bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic introgression from commercial European pigs to the indigenous Chinese Lijiang breed and associated changes in phenotypes
Authors: Yang Ruifei , Jin Siqi , Fang Suyun , Yan Dawei , Zhang Hao , Nie Jingru , Liu Jinqiao , Lv Minjuan , Zhang Bo , Dong Xinxing 
Published: April 2024

Abstract
Background
Gene flow is crucial for enhancing economic traits of livestock. In China, breeders have used hybridization strategies for decades to improve livestock performance. Here, we performed whole-genome sequencing of a native Chinese Lijiang pig (LJP) breed. By integrating previously published data, we explored the genetic structure and introgression of genetic components from commercial European pigs (EP) into the LJP, and examined the impact of this introgression on phenotypic traits.

Results
Our analysis revealed significant introgression of EP breeds into the LJP and other domestic pig breeds in China. Using a haplotype-based approach, we quantified introgression levels and compared EP to LJP and other Chinese domestic pigs. The results show that EP introgression is widely prevalent in Chinese domestic pigs, although there are significant differences between breeds. We propose that LJP could potentially act as a mediator for the transmission of EP haplotypes. We also examined the correlation between EP introgression and the number of thoracic vertebrae in LJP and identified VRTN and STUM as candidate genes for this trait.

Conclusions
Our study provides evidence of introgressed European haplotypes in the LJP breed and describes the potential role of EP introgression on phenotypic changes of this indigenous breed.
Microbiome composition as a potential predictor of longevity in rabbits
Authors: Biada Iliyass , Ibáñez-Escriche Noelia , Blasco Agustín , Casto-Rebollo Cristina , Santacreu Maria A. 
Published: April 2024

Abstract
Background
Longevity and resilience are two fundamental traits for more sustainable livestock production. These traits are closely related, as resilient animals tend to have longer lifespans. An interesting criterion for increasing longevity in rabbit could be based on the information provided by its gut microbiome. The gut microbiome is essential for regulating health and plays crucial roles in the development of the immune system. The aim of this research was to investigate if animals with different longevities have different microbial profiles. We sequenced the 16S rRNA gene from soft faeces from 95 does. First, we compared two maternal rabbit lines with different longevities; a standard longevity maternal line (A) and a maternal line (LP) that was founded based on longevity criteria: females with a minimum of 25 parities with an average prolificacy per parity of 9 or more. Second, we compared the gut microbiota of two groups of animals from line LP with different longevities: females that died/were culled with two parities or less (LLP) and females with more than 15 parities (HLP).

Results
Differences in alpha and beta diversity were observed between lines A and LP, and a partial least square discriminant analysis (PLS-DA) showed a high prediction accuracy (> 91%) of classification of animals to line A versus LP (146 amplicon sequence variants (ASV)). The PLS-DA also showed a high prediction accuracy (> 94%) to classify animals to the LLP and HLP groups (53 ASV). Interestingly, some of the most important taxa identified in the PLS-DA were common to both comparisons (Akkermansia, Christensenellaceae R-7, UnculturedEubacteriaceae, among others) and have been reported to be related to resilience and longevity.

Conclusions
Our results indicate that the first parity gut microbiome profile differs between the two rabbit maternal lines (A and LP) and, to a lesser extent, between animals of line LP with different longevities (LLP and HLP). Several genera were able to discriminate animals from the two lines and animals with different longevities, which shows that the gut microbiome could be used as a predictive factor for longevity, or as a selection criterion for these traits.
Predicting condensate formation of protein and RNA under various environmental conditions
Authors: Chin Ka Yin , Ishida Shoichi , Sasaki Yukio , Terayama Kei 
Published: April 2024

Abstract
Background
Liquid–liquid phase separation (LLPS) by biomolecules plays a central role in various biological phenomena and has garnered significant attention. The behavior of LLPS is strongly influenced by the characteristics of RNAs and environmental factors such as pH and temperature, as well as the properties of proteins. Recently, several databases recording LLPS-related biomolecules have been established, and prediction models of LLPS-related phenomena have been explored using these databases. However, a prediction model that concurrently considers proteins, RNAs, and experimental conditions has not been developed due to the limited information available from individual experiments in public databases.

