bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inhibition kinetics of acetosyringone on xylanase in hydrolysis of hemicellulose
Authors: Liu Feng , Xu Wen-Fei , Mu Hang , Lv Zhi-Rong , Peng Jie , Guo Chao , Zhou Hai-Meng , Ye Zhuo-Ming , Li Xu-Hui 
Published: May 2020

AbstractMany phenolic compounds, derived from lignin during the pretreatment of lignocellulosic biomass, could obviously inhibit the activity of cellulolytic and hemicellulolytic enzymes. Acetosyringone (AS) is one of the phenolic compounds produced from lignin degradation. In this study, we investigated the inhibitory effects of AS on xylanase activity through kinetic experiments. The results showed that AS could obviously inhibit the activity of xylanase in a reversible and noncompetitive binding manner (up to 50% activity loss). Inhibitory kinetics and constants of xylanase on AS were conducted by the HCH-1 model (β = 0.0090 ± 0.0009 mM−1). Furthermore, intrinsic and 8-anilino-1-naphthalenesulfonic (ANS)-binding fluorescence results showed that the tertiary structure of AS-mediated xylanase was altered. These findings provide new insights into the role of AS in xylanase activity. Our results also suggest that AS was an inhibitor of xylanase and targeting AS was a potential strategy to increase xylose production.
Changes in muscle strength and physical function in older patients during and after hospitalisation: a prospective repeated-measures cohort study
Authors: Hartley Peter , Romero-Ortuno Roman , Wellwood Ian , Deaton Christi 
Published: May 2020

Abstract

Aim
to investigate changes in knee-extension strength and physical function in older adults during and after acute hospital admission, and the contributions of illness severity, frailty and sedentary activity to changes in knee-extension strength.

Methods
prospective repeated-measures cohort study on a sample of participants aged ≥75 recruited within 24 hours of acute hospital admission. Knee-extension, grip strength and functional mobility (de Morton Mobility Index, DEMMI) were measured at recruitment, day 7 (or discharge if earlier), and at follow-up 4–6 weeks later. During the first 7 days, continuous measurement of physical activity and daily measurements of muscle strength were taken. Participants recalled the functional ability they had 2-weeks before admission and self-reported it at follow-up (Barthel Index, BI).

Results
sixty-five of 70 participants (median age 84 years) had at least one repeated measure of muscle strength in hospital. Knee-extension strength declined during hospitalisation by 11% (P &lt; 0.001), but did not change post-hospitalisation (P = 0.458). Grip strength did not change during hospitalisation (P = 0.665) or from discharge to follow-up (P = 0.508). General functional ability (BI) deteriorated between 2 weeks before admission and follow-up (P &lt; 0.001). Functional mobility (DEMMI) improved during hospitalisation (P &lt; 0.001), but did not change post-hospitalisation (P = 0.508). A repeated-measures mixed model showed that greater loss in knee-extension strength during hospitalisation was associated with increased sedentary time, frailty and baseline strength and lower baseline inflammatory levels.

Conclusions
our observations add to a growing body of evidence on potential risk factors for hospital-associated deconditioning.
Privacy, Literature, and Public Discourse
Authors: Rosen David , Santesso Aaron 
Published: May 2020

Abstract
In the last few decades, something has changed about how Americans conceive of privacy, which has had consequences for how writers address their publics: how writers write. This essay argues that rapidly evolving and expanding surveillance regimes have profoundly affected our sense of where the private life begins and ends and what can or cannot be concealed from others. Discourses characterized by fragmentation, opacity, and indirection have become both a means by which we communicate information about ourselves to the larger world and a mimetic representation of how that surveillance-mediated world often appears to us. Literature has played a crucial role in these transformations and has served as a laboratory for many of these emerging discourses. This essay focuses on two recent and contrasting cohorts of American writers: a slightly older group of authors who saw the sacrifice of individual privacy as having catastrophic implications for liberal democracy, and a younger group whose views of privacy and communication were, on the whole, less panicked and more tactical. The essay concludes by considering what happens when rhetorical modes meant primarily to preserve the private self reenter the public sphere and assert themselves within a civil-minded conversation.
DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy
Authors: Xie Ruopeng , Li Jiahui , Wang Jiawei , Dai Wei , Leier André , Marquez-Lago Tatiana T , Akutsu Tatsuya , Lithgow Trevor , Song Jiangning , Zhang Yanju 
Published: May 2020

