bluuebunny/crossref_metadata_2025_split huggingface dataset:
Robust Huber-LASSO for improved prediction of protein, metabolite and gene expression levels relying on individual genotype data
Authors: Deutelmoser Heike , Scherer Dominique , Brenner Hermann , Waldenberger Melanie ,   INTERVAL study, Suhre Karsten , Kastenmüller Gabi , Lorenzo Bermejo Justo 
Published: August 2020

AbstractLeast absolute shrinkage and selection operator (LASSO) regression is often applied to select the most promising set of single nucleotide polymorphisms (SNPs) associated with a molecular phenotype of interest. While the penalization parameter λ restricts the number of selected SNPs and the potential model overfitting, the least-squares loss function of standard LASSO regression translates into a strong dependence of statistical results on a small number of individuals with phenotypes or genotypes divergent from the majority of the study population—typically comprised of outliers and high-leverage observations.Robust methods have been developed to constrain the influence of divergent observations and generate statistical results that apply to the bulk of study data, but they have rarely been applied to genetic association studies. In this article, we review, for newcomers to the field of robust statistics, a novel version of standard LASSO that utilizes the Huber loss function. We conduct comprehensive simulations and analyze real protein, metabolite, mRNA expression and genotype data to compare the stability of penalization, the cross-iteration concordance of the model, the false-positive and true-positive rates and the prediction accuracy of standard and robust Huber-LASSO.Although the two methods showed controlled false-positive rates ≤2.1% and similar true-positive rates, robust Huber-LASSO outperformed standard LASSO in the accuracy of predicted protein, metabolite and gene expression levels using individual SNP data. The conducted simulations and real-data analyses show that robust Huber-LASSO represents a valuable alternative to standard LASSO in genetic studies of molecular phenotypes.
Classification in biological networks with hypergraphlet kernels
Authors: Lugo-Martinez Jose , Zeiberg Daniel , Gaudelet Thomas , Malod-Dognin Noël , Przulj Natasa , Radivojac Predrag 
Published: August 2020

AbstractMotivationBiological and cellular systems are often modeled as graphs in which vertices represent objects of interest (genes, proteins and drugs) and edges represent relational ties between these objects (binds-to, interacts-with and regulates). This approach has been highly successful owing to the theory, methodology and software that support analysis and learning on graphs. Graphs, however, suffer from information loss when modeling physical systems due to their inability to accurately represent multiobject relationships. Hypergraphs, a generalization of graphs, provide a framework to mitigate information loss and unify disparate graph-based methodologies.ResultsWe present a hypergraph-based approach for modeling biological systems and formulate vertex classification, edge classification and link prediction problems on (hyper)graphs as instances of vertex classification on (extended, dual) hypergraphs. We then introduce a novel kernel method on vertex- and edge-labeled (colored) hypergraphs for analysis and learning. The method is based on exact and inexact (via hypergraph edit distances) enumeration of hypergraphlets; i.e. small hypergraphs rooted at a vertex of interest. We empirically evaluate this method on fifteen biological networks and show its potential use in a positive-unlabeled setting to estimate the interactome sizes in various species.Availability and implementationhttps://github.com/jlugomar/hypergraphlet-kernelsSupplementary informationSupplementary data are available at Bioinformatics online.
Pathophysiology of atrial fibrillation and chronic kidney disease
Authors: Ding Wern Yew , Gupta Dhiraj , Wong Christopher F , Lip Gregory Y H 
Published: August 2020

Abstract
Atrial fibrillation (AF) and chronic kidney disease (CKD) are closely related conditions with shared risk factors. The growing prevalence of both AF and CKD indicates that more patients will suffer from concurrent conditions. There are various complex interlinking mechanisms with important implications for the management of these patients. Furthermore, there is uncertainty regarding the use of oral anticoagulation (OAC) in AF and CKD that is reflected by a lack of consensus between international guidelines. Therefore, the importance of understanding the implications of co-existing AF and CKD should not be underestimated. In this review, we discuss the pathophysiology and association between AF and CKD, including the underlying mechanisms, risk of thrombo-embolic and bleeding complications, influence on stroke management, and evidence surrounding the use of OAC for stroke prevention.
Surface ammonium loading rate shifts ammonia-oxidizing communities in surface water-fed rapid sand filters
Authors: Hu Jiajie , Zhao Yuxiang , Yang Weiling , Wang Jiaqi , Liu Huan , Zheng Ping , Hu Baolan 
Published: August 2020

