bluuebunny/crossref_metadata_2025_split huggingface dataset:
Community curation of bioinformatics software and data resources
Authors: Ison Jon , Ménager Hervé , Brancotte Bryan , Jaaniso Erik , Salumets Ahto , Raček Tomáš , Lamprecht Anna-Lena , Palmblad Magnus , Kalaš Matúš , Chmura Piotr , Hancock John M , Schwämmle Veit , Ienasescu Hans-Ioan 
Published: June 2019

Abstract
The corpus of bioinformatics resources is huge and expanding rapidly, presenting life scientists with a growing challenge in selecting tools that fit the desired purpose. To address this, the European Infrastructure for Biological Information is supporting a systematic approach towards a comprehensive registry of tools and databases for all domains of bioinformatics, provided under a single portal (https://bio.tools). We describe here the practical means by which scientific communities, including individual developers and projects, through major service providers and research infrastructures, can describe their own bioinformatics resources and share these via bio.tools.
RAISS: robust and accurate imputation from summary statistics
Authors: Julienne Hanna , Shi Huwenbo , Pasaniuc Bogdan , Aschard Hugues 
Published: June 2019

Abstract

Motivation
Multi-trait analyses using public summary statistics from genome-wide association studies (GWASs) are becoming increasingly popular. A constraint of multi-trait methods is that they require complete summary data for all traits. Although methods for the imputation of summary statistics exist, they lack precision for genetic variants with small effect size. This is benign for univariate analyses where only variants with large effect size are selected a posteriori. However, it can lead to strong p-value inflation in multi-trait testing. Here we present a new approach that improve the existing imputation methods and reach a precision suitable for multi-trait analyses.

Results
We fine-tuned parameters to obtain a very high accuracy imputation from summary statistics. We demonstrate this accuracy for variants of all effect sizes on real data of 28 GWAS. We implemented the resulting methodology in a python package specially designed to efficiently impute multiple GWAS in parallel.

Availability and implementation
The python package is available at: https://gitlab.pasteur.fr/statistical-genetics/raiss, its accompanying documentation is accessible here http://statistical-genetics.pages.pasteur.fr/raiss/.

Supplementary information
Supplementary data are available at Bioinformatics online.
RAbHIT: R Antibody Haplotype Inference Tool
Authors: Peres Ayelet , Gidoni Moriah , Polak Pazit , Yaari Gur 
Published: June 2019

Abstract

Summary
Antibody haplotype inference (chromosomal phasing) may have clinical implications for the identification of genetic predispositions to diseases. Yet, our knowledge of the genomic loci encoding for the variable regions of the antibody is only partial, mostly due to the challenge of aligning short reads from genome sequencing to these highly repetitive loci. A powerful approach to infer the content of these loci relies on analyzing repertoires of rearranged V(D)J sequences. We present here RAbHIT, an R Haplotype Antibody Inference Tool, that implements a novel algorithm to infer V(D)J haplotypes by adapting a Bayesian framework. RAbHIT offers inference of haplotype and gene deletions. It may be applied to sequences from naïve and non-naïve B-cells, sequenced by different library preparation protocols.

Availability and implementation
RAbHIT is freely available for academic use from comprehensive R archive network (CRAN) (https://cran.r-project.org/web/packages/rabhit/) under CC BY-SA 4.0 license.

Supplementary information
Supplementary data are available at Bioinformatics online.
Findings From a Longitudinal Qualitative Study of Child Protection Social Workers’ Retention: Job Embeddedness, Professional Confidence and Staying Narratives
Authors: Burns Kenneth , Christie Alastair , O’Sullivan Siobhan 
Published: June 2019