Results
To address this challenge, we have constructed a new dataset, RNAPSEC, which serves each experiment as a data point. This dataset was accomplished by manually collecting data from public literature. Utilizing RNAPSEC, we developed two prediction models that consider a protein, RNA, and experimental conditions. The first model can predict the LLPS behavior of a protein and RNA under given experimental conditions. The second model can predict the required conditions for a given protein and RNA to undergo LLPS.

Conclusions
RNAPSEC and these prediction models are expected to accelerate our understanding of the roles of proteins, RNAs, and environmental factors in LLPS.
Karyotype and LTR-RTs analysis provide insights into oak genomic evolution
Authors: Cao Rui-Bin , Chen Ran , Liao Ke-Xin , Li He , Xu Gang-Biao , Jiang Xiao-Long 
Published: April 2024

Abstract
Background
Whole-genome duplication and long terminal repeat retrotransposons (LTR-RTs) amplification in organisms are essential factors that affect speciation, local adaptation, and diversification of organisms. Understanding the karyotype projection and LTR-RTs amplification could contribute to untangling evolutionary history. This study compared the karyotype and LTR-RTs evolution in the genomes of eight oaks, a dominant lineage in Northern Hemisphere forests.

Results
Karyotype projections showed that chromosomal evolution was relatively conservative in oaks, especially on chromosomes 1 and 7. Modern oak chromosomes formed through multiple fusions, fissions, and rearrangements after an ancestral triplication event. Species-specific chromosomal rearrangements revealed fragments preserved through natural selection and adaptive evolution. A total of 441,449 full-length LTR-RTs were identified from eight oak genomes, and the number of LTR-RTs for oaks from section Cyclobalanopsis was larger than in other sections. Recent amplification of the species-specific LTR-RTs lineages resulted in significant variation in the abundance and composition of LTR-RTs among oaks. The LTR-RTs insertion suppresses gene expression, and the suppressed intensity in gene regions was larger than in promoter regions. Some centromere and rearrangement regions indicated high-density peaks of LTR/Copia and LTR/Gypsy. Different centromeric regional repeat units (32, 78, 79 bp) were detected on different Q. glauca chromosomes.

Conclusion
Chromosome fusions and arm exchanges contribute to the formation of oak karyotypes. The composition and abundance of LTR-RTs are affected by its recent amplification. LTR-RTs random retrotransposition suppresses gene expression and is enriched in centromere and chromosomal rearrangement regions. This study provides novel insights into the evolutionary history of oak karyotypes and the organization, amplification, and function of LTR-RTs.
Joint application of A-InDels and miniSTRs for forensic personal, full and half sibling identifications, and genetic differentiation analyses in two populations from China
Authors: Cai Meiming , Lei Fanzhang , Liu Yanfang , Wang Xi , Wang Hongdan , Xie Weibing , Yang Zi , Yang Shangwu , Zhu Bofeng 
Published: April 2024

Abstract
Background
Previously, a novel multiplex system of 64 loci was constructed based on capillary electrophoresis platform, including 59 autosomal insertion/deletions (A-InDels), two Y-chromosome InDels, two mini short tandem repeats (miniSTRs), and an Amelogenin gene. The aim of this study is to evaluate the efficiencies of this multiplex system for individual identification, paternity testing and biogeographic ancestry inference in Chinese Hezhou Han (CHH) and Hubei Tujia (CTH) groups, providing valuable insights for forensic anthropology and population genetics research.

