bluuebunny/crossref_metadata_2025_split huggingface dataset:
Utopia documents: linking scholarly literature with research data
Authors: Attwood T. K. , Kell D. B. , McDermott P. , Marsh J. , Pettifer S. R. , Thorne D. 
Published: September 2010

Abstract
Motivation: In recent years, the gulf between the mass of accumulating-research data and the massive literature describing and analyzing those data has widened. The need for intelligent tools to bridge this gap, to rescue the knowledge being systematically isolated in literature and data silos, is now widely acknowledged.
Results: To this end, we have developed Utopia Documents, a novel PDF reader that semantically integrates visualization and data-analysis tools with published research articles. In a successful pilot with editors of the Biochemical Journal (BJ), the system has been used to transform static document features into objects that can be linked, annotated, visualized and analyzed interactively (http://www.biochemj.org/bj/424/3/). Utopia Documents is now used routinely by BJ editors to mark up article content prior to publication. Recent additions include integration of various text-mining and biodatabase plugins, demonstrating the system's ability to seamlessly integrate on-line content with PDF articles.
Availability: http://getutopia.com
Contact: teresa.k.attwood@manchester.ac.uk
BioXSD: the common data-exchange format for everyday bioinformatics web services
Authors: Kalaš Matúš , Puntervoll Pål , Joseph Alexandre , Bartaševičiūtė Edita , Töpfer Armin , Venkataraman Prabakar , Pettifer Steve , Bryne Jan Christian , Ison Jon , Blanchet Christophe , Rapacki Kristoffer , Jonassen Inge 
Published: September 2010

Abstract
Motivation: The world-wide community of life scientists has access to a large number of public bioinformatics databases and tools, which are developed and deployed using diverse technologies and designs. More and more of the resources offer programmatic web-service interface. However, efficient use of the resources is hampered by the lack of widely used, standard data-exchange formats for the basic, everyday bioinformatics data types.
Results: BioXSD has been developed as a candidate for standard, canonical exchange format for basic bioinformatics data. BioXSD is represented by a dedicated XML Schema and defines syntax for biological sequences, sequence annotations, alignments and references to resources. We have adapted a set of web services to use BioXSD as the input and output format, and implemented a test-case workflow. This demonstrates that the approach is feasible and provides smooth interoperability. Semantics for BioXSD is provided by annotation with the EDAM ontology. We discuss in a separate section how BioXSD relates to other initiatives and approaches, including existing standards and the Semantic Web.
Availability: The BioXSD 1.0 XML Schema is freely available at http://www.bioxsd.org/BioXSD-1.0.xsd under the Creative Commons BY-ND 3.0 license. The http://bioxsd.org web page offers documentation, examples of data in BioXSD format, example workflows with source codes in common programming languages, an updated list of compatible web services and tools and a repository of feature requests from the community.
Contact: matus.kalas@bccs.uib.no; developers@bioxsd.org; support@bioxsd.org
Modeling associations between genetic markers using Bayesian networks
Authors: Villanueva Edwin , Maciel Carlos Dias 
Published: September 2010

Abstract
Motivation: Understanding the patterns of association between polymorphisms at different loci in a population (linkage disequilibrium, LD) is of fundamental importance in various genetic studies. Many coefficients were proposed for measuring the degree of LD, but they provide only a static view of the current LD structure. Generative models (GMs) were proposed to go beyond these measures, giving not only a description of the actual LD structure but also a tool to help understanding the process that generated such structure. GMs based in coalescent theory have been the most appealing because they link LD to evolutionary factors. Nevertheless, the inference and parameter estimation of such models is still computationally challenging.
Results: We present a more practical method to build GM that describe LD. The method is based on learning weighted Bayesian network structures from haplotype data, extracting equivalence structure classes and using them to model LD. The results obtained in public data from the HapMap database showed that the method is a promising tool for modeling LD. The associations represented by the learned models are correlated with the traditional measure of LD D′. The method was able to represent LD blocks found by standard tools. The granularity of the association blocks and the readability of the models can be controlled in the method. The results suggest that the causality information gained by our method can be useful to tell about the conservability of the genetic markers and to guide the selection of subset of representative markers.
Availability: The implementation of the method is available upon request by email.
Contact: maciel@sc.usp.br
Semi-supervised multi-task learning for predicting interactions between HIV-1 and human proteins
Authors: Qi Yanjun , Tastan Oznur , Carbonell Jaime G. , Klein-Seetharaman Judith , Weston Jason 
Published: September 2010

