bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence of Hepatitis B Virus (HBV) Basal Core Promoter/Precore region molecular variants among HIV/HBV co-infected and HBV mono-infected patients in Ile-Ife, Nigeria
Authors: Osasona Oluwadamilola Gideon , Boudarene Lydia , Adewale-Fasoro Opeoluwa , George Uwem , Oguzie Judith , Ariyo Olumuyiwa Elijah , Olumade Testimony J. , Adeniyi Awe , Adewumi Moses Olubusuyi , Adeniji Adekunle Johnson 
Published: July 2020

AbstractIntroductionEvolution of phenotypic diversity among viruses occurs as an escape mechanism against host immune pressure or drug selective pressure. Among HIV/HBV co-infected individuals, various HBV basal core promoter (BCP)/precore (PC) region molecular mutants had been reported with associated phenotypic defect in HBeAg production. The emergence of HBeAg negative variants of HBV in HIV co-infected individuals have profound implication on the diagnosis, management and prognosis of this subset of individuals. This includes delayed clearance of HBV, early development of adverse hepatic events such as liver cirrhosis and hepatocellular carcinoma. Currently, little is known about HBV BCP/PC region genomic heterogeneity in HIV/HBV co-infected patients in Nigeria. Therefore, this study was focussed on investigating evidence of precore/core region genomic variability among HIV/HBV co-infected patients in Nigeria.Materials and methodsA total of 40 patients (20 HIV/HBV co-infected and 20 HBV mono-infected samples) were enrolled into the study and subsequently tested for HBsAg, HBeAg and HBeAb using specific Enzyme-Linked Immunosorbent Assay (ELISA). The BCP/PC genome regions (nucleotides 1653-1959) were amplified using a nested PCR assay and then subjected to BCP/PC mutational analysis in genome sites affecting HBeAg expression especially at the BCP transcriptional and PC Translational stop codon sites.ResultsOverall, 5(83.3%) of the six exploitable sequences after analysis showed various BCP/PC mutations. Only 1(16.6%) sequence from an HIV/HBV co-infected patient had the BCP transcriptional (double mutation; A1762T/G1764A) mutant. Analysis of the PC translational stop codon showed 4 (66.6%) having the G1896A mutants while 33.3% (2) had G1899A mutants.ConclusionThis study has broadened the available evidence of BCP/PC region molecular mutants among HIV/HBV co-infected patients in Nigeria and assessed the difference of mutation prevalence in comparison with HBV mono-infected cohort. We therefore recommend that HIV/HBV co-infected patients be routinely screened for hepatitis B virus precore region mutants to improve their patient outcome.
The left dorsal stream causally mediates the tone labeling in absolute pitch
Authors: Rogenmoser Lars , Arnicane Andra , Jäncke Lutz , Elmer Stefan 
Published: July 2020

AbstractBackgroundAbsolute pitch (AP) refers to the ability of effortlessly identifying given pitches without the reliance on any reference pitch. Correlative evidence suggests that the left posterior dorsolateral prefrontal cortex (DLPFC) is responsible for the process underlying pitch labeling in AP.ObjectiveHere, we aimed at investigating the causal relationship between the DLPFC and the pitch-labeling process underlying AP.MethodsTo address this, we measured sight-reading performance of right-handed AP possessors and matched control musicians (N=18 per sample) under cathodal and sham transcranial direct current stimulation of the left DLPFC. The participants were instructed to report visually presenting notations as accurately and fast as possible by playing with their right hand on a piano. The notations were simultaneously presented with distracting auditory stimuli that either matched or mismatched them in different semitone degrees.ResultsUnlike the control participants, the AP possessors revealed an interference effect in that they responded slower in mismatching conditions than in the matching one. Under cathodal stimulation, half of the time discrepancies between matching and mismatching conditions vanished; specifically, the ones with small up to moderate deviations.ConclusionsThese findings confirm that the pitch-labeling process underlying AP occurs automatically and is largely non-suppressible when triggered by tone exposure. The improvement of the AP possessors’ sight-reading performance in response to the suppression of the left DLPFC using cathodal stimulation confirms a causal relationship between this brain structure and pitch labeling.
Gut Microbiota Mediates High-Fiber Diet Alleviation of Maternal Obesity-Induced Cognitive and Social Deficits in Offspring
Authors: Liu Xiaoning , Li Xiang , Xia Bing , Jin Xin , Zeng Zhenhua , Yan Shikai , Li Ling , Yuan Shufen , Zhao Shancen , Dai Xiaoshuang , Yin Fei , Cadenas Enrique , Liu Rui Hai , Zhao Beita , Hou Min , Liu Zhigang , Liu Xuebo 
Published: July 2020

