bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cox-nnet v2.0: improved neural-network-based survival prediction extended to large-scale EMR data
Authors: Wang Di , Jing Zheng , He Kevin , Garmire Lana X. 
Published: January 2021

Abstract

Summary
Cox-nnet is a neural-network-based prognosis prediction method, originally applied to genomics data. Here, we propose the version 2 of Cox-nnet, with significant improvement on efficiency and interpretability, making it suitable to predict prognosis based on large-scale population data, including those electronic medical records (EMR) datasets. We also add permutation-based feature importance scores and the direction of feature coefficients. When applied on a kidney transplantation dataset, Cox-nnet v2.0 reduces the training time of Cox-nnet up to 32-folds (n =10 000) and achieves better prediction accuracy than Cox-PH (P&lt;0.05). It also achieves similarly superior performance on a publicly available SUPPORT data (n=8000). The high efficiency and accuracy make Cox-nnet v2.0 a desirable method for survival prediction in large-scale EMR data.

Availability and implementation
Cox-nnet v2.0 is freely available to the public at https://github.com/lanagarmire/Cox-nnet-v2.0.

Supplementary information
Supplementary data are available at Bioinformatics online.
Perforation rate after a diagnosis of uncomplicated appendicitis on CT
Authors: Lastunen K , Leppäniemi A , Mentula P 
Published: January 2021

Abstract

Background
Appendicectomy is a common emergency operation. The aim of this analysis was to study the effect of preoperative delay on disease progression, and whether a novel scoring system (Atema score) could be useful in predicting complicated appendicitis.

Methods
Patients with uncomplicated acute appendicitis on CT and who underwent appendicectomy in 2014–2015 were analysed for patient characteristics, preoperative delay and outcomes.

Results
Of 837 patients with uncomplicated appendicitis on CT, 187 (22.3 per cent) were found to have complicated appendicitis at surgery. The median time estimate for perforation was 25.4 h after CT, with an hourly rate of perforation of 2 per cent. Patients with an Atema score of 6 or less and those with no appendicolith on CT and a C-reactive protein level below 51 mg/l were the slowest to develop perforation, reaching a perforation rate of 5 per cent in 7.1 and 7.6 h respectively.

Conclusion
A substantial proportion of patients with uncomplicated acute appendicitis on CT have complicated appendicitis at surgery. However, in patients with no risk factors, surgery can be postponed safely for up to 7 h.
Systematic Bibliographic Database Searching for Literature Reviews: Case Study on Child Protection Decision-Making
Authors: Alfandari Ravit , Taylor Brian J 
Published: January 2021

Abstract
Skills of the ‘information age’ need to be applied to social work. Conceptual and practical aspects of using online bibliographic databases to identify research were explored using multi-professional decision-making in child protection as a case study. Five databases (Social Science Citation Index, Scopus, Medline, Social Work Abstracts and Cochrane Central Register of Controlled Trials) were searched for relevant studies, retrieving 6,934 records of which fifty-eight studies were identified as relevant. The usefulness of specific search terms and the process of learning from the terminology of previous searches are illustrated, as well as the value of software to manage retrieved studies. Scopus had the highest sensitivity (retrieving the highest number of relevant articles) and retrieved the most articles not retrieved by any other database (exclusiveness). All databases had low precision on this topic, despite extensive efforts in selecting search terms. Cumulative knowledge about search strategies and empirical comparison of database utility helps to increase the efficiency of systematic literature searching. Such endeavours encourage and support professionals to use the best available evidence to inform practice and policy.
Global longitudinal strain by feature-tracking cardiovascular magnetic resonance imaging predicts mortality in patients with end-stage kidney disease
Authors: Rankin Alastair J , Zhu Luke , Mangion Kenneth , Rutherford Elaine , Gillis Keith A , Lees Jennifer S , Woodward Rosie , Patel Rajan K , Berry Colin , Roditi Giles , Mark Patrick B 
Published: January 2021

Abstract

Background
Patients with end-stage kidney disease (ESKD) are at increased risk of premature death, with cardiovascular disease being the predominant cause of death. We hypothesized that left ventricular global longitudinal strain (LV-GLS) measured by feature-tracking cardiovascular magnetic resonance imaging (CMRI) would be associated with all-cause mortality in patients with ESKD.

