bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Plasmid Network from the Gut Microbiome of Semi-isolated Human Groups Reveals Unique and Shared Metabolic and Virulence Traits
Authors: Conteville Liliane Costa , Vicente Ana Carolina Paulo 
Published: August 2021

ABSTRACTThe plasmidome, the set of plasmids in gut microbiomes, has the potential to contribute to the microbiome assembly, as well as human health and physiology. Nevertheless, this niche remains poorly explored, likely due to the difficulties attributed to mining mobile elements from complex environments such as microbiomes. In general, most microbiome studies focus on urban-industrialized groups, but here, we studied semi-isolated groups, which represent a link between the ancestral and modern human groups. Based on metagenomic data, we characterized their plasmidome, including the set of accessory genes and functions from the gut microbiome of the Hadza, Matses, Tunapuco, and Yanomami. In silico analyzes revealed unique plasmid clusters and gene functions for each human group related to their diet and lifestyle. In addition, network analysis revealed a dozen plasmid clusters shared by these distinct groups but that are also circulating in other niches worldwide. Moreover, in these microbiomes, there are novel and unique plasmids associated with their resistome and virulome. A resistome encompassing six antibiotic classes and multiple metals, and a virulome with type VI secretion systems were identified. Functional analysis revealed pathways associated with urban-industrialized groups, such as lipopolysaccharide biosynthesis that was characterized in the Hadza plasmidome. These results demonstrate the richness of features in the semi-isolated human groups’ plasmidome and provide a snapshot of the forces that are acting in their gut microbiome. Their plasmidomes also represent an important source of information with biotechnological and/or pharmaceutical potential.
Structurally complex osteosarcoma genomes exhibit limited heterogeneity within individual tumors and across evolutionary time
Authors: Rajan Sanjana , Zaccaria Simone , Cannon Matthew V. , Cam Maren , Gross Amy C. , Raphael Benjamin J. , Roberts Ryan D. 
Published: August 2021

AbstractOsteosarcoma is an aggressive malignancy characterized by high genomic complexity. Identification of few recurrent mutations in protein coding genes suggests that somatic copy-number aberrations (SCNAs) are the genetic drivers of disease. Models around genomic instability conflict - it is unclear if osteosarcomas result from pervasive ongoing clonal evolution with continuous optimization of the fitness landscape or an early catastrophic event followed by stable maintenance of an abnormal genome. We address this question by investigating SCNAs in >12,000 tumor cells obtained from human osteosarcomas using single cell DNA sequencing, with a degree of precision and accuracy not possible when inferring single cell states using bulk sequencing. Using the CHISEL algorithm, we inferred allele- and haplotype-specific SCNAs from this whole-genome single cell DNA sequencing data. Surprisingly, despite extensive structural complexity, these tumors exhibit a high degree of cell-cell homogeneity with little sub-clonal diversification. Longitudinal analysis of patient samples obtained at distant therapeutic time points (diagnosis, relapse) demonstrated remarkable conservation of SCNA profiles over tumor evolution. Phylogenetic analysis suggests that the majority of SCNAs were acquired early in the oncogenic process, with relatively few structure-altering events arising in response to therapy or during adaptation to growth in metastatic tissues. These data further support the emerging hypothesis that early catastrophic events, rather than sustained genomic instability, give rise to structural complexity, which is then preserved over long periods of tumor developmental time.Significance StatementChromosomally complex tumors are often described as genomically unstable. However, determining whether complexity arises from remote time-limited events that give rise to structural alterations or a progressive accumulation of structural events in persistently unstable tumors has implications for diagnosis, biomarker assessment, mechanisms of treatment resistance, and represents a conceptual advance in our understanding of intra-tumoral heterogeneity and tumor evolution.
Genomic epidemiology of early SARS-CoV-2 transmission dynamics in Gujarat, India
Authors: Raghwani Jayna , du Plessis Louis , McCrone John T , Hill Sarah C. , Parag Kris V. , Thézé Julien , Kumar Dinesh , Puvar Apurva , Pandit Ramesh , Pybus Oliver G. , Fournié Guillaume , Joshi Madhvi , Joshi Chaitanya 
Published: August 2021