SUMMARYMaternal obesity has been reported to be related to the neurodevelopmental disorders in offspring. However, the underlying mechanisms and effective interventions remain unclear. Here, a cross-sectional study on 778 children aged 7-14 years in two cities of China indicates that the maternal obesity is highly associated with the poorer cognition and sociality of their children. Moreover, we also find that the maternal obesity in mice disrupts the behavior and the gut microbiome in the offspring, which are alleviated by a high-fiber diet in either dams or offspring. Co-housing and feces microbiota transplantation experiments reveal a causal relationship between the reshaped microbiota and the behavioral changes. Moreover, treatment of the microbiota-derived short-chain fatty acids exhibits a similar beneficial effect on alleviating the behavioral deficits in offspring. Together, our study purports the microbiota-metabolites-brain axis as a mechanism, and high-dietary fiber intake is a promising intervention against maternal obesity-induced cognitive and social dysfunctions.
PartSeg, a Tool for Quantitative Feature Extraction From 3D Microscopy Images for Dummies
Authors: Bokota Grzegorz , Sroka Jacek , Basu Subhadip , Das Nirmal , Trzaskoma Paweł , Yushkevich Yana , Grabowska Agnieszka , Magalska Adriana , Plewczyński Dariusz 
Published: July 2020

AbstractBackgroundBioimaging techniques offer a robust tool for studying molecular pathways and morphological phenotypes of cell populations subjected to various conditions. As modern high resolution 3D microscopy provides access to an ever-increasing amount of high quality images, there arises a need for their analysis in an automated, unbiased and simple way.Segmentation of structures within cell nucleus, which is the focus of this paper, presents a new layer of complexity in the form of dense packing and significant signal overlap.At the same time the available segmentation tools provide a steep learning curve for new users with limited technical background. This is especially apparent in bulk processing of image sets, which requires the use of some form of programming notation.ResultsIn this paper, we present PartSeg, a tool for segmentation and reconstruction of 3D microscopy images, optimised for the study of cell nucleus. PartSeg integrates refined versions of several state-of-the-art algorithms, including a new multi-scale approach for segmentation and quantitative analysis of 3D microscopy images.The features and user-friendly interface of PartSeg were carefully planned with biologists in mind, based on analysis of multiple use cases and difficulties encountered with other tools, to offer ergonomic interface with a minimal entry barrier. Bulk processing in an ad-hoc manner is possible without the need for programmer support. As the size of datasets of interest grows, such bulk processing solutions become essential for proper statistical analysis of results.Advanced users can use PartSeg components as a library within Python data processing and visualisation pipelines, for example within Jupyter notebooks. The tool is extensible so that new functionality and algorithms can be added by the use of plugins.For biologists the utility of PartSeg is presented in several scenarios, showing the quantitative analysis of nuclear structures.ConclusionsIn this paper, we have presented PartSeg which is a tool for precise and verifiable segmentation and reconstruction of 3D microscopy images. PartSeg is optimised for cell nucleus analysis and offers multiscale segmentation algorithms best-suited for this task. PartSeg can also be used for bulk processing of multiple images and its components can be reused in other systems or computational experiments.Contactg.bokota@cent.uw.edu.pl,a.magalska@nencki.edu.pl,d.plewczynski@cent.uw.edu.pl
A novel bioinformatics approach to reveal the role of circadian oscillations in AD development
Authors: Ji Zhiwei , Shang Dazhi , Kim Pora , Yang Mengyuan , Wu Sijia , Zhao Weiling , Kim Eunju , Wirianto Marvin , Chen Zheng , Yoo Seung-Hee , Zhou Xiaobo 
Published: July 2020