Methods
A pooled analysis of CMRI studies in patients with ESKD acquired within a single centre between 2002 and 2016 was carried out. CMR parameters including LV ejection fraction (LVEF), LV mass index, left atrial emptying fraction (LAEF) and LV-GLS were measured. We tested independent associations of CMR parameters with survival using a multivariable Cox model.

Results
Among 215 patients (mean age 54 years, 62% male), mortality was 53% over a median follow-up of 5 years. The median LVEF was 64.7% [interquartile range (IQR) 58.5–70.0] and the median LV-GLS was −15.3% (IQR −17.24 to −13.6). While 90% of patients had preserved LVEF (&gt;50%), 58% of this group had abnormal LV-GLS (&gt;−16%). On multivariable Cox regression, age {hazard ratio [HR] 1.04 [95% confidence interval (CI) 1.02–1.05]}, future renal transplant [HR 0.29 (95% CI 0.17–0.47)], LAEF [HR 0.98 (95% CI 0.96–1.00)] and LV-GLS [HR 1.08 (95% CI 1.01–1.16)] were independently associated with mortality.

Conclusions
In this cohort of patients with ESKD, LV-GLS on feature-tracking CMRI and LAEF was associated with all-cause mortality, independent of baseline clinical variables and future renal transplantation. This effect was present even when &gt;90% of the cohort had normal LVEF. Using LV-GLS instead of LVEF to diagnose cardiac dysfunction in patients with ESKD could result in a major advance in our understanding of cardiovascular disease in ESKD.
Analyzing Mass Attitudes Toward the International Court of Justice
Authors: Justwan Florian , Fisher Sarah K , Kerr Ashley , Berejikian Jeffrey D 
Published: January 2021

AbstractThis paper analyzes public attitudes about the International Court of Justice (ICJ). We explore two questions: (1) Why are some people in favor of submitting their country's disputes to the ICJ while others are opposed? (2) How can we explain variations in public support for compliance with a costly ICJ ruling? We argue that individual-level attitudes about both issues are driven by different psychological dynamics. While we expect that cost–benefit calculations and cosmopolitan social identity will affect attitudes in both contexts, people's views on compliance should also be shaped by their level of social dominance orientation (SDO). Our statistical analysis is based on original survey data, collected in Belize in April 2019. We obtain three main findings. First, people's ex ante beliefs about the costs of an ICJ ruling have tangible effects on attitudes toward ICJ adjudication. As predicted, higher expected costs lead to decreased support for adjudication. Second, cosmopolitanism is positively associated with support for adjudication, but it has no effect on attitudes about compliance with international court rulings. Third, high-SDO respondents are less likely to favor the implementation of a costly ICJ verdict. However, SDO only reduces support for compliance in individuals with narrow social identity attachments.
Comparative genomics of white and opaque cell states supports an epigenetic mechanism of phenotypic switching in Candida albicans
Authors: Beekman Chapman N , Cuomo Christina A , Bennett Richard J , Ene Iuliana V 
Published: January 2021

Abstract
Several Candida species can undergo a heritable and reversible transition from a ‘white’ state to a mating proficient ‘opaque’ state. This ability relies on highly interconnected transcriptional networks that control cell-type-specific gene expression programs over multiple generations. Candida albicans, the most prominent pathogenic Candida species, provides a well-studied paradigm for the white-opaque transition. In this species, a network of at least eight transcriptional regulators controls the balance between white and opaque states that have distinct morphologies, transcriptional profiles, and physiological properties. Given the reversible nature and the high frequency of white-opaque transitions, it is widely assumed that this switch is governed by epigenetic mechanisms that occur independently of any changes in DNA sequence. However, a direct genomic comparison between white and opaque cells has yet to be performed. Here, we present a whole-genome comparative analysis of C. albicans white and opaque cells. This analysis revealed rare genetic changes between cell states, none of which are linked to white-opaque switching. This result is consistent with epigenetic mechanisms controlling cell state differentiation in C. albicans and provides direct evidence against a role for genetic variation in mediating the switch.
Treatment of the X chromosome in mapping multiple quantitative trait loci
Authors: Tran Quoc , Broman Karl W 
Published: January 2021

