bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative bioinformatics analysis and experimental validation of key biomarkers for risk stratification in primary biliary cholangitis
Authors: Tian Siyuan , Hu Yinan , Zhang Miao , Wang Kemei , Guo Guanya , Li Bo , Shang Yulong , Han Ying 
Published: October 2023

Abstract
Background
Primary biliary cholangitis (PBC) is an autoimmune liver disease, whose etiology is yet to be fully elucidated. Currently, ursodeoxycholic acid (UDCA) is the only first-line drug. However, 40% of PBC patients respond poorly to it and carry a potential risk of disease progression. So, in this study, we aimed to explore new biomarkers for risk stratification in PBC patients to enhance treatment.

Methods
We first downloaded the clinical characteristics and microarray datasets of PBC patients from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified and subjected to enrichment analysis. Hub genes were further validated in multiple public datasets and PBC mouse model. Furthermore, we also verified the expression of the hub genes and developed a predictive model in our clinical specimens.

Results
A total of 166 DEGs were identified in the GSE79850 dataset, including 95 upregulated and 71 downregulated genes. Enrichment analysis indicated that DEGs were significantly enriched in inflammatory or immune-related process. Among these DEGs, 15 risk-related genes were recognized and further validated in the GSE119600 cohort. Then, TXNIP, CD44, ENTPD1, and PDGFRB were identified as candidate hub genes. Finally, we proceeded to the next screening with these four genes in our serum samples and developed a three-gene panel. The gene panel could effectively identify those patients at risk of disease progression, yielding an AUC of 0.777 (95% CI, 0.657–0.870).

Conclusions
In summary, combining bioinformatics analysis and experiment validation, we identified TXNIP, CD44, and ENTPD1 as promising biomarkers for risk stratification in PBC patients.
Binding of Trichinella spiralis C-type lectin with syndecan-1 on intestinal epithelial cells mediates larval invasion of intestinal epithelium
Authors: Wang Zhen , Lu Qi Qi , Weng Min Min , Li Yang Li , Han Lu Lu , Song Yan Yan , Shi Yu Long , Liu Ruo Dan , Cui Jing , Wang Zhong Quan 
Published: October 2023

AbstractC-type lectin (CTL) is a protein that binds to saccharides and plays an important role in parasite adhesion, host cell invasion and immune evasion. Previous studies showed that recombinant T. spiralis C-type lectin (rTsCTL) promotes larval invasion of intestinal epithelium cells (IEC), whereas anti-rTsCTL antibodies inhibits larval invasion. Syndecan-1 (SDC-1) is a member of the heparan sulfate proteoglycan family which is mainly expressed on the surface of IEC and in extracellular matrices where they interact with a plethora of ligands. SDC-1 has a principal role in maintaining cell morphogenesis, establishing cell–cell adhesions, and regulating the gut mucosal barrier. The aim of this study was to investigate whether rTsCTL binds to SDC-1 on IEC, and the binding of rTsCTL with SDC-1 promotes larval invasion and its mechanism. IFA results show that rTsCTL and SDC-1 co-localized on Caco-2 cell membrane. GST pull-down and Co-IP verified the direct interaction between rTsCTL and SDC-1 on Caco-2 cells. qPCR and Western blotting revealed that rTsCTL binding to SDC-1 increased the expression of SDC-1 and claudin-2, and reduced the expression of occludin and claudin-1 in Caco-2 cells incubated with rTsCTL via the STAT3 pathway. β-Xyloside (a syndecan-1 synthesis inhibitor) and Stattic (a STAT3 inhibitor) significantly inhibited rTsCTL binding to syndecan-1 in Caco-2 cells and activation of the STAT3 pathway, abrogated the effects of rTsCTL on the expression of gut tight junctions, and impeded larval invasion. The results demonstrate that binding of rTsCTL to SDC-1 on Caco-2 cells activated the STAT3 pathway, decreased gut tight junction expression, damaged the integrity of the gut epithelial barrier, and mediated T. spiralis invasion of the gut mucosa. TsCTL might be regarded as a candidate vaccine target against T. spiralis invasion and infection.
CD24+LCN2+ liver progenitor cells in ductular reaction contributed to macrophage inflammatory responses in chronic liver injury
Authors: Huang Wei-Jian , Qiu Bi-Jun , Qi Xiao-Shu , Chen Cai-Yang , Liu Wen-Ming , Zhou Shen-ao , Ding Min , Lu Feng-Feng , Zhao Jie , Tang Dan , Zhou Xu , Fu Gong-Bo , Wang Zhen-Yu , Ma Hong-Qian , Wu Yu-Ling , Wu Hong-ping , Chen Xiao-Song , Yu Wei-Feng , Yan He-Xin 
Published: October 2023

