demography
Authors: Hernandez Ryan D. 
Published: October 2008

Abstract
Summary: This article introduces a new forward population genetic simulation program that can efficiently generate samples from populations with complex demographic histories under various models of natural selection. The program (SFS_CODE) is highly flexible, allowing the user to simulate realistic genomic regions with several loci evolving according to a variety of mutation models (from simple to context-dependent), and allows for insertions and deletions. Each locus can be annotated as either coding or non-coding, sex-linked or autosomal, selected or neutral, and have an arbitrary linkage structure (from completely linked to independent).
Availability: The source code (written in the C programming language) is available at http://sfscode.sourceforge.net, and a web server (http://cbsuapps.tc.cornell.edu/sfscode.aspx) allows the user to perform simulations using the high-performance computing cluster hosted by the Cornell University Computational Biology Service Unit.
Contact: rhernandez@uchicago.edu
Supplementary information: An extensive user's manual, perfor-mance statistics, and comparisons of patterns of genetic variation generated by SFS_CODE to theoretical expectations under various non-stationary demographic histories and models of natural selection are available on the project website: http://sfscode.sourceforge.net.
Inhibition of 2-Oxoglutarate Dehydrogenase in Potato Tuber Suggests the Enzyme Is Limiting for Respiration and Confirms Its Importance in Nitrogen Assimilation
Authors: Araújo Wagner L. , Nunes-Nesi Adriano , Trenkamp Sandra , Bunik Victoria I. , Fernie Alisdair R. 
Published: October 2008

AbstractThe 2-oxoglutarate dehydrogenase complex constitutes a mitochondrially localized tricarboxylic acid cycle multienzyme system responsible for the conversion of 2-oxoglutarate to succinyl-coenzyme A concomitant with NAD+ reduction. Although regulatory mechanisms of plant enzyme complexes have been characterized in vitro, little is known concerning their role in plant metabolism in situ. This issue has recently been addressed at the cellular level in nonplant systems via the use of specific phosphonate inhibitors of the enzyme. Here, we describe the application of these inhibitors for the functional analysis of the potato (Solanum tuberosum) tuber 2-oxoglutarate dehydrogenase complex. In vitro experiments revealed that succinyl phosphonate (SP) and a carboxy ethyl ester of SP are slow-binding inhibitors of the 2-oxoglutarate dehydrogenase complex, displaying greater inhibitory effects than a diethyl ester of SP, a phosphono ethyl ester of SP, or a triethyl ester of SP. Incubation of potato tuber slices with the inhibitors revealed that they were adequately taken up by the tissue and produced the anticipated effects on the in situ enzyme activity. In order to assess the metabolic consequences of the 2-oxoglutarate dehydrogenase complex inhibition, we evaluated the levels of a broad range of primary metabolites using an established gas chromatography-mass spectrometry method. We additionally analyzed the rate of respiration in both tuber discs and isolated mitochondria. Finally, we evaluated the metabolic fate of radiolabeled acetate, 2-oxoglutarate or glucose, and 13C-labeled pyruvate and glutamate following incubation of tuber discs in the presence or absence of either SP or the carboxy ethyl ester of SP. The data obtained are discussed in the context of the roles of the 2-oxoglutarate dehydrogenase complex in respiration and carbon-nitrogen interactions.
Differential Accumulation of Retroelements and Diversification of NB-LRR Disease Resistance Genes in Duplicated Regions following Polyploidy in the Ancestor of Soybean
Authors: Innes Roger W. , Ameline-Torregrosa Carine , Ashfield Tom , Cannon Ethalinda , Cannon Steven B. , Chacko Ben , Chen Nicolas W.G. , Couloux Arnaud , Dalwani Anita , Denny Roxanne , Deshpande Shweta , Egan Ashley N. , Glover Natasha , Hans Christian S. , Howell Stacy , Ilut Dan , Jackson Scott , Lai Hongshing , Mammadov Jafar , del Campo Sara Martin , Metcalf Michelle , Nguyen Ashley , O'Bleness Majesta , Pfeil Bernard E. , Podicheti Ram , Ratnaparkhe Milind B. , Samain Sylvie , Sanders Iryna , Ségurens Béatrice , Sévignac Mireille , Sherman-Broyles Sue , Thareau Vincent , Tucker Dominic M. , Walling Jason , Wawrzynski Adam , Yi Jing , Doyle Jeff J. , Geffroy Valérie , Roe Bruce A. , Maroof M.A. Saghai , Young Nevin D. 
Published: October 2008