Results
The cumulative values of power of discrimination (CDP) and probability of exclusion (CPE) for the 59 A-InDels and two miniSTRs were 0.99999999999999999999999999754, 0.99999905; and 0.99999999999999999999999999998, 0.99999898 in CTH and CHH groups, respectively. When the likelihood ratio thresholds were set to 1 or 10, more than 95% of the full sibling pairs could be identified from unrelated individual pairs, and the false positive rates were less than 1.2% in both CTH and CHH groups. Biogeographic ancestry inference models based on 35 populations were constructed with three algorithms: random forest, adaptive boosting and extreme gradient boosting, and then 10-fold cross-validation analyses were applied to test these three models with the average accuracies of 86.59%, 84.22% and 87.80%, respectively. In addition, we also investigated the genetic relationships between the two studied groups with 33 reference populations using population statistical methods of FST, DA, phylogenetic tree, PCA, STRUCTURE and TreeMix analyses. The present results showed that compared to other continental populations, the CTH and CHH groups had closer genetic affinities to East Asian populations.

Conclusions
This novel multiplex system has high CDP and CPE in CTH and CHH groups, which can be used as a powerful tool for individual identification and paternity testing. According to various genetic analysis methods, the genetic structures of CTH and CHH groups are relatively similar to the reference East Asian populations.
Genomic evidence for human-mediated introgressive hybridization and selection in the developed breed
Authors: Du Heng , Liu Zhen , Lu Shi-Yu , Jiang Li , Zhou Lei , Liu Jian-Feng 
Published: April 2024

Abstract
Background
The pig (Sus Scrofa) is one of the oldest domesticated livestock species that has undergone extensive improvement through modern breeding. European breeds have advantages in lean meat development and highly-productive body type, whereas Asian breeds possess extraordinary fat deposition and reproductive performance. Consequently, Eurasian breeds have been extensively used to develop modern commercial breeds for fast-growing and high prolificacy. However, limited by the sequencing technology, the genome architecture of some nascent developed breeds and the human-mediated impact on their genomes are still unknown.

Results
Through whole-genome analysis of 178 individuals from an Asian locally developed pig breed, Beijing Black pig, and its two ancestors from two different continents, we found the pervasive inconsistent gene trees and species trees across the genome of Beijing Black pig, which suggests its introgressive hybrid origin. Interestingly, we discovered that this developed breed has more genetic relationships with European pigs and an unexpected introgression from Asian pigs to this breed, which indicated that human-mediated introgression could form the porcine genome architecture in a completely different type compared to native introgression. We identified 554 genomic regions occupied 63.30 Mb with signals of introgression from the Asian ancestry to Beijing Black pig, and the genes in these regions enriched in pathways associated with meat quality, fertility, and disease-resistant. Additionally, a proportion of 7.77% of genomic regions were recognized as regions that have been under selection. Moreover, combined with the results of a genome-wide association study for meat quality traits in the 1537 Beijing Black pig population, two important candidate genes related to meat quality traits were identified. DNAJC6 is related to intramuscular fat content and fat deposition, and RUFY4 is related to meat pH and tenderness.

Conclusions
Our research provides insight for analyzing the origins of nascent developed breeds and genome-wide selection remaining in the developed breeds mediated by humans during modern breeding.
Influence of PhoPQ and PmrAB two component system alternations on colistin resistance from non-mcr colistin resistant clinical E. Coli strains
Authors: Wang Ching-Hsun , Siu L. Kristopher , Chang Feng-Yee , Tsai Yu-Kuo , Huang Li-Yueh , Lin Jung-Chung 
Published: April 2024

Abstract
Background
The current understanding of acquired chromosomal colistin resistance mechanisms in Enterobacterales primarily involves the disruption of the upstream PmrAB and PhoPQ two-component system (TCS) control caused by mutations in the regulatory genes. Interestingly, previous studies have yielded conflicting results regarding the interaction of regulatory genes related to colistin resistance in Escherichia coli, specifically those surrounding PhoPQ and PmrAB TCS.

