bluuebunny/crossref_metadata_2025_split huggingface dataset:
sc-PDB: a database for identifying variations and multiplicity of ‘druggable’ binding sites in proteins
Authors: Meslamani Jamel , Rognan Didier , Kellenberger Esther 
Published: March 2011

Abstract
Background: The sc-PDB database is an annotated archive of druggable binding sites extracted from the Protein Data Bank. It contains all-atoms coordinates for 8166 protein–ligand complexes, chosen for their geometrical and physico-chemical properties. The sc-PDB provides a functional annotation for proteins, a chemical description for ligands and the detailed intermolecular interactions for complexes. The sc-PDB now includes a hierarchical classification of all the binding sites within a functional class.
Method: The sc-PDB entries were first clustered according to the protein name indifferent of the species. For each cluster, we identified dissimilar sites (e.g. catalytic and allosteric sites of an enzyme).
Scope and applications: The classification of sc-PDB targets by binding site diversity was intended to facilitate chemogenomics approaches to drug design. In ligand-based approaches, it avoids comparing ligands that do not share the same binding site. In structure-based approaches, it permits to quantitatively evaluate the diversity of the binding site definition (variations in size, sequence and/or structure).
Availability: The sc-PDB database is freely available at: http://bioinfo-pharma.u-strasbg.fr/scPDB.
Contact: ekellen@unistra.fr
GeCo++: a C++ library for genomic features computation and annotation in the presence of variants
Authors: Cereda Matteo , Sironi Manuela , Cavalleri Matteo , Pozzoli Uberto 
Published: March 2011

Abstract
Summary: We propose a C++ class library developed to the purpose of making the implementation of sequence analysis algorithms easier and faster when genomic annotations and variations need to be considered. The library provides a class hierarchy to seamlessly bind together annotations of genomic elements to sequences and to algorithm results; it allows to evaluate the effect of mutations/variations in terms of both element position shifts and of algorithm results, limiting recalculation to the minimum. Particular care has been posed to keep memory and time overhead into acceptable limits.
Availability and Implementation: A complete tutorial as well as a detailed doxygen generated documentation and source code is freely available at http://bioinformatics.emedea.it/geco, under the GPL license. The library was written in standard ISO C++, and does not depend on external libraries.
Contact: uberto.pozzoli@bp.lnf.it
fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios
Authors: Excoffier Laurent , Foll Matthieu 
Published: March 2011

Abstract
Motivation: Genetic studies focus on increasingly larger genomic regions of both extant and ancient DNA, and there is a need for simulation software to match these technological advances. We present here a new coalescent-based simulation program fastsimcoal, which is able to quickly simulate a variety of genetic markers scattered over very long genomic regions with arbitrary recombination patterns under complex evolutionary scenarios.
Availability and Implementation: fastsimcoal is a C++ program compiled for Windows, MacOsX and Linux platforms. It is freely available at cmpg.unibe.ch/software/fastsimcoal/, together with its detailed user manual and example input files.
Contact: laurent.excoffier@iee.unibe.ch
Supplementary Information: Supplementary data are available at Bioinformatics online.
High-throughput feature counting and measurement of roots
Authors: Naeem Asad , French Andrew P. , Wells Darren M. , Pridmore Tony P. 
Published: March 2011

Abstract
Summary: The original RootTrace tool has proved successful in measuring primary root lengths across time series image data. Biologists have shown interest in using the tool to address further problems, namely counting lateral roots to use as parameters in screening studies, and measuring highly curved roots. To address this, the software has been extended to count emerged lateral roots, and the tracking model extended so that strongly curved and agravitropic roots can be now be recovered. Here, we describe the novel image analysis algorithms and user interface implemented within the RootTrace framework to handle such situations and evaluate the results.
Availability: The software is open source and available from http://sourceforge.net/projects/roottrace.
Contact: andrew.french@cpib.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Histogram-based DNA analysis for the visualization of chromosome, genome and species information
Authors: Costa António M. , Machado José T. , Quelhas Maria D. 
Published: March 2011

