bluuebunny/crossref_metadata_2025_split huggingface dataset:
A sequential niche multimodal conformational sampling algorithm for protein structure prediction
Authors: Xia Yu-Hao , Peng Chun-Xiang , Zhou Xiao-Gen , Zhang Gui-Jun 
Published: July 2021

Abstract

Motivation
Massive local minima on the protein energy landscape often cause traditional conformational sampling algorithms to be easily trapped in local basin regions, because they find it difficult to overcome high-energy barriers. Also, the lowest energy conformation may not correspond to the native structure due to the inaccuracy of energy models. This study investigates whether these two problems can be alleviated by a sequential niche technique without loss of accuracy.

Results
A sequential niche multimodal conformational sampling algorithm for protein structure prediction (SNfold) is proposed in this study. In SNfold, a derating function is designed based on the knowledge learned from the previous sampling and used to construct a series of sampling-guided energy functions. These functions then help the sampling algorithm overcome high-energy barriers and avoid the re-sampling of the explored regions. In inaccurate protein energy models, the high-energy conformation that may correspond to the native structure can be sampled with successively updated sampling-guided energy functions. The proposed SNfold is tested on 300 benchmark proteins, 24 CASP13 and 19 CASP14 FM targets. Results show that SNfold correctly folds (TM-score ≥ 0.5) 231 out of 300 proteins. In particular, compared with Rosetta restrained by distance (Rosetta-dist), SNfold achieves higher average TM-score and improves the sampling efficiency by more than 100 times. On several CASP FM targets, SNfold also shows good performance compared with four state-of-the-art servers in CASP. As a plug-in conformational sampling algorithm, SNfold can be extended to other protein structure prediction methods.

Availability and implementation
The source code and executable versions are freely available at https://github.com/iobio-zjut/SNfold.

Supplementary information
Supplementary data are available at Bioinformatics online.
UCSC Cell Browser: visualize your single-cell data
Authors: Speir Matthew L , Bhaduri Aparna , Markov Nikolay S , Moreno Pablo , Nowakowski Tomasz J , Papatheodorou Irene , Pollen Alex A , Raney Brian J , Seninge Lucas , Kent W James , Haeussler Maximilian 
Published: July 2021

Abstract

Summary
As the use of single-cell technologies has grown, so has the need for tools to explore these large, complicated datasets. The UCSC Cell Browser is a tool that allows scientists to visualize gene expression and metadata annotation distribution throughout a single-cell dataset or multiple datasets.

Availability and implementation
We provide the UCSC Cell Browser as a free website where scientists can explore a growing collection of single-cell datasets and a freely available python package for scientists to create stable, self-contained visualizations for their own single-cell datasets. Learn more at https://cells.ucsc.edu.

Supplementary information
Supplementary data are available at Bioinformatics online.
Frailty among chronic kidney disease patients on the kidney transplant waiting list: the sex–frailty paradox
Authors: Pérez-Sáez María José , Arias-Cabrales Carlos E , Dávalos-Yerovi Vanesa , Redondo Dolores , Faura Anna , Vera María , Bach Anna , Pedreira Guillermo , Junyent Ernestina , Crespo Marta , Marco Ester , Rodríguez-Mañas Leocadio , Pascual Julio ,   , for the FRAIL-MAR Study Group
Published: July 2021

ABSTRACT

Background
Frailty is defined as decreased physiologic reserve and resistance to stressors that predisposes patients towards poor health results. Its prevalence in chronic kidney disease (CKD) patients who are kidney transplant (KT) candidates is high. Frailty is associated with a higher rate of complications and mortality after transplant. It is unknown whether frailty phenotype differs depending on sex in this population.

Methods
This was a prospective longitudinal study of 455 KT candidates evaluated for frailty by physical frailty phenotype at the time of inclusion on the KT waiting list. Pre-frailty was defined as the presence of two criteria and frailty as three or more criteria. Univariate and multivariate analyses searched for associations of frailty status, frailty components and gender differences.

Results
Thirty percent of the total cohort resulted to be pre-frail (20%) or frail (10.3%), but disparities were observed between sexes, with 22.5% of men and 47.2% of women falling into one of these categories. Among frailty criteria, women presented with a higher percentage of exhaustion (39.6% versus 17%) and slowness (22.2% versus 9.6%) compared with men. Comorbidity burden was higher among frail men, whereas social factors were poorer between frail women. Disability was common among those patients who were frail, both men and women.

