bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computer-assisted curation of a human regulatory core network from the biological literature
Authors: Thomas Philippe , Durek Pawel , Solt Illés , Klinger Bertram , Witzel Franziska , Schulthess Pascal , Mayer Yvonne , Tikk Domonkos , Blüthgen Nils , Leser Ulf 
Published: November 2014

Abstract
Motivation: A highly interlinked network of transcription factors (TFs) orchestrates the context-dependent expression of human genes. ChIP-chip experiments that interrogate the binding of particular TFs to genomic regions are used to reconstruct gene regulatory networks at genome-scale, but are plagued by high false-positive rates. Meanwhile, a large body of knowledge on high-quality regulatory interactions remains largely unexplored, as it is available only in natural language descriptions scattered over millions of scientific publications. Such data are hard to extract and regulatory data currently contain together only 503 regulatory relations between human TFs.
Results: We developed a text-mining-assisted workflow to systematically extract knowledge about regulatory interactions between human TFs from the biological literature. We applied this workflow to the entire Medline, which helped us to identify more than 45 000 sentences potentially describing such relationships. We ranked these sentences by a machine-learning approach. The top-2500 sentences contained ∼900 sentences that encompass relations already known in databases. By manually curating the remaining 1625 top-ranking sentences, we obtained more than 300 validated regulatory relationships that were not present in a regulatory database before. Full-text curation allowed us to obtain detailed information on the strength of experimental evidences supporting a relationship.
Conclusions: We were able to increase curated information about the human core transcriptional network by &gt;60% compared with the current content of regulatory databases. We observed improved performance when using the network for disease gene prioritization compared with the state-of-the-art.
Availability and implementation: Web-service is freely accessible at http://fastforward.sys-bio.net/.
Contact: leser@informatik.hu-berlin.de or nils.bluethgen@charite.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Lipid-Pro: a computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms
Authors: Ahmed Zeeshan , Mayr Michel , Zeeshan Saman , Dandekar Thomas , Mueller Martin J. , Fekete Agnes 
Published: November 2014

Abstract
Summary: A major challenge for mass spectrometric-based lipidomics, aiming at describing all lipid species in a biological sample, lies in the computational and bioinformatic processing of the large amount of data that arises after data acquisition. Lipid-Pro is a software tool that supports the identification of lipids by interpreting large datasets generated by liquid chromatography—tandem mass spectrometry (LC–MS/MS) using the advanced data-independent acquisition mode MSE. In the MSE mode, the instrument fragments all molecular ions generated from a sample and records time-resolved molecular ion data as well as fragment ion data for every detectable molecular ion. Lipid-Pro matches the retention time-aligned mass-to-charge ratio data of molecular- and fragment ions with a lipid database and generates a report on all identified lipid species. For generation of the lipid database, Lipid-Pro provides a module for construction of lipid species and their fragments using a flexible building block approach. Hence, Lipid-Pro is an easy to use analysis tool to interpret complex MSE lipidomics data and also offers a module to generate a user-specific lipid database.
Availability and implementation: Lipid-Pro is freely available at: http://www.neurogenetics.biozentrum.uni-wuerzburg.de/en/project/services/lipidpro/
Contact: zeeshan.ahmed@uni-wuerzburg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Exploiting hidden information interleaved in the redundancy of the genetic code without prior knowledge
Authors: Zur Hadas , Tuller Tamir 
Published: November 2014

