bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Novel Use of Latent Class Analysis to Identify Patterns of Workplace Hazards among Informally Employed Domestic Workers in 14 Cities, United States, 2011–2012
Authors: Wright Emily , Chen Jarvis T , Beckfield Jason , Theodore Nik , González Paulina López , Krieger Nancy 
Published: April 2022

Abstract

Introduction
Few studies, mostly descriptive, have quantitatively analyzed the working conditions of domestic workers (DWers) informally employed by private households in the USA. These workers are explicitly or effectively excluded from numerous workplace protections, and scant data exist on their exposures or how best to categorize them.

Methods
We analyzed data from the sole nationwide survey of informally employed US DWers with work-related hazards data, conducted by the National Domestic Workers Alliance, the University of Illinois Chicago Center for Urban Economic Development, and the DataCenter in 14 US cities (2011–2012; N = 2086). We used exploratory latent class analysis to identify groups of DWers with distinct patterns of exposure to 21 self-reported economic, social, and occupational workplace hazards (e.g. pay violations, verbal abuse, heavy lifting). We then used multinomial logistic latent class regression to examine associations between workers’ individual, household, and occupational characteristics and latent class membership.

Results
Among the 2086 DWers, mean age was 42.6 years, 97.3% were women, 56.0% Latina/o, 26.5% White, 33.2% undocumented immigrants, and 11.7% live-in. 53.5%, 32.0%, and 14.5% primarily worked doing housecleaning, child care, and adult care, respectively. 49.9% of workers reported ≥3 hazards. Latent class analysis identified four groups of DWers doing: ‘Low hazard domestic work’ (lowest exposure to all hazards), ‘Demanding care work’ (moderate exposure to pay violations [item response probability (IRP) = 0.42] and contagious illness care [IRP = 0.39]), ‘Strenuous cleaning work’ (high exposure to cleaning-related occupational hazards, such as climbing to clean [IRP = 0.87]), and ‘Hazardous domestic work’ (highest exposure to all but one hazard). Covariates were strongly associated, in many cases, with latent class membership. For example, compared to other DWers, DWers doing ‘hazardous domestic work’ had the largest predicted probability of being economically insecure (0.53) and living-in with their employers (0.17).

Conclusions
Results indicate that informally employed US DWers experience distinct patterns of workplace hazards, and that it is informative to characterize DWers’ exposures to different sets of multiple hazards using latent class analysis.
Shoaling in the Trinidadian guppy: costs, benefits, and plasticity in response to an ambush predator
Authors: Li Anna , Richardson Jean M L , Helen Rodd F 
Published: April 2022

AbstractShoaling, the formation of social groupings in fish, can provide benefits including reduced predation risk. However, it can also inflict costs including increased competition for resources, transmission of parasites, and salience to predators. Trinidadian guppies exhibit inter-population variation in shoaling behavior where individuals coexisting with large piscivorous predators (high predation localities) spend most of their time in shoals and those coexisting with an ambush predator, Rivulus hartii (recently, Anablepsoides hartii), that preys primarily on smaller guppies (low predation localities) do not. It has been suggested that this predator selects for reduced shoaling because doing so reduces salience to the predator. Here, as far as we know, we perform the first test of this idea. First, we investigated the effectiveness of shoaling in encounters with this predator. In survival trials, where one rivulus interacted with a group of guppies, we found that the predator was more likely to attack individuals in shoals than singletons. However, we also found that attacks directed at shoals were less likely to succeed. This suggests that the optimal strategy for guppies co-existing with this predator is to reduce shoaling to reduce the probability of being attacked, and to form shoals when an attack is initiated. We then asked if guppies modified their shoaling behavior in response to visual and olfactory cues from this predator during development. We found changes in guppy behavior in response to the treatment: guppies increased shoaling behavior when there was heightened risk of predation.
Once an optimist, always an optimist? Studying cognitive judgment bias in mice
Authors: Bračić Marko , Bohn Lena , Siewert Viktoria , von Kortzfleisch Vanessa T , Schielzeth Holger , Kaiser Sylvia , Sachser Norbert , Richter S Helene 
Published: April 2022