Abstract
Statistical methods to map quantitative trait loci (QTL) often neglect the X chromosome and may focus exclusively on autosomal loci. But the X chromosome often requires special treatment: sex and cross-direction covariates may need to be included to avoid spurious evidence of linkage, and the X chromosome may require a separate significance threshold. In multiple-QTL analyses, including the consideration of epistatic interactions, the X chromosome also requires special care and consideration. We extend a penalized likelihood method for multiple-QTL model selection, to appropriately handle the X chromosome. We examine its performance in simulation and by application to a large eQTL data set. The method has been implemented in the package R/qtl.
Improved contiguity of the threespine stickleback genome using long-read sequencing
Authors: Nath Shivangi , Shaw Daniel E , White Michael A 
Published: January 2021

Abstract
While the cost and time for assembling a genome has drastically decreased, it still remains a challenge to assemble a highly contiguous genome. These challenges are rapidly being overcome by the integration of long-read sequencing technologies. Here, we use long-read sequencing to improve the contiguity of the threespine stickleback fish (Gasterosteus aculeatus) genome, a prominent genetic model species. Using Pacific Biosciences sequencing, we assembled a highly contiguous genome of a freshwater fish from Paxton Lake. Using contigs from this genome, we were able to fill over 76.7% of the gaps in the existing reference genome assembly, improving contiguity over fivefold. Our gap filling approach was highly accurate, validated by 10X Genomics long-distance linked-reads. In addition to closing a majority of gaps, we were able to assemble segments of telomeres and centromeres throughout the genome. This highlights the power of using long sequencing reads to assemble highly repetitive and difficult to assemble regions of genomes. This latest genome build has been released through a newly designed community genome browser that aims to consolidate the growing number of genomics datasets available for the threespine stickleback fish.
KH domain containing RNA-binding proteins coordinate with microRNAs to regulate Caenorhabditis elegans development
Authors: Haskell Dustin , Zinovyeva Anna 
Published: January 2021

Abstract
MicroRNAs (miRNAs) and RNA-binding proteins (RBPs) regulate gene expression at the post-transcriptional level, but the extent to which these key regulators of gene expression coordinate their activities and the precise mechanisms of this coordination are not well understood. RBPs often have recognizable RNA binding domains that correlate with specific protein function. Recently, several RBPs containing K homology (KH) RNA binding domains were shown to work with miRNAs to regulate gene expression, raising the possibility that KH domains may be important for coordinating with miRNA pathways in gene expression regulation. To ascertain whether additional KH domain proteins functionally interact with miRNAs during Caenorhabditis elegans development, we knocked down twenty-four genes encoding KH-domain proteins in several miRNA sensitized genetic backgrounds. Here, we report that a majority of the KH domain-containing genes genetically interact with multiple miRNAs and Argonaute alg-1. Interestingly, two KH domain genes, predicted splicing factors sfa-1 and asd-2, genetically interacted with all of the miRNA mutants tested, whereas other KH domain genes showed genetic interactions only with specific miRNAs. Our domain architecture and phylogenetic relationship analyses of the C. elegans KH domain-containing proteins revealed potential groups that may share both structure and function. Collectively, we show that many C. elegans KH domain RBPs functionally interact with miRNAs, suggesting direct or indirect coordination between these two classes of post-transcriptional gene expression regulators.
Lilikoi V2.0: a deep learning–enabled, personalized pathway-based R package for diagnosis and prognosis predictions using metabolomics data
Authors: Fang Xinying , Liu Yu , Ren Zhijie , Du Yuheng , Huang Qianhui , Garmire Lana X 
Published: January 2021

Abstract

Background
previously we developed Lilikoi, a personalized pathway-based method to classify diseases using metabolomics data. Given the new trends of computation in the metabolomics field, it is important to update Lilikoi software.

Results
here we report the next version of Lilikoi as a significant upgrade. The new Lilikoi v2.0 R package has implemented a deep learning method for classification, in addition to popular machine learning methods. It also has several new modules, including the most significant addition of prognosis prediction, implemented by Cox-proportional hazards model and the deep learning–based Cox-nnet model. Additionally, Lilikoi v2.0 supports data preprocessing, exploratory analysis, pathway visualization, and metabolite pathway regression.

