bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide association analysis explores the genetic loci of amino acid content in duck’s breast muscle
Authors: Wang Rui , Lu Yinjuan , Qi Jingjing , Xi Yang , Shen Zhenyang , Twumasi Grace , Bai Lili , Hu Jiwei , Wang Jiwen , Li Liang , Liu Hehe 
Published: May 2024

Abstract
Background
Amino acids are the basic components of protein and an important index to evaluate meat quality. With the rapid development of genomics, candidate regions and genes affecting amino acid content in livestock and poultry have been gradually revealed. Hence, genome-wide association study (GWAS) can be used to screen candidate loci associated with amino acid content in duck meat.

Result
In the current study, the content of 16 amino acids was detected in 358 duck breast muscles. The proportion of Glu to the total amino acid content was relatively high, and the proportion was 0.14. However, the proportion of Met content was relatively low, at just 0.03. By comparative analysis, significant differences were found between males and females in 3 amino acids, including Ser, Met, and Phe. In addition, 12 SNPs were significantly correlated with Pro content by GWAS analysis, and these SNPs were annotated by 7 protein-coding genes; 8 significant SNPs were associated with Tyr content, and these SNPs were annotated by 6 protein-coding genes. At the same time, linkage disequilibrium (LD) analysis was performed on these regions with significant signals. The results showed that three SNPs in the 55–56 Mbp region of chromosome 3 were highly correlated with the leader SNP (chr3:55526954) that affected Pro content (r2 > 0.6). Similarly, LD analysis showed that there were three SNPs in the 21.2–21.6 Mbp region of chromosome 13, which were highly correlated with leader SNP (chr13:21421661) (r2 > 0.6). Moreover, Through functional enrichment analysis of all candidate genes. The results of GO enrichment analysis showed that several significant GO items were associated with amino acid transport function, including amino acid transmembrane transport and glutamine transport. The results further indicate that these candidate genes are closely associated with amino acid transport. Among them, key candidate genes include SLC38A1. For KEGG enrichment analysis, CACNA2D3 and CACNA1D genes were covered by significant pathways.

Conclusion
In this study, GWAS analysis found a total of 28 significant SNPs affecting amino acid content. Through gene annotation, a total of 20 candidate genes were screened. In addition, Through LD analysis and enrichment analysis, we considered that SERAC1, CACNA2D3 and SLC38A1 genes are important candidate genes affecting amino acid content in duck breast muscle.
Genome-wide detections for runs of homozygosity and selective signatures reveal novel candidate genes under domestication in chickens
Authors: Tan Xiaodong , Liu Lu , Dong Jie , Huang Minjie , Zhang Jiawen , Li Qinghai , Wang Huanhuan , Bai Lijuan , Cui Ming , Zhou Zhenzhen , Wu De , Xiang Yun , Li Weifen , Wang Deqian 
Published: May 2024

Abstract
Background
Indigenous chickens were developed through a combination of natural and artificial selection; essentially, changes in genomes led to the formation of these modern breeds via admixture events. However, their confusing genetic backgrounds include a genomic footprint regulating complex traits, which is not conducive to modern animal breeding.

Results
To better evaluate the candidate regions under domestication in indigenous chickens, we considered both runs of homozygosity (ROHs) and selective signatures in 13 indigenous chickens. The genomes of Silkie feather chickens presented the highest heterozygosity, whereas the highest inbreeding status and ROH number were found in Luhua chickens. Short ROH (< 1 Mb), were the principal type in all chickens. A total of 291 ROH islands were detected, and QTLdb mapping results indicated that body weight and carcass traits were the most important traits. An ROH on chromosome 2 covering VSTM2A gene was detected in 12 populations. Combined analysis with the Tajima’s D index revealed that 18 genes (e.g., VSTM2A, BBOX1, and RYR2) were under selection and covered by ROH islands. Transcriptional analysis results showed that RYR2 and BBOX1 were specifically expressed in the heart and muscle tissue, respectively.

Conclusion
Based on genome-wide scanning for ROH and selective signatures, we evaluated the genomic characteristics and detected significant candidate genes covered by ROH islands and selective signatures. The findings in this study facilitated the understanding of genetic diversity and provided valuable insights for chicken breeding and conservation strategies.
Enhancer selectivity across cell types delineates three functionally distinct enhancer-promoter regulation patterns
Authors: Wu Chengyi , Huang Jialiang 
Published: May 2024

Abstract
Background
Multiple enhancers co-regulating the same gene is prevalent and plays a crucial role during development and disease. However, how multiple enhancers coordinate the same gene expression across various cell types remains largely unexplored at genome scale.

