bluuebunny/crossref_metadata_2025_split huggingface dataset:
Glby, is a PBP with β-lactamase activity and is required for in vivo viability of M. abscessus
Authors: Galanis Christos , Maggioncalda Emily C. , Kumar Gaurav , Lamichhane Gyanu 
Published: July 2021

ABSTRACTThe prevalence of Mycobacteroides abscessus, Mab, (also known as Mycobacterium abscessus) has been increasing steadily globally. Patients with structural lung conditions such as bronchiectasis, cystic fibrosis and chronic obstructive pulmonary disease are at high risk of developing pulmonary Mab disease. The disease is often recurrent as the current treatment regimen is considered sub-efficacious. The cell wall peptidoglycan of bacteria is required for their viability and its biosynthetic pathway is enriched in proteins whose inhibition is the basis for two of the most widely used classes of antibiotics to treat bacterial infections. The peptidoglycan of Mab is distinct from that of most bacteria as its synthesis involves penicillin binding proteins (PBP) and L,D-transpeptidases. Here, we demonstrate that Mab gene locus MAB_3167c encodes a PBP (hereafter referred to as Glby) and is required for normal planktonic growth in liquid broth. Glby exhibits a strong β-lactamase activity and is sensitive to β-lactamase inhibitors. In a mouse model of pulmonary Mab disease, mutant lacking this gene was unable to proliferate, gradually cleared and undetectable after three weeks. In a collection of 1.046 Mab clinical isolates, there is evidence that changes in amino acid sequence that compromise Glby function are not favored. These evidences suggest that an agent that can inhibit Glby in vivo has the potential to be an efficacious treatment against Mab disease.
Chemically Induced Senescence in Human Stem Cell-Derived Neurons Promotes Phenotypic Presentation of Neurodegeneration
Authors: Fathi Ali , Mathivanan Sakthikumar , Kong Linghai , Petersen Andrew J , Harder Cole R. K. , Block Jasper , Miller Julia Marie , Bhattacharyya Anita , Wang Daifeng , Zhang Su-Chun 
Published: July 2021

SummaryModeling age-related neurodegenerative disorders with human stem cells is difficult due to the embryonic nature of stem cell derived neurons. We developed a chemical cocktail to induce senescence of iPSC-derived neurons to address this challenge. We first screened small molecules that induce embryonic fibroblasts to exhibit features characteristic of aged fibroblasts. We then optimized a cocktail of small molecules that induced senescence in fibroblasts and cortical neurons without causing DNA damage. The utility of the “senescence cocktail” was validated in motor neurons derived from ALS patient iPSCs which exhibited protein aggregation and axonal degeneration substantially earlier than those without cocktail treatment. Our “senescence cocktail” will likely enhance the manifestation of disease-related phenotypes in neurons derived from iPSCs, enabling the generation of reliable drug discovery platforms.
Evaluating de novo assembly and binning strategies for time-series drinking water metagenomes
Authors: Vosloo Solize , Huo Linxuan , Anderson Christopher L. , Dai Zihan , Sevillano Maria , Pinto Ameet 
Published: July 2021

AbstractReconstructing microbial genomes from metagenomic short-read data can be challenging due to the unknown and uneven complexity of microbial communities. This complexity encompasses highly diverse populations which often includes strain variants. Reconstructing high-quality genomes is a crucial part of the metagenomic workflow as subsequent ecological and metabolic inferences depend on their accuracy, quality, and completeness. In contrast to microbial communities in other ecosystems, there has been no systematic assessment of genome-centric metagenomic workflows for drinking water microbiomes. In this study, we assessed the performance of a combination of assembly and binning strategies for time-series drinking water metagenomes that were collected over a period of 6 months. The goal of this study was to identify the combination of assembly and binning approaches that results in high quality and quantity metagenome-assembled genomes (MAGs), representing most of the sequenced metagenome. Our findings suggest that the metaSPAdes co-assembly strategies had the best performance as they resulted in larger and less fragmented assemblies with at least 85% of the sequence data mapping to contigs greater than 1kbp. Furthermore, a combination of metaSPAdes co-assembly strategies and MetaBAT2 produced the highest number of medium-quality MAGs while capturing at least 70% of the metagenomes based on read recruitment. Utilizing different assembly/binning approaches also assist in the reconstruction of unique MAGs from closely related species that would have otherwise collapsed into a single MAG using a single workflow. Overall, our study suggests that leveraging multiple binning approaches with different metaSPAdes co-assembly strategies may be required to maximize the recovery of good-quality MAGs, which more accurately capture the microbial diversity of drinking water samples.
Pathogenic and transcriptomic differences of emerging SARS-CoV-2 variants in the Syrian golden hamster model
Authors: O’Donnell Kyle L. , Pinski Amanda N. , Clancy Chad S. , Gourdine Tylisha , Shifflett Kyle , Fletcher Paige , Messaoudi Ilhem , Marzi Andrea 
Published: July 2021