Abstract
Motivation: We describe a novel approach to explore DNA nucleotide sequence data, aiming to produce high-level categorical and structural information about the underlying chromosomes, genomes and species.
Results: The article starts by analyzing chromosomal data through histograms using fixed length DNA sequences. After creating the DNA-related histograms, a correlation between pairs of histograms is computed, producing a global correlation matrix. These data are then used as input to several data processing methods for information extraction and tabular/graphical output generation. A set of 18 species is processed and the extensive results reveal that the proposed method is able to generate significant and diversified outputs, in good accordance with current scientific knowledge in domains such as genomics and phylogenetics.
Availability and implementation: Source code freely available for download at http://www4.dei.isep.ipp.pt/etc/dnapaper2010, implemented in Free Pascal and UNIX scripting tools. Study input data available online for download at University of California at Santa Cruz Genome Bioinformatics, http://hgdownload.cse.ucsc.edu/downloads.html.
Contact: acc@isep.ipp.pt
Supplementary information: Supplementary data are available at Bioinformatics online.
UniCarb-DB: a database resource for glycomic discovery
Authors: Hayes Catherine A. , Karlsson Niclas G. , Struwe Weston B. , Lisacek Frederique , Rudd Pauline M. , Packer Nicolle H. , Campbell Matthew P. 
Published: March 2011

Abstract
Summary: Glycosylation is one of the most important post-translational modifications of proteins, known to be involved in pathogen recognition, innate immune response and protection of epithelial membranes. However, when compared to the tools and databases available for the processing of high-throughput proteomic data, the glycomic domain is severely lacking. While tools to assist the analysis of mass spectrometry (MS) and HPLC are continuously improving, there are few resources available to support liquid chromatography (LC)–MS/MS techniques for glycan structure profiling. Here, we present a platform for presenting oligosaccharide structures and fragment data characterized by LC–MS/MS strategies. The database is annotated with high-quality datasets and is designed to extend and reinforce those standards and ontologies developed by existing glycomics databases.
Availability: http://www.unicarb-db.org
Contact: matthew.campbell@mq.edu.au
Microvillous Inclusion Disease: How to Improve the Prognosis of a Severe Congenital Enterocyte Disorder
Authors: Halac Ugur , Lacaille Florence , Joly Francisca , Hugot Jean‐Pierre , Talbotec Cécile , Colomb Virginie , Ruemmele Frank M , Goulet Olivier 
Published: March 2011

ABSTRACTBackground and Objective:Microvillous inclusion disease (MVID) is a rare congenital enterocyte disorder causing severe diarrhea and intestinal failure. The objective of this study was to analyze clinical evolution and the most frequent complications of MVID in children receiving parenteral nutrition (PN) and after small‐bowel transplantation (SBTx) with the aim to improve treatment strategies and prognosis.Patients and Methods:From 1995 to 2009, 24 patients (16 boys, median follow‐up 4.7 years, range: from birth to 23.5 years) with MVID were admitted to our unit. The recorded parameters included growth, neurological development, liver and renal functions, bone disease, and outcome.Results:Almost half of the children were from consanguineous families from the Mediterranean area. All of the patients completely depended on PN. Four children died of PN complications before 4 years of age. Before or without SBTx, growth failure was common (mean height −2.5 standard deviations [SD]), as was developmental delay (12/24), liver (20/22 with fibrosis) or kidney disease (3/23 with moderate renal insufficiency), and osteoporosis (6/24). Thirteen children underwent SBTx (9 isolated, 4 combined with liver Tx) at a median age of 3.5 years. Follow‐up after SBTx was 0.4 to 14 years. Patient survival rates were 63% without SBTx and 77% with SBTx. After SBTx, 4 children experienced catch‐up growth.Conclusions:PN in MVID is difficult to manage and requires expertise. Despite improved results in expert centers, the risk of death or irreversible sequelae is higher with PN than after Tx. SBTx, despite being complicated, remains the only hope to improve the quality of life and long‐term prognosis of these children.
Utility of Simplified Criteria for the Diagnosis of Autoimmune Hepatitis in Children
Authors: Hiejima Eitaro , Komatsu Haruki , Sogo Tsuyoshi , Inui Ayano , Fujisawa Tomoo 
Published: March 2011