Abstract
Background
CD24+CK19+/CD24+SOX9+ resident liver cells are activated and expanded after chronic liver injury in a ductular reaction. However, the sources and functions of these cells in liver damage remain disputed.

Results
The current study combined genetic lineage tracing with in vitro small-molecule-based reprogramming to define liver progenitor cells (LPCs) derived from hepatic parenchymal and non-parenchymal tissues. tdTom+ hepatocytes were isolated from ROSA26tdTomato mice following AAV8-Tbg-Cre-mediated recombination, EpCAM+ biliary epithelial cells (BECs) from wild-type intrahepatic bile ducts and ALB/GFP−EpCAM− cells were isolated from AlbCreERT/R26GFP mice. A cocktail of small molecules was used to convert the isolated cells into LPCs. These in vitro cultured LPCs with CD24 and SOX9 expression regained the ability to proliferate. Transcriptional profiling showed that the in-vitro cultured LPCs derived from the resident LPCs in non-parenchymal tissues expressed Lipocalin-2 (Lcn2) at high levels. Accordingly, endogenous Cd24a+Lcn2+ LPCs were identified by integration of sc-RNA-sequencing and pathological datasets of liver dysfunction which indicates that LPCs produced by ductular reactions might also originate from the resident LPCs. Transplantation of in-vitro cultured Cd24a+Lcn2+ LPCs into CCl4-induced fibrotic livers exacerbated liver damage and dysfunction, possibly due to LCN2-dependent macrophage inflammatory response.

Conclusions
CD24+LCN2+ LPCs constituted the expanding ductular reaction and contributed to macrophage-mediated inflammation in chronic liver damage. The current findings highlight the roles of LPCs from distinct origins and expose the possibility of targeting LPCs in the treatment of chronic hepatic diseases.

Graphical Abstract
The opinions of farm animal veterinarians in Ireland on antibiotic use and their role in antimicrobial stewardship
Authors: O’Connor Sorcha , More Simon J. , Speksnijder David C. , Petti Carloalberto 
Published: October 2023

Abstract
Background
Antibiotic use and resistance in animal production are a concern to public health, and there is an urgent need to reduce antibiotic use in farm animals. To prevent blame shifting, professionals from human medicine, animal medicine and environmental backgrounds must collaborate to tackle this issue. Veterinarians are typically responsible for overseeing and prescribing antibiotic use in animals. There are currently no available studies on the opinions of Irish farm animal veterinarians on antibiotic use, reduction opportunities and their relationships with farmers. A digital survey was developed and sent out to Irish farm animal veterinarians. This paper presents the results of a cross-sectional study of Irish farm animal veterinarians’ attitudes towards antimicrobial stewardship, their prescribing behaviours, antibiotic reduction opportunities and their attitudes for the future of antibiotic use. The veterinarian-farmer relationship is examined and potential interventions to reduce antibiotic use on farms are identified.

Results
In total, 114 complete questionnaires were received, representing approximately 11 per cent of all farm animal veterinarians in Ireland. Respondents were aware of the problem of antibiotic resistance and recognise their role in the fight against it. They realise what actions they must take to reduce antibiotic use and identify barriers that prevent their farmer clients from implementing their advice. Many of them say that they can reduce antibiotic use on farms in the future, but some remain doubtful. There was no statistical difference between veterinarians that had less experience working than those that had more experience in their attitudes towards future reduction in antibiotic use.