Abstract
Motivation: Dozens of studies in recent years have demonstrated that codon usage encodes various aspects related to all stages of gene expression regulation. When relevant high-quality large-scale gene expression data are available, it is possible to statistically infer and model these signals, enabling analysing and engineering gene expression. However, when these data are not available, it is impossible to infer and validate such models.
Results: In this current study, we suggest Chimera—an unsupervised computationally efficient approach for exploiting hidden high-dimensional information related to the way gene expression is encoded in the open reading frame (ORF), based solely on the genome of the analysed organism. One version of the approach, named Chimera Average Repetitive Substring (ChimeraARS), estimates the adaptability of an ORF to the intracellular gene expression machinery of a genome (host), by computing its tendency to include long substrings that appear in its coding sequences; the second version, named ChimeraMap, engineers the codons of a protein such that it will include long substrings of codons that appear in the host coding sequences, improving its adaptation to a new host’s gene expression machinery. We demonstrate the applicability of the new approach for analysing and engineering heterologous genes and for analysing endogenous genes. Specifically, focusing on Escherichia coli, we show that it can exploit information that cannot be detected by conventional approaches (e.g. the CAI—Codon Adaptation Index), which only consider single codon distributions; for example, we report correlations of up to 0.67 for the ChimeraARS measure with heterologous gene expression, when the CAI yielded no correlation.
Availability and implementation: For non-commercial purposes, the code of the Chimera approach can be downloaded from http://www.cs.tau.ac.il/∼tamirtul/Chimera/download.htm.
Contact: tamirtul@post.tau.ac.il
Supplementary information: Supplementary data are available at Bioinformatics online.
Radiation fields of intermediate-age stellar populations with binaries as ionizing sources of H ii regions
Authors: Zhang F. , Li L. , Cheng L. , Wang L. , Kang X. , Zhuang Y. , Han Z. 
Published: November 2014

Abstract
Radiation fields emitted by O- and B-type stars or young stellar populations (SPs) are generally considered as significant central ionizing sources (CISs) of classic H ii regions. In our previous studies, we showed that the inclusion of binary interactions in stellar population synthesis models can significantly increase the ultraviolet spectrum hardness and the number of ionizing photons of intermediate-age (IA) SPs (7 ≲ log(t/yr) ≲ 8). In this work, we present photoionization models of H ii regions ionized by radiation fields emitted by IA SPs, including binary systems, and show that these fields are in theory possible candidates for significant CISs of classic H ii regions. When radiation fields of IA SPs comprising binary systems are used as the CISs of classic H ii regions, the theoretical strengths of a number of lines (such as [O iii] λ4959′, [S ii] λ6716′, etc.), which are weaker than observations, are increased; the border or selection-criterion lines between star-forming galaxies and active galactic nuclei (AGNs) in the diagnostic diagrams (for example, [N ii] λ6583/Hα versus [O iii] λ5007/Hβ), move into the region occupied originally by AGNs; and the He ii λ1640 line, observed in Lyman break and high-redshift gravitationally lensed galaxies, also can be produced.
Rotation measure synthesis revisited
Authors: Schnitzeler D. H. F. M. , Lee K. J. 
Published: November 2014

Abstract
We reformulate rotation measure (RM) synthesis for data sets with discrete frequency channels and an arbitrary channel response function. The most commonly used version of the formalism by Brentjens & De Bruyn assumes a top-hat response function in wavelength squared, while real data sets can often be approximated better with a top-hat in frequency. We simulate mock data sets for various source geometries, using a top-hat response function in frequency, and we compare the quality of the RM spectra that are found with both formalisms. We include the response function of the simulated data to calculate exact RM spectra using our formalism. We show that the formalism by Brentjens & De Bruyn produces accurate results even if depolarization at the lowest frequencies in the observing band is severe. If RMs are large, our formalism reconstructs the emitted signal more accurately, with a higher amplitude and (in most cases) a narrower RM spread function. Our formalism can also detect sources with larger (absolute) RMs for a given sensitivity level of the observations.
An Integrated Modelling Framework for the Forest-based Bioeconomy
Authors: Mubareka Sarah , Jonsson Ragnar , Rinaldi Francesca , Fiorese Giulia , San-Miguel-Ayanz Jesús , Sallnäs Ola , Baranzelli Claudia , Pilli Roberto , Lavalle Carlo , Kitous Alban 
Published: November 2014

AbstractThis paper describes the conceptual design of a regional modelling framework to assess scenarios for the forest-based bioeconomy. The framework consists of a core set of tools: a partial equilibrium model for the forest sector, a forestry dynamics model for forest growth and harvest and a wood resources balance sheet. The framework can be expanded to include an energy model, a land use model and a forest owner decision model. This partially integrated, multi-disciplinary modelling framework is described, with particular emphasis on the structure of the variables to be exchanged between the framework tools. The data exchange is subject to a series of integrity checks to ensure that the model is computing the correct information in the correct format and order of elements.
Comparative performances of the new chronic kidney disease epidemiology equations incorporating cystatin C for use in cancer patients
Authors: Chew‐Harris Janice SC , Florkowski Christopher M , George Peter M , Endre Zoltan H 
Published: December 2014

