bluuebunny/crossref_metadata_2025_split huggingface dataset:
From genotype to phenotype inArabidopsis thaliana:in-silicogenome interpretation predicts 288 phenotypes from sequencing data
Authors: Raimondi Daniele , Corso Massimiliano , Fariselli Piero , Moreau Yves 
Published: October 2021

AbstractIn many cases, the unprecedented availability of data provided by high-throughput sequencing has shifted the bottleneck from a data availability issue to a data interpretation issue, thus delaying the promised breakthroughs in genetics and precision medicine, for what concerns Human genetics, and phenotype prediction to improve plant adaptation to climate change and resistance to bioagressors, for what concerns plant sciences. In this paper, we propose a novel Genome Interpretation paradigm, which aims at directly modeling the genotype-to-phenotype relationship, and we focus on A. thaliana since it is the best studied model organism in plant genetics. Our model, called Galiana, is the first end-to-end Neural Network (NN) approach following the genomes in/phenotypes out paradigm and it is trained to predict 288 real-valued Arabidopsis thaliana phenotypes from Whole Genome sequencing data. We show that 75 of these phenotypes are predicted with a Pearson correlation ≥0.4, and are mostly related to flowering traits. We show that our end-to-end NN approach achieves better performances and larger phenotype coverage than models predicting single phenotypes from the GWAS-derived known associated genes. Galiana is also fully interpretable, thanks to the Saliency Maps gradient-based approaches. We followed this interpretation approach to identify 36 novel genes that are likely to be associated with flowering traits, finding evidence for 6 of them in the existing literature.
Observation of 1D Fermi arc states in Weyl semimetal TaAs
Authors: Zheng Xiaohu , Gu Qiangqiang , Liu Yiyuan , Tong Bingbing , Zhang Jian-Feng , Zhang Chi , Jia Shuang , Feng Ji , Du Rui-Rui 
Published: October 2021

Abstract
Fermi arcs on Weyl semimetals exhibit many exotic quantum phenomena. Usually found on atomically flat surfaces with approximate translation symmetry, Fermi arcs are rooted in the peculiar topology of bulk Bloch bands of 3D crystals. The fundamental question of whether a 1D Fermi arc can be probed remains unanswered. Such an answer could significantly broaden potential applications of Weyl semimetals. Here, we report a direct observation of robust edge states on atomic-scale ledges in TaAs using low-temperature scanning tunneling microscopy/spectroscopy. Spectroscopic signatures and theoretical calculations reveal that the 1D Fermi arcs arise from the chiral Weyl points of bulk crystals. The crossover from 2D Fermi arcs to eventual complete localization on 1D edges was arrested experimentally on a sequence of surfaces. Our results demonstrate extreme robustness of the bulk-boundary correspondence, which offers topological protection for Fermi arcs, even in cases in which the boundaries are at the atomic-scale. The persistent 1D Fermi arcs can be profitably exploited in miniaturized quantum devices.
Optimal Cutoff Concentration of Urinary Cyanoethyl Mercapturic Acid for Differentiating Cigarette Smokers From Nonsmokers
Authors: Bhandari Deepak , Zhang Luyu , Zhu Wanzhe , De Jesús Víctor R , Blount Benjamin C 
Published: October 2021

Abstract

Introduction
Cotinine is a widely used biomarker for classifying cigarette smoking status. However, cotinine does not differentiate between the use of combustible and noncombustible tobacco products. The increasing use of noncombustible tobacco drives the need for a complementary biomarker for distinguishing cigarette smokers from users of noncombustible tobacco products.

Aims and Methods
We evaluated the urinary acrylonitrile metabolite, 2CyEMA, as a biomarker of exposure to cigarette smoke in the US population-representative data from the National Health and Nutritional Examination Survey (NHANES). Smoking status was categorized based on the recent tobacco use questionnaire. The receiver operating characteristic (ROC) curve analysis was performed to identify optimal cutoff concentrations by maximizing Youden’s J index. The area under the curve (AUC) was used to compare 2CyEMA effectiveness with respect to serum cotinine.

Results
The overall cutoff concentration for the classification of cigarette smokers from nonsmokers was 7.32 ng/ml with high sensitivity and specificity (≥0.925). When stratified by demographic variables, the cutoff concentrations varied among subgroups based on age, sex, and race/Hispanic origin. Non-Hispanic Blacks had the highest cutoff concentration (15.3 ng/ml), and Hispanics had the lowest (4.63 ng/ml). Females had higher cutoff concentrations (8.80 ng/ml) compared to males (6.10 ng/ml). Among different age groups, the cutoff concentrations varied between 4.63 ng/ml (21–39 years old) and 10.6 ng/ml (for ≥60 years old). We also explored the creatinine adjusted cutoff values.