Abstract
The retention of social workers in child protection and welfare is an ongoing concern in many countries. While our knowledge based on the turnover of child protection and welfare social workers is growing, much less is known about ‘stayers’—those who undertake this work for over 10+ years. This article draws on the data gathered over a decade in Ireland on these social workers. The article addresses three questions: (i) What can we learn from social workers with 10+ years’ experience of child protection and welfare about their retention? (ii) Does job embeddedness theory help explain their choices to stay? (iii) Does the ‘career preference typology’ (Burns, 2011. British Journal of Social Work, 41(3), pp. 520–38) helps to explain social workers’ retention? The main findings are that if you can retain social workers beyond the 5-year point, their retention narrative intensifies, their embeddedness in the organisation and community strengthens and they have a stronger sense of professional confidence as they move out of the early professional stage. A surprising finding of this study was that nearly all of the social workers in this study had a staying narrative that changed little between their interviews a decade apart.
DNA barcodes fail to accurately differentiate species in Hawaiian plant lineages
Authors: Stallman Jeffery K , Funk Vicki A , Price Jonathan P , Knope Matthew L 
Published: June 2019

AbstractDNA barcoding has been largely successful in differentiating animal species, but the most effective loci and evaluative methods for plants are still debated. Floras of young, oceanic islands are a challenging test of DNA barcodes, because of rapid speciation, high incidence of hybridization and polyploidy. We used character-based, tree-based and genetic distance-based methods to test DNA barcoding of 385 species of native Hawaiian plants constituting 20 lineages at the nuclear ITS(2) locus, nine lineages at each of the plastid loci trnH-psbA and rbcL, eight lineages at the plastid locus matK and four lineages with concatenated data. We also incorporated geographical range information and tested if varying sample sizes within a lineage influenced identification success. Average discrimination success was low (22% maximum) with all methods of analysis across all loci. The character-based method generally provided the highest identification success, there were limited benefits from incorporating geographical data and no relationship between number of species sampled in a lineage and identification success was found. Percentages of identification success are the lowest reported in a DNA barcoding study of comparable scale, and multi-species groups that radiated in the Hawaiian archipelago probably cannot be identified based on current DNA barcoding loci and methodologies.
The nutritional environment determines which and how intestinal stem cells contribute to homeostasis and tumorigenesis
Authors: Li Wenge , Zimmerman Samuel E , Peregrina Karina , Houston Michele , Mayoral Joshua , Zhang Jinghang , Maqbool Shahina , Zhang Zhengdong , Cai Ying , Ye Kenny , Augenlicht Leonard H 
Published: June 2019

Abstract
Sporadic colon cancer accounts for approximately 80% of colorectal cancer (CRC) with high incidence in Western societies strongly linked to long-term dietary patterns. A unique mouse model for sporadic CRC results from feeding a purified rodent Western-style diet (NWD1) recapitulating intake for the mouse of common nutrient risk factors each at its level consumed in higher risk Western populations. This causes sporadic large and small intestinal tumors in wild-type mice at an incidence and frequency similar to that in humans. NWD1 perturbs intestinal cell maturation and Wnt signaling throughout villi and colonic crypts and decreases mouse Lgr5hi intestinal stem cell contribution to homeostasis and tumor development. Here we establish that NWD1 transcriptionally reprograms Lgr5hi cells, and that nutrients are interactive in reprogramming. Furthermore, the DNA mismatch repair pathway is elevated in Lgr5hi cells by lower vitamin D3 and/or calcium in NWD1, paralleled by reduced accumulation of relevant somatic mutations detected by single-cell exome sequencing. In compensation, NWD1 also reprograms Bmi1+ cells to function and persist as stem-like cells in mucosal homeostasis and tumor development. The data establish the key role of the nutrient environment in defining the contribution of two different stem cell populations to both mucosal homeostasis and tumorigenesis. This raises important questions regarding impact of variable human diets on which and how stem cell populations function in the human mucosa and give rise to tumors. Moreover, major differences reported in turnover of human and mouse crypt base stem cells may be linked to their very different nutrient exposures.
Too big to manage: US megabanks’ competition by innovation and the microfoundations of financialization
Authors: Cerpa Vielma Nicole , Cömert Hasan , D’Avino Carmela , Dymski Gary , Kaltenbrunner Annina , Petratou Eirini , Shabani Mimoza 
Published: June 2019

