bluuebunny/crossref_metadata_2025_split huggingface dataset:
Imputation and polygenic score performances of human genotyping arrays in diverse populations
Authors: Nguyen Dat Thanh , Tran Trang , Tran Mai , Tran Khai , Pham Duy , Duong Nguyen Thuy , Nguyen Quan , Vo Nam S. 
Published: June 2022

ABSTRACTRegardless of the overwhelming use of next-generation sequencing technologies, microarray-based genotyping combined with the imputation of untyped variants remains a cost-effective means to interrogate genetic variations across the human genome. This technology is widely used in genome-wide association studies (GWAS) at bio-bank scales, and more recently, in polygenic score (PGS) analysis to predict and to stratify disease risk. Over the last decade, human genotyping arrays have undergone a tremendous growth in both number, and content making a comprehensive evaluation of their performances became more important. Here, we performed a comprehensive performance assessment for 23 available human genotyping arrays in 6 ancestry groups using diverse public, and in-house datasets. The analyses focus on performance estimation of derived imputation (in terms of accuracy and coverage) and PGS (in term of concordance to PGS estimated from whole genome sequencing data) in three different traits and diseases. We found that the arrays with a higher number of SNPs are not necessarily the ones with higher imputation performance, but the arrays that are well-optimized for the targeted population could provide very good imputation performance. In addition, PGS estimated by imputed SNP array data is highly correlated to PGS estimated by whole genome sequencing data in most of cases. When optimal arrays are used, the correlations of key PGS metrics between two types of data can be higher than 0.97, but interestingly, arrays with high density can result in lower PGS performance. Our results suggest the importance of properly selecting a suitable genotyping array for PGS applications. Finally, we developed a web tool that provide interactive analyses of tag SNP contents and imputation performance based on population and genomic regions of interest. This study would act as a practical guide for researchers to design their genotyping arrays-based studies. The tool is available at: https://genome.vinbigdata.org/tools/saa/
HIV skews the SARS-CoV-2 B cell response toward an extrafollicular maturation pathway
Authors: Krause Robert , Snyman Jumari , Shi-Hsia Hwa , Muema Daniel , Karim Farina , Ganga Yashica , Ngoepe Abigail , Zungu Yenzekile , Gazy Inbal , Bernstein Mallory , Khan Khadija , Mazibuko Matilda , Mthabela Ntombifuthi , Ramjit Dirhona ,   COMMIT-KZN Team, Limbo Oliver , Jardine Joseph , Sok Devin , Wilson Ian , Hanekom Willem , Sigal Alex , Kloverpris Henrik , Ndung’u Thumbi , Leslie Alasdair 
Published: June 2022

AbstractBackgroundHIV infection dysregulates the B cell compartment, affecting memory B cell formation and the antibody response to infection and vaccination. Understanding the B cell response to SARS-CoV-2 in people living with HIV (PLWH) may explain the increased morbidity, reduced vaccine efficacy, reduced clearance, and intra-host evolution of SARS-CoV-2 observed in some HIV-1 coinfections.MethodsWe compared B cell responses to COVID-19 in PLWH and HIV negative (HIV-ve) patients in a cohort recruited in Durban, South Africa, during the first pandemic wave in July 2020 using detailed flow cytometry phenotyping of longitudinal samples with markers of B cell maturation, homing and regulatory features.ResultsThis revealed a coordinated B cell response to COVID-19 that differed significantly between HIV-ve and PLWH. Memory B cells in PLWH displayed evidence of reduced germinal center (GC) activity, homing capacity and class-switching responses, with increased PD-L1 expression, and decreased Tfh frequency. This was mirrored by increased extrafollicular (EF) activity, with dynamic changes in activated double negative (DN2) and activated naïve B cells, which correlated with anti-RBD-titres in these individuals. An elevated SARS-CoV-2 specific EF response in PLWH was confirmed using viral spike and RBD bait proteins.ConclusionsDespite similar disease severity, these trends were highest in participants with uncontrolled HIV, implicating HIV in driving these changes. EF B cell responses are rapid but give rise to lower affinity antibodies, less durable long-term memory, and reduced capacity to adapt to new variants. Further work is needed to determine the long-term effects of HIV on SARS-CoV-2 immunity, particularly as new variants emerge.FundingThis work was supported by a grant from the Wellcome Trust to the Africa Health Research Institute (Wellcome Trust Strategic Core Award [grant number 201433/Z/16/Z]). Additional funding was received from the South African Department of Science and Innovation through the National Research Foundation (South African Research Chairs Initiative, [grant number 64809]), and the Victor Daitz Foundation.
F-actin regulates polarized secretion of pollen tube attractants inArabidopsissynergid cell
Authors: Susaki Daichi , Izumi Rie , Oi Takao , Takeuchi Hidenori , Shin Ji Min , Sugi Naoya , Kinoshita Tetsu , Higashiyama Tetsuya , Kawashima Tomokazu , Maruyama Daisuke 
Published: June 2022

