bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trust and Authority in Scholarly Communications in the Light of the Digital Transition: setting the scene for a major study
Authors: NICHOLAS David , WATKINSON Anthony , VOLENTINE Rachel , ALLARD Suzie , LEVINE Kenneth , TENOPIR Carol , HERMAN Eti 
Published: March 2014

ABSTRACTThe paper provides the results of the first phase of the research project Trust and Authority in Scholarly Communications in the Light of the Digital Transition. It provides for an examination of the behaviours and attitudes of academic researchers as producers and consumers of scholarly information resources in the digital era in respect to how they determine authority and trustworthiness in the sources they use, cite, and publish in. The first phase of the study utilized focus groups to formulate research questions for the project as a whole. It provided the direction for the literature review, interviews, and questionnaires studies that would follow. Fourteen focus groups were held in the UK and US in order to obtain this information. A total of 66 science and social science researchers participated. The main findings were: (a) researchers play down difficulties of establishing trustworthiness, not because there are none, but because they have well‐developed methods of establishing trust; (b) citation‐derived metrics are becoming more important in regard to where researchers publish; (c) social media are ancillary to research, but are used for promotion of research and idea generation; (d) researchers are suspicious and confused about open access, but less so if produced by a traditional publisher; (e) there was a uniformity of perceptions/behaviour of researchers irrespective of differences in subject, country, and age; (f) although some early career researchers behave the same as their more senior colleagues this is because of a fear of the system: they actually think differently.
Comparison between user affinity with digital libraries and virtual communities
Authors: YAN Yalan , ZHA Xianjin 
Published: March 2014

ABSTRACTThere is ongoing discussion about the value and reliability of information produced by experts and organized by digital libraries in universities versus information produced by the crowd in virtual communities. This study compares users' perceptions of digital libraries and virtual communities in terms of affinity. In this study, affinity with digital libraries or virtual communities is defined as the degree of importance that users place on digital libraries or virtual communities. Data collected from 334 users of digital libraries and virtual communities were used for data analysis. The statistical method of 'compare means' is employed. We find the mean of affinity with digital libraries is significantly larger than that of virtual communities, suggesting users are likely to perceive higher levels of affinity with digital libraries than with virtual communities. More analysis oriented to different groups is also conducted. The findings and their implications are discussed.
CorMut: an R/Bioconductor package for computing correlated mutations based on selection pressure
Authors: Li Zhenpeng , Huang Yang , Ouyang Yabo , Jiao Yang , Xing Hui , Liao Lingjie , Jiang Shibo , Shao Yiming , Ma Liying 
Published: March 2014

Abstract
Summary: Correlated mutations constitute a fundamental idea in evolutionary biology, and understanding correlated mutations will, in turn, facilitate an understanding of the genetic mechanisms governing evolution. CorMut is an R package designed to compute correlated mutations in the unit of codon or amino acid mutation. Three classical methods were incorporated, and the computation results can be represented as correlation mutation networks. CorMut also enables the comparison of correlated mutations between two different evolutionary conditions.
Availability and implementation: CorMut is released under the GNU General Public License within bioconductor project, and freely available at http://bioconductor.org/packages/release/bioc/html/CorMut.html .
Contact: mal@chinaaids.cn or yshao08@gmail.com
Motifs tree: a new method for predicting post-translational modifications
Authors: Charpilloz Christophe , Veuthey Anne-Lise , Chopard Bastien , Falcone Jean-Luc 
Published: March 2014