AbstractFollowing the discovery of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its rapid spread throughout the world, new viral variants of concern (VOC) have emerged. There is a critical need to understand the impact of the emerging variants on host response and disease dynamics to facilitate the development of vaccines and therapeutics. Syrian golden hamsters are the leading small animal model that recapitulates key aspects of severe coronavirus disease 2019 (COVID-19). In this study, we show that intranasal inoculation of SARS-CoV-2 into hamsters with the ancestral virus (nCoV-WA1-2020) or VOC first identified in the United Kingdom (B.1.1.7) and South Africa (B.1.351) led to similar gross and histopathologic pulmonary lesions. Although differences in viral genomic copy numbers were noted in the lungs and oral swabs of challenged animals, infectious titers in the lungs were comparable. Antibody neutralization capacities varied, dependent on the original challenge virus and cross-variant protective capacity. Transcriptional profiling indicated significant induction of antiviral pathways in response to all three challenges with a more robust inflammatory signature in response to B.1.1.7. Furthermore, no additional mutations in the spike protein were detected at peak disease. In conclusion, the emerging VOC showed distinct humoral responses and transcriptional profiles in the hamster model compared to the ancestral virus.
Population-based structure modeling reveals key roles of nuclear microenviroment in gene functions
Authors: Yildirim Asli , Hua Nan , Boninsegna Lorenzo , Polles Guido , Gong Ke , Hao Shengli , Li Wenyuan , Zhou Xianghong Jasmine , Alber Frank 
Published: July 2021

AbstractThe nuclear folding of chromosomes relative to nuclear bodies is an integral part of gene function. Here, we demonstrate that population-based modeling—from ensemble Hi-C data—can provide a detailed description of the nuclear microenvironment of genes and its role on gene function. We define the microenvironment by the subnuclear positions of genomic regions with respect to nuclear bodies, local chromatin compaction, and preferences in chromatin compartmentalization. These structural descriptors are determined in single cell models on a genome-wide scale, thereby revealing the structural variability between cells. We demonstrate that the structural microenvironment of a genomic region is linked to its functional potential in gene transcription, replication and chromatin compartmentalization. Some chromatin regions are distinguished by their strong preferences to a single microenvironment, due to associations to specific nuclear bodies in most cells. Other chromatin shows high structural variability, which is a strong indicator of functional heterogeneity. Moreover, we identify specialized nuclear microenvironments, which distinguish chromatin in different functional states and reveal a key role of nuclear speckles in chromosome organization. We demonstrate that our method produces highly predictive 3-dimensional genome structures, which accurately reproduce data from TSA-seq, DamID, GPSeq and super-resolution imaging. Thus, our method considerably expands the range of Hi-C data analysis and is widely applicable.
The contributing factors of intellectual capital disclosures in agriculture and mining sectors of Indonesia and Thailand
Authors: Hatane Saarce Elsye , Tarigan Josua , Kuanda Elenne Stefanie , Cornelius Elizabeth 
Published: July 2021

Purpose
This study aims to examine the factors affecting intellectual capital disclosure (ICD), especially in the agriculture and mining sectors in Indonesia and Thailand. Additionally, this study discusses the difference in ICD levels between Indonesia and Thailand.

Design/methodology/approach
The sample used is companies listed on the Indonesia Stock Exchange and Stock Exchange of Thailand from 2013 to 2017. The method used is a content analysis of 380 annual reports (150 from Thailand and 230 from Indonesia). This study uses a panel regression model. Variables tested are firm size, market shares, minority shareholders, profitability, leverage and the focus on ICD components such as human capital disclosure, structural capital disclosure and relational capital disclosure.

Findings
IC disclosures in financial statements are generally oriented to past events and focus more on the human capital component. Overall, ICDs in Thailand are more qualified than in Indonesia. The findings support the stakeholder and legitimacy theories. It was found that the greater the company’s resources, the higher the quality of disclosure of all intellectual capital (IC) components. Conversely, when associated with the position in the market, companies reduce the disclosures. As the company has gained the government’s legitimacy, management’s passion for revealing more about its ICD is diminishing.

Research limitations/implications
This study focuses on the agriculture and mining sectors in Indonesia and Thailand. The annual report is the primary medium to observe IC in qualitative and quantitative ways, yet firms would use other means to disclose their IC. This study deploys the content analysis method, in which the determination of scores is based on the researchers’ judgment.