AbstractIndividuals differ in the way they judge ambiguous information: some individuals interpret ambiguous information in a more optimistic, and others in a more pessimistic way. Over the past two decades, such “optimistic” and “pessimistic” cognitive judgment biases (CJBs) have been utilized in animal welfare science as indicators of animals’ emotional states. However, empirical studies on their ecological and evolutionary relevance are still lacking. We, therefore, aimed at transferring the concept of “optimism” and “pessimism” to behavioral ecology and investigated the role of genetic and environmental factors in modulating CJB in mice. In addition, we assessed the temporal stability of individual differences in CJB. We show that the chosen genotypes (C57BL/6J and B6D2F1N) and environments (“scarce” and “complex”) did not have a statistically significant influence on the responses in the CJB test. By contrast, they influenced anxiety-like behavior with C57BL/6J mice and mice from the “complex” environment displaying less anxiety-like behavior than B6D2F1N mice and mice from the “scarce” environment. As the selected genotypes and environments did not explain the existing differences in CJB, future studies might investigate the impact of other genotypes and environmental conditions on CJB, and additionally, elucidate the role of other potential causes like endocrine profiles and epigenetic modifications. Furthermore, we show that individual differences in CJB were repeatable over a period of seven weeks, suggesting that CJB represents a temporally stable trait in laboratory mice. Therefore, we encourage the further study of CJB within an animal personality framework.
Syotti: scalable bait design for DNA enrichment
Authors: Alanko Jarno N , Slizovskiy Ilya B , Lokshtanov Daniel , Gagie Travis , Noyes Noelle R , Boucher Christina 
Published: April 2022

AbstractMotivationBait enrichment is a protocol that is becoming increasingly ubiquitous as it has been shown to successfully amplify regions of interest in metagenomic samples. In this method, a set of synthetic probes (‘baits’) are designed, manufactured and applied to fragmented metagenomic DNA. The probes bind to the fragmented DNA and any unbound DNA is rinsed away, leaving the bound fragments to be amplified for sequencing. Metsky et al. demonstrated that bait-enrichment is capable of detecting a large number of human viral pathogens within metagenomic samples.ResultsWe formalize the problem of designing baits by defining the Minimum Bait Cover problem, show that the problem is NP-hard even under very restrictive assumptions, and design an efficient heuristic that takes advantage of succinct data structures. We refer to our method as Syotti. The running time of Syotti shows linear scaling in practice, running at least an order of magnitude faster than state-of-the-art methods, including the method of Metsky et al. At the same time, our method produces bait sets that are smaller than the ones produced by the competing methods, while also leaving fewer positions uncovered. Lastly, we show that Syotti requires only 25 min to design baits for a dataset comprised of 3 billion nucleotides from 1000 related bacterial substrains, whereas the method of Metsky et al. shows clearly super-linear running time and fails to process even a subset of 17% of the data in 72 h.Availability and implementationhttps://github.com/jnalanko/syotti.Supplementary informationSupplementary data are available at Bioinformatics online.
PolarMorphism enables discovery of shared genetic variants across multiple traits from GWAS summary statistics
Authors: von Berg Joanna , ten Dam Michelle , van der Laan Sander W , de Ridder Jeroen 
Published: April 2022

AbstractMotivationPleiotropic SNPs are associated with multiple traits. Such SNPs can help pinpoint biological processes with an effect on multiple traits or point to a shared etiology between traits. We present PolarMorphism, a new method for the identification of pleiotropic SNPs from genome-wide association studies (GWAS) summary statistics. PolarMorphism can be readily applied to more than two traits or whole trait domains. PolarMorphism makes use of the fact that trait-specific SNP effect sizes can be seen as Cartesian coordinates and can thus be converted to polar coordinates r (distance from the origin) and theta (angle with the Cartesian x-axis, in the case of two traits). r describes the overall effect of a SNP, while theta describes the extent to which a SNP is shared. r and theta are used to determine the significance of SNP sharedness, resulting in a P-value per SNP that can be used for further analysis.ResultsWe apply PolarMorphism to a large collection of publicly available GWAS summary statistics enabling the construction of a pleiotropy network that shows the extent to which traits share SNPs. We show how PolarMorphism can be used to gain insight into relationships between traits and trait domains and contrast it with genetic correlation. Furthermore, pathway analysis of the newly discovered pleiotropic SNPs demonstrates that analysis of more than two traits simultaneously yields more biologically relevant results than the combined results of pairwise analysis of the same traits. Finally, we show that PolarMorphism is more efficient and more powerful than previously published methods.Availability and implementationcode: https://github.com/UMCUGenetics/PolarMorphism, results: 10.5281/zenodo.5844193.Supplementary informationSupplementary data are available at Bioinformatics online.
Exploring automatic inconsistency detection for literature-based gene ontology annotation
Authors: Chen Jiyu , Goudey Benjamin , Zobel Justin , Geard Nicholas , Verspoor Karin 
Published: April 2022