AbstractAimIn cancer patients receiving chemotherapy treatment, accurate assessment of kidney function is required. The aim of our study was to investigate whether the inclusion of cystatin C together with creatinine in prediction equations would improve the prediction of glomerular filtration rate (GFR).MethodsPlasma creatinine and cystatin C were analyzed in 155 patients (cancer, n = 80, kidney donors, n = 75) undergoing 99mTechnetium diethylenepentaacetic (Tc‐DTPA) GFR clearance. Equations by the CKD‐EPI (chronic kidney disease epidemiology) group (creatinine‐, creatinine + cystatin C‐, cystatin C‐based, respectively) and Cockcroft–Gault were compared with Tc‐DTPA GFR by difference plots, receiver operator characteristics curve analysis, root mean square error, chi‐squared analysis and percentage concordance according to carboplatin dosage. Comparisons between two creatinine methodologies (enzymatic vs Jaffe) were also performed.ResultsIn the overall group, the combination creatinine and cystatin C equation had 69% of results within 20% of GFR (P20), a sensitivity of 86.3% and a specificity of 73.1% to detect reduced GFR at <90 mL/min/1.73 m2, and a concordance of 78%. In contrast, the traditional Cockcroft–Gault equation had a P20 of 38.0%, with a large underestimation to predict GFR, thereby accounting for approximately 45% of dosing discordance. No obvious differences were obtained when comparing the performance of equations using the two creatinine methodologies.ConclusionThe inclusion of cystatin C in the CKD‐EPI equations improved the prediction of kidney function in the overall population, although probably not sufficiently for it to be favored over radioisotopic GFR for guiding chemotherapy. More research is warranted to further improve estimated GFR equations for these purposes.
Identification and examination of a novel 9‐bp insert/deletion polymorphism on porcine SFTPA1 exon 2 associated with acute lung injury using an oleic acid‐acute lung injury model
Authors: Zhang Yuebo , Zhang Longchao , Wang Ligang , Qiao Lijuan , Liang Jing , Yan Hua , Zhao Kebin , Liu Xin , Wang Lixian 
Published: November 2014

AbstractThe pulmonary surfactant‐associated protein (SFTPA1, SP‐A) gene has been studied as a candidate gene for lung disease resistance in humans and livestock. The objective of the present study was to identify polymorphisms of the porcine SFTPA1 gene coding region and its association with acute lung injury (ALI). Through DNA sequencing and the PCR‐single‐strand conformation polymorphism method, a novel 9‐bp nucleotide insertion (+) or deletion (‐) was detected on exon 2 of SFTPA1, which causes a change in three amino acids, namely, alanine (Ala), glycine (Gly) and proline (Pro). Individuals of three genotypes (−/−, +/− and +/+) were divided into equal groups from 60 Rongchang pigs that were genotyped. These pigs were selected for participation in the oleic acid (OA)‐ALI model by 1‐h and 3‐h injections of OA, and there were equal numbers of pigs in the control and injection groups. The lung water content, a marker for acute lung injury, was measured in this study; there is a significant correlation between high lung water content and the presence of the 9‐bp indel polymorphism (P < 0.01). The lung water content of the OA injection group was markedly higher than that of the control group and lung water content for the +/+ genotype was significantly higher than that of the others in the 1‐h group (P < 0.01). No differences in the expression of the SFTPA1 gene were found among individuals with different SFTPA1 genotypes, indicating that the trait is not caused by a linked polymorphism causing altered expression of the gene. The individuals with the −/− genotype showed lower lung water content than the +/+ genotype pigs, which suggests that polymorphism could be a potential marker for lung disease‐resistant pig breeding and that pig can be a potential animal model for human lung disease resistance in future studies.
Burnout prevalence and correlates amongst Colombian dental students: the STRESSCODE study
Authors: Mafla A. C. , Villa‐Torres L. , Polychronopoulou A. , Polanco H. , Moreno‐Juvinao V. , Parra‐Galvis D. , Durán C. , Villalobos M. J. , Divaris K. 
Published: December 2014