Originality/value
This study contributes to the ICD-related literature by focusing on the agriculture and mining industries and multinational scopes. The ICD valuation is extended to the quality of disclosures, in which numerical and monetary figures also support the disclosures. This study also examined minority shareholders’ role in ICD quality, which is infrequent in ICD literature.
Matching external search strategies with radical and incremental innovation and the role of knowledge integration capability
Authors: Liu Bao 
Published: July 2021

PurposeThe purpose of this paper is to analyze the differential effects of two external search strategies on radical innovation (RI) and incremental innovation (II) and explore the mediating role of knowledge integration capability (KIC).Design/methodology/approachThe paper is based on the data collected from a sample of 241 firms from Chinese electronic information industry. The author conducted a hierarchical regression analysis using SPSS and PROCESS to test the proposed hypotheses.FindingsThe results showed that both external search breadth and depth have positive effects on RI/II performance. The author also found that the effect of search breadth on RI is greater than that on II, and the effect of search depth on RI is less than that on II. Moreover, the author discovered that KIC fully or partially mediates the relationship between external search strategies and RI/II.Originality/valueThe paper provides a finer grained understanding concerning the difference in the impacts of the two external search strategies on RI/II performance. The paper also adds to the existing literature by explaining the path in which external knowledge search influences RI/II through the mediation effect of KIC.
Subordinates’ negative workplace gossip leads to supervisor abuse: based on the conservation of resources theory
Authors: Ye Cunjun , He Bin , Sun Xu 
Published: July 2021

PurposeBased on the conservation of resources (COR) theory, this paper aims to explore the potential influence of perceived subordinates’ negative workplace gossip on abusive supervision in China. Moreover, the COR theory helps in examining the mediating role of self-esteem threat and psychological distress and the moderating role of mindfulness on the effects of perceived subordinates’ negative workplace gossip on abusive supervision.Design/methodology/approachData was collected from 305 supervisor-subordinate dyads in China using the time-lagged and multi-source methods and hierarchical regression analysis was used to analyze the data.FindingsResults reveal that perceived subordinates’ negative workplace gossip is positively related to abusive supervision and the relationship is moderated by the supervisor’s traits of mindfulness. In addition, perceived subordinates’ negative workplace gossip has an indirect effect on abusive supervision via self-esteem threat (cognition) and psychological distress (emotion).Originality/valueThe study helps to understand the influence of perceived subordinates’ negative workplace gossip on abusive supervision based on the COR theory. At the same time, it also enriches the understanding of the internal mechanism between perceived subordinates’ negative workplace gossip and abusive supervision.
A numerical modelling investigation of the development of a human cough jet
Authors: Bi Ran , Ali Shady , Savory Eric , Zhang Chao 
Published: July 2021

PurposeThis study aims (1) to numerically investigate the characteristics of a human cough jet in a quiescent environment, such as the variation with time of the velocity field, streamwise jet penetration and maximum jet width. Two different turbulence modelling approaches, the unsteady Reynolds-averaged Navier–Stokes (URANS) and large eddy simulation (LES), are used for comparison purposes. (2) To validate the numerical results with the experimental data.Design/methodology/approachTwo different approaches, the URANS and LES, are used to simulate a human cough jet flow. The numerical results for the velocity magnitude contours and the spatial average of the two-dimensional velocity magnitude over the corresponding particle image velocimetry (PIV) field of view are compared with the relevant PIV measurements. Similarly, the numerical results for the streamwise velocity component at the hot-wire probe location are compared with the hot-wire anemometry (HWA) measurements. Furthermore, the numerical results for the streamwise jet penetration are compared with the data from the previous experimental work.FindingsBased on the comparison with the URANS approach and the experimental data, the LES approach can predict the temporal development of a human cough jet reasonably well. In addition, the maximum width of the cough jet is found to grow practically linearly with time in the far-field, interrupted-jet stage, while the corresponding axial distance from the mouth of the jet front increases with time in an approximately quadratic manner.Originality/valueCurrently, no numerical study of human cough flow has been conducted using the LES approach due to the following challenges: (1) the computational cost is much higher than that of the URANS approach; (2) it is difficult to specify the turbulent fluctuations at the mouth for the cough jet properly; (3) it is necessary to define the appropriate conditions for the droplets to obtain statistically valid results. Therefore, this work fills this research gap.
The role of library user preferences in the willingness to read and pay for e-books: case of the Czech Republic
Authors: Stejskal Jan , Hajek Petr , Prokop Viktor 
Published: July 2021

Purpose
The study aims to analyse library user preferences in the willingness to read and pay for e-books, using a sample of both active readers (users of public library services) and non-users (the general population).

Design/methodology/approach
Two empirical surveys were conducted from August to November of 2019; the research sample consisted of 1,334 users from the Municipal Library of Prague and 1,101 non-users from the general Czech population. The research was focussed on e-book user preferences. The willingness to pay (WTP) for e-book services and the determinants that affect this willingness were also examined.