AbstractAltered circadian gene expression may contribute to Alzheimer’s disease (AD) progression. Unfortunately, sampling the central nervous system (CNS) at multiple time points is not feasible. Moreover, there are no AD-related time-series transcriptome datasets available for studying these circadian patterns and their impacts on AD development. In this study, we introduce a novel computational platform, Event-driven Sample Ordering for Circadian Variation Detection (ESOCVD), to reveal rhythmic patterns of gene expression of AD using untimed transcriptome datasets. ESOCVD was applied to 20 untimed gene expression profiles of 16 brain regions from approximately 3000 AD patients in public transcriptome databases. Our analysis revealed five types of circadian alteration patterns in ~2,000 circadian genes in different brain regions of AD patients. Further analyses of additional databases confirmed that our analytical platform can be applied to identify the evolutionary dynamics of circadian variation during the process of AD development. Through the gene expression correlation analysis for our 8 circadian genes identified from AMP-AD MSBB cohorts, we identified stage-specifically enriched biological processes with anticipated context. Gene expression analysis of AD mouse brain tissues further substantiated the predictions of the ESOCVD model. In summary, ESOCVD is highly versatile in bridging circadian research and precision medicine.
Early acquisition of conserved, lineage-specific proteins currently lacking functional predictions were central to the rise and diversification of archaea
Authors: Méheust Raphaël , Castelle Cindy J. , Jaffe Alexander L. , Banfield Jillian F. 
Published: July 2020

AbstractRecent genomic analyses of Archaea have profoundly reshaped our understanding of their distribution, functionalities and roles in eukaryotic evolution. Within the domain, major supergroups are Euryarchaeota, which includes many methanogens, the TACK, which includes Thaumarchaeaota that impact ammonia oxidation in soils and the ocean, the Asgard, which includes lineages inferred to be ancestral to eukaryotes, and the DPANN, a group of mostly symbiotic small-celled archaea. Here, we investigated the extent to which clustering based on protein family content recapitulates archaeal phylogeny and identified the proteins that distinguish the major subdivisions. We also defined 10,866 archaeal protein families that will serve as a community resource. Clustering based on these families broadly recovers the archaeal phylogenetic tree. Interestingly, all major groups are distinguished primarily by the presence of families of conserved hypothetical proteins that are either novel or so highly diverged that their functions are obscured. Given that these hypothetical proteins are near ubiquitous within phyla, we conclude that they were important in the origin of most of the major archaeal lineages.
Electromyography Classification during Reach-to-Grasp Motion using Manifold Learning
Authors: Lashgari Elnaz , Maoz Uri 
Published: July 2020

AbstractElectromyography (EMG) is a simple, non-invasive, and cost-effective technology for sensing muscle activity. However, EMG is also noisy, complex, and high-dimensional. It has nevertheless been widely used in a host of human-machine-interface applications (electrical wheelchairs, virtual computer mice, prosthesis, robotic fingers, etc.) and in particular to measure reaching and grasping motions of the human hand. Here, we developd a more automated pipeline to predict object weight in a reach-and-grasp task from an open dataset relying only on EMG data. In that we shifted the focus from manual feature-engineering to automated feature-extraction by using raw (filtered) EMG signals and thus letting the algorithms select the features. We further compared intrinsic EMG features, derived from several dimensionality-reduction methods, and then ran some classification algorithms on these low-dimensional representations. We found that the Laplacian Eigenmap algorithm generally outperformed other dimensionality-reduction methods. What is more, optimal classification accuracy was achieved using a combination of Laplacian Eigenmaps (simple-minded) and k-Nearest Neighbors (88% for 3-way classification). Our results, using EMG alone, are comparable to others in the literature that used EMG and EEG together. They also demonstrate the usefulness of dimensionality reduction when classifying movement based on EMG signals and more generally the usefulness of EMG for movement classification.
Ecdysone regulates theDrosophilaimaginal disc epithelial barrier, determining the duration of regeneration checkpoint delay
Authors: DaCrema Danielle , Bhandari Rajan , Karanja Faith , Yano Ryunosuke , Halme Adrian 
Published: July 2020