AbstractIntroductionAccumulating evidence amongst dental students indicates an alarming prevalence of stress, which can precipitate the development of burnout – a state of mental or physical exhaustion and disengagement. Understanding individual and educational correlates of burnout is necessary for its prevention. The aims of this study were to determine the prevalence of burnout amongst a large sample of Colombian dental undergraduates and investigate its psychosocial and educational correlates.Materials and methodsSurvey data collected from 5647 students participating in the Stress in Colombian Dental Education study were used for this analysis. Burnout was measured using the Maslach Burnout Inventory–Student Survey (MBI‐SS). Covariates included participants’ socio‐demographic characteristics and perceived stress, as well as educational environment factors. Descriptive, bivariate and multivariate methods based on multilevel mixed‐effects logistic regression modelling were used for data analysis.ResultsSeven per cent of the students surveyed met the criteria for burnout. The prevalence of burnout was higher amongst upper classes, older and married students, those who reported not having passed all required courses and not having dentistry as their first career choice, as well as students in public institutions and those with large class sizes. Moreover, students’ perceived stress in the domains of workload and self‐efficacy was significantly and positively associated with burnout.ConclusionsBoth personal and educational environment characteristics were found to be associated with burnout. Irrespective of these factors, students’ perceived stress with regard to workload and self‐efficacy was a strong influence on burnout and its alleviation may be a promising avenue to prevent psychological morbidity.
Combination of CD160 and CD200 as a useful tool for differential diagnosis between chronic lymphocytic leukemia and other mature B‐cell neoplasms
Authors: Lesesve J.‐F. , Tardy S. , Frotscher B. , Latger‐Cannard V. , Feugier P. , De Carvalho Bittencourt M. 
Published: December 2014

SummaryIntroductionChronic lymphocytic leukemia is usually diagnosed through the characteristic morphology/immunophenotype of the lymphocytes, but some CLL cases remain atypical resulting in diagnostic uncertainty.MethodsUsing flow cytometry analysis, we investigated the expression of CDs160/200 on B cells from 124 patients (82 CLL, 42 other B‐cell neoplasms) and nine controls. CDs160/200 measurements were determined as a ratio of the mean fluorescence intensities of leukemic cells/controls and were considered positive when the ratios were ≥2 and 20, respectively.ResultsSixty and 83% CLL expressed CDs160/200 as compared to 5% and 10% of other B‐cell neoplasms, respectively. None of the controls showed CDs160/200 expressions. Combination of both markers was observed in 55% of CLL but only in 2% of other B‐cell neoplasms, and absence of both markers occurred in 12% of CLL but in 86% of other B‐cell neoplasms.ConclusionCDs160/200 were associated with markers of the gold standard ‘Matutes score’ and could be useful markers to differentiate atypical CLL from other B‐cell neoplasms in the absence of available biopsies or cytogenetics and molecular studies.
Development of a clinical score system for the diagnosis of photoallergic contact dermatitis using a consensus process: item selection and reliability
Authors: Cazzaniga S. , Lecchi S. , Bruze M. , Chosidow O. , Diepgen T. , Gonçalo M. , Hercogova J. , Pigatto P.D. , Naldi L. 
Published: December 2014

AbstractBackgroundPhotoallergic contact dermatitis (PACD) is an uncommon condition, and there is a lack of validated criteria for its diagnosis.ObjectiveTo identify a set of relevant criteria to be considered when suspecting a diagnosis of PACD and to assess the reproducibility of these criteria.MethodsThis was a diagnostic item selection and reliability study performed between July 2012 and October 2012. A panel of seven recognized experts was invited to consecutive rounds of a Delphi survey and to a conclusive face‐to‐face meeting with the aim of obtaining an agreement on criteria for the diagnosis of PACD. The panel was also provided with a series of 16 reports of suspected PACDs to be classified according to a five‐point likelihood scale. Identified criteria with the weights attributed by experts were used to develop a score system for the diagnosis of PACD. Consensus was measured by calculating the Intraclass Correlation Coefficient (ICC). The performance of the score system was evaluated in terms of overall classification accuracy.ResultsSeven criteria were identified by experts as relevant for the diagnosis of PACD. The criteria were related to the type of skin lesions, accompanying symptoms, skin area involved, general medical history, modality of exposure to the culprit substance, history of exposure to the sun or other light sources and photopatch test results. Experts reached a moderate agreement on PACD cases classification, with ICC = 0.69 (95% Confidence Interval, CI, 0.50–0.86). The score system enabled discrimination of probable and definite PACD cases from possible and unlikely or excluded ones, with a nearly perfect agreement being observed between the score system classification and judgment by experts.ConclusionA diagnostic score was proposed. The score should receive a comprehensive validation on a larger series of cases and with multiple evaluators.
Parents' experiences of healthcare provider actions when their child dies: An integrative review of the literature
Authors: Butler Ashleigh , Hall Helen , Willetts Georgina , Copnell Beverley 
Published: November 2014

