bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenetic analysis of human parainfluenza type 3 virus strains responsible for the outbreak during the COVID-19 pandemic in Seoul, South Korea
Authors: Kim Ha Nui , Yoon Soo-Young , Lim Chae Seung , Lee Chang Kyu , Yoon Jung 
Published: March 2022

AbstractBackgroundHuman parainfluenza virus 3 (HPIV3) is a major respiratory pathogen that causes acute respiratory infections in infants and children. Since September 2021, an out-of-season HPIV3 rebound has been noted in Korea. The objective of this study was to analyze the molecular characteristics of the HPIV3 strains responsible for the outbreak in Seoul, South Korea.MethodsA total of 61 HPIV3-positive nasopharyngeal swab specimens were collected between October and November 2021. Using 33 HPIV3-positive specimens, partial nucleotide sequences of the HPIV3 hemagglutinin-neuraminidase (HN) gene were aligned with previously published HN gene sequences for phylogenetic and genetic distance (p-distance) analyses.ResultsPhylogenetic tree revealed that all Seoul HPIV3 strains grouped within the phylogenetic subcluster C3. However, these strains formed a unique cluster that branched separately from the C3a lineage. This cluster showed 99% bootstrap support with a p-distance < 0.001. Genetic distances within the other C3 lineages ranged from 0.013 (C3a) to 0.023 (C3c). Deduced amino acid sequences of the HN gene revealed four protein substitutions in Seoul HPIV3 strains that have rarely been observed in other reference strains: A22T, K31N, G387S, and E514K.ConclusionsPhylogenetic analysis of Seoul HPIV3 strains revealed that the strain belonged to a separate cluster within subcluster C3. Genetic distances among strains within subcluster C3 suggest the emergence of a new genetic lineage. The emergence of a new genetic lineage could pose a potential risk of a new epidemic. Further monitoring of the circulating HPIV3 strains is needed to understand the importance of newly discovered mutations.
No evidence for environmental transmission risk of SARS-CoV-2 in the UK’s largest urban river system: London as a case study
Authors: Ransome E , Hobbs F , Jones S , Coleman CM , Harris N D , Woodward G , Bell T , Trew J , Kolarević S , Kračun-Kolarević M , Savolainen V 
Published: March 2022

AbstractThe presence of SARS-CoV-2 in untreated sewage has been confirmed in many countries but its incidence and infection risk in contaminated freshwaters is still poorly understood. The River Thames in the UK receives untreated sewage from 57 Combined Sewer Overflows (CSOs), with many discharging dozens of times per year. We investigated if such discharges provide a pathway for environmental transmission of SARS-CoV-2. Samples of wastewater, surface water, and sediment collected close to six CSOs on the River Thames were assayed over 8 months for SARS-CoV-2 RNA and infectious virus. Bivalves were sampled as sentinel species of viral bioaccumulation. Sediment and water samples from the Danube and Sava rivers in Serbia, where raw sewage is also discharged in high volumes, were assayed as a positive control. We found no evidence of SARS-CoV-2 RNA or infectious virus in UK samples, in contrast to RNA positive water and sediment samples from Serbia. Furthermore, we show that infectious SARS-CoV-2 inoculum is stable in Thames water and sediment for < 3 days, while RNA remained detectable for at least seven days. This indicates that dilution of wastewater likely limits environmental transmission, and that infectivity should be embedded in future risk assessments of pathogen spillover.
Unusual patterns of risk for diabetic retinopathy in the Mumbai slums: The Aditya Jyot Diabetic Retinopathy in Urban Mumbai Slums Study (AJ-DRUMSS) Report 3
Authors: Krishnan Radhika , Jain Astha , Nare Siddhita , Shankar Rajkumar , Bartlett Jacquelaine , Iyengar Sudha K. , Williams Scott M. , Sundaram Natarajan 
Published: March 2022