AbstractVirulence factors (VFs) enable pathogens to infect their hosts. A wealth of individual, disease-focused studies has identified a wide variety of VFs, and the growing mass of bacterial genome sequence data provides an opportunity for computational methods aimed at predicting VFs. Despite their attractive advantages and performance improvements, the existing methods have some limitations and drawbacks. Firstly, as the characteristics and mechanisms of VFs are continually evolving with the emergence of antibiotic resistance, it is more and more difficult to identify novel VFs using existing tools that were previously developed based on the outdated data sets; secondly, few systematic feature engineering efforts have been made to examine the utility of different types of features for model performances, as the majority of tools only focused on extracting very few types of features. By addressing the aforementioned issues, the accuracy of VF predictors can likely be significantly improved. This, in turn, would be particularly useful in the context of genome wide predictions of VFs. In this work, we present a deep learning (DL)-based hybrid framework (termed DeepVF) that is utilizing the stacking strategy to achieve more accurate identification of VFs. Using an enlarged, up-to-date dataset, DeepVF comprehensively explores a wide range of heterogeneous features with popular machine learning algorithms. Specifically, four classical algorithms, including random forest, support vector machines, extreme gradient boosting and multilayer perceptron, and three DL algorithms, including convolutional neural networks, long short-term memory networks and deep neural networks are employed to train 62 baseline models using these features. In order to integrate their individual strengths, DeepVF effectively combines these baseline models to construct the final meta model using the stacking strategy. Extensive benchmarking experiments demonstrate the effectiveness of DeepVF: it achieves a more accurate and stable performance compared with baseline models on the benchmark dataset and clearly outperforms state-of-the-art VF predictors on the independent test. Using the proposed hybrid ensemble model, a user-friendly online predictor of DeepVF (http://deepvf.erc.monash.edu/) is implemented. Furthermore, its utility, from the user’s viewpoint, is compared with that of existing toolkits. We believe that DeepVF will be exploited as a useful tool for screening and identifying potential VFs from protein-coding gene sequences in bacterial genomes.
DeepLGP: a novel deep learning method for prioritizing lncRNA target genes
Authors: Zhao Tianyi , Hu Yang , Peng Jiajie , Cheng Liang 
Published: May 2020

Abstract

Motivation
Although long non-coding RNAs (lncRNAs) have limited capacity for encoding proteins, they have been verified as biomarkers in the occurrence and development of complex diseases. Recent wet-lab experiments have shown that lncRNAs function by regulating the expression of protein-coding genes (PCGs), which could also be the mechanism responsible for causing diseases. Currently, lncRNA-related biological data are increasing rapidly. Whereas, no computational methods have been designed for predicting the novel target genes of lncRNA.

Results
In this study, we present a graph convolutional network (GCN) based method, named DeepLGP, for prioritizing target PCGs of lncRNA. First, gene and lncRNA features were selected, these included their location in the genome, expression in 13 tissues and miRNA-mediated lncRNA–gene pairs. Next, GCN was applied to convolve a gene interaction network for encoding the features of genes and lncRNAs. Then, these features were used by the convolutional neural network for prioritizing target genes of lncRNAs. In 10-cross validations on two independent datasets, DeepLGP obtained high area under curves (0.90–0.98) and area under precision-recall curves (0.91–0.98). We found that lncRNA pairs with high similarity had more overlapped target genes. Further experiments showed that genes targeted by the same lncRNA sets had a strong likelihood of causing the same diseases, which could help in identifying disease-causing PCGs.

Availability and implementation
https://github.com/zty2009/LncRNA-target-gene.

Supplementary information
Supplementary data are available at Bioinformatics online.
AlphaFamImpute: high-accuracy imputation in full-sib families from genotype-by-sequencing data
Authors: Whalen Andrew , Gorjanc Gregor , Hickey John M 
Published: May 2020

Abstract

Summary
AlphaFamImpute is an imputation package for calling, phasing and imputing genome-wide genotypes in outbred full-sib families from single nucleotide polymorphism (SNP) array and genotype-by-sequencing (GBS) data. GBS data are increasingly being used to genotype individuals, especially when SNP arrays do not exist for a population of interest. Low-coverage GBS produces data with a large number of missing or incorrect naïve genotype calls, which can be improved by identifying shared haplotype segments between full-sib individuals. Here, we present AlphaFamImpute, an algorithm specifically designed to exploit the genetic structure of full-sib families. It performs imputation using a two-step approach. In the first step, it phases and imputes parental genotypes based on the segregation states of their offspring (i.e. which pair of parental haplotypes the offspring inherited). In the second step, it phases and imputes the offspring genotypes by detecting which haplotype segments the offspring inherited from their parents. With a series of simulations, we find that AlphaFamImpute obtains high-accuracy genotypes, even when the parents are not genotyped and individuals are sequenced at &lt;1x coverage.