Abstract
Motivation: Post-translational modifications (PTMs) are important steps in the maturation of proteins. Several models exist to predict specific PTMs, from manually detected patterns to machine learning methods. On one hand, the manual detection of patterns does not provide the most efficient classifiers and requires an important workload, and on the other hand, models built by machine learning methods are hard to interpret and do not increase biological knowledge. Therefore, we developed a novel method based on patterns discovery and decision trees to predict PTMs. The proposed algorithm builds a decision tree, by coupling the C4.5 algorithm with genetic algorithms, producing high-performance white box classifiers. Our method was tested on the initiator methionine cleavage (IMC) and N α -terminal acetylation (N-Ac), two of the most common PTMs.
Results: The resulting classifiers perform well when compared with existing models. On a set of eukaryotic proteins, they display a cross-validated Matthews correlation coefficient of 0.83 (IMC) and 0.65 (N-Ac). When used to predict potential substrates of N-terminal acetyltransferaseB and N-terminal acetyltransferaseC, our classifiers display better performance than the state of the art. Moreover, we present an analysis of the model predicting IMC for Homo sapiens proteins and demonstrate that we are able to extract experimentally known facts without prior knowledge. Those results validate the fact that our method produces white box models.
Availability and implementation: Predictors for IMC and N-Ac and all datasets are freely available at http://terminus.unige.ch/ .
Contact: jean-luc.falcone@unige.ch
Supplementary information: Supplementary data are available at Bioinformatics online.
VariantAnnotation
: a
Bioconductor
package for exploration and annotation of genetic variants
Authors: Obenchain Valerie , Lawrence Michael , Carey Vincent , Gogarten Stephanie , Shannon Paul , Morgan Martin 
Published: March 2014

Abstract
Summary: VariantAnnotation is an R / Bioconductor package for the exploration and annotation of genetic variants. Capabilities exist for reading, writing and filtering variant call format (VCF) files. VariantAnnotation allows ready access to additional R / Bioconductor facilities for advanced statistical analysis, data transformation, visualization and integration with diverse genomic resources.
Availability and implementation: This package is implemented in R and available for download at the Bioconductor Web site ( http://bioconductor.org/packages/2.13/bioc/html/ VariantAnnotation .html ). The package contains extensive help pages for individual functions and a ‘vignette’ outlining typical work flows; it is made available under the open source ‘Artistic-2.0’ license. Version 1.9.38 was used in this article.
Contact: vobencha@fhcrc.org
molBLOCKS: decomposing small molecule sets and uncovering enriched fragments
Authors: Ghersi Dario , Singh Mona 
Published: March 2014

AbstractSummary: The chemical structures of biomolecules, whether naturally occurring or synthetic, are composed of functionally important building blocks. Given a set of small molecules—for example, those known to bind a particular protein—computationally decomposing them into chemically meaningful fragments can help elucidate their functional properties, and may be useful for designing novel compounds with similar properties. Here we introduce molBLOCKS , a suite of programs for breaking down sets of small molecules into fragments according to a predefined set of chemical rules, clustering the resulting fragments, and uncovering statistically enriched fragments. Among other applications, our software should be a great aid in large-scale chemical analysis of ligands binding specific targets of interest.Availability and implementation: molBLOCKS is available as GPL C++ source code at http://compbio.cs.princeton.edu/molblocks .Contact: mona@cs.princeton.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Combined effects of exploitation and temperature on fish stocks in the Northeast Atlantic
Authors: Rouyer Tristan , Fromentin Jean-Marc , Hidalgo Manuel , Stenseth Nils C. 
Published: March 2014

Abstract
Fish stock fluctuations are affected by two potentially confounding forces: the removal of individuals by fisheries and climatic variations affecting the productivity of fish populations. Disentangling the relative importance of these forces has thus been a question of primary importance for fisheries management and conservation. Through the analysis of long-term time-series for 27 fish stocks from the Northeast Atlantic, the present study shows that the sign and intensity of the effect of temperature on biomass are dependent on the geographical location: the stocks located at the southernmost and northernmost latitudes of our study displayed stronger associations with temperature than the stocks located in the middle range of latitudes. As a consequence, the investigation of the combined effects of exploitation and the environment revealed that the stocks at the northern/southern boundaries of the spatial extent of the species were more prone to combined effects. The interplay between geographic location, climate and exploitation thus plays a significant role in fish stock productivity, which is generally ignored during assessment, thus affecting management procedures.
Overvalued equity, benchmark beating and unexpected accruals
Authors: Coulton Jeffrey J. , Saune Naibuka , Taylor Stephen L. 
Published: March 2014

