bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prebiotic proanthocyanidins inhibit bile reflux-induced esophageal adenocarcinoma through reshaping the gut microbiome and esophageal metabolome
Authors: Weh Katherine M. , Howard Connor L. , Zhang Yun , Tripp Bridget A. , Clarke Jennifer L. , Howell Amy B. , Rubenstein Joel H. , Abrams Julian A. , Westerhoff Maria , Kresty Laura A. 
Published: August 2023

AbstractThe gut and local esophageal microbiome progressively shift from healthy commensal bacteria to inflammatory-linked pathogenic bacteria in patients with gastroesophageal reflux disease, Barrett’s esophagus and esophageal adenocarcinoma (EAC). However, mechanisms by which microbial communities and metabolites contribute to reflux-driven EAC remain incompletely understood and challenging to target. Herein, we utilized a rat reflux-induced EAC model to investigate targeting the gut microbiome-esophageal metabolome axis with cranberry proanthocyanidins (C-PAC) to inhibit EAC progression. Sprague Dawley rats, with or without reflux-induction received water or C-PACad libitum(700 µg/rat/day) for 25 or 40 weeks. C-PAC exerted prebiotic activity abrogating reflux-induced dysbiosis, and mitigating bile acid metabolism and transport, culminating in significant inhibition of EAC through TLR/NF-κB/P53 signaling cascades. At the species level, C-PAC mitigated reflux-induced pathogenic bacteria(Clostridium perfringens, Escherichia coli,andProteus mirabilis).C-PAC specifically reversed reflux-induced bacterial, inflammatory and immune-implicated proteins and genes includingCcl4, Cd14, Crp, Cxcl1, Il6, Il1β, Lbp, Lcn2, Myd88, Nfkb1, Tlr2 and Tlr4aligning with changes in human EAC progression, as confirmed through public databases. C-PAC is a safe promising dietary constituent that may be utilized alone or potentially as an adjuvant to current therapies to prevent EAC progression through ameliorating reflux-induced dysbiosis, inflammation and cellular damage.
Rise in frequency oflasRmutantPseudomonas aeruginosaamong keratitis isolates between 1993 and 2021
Authors: Shanks Robert M. Q. , Atta Sarah , Stella Nicholas A. , Sundar-Raj Chollapadi V. , Romanowski John E. , Grewel Arman S. , Shanks Hazel Q. , Mumper Sonya M. , Dhaliwal Deepinder K. , Mammen Alex , Callaghan Jake D. , Calvario Rachel C. , Romanowski Eric G. , Kowalski Regis P. , Zegans Michael E. , Jhanji Vishal 
Published: August 2023

ABSTRACTPseudomonas aeruginosacauses severe vision threatening keratitis. LasR is a transcription factor that regulates virulence associated genes in response to the quorum sensing molecule N-3-oxo-dodecanoyl-L-homoserine lactone.P. aeruginosaisolates withlasRmutations are characterized by an iridescent high sheen phenotype caused by a build-up of 2-heptyl-4-quinolone. A previous study indicated a high proportion (22 out of 101) ofP. aeruginosakeratitis isolates from India between 2010 and 2016 were sheen positive and had mutations in thelasRgene, and the sheen phenotype correlated with worse clinical outcomes for patients. In this study, a longitudinal collection ofP. aeruginosakeratitis isolates from Eastern North America were screened forlasRmutations by the sheen phenotype and sequencing of thelasRgene. A significant increase in the frequency of isolates with the sheen positive phenotype was observed in isolates between 1993 and 2021. Extracellular protease activity was lower among the sheen positive isolates and a definedlasRmutant. ClonedlasRalleles from the sheen positive isolates were loss of function or dominant negative and differed in sequence from previously reported ocularlasRmutant alleles. Insertion elements were present in a subset of independent isolates and may represent an endemic source from some of the isolates. Retrospective analysis of patient information suggested significantly better visual outcomes for patients with infected by sheen positive isolates. Together, these results indicate an increasing trend towardslasRmutations among keratitis isolates at a tertiary eye care hospital in the United States.
Insight into the emerging insect to human pathogenPhotorhabdusrevealing geographic differences in immune cell tropism
Authors: Addison Max L. , Hapeshi Alexia , Carter Elena , Wong Zi Xin , Connally John E. , Waterfield Nicholas R. 
Published: August 2023