AbstractDiabetes onset precedes diabetic retinopathy (DR) by 5-10 years, but many people with diabetes remain free of this microvascular complication. Our aim was to identify risk factors for DR progression in a unique and diverse population, the slums of Mumbai.We performed a population-based cross-sectional analysis of 1163 diabetics over 40 years of age from slums in 18 wards of Mumbai. Data was collected on 33 variables and assessed for association with DR using both univariate and multivariate analyses. Stratified analyses were also performed on males and females, separately. Among hypertensive individuals we also assessed whether duration of hypertension associated with DR.Of 31 non-correlated variables analysed as risk factors for DR, 15 showed evidence of significant association. The most prominent included sex, where being a female associated with decreased risk of DR, while longer duration of diabetes and poor glycaemic control associated with increased risk. The duration of diabetes risk was partially, but significantly, mediated by age of diabetes diagnoses (8.6% of variance explained, p = 0.012). Obesity as measured by several measures, including body mass index (BMI) and measures of central obesity had a negative association with DR; increased measures of obesity consistently reduced risk of DR.There was some agreement with risk factors described in earlier studies (e.g., duration of diabetes and glycaemic control), but other factors such as obesity measures appeared to have a reversed direction of effect compared to most prior studies. These results indicated that the overall pattern of association in the Mumbai slums was novel. Thus, in previously uncharacterized populations, such as the slums that we examined, it is important to evaluate all risk factors de novo to appropriately assess patterns of risk.
MePMe-seq: Antibody-free simultaneous m6A and m5C mapping in mRNA by metabolic propargyl labeling and sequencing
Authors: Hartstock Katja , Ovcharenko Anna , Kueck Nadine A. , Spacek Petr , Cornelissen Nicolas V. , Hüwel Sabine , Dieterich Christoph , Rentmeister Andrea 
Published: March 2022

AbstractInternal modifications of mRNA have emerged as widespread and versatile regulatory mechanism to control gene expression at the post-transcriptional level. Current insights rely on the ability to make a modified nucleoside amenable to sequencing. Most of the modifications are methylations involving the co-factorS-adenosyl-L-methionine (SAM), however, simultaneous detection of different methylation sites in the same sample has remained elusive. We present metabolic labeling with propargyl-selenohomocysteine (PSH) in combination with click chemistry to detectN6- methyladenosine (m6A) and 5-methylcytidine (m5C) sites in mRNA with single nucleotide precision in the same sequencing run (MePMe-seq). Intracellular formation of the corresponding SAM analogue leads to detectable levels ofN6-propargyl-A (prop6A) and 5-propargyl-C (prop5C). MePMe-seq overcomes the problems of antibodies for enrichment and sequence-motifs for evaluation, limiting previous methodologies. The joint evaluation of m6A and m5C sites opens the door to study their interconnectivity and improve our understanding of mechanisms and functions of the RNA methylome.
Strain-specific alterations in gut microbiome and host immune responses elicited by Bifidobacterium pseudolongum
Authors: Ma Bing , Gavzy Samuel J. , Saxena Vikas , Song Yang , Piao Wenji , Lwin Hnin Wai , Lakhan Ram , Lyyathurai Jegan , Li Lushen , France Michael , Paluskievicz Christina , WillsonShirkey Marina , Hittle Lauren , Munawwar Arshi , Mongodin Emmanuel F. , Bromberg Jonathan S. 
Published: March 2022