ABSTRACTGenomic surveillance of SARS-CoV-2 has played a decisive role in understanding the transmission and evolution of the virus during its emergence and continued circulation. However, limited genomic sampling in many high-incidence countries has impeded detailed studies of SARS-CoV-2 genomic epidemiology. Consequently, critical questions remain about the generation and global distribution of virus genetic diversity. To address this gap, we investigated SARS-CoV-2 transmission dynamics in Gujarat, India, during its first epidemic wave and shed light on virus’ spread in one of the pandemic’s hardest-hit regions. By integrating regional case data and 434 whole virus genome sequences sampled across 20 districts from March to July 2020, we reconstructed the epidemic dynamics and spatial spread of SARS-CoV-2 in Gujarat, India. Our findings revealed that global and regional connectivity, along with population density, were significant drivers of the Gujarat SARS-CoV-2 outbreak. The three most populous districts in Gujarat accounted ∼84% of total cases during the first wave. Moreover, we detected over 100 virus lineage introductions, which were primarily associated with international travel. Within Gujarat, virus dissemination occurred predominantly from densely populated regions to geographically proximate locations with low-population density. Our findings suggest SARS-CoV-2 transmission follows a gravity model in India, with urban centres contributing disproportionately to onward virus spread.
Establishment of reference standards for multifaceted mosaic variant analysis
Authors: Ha Yoo-Jin , Oh Myung Joon , Kim Junhan , Kim Jisoo , Kang Seungseok , Kim Hyun Seok , Kim Sangwoo 
Published: August 2021

AbstractDetection of somatic mosaicism in non-proliferative cells is a new challenge in genome research, however, the accuracy of current detection strategies remains uncertain due to the lack of a ground truth. Herein, we sought to present a set of reference standards based on a total of 386,613 mosaic single-nucleotide variants (SNVs) and insertion-deletion mutations (INDELs) with variant allele frequencies (VAFs) ranging from 0.5% to 56%, as well as 35,113,417 non-variant and 19,936 germline variant sites as a negative control. The whole reference standard set mimics the cumulative aspect of mosaic variant acquisition in the early developmental stage owing to the progressive mixing of cell lines with established genotypes, ultimately unveiling 741 possible inter-sample relationships with respect to variant sharing and asymmetry in VAFs. We expect that our reference standards will be essential for optimizing the current use of mosaic variant detection strategies and for developing algorithms to enable future improvements.
Compassion in custody: developing a trauma sensitive intervention for men with developmental disabilities who have convictions for sexual offending
Authors: Taylor Jon 
Published: August 2021

PurposeThis paper aims to provide a description of a trauma sensitive intervention for men who have committed sexual offences. The intervention aims to support men to process and make sense of their own experience of trauma before inviting them to acknowledge their role in causing harm to others. The intervention draws on compassion focussed therapy (CFT) as the overarching therapeutic modality.Design/methodology/approachAs part of a service evaluation changes in routine repeat measures completed by service users were analysed prior to joining the intervention and after 12 months of intervention. Service users were encouraged to provide regular feedback relating to their experience of the intervention at regular intervals. This feedback was collated and patterns were identified collaboratively to understand the context for assessed change in the measures.FindingsPrior to the intervention men reported high levels of shame and limited experiences of guilt (as compassion for others). Early findings indicate that men experience less shame and increased experiences of guilt after 12 months. An increase in insight into risk was also evident. Service user feedback pointed towards a more engaging therapeutic style and highlighted the importance of both a collaborative and trauma sensitive approach.Originality/valueThis is the first evaluative description of forensic CFT for sexual offending. Findings offer insight into potential future directions for forensic interventions with this population.
Profiling Hungarian hypermarket shoppers
Authors: Fehér Orsolya , Gere Attila , Csiby Ágnes , Szakál Dorina , Dunay Anna 
Published: August 2021

