bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance of five metagenomic classifiers for virus pathogen detection using respiratory samples from a clinical cohort
Authors: Carbo Ellen C. , Sidorov Igor A. , van Rijn-Klink Anneloes L. , Pappas Nikos , van Boheemen Sander , Mei Hailiang , Hiemstra Pieter S. , Eagan Tomas M. , Claas Eric C.J. , Kroes Aloys C.M. , de Vries Jutte J.C. 
Published: January 2022

AbstractViral metagenomics is increasingly being applied in clinical diagnostic settings for detection of pathogenic viruses. While a number of benchmarking studies have been published on the use of metagenomic classifiers for abundance and diversity profiling of bacterial populations, studies on the comparative performance of the classifiers for virus pathogen detection are scarce.In this study, metagenomic data sets (N=88) from a clinical cohort of patients with respiratory complaints were used for comparison of the performance of five taxonomic classifiers: Centrifuge, Clark, Kaiju, Kraken2, and Genome Detective. A total of 1,144 positive and negative PCR results for a total of 13 respiratory viruses were used as gold standard. Sensitivity and specificity of these classifiers ranged from 83-100% and 90-99% respectively, and was dependent on the classification level and data pre-processing. Exclusion of human reads generally resulted in increased specificity. Normalization of read counts for genome length resulted in minor overall performance, however negatively affected the detection of targets with read counts around detection level. Correlation of sequence read counts with PCR Ct-values varied per classifier, data pre-processing (R2 range 15.1-63.4%), and per virus, with outliers up to 3 log10 reads magnitude beyond the predicted read count for viruses with high sequence diversity.In this benchmarking study, sensitivity and specificity were within the ranges of use for diagnostic practice when the cut-off for defining a positive result was considered per classifier.HighlightsThe performance of five metagenomic classifiers was assessed using datasets obtained from respiratory samples from a clinical cohort of patients88 samples were characterized by means of 1,144 respiratory virus PCR resultsUsing PCR as gold standard, sensitivity and specificity ranged from 83-100% and 90-99% respectively, with the overall highest scores resulting from amino-acid based classification by Kaiju classifier. Performance was dependent on classification level and exclusion of human reads prior to classification.Normalization of assigned read counts for corresponding genome lengths generally had minor effect on performance, but negatively affected the detection of target viruses with read counts around detection level.Correlation between sequence read counts and PCR Ct-values varied per classifier (12.1-62.7% at species level), per data pre-processing, and per virus. Outliers were detected of up to 3 log10 reads the predicted read counts for viruses with high sequence diversity.Sensitivity and specificity of the classifiers were within the range of use for diagnostic practice when combined with a determined cut-off for defining a positive result.
Mechanical strain stimulates COPII-dependent trafficking via Rac1
Authors: Phuyal Santosh , Djaerff Elena , Roux Anabel-Lise Le , Baker Martin J. , Fankhauser Daniela , Mahdizadeh Sayyed Jalil , Reiterer Veronika , Kahlhofer Jennifer C. , Teis David , Kazanietz Marcelo G. , Geley Stephan , Eriksson Leif , Roca-Cusachs Pere , Farhan Hesso 
Published: January 2022

AbstractSecretory trafficking from the endoplasmic reticulum (ER) is subject to regulation by extrinsic and intrinsic factors. While much of the focus has been on biochemical triggers, little is known whether and how the ER is subject to regulation by mechanical signals. Here, we show that COPII-dependent ER-export is regulated by mechanical strain. Mechanotransduction to the ER was mediated via a previously unappreciated ER-localized pool of the small GTPase Rac1. Mechanistically, we show that Rac1 interacts with the small GTPase Sar1 to drive budding of COPII carriers and stimulate ER-to-Golgi transport. Altogether, we establish an unprecedented link between mechanical strain and export from the ER.
Extraversion is associated with lower brain amyloid deposition in cognitively normal older adults
Authors: Oh Hwamee 
Published: January 2022

AbstractEmerging evidence suggests that some personality traits may link to the vulnerability to or protection for Alzheimer’s disease (AD). A causal mechanism underlying this relationship, however, remains largely unknown. Using 18F-Florbetaben positron emission tomography (PET) binding to beta-amyloid (Aβ) plaques, a pathological feature of AD, and functional magnetic resonance imaging (fMRI), we investigated pathological and functional correlates of extraversion and neuroticism in a group of healthy young and older subjects. We quantified a level of brain Aβ deposition in older individuals. Brain activity was measured in young adults using a task-switching fMRI paradigm. When we correlated personality scores of extraversion and neuroticism with these pathological and functional measures, higher extraversion, but not neuroticism, was significantly associated with lower global Aβ measures among older adults, accounting for age and sex. This association was present across widespread brain regions. Among young subjects, higher extraversion was associated with lower activity during task switching in anterior cingulate cortex, left anterior insular cortex, left putamen, and middle frontal gyrus bilaterally, while higher neuroticism was associated with increased activity throughout the brain. The present results suggest that possibly via efficient neuronal activity, extraversion, one of lifelong personality traits, may confer the protective mechanism against the development of Aβ pathology during aging.
Extracellular matrix deposition precedes muscle-tendon integration during murine forelimb morphogenesis
Authors: Leng Yue , Lipp Sarah N. , Bu Ye , Larson Hannah , Jacobson Kathryn R. , Calve Sarah 
Published: January 2022