AbstractPhotorhabdus asymbioticais a species of the insect pathogenicPhotorhabdusgenus that has been isolated as an etiological agent in human infections. Since then, multiple isolates have been identified worldwide, however actual clinical infections have so far only been identified in North America, Australia and Nepal. Previous research on the clinical isolates had shown that the strains differed in their behaviour when infecting cultured human cells, based on the geographical site of isolation. In this study we investigate the differences between the pathogenic activities ofP. asymbioticaisolates from different geographic locations. We present findings from the clinical isolates from Australia (Kingscliff) and North America (ATCC43949), and soil borne nematode isolates from Thailand (PB68) and Northern Europe non-clinicalP. asymbioticagenospecies HIT and JUN. We also show the first findings from a new clinical isolate ofP. luminescens(Texas), the first non-asymbioticaspecies to cause a human infection, confirming its ability to infect and survive inside human immune cells. Infection assays were done using both cultured cell lines (THP-1, CHO and HEK cells) and also primary immune cells, Peripheral Blood Mononuclear cells (PBMCs) isolated from human blood. Here for the first time, we show howP. asymbiotica, selectively infects certain immune cells while avoiding others, and that infectivity varies depending on growth temperature. We also show that the infected immune cells vary depending on the geographical location a strain is isolated from, and that the European HIT and JUN strains lack the ability to survive within mammalian cells in tissue culture.
Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles
Authors: Leal J. Luis , Milesi Pascal , Hodková Eva , Zhou Qiujie , James Jennifer , Eklund D. Magnus , Pyhäjärvi Tanja , Salojärvi Jarkko , Lascoux Martin 
Published: August 2023

AbstractIntrogression allows polyploid species to acquire new genomic content from diploid progenitors or from other unrelated diploid or polyploid lineages, contributing to genetic diversity and facilitating adaptive allele discovery. In some cases, high levels of introgression elicit the replacement of large numbers of alleles inherited from the polyploid’s ancestral species, profoundly reshaping the polyploid’s genomic composition. In such complex polyploids it is often difficult to determine which taxa were the progenitor species and which taxa provided additional introgressive blocks through subsequent hybridization. Here, we use population-level genomic data to reconstruct the phylogenetic history ofBetula pubescens(downy birch), a tetraploid species often assumed to be of allopolyploid origin and which is known to hybridize with at least four other birch species. This was achieved by modeling of polyploidization and introgression events under the multispecies coalescent and then using an approximate Bayesian computation (ABC) rejection algorithm to evaluate and compare competing polyploidization models. We provide evidence thatB. pubescensis the outcome of an autoploid genome doubling event in the common ancestor ofB. pendulaand its extant sister species,B. platyphylla, that took place approximately 178,000-188,000 generations ago. Extensive hybridization withB. pendula,B. nana, andB. humilisfollowed in the aftermath of autopolyploidization, with the relative contribution of each of these species to theB. pubescensgenome varying markedly across the species’ range. Functional analysis ofB. pubescensloci containing alleles introgressed fromB. nanaidentified multiple genes involved in climate adaptation, while loci containing alleles derived fromB. humilisrevealed several genes involved in the regulation of meiotic stability and pollen viability in plant species.
Inference of gene regulatory networks using time-series single-cell RNA-seq data with CRISPR perturbations
Authors: Ishikawa Masato , Sugino Seiichi , Masuda Yoshie , Tarumoto Yusuke , Seto Yusuke , Taniyama Nobuko , Wagai Fumi , Yamauchi Yuhei , Kojima Yasuhiro , Kiryu Hisanori , Yusa Kosuke , Eiraku Mototsugu , Mochizuki Atsushi 
Published: August 2023

AbstractSingle-cell RNA-seq analysis coupled with CRISPR-based perturbation (scCRISPR) has enabled the inference of gene regulatory networks (GRNs) with causal relationships. However, a snapshot of scCRISPR data may not lead to an accurate inference, since a gene knockout can influence multi-layered downstream over time. Here, we developed RENGE, a new computational method that infers GRNs using a time-series scCRISPR dataset. RENGE models the propagation process of the effects elicited by a gene knockout on its GRN. It can distinguish between direct and indirect regulations, which allows for the inference of regulations by genes that are not knocked out. RENGE therefore outperforms current methods in the accuracy of inferring GRNs. When used on a dataset we derived from human-induced pluripotent stem cells, RENGE yielded a GRN consistent with multiple databases and literature. Accurate inference of GRNs by RENGE would enable the identification of key factors for various biological systems.
Advancing Protein-DNA Binding Site Prediction: Integrating Sequence Models and Machine Learning Classifiers
Authors: Murad Taslim , Chourasia Prakash , Ali Sarwan , Patterson Murray 
Published: August 2023

