bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity of HBV genotypes and their association with precore/basal core mutations among HBsAg positive patients in Ibadan, Nigeria
Authors: Faneye Adedayo Omotayo , Motayo Babatunde Olanrewaju , Mustafa Aisha , Odiabo Georgina 
Published: September 2024

Background; Hepatis B virus (HBV) is the most implicated cause of severe liver disease and hepatocellular carcinoma worldwide. Studies have shown that the basal core protein (BCP) and precore protein (PC) of HBV play a significant role in HBV related carcinogenesis. There is paucity of data on type and effect of BCP and PC mutations in Nigeria. This study aims to genotype HBV and investigate any mutations within the BCP and PC among HBV patients in Ibadan, Nigeria.
Methods; Forty HBV DNA positive were recruited into this study, viral load assay and genotyping by nested multiplex PCR was done. The partial X gene region was amplified and Sanger sequenced. The BPC and PC genomic regions were then analyzed using bioinformatics.
Results; Twenty-three participants recorded HBV DNA viral load of >20,000 International Units (IU), while 17 had <20,000 IU, while 28 samples were genotyped. Five genotypes A, B, C, D and E and 4 mixed genotypes AC, AD ACD and ABCD were detected. Genotype AC was the most frequently encountered while genotypes E and B were the least encountered. Mutation was highest in ages 34 to 45 years. Double mutation A1762T and G1764A within the BCP region was the most encountered mutation.
Conclusions; We report a diverse HBV genetic landscape, with mixed infections between genotypes with BCP double mutation A1762T/G1764A, signaling the likelihood of poor HBV related liver disease prognosis. Our findings contribute to our understanding of the molecular characteristics of HBV and its potential implications for disease progression and management among HBV infected Nigerians.
Molecular and spatiotemporal characterization of cells in murine atherosclerotic plaques
Authors: Hou Pengbo , Liu Zhanhong , Fang Jiankai , Wang Ziyi , Liu Shisong , Wang Shiqing , Melino Gerry , Li Peishan , Shi Yufang , Shao Changshun 
Published: September 2024

AbstractObjectiveSingle-cell technologies have revolutionized our understanding of the phenotypic and transcriptional diversity of aortic leukocytes in atherosclerotic humans and mice. However, enzymatically dissociated tissues lose the spatial context of plaque cellsin situ. Here we utilized imaging mass cytometry (IMC) combining with single-cell RNA sequencing (scRNA-seq) to characterize the spatial distribution dynamics, phenotypic transitions, metabolic and functional phenotypes, and the intercellular interaction networks of plaque cells during atherosclerotic progression. Additionally, the dynamic immune landscape of circulating leukocytes associated with atherosclerosis was characterized using cytometry of time of flight (CyTOF).Approach and ResultsA highly multiplexed IMC panel with 33 metal-conjugated antibodies was designed to generate 11 highly multiplexed histology images of aortic root tissues fromApoE-/-mice on high-fat diet at different stage of atherosclerosis. Using histoCAT, we identified 8 principal cell subtypes with distinct phenotypic and geographic dynamics. Furthermore, IMC-defined cell subsets partially corresponded to scRNA-seq-annotated aortic cell subtypes, including 4 macrophage subsets, neutrophils, smooth muscle cells (SMCs) and SMC-derived SEMs (Stem cell, endothelial cell and macrophage-like cell). Activation of inflammatory pathways, increased oxidative phosphorylation and augmented osteoclast differentiation were observed in macrophage populations, SMCs and SEMs from an early stage to advanced stage of atherosclerosis. Notably, cell neighborhood analysis by IMC uncovered multifaceted cell-cell interactions within the plaque, in particular in neutrophil-mediated interactions with smooth muscle cells and macrophages, which were confirmed by ligand-receptor interactions based on scRNA-seq data.Additionally, characterization of the peripheral immune cells by CyTOF revealed an increased ratio of myeloid cells to lymphocytes, and certain neutrophil and monocyte subpopulations also exhibited enhanced lipid metabolism and glycolysis as well as activated inflammatory signaling.ConclusionThis study provides a dynamic spatiotemporal landscape of atherosclerotic lesions and peripheral leukocytes. The new information based on IMC may help understand atherosclerotic pathology and develop novel therapeutic strategies.
Functional insights into the effect of feralisation on the gut microbiota of cats worldwide
Authors: Aizpurua Ostaizka , Botnen Amanda Bolt , Eisenhofer Raphael , Odriozola Iñaki , Santos-Bay Luisa , Bjørnsen Mads Bjørn , Gilbert MTP , Alberdi Antton 
Published: September 2024