Results
We develop a computational approach that enables the quantitative assessment of enhancer specificity and selectivity across diverse cell types, leveraging enhancer-promoter (E-P) interactions data. We observe two well-known gene regulation patterns controlled by enhancer clusters, which regulate the same gene either in a limited number of cell types (Specific pattern, Spe) or in the majority of cell types (Conserved pattern, Con), both of which are enriched for super-enhancers (SEs). We identify a previously overlooked pattern (Variable pattern, Var) that multiple enhancers link to the same gene, but rarely coexist in the same cell type. These three patterns control the genes associating with distinct biological function and exhibit unique epigenetic features. Specifically, we discover a subset of Var patterns contains Shared enhancers with stable enhancer-promoter interactions in the majority of cell types, which might contribute to maintaining gene expression by recruiting abundant CTCF.

Conclusions
Together, our findings reveal three distinct E-P regulation patterns across different cell types, providing insights into deciphering the complexity of gene transcriptional regulation.
A novel family of defensin-like peptides from Hermetia illucens with antibacterial properties
Authors: Fahmy Leila , Generalovic Tomas , Ali Youssif M. , Seilly David , Sivanesan Kesavan , Kalmar Lajos , Pipan Miha , Christie Graham , Grant Andrew J 
Published: May 2024

Abstract
Background
The world faces a major infectious disease challenge. Interest in the discovery, design, or development of antimicrobial peptides (AMPs) as an alternative approach for the treatment of bacterial infections has increased. Insects are a good source of AMPs which are the main effector molecules of their innate immune system. Black Soldier Fly Larvae (BSFL) are being developed for large-scale rearing for food sustainability, waste reduction and as sustainable animal and fish feed. Bioinformatic studies have suggested that BSFL have the largest number of AMPs identified in insects. However, most AMPs identified in BSF have not yet undergone antimicrobial evaluation but are promising leads to treat critical infections.

Results
Jg7197.t1, Jg7902.t1 and Jg7904.t1 were expressed into the haemolymph of larvae following infection with Salmonella enterica serovar Typhimurium and were predicted to be AMPs using the computational tool ampir. The genes encoding these proteins were within 2 distinct clusters in chromosome 1 of the BSF genome. Following removal of signal peptides, predicted structures of the mature proteins were superimposed, highlighting a high degree of structural conservation. The 3 AMPs share primary sequences with proteins that contain a Kunitz-binding domain; characterised for inhibitory action against proteases, and antimicrobial activities. An in vitro antimicrobial screen indicated that heterologously expressed SUMO-Jg7197.t1 and SUMO-Jg7902.t1 did not show activity against 12 bacterial strains. While recombinant SUMO-Jg7904.t1 had antimicrobial activity against a range of Gram-negative and Gram-positive bacteria, including the serious pathogen Pseudomonas aeruginosa.

Conclusions
We have cloned and purified putative AMPs from BSFL and performed initial in vitro experiments to evaluate their antimicrobial activity. In doing so, we have identified a putative novel defensin-like AMP, Jg7904.t1, encoded in a paralogous gene cluster, with antimicrobial activity against P. aeruginosa.
Epicardial fat volume is associated with primary coronary slow-flow phenomenon in patients with severe aortic stenosis undergoing transcatheter valve implantation
Authors: Weferling Maren , Rolf Andreas , Treiber Julia , Fischer-Rasokat Ulrich , Liebetrau Christoph , Hamm Christian W. , Dey Damini , Kim Won-Keun 
Published: May 2024