Results
In our study, we focused on two clinical non-mcr colistin-resistant strains of E. coli, TSAREC02 and TSAREC03, to gain a better understanding of their resistance mechanisms. Upon analysis, we discovered that TSAREC02 had a deletion (Δ27–45) in MgrB, as well as substitutions (G206R, Y222H) in PmrB. On the other hand, TSAREC03 exhibited a long deletion (Δ84–224) in PhoP, along with substitutions (M1I, L14P, P178S, T235N) in PmrB. We employed recombinant DNA techniques to explore the interaction between the PhoPQ and PmrAB two-component systems (TCSs) and examine the impact of the mutated phoPQ and pmrB genes on the minimum inhibitory concentrations (MICs) of colistin. We observed significant changes in the expression of the pmrD gene, which encodes a connector protein regulated by the PhoPQ TCS, in the TSAREC02 wild-type (WT)-mgrB replacement mutant and the TSAREC03 WT-phoP replacement mutant, compared to their respective parental strains. However, the expressions of pmrB/pmrA, which reflect PmrAB TCS activity, and the colistin MICs remained unchanged. In contrast, the colistin MICs and pmrB/pmrA expression levels were significantly reduced in the pmrB deletion mutants from both TSAREC02 and TSAREC03, compared to their parental strains. Moreover, we were able to restore colistin resistance and the expressions of pmrB/pmrA by transforming a plasmid containing the parental mutated pmrB back into the TSAREC02 and TSAREC03 mutants, respectively.

Conclusion
While additional data from clinical E. coli isolates are necessary to validate whether our findings could be broadly applied to the E. coli population, our study illuminates distinct regulatory pathway interactions involving colistin resistance in E. coli compared to other species of Enterobacterales. The added information provided by our study contribute to a deeper understanding of the complex pathway interactions within Enterobacterales.
Leaf functional traits and resource use strategies facilitate the spread of invasive plant Parthenium hysterophorus across an elevational gradient in western Himalayas
Authors: Sharma Padma , Rathee Sonia , Ahmad Mustaqeem , Siddiqui Manzer H. , Alamri Saud , Kaur Shalinder , Kohli Ravinder K. , Singh Harminder Pal , Batish Daizy R. 
Published: April 2024

AbstractParthenium hysterophorus L. (Asteraceae) is a highly prevalent invasive species in subtropical regions across the world. It has recently been seen to shift from low (subtropical) to high (sub-temperate) elevations. Nevertheless, there is a dearth of research investigating the adaptive responses and the significance of leaf functional traits in promoting the expansion to high elevations. The current study investigated the variations and trade-offs among 14 leaf traits (structural, photosynthetic, and nutrient content) of P. hysterophorus across different elevations in the western Himalayas, India. Plots measuring 20 × 40 m were established at different elevations (700 m, 1100 m, 1400 m, and 1800 m) to collect leaf trait data for P. hysterophorus. Along the elevational gradient, significant variations were noticed in leaf morphological parameters, leaf nutrient content, and leaf photosynthetic parameters. Significant increases were observed in the specific leaf area, leaf thickness, and chlorophyll a, total chlorophyll and carotenoid content, as well as leaf nitrogen and phosphorus content with elevation. On the other hand, there were reductions in the amount of chlorophyll b, photosynthetic efficiency, leaf dry matter content, leaf mass per area, and leaf water content. The trait-trait relationships between leaf water content and dry weight and between leaf area and dry weight were stronger at higher elevations. The results show that leaf trait variability and trait-trait correlations are very important for sustaining plant fitness and growth rates in low-temperature, high-irradiance, resource-limited environments at relatively high elevations. To summarise, the findings suggest that P. hysterophorus can expand its range to higher elevations by broadening its functional niche through changes in leaf traits and resource utilisation strategies.
The effects of social support and self-efficacy on hopefulness in low-income older adults during COVID-19 pandemic
Authors: Kwon Soonhyung , Benoit Ellen , Windsor Liliane 
Published: April 2024

Abstract
Background
Social support and self-efficacy play a significant role in improving positive psychological well-being in marginalized older adults. However, to date, there are few studies identifying the relationships during the COVID-19 pandemic. We examined the effect of social support and self-efficacy on hopefulness in a majority Black sample of marginalized low-income older adults during the COVID-19 pandemic.