PurposeHungarian economy went through substantial changes in the past few decades and hypermarkets gained high popularity among customers, therefore profiling Hungarian hypermarket shoppers is essential to understand their behavior.Design/methodology/approachThe paper investigates the profile of Hungarian hypermarket shoppers based on a wide questionnaire survey. In the presented research, Computer-Aided Personal Interviewing questionnaires were analyzed using multidimensional scaling and k-means clustering.FindingsResults showed that Hungarian hypermarket shoppers regularly plan their shopping but they buy 8–9 items instead of the planned 4–5 items. However, only 25% of respondents reported the use of shopping list and in spite of the wide digital possibilities, they do not use their mobile devices neither for creating shopping list nor for checking coupons online.Originality/valueThis study explores the profile of Hungarian hypermarket shoppers, which may give additional information for the players of the retail environment about the customers' behavior and preferences.
Governance failure and its impact on financial distress
Authors: Hazami-Ammar Sourour , Gafsi Amal 
Published: August 2021

Purpose
The purpose of this paper is to examine the effects of corporate governance failure, excess remuneration and entrenchment of managers, company variables and corporate governance variables on the company’s financial distress risk (DETR) in the French context.

Design/methodology/approach
Using the regression analysis, this paper is based on 201 observations about 67 companies of SBF 120 from 2015 to 2017. Data are collected on the Thomson Reuters database and in the referenced documents, which are published on the internet.

Findings
The research findings reveal that firm’s DETR is influenced negatively by excess remuneration and entrenchment of managers. In addition, there is a positive and significant relationship between DETR and company variables (performance and ownership structure) and corporate governance variables (power structure). However, a company’s size and board of directors’ independence do not affect firms’ DETR.

Practical implications
The impact highlighted between remuneration and entrenchment of managers and the financial distress of the company is explained by the intention of managers to work for announcing good short-term performance indicators that are most favorable to them.

Originality/value
The shareholder/manager agency problem can be changed when business performance tends to decline. Certainly, the managerial latitude adopted by the managers is used as an external careerism strategy. Its positive impact on the reduction of the firm’s financial distress can benefit shareholders who aim to sell their securities in the short term.
A tale of two contact-tracing apps – comparing Australia’s CovidSafe and New Zealand’s NZ Covid Tracer
Authors: Howell Bronwyn , Potgieter Petrus H. 
Published: August 2021

Purpose
The Australian and New Zealand governments have released smartphone-based apps to complement contact tracing in the event that they face a resurgence of COVID-19 infections. The apps form part of both countries’ policies to support a return to social and economic engagement following extended lockdowns. This paper aims to investigate the extent to which the two approaches are fit for purpose and compare their functional characteristics.

Design/methodology/approach
Using process mapping and analysis, this paper evaluates the potential of the two apps to improve the performance of existing contact tracing systems across a range of efficiency and effectiveness criteria with an emphasis on the framework proposed by Verrall (2020).

Findings
The Bluetooth-based Australian app appears likely to assist that country’s contact tracing system to perform more efficiently and effectively in the event of a resurgence of the virus and should increase confidence in re-engagement. The New Zealand QR code-based app, however, is not well-aligned with these objectives. Its interaction with a range of other regulations and obligations, combined with the inconvenience it imposes on its users, is likely to militate against its use. Bluetooth-based apps based on interactions between individuals likely better support these population-based objectives than QR code-based location-specific apps.