AbstractMotivationLiterature-based gene ontology annotations (GOA) are biological database records that use controlled vocabulary to uniformly represent gene function information that is described in the primary literature. Assurance of the quality of GOA is crucial for supporting biological research. However, a range of different kinds of inconsistencies in between literature as evidence and annotated GO terms can be identified; these have not been systematically studied at record level. The existing manual-curation approach to GOA consistency assurance is inefficient and is unable to keep pace with the rate of updates to gene function knowledge. Automatic tools are therefore needed to assist with GOA consistency assurance. This article presents an exploration of different GOA inconsistencies and an early feasibility study of automatic inconsistency detection.ResultsWe have created a reliable synthetic dataset to simulate four realistic types of GOA inconsistency in biological databases. Three automatic approaches are proposed. They provide reasonable performance on the task of distinguishing the four types of inconsistency and are directly applicable to detect inconsistencies in real-world GOA database records. Major challenges resulting from such inconsistencies in the context of several specific application settings are reported. This is the first study to introduce automatic approaches that are designed to address the challenges in current GOA quality assurance workflows. The data underlying this article are available in Github at https://github.com/jiyuc/AutoGOAConsistency.
Phage–bacterial contig association prediction with a convolutional neural network
Authors: Tang Tianqi , Hou Shengwei , Fuhrman Jed A , Sun Fengzhu 
Published: April 2022

AbstractMotivationPhage–host associations play important roles in microbial communities. But in natural communities, as opposed to culture-based lab studies where phages are discovered and characterized metagenomically, their hosts are generally not known. Several programs have been developed for predicting which phage infects which host based on various sequence similarity measures or machine learning approaches. These are often based on whole viral and host genomes, but in metagenomics-based studies, we rarely have whole genomes but rather must rely on contigs that are sometimes as short as hundreds of bp long. Therefore, we need programs that predict hosts of phage contigs on the basis of these short contigs. Although most existing programs can be applied to metagenomic datasets for these predictions, their accuracies are generally low. Here, we develop ContigNet, a convolutional neural network-based model capable of predicting phage–host matches based on relatively short contigs, and compare it to previously published VirHostMatcher (VHM) and WIsH.ResultsOn the validation set, ContigNet achieves 72–85% area under the receiver operating characteristic curve (AUROC) scores, compared to the maximum of 68% by VHM or WIsH for contigs of lengths between 200 bps to 50 kbps. We also apply the model to the Metagenomic Gut Virus (MGV) catalogue, a dataset containing a wide range of draft genomes from metagenomic samples and achieve 60–70% AUROC scores compared to that of VHM and WIsH of 52%. Surprisingly, ContigNet can also be used to predict plasmid-host contig associations with high accuracy, indicating a similar genetic exchange between mobile genetic elements and their hosts.Availability and implementationThe source code of ContigNet and related datasets can be downloaded from https://github.com/tianqitang1/ContigNet.
DRUMMER—rapid detection of RNA modifications through comparative nanopore sequencing
Authors: Abebe Jonathan S , Price Alexander M , Hayer Katharina E , Mohr Ian , Weitzman Matthew D , Wilson Angus C , Depledge Daniel P 
Published: April 2022