AbstractPollen tube attraction is a key event of sexual reproduction in flowering plants. In the ovule, two synergid cells neighboring the egg cell control pollen tube arrival via the active secretion of attractant peptides such as AtLURE1 and XIUQIU from the filiform apparatus facing toward the micropyle. Distinctive cell polarity together with longitudinal F-actin and microtubules are hallmarks of the synergid cell in various species, though functions of these cellular structures are still unclear. In this study we used genetic and pharmacological approaches to elucidate the roles of cytoskeletal components in filiform apparatus formation and pollen tube guidance inArabidopsis thaliana. Inhibition of microtubule formation reduced invaginations of the plasma membrane but did not abolish micropylar AtLURE1.2 accumulation. In contrast, the expression of a dominant-negative form of ACTIN8 induced disorganization of the filiform apparatus and loss of polar AtLURE1.2 distribution toward the filiform apparatus. Interestingly, after pollen tube reception, F-actin became unclear for a few hours in the persistent synergid cell, which may be involved in pausing and resuming pollen tube attraction during early polytubey block. Our data propose the central role of F-actin in the maintenance of cell polarity and function of male-female communication in the synergid cell.
Cell-type specific transcriptomic signatures of neocortical circuit organization and their relevance to autism
Authors: Moussa Anthony J. , Wester Jason C. 
Published: June 2022

ABSTRACTA prevailing challenge in neuroscience is understanding how diverse neuronal cell types select their synaptic partners to form circuits. In the neocortex, major classes of excitatory projection neurons and inhibitory interneurons are conserved across functionally distinct regions. There is evidence these classes form canonical circuit motifs that depend primarily on their identity; however, regional cues likely also influence their choice of synaptic partners. We mined the Allen Institute’s single-cell RNA-sequencing database of mouse cortical neurons to study the expression of genes necessary for synaptic connectivity and maintenance in two regions: the anterior lateral motor cortex (ALM) and the primary visual cortex (VISp). We used the Allen’s metadata to parse cells by clusters representing major excitatory and inhibitory classes that are common to both ALM and VISp. We then performed two types of pairwise differential gene expression analysis: 1) between different neuronal classes within the same brain region (ALM or VISp), and 2) between the same neuronal class in ALM and VISp. We filtered our results for differentially expressed circuit connectivity related genes and developed a novel bioinformatic approach to determine the sets uniquely enriched in each neuronal class in ALM, VISp, or both. This analysis provides an organized set of genes that may regulate circuit formation in a cell-type-specific manner. Furthermore, it identifies candidate mechanisms for the formation of circuits that are conserved across functionally distinct cortical regions or that are region dependent. Finally, we used the SFARI Human Gene Module to identify genes from this analysis that are related to risk for autism spectrum disorder (ASD). Our analysis provides clear molecular targets for future studies to understand neocortical circuit organization and abnormalities that underly autistic phenotypes.
A single-component luminescent biosensor for the SARS-CoV-2 spike protein
Authors: Ravalin Matthew , Roh Heegwang , Suryawanshi Rahul , Kumar G. Renuka , Pak John , Ott Melanie , Ting Alice Y. 
Published: June 2022