ABSTRACTThe beneficial effects attributed to Bifidobacterium are thought to arise from their host immunomodulatory capabilities, which are likely to be species- and even strain-specific. However, their strain-specificity in direct and indirect immune modulation remain largely uncharacterized. We have shown that B. pseudolongum UMB-MBP-01, a murine isolate, is capable of suppressing inflammation and reducing fibrosis in vivo. To ascertain the mechanism driving this activity and to determine if it is specific to UMB-MBP-01, we compared it to B. pseudolongum type strain ATCC25526 of porcine origin using a combination of in vitro and in vivo experimentation and comparative genomics approaches. Despite many shared features, we demonstrate that these two strains possess distinct genetic repertoires in carbohydrate assimilation, differential activation signatures and cytokine responses in innate immune cells, and differential effects on lymph node morphology with unique local and systemic leukocyte distribution. Importantly, the administration of each B. pseudolongum strain resulted in major divergence in the structure, composition, and function of gut microbiota. This was accompanied by markedly different changes in intestinal transcriptional activities, suggesting strain-specific modulation of the endogenous gut microbiota as a key to host responses of immune modulation and changes in intestinal B. pseudolongum strains. These observations highlight the importance of strain-specificity characteristics of Bifidobacterium for prophylactic supplementation for immune modulation and advance our understanding of the mechanisms which drive the association between Bifidobacterium and health benefit.
Selection on the fly: short term adaptation to an altered sexual selection regime inDrosophila pseudoobscura
Authors: Barata Carolina , Snook Rhonda R. , Ritchie Michael G. , Kosiol Carolin 
Published: March 2022

AbstractExperimental evolution studies are powerful approaches to unveil the evolutionary history of lab populations. Such studies have shed light on how selection changes phenotypes and genotypes. Most of these studies have not examined the time course of adaptation under sexual selection manipulation, by resequencing the populations’ genomes at multiple time points. Here, we analyse allele frequency trajectories inDrosophila pseudoobscurawhere we altered their sexual selection regime for 200 generations and sequenced pooled populations at 5 time points. The intensity of sexual selection was either relaxed in monogamous populations (M) or elevated in polyandrous lines (E). We present a comprehensive study of how selection alters population genetics parameters at the chromosome and gene level. We investigate differences in the effective population size –Ne– between the treatments, and perform a genome-wide scan to identify signatures of selection from the time-series data.We found genomic signatures of adaptation to both regimes inD. pseudoobscura. There are more significant variants on E lines as expected from stronger sexual selection. However, we found that the response on the X chromosome was substantial in both treatments, only more marked in E and restricted to chromosome arm XR in M.Neis lower on the X at the start of the experiment, which might indicate a swift adaptive response at the onset of selection. Additionally, we show that the third chromosome was also affected by elevated polyandry. Its distal end harbours a region showing a strong signal of adaptive divergence in E lines.
Substrate trapping approach identifies TRIM25 ubiquitination targets involved in diverse cellular and antiviral processes
Authors: Yang Emily , Huang Serina , Jami-Alahmadi Yasaman , McInerney Gerald M , Wohlschlegel James A , Li Melody MH 
Published: March 2022

ABSTRACTThe tripartite motif (TRIM) family of E3 ubiquitin ligases is well known for its roles in antiviral restriction and innate immunity regulation, in addition to many other cellular pathways. In particular, TRIM25-mediated ubiquitination affects both carcinogenesis and antiviral response. While individual substrates have been identified for TRIM25, it remains unclear how it regulates diverse processes. Here we characterized a mutation, R54P, critical for TRIM25 catalytic activity, which we successfully utilized to “trap” substrates. We demonstrated that TRIM25 targets proteins implicated in stress granule formation (G3BP1/2), nonsense-mediated mRNA decay (UPF1), and nucleoside synthesis (NME1). R54P abolishes TRIM25 inhibition of alphaviruses independently of the host interferon response, suggesting that this antiviral effect is a direct consequence of ubiquitination. Consistent with that, we observed diminished antiviral activity upon knockdown of several TRIM25-R54P specific interactors including NME1. Our findings highlight that multiple substrates mediate the cellular and antiviral activities of TRIM25, illustrating the multi-faceted role of this ubiquitination network in diverse biological processes.
Mother cells control daughter cell proliferation in intestinal organoids to minimize proliferation fluctuations
Authors: Huelsz-Prince Guizela , Kok Rutger N.U. , Goos Yvonne J. , Bruens Lotte , Zheng Xuan , Ellenbroek Saskia I. , van Rheenen Jacco , Tans Sander J. , van Zon Jeroen S. 
Published: March 2022

