bluuebunny/crossref_metadata_2025_split huggingface dataset:
A method for partitioning trends in genetic mean and variance to understand breeding practices
Authors: Oliveira Thiago P. , Obšteter Jana , Pocrnic Ivan , Heslot Nicolas , Gorjanc Gregor 
Published: June 2023

AbstractBackgroundIn breeding programmes, the observed genetic change is a sum of the contributions of different selection paths represented by groups of individuals. Quantifying these sources of genetic change is essential for identifying the key breeding actions and optimizing breeding programmes. However, it is difficult to disentangle the contribution of individual paths due to the inherent complexity of breeding programmes. Here we extend the previously developed method for partitioning genetic mean by paths of selection to work both with the mean and variance of breeding values.MethodsFirst, we extended the partitioning method to quantify the contribution of different paths to genetic variance assuming that the breeding values are known. Second, we combined the partitioning method with the Markov Chain Monte Carlo approach to draw samples from the posterior distribution of breeding values and use these samples for computing the point and interval estimates of partitions for the genetic mean and variance. We implemented the method in the package . We demonstrated the method with a simulated cattle breeding programme.ResultsWe show how to quantify the contribution of different groups of individuals to genetic mean and variance and that the contributions of different selection paths to genetic variance are not necessarily independent. Finally, we observed that the partitioning method under the pedigree-based model has some limitations, which suggests the need for a genomic extension.ConclusionsWe presented a partitioning method to quantify sources of change in genetic mean and variance in breeding programmes. The method can help breeders and researchers understand the dynamics in genetic mean and variance in a breeding programme. The developed method for partitioning genetic mean and variance is a powerful method for understanding how different selection paths interact within a breeding programme and how they can be optimised.
Genetic analysis of protein efficiency and its association with performance and meat quality traits under a protein-restricted diet
Authors: Ewaoluwagbemiga Esther Oluwada , Bee Giuseppe , Kasper Claudia 
Published: June 2023

Abstract
Background
An essential component in the development of sustainable pig production is the reduction of nitrogen excretion in fattening pigs. Pig feeds typically contain high levels of dietary crude protein, and due to incomplete conversion to muscle tissue, excess nitrogen is excreted, resulting in environmental problems such as nitrate pollution and greenhouse gas emissions. Therefore, improving protein efficiency (PE), i.e., the proportion of dietary protein that remains in the carcass, is desirable. The aim of this study was to estimate the heritability (h2) of PE and its genetic correlations with phosphorus efficiency, three performance, seven meat quality and two carcass quality traits when pigs were fed a 20% protein-restricted diet, using 1071 Swiss Large White pigs. To determine PE, the intake of feed with known nutrient content was accurately recorded for each pig and the nitrogen and phosphorus content of the carcass was determined using dual-energy X-ray absorptiometry.

Results
We found an average PE of 0.39 ± 0.04 and a heritability of 0.54 ± 0.10. PE showed a high genetic correlation with phosphorus efficiency (0.61 ± 0.16), moderate genetic correlations with feed conversion ratio (− 0.55 ± 0.14) and average daily feed intake (− 0.53 ± 0.14), and a low genetic correlation with average daily gain (− 0.19 ± 0.19). While PE has favourable genetic correlations with the performance traits and some meat quality traits, there is a potentially unfavourable correlation of PE with meat colour (redness [rg = − 0.27 ± 0.17]; yellowness [rg = − 0.31 ± 0.18]) and intra-muscular fat (IMF; rg = − 0.39 ± 0.15). Feed conversion ratio (FCR) also showed unfavourable genetic correlations with meat lightness, redness yellowness, IMF and cooking loss.

Conclusions
PE is a heritable trait that can be considered in breeding programs to reduce the environmental impact of pig production. We found no strong negative correlation of PE with meat quality traits, and that there is potential to indirectly select for improved phosphorus efficiency. Selecting nutrient efficiencies might be a more suitable strategy to reduce nitrogen pollution from manure than focusing on FCR because the latter also shows genetic antagonism with some meat quality traits in our population.
A homozygous missense mutation in the fibroblast growth factor 5 gene is associated with the long-hair trait in Angora rabbits
Authors: Fatima Nazira , Jia Linying , Liu Baoning , Li Lu , Bai Liang , Wang Weirong , Zhao Sihai , Wang Rong , Liu Enqi 
Published: June 2023

Abstract
Background
Rabbits are well-domesticated animals. As a crucial economic animal, rabbit has been successfully bred into wool-use, meat-use and fur-use breeds. Hair length is one of the most economically important traits affecting profitability in wool rabbits. In this study, to identify selection signatures with the long-hair trait, whole-genomic resequencing of long-haired rabbits (Angora rabbits) and short-haired rabbits (Rex and New Zealand rabbits) was performed.

Results
By genome-wide selective sweeping analysis based on population comparison, we identified a total of 5.85 Mb regions (containing 174 candidate genes) with strong selection signals. Six of these genes (Dusp1, Ihh, Fam134a, Map3k1, Spata16, and Fgf5) were enriched in the MAPK signalling and Hedgehog signalling pathways, both of which are closely associated with hair growth regulation. Among these genes, Fgf5 encodes the FGF5 protein, which is a well-established regulator of hair growth. There was a nonsynonymous nucleotide substitution (T19234C) in the Fgf5 gene. At this locus, the C allele was present in all of the tested Angora rabbits, while the T allele was dominant in New Zealand and Rex rabbits. We further confirmed that the C allele was conserved in Angora rabbits by screening an additional 135 rabbits. Moreover, the results of functional predictions and co-immunoprecipitation revealed that the T19234C mutation impaired the binding capacity of FGF5 to its receptor FGFR1.