AbstractPurposeTo review, critique and synthesise current research studies that examine parental perceptions of healthcare provider actions during and after the death of a child.ConclusionsFive main themes were synthesised from the literature: staff attitudes and affect; follow‐up care and ongoing contact; communication; attending to the parents; and continuity of care.Practice ImplicationsThis review helps to identify important aspects of paediatric end‐of‐life care as recognised by parents, with the intention of placing the family at the centre of any future end‐of‐life care education or policy/protocol development.
Sylvia's Similes: A Stylistic Approach to Sylvia Townsend Warner
Authors: Swaab Peter 
Published: December 2014

AbstractThis essay notes the prevalence and analyses the excellence of similes in the writing of Sylvia Townsend Warner. Discussing instances from different genres and periods of her work, it argues that the author's imagination, humour and critical intelligence are especially evident in her similes. It goes on to illustrate how and to what ends these similes are often drawn from the natural world, and how they express a range of attitudes to sexuality and homosexuality. The essay proposes that Warner's similes are characteristically what grammarians term ‘catachretic’ and not ‘illustrative’, and that they often function to complicate the stories and disconcert or shock the reader. It suggests that Warner's might be thought a queer practice of simile. The essay concludes that the propositional force of similes, asserting relations of likeness, gives us a window onto the views and perspectives of Warner's narrators.
Is renal hyperfiltration protective in chronic kidney disease‐stage 1 pregnancies? A step forward unravelling the mystery of the effect of stage 1 chronic kidney disease on pregnancy outcomes
Authors: Piccoli Giorgina Barbara , Attini Rossella , Vigotti Federica Neve , Parisi Silvia , Fassio Federica , Pagano Arianna , Biolcati Marilisa , Giuffrida Domenica , Rolfo Alessandro , Todros Tullia 
Published: December 2014

AbstractBackgroundThe correlation between advanced or proteinuric chronic kidney disease (CKD) and adverse pregnancy outcomes is intuitive, although how early CKD affects pregnancy remains unknown. Glomerular hyperfiltration is a physiological response to pregnancy, correlated with outcomes in hypertension or collagen diseases. The aim of the study was to correlate first trimester hyperfiltration with pregnancy outcomes in stage 1 CKD patients.MethodsA historical prospective study was conducted on the database of our Unit, gathering all pregnant CKD patients referred since 1 January 2000. From 383 pregnancies referred in 2000–2013, 75 patients were selected (stage 1 CKD, referred within the 14th gestational week, singleton deliveries, absence of diabetes, hypertension or nephrotic proteinuria at referral, body mass index [BMI] < 30); 267 ‘low‐risk’ pregnancies, followed in the same setting, served as controls. Glomerular filtration rate (GFR) was assessed by Chronic Kidney Disease Epidemiology Collaboration (CKD‐EPI) and dichotomized at 120 mL/min. The odds for Caesarean section, prematurity, need for Neonatal Intensive Care Unit (NICU) were assessed by univariate analysis and logistic regression.ResultsRisk for adverse pregnancy outcomes was not affected by hyperfiltration (univariate OR GFR ≥ 120 mL/min: Caesarean section 1.30 (0.46–3.65); preterm delivery: 0.84 (0.25–2.80)). In contrast, even in these cases with normal kidney function, stage 1 CKD was associated with prematurity (17.3% vs 4.9% P = 0.001), lower birth weight (3027 ± 586 versus 3268 ± 500 P < 0.001) need for NICU (12% vs 1.1% P < 0.001). In the multivariate analysis, the risks were significantly increased by proteinuria and maternal age but not by GFR.ConclusionsIn pregnant Stage 1 CKD patients, hyperfiltration was not associated with maternal‐foetal outcomes, thus suggesting a need to focus attention on qualitative factors, eventually enhanced by age, as vascular stiffness, endothelial damage or oxidative stress.