ABSTRACTNitrification is important in drinking water treatment plants (DWTPs) for ammonia removal and is widely considered as a stepwise process mediated by ammonia- and nitrite-oxidizing microorganisms. The recent discovery of complete ammonia oxidizers (comammox) has challenged the long-held assumption that the division of metabolic labor in nitrification is obligate. However, little is known about the role of comammox Nitrospira in DWTPs. Here, we explored the relative importance of comammox Nitrospira, canonical ammonia-oxidizing archaea (AOA) and bacteria (AOB) in 12 surface water-fed rapid sand filters (RSFs). Quantitative PCR results showed that all the three ammonia-oxidizing guilds had the potential to dominate nitrification in DWTPs. Spearman's correlation and redundancy analysis revealed that the surface ammonium loading rate (SLR) was the key environmental factor influencing ammonia-oxidizing communities. Comammox Nitrospira were likely to dominate the nitrification under a higher SLR. PCR and phylogenetic analysis indicated that most comammox Nitrospira belonged to clade A, with clade B comammox Nitrospira almost absent. This work reveals obvious differences in ammonia-oxidizing communities between surface water-fed and groundwater-fed RSFs. The presence of comammox Nitrospira can support the stability of drinking water production systems under high SLR and warrants further investigation of their impact on drinking water quality.
Chromoendoscopy with targeted biopsies is superior to white-light endoscopy for the long-term follow-up detection of dysplasia in ulcerative colitis patients: a multicenter randomized–controlled trial
Authors: Wan Jian , Zhang Qin , Liang Shu-Hui , Zhong Jie , Li Jing-Nan , Ran Zhi-Hua , Zhi Fa-Chao , Wang Xiao-Di , Zhang Xiao-Lan , Wen Zhong-Hui , Sheng Jian-Qiu , Shi Hua-Xiu , Mei Qiao , Wu Kai-Chun 
Published: August 2020

Abstract

Background
Data from single-center experience or small sample-sized studies have shown that chromoendoscopy (CE) might be superior to white-light endoscopy (WLE) for dysplasia surveillance in ulcerative colitis (UC) patients. We performed a prospective randomized trial with a long-term follow-up to compare the detection rate of dysplasia among WLE with targeted biopsies (WLT), WLE with random biopsies (WLR), and dye-based CE with targeted biopsies (CET) in UC patients.

Methods
Patients with long-standing UC were enrolled from 11 medical centers from March 2012 to December 2013 and randomized into three arms (WLT, WLR, and CET). Only high-definition endoscopy was used in all three groups. The patients were followed up by annual endoscopy with biopsies through December 2017.

Results
With a median follow-up time of 55 months, a total of 122 patients with 447 colonoscopies were finally analysed in the per-protocol set: WLT (n = 43), WLR (n = 40), and CET (n = 39). A total of 34 dysplastic lesions were found in 29 colonoscopies of 21 patients. WLR and CET could identify more colonoscopies that diagnosed dysplasia than WLT (8.1% and 9.7% vs 1.9%; P = 0.014 and 0.004, respectively). WLR obtained more biopsied samples than WLT and CET (16.4 ± 5.1 vs 4.3 ± 1.4 and 4.3 ± 1.4; both P &lt; 0.001). During the second half of the follow-up (37 − 69 months), CET could identify more colonoscopies that diagnosed dysplasia than WLT (13.3% vs 1.6%, P = 0.015) and showed a trend for increasing the detection rate compared with WLR (13.3% vs 4.9%, P = 0.107).

Conclusions
For a better outcome of cancer/dysplasia surveillance in patients with long-standing UC, CET appeared to be more effective than WLT and less tedious than WLR. CET was found to be particularly useful when a long-term (&gt;3 years) follow-up was conducted for dysplasia surveillance. The trial was registered on www.chictr.org.cn (ChiCTR1900023689).
Adaptive Divergence of Meiotic Recombination Rate in Ecological Speciation
Authors: Neupane Swatantra , Xu Sen 
Published: August 2020