AbstractBackgroundPrimary coronary slow flow (CSF) is defined as delayed opacification of the distal epicardial vasculature during coronary angiography in the absence of relevant coronary artery stenoses. Microvascular disease is thought to be the underlying cause of this pathology. Epicardial fat tissue (EFT) is an active endocrine organ directly surrounding the coronary arteries that provides pro-inflammatory factors to the adjacent tissue by paracrine and vasocrine mechanisms. The aim of the present study was to investigate a potential association between EFT and primary CSF and whether EFT can predict the presence of primary CSF.MethodsBetween 2016 and 2017,n = 88 patients with high-grade aortic stenosis who were planned for transcatheter aortic valve implantation (TAVI) were included in this retrospective study. EFT volume was measured by pre-TAVI computed tomography (CT) using dedicated software. The presence of primary CSF was defined based on the TIMI frame count from the pre-TAVI coronary angiograms.ResultsThirty-nine of 88 TAVI patients had CSF (44.3%). EFT volume was markedly higher in patients with CSF (142 ml [IQR 107–180] vs. 113 ml [IQR 89–147];p = 0.009) and was strongly associated with the presence of CSF (OR 1.012 [95%CI 1.002–1.021];p = 0.014). After adjustment, EFT volume was still an independent predictor of CSF (OR 1.016 [95%CI 1.004–1.026];p = 0.009).ConclusionPrimary CSF was independently associated with increased EFT volume. Further studies are needed to validate this finding and elucidate whether a causal relationship exists.
The long-term effects of blood urea nitrogen levels on cardiovascular disease and all-cause mortality in diabetes: a prospective cohort study
Authors: Liu Hongfang , Xin Xiaoqin , Gan Jinghui , Huang Jungao 
Published: May 2024

Abstract
Background
The long-term effects of blood urea nitrogen(BUN) in patients with diabetes remain unknown. Current studies reporting the target BUN level in patients with diabetes are also limited. Hence, this prospective study aimed to explore the relationship of BUN with all-cause and cardiovascular mortalities in patients with diabetes.

Methods
In total, 10,507 participants with diabetes from the National Health and Nutrition Examination Survey (1999–2018) were enrolled. The causes and numbers of deaths were determined based on the National Death Index mortality data from the date of NHANES interview until follow-up (December 31, 2019). Multivariate Cox proportional hazard regression models were used to calculate the hazard ratios (HRs) and 95% confidence interval (CIs) of mortality.

Results
Of the adult participants with diabetes, 4963 (47.2%) were female. The median (interquartile range) BUN level of participants was 5 (3.93–6.43) mmol/L. After 86,601 person-years of follow-up, 2,441 deaths were documented. After adjusting for variables, the HRs of cardiovascular disease (CVD) and all-cause mortality in the highest BUN level group were 1.52 and 1.35, respectively, compared with those in the lowest BUN level group. With a one-unit increment in BUN levels, the HRs of all-cause and CVD mortality rates were 1.07 and 1.08, respectively. The results remained robust when several sensitivity and stratified analyses were performed. Moreover, BUN showed a nonlinear association with all-cause and CVD mortality. Their curves all showed that the inflection points were close to the BUN level of 5 mmol/L.

Conclusion
BUN had a nonlinear association with all-cause and CVD mortality in patients with diabetes. The inflection point was at 5 mmol/L.
Association between migraine and pre-eclampsia among pregnant women: a single hospital-based case–control study in India
Authors: Biswas Shyamashree , Singh Ranjana , Radhika A. G. 
Published: May 2024

AbstractBackgroundPre-eclampsia and migraine share some similar aspects of pathophysiology such as vascular function, platelet activation, and enhanced clotting. A few observational studies from different demographics showed that pregnant women with a history of migraine were at higher risk of developing pre-eclampsia. However, there is no such evidence available from the Indian context. Hence, a hospital-based case–control study was conducted among Indian women to determine the association between migraine and pre-eclampsia.MethodIt was a single-centre case-control study in a tertiary care hospital in India. Cases were pregnant women with clinically diagnosed pre-eclampsia, and controls were normotensive pregnant women. Migraine was diagnosed with a questionnaire adapted from the “International Classification of Headache Disorders (ICHD), 3rd Edition” by the International Headache Society, (IHS). We performed logistic regression to explore the association between migraine and pre-eclampsia.ResultOne hundred sixty-four women (82 women per group) were enrolled. The mean age among the cases (24.5 years, standard deviation of 2.4 years) was slightly higher than the mean age of the controls (23.5 years, standard deviation of 2.5 years) with ap-value of 0.006. We found that women with a history of migraine were more likely to develop pre-eclampsia (Adjusted Odds Ratio 6.17;p-value < 0.001, 95% Confidence Interval of 2.85 to 13.62).ConclusionThe current findings suggest a significant association between migraine and pre-eclampsia aligning with previous study findings; nevertheless, larger follow-up studies including women from different states in India are needed.
Liver cancer in China: the analysis of mortality and burden of disease trends from 2008 to 2021
Authors: Qin Yajun , Tang Changlin , Li Jinhao , Gong Jianping 
Published: May 2024

Abstract
Background
Liver cancer is one of the most common cancers in China. To understand the basic death situation and disease burden change trend, we analyze the death information of liver cancer among Chinese residents from 2008 to 2021.