Originality/value
This paper provides an original and extensive analysis of the functionality and effectiveness of Australia and New Zealand’s official contact-tracing apps.
Multifidelity modeling similarity conditions for airfoil dynamic stall prediction with manifold mapping
Authors: Raul Vishal , Leifsson Leifur 
Published: August 2021

PurposeThe purpose of this work is to investigate the similarity requirements for the application of multifidelity modeling (MFM) for the prediction of airfoil dynamic stall using computational fluid dynamics (CFD) simulations.Design/methodology/approachDynamic stall is modeled using the unsteady Reynolds-averaged Navier–Stokes equations and Menter's shear stress transport turbulence model. Multifidelity models are created by varying the spatial and temporal discretizations. The effectiveness of the MFM method depends on the similarity between the high- (HF) and low-fidelity (LF) models. Their similarity is tested by computing the prediction error with respect to the HF model evaluations. The proposed approach is demonstrated on three airfoil shapes under deep dynamic stall at a Mach number 0.1 and Reynolds number 135,000.FindingsThe results show that varying the trust-region (TR) radius (λ) significantly affects the prediction accuracy of the MFM. The HF and LF simulation models hold similarity within small (λ ≤ 0.12) to medium (0.12 ≤ λ ≤ 0.23) TR radii producing a prediction error less than 5%, whereas for large TR radii (0.23 ≤ λ ≤ 0.41), the similarity is strongly affected by the time discretization and minimally by the spatial discretization.Originality/valueThe findings of this work present new knowledge for the construction of accurate MFMs for dynamic stall performance prediction using LF model spatial- and temporal discretization setup and the TR radius size. The approach used in this work is general and can be used for other unsteady applications involving CFD-based MFM and optimization.
Enhancing critical thinking and media literacy in the context of IVET: a systematic scoping review
Authors: Tommasi Francesco , Ceschi Andrea , Sartori Riccardo , Gostimir Marija , Passaia Giulia , Genero Silvia , Belotto Silvia 
Published: August 2021

Purpose
The alignment between the labour market and initial vocational education and training (IVET) is placing always more importance on technical knowledge and skills, whilst metacognitive competences such as critical thinking and media literacy are increasingly neglected. In the context of IVET, this results in authors and practitioners paying always more attention to how to devise possible training interventions, with the double aim of implementing their educational pathways and enhancing students’ critical thinking and media literacy. This paper aims to report the state of the art concerning such processes of enhancement in IVET students.

Design/methodology/approach
The study adopted the method of systematic scoping review to address the research questions on how to enhance critical thinking and media literacy in the context of IVET.

Findings
The paper presents the analyses of the n = 19 contributions collected. Then, it proposes an initial conceptualization of the dimensions of critical thinking and media literacy. Moreover, by combining evidence from various contributions, the review proposes implications for educational practices and strategies. Around these pieces of knowledge, further avenues of research and practice are proposed.

Research limitations/implications
This study contributes to the literature on critical thinking and media literacy in the context of IVET by advancing initial comprehensive conceptualizations of the two dimensions. Moreover, the study advances initial practical implications for teachers and trainers for the development of training interventions.

Originality/value
The originality of the present review rests in its proposal of definitions of critical thinking and media literacy; moreover, it widens the discussion of practices on how to enhance such metacognitive competences. Indeed, the study identifies the teaching and training practices meant to enhance critical thinking and media literacy and proposes applied implications in the context of IVET.
Knowledge, attitudes and practices towards the spread of COVID-19: a health counseling initiative among potential entrepreneurs of FUUAST
Authors: Soomro Bahadur Ali , Lakhan Ghulam Rasool , Shah Naimatullah 
Published: August 2021