AbstractWe investigate the extent to which the overvaluation hypothesis provides incentives for managers to beat earnings benchmarks, and whether this benchmark beating can be reliably interpreted as evidence of earnings management. We carefully identify firms immediately above earnings benchmarks that have a priori, overvaluation‐based incentives to achieve the benchmark. We therefore focus on benchmark‐beating observations where manipulation is most likely, providing a more powerful test of the existence of opportunistic financial reporting. Consistent with overvaluation‐related incentives encouraging earnings management, we find that overvalued firms that just exceed levels‐related earnings benchmarks have higher unexpected accruals than firms with less extreme valuations.
Footprints of recent selection and variability in breed composition in the Göttingen Minipig genome
Authors: Gärke C. , Ytournel F. , Sharifi A. R. , Pimentel E. C. G. , Ludwig A. , Simianer H. 
Published: March 2014

SummaryThe Göttingen Minipig (GMP) developed at the University of Göttingen is a synthetic breed that is widely used in medical research and toxicology. It combines the high fertility of the Vietnamese potbellied pig, the low body weight of the Minnesota Minipig and the white coat colour of the German Landrace pig. The aim of this study was to find genomic regions that may have undergone selection since the creation of the breed in the 1960s. Therefore, the whole genome was screened for footprints of recent selection based on single nucleotide polymorphism (SNP) genotypes from the Illumina Porcine SNP60 BeadChip using two methods: the extended haplotype homozygosity (EHH) test and the estimation of the genomic proportion of the three original breeds at each SNP using a Bayesian approach. Local deviations from the average genome‐wide breed composition were tested with a permutation‐based empirical test. Results for a comprehensive whole‐genome scan for both methods are presented. Several regions showing the highest P‐values in the EHH test are related to breeding goals relevant in the GMP, such as growth (SOCS2, TXN, DDR2 and GRB10 genes) and white colour (PRLR gene). Additionally, the calculated proportion of the founder breeds diverged significantly in many regions from the pedigree‐based expectations and the genome average. The results provide a genome‐wide map of selection signatures in the GMP, which leads to a better understanding of selection that took place over the last decades in GMP breed development.
Influence of maternal body mass index on accuracy and reliability of external fetal monitoring techniques
Authors: Cohen Wayne R. , Hayes‐Gill Barrie 
Published: March 2014

AbstractObjectiveTo evaluate the performance of external electronic fetal heart rate and uterine contraction monitoring according to maternal body mass index.DesignSecondary analysis of prospective equivalence study.SettingThree US urban teaching hospitals.SampleSeventy‐four parturients with a normal term pregnancy.MethodsThe parent study assessed performance of two methods of external fetal heart rate monitoring (abdominal fetal electrocardiogram and Doppler ultrasound) and of uterine contraction monitoring (electrohystero‐graphy and tocodynamometry) compared with internal monitoring with fetal scalp electrode and intrauterine pressure transducer. Reliability of external techniques was assessed by the success rate and positive percent agreement with internal methods. Bland–Altman analysis determined accuracy. We analyzed data from that study according to maternal body mass index.Main outcome measuresWe assessed the relationship between body mass index and monitor performance with linear regression, using body mass index as the independent variable and measures of reliability and accuracy as dependent variables.ResultsThere was no significant association between maternal body mass index and any measure of reliability or accuracy for abdominal fetal electrocardiogram. By contrast, the overall positive percent agreement for Doppler ultrasound declined (p = 0.042), and the root mean square error from the Bland–Altman analysis increased in the first stage (p = 0.029) with increasing body mass index. Uterine contraction recordings from electrohysterography and tocodynamometry showed no significant deterioration related to maternal body mass index.ConclusionsAccuracy and reliability of fetal heart rate monitoring using abdominal fetal electrocardiogram was unaffected by maternal obesity, whereas performance of ultrasound degraded directly with maternal size. Both electrohysterography and tocodynamometry were unperturbed by obesity.
Three‐dimensional reconstruction of the human skeletal muscle mitochondrial network as a tool to assess mitochondrial content and structural organization
Authors: Dahl R. , Larsen S. , Dohlmann T. L. , Qvortrup K. , Helge J. W. , Dela F. , Prats C. 
Published: March 2014

