bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Analysis of SARS-CoV-2 Antigenicity across Assays and in Human and Animal Model Sera
Authors: Mühlemann Barbara , Wilks Samuel H , Baracco Lauren , Bekliz Meriem , Carreño Juan Manuel , Corman Victor M , Davis-Gardner Meredith E. , Dejnirattisai Wanwisa , Diamond Michael S , Douek Daniel C. , Drosten Christian , Eckerle Isabella , Edara Venkata-Viswanadh , Ellis Madison , Fouchier Ron A M , Frieman Matthew , Godbole Sucheta , Haagmans Bart , Halfmann Peter J , Henry Amy R , Jones Terry C , Katzelnick Leah C , Kawaoka Yoshihiro , Kimpel Janine , Krammer Florian , Lai Lilin , Liu Chang , Lusvarghi Sabrina , Meyer Benjamin , Mongkolsapaya Juthathip , Montefiori David C , Mykytyn Anna , Netzl Antonia , Pollett Simon , Rössler Annika , Screaton Gavin R , Shen Xiaoying , Sigal Alex , Simon Viviana , Subramanian Rahul , Supasa Piyada , Suthar Mehul , Türeli Sina , Wang Wei , Weiss Carol D , Smith Derek J 
Published: September 2023

AbstractThe antigenic evolution of SARS-CoV-2 requires ongoing monitoring to judge the immune escape of newly arising variants. A surveillance system necessitates an understanding of differences in neutralization titers measured in different assays and using human and animal sera. We compared 18 datasets generated using human, hamster, and mouse sera, and six different neutralization assays. Titer magnitude was lowest in human, intermediate in hamster, and highest in mouse sera. Fold change, immunodominance patterns and antigenic maps were similar among sera. Most assays yielded similar results, except for differences in fold change in cytopathic effect assays. Not enough data was available for conclusively judging mouse sera, but hamster sera were a consistent surrogate for human first-infection sera.
Novel insights into phage biology of the pathogenClostridioides difficilebased on the active virome
Authors: Schüler Miriam A. , Daniel Rolf , Poehlein Anja 
Published: September 2023

AbstractThe global pathogenClostridioides difficileis a well-studied organism, and researchers work on unravelling its fundamental virulence mechanisms and biology. Prophages have been demonstrated to influenceC. difficiletoxin expression and contribute to the distribution of advantageous genes. All this underlines the importance of prophages inC. difficilevirulence. Although severalC. difficileprophages were sequenced and characterized, investigations on the entire active virome of a strain are still missing. Phages were mainly isolated after mitomycin C-induction, which does not resemble natural stressor forC. difficile.We examined active prophages from differentC. difficilestrains after cultivation in the absence of mitomycin C by sequencing and characterization of particle-protected DNA. Phage particles were collected after standard cultivation, or after cultivation in the presence of the secondary bile salt deoxycholate (DCA). DCA is a natural stressor forC. difficileand a potential prophage-inducing agent. We also investigated differences in prophage activity between clinical and non-clinicalC. difficilestrains. Our experiments demonstrated that spontaneous prophage release is common inC. difficile, and that DCA presence induces prophages. Fourteen different, active phages were identified by this experimental procedure. We could not identify a definitive connection between clinical background and phage activity. However, one phage exhibited distinctively higher activity upon DCA-induction in the clinical strain than in the corresponding non-clinical strain, although the phage is identical in both strains. We recorded that enveloped DNA mapped to genome regions with characteristics of mobile genetic elements other than prophages. This pointed to mechanisms of DNA mobility that are not well-studied inC. difficileso far. We also detected phage-mediated lateral transduction of bacterial DNA, which is the first described case inC. difficile. This study significantly contributes to our knowledge on prophage activity inC. difficileand revealed novel aspects onC. difficile(phage) biology.
Starch can expedite the screening for bacterial aflatoxin degraders
Authors: Sandlin Natalie , Momeni Babak 
Published: September 2023