AbstractFeralisation, the process by which domesticated organisms revert to a wild state, is a widespread phenomenon across various species. Successfully adapting to a new environment with different access to food, shelter, and other resources requires rapid physiological and behavioural changes, which could potentially be facilitated by gut microbiota plasticity. To investigate whether alterations in gut microbiota support this transition to a feral lifestyle, we analysed the gut microbiomes of domestic and feral cats from six geographically diverse locations using genome-resolved metagenomics. By reconstructing 229 draft genomes from 92 cats, we identified a typical carnivore microbiome structure, with notable diversity and taxonomic differences across regions. While overall diversity metrics did not differ significantly between domestic and feral cats, hierarchical modelling of species communities, accounting for geographic and sex covariates, revealed distinct taxonomic and functional profiles between the two groups. While taxonomic enrichment was balanced, microbial functional capacities were significantly enriched in feral cats. These functional enhancements, particularly in amino acid and lipid degradation, correspond to feral cats’ dietary reliance on crude protein and fat. Additionally, functional differences were consistent with behavioural contrasts, such as the more aggressive and elusive behaviour measured in feral cats compared to the docile behaviour of domestic cats. Finally, the observed enrichment in short-chain fatty acid, neurotransmitter, and vitamin B12 production in feral cats aligns with improved cognitive function and potentially contributes to their heightened aggression and elusiveness. Our findings suggest that microbiome shifts may play a significant role in the development of physiological and behavioural traits advantageous for a feral lifestyle, supporting the adaptive success of feral cats in the wild.
Patient involvement in the biopsychosocial model of care integrated with primary health services: Experience from three health districts in South Kivu, Democratic Republic of Congo
Authors: Kasongo Bertin Mutabesha , Molima Christian Eboma Ndjangulu , Mparanyi Gérard Jacques , Makali Samuel Lwamushi , Mwene-Batu Pacifique Lyabayungu , Tambwe Albert Mwembo , Karemere Hermès , Bisimwa Ghislain Balaluka , Mukalay Abdon Mukalay wa 
Published: September 2024

AbstractIntroductionInvolving people in the provision of care and in decision-making about their health is one of the keys to success and to improving service delivery in the provision of quality health care. Patient involvement in the biopsychosocial model of care is poorly documented in the Democratic Republic of Congo (DRC). The aim of this study is to describe patients’ involvement in the choice of their health policy, their responsibility in holistic care and their capacity to support the biopsychosocial model.MethodsThis qualitative research was conducted in three health districts in the province of South Kivu, DRC. Using a tool inspired by the International Alliance of Patients’ Organizations’ Declaration of Patient-Centered Healthcare, we conducted 27 individual interviews between February and April 2024. These interviews concerned people in complex situations, attending health centers and belonging to patient clubs in six health areas covered by the study. A content analysis of the discourse from the various interviews was carried out.ResultsPatient involvement in the biopsychosocial model of care depended on multiple factors, including relational aspects (partnership between providers and patients, discussion of therapeutic possibilities and guidance for choice), educational aspects (advice and teaching received from caregivers, development of skills), empowerment (responsibility for care), organizational aspects (inclusive and participatory planning, access to different health services) and community aspects (role of entourage and patient clubs).ConclusionsThe various factors influencing patient involvement in the BPS model should be taken into account in the definition of policies and the process of integrating biopsychosocial care. Some of the strategies suggested to support the model, such as raising awareness of the humanization of care, improving the availability of resources and strengthening financial autonomy, will help to improve the quality of care and accessibility to quality health services.
Salicylic Acid restricts cell elongation and induces changes of vacuolar morphology and pH
Authors: Müller Jonas , König Yvonne , Kaiser Sabrina , Löfke Christian , Krebs Melanie , Scheuring David 
Published: September 2024