AbstractAimMitochondria undergo continuous changes in shape as result of complex fusion and fission processes. The physiological relevance of mitochondrial dynamics is still unclear. In the field of mitochondria bioenergetics, there is a need of tools to assess cell mitochondrial content. To develop a method to visualize mitochondrial networks in high resolution and assess mitochondrial volume.MethodsConfocal fluorescence microscopy imaging of mitochondrial network stains in human vastus lateralis single muscle fibres and focused ion beam/ scanning electron microscopy (FIB/SEM) imaging, combined with 3D reconstruction was used as a tool to analyse mitochondrial morphology and measure mitochondrial fractional volume.ResultsMost type I and type II muscle fibres have tubular highly interconnected profusion mitochondria, which are thicker and more structured in type I muscle fibres (Fig. 1). In some muscle fibres, profission‐isolated ellipsoid‐shaped mitochondria were observed. Mitochondrial volume was significantly higher in type I muscle fibres and showed no correlation with any of the investigated molecular and biochemical mitochondrial measurements (Fig. 2). Three‐dimensional reconstruction of FIB/SEM data sets shows that some subsarcolemmal mitochondria are physically interconnected with some intermyofibrillar mitochondria (Fig. 3).ConclusionTwo microscopy methods to visualize skeletal muscle mitochondrial networks in 3D are described and can be used as tools to investigate mitochondrial dynamics in response to life‐style interventions and/or in certain pathologies. Our results question the classification of mitochondria into subsarcolemmal and intermyofibrillar pools, as they are physically interconnected.
Severe 25‐hydroxyvitamin D deficiency identifies a poor prognosis in patients with hepatocellular carcinoma – a prospective cohort study
Authors: Finkelmeier F. , Kronenberger B. , Köberle V. , Bojunga J. , Zeuzem S. , Trojan J. , Piiper A. , Waidmann O. 
Published: March 2014

SummaryBackgroundVitamin D is involved in many biological processes. The role of vitamin D in patients with hepatocellular carcinoma (HCC) remains inconclusive, although there is evolving evidence that vitamin D may modulate cancer development and progression.AimTo evaluate serum vitamin D as prognostic parameter in HCC, we performed a prospective cohort study.MethodsHCC patients were prospectively recruited and 25‐hydroxyvitamin D3 (25(OH)D3) levels were determined. 25(OH)D3 levels were compared to stages of cirrhosis and HCC stages with nonparametric Kruskal–Wallis tests and Spearman correlations in 200 HCC patients. The association of the 25(OH)D3 levels and overall survival (OS) was assessed in uni‐ and multivariate Cox regression models.ResultsTwo‐hundred patients with HCC were included. The mean follow‐up time was 322 ± 342 days with a range of 1–1508 days. Nineteen patients underwent liver transplantation and 60 patients died within the observation time. The mean serum 25(OH)D3 concentration was 17 ± 13 ng/mL with a range of 1–72 ng/mL. 25(OH)D3 serum levels negatively correlated with the stage of cirrhosis as well as with stages of HCC. Patients with severe 25(OH)D3 deficiency had the highest mortality risk (hazard ratio 2.225, 95% confidence interval 1.331–3.719, P = 0.002). Furthermore, very low 25(OH)D3 levels were associated with mortality independently from the MELD score and high alpha‐Fetoprotein levels (>400 ng/mL) in a multivariate Cox regression model.ConclusionsWe conclude that 25(OH)D3 deficiency is associated with advanced stages of hepatocellular carcinoma and it is a prognostic indicator for a poor outcome.
In Vitro and Modelling Approaches to Risk Assessment from the U.S. Environmental Protection Agency ToxCast Programme
Authors: Judson Richard , Houck Keith , Martin Matt , Knudsen Thomas , Thomas Russell S. , Sipes Nisha , Shah Imran , Wambaugh John , Crofton Kevin 
Published: March 2014