AbstractRegeneration ofDrosophilaimaginal discs, larval precursors to adult tissues, produces a systemic response, a regeneration checkpoint that coordinates regenerative growth with developmental progression. This regeneration checkpoint is coordinated by the release of the relaxin-family peptide Dilp8 from regenerating tissues. Secreted Dilp8 protein can be detected within the imaginal disc lumen. The disc epithelium separates from the lumen from the larval hemolymph and the targets for Dilp8 activity in the brain and prothoracic gland. Here we demonstrate that the imaginal disc epithelial barrier limits Dilp8 signaling and checkpoint delay. We also observe that the wing imaginal disc barrier becomes more restrictive during development, becoming impermeable only at end of the final larval instar. This change in barrier permeability is driven by the steroid hormone ecdysone and correlates with changes in localization of Coracle, a component of the septate junctions that is required for the late, impermeable epithelial barrier. Based on these observations, we propose that the imaginal disc epithelial barrier regulates the duration of the regenerative checkpoint, providing a mechanism by which tissue function can signal the completion of regeneration.Summary StatementEcdysone signaling directs theDrosophilathird instar imaginal disc epithelial barrier to mature, becoming more restrictive. This mature barrier limits Dilp8 signaling and determines the duration of the regeneration checkpoint.
DLPAlign: A Deep Learning based Progressive Alignment for Multiple Protein Sequences
Authors: Kuang Mengmeng 
Published: July 2020

AbstractThis paper proposed a novel and straightforward approach to improve the accuracy of progressive multiple protein sequence alignment. We trained a decision-making model based on the convolutional neural networks and bi-directional long short term memory networks, and based on this model, we progressively aligned the input sequences by calculating different posterior probability matrixes.To test the accuracy of this approach, we have implemented a multiple sequence alignment tool called DLPAlign and compared its performance with eleven leading alignment methods on three empirical alignment benchmarks (BAliBASE, OXBench and SABMark). Our results show that DLPAlign can get the best total-column scores on the three benchmarks. When evaluated against the 711 low similarity families with average PID ≤ 30%, DLPAlign improved about 2.8% over the second-best MSA software.Besides, we also compared the performance of DLPAlign and other alignment tools on a real-life application, namely protein secondary structure prediction on four protein sequences related to SARS-COV-2, and DLPAlign provides the best result in all cases.
Antifibrotic activity of a rho-kinase inhibitor restores outflow function and intraocular pressure homeostasis
Authors: Li Guorong , Lee Chanyoung , Read A. Thomas , Wang Ke , Navarro Iris , Cui Jenny , Young Katherine M. , Gorijavolu Rahul , Sulchek Todd , Kopczynski Casey C. , Farsiu Sina , Samples John R. , Challa Pratap , Ethier C. Ross , Stamer W. Daniel 
Published: July 2020

AbstractGlucocorticoids are widely used as an ophthalmic medication. A common, sight-threatening adverse event of glucocorticoid usage is ocular hypertension, caused by dysfunction of the conventional outflow pathway. We report that netarsudil, a rho-kinase inhibitor, rapidly reversed glucocorticoid-induced ocular hypertension in patients whose intraocular pressures were uncontrolled by standard medications. Mechanistic studies in our established mouse model of glucocorticoid-induced ocular hypertension show that netarsudil both prevented and reversed intraocular pressure elevation. Further, netarsudil reversed characteristic steroid-induced pathologies as assessed by quantification of outflow function and tissue stiffness, and morphological and immunohistochemical indicators of tissue fibrosis. Thus, rho-kinase inhibitors act directly on conventional outflow cells to efficaciously prevent or reverse fibrotic disease processes in glucocorticoid-induced ocular hypertension. These data motivate a novel indication for these agents to prevent or treat ocular hypertension secondary to glucocorticoid administration, and demonstrate the antifibrotic effects of rho-kinase inhibitors in an immune-privileged environment.
Tensor-decomposition-based unsupervised feature extraction applied to prostate cancer multiomics data
Authors: Taguchi Y-h. , Turki Turki 
Published: July 2020