AbstractPredicting protein-DNA binding sites is a challenging computational problem in the field of bioinformatics. Identifying the specific residues where proteins bind to DNA is of paramount importance, as it enables the modeling of their interactions and facilitates downstream studies. Nevertheless, the development of accurate and efficient computational methods for this task remains a persistent challenge. Accurate prediction of protein-DNA binding sites has far-reaching implications for understanding molecular mechanisms, disease processes, drug discovery, and synthetic biology applications. It helps bridge the gap between genomics and functional biology, enabling researchers to uncover the intricacies of cellular processes and advance our knowledge of the biological world. The method used to predict DNA binding residues in this study is a potent combination of conventional bioinformatics tools, protein language models, and cutting-edge machine learning and deep learning classifiers. On a dataset of protein-DNA binding sites, our model is meticulously trained, and it is then rigorously examined using several experiments. As indicated by higher predictive behavior with AUC values on two benchmark datasets, the results show superior performance when compared to existing models. The suggested model has a strong capacity for generalization and shows specificity for DNA-binding sites. We further demonstrated the adaptability of our model as a universal framework for binding site prediction by training it on a variety of protein-ligand binding site datasets. In conclusion, our innovative approach for predicting protein-DNA binding residues holds great promise in advancing our understanding of molecular interactions, thus paving the way for several groundbreaking applications in the field of molecular biology and genetics. Our approach demonstrated efficacy and versatility underscore its potential for driving transformative discoveries in biomolecular research.
Knowledge-sharing attitude and behavior of civil servants: motivations behind rewards
Authors: Lam Kristy , Kong Elaine W.S. , Chiu Dickson K.W. , Ho Kevin K.W. 
Published: August 2023

PurposeTo a large extent, knowledge in government workplaces resides within the hierarchy as it provides unique services to the public. Governments should preserve and pass on valuable and irreplaceable knowledge in providing their services through learning by sharing. Yet, sharing requires time and effort. This study examines the motivations of civil servants to share knowledge and their knowledge-sharing behaviors.Design/methodology/approachThe authors conducted an online survey to collect quantitative data from civil servants in the Hong Kong Government and obtained 104 useable responses to test the eight hypotheses comprising six constructs by structural equation modeling to explore the participants' knowledge-sharing behaviors.FindingsResults indicated that (1) expected contribution was the primary source of motivation behind knowledge sharing; (2) participants engaged more frequently in informal than formal knowledge-sharing activities; and (3) there was a dire need for knowledge sharing focusing on explicit knowledge of work procedures.Originality/valueThe research focuses on motivational factors for knowledge sharing. Despite abundant literature about knowledge sharing in public or governmental organizations, scant studies focus on the motivations behind why expected rewards and expected associations have less significant impacts on the attitude toward knowledge sharing than expected contribution.
The system for distributed energy resources testing according to the IEEE 1547-2018 standard
Authors: Dimitrijević Marko A. , Petronijević Milutin 
Published: August 2023

Purpose
This paper aims to propose a new approach to testing distributed energy resources (DERs) in compliance with the IEEE 1547-2018 standard and describes a new, integrated testing and validation system.

Design/methodology/approach
The system is built on the virtual instrumentation paradigm, using acquisition modules to measure physical quantities, while signal processing, including intensive calculations of required parameters, data processing, manipulation and reporting are performed on a computing device.

Findings
Intensive laboratory measurements were performed on a laboratory prototype of a microgrid that emulates DERs. The results obtained using the system described were compared with the measurements obtained by the reference instruments. As all the results match, the usability of the system was verified.

Practical implications
This approach to the realization of the testing and validation system has obvious advantages compared to the classical instruments and provides significant flexibility in multiple aspects. First, the system described integrates all the functions of different instruments into one measuring system, making the entire testing and validation process significantly cheaper and faster. Second, the implementation of the system is possible on different computing platforms depending on specific needs. Third, the software implementation of the system functions enables simple upgrading and the introduction of new functions or changes to existing ones according to changes in the standard. Finally, the system described is designed to automatically provide reports on compliance with the standard.

Originality/value
This paper emphasizes the advantages of the proposed approach over classical testing. The value of the paper is reflected in the applicability and practical implications of the proposed and described hardware and software technical solutions.
Taming wicked problems through international business policy: recommendations for addressing modern slavery
Authors: Rašković Matevž (Matt) 
Published: August 2023

Purpose
The paper frames modern slavery as a global wicked problem and aims to provide a set of international business (IB) policy recommendations for taming it. The outlined approach can also guide IB policymaking to address other kinds of wicked problems.

Design/methodology/approach
This is a conceptual paper that reviews existing literature on wicked problems and integrates it with an IB policy double helix framework. The paper focuseses on the role multinational enterprises (MNEs) play in moderl slavery globally, either through global value chains or within global factory modes of operation.

Findings
As a global wicked problem, modern slavery will never be solved, but it can be re-solved time and time over. Understanding the social reproduction of modern slavery can help shift the focus from labor governance and a narrow supply chain focus toward the role of transnational governance and the need to address institutional, market and organizational failures.