Availability and implementation
AlphaFamImpute is available as a Python package from the AlphaGenes website http://www.AlphaGenes.roslin.ed.ac.uk/AlphaFamImpute.

Supplementary information
Supplementary data are available at Bioinformatics online.
bGWAS: an R package to perform Bayesian genome wide association studies
Authors: Mounier Ninon , Kutalik Zoltán 
Published: May 2020

Abstract

Summary
Increasing sample size is not the only strategy to improve discovery in Genome Wide Association Studies (GWASs) and we propose here an approach that leverages published studies of related traits to improve inference. Our Bayesian GWAS method derives informative prior effects by leveraging GWASs of related risk factors and their causal effect estimates on the focal trait using multivariable Mendelian randomization. These prior effects are combined with the observed effects to yield Bayes Factors, posterior and direct effects. The approach not only increases power, but also has the potential to dissect direct and indirect biological mechanisms.

Availability and implementation
bGWAS package is freely available under a GPL-2 License, and can be accessed, alongside with user guides and tutorials, from https://github.com/n-mounier/bGWAS.

Supplementary information
Supplementary data are available at Bioinformatics online.
Eocene palms from central Myanmar in a South-East Asian and global perspective: evidence from the palynological record
Authors: Huang Huasheng , Morley Robert , Licht Alexis , Dupont-Nivet Guillaume , Grímsson Friðgeir , Zetter Reinhard , Westerweel Jan , Win Zaw , Wa Aung Day , Hoorn Carina 
Published: May 2020

AbstractIn the Palaeogene, pollen assemblages at low and mid latitudes are characterized by abundant palm and palm-like (PPL) taxa. Although these taxa have been widely reported, their occurrence in the Palaeogene of Myanmar remains poorly documented. Here we report on the morphology of PPL pollen along a middle to upper Eocene sedimentary sequence in central Myanmar and discuss their nearest living relatives (NLRs). Principal components analysis (PCA) indicates that Palmaepollenites kutchensis, Dicolpopollis and Longapertites were dispersed from freshwater plants, whereas the parent taxon of Proxapertites operculatus was probably a member of the coastal vegetation in the manner of Spinizonocolpites. This, with sedimentological data, suggests a palaeoenvironmental change from a brackish, tidally influenced environment to a fully freshwater setting through the late Eocene. Additionally, we mapped and compared the geographical distribution of selected Eocene palm taxa and their NLRs, and found that their distributions shrank after the Eocene. Moreover, in the Palaeogene, species diversity of selected PPL taxa seems lower in Myanmar than in the Indian subcontinent and other regions in South-East Asia. We hypothesize that in the Eocene the Indo–Asian collision zone formed a ‘hotspot’ for palm diversity, which is reflected in species-rich palynofloras. However, the local palm diversity declined after the Eocene, whereas, at the global level, palm distribution was distinctly reduced between the Eocene and the present. We propose that the retreat of the palms may have occurred as early as the Eocene – Oligocene Transition (EOT), but this remains to be confirmed by the study of EOT pollen records in tropical regions.
Personalized Nutrition for Inflammatory Bowel Disease
Authors: Collins Colm B , Roche Helen M 
Published: May 2020

Lay SummaryA person’s diet may impact inflammatory bowel disease (IBD) risk. IBD is an inflammatory condition. We explore how certain foods may trigger, or indeed attenuate, inflammation in some IBD patients, but not others. Greater knowledge is needed underpinning personalized nutrition within effective medical management.
GTDB: an integrated resource for glycosyltransferase sequences and annotations
Authors: Zhou Chenfen , Xu Qingwei , He Sheng , Ye Wei , Cao Ruifang , Wang Pengyu , Ling Yunchao , Yan Xing , Wang Qingzhong , Zhang Guoqing 
Published: May 2020