Conclusions
2CyEMA is an effective biomarker for distinguishing cigarette smokers from nonsmokers (users of noncombustible tobacco products or nonusers).

Implications
Distinguishes smokers from noncombustible tobacco product users.
Finite-N superconformal index via the AdS/CFT correspondence
Authors: Imamura Yosuke 
Published: October 2021

Abstract
We propose a prescription to calculate the superconformal index of the ${\cal N}=4$U(N) supersymmetric Yang–Mills theory with finite N on the anti-de Sitter side. The finite-N corrections are included as contributions of D3-branes wrapped around three-cycles in ${\boldsymbol S}^5$, which are calculated as the index of the gauge theories realized on the wrapped branes. The single-wrapping contribution has been studied in a previous work, and we further confirm that the inclusion of multiple-wrapping contributions correctly reproduces the higher-order terms as far as we have checked numerically.
Patient Preferences for Antipsychotic Drug Side Effects: A Discrete Choice Experiment
Authors: McCrone Paul , Mosweu Iris , Yi Deokhee , Ruffell Tamatha , Dalton Bethan , Wykes Til 
Published: October 2021

Abstract

Background
Development of pharmaceutical interventions for schizophrenia emphasizes clinical efficacy and subsequent effectiveness and cost-effectiveness. However, given the many side effects of antipsychotic medication, it is important to consider the importance of different side effects on the preferences that people with schizophrenia have for different drugs. This study aims to use a discrete choice experiment to elicit patient preferences for antipsychotic medication with different side effects profiles.

Method
Preferences for antipsychotic side effects were investigated using a discrete choice experiment conducted in south London. 297 participants with a schizophrenia diagnosis who had been in receipt of anti-psychotic medication for a minimum of one month were included. Participants were presented with a sequence of choices involving five antipsychotic side effects (attributes) each with four levels. Conditional logit models were used to determine the side effects most (and least) likely to be preferred by people prescribed antipsychotics. Subgroup analyses explored the impact of side effects by gender, ethnicity, age, and symptoms.

Results
As expected, participants tended to value antipsychotic medications offering the least side effects, and the model coefficients were in the expected direction. For the whole sample and subgroups, memory and fatigue were the most important side effects, whereas palpations and mobility were the least important.

Conclusions
Participants had a strong preference for medications with the least side effects on memory and fatigue. These findings should inform drug development by pharmaceutical companies and prescribing practice by clinicians.
Longitudinal association of actigraphy-assessed sleep with physical growth in the first 6 months of life
Authors: Li Xiaoyu , Haneuse Sebastien , Rueschman Michael , Kaplan Emily R , Yu Xinting , Davison Kirsten K , Redline Susan , Taveras Elsie M 
Published: October 2021

AbstractStudy ObjectivesSuboptimal sleep is associated with obesity and its sequelae in children and adults. However, few studies have examined the association between sleep and physical growth in infants who experience rapid changes in sleep/wake patterns. We examined the longitudinal association of changes in objectively assessed sleep/wake patterns with changes in growth between ages 1 and 6 months.MethodsWe studied 298 full-term infants in the longitudinal Rise & SHINE cohort study. Changes from 1 and 6 months in nighttime sleep duration, wake after sleep onset (WASO), and number of waking bouts ≥5 min were assessed using ankle actigraphy. Overweight was defined as age- and sex-specific weight for length ≥95th percentile. Generalized estimating equation analyses adjusted for infants′ and mothers′ characteristics.ResultsThe mean (SD) birth weight was 3.4 (0.4) kg; 48.7% were boys. In multivariable adjusted models, each 1-h increase in nighttime sleep duration between months 1 and 6 was associated with a 26% decrease in the odds of overweight from 1 to 6 months (odds ratio [OR] = 0.74; 95% confidence interval [CI, 0.56, 0.98]). Each 1-unit decrease in number of waking bouts was associated with a 16% decrease in the odds of overweight (OR = 0.84; 95% CI [0.72, 0.98]). Changes in WASO were not associated with the odds of overweight.ConclusionsGreater increases in nighttime sleep duration and more consolidation of nighttime sleep were associated with lower odds of overweight from 1 to 6 months. Adverse sleep patterns as early as infancy may contribute to excess adiposity.
Predictors for Screen Time Exposure among Children between 3 and 5 Years Old in Southern Brazil
Authors: Frata Bruna , Souza Janaina M , Montemezzo Dayane , Henning Elisa , Menegol Natalia A , Okubo Rodrigo , Sonza Anelise , Sanada Luciana S 
Published: October 2021

Abstract

Background
The use of technology is an increasingly common practice among preschoolers. Little is known about the relationship between screen time exposure (STE) and aspects related to family and the environment.