Conclusions
Frailty is twice as frequent in advanced CKD women as men. Frailty criteria distribution and phenotype seem to differ among sexes, which might have implications in terms of specific and individualized interventions to improve their status before transplantation.
Identification of Ulcers and Erosions by the Novel Pillcam™ Crohn’s Capsule Using a Convolutional Neural Network: A Multicentre Pilot Study
Authors: Ferreira João Pedro Sousa , de Mascarenhas Saraiva Miguel José da Quinta e Costa , Afonso João Pedro Lima , Ribeiro Tiago Filipe Carneiro , Cardoso Hélder Manuel Casal , Ribeiro Andrade Ana Patrícia , de Mascarenhas Saraiva Miguel Nuno Gameiro , Parente Marco Paulo Lages , Natal Jorge Renato , Lopes Susana Isabel Oliveira , de Macedo Guilherme Manuel Gonçalves 
Published: July 2021

Abstract

Background and Aims
Capsule endoscopy is a central element in the management of patients with suspected or known Crohn’s disease. In 2017, PillCam™ Crohn’s Capsule was introduced and demonstrated to have greater accuracy in the evaluation of extension of disease in these patients. Artificial intelligence [AI] is expected to enhance the diagnostic accuracy of capsule endoscopy. This study aimed to develop an AI algorithm for the automatic detection of ulcers and erosions of the small intestine and colon in PillCam™ Crohn’s Capsule images.

Methods
A total of 8085 PillCam™ Crohn’s Capsule images were extracted between 2017 and 2020, comprising 2855 images of ulcers and 1975 erosions; the remaining images showed normal enteric and colonic mucosa. This pool of images was subsequently split into training and validation datasets. The performance of the network was subsequently assessed in an independent test set.

Results
The model had an overall sensitivity and specificity of 90.0% and 96.0%, respectively. The precision and accuracy of this model were 97.1% and 92.4%, respectively. In particular, the algorithm detected ulcers with a sensitivity of 83% and specificity of 98%, and erosions with sensitivity and specificity of 91% and 93%, respectively.

Conclusion
A deep learning model capable of automatically detecting ulcers and erosions in PillCam™ Crohn’s Capsule images was developed for the first time. These findings pave the way for the development of automatic systems for detection of clinically significant lesions, optimizing the diagnostic performance and efficiency of monitoring Crohn’s disease activity.
Safety and efficacy of flecainide associated with beta-blockers in arrhythmogenic right ventricular cardiomyopathy
Authors: Rolland Thomas , Badenco Nicolas , Maupain Carole , Duthoit Guillaume , Waintraub Xavier , Laredo Mikael , Himbert Caroline , Frank Robert , Hidden-Lucet Francoise , Gandjbakhch Estelle 
Published: July 2021

Abstract

Aims
Arrhythmogenic right ventricular cardiomyopathy (ARVC) is an inherited cardiomyopathy associated with a high risk of ventricular arrhythmia (VA). Current guidelines recommend beta-blockers as first-line medical therapy and if ineffective, sotalol or amiodarone. We describe our experience, as a tertiary centre for ARVC, with the effectiveness and tolerance of flecainide in addition to beta-blockers to prevent VA in ARVC.

Methods and results
We retrospectively included 100 consecutive ARVC patients who received flecainide with beta-blockers between May 1999 and November 2017. Treatment persistence and related side effects were assessed, as was VA-free survival on treatment, 24-h Holter monitoring and programmed ventricular stimulation (PVS) off- and on-treatment. Tolerance was good, with 10% flecainide discontinuations (lack of efficacy in six, atrial fibrillation in one, and side effects in three). No Brugada-induced electrocardiography pattern on flecainide or haemodynamic impairment was reported. Premature ventricular contraction burden at 24-h Holter monitoring was significantly decreased under treatment [median 415 (interquartile range, IQR 97–730) vs. 2370 (1572–3400) at baseline, P &lt; 0.0001, n = 46]. Among the 33 patients with PVS under treatment, PVS was positive in 40% on-treatment vs. 94% off-treatment (P &lt; 0.001). During a median follow-up of 47 months (IQR 23–73), 22 patients presented sustained VA on treatment, corresponding to an event rate of 5% [95% confidence interval (CI) (0.6–9)] at 1 year and 25% [95% CI (14–35)] at 5 years under treatment. No patient died.