Abstract
Disagreements over the systemic implications—the future—of financialization can be traced in part to the absence of sustained attention to the role of banking firms in driving this secular shift forward. That is, the financialization literature lacks an adequate microfoundation. Accounting for the drivers of financialization processes solely at the macro level overlooks the problems of how these processes came about and whether they are sustainable. This paper addresses this explanatory gap, arguing that a key independent microeconomic driver of increasing financialization did exist: the incessant efforts by money-centre banks in the USA to break out of Depression-era restrictions on their size, activities, and markets. These banks’ growth strategies in turbulent times led to an institutional (meso) shift—the rise of a megabank-centred shadow banking system—that now shapes global financial architecture even while operating in ways that are unsustainable. In short, too-big-to-manage megabanks are at the heart of the fragility and instability of the economy today.
Imaging for screening cardiovascular involvement in patients with systemic rheumatologic diseases: more questions than answers
Authors: Sade Leyla Elif , Akdogan Ali 
Published: June 2019

Abstract
Cardiovascular involvement due to systemic rheumatologic diseases (SRDs) remains largely underdiagnosed despite causing excess mortality and limiting the favourable effect of therapeutic developments on survival. Traditional risk scoring systems are poorly calibrated for SRD patients. There is an unmet need to develop a cardiovascular (CV) risk stratification tool and screening algorithm for CV involvement dedicated to asymptomatic patients with SRDs. Even though accelerated atherosclerosis is the most prominent cause of major CV events, a more comprehensive approach is crucial to detect different pathological processes associated with SRDs that are leading to CV complications. In that regard, incorporation of imaging parameters obtained from echocardiography and carotid ultrasound (CUS) might help to improve risk models, to detect and monitor subclinical CV involvement. These two imaging modalities should be an integral part of screening SRD patients with suspicion of CV involvement on top of electrocardiogram (ECG). Cardiac magnetic resonance and multi-slice computerized tomography angiography and nuclear imaging modalities seem very important to complement echocardiography and CUS for further evaluation. However, to answer the question ‘Should asymptomatic patients with SRDs undergo screening with echocardiography and CUS on top of ECG?’ necessitates large studies performing cardiac screening with a standard approach by using these imaging methods to obtain longitudinal data with hard CV outcomes.
Vocal cord paralysis after cardiovascular surgery in children: incidence, risk factors and diagnostic options
Authors: García-Torres Enrique , Antón-Pacheco Juan L , Luna-Paredes Mª Carmen , Morante-Valverde Rocío , Ezquerra-Pozo Elena , Ferrer-Martínez Alicia , Villafruela Miguel A , Jiménez-Huerta Ignacio , López-Díaz María , Carrillo-Arroyo Isabel , Boni Lorenzo 
Published: June 2019

Abstract

OBJECTIVES
The aim of this study was to assess the incidence of vocal cord paralysis (VCP) in children after cardiovascular surgery. The secondary aims were to identify the factors potentially associated with VCP and to assess the diagnostic utility of laryngeal ultrasound (US).

METHODS
This study is a retrospective review of patients who underwent aortic repair, patent ductus arteriosus ligation and left pulmonary artery surgeries from 2007 to 2017. The following data were collected: patient demographics, gestational age, weight and age at surgery, comorbidities, cardiovascular anomaly and type of procedure, laryngoscopic and US evaluation results. Univariable and multivariable logistic regression models were used to identify the variables associated with VCP.

RESULTS
Two hundred and six patients were included in the study. Seventy-two patients (35%) were preterm and 32.5% showed comorbidities. At surgery, median age and weight were 0.6 months [interquartile range (IQR) 0.3–2.1] and 3.0 kg (IQR 1.3–4.0), respectively. Postoperatively, symptomatic patients underwent endoscopic evaluation and VCP was detected in 25 cases (12.1%). Laryngeal US was performed in 8 of these showing an excellent diagnostic relationship. On univariable analysis, factors significantly associated with VCP were prematurity, young age and lower weight at surgery and the presence of comorbidities. The presence of comorbidities and weight at surgery exhibited a significant risk of developing VCP postoperatively on multivariable analysis.