AbstractMotivationThe chemical modification of ribonucleotides regulates the structure, stability and interactions of RNAs. Profiling of these modifications using short-read (Illumina) sequencing techniques provides high sensitivity but low-to-medium resolution i.e. modifications cannot be assigned to specific transcript isoforms in regions of sequence overlap. An alternative strategy uses current fluctuations in nanopore-based long read direct RNA sequencing (DRS) to infer the location and identity of nucleotides that differ between two experimental conditions. While highly sensitive, these signal-level analyses require high-quality transcriptome annotations and thus are best suited to the study of model organisms. By contrast, the detection of RNA modifications in microbial organisms which typically have no or low-quality annotations requires an alternative strategy. Here, we demonstrate that signal fluctuations directly influence error rates during base-calling and thus provides an alternative approach for identifying modified nucleotides.ResultsDRUMMER (Detection of Ribonucleic acid Modifications Manifested in Error Rates) (i) utilizes a range of statistical tests and background noise correction to identify modified nucleotides with high confidence, (ii) operates with similar sensitivity to signal-level analysis approaches and (iii) correlates very well with orthogonal approaches. Using well-characterized DRS datasets supported by independent meRIP-Seq and miCLIP-Seq datasets we demonstrate that DRUMMER operates with high sensitivity and specificity.Availability and implementationDRUMMER is written in Python 3 and is available as open source in the GitHub repository: https://github.com/DepledgeLab/DRUMMER.Supplementary informationSupplementary data are available at Bioinformatics online.
An atlas of human viruses provides new insights into diversity and tissue tropism of human viruses
Authors: Ye Sifan , Lu Congyu , Qiu Ye , Zheng Heping , Ge Xingyi , Wu Aiping , Xia Zanxian , Jiang Taijiao , Zhu Haizhen , Peng Yousong 
Published: April 2022

AbstractMotivationViruses continue to threaten human health. Yet, the complete viral species carried by humans and their infection characteristics have not been fully revealed.ResultsThis study curated an atlas of human viruses from public databases and literature, and built the Human Virus Database (HVD). The HVD contains 1131 virus species of 54 viral families which were more than twice the number of the human-infecting virus species reported in previous studies. These viruses were identified in human samples including 68 human tissues, the excreta and body fluid. The viral diversity in humans was age-dependent with a peak in the infant and a valley in the teenager. The tissue tropism of viruses was found to be associated with several factors including the viral group (DNA, RNA or reverse-transcribing viruses), enveloped or not, viral genome length and GC content, viral receptors and the virus-interacting proteins. Finally, the tissue tropism of DNA viruses was predicted using a random-forest algorithm with a middle performance. Overall, the study not only provides a valuable resource for further studies of human viruses but also deepens our understanding toward the diversity and tissue tropism of human viruses.Availability and implementationThe HVD is available at http://computationalbiology.cn/humanVirusBase/#/.Supplementary informationSupplementary data are available at Bioinformatics online.
Deephos: predicted spectral database search for TMT-labeled phosphopeptides and its false discovery rate estimation
Authors: Na Seungjin , Choi Hyunjin , Paek Eunok 
Published: April 2022

AbstractMotivationTandem mass tag (TMT)-based tandem mass spectrometry (MS/MS) has become the method of choice for the quantification of post-translational modifications in complex mixtures. Many cancer proteogenomic studies have highlighted the importance of large-scale phosphopeptide quantification coupled with TMT labeling. Herein, we propose a predicted Spectral DataBase (pSDB) search strategy called Deephos that can improve both sensitivity and specificity in identifying MS/MS spectra of TMT-labeled phosphopeptides.ResultsWith deep learning-based fragment ion prediction, we compiled a pSDB of TMT-labeled phosphopeptides generated from ∼8000 human phosphoproteins annotated in UniProt. Deep learning could successfully recognize the fragmentation patterns altered by both TMT labeling and phosphorylation. In addition, we discuss the decoy spectra for false discovery rate (FDR) estimation in the pSDB search. We show that FDR could be inaccurately estimated by the existing decoy spectra generation methods and propose an innovative method to generate decoy spectra for more accurate FDR estimation. The utilities of Deephos were demonstrated in multi-stage analyses (coupled with database searches) of glioblastoma, acute myeloid leukemia and breast cancer phosphoproteomes.Availability and implementationDeephos pSDB and the search software are available at https://github.com/seungjinna/deephos.
Magnet and button battery ingestion in children: multicentre observational study of management and outcomes
Authors:   Paediatric Surgery Trainee Research Network, Neville Jonathan J. , Harwood Rachel , Bethell George S. , Rhodes Hannah , Arthur Felicity , Eastwood Mary P. , Hotonu Sesi , Tullie Lucinda , Hall Nigel J. , Coulson R. , Lawther S. , Burns K. , Chacon C. S. , Boam T. , Clarke S. A. , Hallett J. , Valliant N. , Hemanshoo T. , Tahira A. , Decker E. , Ahmed T. , Cave J. , Ram A. , Shenoy M. , John M. , Wyn M. , Wilkins L. , Allin B. , Fagelnor A. , Bough G. , Mohd-Amin A. T. , Trenear R. 
Published: April 2022