Conclusion
Most of the respondents seek to use antibiotics as judiciously as they can. The majority agree that antibiotic overuse is the main contributor to antibiotic resistance. Possible solutions to reduce antibiotic use include the development of antibiotic treatment guidelines, assigning one unique practice to each farm and compulsory CPD (Continuous Professional Development) courses.
RETRACTED ARTICLE: Blockchain managed federated learning for a secure IoT framework
Authors: Chai Jiayong , Li Jian , Wei Muhua , Zhu Chuangying 
Published: October 2023

AbstractIn this work, we present a blockchain-based federated learning (FL) framework that aims achieving high system efficiency while simultaneously addressing issues relating to data sparsity and the disclosure of private information. It is more efficient to build a number of smaller clusters rather than one big cluster for multiple networks. Blockchain-based FL is carried out in each cluster, with the model changes being compiled at the end of the process. Following that, the accumulated updates are swapped across the clusters, which, in practise, improves the updates that are accessible for each cluster. When compared to the extensive interactions that take place in blockchain-based FL, cluster-based FL only sends a limited number of aggregated updates across a substantial distance. This is in contrast to the extensive interactions that take place in blockchain-based FL. In order to conduct an analysis of our system, we have implemented the prototypes of both cluster and blockchain-based FL models. The findings of the experiments show that cluster-based FL model raise the accuracy goes upto 72.6%, and goes down to 11%. The loss goes upto 3.6 and goes down to 0.8. In addition, cluster-based FL model has the potential to hasten the convergence of the model, provided that the same quantity of data is input into it. The reason for this is due to the fact that during a training cycle, cluster-based FL model combines the computational resources of many different clusters.
RETRACTED ARTICLE: Switching mode allocation in planning paths for vehicular network communication
Authors: Lu Dingzhu 
Published: October 2023

AbstractBecause of the increased mobility of vehicle users, it might be difficult to keep communication services in vehicle networks effective and dependable. Huge hurdles have been presented to vehicular networks as a result of the meteoric rise in the amount of data, which comes with the needs of high dependability and low latency. The deployment of access point servers at geographic locations that are closer to the vehicles in order to provide real-time service to applications that are based on the vehicles is one possible option. However, there is a limited amount of cache store space, and there is also a lack of a tractable access mode allocation method. As a result of these factors, it is very difficult to strike a compromise between the network transmission performance and fronthaul savings. Because the signal-to-interference-ratio (SIR) can be enhanced with switching mode in vehicular infrastructure, it may be possible to achieve higher levels of dependability. To serve all of the vehicles, the conventional allocation in vehicular network may not be sufficient on its own for two reasons: (1) the number of vehicles exceeds the number of paths, and (2) a vehicle may be located outside of the coverage path. Therefore, the implementation of switching mode allocation in vehicular communication is very necessary in order to increase the number of vehicles that can be supplied. In this paper, allocation using V2I, V2V, and V2X modes have been analyzed to provide dependable coverage for vehicles. These methods are used for communicating with other vehicles. In this paper, the numerical analysis has been performed such that SIR is optimized. In switching mode allocation, it has been shown that establishing a variable SIR threshold is helpful in achieving a path coverage that can be relied upon. It has been shown beyond a reasonable doubt that the coverage probability is likewise directly dependent on SIR thresholds. The theoretical analysis is verified, and it is confirmed that the suggested method is capable of achieving significant performance improvement in terms of coverage probability and data rate.
Certain investigations of sequential warped product submanifolds on cosymplectic manifolds
Authors: Sharma Anil , Kumar Anuj , Bin Turki Nasser , Shenawy Sameh 
Published: October 2023

AbstractIn a special class of almost contact metric manifolds known as cosymplectic manifolds, the current study aims to establish the existence result and a few inequalities for sequential warped product submanifolds. These results and inequalities represent fruitful connections between the primary intrinsic and extrinsic invariants. Furthermore, findings related to Dirichlet energy have been addressed. Finally, some exceptional cases resulting in several inequities are examined.
A computational framework for improving genetic variants identification from 5,061 sheep sequencing data
Authors: Xie Shangqian , Isaacs Karissa , Becker Gabrielle , Murdoch Brenda M. 
Published: October 2023

Abstract
Background
Pan-genomics is a recently emerging strategy that can be utilized to provide a more comprehensive characterization of genetic variation. Joint calling is routinely used to combine identified variants across multiple related samples. However, the improvement of variants identification using the mutual support information from multiple samples remains quite limited for population-scale genotyping.