Findings
The results show the specific approach of Czech readers, whose main determinant of WTP is not the content, but the price and method of its payment (allocation). Some people prefer a cheaper annual lump sum, whereas others may prefer a charge of small regular fees. The decision to pay depends on their reading or payment habits.

Originality/value
This study also aims to clarify the demand for various types of digital media in Czech libraries and the preferred distribution models. Furthermore, the study determines the dependence of the preferences of library users in their WTP for e-books using different evaluation models. The originality of this study is in the evaluation of the determinants of WTP for e-books, which makes this study unique, and the findings should contribute to the expansion of existing knowledge in the field of information science.
Towards evolutionary knowledge representation under the big data circumstance
Authors: Li Xuhui , Liu Liuyan , Wang Xiaoguang , Li Yiwen , Wu Qingfeng , Qian Tieyun 
Published: July 2021

Purpose
The purpose of this paper is to propose a graph-based representation approach for evolutionary knowledge under the big data circumstance, aiming to gradually build conceptual models from data.

Design/methodology/approach
A semantic data model named meaning graph (MGraph) is introduced to represent knowledge concepts to organize the knowledge instances in a graph-based knowledge base. MGraph uses directed acyclic graph–like types as concept schemas to specify the structural features of knowledge with intention variety. It also proposes several specialization mechanisms to enable knowledge evolution. Based on MGraph, a paradigm is introduced to model the evolutionary concept schemas, and a scenario on video semantics modeling is introduced in detail.

Findings
MGraph is fit for the evolution features of representing knowledge from big data and lays the foundation for building a knowledge base under the big data circumstance.

Originality/value
The representation approach based on MGraph can effectively and coherently address the major issues of evolutionary knowledge from big data. The new approach is promising in building a big knowledge base.
Examining the mediating role of work-family balance in the core self-evaluations – organizational performance relationship: a multilevel study
Authors: Katou Anastasia 
Published: July 2021

PurposeThe relationship between core self-evaluations (CSEs) and organizational performance is yet to be explained. The purpose of this study is to examine the mediating role of work-family enrichment (WFE), family-work enrichment (FWE) and work-family balance (WFB) in the relationship between CSE and organizational performance.Design/methodology/approachData were obtained from a sample of 2,312 employees working within 188 public and private organizations operating in the current context of the post-2008 economic and financial crises that lasted until up to 2019 in Greece. Multilevel structural equation modeling (MSEM) analyses were used due to the nested nature of data.FindingsThe results showed that (1) WFE and WFB serially and positively mediate the relationship between CSE and organizational performance; (2) FWE and WFB serially and positively mediate the relationship between CSE and organizational performance; (3) the constructs of the operating framework depend on factors such as gender, working hours, level of education and position of employees in the organizational hierarchy.Research limitations/implicationsData were collected at a short period in 2019, thus, restricting dynamic causal inferences into instant changes. The findings suggest that organizations will benefit from developing WFB policies and practices that can improve organizational performance.Originality/valueOnly a handful of studies have previously examined the relations between CSEs, WFE, WFB and organizational performance in an economic and financial crises environment.
Ethnicity and bank lending before and during COVID-19
Authors: Cowling Marc , Liu Weixi , Conway Elaine 
Published: July 2021

PurposeUsing ethnicity as our point of focus, the authors consider the dynamics of the demand for bank loans, and the willingness of banks to supply them, as the UK economy entered the COVID-19 pandemic in early 2020 with a particular focus on potential behavioural differences on the demand-side and discrimination on the supply-side. In doing so we directly address crisis induced financial concerns and how they played out in the context of ethnicity.Design/methodology/approachUsing the most recent ten quarterly waves of the UK SME Finance Monitor survey the authors consider whether ethnicity of the business owner impacts on the decision to apply for bank loans in the first instance. The authors then question whether ethnicity influences the banks decision to meet or reject the request for a bank loan.FindingsThe authors’ pre-COVID-19 results show that there were no ethnic differences in loan application and success rates. During COVID-19, both white and ethnic business loan application rates rose significantly, but the scale of this increase was greater for ethnic businesses. The presence of government 100% guaranteed lending also increased general loan success rates, but again the scale of this improvement was greater for ethnic businesses.Research limitations/implicationsThe authors show very clearly that differences in the willingness of banks to supply loans to SMEs relate very explicitly to firm specific characteristics and ethnicity either plays no additional role or actually leads to improved loan outcomes. The data is for the UK and for a very unique COVID time which may mean that wider generalisability is unwise.Practical implicationsEthnic business owners should not worry about lending discrimination or be discouraged from applying for loans.Social implicationsThe authors identify at worst no lending discrimination and at best positive ethnic discrimination.Originality/valueThis is one of the largest COVID-19 period studies into the financing of ethnic businesses.