AbstractTheories predict that directional selection during adaptation to a novel habitat results in elevated meiotic recombination rate. Yet the lack of population-level recombination rate data leaves this hypothesis untested in natural populations. Here, we examine the population-level recombination rate variation in two incipient ecological species, the microcrustacean Daphnia pulex (an ephemeral-pond species) and Daphnia pulicaria (a permanent-lake species). The divergence of D. pulicaria from D. pulex involved habitat shifts from pond to lake habitats as well as strong local adaptation due to directional selection. Using a novel single-sperm genotyping approach, we estimated the male-specific recombination rate of two linkage groups in multiple populations of each species in common garden experiments and identified a significantly elevated recombination rate in D. pulicaria. Most importantly, population genetic analyses show that the divergence in recombination rate between these two species is most likely due to divergent selection in distinct ecological habitats rather than neutral evolution.
The Genome of the Cauliflower Coral Pocillopora verrucosa
Authors: Buitrago-López Carol , Mariappan Kiruthiga G , Cárdenas Anny , Gegner Hagen M , Voolstra Christian R 
Published: August 2020

Abstract
Climate change and ocean warming threaten the persistence of corals worldwide. Genomic resources are critical to study the evolutionary trajectory, adaptive potential, and genetic distinctiveness of coral species. Here, we provide a reference genome of the cauliflower coral Pocillopora verrucosa, a broadly prevalent reef-building coral with important ecological roles in the maintenance of reefs across the Red Sea, the Indian Ocean, and the Pacific Ocean. The genome has an assembly size of 380,505,698 bp with a scaffold N50 of 333,696 bp and a contig N50 of 75,704 bp. The annotation of the assembled genome returned 27,439 gene models of which 89.88% have evidence of transcription from RNA-Seq data and 97.87% show homology to known genes. A high proportion of the genome (41.22%) comprised repetitive elements in comparison to other cnidarian genomes, in particular in relation to the small genome size of P. verrucosa.
Nursing Home Social Workers Perceptions of Preparedness and Coping for COVID-19
Authors: Miller Vivian J , Fields Noelle L , Anderson Keith A , Kusmaul Nancy , Maxwell Christy 
Published: August 2020

Abstract

Objectives
Social work has a long history of responding to the needs of vulnerable populations during times of crisis and disaster. Social workers are working at the front lines responding to the current COVID-19 pandemic in a variety of health care practice settings, including nursing homes; however, it is unclear how social workers perceive their preparedness during this time.

Methods
This study employed a cross-sectional survey to nursing home social workers via social media on feelings of preparedness for COVID-19, what has been most professionally helpful for social workers during these times in their role in COVID-19, as well as demographic questions. Demographic data were analyzed using SPSS and qualitative data were analyzed using the rigorous and accelerated data reduction technique.

Results
Data are based on a sample of 63 (N = 63) nursing home social workers. Findings revealed that while some social workers felt prepared for the coronavirus, many respondents stated that they were unprepared to meet the demands and challenges they were facing. Moreover, participants shared that professional support was critically important to get through COVID-19.

Discussion
These findings are important, as social workers are tasked with ensuring each resident attains their highest level of psychosocial well-being, which can be achieved only when nursing home staff are supported. Findings from the present study suggest that additional support for nursing home staff ought to include peer mentoring and mutual support. Additionally, improved leadership across health care settings is worth assessing.
Site-specific characterization of SARS-CoV-2 spike glycoprotein receptor-binding domain
Authors: Antonopoulos Aristotelis , Broome Steven , Sharov Victor , Ziegenfuss Christopher , Easton Richard L , Panico Maria , Dell Anne , Morris Howard R , Haslam Stuart M 
Published: August 2020

Abstract
The novel coronavirus SARS-CoV-2, the infective agent causing COVID-19, is having a global impact both in terms of human disease as well as socially and economically. Its heavily glycosylated spike glycoprotein is fundamental for the infection process, via its receptor-binding domains interaction with the glycoprotein angiotensin-converting enzyme 2 on human cell surfaces. We therefore utilized an integrated glycomic and glycoproteomic analytical strategy to characterize both N- and O- glycan site-specific glycosylation within the receptor-binding domain. We demonstrate the presence of complex-type N-glycans with unusual fucosylated LacdiNAc at both sites N331 and N343 and a single site of O-glycosylation on T323.
Temperature and body size affect recruitment and survival of sandeel across the North Sea
Authors: Henriksen Ole , Rindorf Anna , Brooks Mollie E , Lindegren Martin , van Deurs Mikael 
Published: August 2020