Aim
The aim is to characterize STE in Brazilian children aged between 3 and 5 years. Furthermore, the objective of this study is to associate the STE of children and of their parents with sociodemographic variables.

Methods
Children aged between 3 and 5 years from southern Brazil and their parents participated in this study. To investigate STE, the researchers developed a specific questionnaire. To compare STE between age groups, the Kruskal–Wallis test was performed, followed by Dunn’s post hoc test. Spearman’s correlation and linear regression were used to correlate the variables.

Results
Children (n = 237) spend an average of 3.7 ± 0.8 h/day in front of screens. The STE of children had a moderately positive correlation with the STE of their parents (r = 0.4; p-value &lt; 0.001). Only the variables of the children’s and parents’ STE had a significant and positive association. The model is significant (F = 6164, p-value &lt; 0.001) and the residuals of the model met the necessary assumptions, with normal distribution, constant variance and without the presence of outliers.

Conclusion
Children in southern Brazil remain in front of screens four times longer than the recommended amount of time. It was also found that the STE of parents directly influences that of their children.
Belatacept Conversion in Kidney After Liver Transplantation
Authors: Cristea Octav , Karadkhele Geeta , Kitchens William H. , Vasanth Payaswini , Larsen Christian P. , Badell Idelberto R. 
Published: October 2021

Background.
Costimulatory blockade with belatacept has demonstrated long-term benefits in renal transplantation, but de novo use in liver transplant recipients has resulted in increased rejection, graft loss, and death. However, belatacept conversion as a calcineurin inhibitor (CNI) avoidance strategy has not been studied and may be of benefit in liver transplantation where CNI-induced renal dysfunction and toxicity are barriers to improved outcomes.

Methods.
Using clinical data extracted from our institutional medical record, we report on 8 patients who underwent kidney after liver transplantation and were treated with belatacept-based immunosuppression and transient CNI therapy.

Results.
All patients tolerated belatacept therapy without any patient deaths or graft losses. No episodes of rejection, de novo donor-specific antibody formation, or major systemic infections were observed, and all patients demonstrated preserved liver and excellent renal allograft function. Patients received belatacept for a median duration of 13.2 mo, and at a median follow-up of 15.9 mo post–kidney transplant, 6 of 8 patients continued on belatacept with 3 completely off and 3 poised to transition off CNI.

Conclusions.
These findings are the first evidence that in liver transplant recipients requiring subsequent kidney transplantation, belatacept-based therapy can potentially facilitate CNI-free maintenance immunosuppression. This supports the possibility of belatacept conversion in stand-alone liver transplant recipients as a viable method of CNI avoidance.
Attitudes towards glaucoma genetic risk assessment in unaffected individuals
Authors: Hollitt Georgina L , Siggs Owen M , Ridge Bronwyn , Keane Miriam C , Mackey David A , MacGregor Stuart , Hewitt Alex W , Craig Jamie E , Souzeau Emmanuelle 
Published: October 2021

ABSTRACTIntegrating polygenic risk scores (PRS) into healthcare has the potential to stratify an individual’s risk of glaucoma across a broad population. Glaucoma is the most common cause of irreversible blindness worldwide, therefore effective screening for glaucoma endorsed by the population is highly important. This study assessed the attitude of unaffected individuals towards PRS testing for glaucoma, and sought to identify factors associated with interest in testing. We surveyed 418 unaffected individuals including those with a first-degree relative with glaucoma (n=193), those who had a recent eye examination (n=117), and general members of the community (n=108). Overall, 71.3% indicated an interest in taking a polygenic risk test for glaucoma. Interest was more likely in those who believed glaucoma to be a severe medical condition (OR 14.58, 95%CI (1.15-185.50), p=0.039), those concerned about developing glaucoma (OR 4.37, 95%CI (2.32-8.25), p<0.001), those with an intention to take appropriate measures regarding eye health (OR 2.39, 95%CI (1.16-4.95), p=0.019), and those preferring to know if considered to be at-risk or not (OR 4.52, 95%CI (2.32-8.83), p<0.001). These findings represent a valuable assessment of general public interest in glaucoma polygenic risk testing, which will be integral to the implementation and uptake of novel PRS based tests into clinical practice.
COVID-19: Knowledge, Perception of Risk, Preparedness and Vaccine Acceptability among Healthcare Workers in Kenya
Authors: Abdulle Hafso Mohamed , Masika Moses Muia , Oyugi Julius Otieno 
Published: October 2021

