bluuebunny/crossref_metadata_2025_split huggingface dataset:
A meta-analysis of genetic and phenotypic diversity of European local pig breeds reveals genomic regions associated with breed differentiation for production traits
Authors: Poklukar Klavdija , Mestre Camille , Škrlep Martin , Čandek-Potokar Marjeta , Ovilo Cristina , Fontanesi Luca , Riquet Juliette , Bovo Samuele , Schiavo Giuseppina , Ribani Anisa , Muñoz Maria , Gallo Maurizio , Bozzi Ricardo , Charneca Rui , Quintanilla Raquel , Kušec Goran , Mercat Marie-José , Zimmer Christoph , Razmaite Violeta , Araujo Jose P. , Radović Čedomir , Savić Radomir , Karolyi Danijel , Servin Bertrand 
Published: December 2023

Abstract
Background
Intense selection of modern pig breeds has resulted in genetic improvement of production traits while the performance of local pig breeds has remained lower. As local pig breeds have been bred in extensive systems, they have adapted to specific environmental conditions, resulting in a rich genotypic and phenotypic diversity. This study is based on European local pig breeds that have been genetically characterized using DNA-pool sequencing data and phenotypically characterized using breed level phenotypes related to stature, fatness, growth, and reproductive performance traits. These data were analyzed using a dedicated approach to detect signatures of selection linked to phenotypic traits in order to uncover potential candidate genes that may underlie adaptation to specific environments.

Results
Analysis of the genetic data of European pig breeds revealed four main axes of genetic variation represented by the Iberian and three modern breeds (i.e. Large White, Landrace, and Duroc). In addition, breeds clustered according to their geographical origin, for example French Gascon and Basque breeds, Italian Apulo Calabrese and Casertana breeds, Spanish Iberian, and Portuguese Alentejano breeds. Principal component analysis of the phenotypic data distinguished the larger and leaner breeds with better growth potential and reproductive performance from the smaller and fatter breeds with low growth and reproductive efficiency. Linking the signatures of selection with phenotype identified 16 significant genomic regions associated with stature, 24 with fatness, 2 with growth, and 192 with reproduction. Among them, several regions contained candidate genes with possible biological effects on stature, fatness, growth, and reproductive performance traits. For example, strong associations were found for stature in two regions containing, respectively, the ANXA4 and ANTXR1 genes, for fatness in a region containing the DNMT3A and POMC genes and for reproductive performance in a region containing the HSD17B7 gene.

Conclusions
In this study on European local pig breeds, we used a dedicated approach for detecting signatures of selection that were supported by phenotypic data at the breed level to identify potential candidate genes that may have adapted to different living environments and production systems.
Genetic parameters, reciprocal cross differences, and age-related heterosis of egg-laying performance in chickens
Authors: Ni Aixin , Calus Mario P. L. , Bovenhuis Henk , Yuan Jingwei , Wang Yuanmei , Sun Yanyan , Chen Jilan 
Published: December 2023

AbstractBackgroundEgg-laying performance is economically important in poultry breeding programs. Crossbreeding between indigenous and elite commercial lines to exploit heterosis has been an upward trend in traditional layer breeding for niche markets. The objective of this study was to analyse the genetic background and to estimate the heterosis of longitudinal egg-laying traits in reciprocal crosses between an indigenous Beijing-You and an elite commercial White Leghorn layer line. Egg weights were measured for the first three eggs, monthly from 28 to 76 weeks of age, and at 86 and 100 weeks of age. Egg quality traits were measured at 32, 54, 72, 86, and 100 weeks of age. Egg production traits were measured from the start of lay until 43, 72, and 100 weeks of age. Heritabilities and phenotypic and genetic correlations were estimated. Heterosis was estimated as the percentage difference of performance of a crossbred from that of the parental average. Reciprocal cross differences were estimated as the difference between the reciprocal crossbreds as a percentage of the parental average.ResultsEstimates of heritability of egg weights ranged from 0.29 to 0.75. Estimates of genetic correlations between egg weights at different ages ranged from 0.72 to 1.00. Estimates of heritability for cumulative egg numbers until 43, 72, and 100 weeks of age were around 0.15. Estimates of heterosis for egg weight and cumulative egg number increased with age, ranging from 1.0 to 9.0% and from 1.4 to 11.6%, respectively. From 72 to 100 weeks of age, crossbreds produced more eggs per week than the superior parent White Leghorn (3.5 eggs for White Leghorn, 3.8 and 3.9 eggs for crossbreds). Heterosis for eggshell thickness ranged from 2.7 to 6.6% when using Beijing-You as the sire breed. No significant difference between reciprocal crosses was observed for the investigated traits, except for eggshell strength at 54 weeks of age.ConclusionsThe heterosis was substantial for egg weight and cumulative egg number, and increased with age, suggesting that non-additive genetic effects are important in crossbreds between the indigenous and elite breeds. Generally, the crossbreds performed similar to or even outperformed the commercial White Leghorns for egg production persistency.
Incorporating mutational heterogeneity to identify genes that are enriched for synonymous mutations in cancer
Authors: Rao Yiyun , Ahmed Nabeel , Pritchard Justin , O’Brien Edward P. 
Published: December 2023