AbstractThe phytohormone salicylic acid (SA) is a key factor to balance plant defence as well as growth and development. While its role in plant defence has been investigated for decades, regulation of plant growth and development has only come into focus recently. It has been demonstrated that SA application inhibits growth independently of the established Non-expressor of Pathogenesis Related (NPR) receptors. However, the underlying mechanism of this growth inhibition on the cellular level remains largely elusive. Here we show that SA restricts cell elongation and induces changes of vacuolar morphology and pH. Rapidly upon SA application we observe homotypic vacuole fusion and a significant increase in vacuolar pH. These changes seem to be independent of the phytohormone auxin which has been reported to crosstalk with SA. By increasing vacuolar pH, SA directly impacts basic cellular functions such as vesicle trafficking or nutrient storage, leading eventually to cell size restriction and limited growth. Our results demonstrate an NPR-independent mechanism to attenuate growth, potentially allowing free resources to be relocated to withstand environmental stresses.Graphical abstractSalicylic Acid (SA) triggers a reduction in cell size and leads to a spherical vacuolar phenotype. This morphological change is accompanied by an increase in vacuolar pH, potentially due to the enhanced activity of a glycosylated SA (SAG) H+-antiporter and/or the inhibition of V-ATPase activity. In addition, SA disrupts the polarity of PIN2 auxin transporters, resulting in their uniform distribution across the cell membrane.
Deciphering the Cell-Specific Transcript Heterogeneity and Alternative Splicing during the Early Embryonic Development of Zebrafish
Authors: Lin Xiumei , Wang Xue , Liu Chang , Liu Chuanyu , Zeng Tao , Yuan Ziqi , Hu Meidi , Xiang Rong , Zhao Kaichen , Zhou Jie , Yang Shichen , Wang Yang , Meng Kaifeng , Wang Hui , He Guangli , Zhao Rui , Liu Jiaheng , Huang Yunqi , Pan Jingfang , Wang Jialu , Chen Junyi , Guo Fei , Dong Yuliang , Xu Xun , Luo Daji , Gu Ying , Liu Longqi , Dong Zhiqiang , Chen Liang 
Published: September 2024

AbstractCell fate determination during early embryonic development is a complex process modulated by gene expression. The intricate interplay of transcriptional and post-transcriptional regulation is integral to the developmental trajectory of embryogenesis, yet how RNA processing may contribute to early development programming is largely elusive. Leveraging recent technological advances in single-molecule nanopore sequencing, we developed a single-cell long-read transcriptome sequencing technology, allowing a clear view of transcript diversity during zebrafish embryogenesis during pre- and post-zygotic genome activation (ZGA). A closer examination of the dynamic transcript usage and potential alternative splicing revealed that abundant stage-specific transcripts with differential coding potentials are involved in distinct biological functions. Specifically, we identified two cell populations at the onset of ZGA based on isoform diversity instead of gene profiling, which followed divergent developmental trajectories toward the ectoderm and the presumptive ectoderm. These two populations of cells were characterized by divergent splicing regulations linked to differential RNA-binding proteins, including SNRPA and SFPQ. Altogether, using the single-cell long-read transcriptome sequencing strategy, we work has revealed the cell-specific transcriptome dynamics contributing to the cell fate determination during embryogenesis.
3D nanoscale architecture of the respiratory epithelium reveals motile cilia-rootlets-mitochondria axis of communication
Authors: Vijayakumaran Aaran , Godbehere Christopher , Abuammar Analle , Breusegem Sophia Y. , Hurst Leah R. , Morone Nobuhiro , Llodra Jaime , Dalbay Melis T. , Tanvir Niaj M. , MacLellan-Gibson K. , O’Callaghan Chris , Lorentzen Esben ,   CellMap Project Team,   FIB-SEM Technology, Murray Andrew J. , Narayan Kedar , Mennella Vito 
Published: September 2024