Conclusion
This study suggests that flecainide and beta-blockers association is complementary to implantable cardioverter-defibrillator and catheter ablation and is safe for treating persistent symptomatic VA in patients with ARVC.
Stronger alcohol-violence association when adolescents drink less? Evidence from three Nordic countries
Authors: Moan Inger Synnøve , Bye Elin K , Rossow Ingeborg 
Published: July 2021

Abstract

Background
Since 2000, adolescents’ alcohol use and heavy episodic drinking (HED) have declined in the Nordic countries. However, little is known about corresponding trends in alcohol-related harm and possible changes in the alcohol-harm association. The aims are to examine (i) whether the decline in HED was accompanied by a decline in alcohol-related violence (AV) and (ii) whether the strength of the HED-AV association changed concomitant with the decline.

Methods
Analysis of data from the European School Survey Project on Alcohol and Other Drugs (ESPAD), conducted among 15–16-year-olds in Iceland, Norway and Sweden in 2007 and 2015 (n = 17 027). Changes in proportions of AV and alcohol use past 12 months, and mean frequency of HED past 30 days were examined using Pearsons χ2-test and F-test, respectively. The HED-AV associations were estimated using logistic regression analysis.

Results
HED and AV proportions decreased from 2007 to 2015 in all countries. Among current drinkers (n = 8927), both HED frequency and AV proportion decreased in Norway (P &lt; 0.001) and remained stable in Iceland. In Sweden, AV decreased (P &lt; 0.001) whereas HED remained stable. The magnitude of the HED-AV association increased in Norway (Beta2015–2007 = 0.145, 95% CI 0.054–0.236), remained the same in Iceland and decreased in Sweden (Beta2015–2007 = −0.082, 95% CI −0.158 to −0.005).

Conclusions
Among youth in Iceland, Norway and Sweden, heavy episodic drinking and alcohol-related violence declined from 2007 to 2015. Among drinkers, the strength of the alcohol-violence association was moderated by the extent of heavy episodic drinking.
Long-term Trajectories of C-Reactive Protein Among Men Living With and Without HIV Infection in the Multicenter AIDS Cohort Study
Authors: Wada Nikolas I , Breen Elizabeth C , Post Wendy S , Stosor Valentina , Macatangay Bernard J , Margolick Joseph B 
Published: July 2021

Abstract

Background
C-reactive protein (CRP) is an inflammatory biomarker associated with all-cause mortality and morbidities such as cardiovascular disease. CRP is increased with HIV infection and thought to increase with age, though trajectories of CRP with aging have not been well characterized. We investigated trajectories of CRP in men from the Multicenter AIDS Cohort Study, according to HIV infection and HIV viral load status.

Methods
CRP measurements from 12 250 serum samples, provided by 2132 men over a span of 30 years, were categorized by HIV status at sample collection: HIV uninfected (HIV−, n = 1717), HIV infected with undetectable RNA (HIV+ suppressed, n = 4075), and detectable HIV RNA (HIV+ detectable, n = 6458). Age-related trajectories of CRP were fit to multivariable linear mixed models; we tested for differences in trajectories by HIV status.

Results
CRP increased with age in all sample groups. HIV+ detectable and HIV+ suppressed samples had higher CRP than HIV− samples throughout the observed age range of 20–70 years (p &lt; .05). CRP concentrations at age 45 years were 38% (95% CI: 26%–50%) and 26% (15%–38%) higher in HIV+ detectable and HIV+ suppressed samples, respectively, relative to HIV− samples. HIV+ detectable samples showed more rapid linear increases with age (8% higher/decade, 0.3%–16%) than HIV− samples.