AbstractGlycosyltransferases (GTs), a large class of carbohydrate-active enzymes, adds glycosyl moieties to various substrates to generate multiple bioactive compounds, including natural products with pharmaceutical or agrochemical values. Here, we first collected comprehensive information on GTs, including amino acid sequences, coding region sequences, available tertiary structures, protein classification families, catalytic reactions and metabolic pathways. Then, we developed sequence search and molecular docking processes for GTs, resulting in a GTs database (GTDB). In the present study, 520 179 GTs from approximately 21 647 species that involved in 394 kinds of different reactions were deposited in GTDB. GTDB has the following useful features: (i) text search is provided for retrieving the complete details of a query by combining multiple identifiers and data sources; (ii) a convenient browser allows users to browse data by different classifications and download data in batches; (iii) BLAST is offered for searching against pre-defined sequences, which can facilitate the annotation of the biological functions of query GTs; and lastly, (iv) GTdock using AutoDock Vina performs docking simulations of several GTs with the same single acceptor and displays the results based on 3Dmol.js allowing easy view of models.
Influence of prosthesis-related factors on the occurrence of early leaflet thrombosis after transcatheter aortic valve implantation
Authors: Breitbart Philipp , Pache Gregor , Minners Jan , Hein Manuel , Schröfel Holger , Neumann Franz-Josef , Ruile Philipp 
Published: May 2020

Abstract

Aims
Early leaflet thrombosis (LT) is a well-described phenomenon after transcatheter aortic valve implantation (TAVI) with an incidence around 15%. Data about predictors of LT are scarce. The purpose of the study was to investigate the influence of prosthesis-related factors on the occurrence of LT.

Materials and results
Fusion imaging of pre- and post-procedural computed tomography angiography was performed in 55 TAVI patients with LT and 140 selected patients as control groups (85 patients in an unmatched and 55 in a matched control) to obtain a 3D reconstruction of the transcatheter heart valve (THV) within the native annulus region. All patients received a balloon-expandable Sapien 3 THV. The THV length above and below the native annulus was measured within the fused images to assess the implantation depth. The deployed THV area was quantified on three heights (left ventricular outflow tract end, stent centre, and aortic end) to determine the average expansion of the prosthesis as percent of the nominal area. We also calculated the extent of prosthesis waist in percent of maximum area. After multivariate adjustment, the extent of THV waist [odds ratio (OR) per 10% (confidence interval, CI) 0.636 (0.526–0.769), P &lt; 0.001] as prosthesis-related factor and previous oral anticoagulation [OR (CI) 0.070 (0.020–0.251), P &lt; 0.001] had significant, independent influence on the occurrence of LT. The implantation depth showed no influence on LT manifestation (P = 0.704).

Conclusion
Besides the absence of previous oral anticoagulation, a less pronounced waist of the implanted THV was a prosthesis-position-related independent predictor of LT after TAVI using the Sapien 3.
Unreliable Protection: An Experimental Study of Experts’ In Bello Proportionality Decisions
Authors: Statman Daniel , Sulitzeanu-Kenan Raanan , Mandel Micha , Skerker Michael , de Wijze Stephen 
Published: May 2020

Abstract
The proportionality principle is an international humanitarian law requirement intended to constrain the use of military force in order to protect civilians in armed conflicts. This research experimentally assesses the reliability of its application by legal and moral experts (in 11 countries), by military officers (in two countries) and by laypeople. Reliability was evaluated according to three criteria: inter-expert convergence; sensitivity to relevant factors; and robustness – relative (lack of) susceptibility to biases. Unlike laypeople, experts and military officers performed well on the sensitivity criterion and manifested an appropriate understanding of the principle at the abstract level. However, both groups of experts failed to reach reasonable judgment convergence. These findings cast doubt on the reliability of the protection provided to civilians during warfare, even when warring parties attempt to abide by the proportionality principle.
Acute and mid-term outcome of ethanol infusion of vein of Marshall for the treatment of perimitral flutter
Authors: Takigawa Masateru , Vlachos Konstantinos , Martin Claire A , Bourier Felix , Denis Arnaud , Kitamura Takeshi , Cheniti Ghassen , Lam Anna , Martin Ruairidh , Frontera Antonio , Thompson Nathaniel , Massoullié Grégoire , Wolf Michael , Escande William , André Clémentine , Zeng Li-Jun , Nakatani Yosuke , Nakashima Takashi , Pillois Xavier , Ramirez Daniel , Duchateau Josselin , Pambrun Thomas , Sacher Frederic , Cochet Hubert , Hocini Mélèze , Haïssaguerre Michel , Jaïs Pierre , Derval Nicolas 
Published: May 2020

Abstract

Aims
We hypothesized that an epicardial approach using ethanol infusion in the vein of Marshall (EIVOM) may improve the result of ablation for perimitral flutter (PMF).