Conculsion
Lilikoi v2.0 is a modern, comprehensive package to enable metabolomics analysis in R programming environment.
A framework for mapping local knowledge on ciguatera and artisanal fisheries to inform systematic conservation planning
Authors: André Laure Vaitiare , Van Wynsberge Simon , Chinain Mireille , Gatti Clémence Mahana Iti , Dempsey Alexandra , Andréfouët Serge 
Published: January 2021

Abstract
Millions of people’s livelihoods rely on artisanal fisheries. However, in many regions fishers are increasingly facing ciguatera poisoning, a seafood-borne illness. The toxin, produced by benthic dinoflagellates, can spread through marine food webs and to humans by direct consumption. Ciguatera risk can play a major role in fisher’s activities but has never been considered in any marine spatial plans thus far. To fill this gap, we examined if integrating ciguatera in systematic conservation plans could affect these decisions. We developed through map-based interviews, a novel seven-step framework to collect and map local knowledge on ciguatera risk and fisheries activities with two innovations: (i) better mapping of fishing grounds by combining geomorphological habitat and fishing gear information, and (ii) integrating ciguatera risk directly into systematic spatial planning designs and scenarios conceived to maximize benthic habitat conservation while minimizing impacts to fishers. The approach is illustrated for Raivavae Island, in French Polynesia, Pacific Ocean. We found that integrating ciguatera significantly improved prioritization solutions with a 24–38% decrease of costs to fishers compared with scenarios based solely on fishery data. This framework was designed for scientists and managers to optimize the implementation of conservation plans and could be generalized to ciguatera-prone areas.
Huehue constitutionalism
Authors: Xavier Fernando César Costa 
Published: January 2021

Abstract
The article describes the characteristics of the disruptive behavior of Brazilian users in multiplayer online games (MOGs), which has come to be termed—including in the literature—as huehue. It then argues that the main features pointed out—spamming, trolling, and griefing—could also be perceived to some extent in the behavior of players acting in Brazilian high politics. The persona behind this disruptive subjectivity, so characteristic of Brazilian culture, could be called “griefer” (in Portuguese: zoeiro). “Huehue constitutionalism” or “griefer constitutionalism” would be a type of dysfunctional constitutional environment, markedly Brazilian, characterized by the fact that, in the political game, subjects who perform constitutional functions feel free to act, raising the levels of disruptive behavior to unprecedented levels (huehueing), so that while benefiting from constitutional rules to act freely, they abuse and corrupt the democratic stability proper to constitutional order. Although more serious in terms of dysfunctionality than the so-called “constitutional rot,” huehue constitutionalism would foreshadow a moment of constitutional crisis and would be sufficient to thwart any attempt at experimenting with popular collaborative constitutionalism using digital tools.
Human papillomavirus vaccination and all-cause morbidity in adolescent girls: a cohort study of absence from school due to illness
Authors: Hviid Anders , Thorsen Nicklas M , Thomsen Louise N , Møller Frederik T , Wiwe Andreas , Frisch Morten , Valentiner-Branth Palle , Rytter Dorte , Mølbak Kåre 
Published: January 2021

Abstract

Background
A growing body of evidence supports the safety of the human papillomavirus (HPV) vaccines. However, concerns about autonomic dysfunction syndromes and non-specific symptoms continue to linger. These conditions are not easily captured by traditional diagnostic classification schemes and call for innovative approaches to the study of vaccine safety which take more general measures of all-cause morbidity into account.

Methods
Taking advantage of the unique Danish registers, including regional registration of absence from school, we conducted a cohort study of 14 068 adolescent Danish girls attending 5th through 9th grade in public schools in the municipality of Copenhagen during 1 August 2013–23 January 2018. We obtained time-varying HPV vaccination status and demographic information from nationwide registers. Using Poisson regression with random effects, we estimated rate ratios (RRs) of absence due to illness, comparing HPV-vaccinated girls with unvaccinated girls with adjustment for grade, season, calendar period, demographic factors and random effects at the individual, class and school levels.

Results
Our study included 6 206 188 school days with 213 221 days of absence from school due to illness (absence rate, 3.4%). Comparing absence rates due to illness in HPV-vaccinated and unvaccinated girls yielded an adjusted RR of 1.00 (95% confidence interval [CI], 0.98–1.03).