Methods
Data was collected from the Cause-of-Death Surveillance dataset of the National Cause-of-Death Surveillance System from 2008 to 2021. Excel 2016 was used for data entry and to calculate the Crude Mortality Rate (CMR), Age-Standardized Mortality Rate (ASMR), Potential Years of Life Lost (PYLL), and Potential Years of Life Lost Rate (PYLLR). SPSS 25.0 was used to statistically analyze CMR, ASMR, PYLL, and other indicators. Annual percent change (APC) and average APC(AAPC) was used for trend analysis and tested by t tests. Joinpoint 4.9.1.0 was used to calculate APC and AAPC. Age-Period-Cohort model was used to assess the effects of age, period, and birth cohort on liver cancer mortality.

Results
From 2008 to 2021, 491,701 liver cancer deaths were reported in the National Disease Surveillance Points System. The ASMR of liver cancer in Chinese residents decreased from 27.58/100,000 in 2008 to 17.95/100,000 in 2021 at an average annual rate of 3.40% (t = -5.10, P < 0.001). The mortality rate was higher in males than in females (all P < 0.001) and higher in rural areas than in urban areas (all P < 0.001). The mortality rate of liver cancer varied significantly among eastern, central, and western China (all P < 0.001). The PYLLR of liver cancer in Chinese residents decreased from 2.89‰ in 2008 to 2.06‰ in 2021 at an average annual rate of 2.40% (t = -5.10, P < 0.001). Males had a lower PYLLR than females, decreasing at average annual rates of 2.20% (t = -5.40, P < 0.001) and 2.90% (t = -8.40, P < 0.001), respectively. Urban areas had a lower PYLLR than rural areas, decreasing at average annual rate of 3.30% (t = -4.00, P < 0.001) and 2.50% (t = -11.60, P < 0.001), respectively. Eastern, central, and western China decreased at average annual rates of 3.40%, 2.30%, and 2.10%, respectively (t = -7.80, -3.60, -7.10, P < 0.001 for all). The risk of China liver cancer mortality increased with age, decreased with birth cohort.

Conclusions
The mortality and disease burdens of liver cancer in China decreased yearly and were higher in males and in people living in rural areas, with significant differences among those living in eastern, central, and western China.
Prediction of esophageal cancer risk based on genetic variants and environmental risk factors in Chinese population
Authors: Liu Haiyan , Li Keming , Xia Junfen , Zhu Jicun , Cheng Yifan , Zhang Xiaoyue , Ye Hua , Wang Peng 
Published: May 2024

Abstract
Background
Results regarding whether it is essential to incorporate genetic variants into risk prediction models for esophageal cancer (EC) are inconsistent due to the different genetic backgrounds of the populations studied. We aimed to identify single-nucleotide polymorphisms (SNPs) associated with EC among the Chinese population and to evaluate the performance of genetic and non-genetic factors in a risk model for developing EC.

Methods
A meta-analysis was performed to systematically identify potential SNPs, which were further verified by a case-control study. Three risk models were developed: a genetic model with weighted genetic risk score (wGRS) based on promising SNPs, a non-genetic model with environmental risk factors, and a combined model including both genetic and non-genetic factors. The discrimination ability of the models was compared using the area under the receiver operating characteristic curve (AUC) and the net reclassification index (NRI). The Akaike information criterion (AIC) and Bayesian information criterion (BIC) were used to assess the goodness-of-fit of the models.

Results
Five promising SNPs were ultimately utilized to calculate the wGRS. Individuals in the highest quartile of the wGRS had a 4.93-fold (95% confidence interval [CI]: 2.59 to 9.38) increased risk of EC compared with those in the lowest quartile. The genetic or non-genetic model identified EC patients with AUCs ranging from 0.618 to 0.650. The combined model had an AUC of 0.707 (95% CI: 0.669 to 0.743) and was the best-fitting model (AIC = 750.55, BIC = 759.34). The NRI improved when the wGRS was added to the risk model with non-genetic factors only (NRI = 0.082, P = 0.037).