Abstract
Background
Synonymous mutations, which change the DNA sequence but not the encoded protein sequence, can affect protein structure and function, mRNA maturation, and mRNA half-lives. The possibility that synonymous mutations might be enriched in cancer has been explored in several recent studies. However, none of these studies control for all three types of mutational heterogeneity (patient, histology, and gene) that are known to affect the accurate identification of non-synonymous cancer-associated genes. Our goal is to adopt the current standard for non-synonymous mutations in an investigation of synonymous mutations.

Results
Here, we create an algorithm, MutSigCVsyn, an adaptation of MutSigCV, to identify cancer-associated genes that are enriched for synonymous mutations based on a non-coding background model that takes into account the mutational heterogeneity across these levels. Using MutSigCVsyn, we first analyzed 2572 cancer whole-genome samples from the Pan-cancer Analysis of Whole Genomes (PCAWG) to identify non-synonymous cancer drivers as a quality control. Indicative of the algorithm accuracy we find that 58.6% of these candidate genes were also found in Cancer Census Gene (CGC) list, and 66.2% were found within the PCAWG cancer driver list. We then applied it to identify 30 putative cancer-associated genes that are enriched for synonymous mutations within the same samples. One of the promising gene candidates is the B cell lymphoma 2 (BCL-2) gene. BCL-2 regulates apoptosis by antagonizing the action of proapoptotic BCL-2 family member proteins. The synonymous mutations in BCL2 are enriched in its anti-apoptotic domain and likely play a role in cancer cell proliferation.

Conclusion
Our study introduces MutSigCVsyn, an algorithm that accounts for mutational heterogeneity at patient, histology, and gene levels, to identify cancer-associated genes that are enriched for synonymous mutations using whole genome sequencing data. We identified 30 putative candidate genes that will benefit from future experimental studies on the role of synonymous mutations in cancer biology.
Efficient design of synthetic gene circuits under cell-to-cell variability
Authors: Turpin Baptiste , Bijman Eline Y. , Kaltenbach Hans-Michael , Stelling Jörg 
Published: December 2023

Abstract
Background
Synthetic biologists use and combine diverse biological parts to build systems such as genetic circuits that perform desirable functions in, for example, biomedical or industrial applications. Computer-aided design methods have been developed to help choose appropriate network structures and biological parts for a given design objective. However, they almost always model the behavior of the network in an average cell, despite pervasive cell-to-cell variability.

Results
Here, we present a computational framework and an efficient algorithm to guide the design of synthetic biological circuits while accounting for cell-to-cell variability explicitly. Our design method integrates a Non-linear Mixed-Effects (NLME) framework into a Markov Chain Monte-Carlo (MCMC) algorithm for design based on ordinary differential equation (ODE) models. The analysis of a recently developed transcriptional controller demonstrates first insights into design guidelines when trying to achieve reliable performance under cell-to-cell variability.