CONCLUSIONS
VCP is not an unusual complication of cardiovascular surgery. Certain factors were associated with VCP development but only the presence of comorbidities and weight at surgery were statistically significant on multivariable analysis. Flexible laryngoscopy is the standard diagnostic technique and laryngeal US appears to be a reliable complement.
Predicting cardiac electrical response to sodium-channel blockade and Brugada syndrome using polygenic risk scores
Authors: Tadros Rafik , Tan Hanno L ,   ESCAPE-NET Investigators, el Mathari Sulayman , Kors Jan A , Postema Pieter G , Lahrouchi Najim , Beekman Leander , Radivojkov-Blagojevic Milena , Amin Ahmad S , Meitinger Thomas , Tanck Michael W , Wilde Arthur A , Bezzina Connie R 
Published: June 2019

Abstract

Aims
Sodium-channel blockers (SCBs) are associated with arrhythmia, but variability of cardiac electrical response remains unexplained. We sought to identify predictors of ajmaline-induced PR and QRS changes and Type I Brugada syndrome (BrS) electrocardiogram (ECG).

Methods and results
In 1368 patients that underwent ajmaline infusion for suspected BrS, we performed measurements of 26 721 ECGs, dose–response mixed modelling and genotyping. We calculated polygenic risk scores (PRS) for PR interval (PRSPR), QRS duration (PRSQRS), and Brugada syndrome (PRSBrS) derived from published genome-wide association studies and used regression analysis to identify predictors of ajmaline dose related PR change (slope) and QRS slope. We derived and validated using bootstrapping a predictive model for ajmaline-induced Type I BrS ECG. Higher PRSPR, baseline PR, and female sex are associated with more pronounced PR slope, while PRSQRS and age are positively associated with QRS slope (P &lt; 0.01 for all). PRSBrS, baseline QRS duration, presence of Type II or III BrS ECG at baseline, and family history of BrS are independently associated with the occurrence of a Type I BrS ECG, with good predictive accuracy (optimism-corrected C-statistic 0.74).

Conclusion
We show for the first time that genetic factors underlie the variability of cardiac electrical response to SCB. PRSBrS, family history, and a baseline ECG can predict the development of a diagnostic drug-induced Type I BrS ECG with clinically relevant accuracy. These findings could lead to the use of PRS in the diagnosis of BrS and, if confirmed in population studies, to identify patients at risk for toxicity when given SCB.
Comparative analysis of gut bacterial communities in housefly larvae fed different diets using a high-throughput sequencing approach
Authors: Xue Zhijing , Zhang Junli , Zhang Ruiling , Huang Zhendong , Wan Qing , Zhang Zhong 
Published: June 2019

ABSTRACT
Housefly larvae are a synanthropic host for various bacteria, including pathogens and commensals and an important protein source for monogastric animal feed. Many factors, such as diets, life stages, host habitats can influence microbial community structure. In this study, the diversity of bacterial communities in the gut of housefly larvae fed on different artificial diets was comprehensively characterized using high-throughput sequencing with the aim shedding light on an optimal larval diet. The results showed that the dominant bacteria belonging to Proteobacteria, Firmicutes and Bacteroidetes phyla were related to polysaccharide degradation. The comparative analysis indicated that the dominant intestinal bacteria of larvae fed on high-protein were similar to those on high-fat diet. The same was the case in larvae fed high-starch diet and wheat bran alone. In addition, the diversity of intestinal bacteria at genus level in larvae fed high-protein and high-fat diet was higher than in larvae fed the other two diets. Further analysis indicated that the increase of potential commensals and decrease of pathogens in larvae fed on high-fat diet contributed to the increase of housefly larvae immunity. It established a foundation for further research on improvement of nutrition of housefly larvae used for poultry and fish feed.
Estimating lateral and vertical resolution in receiver function data for shallow crust exploration
Authors: Subašić Senad , Piana Agostinetti Nicola , Bean Christopher J 
Published: June 2019