AbstractDuring renewal of the intestine, cells are continuously generated by proliferation. Proliferation and differentiation must be tightly balanced, as any bias towards proliferation results in uncontrolled exponential growth. Yet, the inherently stochastic nature of cells raises the question how such fluctuations are limited. We used time-lapse microscopy to track all cells in crypts of growing mouse intestinal organoids for multiple generations, allowing full reconstruction of the underlying lineage dynamics in space and time. Proliferative behavior was highly symmetric between sister cells, with both sisters either jointly ceasing or continuing proliferation. Simulations revealed that such symmetric proliferative behavior minimizes cell number fluctuations, explaining our observation that proliferating cell number remained constant even as crypts increased in size considerably. Proliferative symmetry did not reflect positional symmetry, but rather lineage control through the mother cell. Our results indicate a concrete mechanism to balance proliferation and differentiation with minimal fluctuations, that may be broadly relevant for other tissues.
Managing the dynamic change of organizational knowledge base in collaboration networks
Authors: Wang Jingbei , Nie Yafei 
Published: March 2022

PurposePrevious studies have addressed the importance of knowledge base and its effect on innovation outputs. However, few studies have focused on the antecedents of dynamic changes of the organizational knowledge base. This study aims to shed light on the antecedents of dynamic change of the organizational knowledge base by examining how network centrality in an organization's collaboration network impacts this change and the moderating role of knowledge network cohesion.Design/methodology/approachThe empirical setting of this study is the smartphone collaboration network. The authors selected patent data from the Derwent Innovation Database. A negative binomial model was used to test the hypotheses.FindingsThe results verified that network centrality has a positive effect on the change in coupling among existing knowledge domains and has an invertedU-shaped relationship with the coupling between new and existing knowledge domains. Furthermore, when local cohesion is high, network centrality has a stronger positive effect on the change in coupling among existing knowledge domains. Global cohesion moderates this process in such a way that when it is at a high level, the coupling between new and existing knowledge domains can benefit more from a moderate level of network centrality.Originality/valueThis study sheds light on the antecedents of dynamic change of the organizational knowledge base and links the literature on collaboration and knowledge networks by providing novel insights to match collaboration network centrality with knowledge network cohesion for successful improvement of the organizational knowledge base.
Ownership concentration and Covid-19 disclosure: the mediating role of corporate leverage
Authors: Albitar Khaldoon , Elmarzouky Mahmoud , Hussainey Khaled 
Published: March 2022

Purpose
This paper aims to examine the impact of ownership concentration on Covid-19 disclosure in the narrative sections of corporate annual reports. It also explores the mediating role of corporate leverage on the ownership concentration–Covid-19 disclosure relationship.

Design/methodology/approach
This paper uses automated textual analysis to measure Covid-19 disclosure in annual reports. It also applies different regression models to test the research hypotheses and to address the endogeneity problem. It uses univariate and multivariate analyses through correlations and ordinary least squares.

Findings
The analysis shows that ownership concentration has a negative impact on Covid-19 disclosure. It also shows that corporate leverage negatively affects Covid-19 disclosure, and it has a partial mediating effect on the ownership concentration–Covid-19 disclosure relationship.

Practical implications
The results offer important practical implications for the government, management, shareholders and policymakers. For example, corporate managers are encouraged to consider small shareholders’ interests and provide a sufficient level of Covid-19 disclosure to avoid violating their rights. Also, the government may consider forming a mechanism for balancing the ownership structure to protect small investors and weaken large shareholders’ tunnelling behaviours.