AbstractThe genomes of most, if not all, flowering plants have undergone whole genome duplication events during their evolution. The impact of such polyploidy events is poorly understood, as is the fate of most duplicated genes. We sequenced an approximately 1 million-bp region in soybean (Glycine max) centered on the Rpg1-b disease resistance gene and compared this region with a region duplicated 10 to 14 million years ago. These two regions were also compared with homologous regions in several related legume species (a second soybean genotype, Glycine tomentella, Phaseolus vulgaris, and Medicago truncatula), which enabled us to determine how each of the duplicated regions (homoeologues) in soybean has changed following polyploidy. The biggest change was in retroelement content, with homoeologue 2 having expanded to 3-fold the size of homoeologue 1. Despite this accumulation of retroelements, over 77% of the duplicated low-copy genes have been retained in the same order and appear to be functional. This finding contrasts with recent analyses of the maize (Zea mays) genome, in which only about one-third of duplicated genes appear to have been retained over a similar time period. Fluorescent in situ hybridization revealed that the homoeologue 2 region is located very near a centromere. Thus, pericentromeric localization, per se, does not result in a high rate of gene inactivation, despite greatly accelerated retrotransposon accumulation. In contrast to low-copy genes, nucleotide-binding-leucine-rich repeat disease resistance gene clusters have undergone dramatic species/homoeologue-specific duplications and losses, with some evidence for partitioning of subfamilies between homoeologues.
Dental and anaesthetic management of children with dystrophic epidermolysis bullosa
Authors: LINDEMEYER ROCHELLE , WADENYA ROSE , MAXWELL LYNNE 
Published: October 2008

Background.  Epidermolysis bullosa (EB) is a genetic disease associated with fragility and bullous lesions of the skin and mucous membranes. There are various patterns of inheritance and histopathology. The disease is associated with systemic and oral manifestations, among which may be dental decay necessitating oral rehabilitation. General anaesthesia is frequently required for oral rehabilitation in children with dystrophic EB. Paediatric dentists should be aware of the implications of dystrophic EB for dental and anaesthetic management.Case report.  Two siblings with moderate to severe systemic and oral manifestations of dystrophic EB requiring extensive oral rehabilitation for rampant decay are described, including special anaesthetic techniques required for airway management and maintenance of skin integrity.Conclusion.  Dystrophic EB is a rare genetic disorder in which vesiculobullous lesions occur with erosions and scarring of cutaneous and extracutaneous surfaces in the oral cavity. Poor oral hygiene results from efforts to avoid mucosal trauma, resulting in decay. The comprehensive care of children with dystrophic EB impacts not only dental management but anaesthesia administration as well.
Psychometric validation of the Chinese version of the Illness Perception Questionnaire‐Revised for patients with hypertension
Authors: Chen Shiah‐Lian , Tsai Jen‐Chen , Lee Wen‐Lieng 
Published: October 2008

AbstractTitle.  Psychometric validation of the Chinese version of the Illness Perception Questionnaire‐Revised for patients with hypertension. Aim.  This paper is a report of a study to evaluate the psychometric properties of the Chinese version of the Illness Perception Questionnaire‐Revised using the technique of confirmatory factor analysis.Background.  The Illness Perception Questionnaire‐Revised is the most commonly used instrument for assessing patients’ views of illness, and there is good evidence for the psychometric properties of the English version. However, there is inconsistency in the literature about how scores of the Illness Perception Questionnaire‐Revised should be used.Method.  A cross‐sectional survey was conducted in three teaching hospitals in central Taiwan. The Chinese Illness Perception Questionnaire‐Revised was administered to a purposive sample of 358 patients with hypertension in 2005–2006.Results.  Confirmatory factor analysis provided evidence of satisfactory factorial validity, convergent validity and discriminant validity of the Chinese Illness Perception Questionnaire‐Revised. Internal consistency was supported by adequate Cronbach’s alphas (ranging 0·67–0·87) and composite reliability (0·57–0·88). The factor structures of the identity and cause subscales were found to be an acceptable fit to the data. The findings of model evaluations supported the seven‐factor structure, after removal of six poorly fitting items. Second‐order analysis indicated two factors (control and negative illness representation) representing latent constructs underlying the factors of personal control, treatment control, consequence, timeline‐cyclic and emotional representation.Conclusion.  The Chinese Illness Perception Questionnaire‐Revised is a reliable and valid instrument for the measurement of illness perceptions in patients with hypertension.
Collision fatality of raptors in wind farms does not depend on raptor abundance
Authors: De Lucas Manuela , Janss Guyonne F. E. , Whitfield D. P. , Ferrer Miguel 
Published: October 2008