Abstract
Motivation: Protein–protein interactions (PPIs) are critical for virtually every biological function. Recently, researchers suggested to use supervised learning for the task of classifying pairs of proteins as interacting or not. However, its performance is largely restricted by the availability of truly interacting proteins (labeled). Meanwhile, there exists a considerable amount of protein pairs where an association appears between two partners, but not enough experimental evidence to support it as a direct interaction (partially labeled).
Results: We propose a semi-supervised multi-task framework for predicting PPIs from not only labeled, but also partially labeled reference sets. The basic idea is to perform multi-task learning on a supervised classification task and a semi-supervised auxiliary task. The supervised classifier trains a multi-layer perceptron network for PPI predictions from labeled examples. The semi-supervised auxiliary task shares network layers of the supervised classifier and trains with partially labeled examples. Semi-supervision could be utilized in multiple ways. We tried three approaches in this article, (i) classification (to distinguish partial positives with negatives); (ii) ranking (to rate partial positive more likely than negatives); (iii) embedding (to make data clusters get similar labels). We applied this framework to improve the identification of interacting pairs between HIV-1 and human proteins. Our method improved upon the state-of-the-art method for this task indicating the benefits of semi-supervised multi-task learning using auxiliary information.
Availability: http://www.cs.cmu.edu/∼qyj/HIVsemi
Contact: qyj@cs.cmu.edu
Candidate gene prioritization based on spatially mapped gene expression: an application to XLMR
Authors: Piro Rosario M. , Molineris Ivan , Ala Ugo , Provero Paolo , Di Cunto Ferdinando 
Published: September 2010

Abstract
Motivation: The identification of genes involved in specific phenotypes, such as human hereditary diseases, often requires the time-consuming and expensive examination of a large number of positional candidates selected by genome-wide techniques such as linkage analysis and association studies. Even considering the positive impact of next-generation sequencing technologies, the prioritization of these positional candidates may be an important step for disease-gene identification.
Results: Here, we report a large-scale analysis of spatial, i.e. 3D, gene-expression data from an entire organ (the mouse brain) for the purpose of evaluating and ranking positional candidate genes, showing that the spatial gene-expression patterns can be successfully exploited for the prediction of gene–phenotype associations not only for mouse phenotypes, but also for human central nervous system-related Mendelian disorders. We apply our method to the case of X-linked mental retardation, compare the predictions to the results obtained from a previous large-scale resequencing study of chromosome X and discuss some promising novel candidates.
Contact: rosario.piro@unito.it
Supplementary information: Supplementary data are available at Bioinformatics online.
Detecting host factors involved in virus infection by observing the clustering of infected cells in siRNA screening images
Authors: Suratanee Apichat , Rebhan Ilka , Matula Petr , Kumar Anil , Kaderali Lars , Rohr Karl , Bartenschlager Ralf , Eils Roland , König Rainer 
Published: September 2010