Conclusions
Among the three risk models for EC, the combined model showed optimal predictive performance and can help to identify individuals at risk of EC for tailored preventive measures.
Identification of shared gene signatures in major depressive disorder and triple-negative breast cancer
Authors: Xie Hua , Ding Chenxiang , Li Qianwen , Sheng Wei , Xu Jie , Feng Renjian , Cheng Huaidong 
Published: May 2024

Abstract
Background
Patients with major depressive disorder (MDD) have an increased risk of breast cancer (BC), implying that these two diseases share similar pathological mechanisms. This study aimed to identify the key pathogenic genes that lead to the occurrence of both triple-negative breast cancer (TNBC) and MDD.

Methods
Public datasets GSE65194 and GSE98793 were analyzed to identify differentially expressed genes (DEGs) shared by both datasets. A protein-protein interaction (PPI) network was constructed using STRING and Cytoscape to identify key PPI genes using cytoHubba. Hub DEGs were obtained from the intersection of hub genes from a PPI network with genes in the disease associated modules of the Weighed Gene Co-expression Network Analysis (WGCNA). Independent datasets (TCGA and GSE76826) and RT-qPCR validated hub gene expression.

Results
A total of 113 overlapping DEGs were identified between TNBC and MDD. The PPI network was constructed, and 35 hub DEGs were identified. Through WGCNA, the blue, brown, and turquoise modules were recognized as highly correlated with TNBC, while the brown, turquoise, and yellow modules were similarly correlated with MDD. Notably, G3BP1, MAF, NCEH1, and TMEM45A emerged as hub DEGs as they appeared both in modules and PPI hub DEGs. Within the GSE65194 and GSE98793 datasets, G3BP1 and MAF exhibited a significant downregulation in TNBC and MDD groups compared to the control, whereas NCEH1 and TMEM45A demonstrated a significant upregulation. These findings were further substantiated by TCGA and GSE76826, as well as through RT-qPCR validation.

Conclusions
This study identified G3BP1, MAF, NCEH1 and TMEM45A as key pathological genes in both TNBC and MDD.
Temporal change in prevalence of BMI categories in India: patterns across States and Union territories of India, 1999–2021
Authors: Sung Meekang , Kumar Akhil , Mishra Raman , Kulkarni Bharati , Kim Rockli , Subramanian S. V. 
Published: May 2024

Abstract
Background
The problem of overweight/obesity often coexists with the burden of undernutrition in most low- and middle-income countries. BMI change in India incorporating the most recent trends has been under-researched.

Methods
This repeated cross-sectional study of 1,477,885 adults in India analyzed the prevalence of different categories of BMI among adults (age 20–54) in 4 rounds of National Family Health Surveys (1998–1999, 2005–2006, 2015–2016, and 2019–2021) for 36 states/UTs. State differences across time were harmonized for accurate analysis. The categories were Severely/Moderately Thin (BMI < 17.0), Mildly Thin (17.0-18.4), Normal (18.5–24.9), Overweight (25.0-29.9), and Obese (≥ 30.0). We also estimated change in Standardized Absolute Change (SAC), ranking of states, and headcount burden to quantify the trend of BMI distribution across time periods for all-India, urban/rural residence, and by states/UTs.

Results
The prevalence of thinness declined from 31.7% in 1999 to 14.2% in 2021 for women, and from 23.4% in 2006 to 10.0% in 2021 for men. Obesity prevalence increased from 2.9% (1999) to 6.3% (2021) for women, and from 2.0% (2006) to 4.2% (2021) for men. In 2021, the states with the highest obesity prevalence were Puducherry, Chandigarh, and Delhi. These states also had a high prevalence of overweight. Dadra and Nagar Haveli and Diu, Gujarat, Jharkhand, and Bihar had the highest prevalence of severe/moderately thin. Prevalence of extreme categories (severely/moderately thin and obese) was larger in the case of women than men. While States/UTs with a higher prevalence of thin populations tend to have a larger absolute burden of severe or moderate thinness, the relationship between headcount burden and prevalence for overweight and obese is unclear.

Conclusions
We found persistent interstate inequalities of undernutrition. Tailored efforts at state levels are required to further strengthen existing policies and develop new interventions to target both forms of malnutrition.