Conclusion
We anticipate that our method not only facilitates the rational design of synthetic networks under cell-to-cell variability, but also enables novel applications by supporting design objectives that specify the desired behavior of cell populations.
Multi-omics analysis of fecal microbiota transplantation’s impact on functional constipation and comorbid depression and anxiety
Authors: Yang Chuanli , Hu Tianjiao , Xue Xin , Su Xiaohu , Zhang Xuan , Fan Yunhe , Shen Xiaobing , Dong Xiushan 
Published: December 2023

Abstract
Background
Depression and anxiety are common comorbid diseases of constipation. Fecal microbiota transplantation (FMT) significantly relieves gastrointestinal-related symptoms, but its impact on psychiatric symptoms remains uncharted.

Methods
We collected fecal and serum samples before and after FMT from 4 functional constipation patients with psychiatric symptoms and corresponding donor stool samples. We categorized the samples into two groups: before FMT (Fb) and after FMT (Fa). Parameters associated with constipation, depression, and anxiety symptoms were evaluated. Metagenomics and targeted neurotransmitter metabolomics were performed to investigate the gut microbiota and metabolites. 5-hydroxytryptamine (5-HT) biosynthesis was detected in patients’ fecal supernatants exposed to the QGP-1 cell model in vitro.

Results
Our study demonstrated that patient’s constipation, depression, and anxiety were improved after FMT intervention. At the genus level, relative abundance of g_Bacteroides and g_Klebsiella decreased in the Fa group, while g_Lactobacillus, and g_Selenomonas content increased in the same group. These observations suggest a potential involvement of these genera in the pathogenesis of constipation with psychiatric symptoms. Metabolomics analysis showed that FMT intervention decreased serum 5-HT levels. Additionally, we found that species, including s_Klebsiella sp. 1_1_55, s_Odoribacter splanchnicus, and s_Ruminococcus gnavus CAG:126, were positively correlated with 5-HT levels. In contrast, s_Acetobacterium bakii, s_Enterococcus hermanniensis, s_Prevotella falsenii, s_Propionispira arboris, s_Schwartzia succinivorans, s_Selenomonas artemidis, and s_Selenomonas sp. FC4001 were negatively correlated with 5-HT levels. Furthermore, we observed that patients’ fecal supernatants increased 5-HT biosynthesis in QGP-1 cells.

Conclusion
FMT can relieve patients’ constipation, depression, and anxiety symptoms by reshaping gut microbiota. The 5-HT level was associated with an altered abundance of specific bacteria or metabolites. This study provides specific evidence for FMT intervention in constipation patients with psychiatric symptoms.
Genome-wide association study on resistance of cultivated soybean to Fusarium oxysporum root rot in Northeast China
Authors: Sang Yongsheng , Liu Xiaodong , Yuan Cuiping , Yao Tong , Li Yuqiu , Wang Dechun , Zhao Hongkun , Wang Yumin 
Published: December 2023

Abstract
Background
Fusarium oxysporum is a prevalent fungal pathogen that diminishes soybean yield through seedling disease and root rot. Preventing Fusarium oxysporum root rot (FORR) damage entails on the identification of resistance genes and developing resistant cultivars. Therefore, conducting fine mapping and marker development for FORR resistance genes is of great significance for fostering the cultivation of resistant varieties. In this study, 350 soybean germplasm accessions, mainly from Northeast China, underwent genotyping using the SoySNP50K Illumina BeadChip, which includes 52,041 single nucleotide polymorphisms (SNPs). Their resistance to FORR was assessed in a greenhouse. Genome-wide association studies utilizing the general linear model, mixed linear model, compressed mixed linear model, and settlement of MLM under progressively exclusive relationship models were conducted to identify marker-trait associations while effectively controlling for population structure.

Results
The results demonstrated that these models effectively managed population structure. Eight SNP loci significantly associated with FORR resistance in soybean were detected, primarily located on Chromosome 6. Notably, there was a strong linkage disequilibrium between the large-effect SNPs ss715595462 and ss715595463, contributing substantially to phenotypic variation. Within the genetic interval encompassing these loci, 28 genes were present, with one gene Glyma.06G088400 encoding a protein kinase family protein containing a leucine-rich repeat domain identified as a potential candidate gene in the reference genome of Williams82. Additionally, quantitative real-time reverse transcription polymerase chain reaction analysis evaluated the gene expression levels between highly resistant and susceptible accessions, focusing on primary root tissues collected at different time points after F. oxysporum inoculation. Among the examined genes, only this gene emerged as the strongest candidate associated with FORR resistance.