Originality/value
The paper contributes to the gap in an overarching theory of modern slavery and systematically applies the concept of wicked problems and wickedness theory to modern slavery. Drawing on an IB policy double helix framework, the paper addresses the governance nexus between modern slavery, IB and policymaking which can in turn advance IB policy research and theory.
ESG and share price volatility in energy sector firms: does the development phase of countries matter?
Authors: Singh Kuldeep , Jaiwani Megha 
Published: August 2023

Purpose
The global energy sector draws significant stakeholder attention due to never-ending controversies surrounding its environmental impacts. Investors’ response to such controversies causes direct financial implications for these firms. Furthermore, environmental, social and governance (ESG) sensitivity, which is likely to safeguard the energy sector firms from such controversies, is itself conditional to the development stage of a country and its regulatory environment. Therefore, this study aims to investigate if the influence of ESG on the share price volatility (SPV) of energy sector firms is subject to the development stage of the countries.

Design/methodology/approach
The study investigates nine years of panel data of 93 global energy sector firms from developing and developed nations. Using dynamic two-way fixed effects estimation and computing robust standard errors to obtain the econometric results.

Findings
The main finding reveals that the impact of ESG on SPV is, indeed, subject to the development stage of the nations. Similar results are observed for the effects of the social dimension of ESG on SPV. While ESG impacts the SPV negatively for firms in developing economies, the impact is the opposite for firms in developed nations. In other words, strong ESG propositions induce share price stability for developing countries while destabilizing the firms in developed nations.

Practical implications
The policymakers should further streamline the regulations and policies related to ESG adoption and adherence. In practice, the energy sectors should streamline their operations. Firm managers, especially in the energy sector, should devise strategies with ESG as an essential component to safeguard their firms against environmental and market volatility and adversatives. The firms in developing nations should further strengthen their social dimension of ESG to foster social equity and harmony.

Originality/value
The study contributes through its niche investigations on the energy sector, which is very important for the world economy. The study is relevant in the current scenario when the world faces a severe energy crisis due to global supply chain issues.
Enhancing supply chain resilience in SMEs: a deep Learning-based approach to managing Covid-19 disruption risks
Authors: Sun Kai-Xiang , Ooi Keng-Boon , Tan Garry Wei-Han , Lee Voon-Hsien 
Published: August 2023

PurposeThis research examines the relationships between the components of supply chain integration (SCI) (i.e. internal integration (INI), customer integration (CI) and supplier integration (SI)), supply chain risk management (SCRM) and supply chain resilience (SCRE), with disruption impact (DI) as the moderator, among small and medium-sized enterprises (SMEs).Design/methodology/approach271 useable data were collected from Chinese SMEs to test the research model with two statistical approaches of PLS-SEM and ANN analysis.FindingsResults show that SCI (i.e. INI, CI and SI) positively affects SCRM, and subsequently affects SCRE. Moreover, SCRM has also been found to fully mediate the relationship between INI, CI and SI with SCRE. Additionally, DI was also found to moderate the relationship between SCRM and SCRE.Research limitations/implicationsThis study expands the supply chain management-related knowledge by empirically validating the mediating role of SCRM between the elements of SCI and SCRE, as well as empirically identifying DI as the moderator between SCRM and SCRE.Practical implicationsThe findings offer valuable understanding that can guide SME managers, owners and stakeholders in developing strategies for integrating with customers, suppliers and internal departments, as well as implementing SCRM practices to enhance SCRE performance.Originality/valueThe research expands the existing literature on the elements of SCI and SCRM in maintaining SCRE from an Asian developing country's perspective.
The state of embedded librarianship in the university research processes in selected African academic libraries
Authors: Leonard Anna , Chigwada Josiline , Mushi Gilbert 
Published: August 2023

PurposeThis study aims to examine the state of embedded librarianship in African academic libraries by exploring the extent of librarian embedment in research processes in selected academic libraries in Africa.Design/methodology/approachA survey was conducted to collect data using an online questionnaire. The study population was comprised of librarians who directly support researchers throughout the research process in the scholarly communication and information services sections. Purposive sampling was used to select librarians, and 63 responses were received from the target of 100. The collected data were analysed using the statistical package for the social sciences (SPSS) software, and content analysis was used to analyse open-ended questions.FindingsThe study results showed that the extent and nature of librarians' embeddedness in the research process vary across different university contexts in Africa. Challenges and areas of research skill gaps among librarians were identified, and propositions to address the research skill gaps were provided.Practical implicationsThe study findings can be used as a framework for libraries to embed librarians in the research process. The study made recommendations with practical implications for library practitioners in academia, and institutions offering library and information science education, and the library management responsible for the research process.Originality/valueA study brings a novel perspective by examining the state of embedded librarianship in the African context. Its contribution generates knowledge and insights that inform the development of effective embedded librarianship practices in African academic libraries to enhance research support services and advancement of scholarly research in the region.