SUMMARYIn order to test the horizontal and vertical resolution of teleseismic receiver functions, we perform a complete receiver function analysis and inversion using data from the La Barge array. The La Barge Passive Seismic Experiment was a seismic deployment in western Wyoming, recording continuously between November 2008 and June 2009, with 55 instruments deployed 250 m apart—up to two orders of magnitude closer than in typical receiver function studies. We analyse each station separately. We calculate receiver functions and invert them using a Bayesian algorithm. The inversion results are in agreement with measurements from nearby wells, and from other studies using the same data set. The resulting posterior probability distributions (PPDs), obtained for each station, are compared to each other by computing the Bhattacharyya coefficients, which quantify the overlap between two PPDs. Our results indicate that (a) the lateral resolution of 8 Hz receiver functions is approximately equal to the width of their first Fresnel zone, (b) minimum investigable depth is about 400 m at 8 Hz, (c) lateral resolution depends on the local geology as expected and (d) velocity inversion in the shallow-crust can be resolved in the first few kilometres, even in case of dipping interfaces.
The tree-canopy effect in gravity forward modelling
Authors: Yang Meng , Hirt Christian , Rexer Moritz , Pail Roland , Yamazaki Dai 
Published: June 2019

SUMMARY
High resolution and accurate digital terrain models (DTMs) are frequently used as input data sets to define the topographic masses in gravity forward modelling, for example, for terrain corrections in the context of regional gravity modelling. However, over vegetated areas such as forests and scrublands, the radar- and image-based digital elevation models (DEMs) may contain a tree bias, and therefore do not represent the bare-ground surface. The presence of vegetation-induced signals in DEMs, denoted here the tree-canopy effect, will introduce errors in the gravity forward modelling. In this study, the role of the tree-canopy effect in gravity forward modelling calculations is numerically investigated. First, spectral forward modelling techniques were applied to analyse a global tree-canopy bias model with a horizontal resolution of 1 km x 1 km and to quantify its effect on global gravity forward modelling results. We demonstrate that tree-canopy signals in the DEM produce a positive bias in the topographic gravitational field over vegetated areas, with values ranging from 0 to ∼2.7 mGal for gravity disturbances. Second, the role of the tree-canopy effect in high-frequency gravity forward modelling is studied using well-known residual terrain modelling (RTM) techniques. As DEM data sets, we used the 3″ SRTM (Shuttle Radar Topography Mission Digital 9 m Elevation Database) V4.1 (containing vegetation biases) and the 3″ MERIT-DEM (Multi-Error-Removed Improved-Terrain Digital elevation model) as a representation of the bare-ground elevations. Using Tasmania and the Amazon rainforest regions as test areas with significant tree-canopy signals we show that the tree-height effect on RTM calculations is of high-frequency nature, with rather small signals which reach in extreme cases amplitudes of ∼1–2 mGal occurring at forest boundaries. Third, using ground gravity observations, validation experiments were performed over the Australian Alps, Tasmania and the Canadian Rocky Mountains. All validation experiments show that the bare-ground elevation model MERIT-DEM performs better than SRTM V4.1 in terms of reduction of the discrepancies between modelled and observed gravity values. As a general conclusion, bare-ground DEM models should be preferred in any gravity forward modelling application to avoid or reduce the tree-canopy effect.
Judging constitutional conventions
Authors: Ahmed Farrah , Albert Richard , Perry Adam 
Published: June 2019

Abstract
The study of constitutional conventions is anchored in three assumptions that have so far remained largely unchallenged: that there is a shared “Commonwealth approach” to constitutional conventions; that Commonwealth courts will recognize and employ conventions but never enforce them; and that conventions are always distinguishable from rules of law. After setting out a new taxonomy of modes of judicial engagement with constitutional conventions, we overturn each of these assumptions. We draw on recent case law from Canada, India, and the United Kingdom to show that there is no shared “Commonwealth approach” to the treatment of constitutional conventions. We show that some Commonwealth courts do, in fact, enforce conventions. Finally, we show that at least some constitutional conventions have crystallized into law. These insights disrupt much of what is foundational in the study of constitutional conventions.
The Double Complex of a Blow-up
Authors: Stelzig Jonas 
Published: June 2019

Abstract
We compute the double complex of smooth complex-valued differential forms on projective bundles over and blow-ups of compact complex manifolds up to a suitable notion of quasi-isomorphism. This simultaneously yields formulas for “all” cohomologies naturally associated with this complex (in particular, de Rham, Dolbeault, Bott–Chern, and Aeppli).