AbstractAflatoxins (AFs) are secondary fungal metabolites that contaminate common food crops and are harmful to humans and animals. The ability to degrade or remove aflatoxins from common feed commodities will improve health standards and counter the economic drain inflicted by AF contamination. Bioremediation is a promising solution to AF contamination because of its low cost and few undesired environmental side-effects. Identifying new degrader species is highly beneficial in that it can offer alternatives to overcome the limitations of existing biodegraders, such as narrow working conditions and low degradation rates. Here, we screen several environmental isolates for their AF detoxification ability, using aflatoxin G2. We use different carbon sources (glucose and starch) as isolation and culturing media to examine the effect of the environment on degradation ability. Strains isolated in media with starch as the primary carbon source showed a higher percentage of good AF degraders, 16% compared to 2% when glucose was the primary carbon source. Additionally, the majority of species isolated in glucose medium exhibited improved degradation efficiency when moved into starch medium, with one isolate improving degradation levels from 30% to 70%. Our starch screen also revealed three previously unidentified AF degrader bacterial species. Good aflatoxin G2degraders also appear to perform well against aflatoxin B1. Overall, for AF degradation, starch medium expedites the screening process and generally improves the performance of isolates. We thus propose that using starch as the carbon source is a promising means to identify new AF degraders in the environment.
Host metabolic pathways essential for malaria and related hemoparasites in the infection of nucleated cells
Authors: Maurizio Marina , Masid Maria , Woods Kerry , Caldelari Reto , Doench John G. , Naguleswaran Arunasalam , Joly Denis , Fernández Martín González , Zemp Jonas , Borteele Mélanie , Hatzimanikatis Vassily , Heussler Volker , Rottenberg Sven , Olias Philipp 
Published: September 2023

SUMMARYApicomplexan parasite diseases, including malaria (Plasmodium) and theileriosis (Theileria), pose a significant threat to global health and the socioeconomic well-being of low-income countries. Despite recent advances, the common host metabolic proteins essential for these highly auxotrophic pathogens remain elusive. Here, we present a comprehensive investigation integrating a metabolic model ofP. falciparumparasites in hepatocytes and a genome-wide CRISPR screen targetingTheileriaschizont-infected macrophages. We reveal unifying host metabolic enzymes critical for the intracellular survival of these related hematozoa. We show that pathways such as host purine and heme biosynthesis are essential for bothTheileriasurvival andPlasmodiumliver development, while genes involved in glutathione and polyamine biosynthesis are predicted to be essential forPlasmodiumonly under certain metabolic conditions. Our work highlights the importance of host porphyrins for the viability of liver-stagePlasmodium. Shared parasite vulnerabilities provide a resource for exploring alternative therapeutic approaches to combat these crippling diseases.
Reconstitution of Early Paclitaxel Biosynthetic Network
Authors: Liu Jack Chun-Ting , De La Pena Ricardo , Tocol Christian , Sattely Elizabeth S. 
Published: September 2023

AbstractPaclitaxel is an anticancer therapeutic produced by the yew tree. Over the last two decades, a significant bottleneck in the reconstitution of early paclitaxel biosynthesis has been the propensity of heterologously expressed pathway cytochromes P450, including taxadiene 5α-hydroxylase (T5αH), to form multiple products. This diverts metabolic flux away from the paclitaxel precursor, taxadien-5α-ol, thus previous attempts of reconstitution have not yielded sufficient material for characterization, regardless of the heterologous host. Here, we structurally characterized four new products of T5αH, many of which appear to be over-oxidation of the primary mono-oxidized products. By tuning the promoter strength for T5αH expression, levels of these proposed byproducts decrease with a concomitant increase in the accumulation of taxadien-5α-ol by four-fold. This engineered system enabled the reconstitution of a six step biosynthetic pathway to produce isolatable 5α,10β-diacetoxy-taxadien-13α-ol. Furthermore, we showed that this pathway may function as a metabolic network rather than a linear pathway. The engineering of the paclitaxel biosynthetic network demonstrates thatTaxusgenes can coordinatively function for the biosynthetic production of key early stage paclitaxel intermediates and serves as a crucial platform for the discovery of the remaining biosynthetic genes.
Discovering paracrine regulators of cell type composition from spatial transcriptomics using SPER
Authors: Zhao Tianxiao , Haber Adam L. 
Published: September 2023