AbstractThe development of a functional vertebrate musculoskeletal system requires the combination of contractile muscle and extracellular matrix (ECM)-rich tendons that transmit muscle-generated force to bone. Despite the different embryologic origins, muscle and tendon integrate at the myotendinous junction (MTJ) to seamlessly connect cells and ECM across this interface. While the cell-cell signaling factors that direct development have received considerable attention, how and when the ECM linking these tissues is deposited remains unknown. To address this gap, we analyzed the 3D distribution of different ECM and the influence of skeletal muscle in forelimbs from wildype (WT) and muscle-less Pax3Cre/Cre mice. At E11.5, prior to MTJ integration, an aligned ECM was present at the presumptive insertion of the long triceps into the WT ulna. Mechanically robust tendon-like and muscle compartmentalization structures, positive for type I collagen, type V collagen, and fibrillin-2, still formed when muscle was knocked out. However, MTJ-specific ECM was not observed when muscle was absent. Our results show that an ECM-based template forms independent of muscle, but muscle is needed for the proper assembly of ECM at the MTJ.Summary statementAn aligned ECM template connects tendon and muscle during limb development, independent of muscle progenitor migration into the limb; however, the assembly of MTJ-specific ECM requires the presence of muscle.
Ion transfer mechanisms in Mrp-type antiporters from high resolution cryoEM and molecular dynamics simulations
Authors: Lee Yongchan , Haapanen Outi , Altmeyer Anton , Kühlbrandt Werner , Sharma Vivek , Zickermann Volker 
Published: January 2022

AbstractMultiple resistance and pH adaptation (Mrp) cation/proton antiporters are essential for growth of a variety of halophilic and alkaliphilic bacteria under stress conditions. Mrp-type antiporters are closely related to the membrane domain of respiratory complex I. We determined the structure of the Mrp antiporter from Bacillus pseudofirmus by electron cryo-microscopy at 2.2 Å resolution. The structure resolves more than 99% of the sidechains of the seven membrane subunits MrpA to MrpG plus 360 water molecules, including ∼70 in putative ion translocation pathways. Molecular dynamics simulations based on the high-resolution structure revealed details of the antiport mechanism. We find that switching the position of a histidine residue between three hydrated pathways in the MrpA subunit is critical for proton transfer that drives gated transmembrane sodium translocation. Several lines of evidence indicate that the same histidine-switch mechanism operates in respiratory complex I.
The AAA-ATPase ATAD1 and its partners promote degradation of desmin intermediate filaments in muscle
Authors: Aweida Dina , Cohen Shenhav 
Published: January 2022

ABSTRACTMaintenance of desmin intermediate filaments (IF) is vital for muscle plasticity and function, and their perturbed integrity due to accelerated loss or aggregation causes atrophy and myopathies. Calpain-1-mediated disassembly of ubiquitinated desmin IF is a prerequisite for desmin loss, myofibril breakdown and atrophy. Because calpain-1 does not harbor a bona fide ubiquitin binding domain, the precise mechanism for desmin IF disassembly remains unknown. Here, we demonstrate that the AAA-ATPase, ATAD1, is required to facilitate disassembly and turnover of ubiquitinated desmin IF. We identified PLAA and UBXN4 as ATAD1’s interacting partners, and show they are required for desmin filaments turnover because their downregulation attenuated desmin loss upon denervation. The ATAD1-PLAA-UBXN4 complex binds desmin filaments and promotes a release of phosphorylated and ubiquitinated species into the cytosol, presenting ATAD1 as the only known AAA-ATPase that preferentially acts on phosphorylated substrates. Desmin filaments disassembly was accelerated by the coordinated functions of Atad1 and calpain-1, which interact in muscle. Thus, by extracting ubiquitinated desmin from the insoluble filament, ATAD1 may expose calpain-1 cleavage sites on desmin, consequently enhancing desmin solubilization and degradation in the cytosol.
Rural cooperatives in disaster risk reduction and management: contributions and challenges
Authors: Lawangen Abner 
Published: January 2022