Conclusions
The identification of this candidate gene Glyma.06G088400 improves our understanding of soybean resistance to FORR and the markers strongly linked to resistance can be beneficial for molecular marker-assisted selection in breeding resistant soybean accessions against F. oxysporum.
Genome-wide analysis of UDP-glycosyltransferase gene family and identification of a flavonoid 7-O-UGT (AhUGT75A) enhancing abiotic stress in peanut (Arachis hypogaea L.)
Authors: Ouyang Lei , Liu Yue , Yao Ruonan , He Dongli , Yan Liying , Chen Yuning , Huai Dongxin , Wang Zhihui , Yu Bolun , Kang Yanping , Jiang Huifang , Lei Yong , Liao Boshou , Wang Xin 
Published: December 2023

Abstract
Background
Glycosylation, catalyzed by UDP-glycosyltransferase (UGT), was important for enhancing solubility, bioactivity, and diversity of flavonoids. Peanut (Arachis hypogaea L.) is an important oilseed and cash crop worldwide. In addition to provide high quality of edible oils and proteins, peanut seeds contain a rich source of flavonoid glycosides that benefit human health. However, information of UGT gene family was quite limited in peanut.

Results
In present study, a total of 267 AhUGTs clustered into 15 phylogenetic groups were identified in peanut genome. Group I has greatly expanded to contain the largest number of AhUGT genes. Segmental duplication was the major driving force for AhUGT gene family expansion. Transcriptomic analysis of gene expression profiles in various tissues and under different abiotic stress treatments indicated AhUGTs were involved in peanut growth and abiotic stress response. AhUGT75A (UGT73CG33), located in mitochondria, was characterized as a flavonoid 7-O-UGT by in vitro enzyme assays. The transcript level of AhUGT75A was strongly induced by abiotic stress. Overexpression of AhUGT75A resulted in accumulating less amount of malondialdehyde (MDA) and superoxide, and enhancing tolerance against drought and/or salt stress in transgenic Arabidopsis. These results indicated AhUGT75A played important roles in conferring abiotic stress tolerance through reactive oxygen species scavenging.

Conclusions
Our research only not provides valuable information for functional characterization of UGTs in peanut, but also gives new insights into potential applications in breeding new cultivars with both desirable stress tolerance and health benefits.
Higher baseline resting metabolic rate is associated with 1-year frailty decline among older adults residing in an urban area
Authors: Gonzalez A , Soto J , Babiker N , Wroblewski K , Sawicki S , Schoeller D , Luke A , Huisingh-Scheetz Megan 
Published: December 2023

Abstract
Background
Dysregulated energy metabolism is one hypothesized mechanism underlying frailty. Resting energy expenditure, as reflected by resting metabolic rate (RMR), makes up the largest component of total energy expenditure. Prior work relating RMR to frailty has largely been done in cross section with mixed results. We investigated whether and how RMR related to 1-year frailty change while adjusting for body composition.

Methods
N = 116 urban, predominantly African-American older adults were recruited between 2011 and 2019. One-year frailty phenotype (0–5) was regressed on baseline RMR, frailty phenotype, demographics and body composition (DEXA) in an ordinal logistic regression model. Multimorbidity (Charlson comorbidity scale, polypharmacy) and cognitive function (Montreal Cognitive Assessment) were separately added to the model to assess for change to the RMR-frailty relationship. The model was then stratified by baseline frailty status (non-frail, pre-frail) to explore differential RMR effects across frailty.

Results
Higher baseline RMR was associated with worse 1-year frailty (odds ratio = 1.006 for each kcal/day, p = 0.001) independent of baseline frailty, demographics, and body composition. Lower fat-free mass (odds ratio = 0.88 per kg mass, p = 0.008) was independently associated with worse 1-year frailty scores. Neither multimorbidity nor cognitive function altered these relationships. The associations between worse 1-year frailty and higher baseline RMR (odds ratio = 1.009, p < 0.001) and lower baseline fat-free mass (odds ratio = 0.81, p = 0.006) were strongest among those who were pre-frail at baseline.