Methods and results
We studied 103 consecutive patients with PMF undergoing high-resolution mapping. The first 71 were treated with radiofrequency (RF) ablation alone (RF-group), and the next 32 underwent EIVOM followed by RF on the endocardial and epicardial mitral isthmus (EIVOM/RF-group). Contact force was not measured during ablation. Acute and 1-year outcomes were compared. Flutter termination rates were similar between the RF-group (63/71, 88.7%) and EIVOM/RF-group (31/32, 96.8%, P = 0.27). Atrial tachycardia (AT) terminated with EIVOM alone in 22/32 (68.6%) in the EIVOM/RF-group. Bidirectional block of mitral isthmus was always achieved in the EIVOM/RF-group, but significantly less frequently achieved in the RF-group (62/71, 87.3%; P = 0.05). Median RF duration for AT termination/conversion was shorter [0 (0–6) s in the EIVOM/RF-group than 312 (55–610) s in the RF-group, P &lt; 0.0001], as well as for mitral isthmus block in the EIVOM/RF-group [246 (0–663) s] than in the RF-group [900 (525–1310) s, P &lt; 0.0001]. Pericardial effusion was observed in 1/32 (3.2%) in EIVOM/RF-group and 5/71 (7.0%) in RF-group (P = 0.66); two in RF-group required drainage and one of them developed subsequent ischaemic stroke. One-year follow-up demonstrated fewer recurrences in the EIVOM/RF-group [6/32 (18.8%)] than in the RF-group [29/71 (40.8%), P = 0.04]. By multivariate analysis, only EIVOM was significantly associated with less AT recurrence (hazard ratio = 0.35, P = 0.018).

Conclusion
Ethanol infusion in the vein of Marshall may reduce RF duration required for PMF termination as well as for mitral isthmus block without severe complications, and the mid-term outcome may be improved by this approach.
Remote monitoring of cardiac implanted electronic devices: legal requirements and ethical principles - ESC Regulatory Affairs Committee/EHRA joint task force report
Authors: Nielsen Jens Cosedis , Kautzner Josef , Casado-Arroyo Ruben , Burri Haran , Callens Stefaan , Cowie Martin R , Dickstein Kenneth , Drossart Inga , Geneste Ginger , Erkin Zekeriya , Hyafil Fabien , Kraus Alexander , Kutyifa Valentina , Marin Eduard , Schulze Christian , Slotwiner David , Stein Kenneth , Zanero Stefano , Heidbuchel Hein , Fraser Alan G 
Published: May 2020

Abstract
The European Union (EU) General Data Protection Regulation (GDPR) imposes legal responsibilities concerning the collection and processing of personal information from individuals who live in the EU. It has particular implications for the remote monitoring of cardiac implantable electronic devices (CIEDs). This report from a joint Task Force of the European Heart Rhythm Association and the Regulatory Affairs Committee of the European Society of Cardiology (ESC) recommends a common legal interpretation of the GDPR. Manufacturers and hospitals should be designated as joint controllers of the data collected by remote monitoring (depending upon the system architecture) and they should have a mutual contract in place that defines their respective roles; a generic template is proposed. Alternatively, they may be two independent controllers. Self-employed cardiologists also are data controllers. Third-party providers of monitoring platforms may act as data processors. Manufacturers should always collect and process the minimum amount of identifiable data necessary, and wherever feasible have access only to pseudonymized data. Cybersecurity vulnerabilities have been reported concerning the security of transmission of data between a patient’s device and the transceiver, so manufacturers should use secure communication protocols. Patients need to be informed how their remotely monitored data will be handled and used, and their informed consent should be sought before their device is implanted. Review of consent forms in current use revealed great variability in length and content, and sometimes very technical language; therefore, a standard information sheet and generic consent form are proposed. Cardiologists who care for patients with CIEDs that are remotely monitored should be aware of these issues.