Conclusions
Our study provides an important and novel contribution to HPV vaccine safety. Using absence from school records, we were able to address important safety concerns without relying on medical diagnoses. We conclude that HPV vaccination does not increase the risk of morbidity in any manner that manifests as absence from school due to illness.
Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Replication and Tropism in the Lungs, Airways, and Vascular Endothelium of Patients With Fatal Coronavirus Disease 2019: An Autopsy Case Series
Authors: Bhatnagar Julu , Gary Joy , Reagan-Steiner Sarah , Estetter Lindsey B , Tong Suxiang , Tao Ying , Denison Amy M , Lee Elizabeth , DeLeon-Carnes Marlene , Li Yan , Uehara Anna , Paden Clinton R , Leitgeb Brooke , Uyeki Timothy M , Martines Roosecelis B , Ritter Jana M , Paddock Christopher D , Shieh Wun-Ju , Zaki Sherif R 
Published: January 2021

Abstract

Background
The coronavirus disease 2019 (COVID-19) pandemic continues to produce substantial morbidity and mortality. To understand the reasons for the wide-spectrum complications and severe outcomes of COVID-19, we aimed to identify cellular targets of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) tropism and replication in various tissues.

Methods
We evaluated RNA extracted from formalin-fixed, paraffin-embedded autopsy tissues from 64 case patients (age range, 1 month to 84 years; 21 COVID-19 confirmed, 43 suspected COVID-19) by SARS-CoV-2 reverse-transcription polymerase chain reaction (RT-PCR). For cellular localization of SARS-CoV-2 RNA and viral characterization, we performed in situ hybridization (ISH), subgenomic RNA RT-PCR, and whole-genome sequencing.

Results
SARS-CoV-2 was identified by RT-PCR in 32 case patients (21 COVID-19 confirmed, 11 suspected). ISH was positive in 20 and subgenomic RNA RT-PCR was positive in 17 of 32 RT-PCR–positive case patients. SARS-CoV-2 RNA was localized by ISH in hyaline membranes, pneumocytes, and macrophages of lungs; epithelial cells of airways; and endothelial cells and vessel walls of brain stem, leptomeninges, lung, heart, liver, kidney, and pancreas. The D614G variant was detected in 9 RT-PCR–positive case patients.

Conclusions
We identified cellular targets of SARS-CoV-2 tropism and replication in the lungs and airways and demonstrated its direct infection in vascular endothelium. This work provides important insights into COVID-19 pathogenesis and mechanisms of severe outcomes.
Novel Sterile Insect Technology Program Results in Suppression of a Field Mosquito Population and Subsequently to Reduced Incidence of Dengue
Authors: de Castro Poncio Lisiane , dos Anjos Filipe Apolinário , de Oliveira Deborah A , Rebechi Débora , de Oliveira Rodrigo Neves , Chitolina Rodrigo Faitta , Fermino Marise Lopes , Bernardes Luciano G , Guimarães Danton , Lemos Pedro A , Silva Marcelo N E , Silvestre Rodrigo G M , Bernardes Emerson Soares , Paldi Nitzan 
Published: January 2021

Abstract

Background
There is a steady rise in the global incidence of Aedes-borne arbovirus disease. It has become urgent to develop alternative solutions for mosquito vector control. We developed a new method of sterilization of male mosquitoes with the goal to suppress a local Aedes aegypti population and to prevent the spread of dengue.

Methods
Sterile male mosquitoes were produced from a locally acquired Ae. aegypti colony by using a treatment that includes double-stranded RNA and thiotepa. A field study was conducted with sterile mosquito releases being performed on a weekly basis in predefined areas. There were 2 intervention periods (INT1 and INT2), with treatment and control areas reversed between INT1 and INT2.

Results
During INT1, releases in the treated area resulted in up to 91.4% reduction of live progeny of field Ae. aegypti mosquitoes recorded over time, while the control neighborhoods (no releases of sterile male mosquitoes) remained highly infested. The successful implementations of the program during INT1 and INT2 were associated with 15.9-fold and 13.7-fold lower incidences of dengue in the treated area compared to the control areas, respectively.

Conclusions
Our data show the success of this new sterile insect technology-based program in preventing the spread of dengue.