Results
In this study, we developed a computational framework for joint calling genetic variants from 5,061 sheep by incorporating the sequencing error and optimizing mutual support information from multiple samples' data. The variants were accurately identified from multiple samples by using four steps: (1) Probabilities of variants from two widely used algorithms, GATK and Freebayes, were calculated by Poisson model incorporating base sequencing error potential; (2) The variants with high mapping quality or consistently identified from at least two samples by GATK and Freebayes were used to construct the raw high-confidence identification (rHID) variants database; (3) The high confidence variants identified in single sample were ordered by probability value and controlled by false discovery rate (FDR) using rHID database; (4) To avoid the elimination of potentially true variants from rHID database, the variants that failed FDR were reexamined to rescued potential true variants and ensured high accurate identification variants. The results indicated that the percent of concordant SNPs and Indels from Freebayes and GATK after our new method were significantly improved 12%−32% compared with raw variants and advantageously found low frequency variants of individual sheep involved several traits including nipples number (GPC5), scrapie pathology (PAPSS2), seasonal reproduction and litter size (GRM1), coat color (RAB27A), and lentivirus susceptibility (TMEM154).

Conclusion
The new method used the computational strategy to reduce the number of false positives, and simultaneously improve the identification of genetic variants. This strategy did not incur any extra cost by using any additional samples or sequencing data information and advantageously identified rare variants which can be important for practical applications of animal breeding.
Stable functional structure despite high taxonomic variability across fungal communities in soils of old-growth montane forests
Authors: Zeng Qingchao , Lebreton Annie , Auer Lucas , Man Xiaowu , Jia Liukun , Wang Gengshen , Gong Sai , Lombard Vincent , Buée Marc , Wu Gang , Dai Yucheng , Yang Zhuliang , Martin Francis M. 
Published: October 2023

AbstractBackgroundMajor advances over the past decade in molecular ecology are providing access to soil fungal diversity in forest ecosystems worldwide, but the diverse functions and metabolic capabilities of this microbial community remain largely elusive. We conducted a field survey in montane old-growth broadleaved and conifer forests, to investigate the relationship between soil fungal diversity and functional genetic traits. To assess the extent to which variation in community composition was associated with dominant tree species (oak, spruce, and fir) and environmental variations in the old-growth forests in the Jade Dragon Snow Mountain in Yunnan Province, we applied rDNA metabarcoding. We also assessed fungal gene expression in soil using mRNA sequencing and specifically assessed the expression of genes related to organic matter decomposition and nutrient acquisition in ectomycorrhizal and saprotrophic fungi.ResultsOur taxonomic profiling revealed striking shifts in the composition of the saprotrophic and ectomycorrhizal guilds among the oak-, fir-, and spruce-dominated forests. The core fungal microbiome comprised only ~ 20% of the total OTUs across all soil samples, although the overlap between conifer-associated communities was substantial. In contrast, seasonality and soil layer explained only a small proportion of the variation in community structure. However, despite their highly variable taxonomic composition, fungal guilds exhibited remarkably similar functional traits for growth-related and core metabolic pathways across forest associations, suggesting ecological redundancy. However, we found that the expression profiles of genes related to polysaccharide and protein degradation and nutrient transport notably varied between and within the fungal guilds, suggesting niche adaptation.ConclusionsOverall, our metatranscriptomic analyses revealed the functional potential of soil fungal communities in montane old-growth forests, including a suite of specialized genes and taxa involved in organic matter decomposition. By linking genes to ecological traits, this study provides insights into fungal adaptation strategies to biotic and environmental factors, and sheds light on the importance of understanding functional gene expression patterns in predicting ecosystem functioning.
Coexistence of two sympatric predators in a transitional ecosystem under constraining environmental conditions: a perspective from space and habitat use
Authors: Warret Rodrigues Chloé , Roth James D. 
Published: October 2023

Abstract
Background
Range expansion of species, a major consequence of climate changes, may alter communities substantially due to competition between expanding and native species.