Methods
This study used baseline data from a clinical trial designed to increase COVID-19 testing in Essex County, NJ, United States. The dataset involved participants 50 years old or older. We conducted: 1) cross-sectional descriptive/frequency statistics to understand the sociodemographic characteristics, 2) multivariate linear regression to investigate the direct relationships between social support subscales or self-efficacy and hopefulness, and 3) mediation analyses to examine the mediating role of self-efficacy in the relationship between social support and hopefulness.

Results
Our findings showed that self-efficacy had a partial mediating effect on the relationship between social support and hopefulness. After adjusting for covariate variables, social support subscales (i.e., emotional/informational, tangible, affectionate, positive social interaction social support) and self-efficacy were significantly associated with hopefulness. The indirect effect of social support via self-efficacy was positive and statistically significant.

Conclusion
Self-efficacy mediated the relationship between social support and hopefulness in marginalized older adults aged 50 and over. Further research is needed to identify the various facets of positive psychological well-being using longitudinal data and a larger sample size.
Trends in immunological markers of transfusion transmissible infections among blood donors in Mamfe District Hospital, Southwest Cameroon
Authors: Ngomtcho Sen Claudine Henriette , Njike Ngo Biyong Olive , Ekwere Timothy Amos , Wandji Takemegni Jonas Merlin , Mbah Henrietta , Makamdoum Bogne Sandra Maella , Nkengkanna Omer Aurelle , Fouamno Kamga Henri Lucien 
Published: April 2024

Abstract
Background
Blood transfusion is associated with exposure to blood Transfusion Transmissible Infection (TTIs). The threat posed by the blood-borne pathogens is disproportionately distributed in different healthcare facilities in Cameroon. Thus, there is a need for continuous surveillance of TTIs in the country. This study aimed to assess the screening procedure for blood transfusion and determine the trend in immunological markers of TTIs among blood donors at the Mamfe District Hospital.

Methods
A prospective descriptive, cross-sectional and analytical study was conducted at Mamfe District Hospital from March to May 2022. A total of 165 blood donors were recruited by the consecutive sampling method. Donors were screened using both Rapid diagnostic tests,T. pallidum haemagglutination test and indirect enzyme-linked immunosorbent assay (ELISA) for the detection of TTIs. Data generated was entered into an Excel spreadsheet and analysed using the statistical software R, version 4.2.0. Statistical analysis included descriptive statistics of percentages, means ± standard deviation, and student t-test was used to compare both diagnostic techniques, and was considered significant when p < 0.05.

Results
A hundred and sixty-five donors were enrolled in the study with a male preponderance giving a male-female sex ratio of 22.5 and a mean age of 32.23 ± 8.60 years. The majority (75.2%) of the donors were of the O-positive blood type, repeat donors (69.1%) and were mainly family replacement and paid donors as against the voluntary blood donors (39.4% and 37.0% vs. 23.6% respectively). overall TTIs prevalence was 18.78% (31/165) (), with HBsAg being the most predominant marker at 12.12% (20/165) followed by Treponema pallidum, HCV and HIV antibodies at 4.85 (8/165), 1.21%(2/165), 0.60% (1/165) respectively. Except for the HBV, The prevalence of TTIs was higher when using a single RDT than the ELISA test, and the difference was significant (p < 0.05).

Conclusion
Bloodborne pathogens remain a major menace to safe blood transfusion practice in Mamfe district hospital and their detection could be easily missed if the RDT method alone is used for donor screening. Therefore, the donor screening protocol in Mamfe District Hospital should systematically incorporate a confirmation diagnostic test such as ELISA.