Discussion
We are among the first to relate RMR to 1-year change in frailty scores. Those with higher baseline RMR and lower fat-free mass had worse 1-year frailty scores, but these relationships were strongest among adults who were pre-frail at baseline. These relationships were not explained by chronic disease or impaired cognition. These results provide new evidence suggesting higher resting energy expenditure is associated with accelerate frailty decline.
Association between prior-night sleep and next-day fatigue in older adults: a daily diary study
Authors: Nakagawa Takeshi , Yasumoto Saori , Kabayama Mai , Matsuda Ken’ichi , Gondo Yasuyuki , Kamide Kei , Ikebe Kazunori 
Published: December 2023

Abstract
Background
Fatigue is known as an element of frailty. Sleep problems (e.g., short sleep duration and low sleep quality) can increase fatigue, but the day-to-day relationship between sleep and fatigue has not been studied well in older adults. Using a daily diary method, this study examined the within- and between-person associations between sleep and fatigue in older adults.

Methods
The study recruited 56 Japanese community dwellers (age: 82–86 years; female: 37.5%). Participants responded to a daily diary questionnaire at the end of each day. Over seven days, time in bed and satisfaction were measured after waking up, whereas fatigue was assessed before going to bed. We included person-level covariates (demographic factors, and physical and mental health) and day-level covariates (time in study, and positive and negative emotions). Multilevel models were estimated to examine within- and between-person associations.

Results
At the within-person level, on days following short and long time in bed and days following low levels of sleep satisfaction, individuals felt higher levels of fatigue compared with usual days. At the between-person level, no statistically significant differences in fatigue were observed between individuals with long and short time in bed.

Conclusions
The findings suggest that prior-day sleep is associated with next-day fatigue in older adults. Long and short sleep duration and low sleep quality can lead to fatigue. Considering that sleep is a modifiable health behavior, appropriate management of sleep behavior may reduce fatigue.
Assessing health-related quality of life among cancer survivors during systemic and radiation therapy in Bangladesh: a cancer-specific exploration
Authors: Shahjalal Md. , Sultana Marufa , Gow Jeff , Hoque Mohammad Enamul , Mistry Sabuj Kanti , Hossain Ahmed , Mahumud Rashidul Alam 
Published: December 2023

Abstract
Background
Evaluating the effects of cancer diagnosis and treatment on a patient’s overall well-being is crucial and health-related quality of life (HRQoL) is a reliable metric for assessing this impact. Little is known about HRQoL among cancer survivors across various stages and treatments. The study examined individual and clinical factors influencing HRQoL among cancer survivors.

Methods
A cross-sectional study was conducted in two specialised cancer care hospitals in Dhaka, Bangladesh. Cancer-diagnosed adults receiving treatment at selected hospitals from January to May 2022 were enrolled. The 5-level EuroQol-5 Dimensions version (EQ-5D-5L) instrument was used to collect HRQoL data. HRQoL scores were derived using UK value sets. The investigation used a multivariable Tobit regression model to determine the association between independent variables and HRQoL scores.

Results
A total of 607 adult patients were enrolled, with 55% being females and 66% aged 36 to 64 years. Reported health problems in five EQ-5D domains include mobility (11%), self-care (11%), usual daily activities (19%), pain/discomfort (21%), and anxiety/depression (46%). Patients with throat, brain, lung, blood, and liver cancer had lower utility scores. Advanced-stage cancer survivors had lower utility scores (β = -49 units, 95% codfidence interval [CI]: -0.75 to -0.22) compared to early-stage survivors. Physically inactive survivors had lower utility scores by 0.41 units (95% CI: -0.51 to -0.30) compared to their counterparts. Private hospital patients had higher utility scores, whereas patients belonged to poor socioeconomic groups scored worse than wealthier ones.

Conclusions
This study highlights the impact of clinical and individual characteristics on HRQoL among cancer survivors. These findings advocate for an enhanced Bangladeshi cancer patient care model through timely interventions or programs, early detection or diagnosis, tailored treatments, and the promotion of physical activity to bolster HRQoL outcomes.