Methods
We first quantified size differences between an expanding habitat generalist, the red fox (Vulpes vulpes), and a circumpolar habitat specialist, the Arctic foxes (Vulpes lagopus), at the edge of the Arctic, where climate-related changes occur rapidly, to predict the likelihood of the larger competitor escalating interference to intraguild killing. We then used satellite telemetry to evaluate competition in a heterogeneous landscape by examining space use early during the foxes' reproductive period, when resource scarcity, increased-food requirements and spatial constraints likely exacerbate the potential for interference. We used time-LoCoH to quantify space and habitat use, and Minta's index to quantify spatio-temporal interactions between neighbors.

Results
Our morphometric comparison involving 236 foxes found that the potential for escalated interference between these species was high due to intermediate size difference. However, our results from 17 collared foxes suggested that expanding and native competitors may coexist when expanding species occur at low densities. Low home-range overlap between neighbors suggested territoriality and substantial exploitation competition for space. No obvious differential use of areas shared by heterospecific neighbors suggested low interference. If anything, intraspecific competition between red foxes may be stronger than interspecific competition. Red and Arctic foxes used habitat differentially, with near-exclusive use of forest patches by red foxes and marine habitats by Arctic foxes.

Conclusion
Heterogeneous landscapes may relax interspecific competition between expanding and native species, allowing exclusive use of some resources. Furthermore, the scarcity of habitats favored by expanding species may emphasize intraspecific competition between newcomers over interspecific competition, thus creating the potential for self-limitation of expanding populations. Dominant expanding competitors may benefit from interference, but usually lack adaptations to abiotic conditions at their expansion front, favoring rear-edge subordinate species in exploitation competition. However, due to ongoing climate change, systems are usually not at equilibrium. A spread of habitats and resources favorable to expanding species may promote higher densities of antagonistically dominant newcomers, which may lead to extirpation of native species.
Higher angiotensin-converting enzyme 2 (ACE2) levels in the brain of individuals with Alzheimer’s disease
Authors: Reveret Louise , Leclerc Manon , Emond Vincent , Tremblay Cyntia , Loiselle Andréanne , Bourassa Philippe , Bennett David A. , Hébert Sébastien S. , Calon Frédéric 
Published: October 2023

AbstractCognitive decline due to Alzheimer’s disease (AD) is frequent in the geriatric population, which has been disproportionately affected by the COVID-19 pandemic. In this study, we investigated the levels of angiotensin-converting enzyme 2 (ACE2), a regulator of the renin-angiotensin system and the main entry receptor of SARS-CoV-2 in host cells, in postmortem parietal cortex samples from two independent AD cohorts, totalling 142 persons. Higher concentrations of ACE2 protein (p < 0.01) and mRNA (p < 0.01) were found in individuals with a neuropathological diagnosis of AD compared to age-matched healthy control subjects. Brain levels of soluble ACE2 were inversely associated with cognitive scores (p = 0.02) and markers of pericytes (PDGFRβ, p = 0.02 and ANPEP, p = 0.007), but positively correlated with concentrations of soluble amyloid-β peptides (Aβ) (p = 0.01) and insoluble phospho-tau (S396/404, p = 0.002). However, no significant differences in ACE2 were observed in the 3xTg-AD mouse model of tau and Aβ neuropathology. Results from immunofluorescence and Western blots showed that ACE2 protein is predominantly localized in microvessels in the mouse brain whereas it is more frequently found in neurons in the human brain. The present data suggest that higher levels of soluble ACE2 in the human brain may contribute to AD, but their role in CNS infection by SARS-CoV-2 remains unclear.