AbstractA major frontier in single cell biology is decoding how transcriptional states result in cellular-level architectural changes, ultimately driving function. A remarkable example of this cellular remodelling program is the differentiation of airway stem cells into the human respiratory multiciliated epithelium, a tissue barrier protecting against bacteria, viruses and particulate matter. Here, we present the first isotropic three-dimensional map of the airway epithelium at the nanometre scale unveiling the coordinated changes in cellular organisation, organelle topology and contacts, occurring during multiciliogenesis. This analysis led us to discover a cellular mechanism of communication whereby motile cilia relay mechanical information to mitochondria through striated cytoskeletal fibres, the rootlets, to promote effective ciliary motility and ATP generation. Altogether, this study integrates nanometre-scale structural, functional and dynamic insights to elucidate fundamental mechanisms responsible for airway defence.
Detecting imported malaria infections in endemic settings using molecular surveillance: current state and challenges
Authors: Safarpour Mahdi , Sosa Luis Cabrera , Gamboa Dionicia , Van geertruyden Jean-Pierre , Delgado-Ratto Christopher 
Published: September 2024

AbstractThe Global Technical Strategy for Malaria 2016–2030 targets eliminating malaria from at least 35 countries and reducing case incidence by 90% globally. The importation of parasites due to human mobilization presents a significant challenge to achieve elimination as it can undermine local interventions. A thorough understanding of importation is necessary to support efforts to control and further lead to elimination. Parasite genetic data is extensively deployed to investigate the space-time spread of imported infections. In this matter, this systematic review aimed to aggregate evidence on the use of parasite genetic data for mapping imported malaria and the statistical analytical methods. We discuss the advantages and limitations of the deployed genetic approaches and propose a suitable type of genetic data and statistical framework to discriminate imported malaria infections from local infections. The findings provide actionable insights for national control programs, helping them select the most suitable methods for detecting imported cases while supporting the evaluation of elimination program performance, particularly in low transmission settings.
Evaluating and Addressing Demographic Disparities in Medical Large Language Models: A Systematic Review
Authors: Omar Mahmud , Sorin Vera , Agbareia Reem , Apakama Donald U. , Soroush Ali , Sakhuja Ankit , Freeman Robert , Horowitz Carol R , Richardson Lynne D. , Nadkarni Girish N , Klang Eyal 
Published: September 2024

AbstractBackgroundLarge language models (LLMs) are increasingly evaluated for use in healthcare. However, concerns about their impact on disparities persist. This study reviews current research on demographic biases in LLMs to identify prevalent bias types, assess measurement methods, and evaluate mitigation strategies.MethodsWe conducted a systematic review, searching publications from January 2018 to July 2024 across five databases. We included peer-reviewed studies evaluating demographic biases in LLMs, focusing on gender, race, ethnicity, age, and other factors. Study quality was assessed using the Joanna Briggs Institute Critical Appraisal Tools.ResultsOur review included 24 studies. Of these, 22 (91.7%) identified biases in LLMs. Gender bias was the most prevalent, reported in 15 of 16 studies (93.7%). Racial or ethnic biases were observed in 10 of 11 studies (90.9%). Only two studies found minimal or no bias in certain contexts. Mitigation strategies mainly included prompt engineering, with varying effectiveness.However, these findings are tempered by a potential publication bias, as studies with negative results are less frequently published.ConclusionBiases are observed in LLMs across various medical domains. While bias detection is improving, effective mitigation strategies are still developing. As LLMs increasingly influence critical decisions, addressing these biases and their resultant disparities is essential for ensuring fair AI systems. Future research should focus on a wider range of demographic factors, intersectional analyses, and non- Western cultural contexts.
Flame stabilization and emission reduction: a comprehensive study on the influence of swirl velocity in hydrogen fuel-based burner design
Authors: Paramasivam Prabhu , Obaid Sami Al , Balasubramanian Arun 
Published: September 2024

Purpose
This study aims to numerically analyse a full-scale burner across a wide range of operating pressure conditions and determine the effect of swirl velocity on flame stabilization, flame holding and combustion performance.