AbstractMotivation: Detecting human proteins that are involved in virus entry and replication is facilitated by modern high-throughput RNAi screening technology. However, hit lists from different laboratories have shown only little consistency. This may be caused by not only experimental discrepancies, but also not fully explored possibilities of the data analysis. We wanted to improve reliability of such screens by combining a population analysis of infected cells with an established dye intensity readout.Results: Viral infection is mainly spread by cell–cell contacts and clustering of infected cells can be observed during spreading of the infection in situ and in vivo. We employed this clustering feature to define knockdowns which harm viral infection efficiency of human Hepatitis C Virus. Images of knocked down cells for 719 human kinase genes were analyzed with an established point pattern analysis method (Ripley's K-function) to detect knockdowns in which virally infected cells did not show any clustering and therefore were hindered to spread their infection to their neighboring cells. The results were compared with a statistical analysis using a common intensity readout of the GFP-expressing viruses and a luciferase-based secondary screen yielding five promising host factors which may suit as potential targets for drug therapy.Conclusion: We report of an alternative method for high-throughput imaging methods to detect host factors being relevant for the infection efficiency of viruses. The method is generic and has the potential to be used for a large variety of different viruses and treatments being screened by imaging techniques.Contact: r.eils@dkfz.de; r.koenig@dkfz.deSupplementary information: Supplementary data are available at Bioinformatics online.
Higher parasite resistance in Daphnia populations with recent epidemics
Authors: SCHOEBEL C. N. , WOLINSKA J. , SPAAK P. 
Published: September 2010

AbstractNatural populations often show genetic variation in parasite resistance, forming the basis for evolutionary response to selection imposed by parasitism. We investigated whether previous epidemics selected for higher resistance to novel parasite isolates in a Daphnia galeata–microparasite system by comparing susceptibility of host clones from populations with varying epidemic history. We manipulated resource availability to evaluate whether diet influences Daphnia susceptibility as epidemics are common in nutrient‐rich lakes. Exposing clones from 10 lakes under two food treatments to an allopatric protozoan parasite, we found that Daphnia originating from lakes (mainly nutrient rich) with previous epidemics better resist infection. Despite this result, there was a tendency of higher susceptibility in the low food treatment, suggesting that higher resistance of clones from populations with epidemic background is not directly caused by lake nutrient level. Rather, our results imply that host populations respond to parasite‐mediated selection by evolving higher parasite resistance.
The lifetime costs of increased male reproductive effort: courtship, copulation and the Coolidge effect
Authors: JORDAN L. A. , BROOKS R. C. 
Published: September 2010

AbstractThe reproductive effort that a male directs to a familiar female declines over time, suggesting decreasing marginal returns. But is this diminishing returns a function of increasing reproductive costs or decreasing benefits of sustained effort? Here, we use the restoration of male reproductive effort with unfamiliar females to differentiate the role of diminishing returns and lifetime costs of increased reproductive effort of male guppies. We kept males with familiar or unfamiliar females throughout their lives and manipulated their ability to either court or mate with females. We found that increased male reproductive effort with novel mates lead to an immediate trade‐off in the form of reduced foraging effort. Further, males able to mate with a series of unfamiliar females had lower lifetime growth, indicating the primary cost of male reproductive effort in guppies arises from copulation rather than courtship. The lifetime growth trade‐offs were significant only when males mated with unfamiliar mates, suggesting that male reproductive effort with familiar females declines before it is restricted by physical exhaustion. These findings provide some of the first evidence of longitudinal costs of increased male reproductive effort in a vertebrate.
First description of giant Archaea (Thaumarchaeota) associated with putative bacterial ectosymbionts in a sulfidic marine habitat
Authors: Muller Félix , Brissac Terry , Le Bris Nadine , Felbeck Horst , Gros Olivier 
Published: September 2010