AbstractBackgroundCoronaviruses are highly contagious and healthcare workers are at a higher risk of contracting the disease. The objective of this study was to assess the level of knowledge, risk perception, preparedness for coronavirus disease 2019 and vaccine acceptability among healthcare workers in Kenya.MethodsA cross-sectional study was conducted from December 2020 to January 2021. A link to an online self-administered questionnaire was disseminated to health workers across the country. SPSS version 20 was used for data analysis. Bivariate correlation analyses were used to determine associations between variables. P-value of <0.05 was considered statistically significant.ResultsA total of 997 participants were enrolled in the study. About half (53%) of the participants were female. The mean age was 36.54 years (SD = 8.31) and 46% of the participants were aged between 31-40years. The overall knowledge score of health workers for COVID-19 was 80%. Most of the health workers (89%) perceived that they were at high risk of infection. Seventy-two percent of the participants felt that they were either partially or fully prepared to handle patients with COVID-19. Overall, 71% of all health workers would take a vaccine if provided free by the government.ConclusionHealth workers’ knowledge on transmission, clinical manifestations and risk factors for development of severe COVID-19 was good. Majority of the health workers perceived the risk of infection with COVID-19 as high and a significant number felt that they were not fully prepared to handle the pandemic. Majority of health workers would take a COVID-19 vaccine.
Small Airway Disease as long-term Sequela of COVID-19: Use of Expiratory CT despite Improvement in Pulmonary Function test
Authors: Garg Alpana , Nagpal Prashant , Goyal Sachin , Comellas Alejandro P. 
Published: October 2021

AbstractBackgroundIt is important to understand the spectrum of pulmonary diseases that patients are presenting after recovery from initial SARS-CoV-2 infection. We aim to study small airway disease and changes in Computed Tomography (CT)and pulmonary function tests (PFTs) with time.MethodsThis is retrospective observation study including adult patients with confirmed SARS-CoV-2 infection with at-least two CT scans either during acute (defined as <1 month) or subacute (1-3 months) or chronic (>3months) phase after positive test. Radiological features and follow up PFTs were obtained.Results22 patients met the inclusion criteria with mean age 57.6 years (range 36-83). Out of these,18 (81.81%) were hospitalized. Mean duration of diagnosis to CT and PFT was 192.68(112-385) days and 161.54(31-259) days respectively. On PFTs, restrictive pulmonary physiology was predominant finding during subacute 56.25% (9/16) and chronic phases 47% (7/15). PFTs improved significantly with time {FEV1((p=0.0361), FVC (p=0.0341), FEF 25%-75% (p=0.0259) and DLCO (p=0.0019)}, but there was persistent air trapping in the expiratory chronic phase CT. There was resolution of ground glass opacity, consolidation, and bronchiectasis however air trapping increased with time in 41.61% (10/21) of subacute CTs compared to 81.25% (13/16) in chronic CTs.ConclusionOur study shows evidence of airway as well as parenchymal disease as relatively long-term sequel of SARS-CoV-2 infection. It also highlights the natural course and spontaneous recovery of some radiological and pulmonary function test abnormalities over time with evidence of persistent small airway disease (air trapping) on expiratory CT imaging months after infection.HighlightsLong term pulmonary complication of SARS-CoV-2 infection include small airway diseaseThere is role of inspiratory and expiratory Computed tomography (CT) scan to identify air trapping in patients with persistent respiratory symptoms after SARS-CoV-2 infectionNormal spirometry and normal routine CT may not be sufficient to characterize and identify cause of persistent respiratory complains in patients after COVID-19This study highlights persistent parenchymal and physiological airway abnormalities more than six months after recovery from initial SARS-CoV-2 infection
Metagenomic analysis of the abundance and composition of antibiotic resistance genes in hospital wastewater in Benin, Burkina Faso, and Finland
Authors: Markkanen Melina A. , Haukka Kaisa , Pärnänen Katariina M. M. , Dougnon Victorien Tamegnon , Bonkoungou Isidore Juste O. , Garba Zakaria , Tinto Halidou , Sarekoski Anniina , Karkman Antti , Kantele Anu , Virta Marko P. J. 
Published: October 2021