Summary

The number of wind farms is increasing worldwide. Despite their purported environmental benefits, wind energy developments are not without potential adverse impacts on the environment, and the current pace and scale of development proposals, combined with a poor understanding of their impacts, is a cause for concern.
Avian mortality through collision with moving rotor blades is one of the main adverse impacts of wind farms, yet long‐term studies are rare. We analyse bird fatalities in relation to bird abundance, and test several factors which have been hypothesized to be associated with bird mortality.
Bird abundance was compared with collision fatality records to identify species‐specific death risk. Failure time analysis incorporated censored mortality data in which the time of event occurrence (collision) was not known. The analysis was used to test null hypotheses of homogeneity in avian mortality distribution according to several factors.
There was no clear relationship between species mortality and species abundance, although all large‐bird collision victims were raptors and griffon vulture Gyps fulvus was most frequently killed. Bird mortality and bird abundance varied markedly among seasons, but mortality was not highest in the season with highest bird abundance. Mortality rates of griffon vultures did not differ significantly between years.
Bird collision probability depended on species, turbine height (taller = more victims) and elevation above sea level (higher = more victims), implicating species‐specific and topographic factors in collision mortality. There was no evidence of an association between collision probability and turbine type or the position of a turbine in a row.
Synthesis and applications. Bird abundance and bird mortality through collision with wind turbines were not closely related; this result challenges a frequent assumption of wind‐farm assessment studies. Griffon vulture was the most frequently killed species, and species‐specific flight behaviour was implicated. Vultures collided more often when uplift wind conditions were poor, such as on gentle slopes, when thermals were weak, and when turbines were taller at higher elevations. New wind installations and/or repowering of older wind farms with griffon vulture populations nearby, should avoid turbines on the top of hills with gentle slopes.
Forecasting the potential distribution of the invasive tunicate Didemnum vexillum
Authors: Herborg Leif‐Matthias , O’Hara Patrick , Therriault Thomas W. 
Published: October 2008

Summary

Invasive species are a major threat to global biodiversity and their introduction can have significant economic consequences. The invasive tunicate Didemnum vexillum is a notorious invader with significant negative impacts on cultured shellfish and natural benthic communities, including commercially important ones.
We conducted an expert survey, identifying the five most important transport vectors for D. vexillum along the west coast of North America. We determined the spatially explicit vector density for all vectors in order to identify introduction hotspots. Additionally, we developed an environmental niche model based on 46 occurrence points and nine environmental variables to identify areas suitable for D. vexillum.
Spatial distribution of the most important transport vectors (slow‐moving vessels, aquaculture, fishing vessels, small vessels, and large commercial vessels) identified several hotspots with high vector densities. These proved to be a very good predictor of current D. vexillum occurrence in British Columbia (BC). Ecological niche modelling (Genetic Algorithm for Rule‐set Prediction) predicted suitable environments in southern BC, parts of central BC and along the east coast of the Queen Charlotte Islands. Independent validation of the model based on the current distribution in BC indicated good predictive accuracy. Additional analytical steps confirmed that no environmental variable dominated the predictions and we identified ranges of environmental conditions predicted suitable by the model.
We identified areas of high establishment probability for D. vexillum by combining the vector model and environmental niche model. Parts of central BC, the west coast of Vancouver Island and the Strait of Georgia are areas where D. vexillum is most likely to establish.
Synthesis and applications. Spatially explicit predictions of the potential distribution of biological invaders are crucial for informing risk assessments, development of management strategies, and resource allocation. While most studies only focus on one step in the invasion process, we successfully combined the likelihood of introduction and establishment. Results from this study are informing the canadian risk assessment of invasive tunicates, guiding current monitoring efforts, and providing a basis for potential intervention/mediation measures.
Insect seed predators and environmental change
Authors: Lewis Owen T. , Gripenberg Sofia 
Published: October 2008