Summary Archaea may be involved in global energy cycles, and are known for their ability to interact with eukaryotic species (sponges, corals and ascidians) or as archaeal–bacterial consortia. The recently proposed phylum Thaumarchaeota may represent the deepest branching lineage in the archaeal phylogeny emerging before the divergence between Euryarchaeota and Crenarchaeota. Here we report the first characterization of two marine thaumarchaeal species from shallow waters that consist of multiple giant cells. One species is coated with sulfur‐oxidizing γ‐Proteobacteria. These new uncultured thaumarchaeal species are able to live in the sulfide‐rich environments of a tropical mangrove swamp, either on living tissues such as roots or on various kinds of materials such as stones, sunken woods, etc. These archaea and archaea/bacteria associations have been studied using light microscopy, transmission electron microscopy and scanning electron microscopy. Species identification of archaeons and the putative bacterial symbiont have been assessed by 16S small subunit ribosomal RNA analysis. The sulfur‐oxidizing ability of the bacteria has been assessed by genetic investigation on alpha‐subunit of the adenosine‐5′‐phosphosulfate reductase/oxidase's (AprA). Species identifications have been confirmed by fluorescence in situ hybridization using specific probes designed in this study. In this article, we describe two new giant archaeal species that form the biggest archaeal filaments ever observed. One of these species is covered by a specific biofilm of sulfur‐oxidizing γ‐Proteobacteria. This study highlights an unexpected morphological and genetic diversity of the phylum Thaumarchaeota.
Association of the POU class 2 homeobox 1 gene (POU2F1) with susceptibility to Type 2 diabetes in Chinese populations
Authors: Ng M. C. Y. , Lam V. K. L. , Tam C. H. T. , Chan A. W. H. , So W.‐Y. , Ma R. C. W. , Zee B. C. Y. , Waye M. M. Y. , Mak W. W. , Hu C. , Wang C. R. , Tong P. C. Y. , Jia W. P. , Chan J. C. N. ,   for the International Type 2 Diabetes 1q Consortium
Published: September 2010

Diabet. Med. 27, 1443–1449 (2010)AbstractAims  POU class 2 homeobox 1 (POU2F1), also known as octamer‐binding transcription factor‐1 (OCT‐1), is a ubiquitous transcription factor that plays a key role in the regulation of genes related to inflammation and cell cycles. POU2F1 is located on chromosome 1q24, a region with linkage for Type 2 diabetes in Chinese and other populations. We examined the association of POU2F1 genetic variants with Type 2 diabetes in Hong Kong Chinese using two independent cohorts.Methods  We genotyped five haplotype‐tagging single nucleotide polymorphisms at POU2F1 in 1378 clinic‐based patients with Type 2 diabetes and 601 control subjects, as well as 707 members from 179 families with diabetes.Results  We found significant associations of rs4657652, rs7532692, rs10918682 and rs3767434 (OR = 1.26–1.59, 0.0003 < Punadjusted < 0.035) with Type 2 diabetes in the clinic‐based case–control cohorts. Rs3767434 was also associated with Type 2 diabetes (OR = 1.55, Punadjusted = 0.013) in the family‐based cohort. Meta‐analysis revealed similar associations. In addition, the risk G allele of rs10918682 showed increased usage of insulin treatment during a mean follow‐up period of 7 years [hazard ratio = 1.50 (1.05–2.14), P = 0.025].Conclusions  Using separate cohorts, we observed consistent results showing the contribution of multiple variants at POU2F1 to the risk of Type 2 diabetes.
More co‐morbid depression in patients with Type 2 diabetes with multiple complications. An observational study at a specialized outpatient clinic
Authors: van Steenbergen‐Weijenburg K. M. , van Puffelen A. L. , Horn E. K. , Nuyen J. , Sytze van Dam P. , van Benthem T. B. , Beekman A. T. F. , Rutten F. F. H. , Hakkaart‐van Roijen L. , van der Feltz‐Cornelis C. M. 
Published: September 2010

Diabet. Med. 28, 86–89 (2011)AbstractAims  The impact of depression on patients with chronic medical illnesses such as diabetes is well documented. Depression is relatively common in diabetes patients with diabetes‐related complications and they are more likely to be referred to specialized outpatient facilities. Only a few studies have addressed the association between depression and multiple diabetes‐related complications at these specialized outpatient facilities. The aim of this study was to determine the association between diabetes with multiple complications and depression in patients with Type 2 diabetes at a specialized outpatient clinic.Methods  After giving informed consent, 1194 patients were screened for depression using the Patient Health Questionnaire (PHQ‐9). Additional data on the type of diabetes and complications were taken from the medical records. Logistic regression analysis was conducted, with complications as the predictor variable and the probability of depression as the dependent variable.Results  A total of 596 (63%) patients with Type 2 diabetes participated in the study. The presence of two or more complications (OR 2.23, 95% CI 1.02–2.94) was significantly associated with depression. Neuropathy (OR 1.7, 95% CI 1.10–2.77) and nephropathy (OR 1.68, 95% CI 1.00–2.48) were especially related to depression.Conclusions  Patients with Type 2 diabetes with two or more complications, especially neuropathy or nephropathy, are at high risk of depression. Knowing this can help clinicians identify patients at risk for depression and facilitate timely and adequate treatment.
A comparison of the health and related quality of life between middle‐aged Korean and Chinese women
Authors: Kim K.‐B. , Sok S.R. 
Published: September 2010