AbstractAntibiotic resistance is one of the greatest global threats to human health, but substantial gaps in antibiotic resistance data exist in West African countries. We explored the presence of antibiotic resistance genes (ARGs) in the hospital wastewater (HWW) of nine hospitals in Benin and Burkina Faso and, for comparison, four hospitals in Finland using shotgun metagenomic sequencing. The highest sum of the relative abundance of ARGs in the 68 HWW samples was detected in Benin and the lowest in Finland. HWW resistomes and mobilomes in Benin and Burkina Faso resembled more of each other than those in Finland. Different carbapenemases were detected in varying abundances, especially in HWW from Burkina Faso and Finland. TheblaGES genes, the most widespread carbapenemase genes in the Beninese HWW, were also found in water intended for hand-washing and in a puddle at the hospital yard in Benin.mcrwere detected in the HWW of all three countries, withmcr-5being the most commonmcrgene. These and othermcrgenes were observed in very high relative abundances, even in treated wastewater in Burkina Faso and in a street gutter in Benin. The results provide evidence for public health decision-makers for the dire need to increase wastewater treatment capacity, with particular attention to HWW.ImportanceThe global emergence and increased spread of antibiotic resistance threaten the effectiveness of antibiotics and, thus, the health of the entire population. Therefore, understanding the resistomes in different geographical locations is crucial in the global fight against the antibiotic crisis. However, this information is scarce in many low- and middle-income countries (LMICs), such as those in West Africa. In this study, we describe the resistomes of hospital wastewater in Benin and Burkina Faso and, as a comparison, in Finland. Our results help to understand the hitherto unrevealed resistance in Beninese and Burkinabe hospitals. Furthermore, the results emphasize the importance of wastewater management infrastructure design to minimize exposure events between humans, HWW, and the environment, preventing the circulation of resistant bacteria and ARGs between humans (hospitals and community) and the environment.
Escherichia colistrains from patients with inflammatory bowel diseases have disease-specific genomic adaptations
Authors: Dubinsky Vadim , Reshef Leah , Rabinowitz Keren , Wasserberg Nir , Dotan Iris , Gophna Uri 
Published: October 2021

ABSTRACTObjectiveEscherichia coliis over-abundant in the gut microbiome of patients with IBD, yet most studies have focused on the adherent-invasiveE. colipathotype. Here, we aimed to identify IBD-specific or phenotype-specific genomic functions of diverseE. colilineages.DesignWe investigatedE. colifrom patients with UC, CD and a pouch and healthy subjects. The majority ofE. coligenomes were reconstructed directly from metagenomic samples, including publicly available and newly sequenced fecal metagenomes. Clinical metadata and biomarkers were collected. Functional analysis at the gene and mutation level and genome replication rates ofE. coli strainswere performed, and correlated with IBD phenotypes and biomarkers.ResultsOverall, 530E. coligenomes were analysed. A specificE. colilineage (B2) was more prevalent in UC compared to other IBD phenotypes. Genomic metabolic capacities varied acrossE. colilineages and IBD phenotypes. Specifically,sialidases involved in host mucin utilization, were exclusively present in a single lineage and were depleted in patients with a pouch. In contrast, enzymes that hydrolyze inulin were enriched in patients with a pouch.E. colifrom patients with UC were twice as likely to encode the genotoxic molecule colibactin than strains from patients with CD or pouch. Strikingly, patients with a pouch showed the highestE. coligrowth rates, even in the presence of antibiotics. Fecal calprotectin did not correlate with the relative abundance ofE. coli. Finally, we identified multiple IBD-specific loss-of function mutations inE. coligenes encoding for bacterial cell envelope and secretion components.ConclusionThis study presentsE. colias a commensal species better adapted to the overly-active mucosal immune milieu in IBD, that may benefit from intestinal inflammation, rather than causing it. The evidence given here suggests adaptive evolution toward attenuated virulence in someE. colistrains, coupled with a rapid growth despite the presence of antibiotics.