ABSTRACTBackground and Aim:Although the diagnostic scoring system of autoimmune hepatitis (AIH) has been used, these criteria are intended mainly as research tools and are complicated to apply. To resolve these difficulties and allow quick diagnosis, a simplified scoring system was proposed in 2007. We retrospectively compared the simplified AIH scoring system with the 1999 revised original AIH scoring system in children.Patients and Methods:Twenty children (boys/girls 10/10, age 1–15 years, mean age ± SD 8.4 ± 4.4 years) who were diagnosed with AIH based on clinical, biochemical, immunological, and histological data were enrolled in this study. In addition, 36 children with non‐AIH liver diseases (boys/girls 22/14, age 1–16 years, mean age ± SD 7.8 ± 4.4 years) were available for evaluation of both the simplified and the 1999 revised scoring system.Results:The sensitivity and specificity of the 1999 revised scoring system were 100% and 81%, respectively. In contrast, the sensitivity and specificity of the simplified scoring system were 55% and 86%, respectively. Of the 20 children with AIH, 9 (45%) were classified as not having AIH using the simplified scoring system. Of the 9 children, 2 and 7 were classified as having definite AIH and probable AIH using the 1999 revised scoring system, respectively. All 5 children with primary sclerosing cholangitis were graded as having AIH using the simplified AIH criteria and the 1999 revised criteria.Conclusions:Although the simplified AIH scoring system has low sensitivity for the diagnosis of AIH in children, the specificity of the simplified AIH scoring system is high. However, the simplified AIH scoring system could not differentiate between AIH and primary sclerosing cholangitis. Therefore, the simplified AIH scoring system does not seem to be a reliable diagnostic tool in children.
Parents' Willingness to Pay for Coeliac Disease Screening of Their Child
Authors: Norström Fredrik , Ivarsson Anneli , Lindholm Lars , Carlsson Annelie , Danielsson Lars , Högberg Lotta , Karlsson Eva , Löfgren Curt 
Published: March 2011

ABSTRACTObjective:The aim of this study is to determine Swedish parents' willingness to pay (WTP) for coeliac disease (CD) screening of their child.Subjects and Methods:CD screening was undertaken involving 10,041 12‐year‐old children, with 7567 (75%) agreeing to participate. Blood samples from the children were analysed for CD serological markers. Parents received a questionnaire including a scenario describing the health‐related risks of having CD and screening and diagnostic procedures. Parents were also asked whether they were willing to pay for CD screening, should this not be offered free of charge, and, if so, what their maximum WTP would be. Their WTP was compared with the average cost per child for the screening and case ascertainment procedures.Results:The questionnaire was answered by 6524 parents, and of 6057 valid responses 63% stated that they were willing to pay something. The mean WTP was 79 EUR and the median 10 EUR. The average cost per child for the screening and case ascertainment procedures was 47 EUR, which 23% of the parents stated they were willing to pay. Parents' WTP increased with higher education and income, and with child symptoms that may indicate CD.Conclusions:Swedish parents' WTP for school‐based CD screening of their child was higher than the average cost per child; however, only a minority of the parents were willing to pay that amount.
Development of a Farsi translation of the AGREE instrument, and the effects of group discussion on improving the reliability of the scores
Authors: Rashidian Arash , Yousefi‐Nooraie Reza 
Published: March 2011