SUMMARYA defining characteristic of each biological tissue is its cell type composition. Many pathologies and chronic diseases are associated with perturbations from the homeostatic composition, which can lead to aberrant tissue function. Spatial transcriptomics now enables simultaneous measurement of gene expression and cell type composition, creating an opportunity to discover the transcripts most strongly associated with changes in nearby cell composition. However, no method yet exists to systematically identify such signals. Here, we develop Spatial Paired Expression Ratio (SPER), a computational approach to evaluate the spatial dependence between transcript abundance and cell type proportions in spatial transcriptomics data. We demonstrate the ability of SPER to accurately detect paracrine drivers of cellular abundance using simulated datasets. Using publicly available spatial transcriptomic data from mouse brain, we show that genes identified by SPER are highly likely to be both extracellularly secreted and to participate in known receptor-ligand interactions. This provides evidence of SPER’s ability to detect compositional regulatory signals. In addition to recovering known interactions, SPER identified novel spatial associations, such as between the Wnt ligandRpso3and its cognate receptorLgr5, not previously known to regulate neural cell type composition in the motor cortex. SPER thus presents a general approach to discovering paracrine drivers of cellular compositional changes.
Measuring the changes: how can a perceived cultural mega-event evidence its “value”? Insights from implementing evaluation methodologies for Coventry 2021
Authors: Scott Mark , Neelands Jonothan , Beer Haley , Bharatan Ila , Healey Tim , Henry Nick , Lam Si Chun , Tomlins Richard 
Published: September 2023

PurposeIt is well known that culture is a catalyst for change, helping economies respond to societal problems and demands and that culture is where people turn to in moments of crisis. In this case study around designing and implementing evaluation methodologies/frameworks for Coventry UK City of Culture 2021, it is suggested that in English public policy and within publicly invested arts there is a maturation of thinking around recognising/measuring the public value of culture including its social value. The purpose of this paper is to chart the recent policy of justifying cultural expenditure with social value claims and highlight challenges for evaluating activity within Coventry UK CoC 2021 as a change in wider policy is taking place.Design/methodology/approachThis paper provides creative insights into the design and implementation of the evaluation methodologies/frameworks for Coventry UK City of Culture 2021. The authors of this paper as the collective team undertaking the evaluation of Coventry's year as UK City of Culture 2021 bring first-hand experiences of challenges faced and the need for a cultural mega-event to evidence its value.FindingsThe case study aims to address the concepts of measuring value within cultural events and argues that a paradigm shift is occurring in methods and concepts for evidencing the aforementioned value.Research limitations/implicationsThe case study within this paper focuses on the build-up period to the UK City of Culture 2021 year and the thinking and logic behind the creation of the evaluation/measurement framework and therefore does not include findings from the actual cultural year.Originality/valueIt is acknowledged that there are papers examining measuring and evidencing the “value” of cultural mega-events, the authors bring real-life first-hand experience of the concepts being utilised by them on the ground in the delivery and evaluation design of Coventry, UK City of Culture 2021.
Assessment of the impacts of the life cycle of construction waste on human health: lessons from developing countries
Authors: Wang Li , Lv Yanhong , Wang Tao , Wan Shuting , Ye Yanling 
Published: September 2023