AbstractMany existing protein detection strategies depend on highly functionalized antibody reagents. A simpler and easier to produce class of detection reagent is highly desirable. We designed a single-component, recombinant, luminescent biosensor that can be expressed in laboratory strains of E. coli and S. cerevisiae. This biosensor is deployed in multiple homogenous and immobilized assay formats to detect recombinant SARS-CoV-2 spike antigen and cultured virus. The chemiluminescent signal generated facilitates detection by an un-augmented cell phone camera. Binding Activated Tandem split-enzyme (BAT) biosensors may serve as a useful template for diagnostics and reagents that detect SARS-CoV-2 antigens and other proteins of interest.
“I felt goosebumps”: emotional experiences of pre-service English teachers and the critical use of narratives
Authors: Abruzzo Emma , Bartow Jacobs Katrina 
Published: June 2022

PurposeThis paper aims to suggest a new way for structuring English teacher preparation within traditional university programs, challenging the age-old use of formal lesson plan reflections and introducing critical narratives as course texts to better understand pre-service teacher experiences. Through this reimagined English methods curriculum, the authors establish increased cohesion between practice and theory, facilitate the development of teacher reflective practice and establish methods for apprehending the emotional experience of pre-service educators.Design/methodology/approachThis study of 18 pre-service English language arts students considers how teacher education programs could better emphasize socio-emotional elements of teaching by asking students to produce and engage with critical narratives that require more than just an appraisal of learning outcomes of direct instruction, but merge critical inquiry, ethical teaching considerations, self-reflection and perceptions of practice.FindingsThe findings indicate that when compared with traditional lesson plan reflections, critical narrative reflections of field experiences increase student focus on emotional aspects of teaching, provide a more nuanced lens into emotional experiences and establish a more complex conception of the teaching practice.Originality/valueThis curricular design challenges the prevailing ways that English pre-service educators are understood and taught through a reimagined understanding and application of narrative writing as course texts.
Approaching systems change at Fulfilling Lives South East in efforts to improve unsupported temporary accommodation: a qualitative case study
Authors: Cooke Charlotte , Jones Kate , Rieley Rebecca , Sylvester Sandra 
Published: June 2022

Purpose
The purpose of this paper is to consider how a South East project approached systems change to improve unsupported temporary accommodation (UTA) and the changes made for people experiencing multiple disadvantage (“multiple and complex needs”). This paper also covers some matters that are hard to change or uncertain, such as housing shortages and financial constraints. The paper focuses on a case study of the East Sussex Temporary Accommodation Action Group (TAAG) – a multi-agency action group.

Design/methodology/approach
A qualitative case study involving a thematic analysis of seven semi-structured interviews, with a review of published literature and internal documentation.

Findings
This example of setting up a TAAG shows us the value of having a dedicated forum to look at a part of the system that requires changing and to identify what works well. Creating a collaborative and democratic space with a common purpose brings different stakeholders and perspectives together and opens discussions to new ways of working. Equalising partners creates an opportunity to create change from the bottom-up within a system traditionally governed by statutory bodies. This study found that the TAAG has facilitated learning around trauma-informed practice and nurtured more sustainable changes towards a Standards Charter and women-only safe UTA.

Originality/value
This is one of the first qualitative case studies of a local systems change approach to improving UTA for people experiencing multiple disadvantage in East Sussex.
Heat transmission in Darcy-Forchheimer flow of Sutterby nanofluid containing gyrotactic microorganisms
Authors: Khan Ambreen A. , Arshad Alina , Ellahi R. , Sait Sadiq M. 
Published: June 2022