Conclusions
We observed higher concentrations of CRP across 5 decades of age in men living with HIV, and steeper increases with age in men with detectable HIV RNA, relative to HIV− men. These results are consistent with a contribution of inflammation to the higher risk of age-related comorbidities with HIV infection.
Risks and rewards of the surgical treatment of lung cancer in octogenarians
Authors: Saftic Igor , Bille Andrea , Asemota Nicole , Berjon de la Vega Loreto , Routledge Tom , King Juliet , Phipps Karen Harrison , Pilling John 
Published: July 2021

Abstract OBJECTIVESSurgeons will face an increasing number of octogenarians with lung cancer potentially curable by surgery. The goal of this study was to evaluate short- and long-term outcomes after lung resection.METHODSWe performed a single-centre study of consecutive patients ≥80 years old, surgically treated for suspected lung cancer between 2009 and 2016. Age, sex, performance status, lung function, surgical approach, type of lung resection, complications, in-hospital and 30- and 90-day deaths and long-term survival were analysed.RESULTSTwo hundred and fifty-seven patients were enrolled. The median age was 82 years (range 80–97). One hundred and thirty-four patients were treated by thoracotomy and 123 by video-assisted thoracic surgery [10 (8.1%) converted]. Two hundred and thirty-two underwent lobar resection and 25 underwent sublobar resection. There were no intraoperative deaths and 9 admissions to the intensive therapy unit; 112 (43.6%) patients suffered complications: More complications occurred after lobar versus after sublobar resections [45.7% vs 24% (P = 0.037)] and in those with chronic obstructive pulmonary disease (COPD) [57.4% vs 40% (P = 0.02)]. The 30-day mortality was 3.9% (n = 10) and the 90-day mortality was 6.22% (n = 16). One hundred and sixty-seven patients died during the study period; patients with non-small-cell lung cancer (n = 233) had a median survival of 46.5 months with 67.2% alive at 2 years and 40.8% at 5 years. Pathological stage and R status were independent prognostic factors for survival.CONCLUSIONSSurgery for malignancies in octogenarians is feasible and safe with good long-term outcomes. The risk of postoperative complications, especially in those with COPD, is high but can be minimized with sublobar resection. Postoperative mortality is acceptable, and long-term survival is primarily governed by lung cancer stage. Age is no reason to deny patients surgery for early-stage disease.
Antimicrobial use in hospitalized patients: a multicentre point prevalence survey across seven hospitals in Ghana
Authors: Labi Appiah-Korang , Obeng-Nkrumah Noah , Dayie Nicholas T K D , Egyir Beverly , Sampane-Donkor Eric , Newman Mercy Jemima , Opintan Japheth Awuletey 
Published: July 2021

Abstract

Background
Antimicrobial resistance (AMR) is a public health crisis of global proportions. Data is required to understand the local drivers of antimicrobial resistance and support decision-making processes including implementation of appropriate antimicrobial stewardship strategies.

Objectives
To measure antimicrobial usage in hospitals in Ghana.

Methods
Using the Global Point Prevalence instruments and processes, we conducted point prevalence surveys across AMR surveillance sentinel hospitals in Ghana, between September and December 2019. Hospital records of all inpatients on admission at 0800 hours on a specific day were reviewed for antimicrobial use at the time of the survey. Data on antibiotic use, including indication for use and quality of prescribing were recorded.

Results
Overall prevalence of antibiotic use across the sentinel sites was 54.9% (n = 1591/2897), ranging between 48.4% (n = 266/550) and 67.2% (n = 82/122). The highest prevalence of antibiotic use 89.3% (n = 25/28) was observed in adult ICUs. The average number of antibiotics prescribed per patient was 1.7 (n = 1562/2620), with the majority (66%, n = 728/2620) administered via the parenteral route. The five most-commonly used antibiotics were metronidazole (20.6%, n = 541/2620), cefuroxime (12.9%, n = 338/2620), ceftriaxone (11.8%, n = 310/2620), amoxicillin/clavulanic acid (8.8%, n = 231/2620) and ciprofloxacin (7.8%, n = 204/2620). The majority (52.2%; n = 1367/2620) of antibiotics were prescribed to treat an infection, whilst surgical prophylaxis accounted for 26.1% (n = 684/2620).

Conclusions
We observed a high use of antibiotics including metronidazole and cephalosporins at the participating hospitals. Most antibiotics were empirically prescribed, with low use of microbiological cultures. High usage of third-generation cephalosporins especially for community-acquired infections offers an opportunity for antibiotic stewardship interventions.
The First Climate Judgment before the Norwegian Supreme Court: Aligning Law with Politics
Authors: Voigt Christina 
Published: July 2021