PurposeThis paper is to contribute to addressing the knowledge gap on the roles of rural cooperatives in disaster risk reduction and management (DRRM).Design/methodology/approachThis study adopts a mixed-methods approach highlighting indigenous strategies of community engagement – the pantatabtaval/tong tongan (brainstorming and dialogs), pan-iestorya/dad-at (storytelling session) and field observations with 50 village-level cooperatives in Benguet, Philippines to understand their contributions to local DRRM.FindingsRural cooperatives in Benguet have evolved on their context of service from mere rural development to now include DRRM donations and aid for disaster-affected families, credit and loans are the most common services of these rural cooperative extended to their members to deal with risks of disasters.Originality/valueMost research on cooperatives focuses on their contribution to socio-economic development and only few dealt with DRRM. This paper explores the link of these rural organizations with DRRM drawing evidence from cooperatives in the rural communities of Benguet, Philippines.
Consumer adoption of mobile payment services during COVID-19: extending meta-UTAUT with perceived severity and self-efficacy
Authors: Upadhyay Nitin , Upadhyay Shalini , Abed Salma S. , Dwivedi Yogesh K. 
Published: January 2022

PurposeThe purpose of this paper is to identify and examine the important factors that could affect consumers' behavioural intention and use behaviour towards mobile payment services during COVID-19.Design/methodology/approachThe proposed model extends meta-Unified Theory of Acceptance and Use of Technology (meta-UTAUT) model with perceived severity and self-efficacy factors affecting consumers' behavioural intention and use behaviour towards mobile payment services. A convenient sampling technique has been utilized to gather data from a self-administered questionnaire. The data collection was restricted to the online mode to avoid any physical contact considering the COVID-19 situation.FindingsThe findings revealed that performance expectancy, effort expectancy and perceived severity have a significant positive impact on consumers' attitude; facilitating conditions has a significant positive impact on effort expectancy; self-efficacy has a significant positive impact on effort expectancy; attitude has a significant positive impact on behavioural intention; and behavioural intention has a significant positive impact on use behaviour. Social influence did not confirm any significant relationship.Research limitations/implicationsThe current research study has utilized a non-probability convenient sampling technique to gather data through a self-administered questionnaire. The data collection was restricted to the online mode to avoid any physical contact considering the COVID-19 situation. The respondents were adopters of mobile payment services. The scope of the study is the COVID-19 context or related chronic diseases context where major preventive mechanisms such as social distancing and avoidance of physical contacts are vital.Originality/valueThis study has extended the meta-UTAUT model with the COVID-19 context-specific constructs and relationships. The undertaken work has strengthened the explanability of the model. The inclusion of context relevant variables such as perceived severity and self-efficacy and their association with the existing meta-UTAUT framework have enriched the context of the study. The current study offers a holistic understanding of significant factors influencing Indian consumers’ adoption of mobile payment services in the COVID-19 context.
Framework and determinants of benchmarking: a theoretical analysis and case study in Vietnam
Authors: Hoang Viet , Nguyen Khanh-Duy , Nguyen Hoang-Le 
Published: January 2022

PurposeThis study aims to develop a benchmarking model with productivity, management, and sustainability indicators (PMS), measure the performance of furniture firms in Vietnam, explore the causes of performance gaps, and identify the barriers and factors of benchmarking practice.Design/methodology/approachThe article uses both qualitative and quantitative methods. Literature review, exploratory interviews and a grounded-theory process are employed to develop a benchmarking framework and identify performance gaps, barriers and factors of benchmarking practice. The PMS benchmarking model and quantitative analysis are utilized to assess performance indicators.FindingsThe study proposes the PMS benchmarking model and measures performance indicators of furniture firms. The sources of performance gaps are explored as design, material supply, the economy of scale, market, management systems and openness. Benchmarking practice encounters barriers of difficult indicators, unsuitable firms, insufficient benchmarking knowledge, reluctance to share data, unavailable and unreliable data, and weak engagement. Benchmarking practice is determined by core factors: leader; internal factors: systems, engagement, strategy, scope, culture; external factors: customers, suppliers, associations, support, competition.Practical implicationsFirms could learn benchmarking indicators and the causes of these gaps to improve their performance. When implementing a benchmarking study, scholars and practitioners need to pay attention to barriers and factors of the benchmarking practice to ensure effective results.Originality/valueThis study develops the PMS benchmarking model and estimates performance indicators in an emerging country with the performance gap justification. It provides readers with benchmarking barriers with solutions and success factors of benchmarking practice.
Debt maturity structure and firm investment in the financially constrained environment
Authors: Nouman Muhammad , Ahmad Ijaz , Siddiqi Muhammad Fahad , Khan Farman Ullah , Fayaz Mohammad , Shah Idrees Ali 
Published: January 2022