PurposeThis paper aims to deal with the heat transmission of Sutterby fluid-containing gyrotactic microorganism by incorporating non-Darcy resistance law. The mathematical modeling is based on nanoparticle concentration, energy, momentum and motile microorganism equations.Design/methodology/approachThe governing nonlinear coupled equations are first rendered into nonlinear ordinary equations using appropriate transformation and are then solved analytically by using the optimal homotopy.FindingsGraphical illustration of results depict the behavior of flow involved physical parameters on temperature, gyrotactic microorganism, concentration and velocity. Additionally, local Nusselt number and skin friction coefficient are computed numerically and validated through comparison with existing literature as a special case of proposed model. It is found that the temperature profile decreases by increasing values of Brownian-motion parameter and Prandtl number. An increase in thermophoresis parameter and Schmidt number results in decrease in concentration of nanoparticles. Bioconvection Peclet number corresponds to decreasing behavior of nondimensional gyrotactic microorganism field is observed. Finally, a comparison with the existing literature is made, and an excellent agreement is seen.Originality/valueTo the best of the authors’ knowledge, this study is reported for the first time.
Understanding virtual organizational identity through the intersection of information technology and narratives
Authors: Davis Daniel J. 
Published: June 2022

Purpose
Virtual organizations present numerous challenges for managers, especially in regards to organizational identity formation. This paper aims to address this gap in the extant literature by exploring how organizational narratives can foster identification with the virtual organization. Moreover, information technology can further catalyze the positive effects of narratives on identity formation.

Design/methodology/approach
Qualitative data from in-depth interviews with 18 members of a nonprofit, virtual organization – DiverseCS – were collected. Participants were asked about their roles in the organization, challenges and collaborative efforts. Grounded theory methodology was used to analyze the data.

Findings
Efforts to instill a sense of identity and community through the adoption of information technology was met with resistance. Rather, senior leaders encouraged and institutionalized the creation of organizational narratives. Novel use of information technology – social media and hyperlinks – became a means to amplify the positive effects of narrative creation and sharing by organizational members.

Originality/value
This study investigates how some members of a virtual organization use information technology in novel ways to further spread organizational narratives to other organizational members and also to external collaboration partners. This research contributes to the extant literature on virtual organizational identity and also proposes a research agenda.
Proposed flood evacuation routes for heritage areas based on spatial configuration analysis: a case study of Penang, Malaysia
Authors: Safizadeh Mina , Hedayati Marzbali Massoomeh , Abdullah Aldrin , Maliki Nor Zarifah 
Published: June 2022

Purpose
Because of the global increase of climate change effects, floods are becoming more frequent and severer, especially in urban areas of coastal cities and islands where floodplains have turned into buildings because of rapid urbanisation, leading to a higher risk of damages. Urban heritage areas should be highly considered in the time of evacuation because of the vulnerability of streets and buildings and limitations on taking counteractions. Given these limitations, this study aims to propose a network of potential evacuation routes based on spatial configuration analysis of the heritage areas.

Design/methodology/approach
Penang Island's heritage site, namely, George Town, located on the northwest coast of Malaysia, is chosen as the case study. By using an approach of spatial configuration analysis using space syntax techniques in addition to considering the potential starting points for evacuation and flood risk map of the area, this study analysed the area's street network values for evacuation function during flood crisis time.

Findings
Potential evacuation routes were identified for flood disasters in the George Town heritage area. Furthermore, the proposed evacuation routes were evaluated in terms of time for evacuation by metric step-depth analysis of space syntax.

Originality/value
A few studies have focused on practical guidelines for evacuation routes based on spatial configuration analysis, an important yet neglected approach in this regard, especially concerning urban island areas. This study can contribute to providing strategies to reduce vulnerability and casualties in urban heritage areas.
Virtue or vice? Public policies and Nigerian entrepreneurial venture performance
Authors: Olorunshola Damilola Temitope , Odeyemi Temitayo Isaac 
Published: June 2022