Abstract
Climate effects on marine fish depend on life stage, particularly when life stages differ in habitat utilization. In the present study, we investigated life stage-dependent responses of lesser sandeel (Ammodytes marinus) to temperature at contrasting geographical scales. We related population density and individual growth to temperature and found different temperature responses between the first and the second years of life. During the first year of life, fish size was the single most important factor influencing sandeel abundances, indicating a positive relationship between growth and survival. In contrast, during the second year of life, autumn bottom temperature was negatively correlated with sandeel abundance, suggesting elevated mortality in warm years. Southerly areas, experiencing higher temperatures in general, were also the areas showing the strongest response to temperature. This study sheds light on how warming impacts population dynamics of one of the most important forage fishes in the North Sea and supports the discussion of underlying mechanisms.
Slipping Through the Cracks in e-Lexicography
Authors: Frankenberg-Garcia Ana , Rees Geraint Paul , Lew Robert 
Published: August 2020

Abstract
Despite the remarkable advances made in recent years to facilitate the lexicographer’s work of interpreting and synthesizing the complexity of language uncovered by corpora, an uncritical use of cutting-edge corpus tools and resources can instill a false sense of assurance. In this paper, authentic examples pertaining to wordlist use, collocation research and example selection that arose when compiling a real-world lexical database are discussed through the lens of problems that can easily slip through the cracks in e-lexicography. In doing so, we emphasize the importance of solid training and sound lexicographic judgment when using corpora, corpus tools and corpus-derived resources, and provide an opportunity to reflect on how e-lexicography can be further refined in the future.
Esketamine Nasal Spray for Rapid Reduction of Depressive Symptoms in Patients With Major Depressive Disorder Who Have Active Suicide Ideation With Intent: Results of a Phase 3, Double-Blind, Randomized Study (ASPIRE II)
Authors: Ionescu Dawn F , Fu Dong-Jing , Qiu Xin , Lane Rosanne , Lim Pilar , Kasper Siegfried , Hough David , Drevets Wayne C , Manji Husseini , Canuso Carla M 
Published: August 2020

AbstractBackgroundPatients with major depressive disorder (MDD) having active suicidal ideation with intent require immediate treatment.MethodsThis double-blind study (ASPIRE II) randomized adults (aged 18–64 years) with MDD having active suicidal ideation with intent to esketamine 84 mg or placebo nasal spray twice weekly for 4 weeks, given with comprehensive standard of care (hospitalization ≥5 days and newly initiated or optimized oral antidepressant[s]). Change from baseline to 24 hours post-first dose in Montgomery-Asberg Depression Rating Scale total score (primary efficacy endpoint) was analyzed using ANCOVA. Clinical Global Impression–Severity of Suicidality–revised (key secondary endpoint) was analyzed using ANCOVA on ranks of change.ResultsOf 230 patients who were randomized (115 per arm), 227 received study drug and were included in efficacy/safety analyses; 184 (80.0%) completed double-blind treatment. Greater improvement in Montgomery-Asberg Depression Rating Scale total score was observed with esketamine (mean [SD]: –15.7 [11.56]) vs placebo (–12.4 [10.43]), each with standard of care, at 24 hours (least-squares mean difference [SE]: –3.9 [1.39], 95% CI: –6.60, –1.11; 2-sided P = .006). This was also noted at the earlier (4-hour) timepoint (least-squares mean difference –4.2, 95% CI: –6.38, –1.94). Patients in both treatment groups experienced rapid reduction in Clinical Global Impression–Severity of Suicidality–revised score; the between-group difference was not statistically significant. The most common adverse events among esketamine-treated patients were dizziness, dissociation, nausea, dysgeusia, somnolence, headache, and paresthesia.ConclusionThis study confirmed rapid and robust reduction of depressive symptoms with esketamine nasal spray in severely ill patients with MDD who have active suicidal ideation with intent.Trial Registration: Clinical Trials.gov identifier: NCT03097133
On the Zeros of Non-Analytic Random Periodic Signals
Authors: Angst Jürgen , Poly Guillaume 
Published: August 2020