AbstractObjective  We aimed to develop a formal Farsi (Persian) translation of the Appraisal of Guidelines for Research and Evaluation (AGREE) clinical guideline appraisal instrument. We considered the effect of group discussion in improving the reliability of scores.Methods  We followed a multi‐step process of translation including independent translations of the instrument and extensive assessment of face validity and fluency. We used the instruments to appraise 11 guidelines from three specialities. After the first appraisal, the raters discussed about each guideline in groups, and had the opportunity to revise their scores individually. In total 96 appraisals were conducted. The intra‐class correlations (1,1) were calculated for domain scores obtained by two versions at each time point.Results  We observed no statistically significant differences between the mean values obtained from the English and the translated versions of AGREE, and the scores at two time points. The average domain scores, as well as the reliability rose significantly after discussion.Conclusion  The Farsi version of the AGREE instrument yields in the scores comparable to the original version, despite a lower reliability. Revision of scores after group discussion leads to higher reliability, probably by helping the raters recognize what they might have overlooked during the short time of assessment.
Functional genomics of life history variation in a butterfly metapopulation
Authors: WHEAT CHRISTOPHER W. , FESCEMYER HOWARD W. , KVIST J. , TAS EVA , VERA J. CRISTOBAL , FRILANDER MIKKO J. , HANSKI ILKKA , MARDEN JAMES H. 
Published: March 2011

AbstractIn fragmented landscapes, small populations frequently go extinct and new ones are established with poorly understood consequences for genetic diversity and evolution of life history traits. Here, we apply functional genomic tools to an ecological model system, the well‐studied metapopulation of the Glanville fritillary butterfly. We investigate how dispersal and colonization select upon existing genetic variation affecting life history traits by comparing common‐garden reared 2‐day adult females from new populations with those from established older populations. New‐population females had higher expression of abdomen genes involved in egg provisioning and thorax genes involved in the maintenance of flight muscle proteins. Physiological studies confirmed that new‐population butterflies have accelerated egg maturation, apparently regulated by higher juvenile hormone titer and angiotensin converting enzyme mRNA, as well as enhanced flight metabolism. Gene expression varied between allelic forms of two metabolic genes (PgiandSdhd), which themselves were associated with differences in flight metabolic rate, population age and population growth rate. These results identify likely molecular mechanisms underpinning life history variation that is maintained by extinction–colonization dynamics in metapopulations.
The genetic effects of Late Quaternary climatic changes over a tropical latitudinal gradient: diversification of an Atlantic Forest passerine
Authors: D’HORTA FERNANDO M. , CABANNE GUSTAVO S. , MEYER DIOGO , MIYAKI CRISTINA Y. 
Published: March 2011

AbstractThe increase in biodiversity from high to low latitudes is a widely recognized biogeographical pattern. According to the latitudinal gradient hypothesis (LGH), this pattern was shaped by differential effects of Late Quaternary climatic changes across a latitudinal gradient. Here, we evaluate the effects of climatic changes across a tropical latitudinal gradient and its implications to diversification of an Atlantic Forest (AF) endemic passerine. We studied the intraspecific diversification and historical demography of Sclerurus scansor, based on mitochondrial (ND2, ND3 and cytb) and nuclear (FIB7) gene sequences. Phylogenetic analyses recovered three well‐supported clades associated with distinct latitudinal zones. Coalescent‐based methods were applied to estimate divergence times and changes in effective population sizes. Estimates of divergence times indicate that intraspecific diversification took place during Middle–Late Pleistocene. Distinct demographic scenarios were identified, with the southern lineage exhibiting a clear signature of demographic expansion, while the central one remained more stable. The northern lineage, contrasting with LGH predictions, exhibited a clear sign of a recent bottleneck. Our results suggest that different AF regions reacted distinctly, even in opposite ways, under the same climatic period, producing simultaneously favourable scenarios for isolation and contact among populations.
Metabolism of reactive oxygen species and reactive nitrogen species in pepper (Capsicum annuum L.) plants under low temperature stress
Authors: AIRAKI MORAD , LETERRIER MARINA , MATEOS ROSA M. , VALDERRAMA RAQUEL , CHAKI MOUNIRA , BARROSO JUAN B. , DEL RÍO LUIS A. , PALMA JOSÉ M. , CORPAS FRANCISCO J. 
Published: March 2011