PurposeThe purpose of this paper is to explore how inter-agency engagement across levels of government and the agencies' policies impact the development of Micro, Small and Medium Scale Enterprises (MSMEs) in Nigeria, with focus on taxation, business registration and access to finance.Design/methodology/approachThe empirical study involved data sourced through questionnaire administered to 192 MSMEs owners, semi-structured interviews with key officials, and Focus Group Discussion (FGD) with leading members of the Osun State Chamber of Commerce, Mines, Industry and Agriculture (OSUCCIMA).FindingsAmidst increasing levels of engagement amongst public agencies, most MSMEs had not benefited from MSMEs' support programmes. Also, although agencies increasingly utilised the mediating roles of OSUCCIMA in policies for MSMEs, gaps remain because of not factoring in OSUCCIMA's inputs into final policy/programme drafts. Again, policies and programmes were tangential to the desired development outcomes amongst MSMEs, irrespective of size.Research limitations/implicationsConsidering differences in socio-economic and psycho-social orientations of residents/business owners across the various states, further studies focussing on other parts of Nigeria will help to strengthen the argument on how Nigeria aligns with the developing countries literature on the subject.Originality/valueExisting literature demonstrates government's recognition of the significance of MSMEs and policy actions taken in setting the right atmosphere for them to thrive, focussing on the national or local governments. This study draws on these but also explores actions at the subnational level and the role of mediating institutions, thereby showing how a multi-level governance approach could influence outcomes.
Narrative forward-looking information disclosure, do ownership concentration, boardroom gender diversity and cultural values matter? A cross country study
Authors: Abdallah Maysa Ali Mohamed , Eltamboly Nayera Adeldayem 
Published: June 2022

PurposeThis study aims to identify the main factors that drive the differences in the levels of forward-looking information disclosure (FLID) across four countries. This study goes beyond the firm-specific characteristics to the countries-specific factors to explain the observable differences in the level of FLID among the UK, Italian, Hong Kong and Chinese American Depositary Receipts (ADRs) firms trading in US Exchanges.Design/methodology/approachTo validate the levels of FLID, corporate financial information environment (CFIE)-final reports structure extractor (FRSE) was conducted on the annual reports of a sample of 353 listed firm observations in 2020 across four different countries. Also, the ordinary least square regression model was used to examine the proposed relationships.FindingsThe empirical results indicate that the level of FLID is highest among the Chinese ADRs firms trading in US Exchanges and UK listed firms. Also, ownership concentration and gender diversity have a positive correlation with the level of FLID. Additionally, long-term orientation positively influences the level of FLID. Considering the moderation effect of power distance and masculinity dimensions, countries with larger power distance tend to have a lower impact of ownership concentration on the level of FLID, whereas countries with higher masculinity tend to have a lesser positive relationship between gender diversity and the level of FLID.Originality/valueNotwithstanding, this study provides novel and persuasive evidence regarding the effects of firm- and country-specific characteristics as possible determinants of forward-looking disclosures, drawing on evidence from international companies with free floats, boards with female quotas and cultural values including masculinity and long-term orientation. This work offers unique insights from the upper echelons lens, which implies that firms need to obtain a critical mass of gender diversity to achieve a more balanced forward-looking perspective on their annual reports.
Distribution and functional data of fungal families
Authors: Matsuoka Shunsuke , Hatano Yuki , Osono Takashi 
Published: June 2022

AbstractFungi have unique ecosystem functions, such as organic matter decomposition, parasitism, and symbiosis with other organisms in terrestrial and aquatic ecosystems. Their taxonomic and functional diversities are essential factors for predicting ecosystem functions and their responses to environmental changes. With the widespread use of high‐throughput sequencing (HTS) in recent years, the detection of fungal DNA sequences in various regions and on different environmental substrates has advanced. HTS‐obtained DNA sequences can be compared with those in databases to identify the taxa of organisms from which they are derived. Therefore, a global DNA database containing taxonomic information has been developed. However, functional data on the distribution and function of individual taxa remain scarce. In this study, the ecological information of each fungal family was compiled from review papers and published books. Specifically, the following information was collected: reported distribution (11 categories including information on the presence of fungi in Japan) and function (38 categories related to ecological functional data, such as guilds and habitats) of 553 families included in the literature. These data will provide information on the ecology of specific fungi detected in the field and help estimate the functional group composition and diversity of fungi from their DNA assemblage data. The detailed Metadata for this abstract published in the Data Article section of the journal is available in MetaCat in JaLTER at http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2022-02.1/jalter-en.