Design/methodology/approach
This study uses a numerical analysis approach to investigate a three-dimensional full-scale burner. Modified governing equations are used to determine the effect of swirl velocity on flame stabilization and flame holding. The GR-Mech 3.0 chemical reaction mechanism is used to predict the combustion process. To validate the model, a grid independence study is performed.

Findings
The study reveals that swirl velocity enhances flame stability, resulting in better combustion rates. As the swirl velocity increases, higher flame temperatures are observed due to high convective heat recirculation. The heat transfer coefficient and high radiative extinction coefficient are found to vary based on fuel swirl velocity. The mass fraction of CH4 and CO emphasizes the role of swirl velocity on flame structure. Increasing velocity potentially improves combustion by delaying the process, leading to better combustion and lower emissions.

Originality/value
The findings of this study contribute to the understanding of swirl-stabilized combustion and can guide the development of advanced combustion technologies, making it a valuable addition to the existing combustion field.
How demographic and appearance cues of a potential social engineer influence trust perception and risk-taking among targets?
Authors: Abuelezz Israa , Barhamgi Mahmoud , Nhlabatsi Armstrong , Khan Khaled Md. , Ali Raian 
Published: September 2024

PurposeThe aim of this study is to investigate how the demographics and appearance cues of potential social engineers influence the likelihood that targets will trust them and accept security risk.Design/methodology/approachData were collected through an online survey of 635 participants, including 322 participants from Arab countries and 313 participants from the UK. The survey presented scenarios with 16 personas who offered participants the use of their mobile internet hotspot. These personas were characterized by combinations of age (young vs aged), gender (male vs female), ethnicity (Arab vs UK) and look formality (casual vs formal). The study measured both participants’ offer acceptance and trust in the persona.FindingsResults indicated a higher likelihood of offer acceptance from female and aged personas, as well as a greater trust in these groups. Arab participants showed a preference for personas with Arabian ethnic features. In both samples, trust and acceptance were influenced by the persona’s appearance, which was found to be gender-dependent; with female personas in casual attire and male personas in formal attire being trusted more in comparison to female with formal attire and male with informal, respectively.Practical implicationsFindings highlight the importance of incorporating awareness of appearance-based biases in cybersecurity training, suggesting the need for culturally sensitive training programs to enhance defense against social engineering.Originality/valueThis study distinguishes itself by elucidating the influence of social engineers’ demographic and appearance cues on the likelihood of individuals to take security risks, thus addressing a significant gap in the literature which has traditionally emphasized the profiles of targets.
What drives problematic Bitcoin investment behavior?: The role of financial literacy
Authors: Ryu Hyun-Sun 
Published: September 2024

PurposeAlongside its remarkable growth, problematic Bitcoin investment (BI) behavior and its associated negative consequences have become prevalent, and only a few studies have examined it. Therefore, this study aims to examine problematic BI behavior by investigating its specific antecedents and consequences and identifying which antecedents were more influential in it. In addition, we also examine the role of financial literacy on the relationship between the antecedents and problematic BI behavior.Design/methodology/approachWe collected survey data from 413 investors with Bitcoin investment experience in 2018, when a Bitcoin frenzy occurred. The partial least squares method was used to test the proposed research model.FindingsThe results show that prudent, negative urgency, overexpectation and sensation seeking are positively associated with problematic BI behavior, while restraint is negatively associated. Problematic BI behavior is negatively related to investor well-being. Our findings also indicate that both objective and subjective financial literacy moderate the relationship between the antecedents and problematic BI behavior. Four types of investors in terms of their objective and subjective Bitcoin knowledge show different patterns in the relationship between the antecedents and problematic BI behavior.Originality/valueThis study offers insights for researchers by providing a deeper understanding of the contextual antecedents of problematic BI behavior and the role of financial literacy in it. This study provides detailed implications for financial institutions, policymakers, and regulators to guide rational Bitcoin investment behaviors.