Abstract

Background
Magnets and button batteries (BBs) are dangerous ingested foreign bodies in children. The scale and consequences of this public health issue in the UK are unknown. This study aims to report the current management strategies and outcomes associated with paediatric magnet and BB ingestion in the UK.

Methods
This multicentre, retrospective observational study involved 13 UK tertiary paediatric surgery centres. Children aged under 17 years, admitted between 1 October 2019 and 30 September 2020, following magnet, or BB ingestion were included. Demographics, investigations, management, and complications were recorded.

Results
In total, 263 patients were identified, comprising 146 (55.5 per cent) magnet, 112 (42.6 per cent) BB, and 5 (1.9 per cent) mixed magnet BB ingestions. Median (interquartile range) age was 4.8 (2.0–9.1) years and 47.5 per cent were female. In the magnet group, 38 (26.0 per cent) children swallowed single magnets, 3 of whom underwent endoscopic retrieval for oesophageal or gastric impaction. Of the 108 (74.0 per cent) children who swallowed multiple magnets, 51 (47.2 per cent) required endoscopic or surgical intervention, predominantly for failure of magnets to progress on serial imaging. Bowel perforations occurred in 10 children (9.3 per cent). Younger age and ingestion of greater numbers of multiple magnets were independently associated with surgery. BB ingestion caused morbidity in 14 children (12.5 per cent) and life-threatening injuries in two (1.8 per cent); the majority were caused by oesophageal BBs (64.3 per cent).

Conclusion
Multiple magnet and BB ingestions are associated with significant morbidity. Action must be taken at an international level to regulate the sale of magnets and BBs, and to raise awareness of the risks that these objects pose to children.
Association of anaesthesia technique with 30-day primary graft patency after open lower limb revascularization: retrospective cohort study
Authors: Ke Janny Xue Chen , Flexman Alana M. , Schwarz Stephan K. W. , MacDonald Shaun , Prabhakar Christopher 
Published: April 2022

Abstract

Background
The relationship between anaesthetic technique and graft patency after open lower limb revascularization is unclear. The aim of this study was to evaluate the association between 30-day graft patency after elective infrainguinal bypass and anaesthetic technique (regional anaesthesia (RA, i.e. neuraxial and/or peripheral nerve blockade) compared with general anaesthesia (GA)).

Methods
Patients who underwent elective infrainguinal bypass in the 2014–2019 National Surgical Quality Improvement Program Vascular Procedure Targeted Lower Extremity Open data set were included. Excluded patients were those under 18 years old, those who did not receive RA or GA, and/or had an international normalized ratio of 1.5 of greater, a partial thromboplastin time more than 35 s, or a platelet count less than 80 × 109/L. The primary outcome was primary graft patency without reintervention. The relationship between anaesthetic technique and patency was analysed with multivariable logistic regression.

Results
Included were 8893 patients with a mean(s.d.) age of 68(11) years and 31.5 per cent female. Within the cohort, 7.7 per cent (n = 688) patients received RA only, 90.4 per cent (n = 8039) GA only, and 1.9 per cent (n = 166) both GA and RA. In the RA-only group, 91.7 per cent (631 of 688) received neuraxial anaesthesia. The primary patency rate was 93.2 per cent (573 of 615) for RA only, and 91.5 per cent (6390 of 6983) for GA only (standardized mean difference, 0.063). RA was not associated with a higher rate of patency compared with GA (adjusted OR, 1.16; 95 per cent c.i., 0.83 to 1.63; P = 0.378).

Conclusion
There was no association between anaesthetic technique and 30-day graft patency after elective infrainguinal bypass surgery. Further prospective studies would be useful to study the impact of anaesthesia technique on important patient-centred outcomes such as long-term patency and non-home discharge.