PurposeThe present study examines the knowledge, attitude and practice towards the reduction of COVID-19 spread among entrepreneurs of the Federal Urdu University of Arts, Sciences and Technology (FUUAST), Karachi Pakistan.Design/methodology/approachThe authors employed cross-sectional data to infer the results. The data are collected through an online survey questionnaire. To target the respondents; a convenience sampling technique is adopted. In total, 222 usable answers proceed with final results. The structural equation model (SEM) is applied for the data analysis.FindingsThe study outcomes found a significant and positive role of knowledge about COVID-19, attitudes towards a stay at home and practices against COVID-19 in reducing the spread of the pandemic.Practical implicationsThe study provides coherent knowledge about the factors that fight against the pandemic's further spread. The findings would provide the guidelines to policymakers to think about such factors and boost them enormously. Further, the results would contribute to the literature of COVID-19.Originality/valueThis study is original, which empirically confirmed the effect of knowledge about COVID-19, attitudes towards a stay at home and practices against COVID-19 in an academic institute.
A note on the relationship between COVID-19 and stock market return: evidence from South Asia
Authors: Rahman Md Arafat , Khudri Md Mohsan , Kamran Muhammad , Butt Pakeezah 
Published: August 2021

PurposeThe transformation of coronavirus disease (COVID-19) from a regional health crisis in a Chinese city to a global pandemic has caused severe damage not only to the natural and economic lives of human beings but also to the financial markets. The rapidly pervading and daunting consequences of COVID-19 spread have plummeted the stock markets to their lowest levels in many decades especially in South Asia. This concern motivates us to investigate the stock markets’ response to the COVID-19 pandemic in four South Asian countries: Bangladesh, India, Pakistan and Sri Lanka. This study aims to investigate the causal impact of the number of confirmed COVID-19 cases on stock market returns using panel data of the countries stated above.Design/methodology/approachThis study collects and analyzes the daily data on COVID-19 spread and stock market return over the period May 28, 2020 to October 01, 2020. Using Dumitrescu and Hurlin panel Granger non-causality test, the empirical results demonstrate that the COVID-19 spread measured through its daily confirmed cases in a country significantly induces stock market return. This paper cross-validates the results using the pairwise Granger causality test.FindingsThe empirical results suggest unidirectional causality from COVID-19 to stock market returns, indicating that the spread of COVID-19 has a dominant short-term influence on the stock movements. To the best of the knowledge, this study provides the first empirical insights into the impact of COVID-19 on the stock markets of selected South Asian countries taking the cross-sectional dependence into account. The results are also in line with the findings of other existing literature on COVID-19. Moreover, the results are robust across the two tests used in this study.Originality/valueThe findings are equally insightful to the fund managers and investors in South Asian countries. Taking into account the possible impact of COVID-19 on stock markets’ returns, investors can design their optimal portfolios more effectively. This study has another important implication in the sense that the impact of COVID-19 on the stock markets of South Asian countries may have spillover effects on other developing or even developed countries.
Non-radial two-stage network DEA model to estimate returns to scale
Authors: Fakhr Mousavi Seyed Mohamad , Amirteimoori Alireza , Kordrostami Sohrab , Vaez-Ghasemi Mohsen 
Published: August 2021

Purpose
As returns to scale (RTS) describes the long run connection of the changes of outputs relative to increases in the inputs, the purpose of this study is to answer the following questions: If the proportionate changes exist in the inputs, what is the rate of changes in outputs with respect to the inputs’ variations in the two-stage networks over the long term? How can the authors investigate quantitative RTS in the two-stage networks? In other words, the purpose of this research is to introduce a different approach to estimate the performance, RTS and scale economies (SE) in network structures.

Design/methodology/approach
This paper proposes a novel non-radial approach based on data envelopment analysis to analyze the performance and to investigate RTS and SE in two-stage processes.

Findings
The findings show that the range adjusted measure (RAM)/RTS approach can identify reference sets for overall systems and each stage. In addition, the models presented in this paper can classify decision-making units and determine the increasing/decreasing trends of RTS.

Originality/value
The majority of previous RTS studies have been examined in black-box structures and have been discussed in a radial framework. Therefore, in this study, RTS and SE in the two-stage networks are dealt with using an extended RAM approach. Actually, the efficiency and RTS for each stage and the overall model are calculated using the proposed technique.