PurposeThe purpose of this research is to address the existing gap in the study of construction and demolition waste (C&DW) by focusing on its impact on human health throughout the entire life cycle. And this research provides a comprehensive assessment model that incorporates the release of gaseous pollutants and particulate matter during the whole life cycle of C&DW, thereby contributing to a more holistic understanding of its impact on human health.Design/methodology/approachThe research was conducted in two stages. Firstly, the quantitative model framework of pollutants emitted by C&DW was established. Three types of pollutants were considered, namely nitrogen dioxide (NO2), sulfur dioxide (SO2) and inhalable particulate matter (PM10). Second, disability-adjusted life year (DALY) and willingness to pay (WTP) assessments were used to provide a monetary quantified health impact for pollutants released by C&DW.FindingsThe results show that the WTP value of PM10 is the highest among all pollutants and 8.68E+07 dollars/a, while the WTP value in the disposal stage accounts for the largest proportion compared to the generation and transportation stage. These findings emphasize the importance of PM10 and C&DW treatment stage for pollutant treatment.Originality/valueThe results of this study are of great significance for the management department to optimize the construction management scheme to reduce the total amount of pollutants produced by C&DW and its harm to human health. Meanwhile, this study fills the gap in existing research on the impact assessment of C&DW on human health throughout the whole life cycle, and provides reference and basis for future research and policy formulation.
Towards a typology of logistics “work” beyond formal employment: a synthesised literature review
Authors: Wang Xueqin , Yuen Kum Fai 
Published: September 2023

PurposeLogistics at work is rapidly changing. The changing trend is especially prominent when considering the active involvement of individuals that perform diverse forms of formal/informal “logistics work” (e.g. crowd logistics and self-collection). Thus, by conducting a synthesised review (n = 55), this study aims to provide a typology of individuals' logistics work.Design/methodology/approachThe total social organisation of labour is used as a guiding framework. A deductive literature analysis is performed based on the identified journal articles.FindingsThe review findings reveal three major contexts where individuals perform logistics work: formal organisation, social community and private household, with a decreased level of formality. Under each context, individuals may be engaged in paid or unpaid activities, creating six forms of logistics work, termed as paid/voluntary professional logistics, incentivised/friendly social logistics and rewarded/free consumer logistics. Furthermore, an actor–sphere–resource–value conceptualisation of individual logistics is proposed, focussing on the chains of actors, work settings, resource input and value outcome.Originality/valueThe results provide a theoretical foundation for further research in individual- or consumer-centrism in logistics. Two research directions and seven research questions are presented for future investigation.
Strategic divestment of emerging market firms: the influence of returnee managers and CEO characteristics
Authors: Kalasin Kiattichai 
Published: September 2023

PurposeThis study aims to examine the role of returnee managers that can affect the strategic-divestment decision of emerging-market firms (EM firms). Drawing on arguments from the upper echelons theory and international human resource mobility perspectives, this study aims to propose that returnee managers influence corporate divestitures when the business outlook is negative. In addition, this study aims to examine the interplay between returnee managers and CEOs, whose characteristics can foster or undermine the efforts of returnee managers to engage in corporate divestments.Design/methodology/approachThis study examines 278 firms from nine emerging economies. The negative binomial regression was employed to estimate the model. In the robustness checks, the logistic regression was adopted to confirm the earlier findings.FindingsThe empirical results support the notion that returnee managers strengthen the relationship between firm performance and divestments. Because of the limited liabilities of foreignness and outsidership, returnee managers can gain social trust and credibility through communication and social interaction. Furthermore, the results provide mixed support for the moderating effect of CEO characteristics on the performance–divestment relationship.Practical implicationsThis study reveals that returnee managers are a great asset for EM firms that aim to find synergies and upgrade their capabilities through asset reconfiguration, which is an essential activity of emerging market firms to integrate themselves into the global competition. Meanwhile, CEO characteristics can foster (through their education level) or hinder (due to their age) divestment attempts, influenced by returnee managers.Originality/valueThis study explores an understudied phenomenon in international business (IB): strategic divestment of EM firms. The literature that examines strategic divestment and corporate refocusing in emerging markets is extremely limited. Furthermore, this study explores the novel topic that intersects the international business (IB) and international human resource management (IHRM) research areas. Specifically, this study investigates the impact of returnee managers on strategic divestments.
A bibliometric analysis of halal tourism: future research agenda
Authors: Supardin Lalu , Suyanto Mohammad , Hidayat Anas , Wijaya Tony 
Published: September 2023

Purpose
Over the past few decades, a large number of research studies have examined tourism. However, studies that examine halal tourism are still limited. Therefore, the purpose of this study is to conduct a bibliometric analysis related to halal tourism based on the results of empirical research studies that have been published.