AbstractThe largepsmallnproblem is a challenge without a de facto standard method available to it. In this study, we propose a tensor-decomposition (TD)-based unsupervised feature extraction (FE) formalism applied to multiomics datasets, in which the number of features is more than 100,000 whereas the number of samples is as small as about 100, hence constituting a typical largepsmallnproblem. The proposed TD-based unsupervised FE outperformed other conventional supervised feature selection methods, random forest, categorical regression (also known as analysis of variance, or ANOVA), penalized linear discriminant analysis, and two unsupervised methods, multiple non-negative matrix factorization and principal component analysis (PCA) based unsupervised FE when applied to synthetic datasets and four methods other than PCA based unsupervised FE when applied to multiomics datasets. The genes selected by TD-based unsupervised FE were enriched in genes known to be related to tissues and transcription factors measured. TD-based unsupervised FE was demonstrated to be not only the superior feature selection method but also the method that can select biologically reliable genes. To our knowledge, this is the first study in which TD-based unsupervised FE has been successfully applied to the integration of this variety of multiomics measurements.
Overcoming barriers to disseminate effective smoking cessation treatments globally
Authors: Patwardhan Sudhanshu , Rose Jed E. 
Published: July 2020

Purpose
The purpose of this paper is to review the barriers in the dissemination of effective smoking cessation treatments and services globally. Offering tobacco users help to stop using tobacco is a key demand reduction measure outlined under Article 14 of the World Health Organisation (WHO) Framework Convention on Tobacco Control (FCTC). Implementing Article 14 can reap great dividends for the billion plus tobacco users around the world and their families, friends and societies.

Design/methodology/approach
A review of the status of the global implementation of Article 14 using available literature on smoking cessation products, services and national guidelines. Discussing innovative approaches being currently explored in South Asia that can lead to faster adoption and implementation of Article 14 globally.

Findings
Major gaps remain in cessation products’ availability and resource allocation for cessation services globally. Current licensed products are falling short on delivering and sustaining smoking cessation. Innovation in cessation products and services needs to build on learnings in nicotine pharmacokinetics, behavioural insights from consumer research and tap into 21st century tools such as mobile based apps. National implementation of FCTC’s Article 14 needs to follow guidelines that encourage integration into existing health programmes and health-care practitioners’ (HCPs) upskilling.

Originality/value
Smoking cessation is a desirable health outcome and nicotine replacement products are a means of achieving cessation through tobacco harm reduction. E-cigarettes are sophisticated nicotine replacement products. Innovation is urgently needed to fill the gaps in smoking cessation products and services, and for converting global policy into local practice. In low- and middle-income countries (LMICs), HCPs’ knowledge, attitudes and practice regarding tobacco use and cessation may hold the key to rapidly scaling up cessation support and delivery to achieve FCTC objectives sooner. Additionally, HCPs can play an important role in offering smoking cessation support in existing national health programmes for TB, cancer screening and maternal and child health. Also, widely prevalent smartphone devices may deliver smoking cessation through telemedicine in LMICs sooner, leapfrogging the hurdles of the existing health-care infrastructure.
Government intervention in the market for electronic nicotine delivery systems (ENDS). The known, the unknown and challenges
Authors: Yurekli Ayda A. , Kovacevic Patricia , Sunley Emil , Ranganathan Karthik 
Published: July 2020

Purpose
This paper aims to describe the various government measures that regulate the market for novel tobacco harm reduction products (THRPs), with an emphasis on e-cigarettes [electronic nicotine delivery systems (“ENDS”)], and evaluates the public health impact of excise taxes levied on these products.

Design/methodology/approach
The paper reviews the economic research on the impact ENDS. Using cited evidence, the paper compares the tax treatment of ENDS and cigarettes and provides a simulation of potential lives that can be saved under alternative tax treatment of ENDS.

Findings
ENDS are considerably less harmful than cigarettes. Imposing the same tax burden on them (per unit of “harm”) as on cigarettes leads to poorer health outcomes. Differential tax treatment of ENDS will encourage more cigarette smokers to switch to ENDS and could save millions of lives worldwide.

Research limitations/implications
Country experiences with regulatory measures on ENDS are limited to those with high THRP penetration. The paper’s simulation analysis used evidence from a limited number of studies. Rigorous economic analysis is needed to understand how ENDS could save lives and could prevent expected one billion premature deaths by the end of this century.

Originality/value
The paper uses research evidence in its analysis of the impact that the differential taxation of cigarettes and ENDS would have. It also provides a rough estimate of the number of lives that could be saved if more smokers who are trying to quit can make the switch to ENDS.