ABSTRACTLow temperature is an environmental stress that affects crop production and quality and regulates the expression of many genes, and the level of a number of proteins and metabolites. Using leaves from pepper (Capsicum annum L.) plants exposed to low temperature (8 °C) for different time periods (1 to 3 d), several key components of the metabolism of reactive nitrogen and oxygen species (RNS and ROS, respectively) were analysed. After 24 h of exposure at 8 °C, pepper plants exhibited visible symptoms characterized by flaccidity of stems and leaves. This was accompanied by significant changes in the metabolism of RNS and ROS with an increase of both protein tyrosine nitration (NO2‐Tyr) and lipid peroxidation, indicating that low temperature induces nitrosative and oxidative stress. During the second and third days at low temperature, pepper plants underwent cold acclimation by adjusting their antioxidant metabolism and reverting the observed nitrosative and oxidative stress. In this process, the levels of the soluble non‐enzymatic antioxidants ascorbate and glutathione, and the activity of the main NADPH‐generating dehydrogenases were significantly induced. This suggests that ascorbate, glutathione and the NADPH‐generating dehydrogenases have a role in the process of cold acclimation through their effect on the redox state of the cell.
Root‐to‐shoot signalling when soil moisture is heterogeneous: increasing the proportion of root biomass in drying soil inhibits leaf growth and increases leaf abscisic acid concentration
Authors: MARTIN‐VERTEDOR ANA ISABEL , DODD IAN C. 
Published: March 2011

ABSTRACTTo determine whether root‐to‐shoot signalling of soil moisture heterogeneity depended on root distribution, wild‐type (WT) and abscisic acid (ABA)‐deficient (Az34) barley (Hordeum vulgare) plants were grown in split pots into which different numbers of seminal roots were inserted. After establishment, all plants received the same irrigation volumes, with one pot watered (w) and the other allowed to dry the soil (d), imposing three treatments (1 d : 3 w, 2 d : 2 w, 3 d : 1 w) that differed in the number of seminal roots exposed to drying soil. Root distribution did not affect leaf water relations and had no sustained effect on plant evapotranspiration (ET). In both genotypes, leaf elongation was less and leaf ABA concentrations were higher in plants with more roots in drying soil, with leaf ABA concentrations and water potentials 30% and 0.2 MPa higher, respectively, in WT plants. Whole‐pot soil drying increased xylem ABA concentrations, but maximum values obtained when leaf growth had virtually ceased (100 nm in Az34, 330 nm in WT) had minimal effects (<40% leaf growth inhibition) when xylem supplied to detached shoots. Although ABA may not regulate leaf growth in vivo, genetic variation in foliar ABA concentration in the field may indicate different root distributions between upper (drier) and lower (wetter) soil layers.
Effects of elevated CO2, warming and drought episodes on plant carbon uptake in a temperate heath ecosystem are controlled by soil water status
Authors: ALBERT K. R. , RO‐POULSEN H. , MIKKELSEN T. N. , MICHELSEN A. , VAN DER LINDEN L. , BEIER C. 
Published: March 2011

ABSTRACTThe impact of elevated CO2, periodic drought and warming on photosynthesis and leaf characteristics of the evergreen dwarf shrub Calluna vulgaris in a temperate heath ecosystem was investigated. Photosynthesis was reduced by drought in midsummer and increased by elevated CO2 throughout the growing season, whereas warming only stimulated photosynthesis early in the year. At the beginning and end of the growing season, a T × CO2 interaction synergistically stimulated plant carbon uptake in the combination of warming and elevated CO2. At peak drought, the D × CO2 interaction antagonistically down‐regulated photosynthesis, suggesting a limited ability of elevated CO2 to counteract the negative effect of drought. The response of photosynthesis in the full factorial combination (TDCO2) could be explained by the main effect of experimental treatments (T, D, CO2) and the two‐factor interactions (D × CO2, T × CO2). The interactive responses in the experimental treatments including elevated CO2 seemed to be linked to the realized range of treatment variability, for example with negative effects following experimental drought or positive effects following the relatively higher impact of night‐time warming during cold periods early and late in the year. Longer‐term experiments are needed to evaluate whether photosynthetic down‐regulation will dampen the stimulation of photosynthesis under prolonged exposure to elevated CO2.