AbstractA significant challenge in toxicology is the ‘too many chemicals’ problem. Human beings and environmental species are exposed to tens of thousands of chemicals, only a small percentage of which have been tested thoroughly using standard in vivo test methods. This study reviews several approaches that are being developed to deal with this problem by the U.S. Environmental Protection Agency, under the umbrella of the ToxCast programme (http://epa.gov/ncct/toxcast/). The overall approach is broken into seven tasks: (i) identifying biological pathways that, when perturbed, can lead to toxicity; (ii) developing high‐throughput in vitro assays to test chemical perturbations of these pathways; (iii) identifying the universe of chemicals with likely human or ecological exposure; (iv) testing as many of these chemicals as possible in the relevant in vitro assays; (v) developing hazard models that take the results of these tests and identify chemicals as being potential toxicants; (vi) generating toxicokinetics data on these chemicals to predict the doses at which these hazard pathways would be activated; and (vii) developing exposure models to identify chemicals for which these hazardous dose levels could be achieved. This overall strategy is described and briefly illustrated with recent examples from the ToxCast programme.
At the Centennial of Michaelis and Menten, Competing Michaelis–Menten Steps Explain Effect of GLP‐1 on Blood–Brain Transfer and Metabolism of Glucose
Authors: Gejl Michael , Rungby Jørgen , Brock Birgitte , Gjedde Albert 
Published: March 2014

AbstractGlucagon‐like peptide‐1 (GLP‐1) is a potent insulinotropic incretin hormone with both pancreatic and extrapancreatic effects. Studies of GLP‐1 reveal significant effects in regions of brain tissue that regulate appetite and satiety. GLP‐1 mimetics are used for the treatment of type 2 diabetes mellitus. GLP‐1 interacts with peripheral functions in which the autonomic nervous system plays an important role, and emerging pre‐clinical findings indicate a potential neuroprotective role of the peptide, for example in models of stroke and in neurodegenerative disorders. A century ago, Leonor Michaelis and Maud Menten described the steady‐state enzyme kinetics that still apply to the multiple receptors, transporters and enzymes that define the biochemical reactions of the brain, including the glucose‐dependent impact of GLP‐1 on blood–brain glucose transfer and metabolism. This MiniReview examines the potential of GLP‐1 as a molecule of interest for the understanding of brain energy metabolism and with reference to the impact on brain metabolism related to appetite and satiety regulation, stroke and neurodegenerative disorders. These effects can be understood only by reference to the original formulation of the Michaelis–Menten equation as applied to a chain of kinetically controlled steps. Indeed, the effects of GLP‐1 receptor activation on blood–brain glucose transfer and brain metabolism of glucose depend on the glucose concentration and relative affinities of the steps both in vitro and in vivo, as in the pancreas.
Age disparities in survival from lymphoma and myeloma: a comparison between US and England
Authors: Pulte Dianne , Redaniel Maria T. , Lowry Lisa , Bird Jenny , Jeffreys Mona 
Published: March 2014

SummaryPopulation‐level survival in older patients with lymphoma is significantly lower than in younger patients. In this study, data were obtained from cancer registries in England and the United States (US) for patients diagnosed with Hodgkin lymphoma (HL), non‐Hodgkin lymphoma (NHL) and myeloma. Five‐year relative survival was calculated using period analysis. Generalised linear models were used to determine excess hazard ratios (EHR) for older compared to younger patients. Five‐year relative survival was lower for older patients diagnosed with HL, NHL and myeloma in both countries. The greatest age‐related survival inequality was observed for patients with HL: in 2006–10 the EHR comparing patients aged 75 + years with those aged 15–24 years was 14·02 in the US and 15·69 in England. For NHL, the EHR was 1·91 in the US and 3·81 in England. For myeloma, comparing patients aged 75 + years with those aged 25–44 years, the EHR was 2·79 in the US and 3·60 in England. Survival of patients with lymphoma is lower for older patients in both the US and England but the discrepancy is less in the US. Physicians should be encouraged to evaluate patients' frailty and co‐morbidities as well as their age when considering treatment options for patients with lymphoma and myeloma.