Abstract
On 22 December 2020, the Norwegian Supreme Court ruled on its first climate case. It dealt with the claim that petroleum licences, issued by the Norwegian government, violate the ‘right to a healthy environment’ as contained in the Norwegian Constitution. The Court rejected the claim and found that the constitutional protection of the environment applies not as a right but as a substantive limit to governmental action, and only in very limited circumstances. Rather than taking the opportunity to give guidance on this constitutional provision, the Court provided a judgment that aligned law with the current politics in favour of continuous petroleum extraction on Norwegian territory.
Role ofSalix reiniipatches in spatio-temporal patterns of cohabitants on a Japanese volcano
Authors: Matsuda Miyuki , Tsuyuzaki Shiro 
Published: July 2021

AbstractShrub patches often support the colonizers particularly under stressful and/or disturbed environments. The intensities of stresses and disturbances on mountains are often related to an elevation gradient and are decreased by shrub patches (canopy and litter). We aim to clarify these relationships by using shrub patches at different elevations on a volcano. We monitored all shoots in plots established inside and outside of patches of Salix reinii (Salicaceae) and their related environments, such as temperature, light, moisture and chemistry, at three elevations on Mount Koma (1131 m a.s.l.), northern Japan, from early spring in 2005 to summer in 2006. The patch structures were evaluated by area, branch density and litter thickness. The structures of shrub patches did not differ among the elevations. The patches increased the diversity of rare species, by an overall increase in plant species richness. The moisture, nitrogen and phosphate contents in the patches were higher than outside of patches. The effects of shrub patches on the cohabitants were overall positive, although the effects were negative on seedling abundance, shoot survival and flowering. These results suggest that the growth patterns of shrub patches determine the plant community structures and facilitate plant diversity.
Large-scale clustering amongst Fermi blazars; evidence for axis alignments?
Authors: Marchã M J M , Browne I W A 
Published: July 2021

ABSTRACT
We find evidence for large-scale clustering amongst Fermi-selected BL Lac objects but not amongst Fermi-selected flat spectrum radio quasars (FSRQs). Using two-point correlation functions, we have investigated the clustering properties of different classes of objects from the Fermi–LAT(Large Area Telescope) 4FGL catalogue. We wanted to test the idea based on optical polarization observations that there might be large volumes of space in which AGN axes are aligned. To do this, we needed a clean sample of blazars as these are objects with their jet axes pointing towards the observer and Fermi sources provide such a sample. We find that high latitude Fermi sources taken as a whole show a significant clustering signal on scales up to 30°. To investigate if all blazars behave in the same way we used he machine learning classifications from the literature, which are based only on gamma-ray information, to separate BL Lac-like objects from FSRQ-like objects. A possible explanation for the clustering signal we find amongst the BL Lac-like objects is that there are indeed large volumes of space in which AGN axes are aligned. This signal might be washed out in FSRQs since they occupy a much larger volume of space. Thus, our results support the idea that large scale polarization alignments could originate from coherent alignments of AGN axes. We speculate that these axis alignments may be related to the well-known intrinsic alignments of galaxy optical position angles.
The BACCO simulation project: a baryonification emulator with neural networks
Authors: Aricò Giovanni , Angulo Raul E , Contreras Sergio , Ondaro-Mallea Lurdes , Pellejero-Ibañez Marcos , Zennaro Matteo 
Published: July 2021

ABSTRACT
We present a neural network emulator for baryonic effects in the non-linear matter power spectrum. We calibrate this emulator using more than 50 000 measurements in a 15D parameter space, varying cosmology and baryonic physics. Baryonic physics is described through a baryonification algorithm, which has been shown to accurately capture the relevant effects on the power spectrum and bispectrum in state-of-the-art hydrodynamical simulations. Cosmological parameters are sampled using a cosmology-rescaling approach including massive neutrinos and dynamical dark energy. The specific quantity we emulate is the ratio between matter power spectrum with baryons and gravity only, and we estimate the overall precision of the emulator to be $2\!-\!3{{\ \rm per\ cent}}$, at scales $k \lt 5 \, h\, {\rm Mpc}^{-1}$ and redshifts 0 &lt; z &lt; 1.5. We obtain an accuracy of $1\!-\!2{{\ \rm per\ cent}}$, when testing the emulator against a collection of 74 different cosmological hydrodynamical simulations and their respective gravity-only counterparts. We also show that only one baryonic parameter, namely Mc, which sets the gas fraction retained per halo mass, is enough to have accurate predictions of most of the baryonic feedbacks at a given epoch. Our emulator is publicly available at http://www.dipc.org/bacco.