Originality/value
This paper offers two important contributions to governance and disclosure literature. First, it provides new empirical evidence on the relationship between ownership concentration and Covid-19 disclosure. Second, it provides new evidence on the mediating role of the leverage ratio on the ownership concentration–Covid-19 disclosure relationship.
Luxury hotels as orchestrators in gastronomic destination development and management: the case of Borgo Egnazia and the Itria Valley
Authors: Franco Stefano , Presenza Angelo , Messeni Petruzzelli Antonio 
Published: March 2022

PurposeThe aim of this paper is to uncover the main capabilities that a luxury hotel needs to develop when functioning as the orchestrator of a local gastronomic business ecosystem.Design/methodology/approachGiven the limited attention previous literature has placed on the role of luxury hotels as orchestrators in luxury gastronomic business ecosystems, this paper adopts a qualitative approach, i.e. the exploratory analysis of a single case study: the Italian high-end hotel Borgo Egnazia.FindingsThe paper highlights the main capabilities developed by the orchestrator: relational, combinative and promotional capabilities.Originality/valueTo the best of the authors’ knowledge, this is among the first studies to explore what capabilities are needed by a company to orchestrate a destination that builds its product and service offerings upon the local food culture.
Women entrepreneurs’ opportunity identification of digital platform start-ups: emerging evidence from South Africa
Authors: Swartz Ethné M. , Scheepers Caren Brenda , Toefy Tracey 
Published: March 2022

PurposeCognitive drivers of opportunity identification and development are important in entrepreneurship. This study examines antecedents of opportunity development among women founders of digital platform start-ups, defined as technology-mediated sites that facilitate user interactions, processing of transactions or other innovative practices. The opportunity identification and development literature framed our exploration of drivers into digital entrepreneurship among women in a middle-income economy, an area under-represented in prior research.Design/methodology/approachThis research uses in-depth interview data with women founders of five digital platform start-ups in South Africa. The authors supplemented primary interviews with secondary data from a global big data site to provide context for how investors are funding women-owned start-ups in the country.FindingsEntrepreneurs’ heightened alertness to opportunity developed from a confluence of factors such as personal values, impatience at the slow pace of change in post-Apartheid South Africa, corporate ennui and building for-profit business models driven by social purpose. Respondents had multiple identities, including gender, culture and generation that influenced their development as entrepreneurs and their adoption of digital platform strategy for start-up ventures.Research limitations/implicationsMultiple factors influence women entrepreneurs during the opportunity identification and development process as they enact the creation of digital platform start-ups. The authors recommend additional research linking opportunity identification and development to gender in emerging markets.Practical implicationsSouth Africa is witnessing the emergence of women-owned digital platform start-ups that attract risk capital investment. These entrepreneurs are university educated and use prior corporate experience to create growth-oriented companies that government should support.Originality/valueThe study contributes to opportunity identification theory building based on context, specifically how the concepts and strategies can inform new models that include women entrepreneurs.
Working together in emergency care? How professional boundaries influence integration efforts and operational performance
Authors: Gifford Rachel , van der Vaart Taco , Molleman Eric , van der Linden M. Christien 
Published: March 2022

PurposeEmergency care delivery is a process requiring input from various healthcare professionals within the hospital. To deliver efficient and effective emergency care, professionals must integrate rapidly at multiple interfaces, working across functional, spatial and professional boundaries. Yet, the interdisciplinary nature of emergency care presents a challenge to the optimization of patient flow, as specialization and functional differentiation restrict integration efforts. This study aims to question what boundaries exist at the level of professionals and explores how these boundaries may come to influence integration and operational performance.Design/methodology/approachTo provide a more holistic understanding of the inherent challenges to integration at the level of professionals and in contexts where professionals play a key role in determining operational performance, the authors carried out an in-depth case study at a busy, Level 1 trauma center in The Netherlands. In total, 28 interviews were conducted over an 18-month period.FindingsThe authors reveal the existence of structural, relational and cultural barriers between (medical) professionals from different disciplines. The study findings demonstrate how relational and cultural boundaries between professionals interrupt flows and delay service processes.Originality/valueThis study highlights the importance of interpersonal and cultural dynamics for internal integration and operational performance in emergency care processes. The authors unveil how the presence of professional boundaries creates opportunity for conflict and delays at important interfaces within the emergency care process, and can ultimately accumulate, disrupting patient flow and increasing lead times.