Summary

The seed‐to‐seedling transition may be a critical stage in determining the dynamics of plant populations. Insects which kill seeds either before or after dispersal can influence the population dynamics of individual plant species, and ultimately, plant diversity and assemblage composition.
We discuss the potential for insect seed predators to maintain diversity in plant assemblages and to structure their composition, with a particular focus on diverse tropical forest habitats. We suggest that our ability to understand the functional effects of insect seed predators is hampered by a shortage of unbiased information on (i) their responses to the density of prey seeds at different spatial scales, and (ii) their host plant specificity.
Density‐dependence and its implications may be best assessed using manipulative field experiments. Such approaches can reveal how insect seed predators respond behaviourally and demographically to the density of individual host species and multiple host species across a range of spatial scales.
Host specificity and its implications may be best addressed through quantitative food web approaches previously applied largely to host–parasitoid interactions. Food webs will allow ecologists to assess the likely importance of indirect interactions such as apparent competition and apparent mutualism in structuring plant assemblages, and the functional consequences of adding or removing individual resource or consumer species.
Fully quantifying the wider effects of seed predators will require studies that better integrate seed stage‐specific demographic information, and which quantify the long‐term effects of variations in seed predation rates for plant recruitment.
Synthesis and applications. Compared to other functionally important insect groups such as pollinators, seed predators have received relatively little attention in the context of the functioning and sustainability of agro‐ecosystems and the consequences of global environmental change for ecological communities. A fuller understanding of the ecology of insect seed predator–plant interactions will be valuable to conservation and management in a range of natural and agricultural systems. For example, seed predator community ecology is relevant to predicting the consequences of deliberately or unintentionally introducing novel resource or consumer species; the process of habitat recovery following local disturbances; and managing the effects of pest or beneficial seed predators in agricultural crops. Furthermore, patterns of insect seed predation on a larger scale are likely to be highly sensitive to global environmental change drivers such as climate change and systematic habitat modification and fragmentation, with implications for the structure and organization of ecological communities more widely.
Living with a relative who has a spinal cord injury: a grounded theory approach
Authors: Chen Hsiao‐Yu , Boore Jennifer R P 
Published: October 2008

Aims.  This paper reports a study which explored family carers’ experiences of taking care of a relative who has a spinal cord injury.Background.  Spinal cord injury is one of the most disastrous injuries a person may experience. Although one family member experiences the injury, the entire family is affected. In Taiwan, family carers carry the primary responsibility of providing care on a 24‐hour basis during the rehabilitation hospitalisation. However, very limited research exists regarding their experiences.Design.  This qualitative study has a cross‐sectional and descriptive‐explorative design.Method.  Grounded theory was used to explore the psychosocial implications for family carer who has a relative with spinal cord injury.Data collection and analysis.  Data were collected through in‐depth, tape‐recorded, semi‐structured interviews and observation of a group discussion and two religious activities in a rehabilitation hospital in Taiwan. Fifteen family carers participated in this study comprising eight individual interviews and seven participating in the group discussion. Data collection and analysis occurred concurrently.Results.  The findings resulted in the core category ‘living with a relative who has a spinal cord injury’ and identified the experience of taking care of a relative who has a spinal cord injury. Three stages, including four categories: stage 1 ‘A catastrophic life event’; stage 2 ‘Confronting challenges’; and stage 3 ‘Family resilience’ or ‘Family breakdown’.Conclusions.  This study shows that family carers experience a catastrophic life event, they have to confront challenges and the positive consequence is family resilience, the negative consequence is family breakdown.Relevance to clinical practice.  Knowing how prospective family carers view their own situation and what they need is essential to provide effective nursing care for the family that has been changed dramatically by a spinal cord injury.