KIM K.‐B. & SOK S.R. (2010) A comparison of the health and related quality of life between middle‐aged Korean and Chinese women.International Nursing ReviewBackground: The proportion of middle‐aged people in one's total life cycle has increased. Health providers are required to promote and manage their health, and improve the quality of their life, especially middle‐aged women. As international interchanges in nursing are growing between Korea and China, understanding of the level related to health and quality of life between middle‐aged Korean and Chinese women is critical to improve their health and quality of life.Aim: To compare and examine the health perception, anger expression, self‐esteem and quality of life between middle‐aged Korean and Chinese women.Methods: A cross‐sectional survey was conducted. The participants were comprised of a total 430 middle‐aged Korean (n = 220) and Chinese (n = 210) women aged 40–64 years. The survey included a set of four questionnaires. All measures were self‐administered. Data were analysed using the statistical package, SPSS/WIN Ver16.0 (SPSS, Inc., Chicago, IL, USA).Results: Middle‐aged Chinese women had higher health perception than middle‐aged Korean women. Anger expression, self‐esteem and quality of life of middle‐aged Korean women were higher than in middle‐aged Chinese women. Also, there were the differences in the health perception, anger expression and self‐esteem according to the general characteristics in all middle‐aged Korean and Chinese women.Conclusions: Various nursing intervention strategies should be developed and adjusted to improve the self‐esteem and quality of life for all middle‐aged Korean and Chinese women, especially middle‐aged Chinese women. Additionally, the individual characteristics and national culture of the middle‐aged women should be considered as a basis for the nursing intervention.
Exogenous attention influences visual short‐term memory in infants
Authors: Ross‐Sheehy Shannon , Oakes Lisa M. , Luck Steven J. 
Published: September 2010

AbstractTwo experiments examined the hypothesis that developing visual attentional mechanisms influence infants’ Visual Short‐Term Memory (VSTM) in the context of multiple items. Five‐ and 10‐month‐old infants (N = 76) received a change detection task in which arrays of three differently colored squares appeared and disappeared. On each trial one square changed color and one square was cued; sometimes the cued item was the changing item, and sometimes the changing item was not the cued item. Ten‐month‐old infants exhibited enhanced memory for the cued item when the cue was a spatial pre‐cue (Experiment 1) and 5‐month‐old infants exhibited enhanced memory for the cued item when the cue was relative motion (Experiment 2). These results demonstrate for the first time that infants younger than 6 months can encode information in VSTM about individual items in multiple‐object arrays, and that attention‐directing cues influence both perceptual and VSTM encoding of stimuli in infants as in adults.
A new measure for assessing executive function across a wide age range: children and adults find happy‐sad more difficult than day‐night
Authors: Lagattuta Kristin Hansen , Sayfan Liat , Monsour Michael 
Published: September 2010

AbstractTwo experiments examined 4‐ to 11‐year‐olds’ and adults’ performance (N = 350) on two variants of a Stroop‐like card task: the day‐night task (say ‘day’ when shown a moon and ‘night’ when shown a sun) and a new happy‐sad task (say ‘happy’ for a sad face and ‘sad’ for a happy face). Experiment 1 featured colored cartoon drawings. In Experiment 2, the happy‐sad task featured photographs, and pictures for both measures were grayscale. All age groups made more errors and took longer to respond to the happy‐sad versus the day‐night versions. Unlike the day‐night task, the happy‐sad task did not suffer from ceiling effects, even in adults. The happy‐sad task provides a methodological advance for measuring executive function across a wide age range.