AbstractIn this paper, we investigate the local universality of the number of zeros of a random periodic signal of the form $S_n(t)=\sum _{k=1}^n a_k f(k t)$, where $f$ is a $2\pi -$periodic function satisfying weak regularity conditions and where the coefficients $a_k$ are i.i.d. random variables, which are centered with unit variance. In particular, our results hold for continuous piecewise linear functions. We prove that the number of zeros of $S_n(t)$ in a shrinking interval of size $1/n$ converges in law as $n$ goes to infinity to the number of zeros of a Gaussian process whose explicit covariance only depends on the function $f$ and not on the common law of the random coefficients $(a_k)$. As a byproduct, this entails that the point measure of the zeros of $S_n(t)$ converges in law to an explicit limit on the space of locally finite point measures on $\mathbb R$ endowed with the vague topology. The standard tools involving the regularity or even the analyticity of $f$ to establish such kind of universality results are here replaced by some high-dimensional Berry–Esseen bounds recently obtained in [ 7]. The latter allow us to prove functional Central Limit Theorems in $C^1$ or Lipschitz topology in situations where usual criteria cannot be applied due to the lack of regularity.
Towards a fair and transparent research participant compensation and reimbursement framework in Vietnam
Authors: Sansom Lucy J , Minh Trang Pham Nguyen , Hill Iona E , Ha Quyen Nguyen Than , Trong Thuan Dang , Vidaillac Celine , Quynh Nhu Dong , Turner Hugo C , Van Nuil Jennifer Ilo , Phuong Dung Nguyen Thi , Kestelyn Evelyne 
Published: August 2020

Abstract

Background
Providing compensation for participants in clinical research is well established and while international guidelines exist, defining a context-specific and fair compensation for participants in low-resource settings is challenging due to ethical concerns and the lack of practical, national compensation and reimbursement frameworks.

Methods
We reviewed Oxford University Clinical Research Unit (OUCRU) internal reimbursement documentation over a 10-y period and conducted a scoping literature review to expand our knowledge of compensation and reimbursement practices including ethical concerns. We developed a preliminary reimbursement framework that was presented to community advisory boards (CAB) and clinical investigators to assess its applicability, fairness and transparency.

Results
The main topics discussed at the workshops centered on fairness and whether the reimbursements could be perceived as financial incentives. Other decisive factors in the decision-making process were altruism and the loss of caregivers’ earnings. Investigators raised the issue of additional burdens, whereas the CAB members were focused on non-monetary elements such as the healthcare quality the patients would receive. All elements discussed were reviewed and, where possible, incorporated into the final framework.

Conclusion
Our new reimbursement framework provides a consistent, fair and transparent decision-making process and will be implemented across all future OUCRU clinical research in Vietnam.
Associations between maternal milk protein genotypes with preweaning calf growth traits in beef cattle
Authors: Hohmann Lisa G , Weimann Christina , Scheper Carsten , Erhardt Georg , König Sven 
Published: August 2020

AbstractThe objectives of this study were to investigate milk casein polymorphisms in dams and to determine the impacts of maternal casein genotypes on growth traits of their sucking calves. Milk samples from 433 dams of the breeds German Angus (GA) and German Simmental (GS) were typed at the milk protein loci α s1-casein (αs1-CN), β-casein (β-CN), α s2-casein (αs2-CN), and κ-casein (κ-CN) via isoelectric focusing. Associations between casein genotypes in maternal milk with growth traits of their 1,872 calves were analyzed until the age of weaning using linear mixed models, considering either genotypes of individual casein loci (model 1) or composite α s1-β-α s2-κ-CN genotypes within the casein cluster (model 2). Besides environmental effects such as sex, age of the dam, and calving year-season, genetic effects (breed group and maternal and paternal effects) were considered in statistical models. The composite casein genotype BBǀA2A2ǀAAǀAB (order of genes on bovine chromosome 6: α s1-ǀβ-ǀα s2-ǀκ-CN) was associated with greater average daily weight gains (ADG) and heavier age-adjusted weaning weights (WW) of calves (P &lt; 0.05). The effects of composite genotypes on birth weight of calves were similar (P &gt; 0.05; model 2). With regard to individual casein loci, greater ADG and WW were observed for calves from dams with the genotypes κ-CN BB and α s1-CN BB, respectively (P &lt; 0.05; model 1). Age-adjusted WW was largest for calves from dams carrying the κ-CN genotype BB (215 kg) compared with calves representing the maternal AB and AA genotypes (both 204 kg). Results from the present study suggested selectable casein genotypes due to their nutritional value of milk (value in terms of offspring performances), offering new perspectives for breeding strategies in beef cattle to improve preweaning calf performance.