Design/methodology/approach
The approach in this study uses a systematic literature review related to halal tourism as a reference in “Article Title, Abstract and Keywords” based on the Scopus database from 1997 to 2023. The analysis was conducted on January 8, 2023. The data that has been collected will be analyzed bibliometrically using VOSviewer.

Findings
The research findings show that research related to halal tourism is still relatively rare, especially in countries/locations where the majority of the population is non-Muslim. This can be seen from the majority of previous studies conducted in Muslim-majority countries/locations, such as Malaysia and Indonesia. Future research should be conducted in countries/locations where the majority of the population is non-Muslim.

Research limitations/implications
This study relies on research in halal tourism literature in the Scopus database. Future studies can combine with the Web of Science database to expand generalization.

Practical implications
The results of this study include implications for managing and developing sustainable halal tourism in the future for practitioners.

Social implications
The results of this study provide a strategic perspective to practitioners and society in general to find out how the concept of sustainable halal tourism development in the future is in accordance with Islamic sharia.

Originality/value
Research related to halal tourism is currently starting to develop in various countries, both with a majority Muslim and non-Muslim population. In addition, until now research related to halal tourism is still limited literature that discusses.
The experience of hurt in the deepest part of self; a phenomenological study in young people with non-suicidal self-injury (NSSI)
Authors: AghaMohammadi Soudeh , Mazaheri Mohammad Ali , Fata Ladan , Mootabi Fereshteh , Moghadasiyan Basir 
Published: September 2023

PurposeWhat is happening in the perceived world of young people who have non-suicidal self-injury? The answer to this question explains many quantitative research findings in the field of NSSI. The current qualitative research design is Husserl's descriptive phenomenology.Design/methodology/approachThe participants included 17–29-year-old youths with self-injury and were selected with a targeted sampling approach and a conspicuous sampling method based on the theoretical saturation criterion of 21 people. Data were collected in a semi-structured interview and analyzed in the MAXQDA2022 software using the Attride-Stirling (2001) method. Validation of data was done by the method of simultaneous review of colleagues and simultaneous review of participants.FindingsThe themes emerging from the analysis of the findings are the three organizing themes of “vulnerable temperament” which includes height and head, high pain sensitivity threshold and desire for nothingness, “traumatic family” which includes disorganization, crisis and devaluation in the family and “developmental injuries” that are associated with physical, sexual and emotional abuse and neglect. The content of these themes seriously harms a person's self-perception through the emotions of fear, shame, anger and despair and is integrated into the overarching theme of “damaged self”.Originality/value“Damaged Self” provides causal explanations related to the formation of self-injurious behaviors and these behaviors are in harmony with the damage that a person observes in his perception of himself.
Operationalising critical realism for case study research
Authors: Fuchs Olivier , Robinson Craig 
Published: September 2023

PurposeCritical realism is an increasingly popular “lens” through which complex events, entities and phenomena can be studied. Yet detailed operationalisations of critical realism are at present relatively scarce. This study's objective here is built on existing debates by developing an open systems model of reality, a basis for designing appropriate, internally consistent methodologies.Design/methodology/approachThe authors use a qualitative case study examining changing practices for client contact management in professional services firms during restrictions imposed by the COVID-19 crisis to show how the model can be operationalised across all stages of a research study.FindingsThis study contributes to the literature on qualitative applications of critical realism by providing a detailed example of how the research paradigm influenced choices at every stage of the case study process.Originality/valueMore importantly, this model of reality as an open system provides a tool for other researchers to use in their own operationalisation of critical realism in a variety of different settings.