PurposeThe financial policies of the modern world corporations and their investment decisions are generally considered as interrelated because the agency problems, associated with the debt level and its maturity structure, give rise to incentives for overinvestment or underinvestment. The present study empirically investigates the linkage between debt maturity structure and firm investment in a financially constrained environment, using Pakistan as a case study, to determine how the institutional environment in which firms operate affect these decisions and their linkage.Design/methodology/approachThe empirical analysis is carried in a panel data setting using panel regression models as the baseline methods. Moreover, generalized methods of moments (GMM) estimators are used, coupled with the instrumental variables approach, for robustness and improving the efficiency and consistency of estimates.FindingsResults suggest that firms rely more on short financing in Pakistan. Thus, given the capital structure which is characterized by higher proportion of short-term financing, the higher level of leverage is less likely to cause underinvestment problem. However, the underinvestment problem do persists in the firms that have higher portion of long-term debt. These findings imply that the debt-overhang problem may persist even in the financially constrained environments where attractive investment opportunities are limited, and long-term financing is difficult to acquire.Originality/valueThis study contributes to the literature by revealing how corporate investment and financing decisions and their linkage is influenced by the institutional environment of the less developed countries which is characterized by underdeveloped financial markets, inefficient legal system and weak investor protection system.
Formation and development of taxation and legislation on administrative responsibility for tax offences in the Republic of Kazakhstan
Authors: Kussainova Aigul K. , Sabitova Ainur A. , Sabitova Shynar A. , Saparaliyeva Saule M. , Begaliyev Yernar N. 
Published: January 2022

Purpose
The relevance of this research topic lies in the fact that administrative responsibility for tax offences is one of the most complex sections of legislation providing for administrative responsibility, because an administrative offence in the field of taxation is considered inextricably with the norms of tax legislation. The purpose of this study is a comparative legal and historical analysis of the legislation on administrative responsibility for offences in the field of taxation and tax legislation of the Republic of Kazakhstan.

Design/methodology/approach
The research used general scientific, private scientific and legal methods of cognition, such as analysis, synthesis, historical, formal and logical methods, as well as the comparative-legal method, which was the main method of cognition in the study.

Findings
To reduce the number of administrative offences in the field of taxation, the study proposed the introduction of an open source of financial information on the income and taxes of tax collectors. The novelty of the research lies in the fact that taxation and administrative responsibility for the commission of offences in the field of taxation are studied in a simultaneous relationship with their formation and subsequent stages of development. The study examines the impact of the coronavirus pandemic on the development of legislation in the field of taxation and on administrative responsibility in the field of taxation.

Originality/value
This paper is devoted to the study of legal norms establishing administrative responsibility for offences in the field of taxation.
Financial risks and performance of conventional and Islamic banks: do reputational risk matters?
Authors: Butt Mahnoor Anjum , Ayub Huma , Latif Bilal , Asif Fawad , Shabbir Malik Shahzad , Raja Ammar Aftab 
Published: January 2022

Purpose
The purpose of this paper is to shed light on the reputational risk, which is elusive and difficult to measure due to the lack of its conclusive definition. Literature supports the notion that financial risks may translate into reputational risks that pose threat to bank performance. However, empirical investigations in this context are still at their nascent stage.

Design/methodology/approach
This study has used a panel dataset for the sample of 24 conventional and Islamic banks regarding the period 2007–2017 by using a structural equation model.

Findings
The results of this study show that reputational risk partially mediates the relationship between financial risks and the performance of conventional banks. However, for Islamic banks, the reputational risk remains insignificant as a mediator. This study provides significant implications to risk managers in banks, regulators and academics to understand the role of reputational risk linked to financial risks for the improvement of bank performance.

Originality/value
This study aims to add to the literature by measuring reputational risk through the shareholders reputational score index, which is used as a mediator to determine whether financial risks of banks affect the performance of conventional and Islamic banks in Pakistan.
Wavelet power spectrum analysis of ETF’s tracking error
Authors: Nieves-González Aniel , Rodríguez Javier , Vega Vilca José 
Published: January 2022

PurposeThis study examines the tracking error (TE) of a sample of sector exchange traded funds (ETFs) using spectral techniques.Design/methodology/approachTE is examined by computing its power spectrum using the wavelet transform. The wavelet transform maps the TE time series from the time domain to the time–frequency domain. Albeit the wavelet transform is a more complicated mathematical tool compared with the Fourier transform, it also has important advantages such as that it allows to analyze non-stationary data and to detect transient behavior.FindingsResults show that changes in the TE of a sample of sector ETFs are captured by the wavelet transform. Moreover, the authors also find that the wavelet coherence function can be used as a measure of TE in the time–frequency domain.Originality/valueThe study shows that the wavelet coherence function can be used as a reliable measure of TE.