Conclusions
We discovered that the homozygous missense mutation T19234C within Fgf5 might contribute to the long-hair trait of Angora rabbits by reducing its receptor binding capacity. This finding will provide new insights into the genetic basis underlying the genetic improvement of Angora rabbits and benefit the improvement of rabbit breeding in the future.
Bioinformatics and experimental analyses of glutamate receptor and its targets genes in myocardial and cerebral ischemia
Authors: Liao Wei , He Chunming , Yang Shaochun , Zhou Man , Zeng Chuan , Luo Muyun , Yu Junjian , Hu Shuo , Duan Yanyu , Liu Ziyou 
Published: June 2023

Abstract
Background
There is a mutual hemodynamic and pathophysiological basis between the heart and brain. Glutamate (GLU) signaling plays an important role in the process of myocardial ischemia (MI) and ischemic stroke (IS). To further explore the common protective mechanism after cardiac and cerebral ischemic injuries, the relationship between GLU receptor-related genes and MI and IS were analyzed.

Results
A total of 25 crosstalk genes were identified, which were mainly enriched in the Toll-like receptor signaling pathway, Th17 cell differentiation, and other signaling pathways. Protein-protein interaction analysis suggested that the top six genes with the most interactions with shared genes were IL6, TLR4, IL1B, SRC, TLR2, and CCL2. Immune infiltration analysis suggested that immune cells such as myeloid-derived suppressor cells and monocytes were highly expressed in the MI and IS data. Memory B cells and Th17 cells were expressed at low levels in the MI and IS data; molecular interaction network construction suggested that genes such as JUN, FOS, and PPARA were shared genes and transcription factors; FCGR2A was a shared gene of MI and IS as well as an immune gene. Least absolute shrinkage and selection operator logistic regression analysis identified nine hub genes: IL1B, FOS, JUN, FCGR2A, IL6, AKT1, DRD4, GLUD2, and SRC. Receiver operating characteristic analysis revealed that the area under the curve of these hub genes was > 65% in MI and IS for all seven genes except IL6 and DRD4. Furthermore, clinical blood samples and cellular models showed that the expression of relevant hub genes was consistent with the bioinformatics analysis.

Conclusions
In this study, we found that the GLU receptor-related genes IL1B, FOS, JUN, FCGR2A, and SRC were expressed in MI and IS with the same trend, which can be used to predict the occurrence of cardiac and cerebral ischemic diseases and provide reliable biomarkers to further explore the co-protective mechanism after cardiac and cerebral ischemic injury.
Identification of C2H2 zinc finger genes through genome-wide association study and functional analyses of LkZFPs in response to stresses in Larix kaempferi
Authors: Shao Liying , Li Lu , Huang Xun , Fu Yanrui , Yang Da , Li Chenghao , Yang Jingli 
Published: June 2023

Abstract
Background
C2H2 zinc finger proteins (C2H2-ZFPs), one of the largest transcription factors, play a variety of roles in plant development and growth as well as stress response. While, the evolutionary history and expression profile of the C2H2-ZFP genes in Larix kaempferi (LkZFPs) have not been reported so far.

Results
In this study, the whole genome of the LkZFPs was identified and characterized, including physicochemical properties, phylogenetic relationships, conservative motifs, the promoter cis-elements and Gene Ontology (GO) annotation. We identified 47 LkZFPs and divided them into four subfamilies based on phylogenetic analysis and conserved motifs. Subcellular localization prediction showed that most of the LkZFPs were located in the nucleus. Promoter cis-element analysis suggested that the LkZFPs may be involved in the regulation of stress responses. Moreover, Real-time quantitative PCR (RT-qPCR) results showed that Q-type LkZFP genes were involved in the response to abiotic stress, such as salt, drought and hormone stresses. Subcellular localization results showed that LkZFP7 and LkZFP37 were located in the nucleus, LkZFP32 was located in both cytoplasm and nucleus.

Conclusion
The identification and functional analysis of LkZFPs suggested that some LkZFP genes might play important roles in coping with both biological and abiotic stresses. These results could further increase understanding of the function of the LkZFPs, and provide some research direction and theoretical support.
The Arabidopsis thaliana onset of leaf death 12 mutation in the lectin receptor kinase P2K2 results in an autoimmune phenotype
Authors: Zhao Liming , Wang Hao-Jie , Martins Patricia Dalcin , van Dongen Joost T. , Bolger Anthony M. , Schmidt Romy R. , Jing Hai-Chun , Mueller-Roeber Bernd , Schippers Jos H. M. 
Published: June 2023

AbstractBackgroundPlant immunity relies on the perception of immunogenic signals by cell-surface and intracellular receptors and subsequent activation of defense responses like programmed cell death. Under certain circumstances, the fine-tuned innate immune system of plants results in the activation of autoimmune responses that cause constitutive defense responses and spontaneous cell death in the absence of pathogens.ResultsHere, we characterized theonset of leaf death 12(old12) mutant that was identified in the Arabidopsis accession Landsbergerecta. Theold12mutant is characterized by a growth defect, spontaneous cell death, plant-defense gene activation, and early senescence. In addition, theold12phenotype is temperature reversible, thereby exhibiting all characteristics of an autoimmune mutant. Mapping the mutated locus revealed that theold12phenotype is caused by a mutation in theLectin Receptor Kinase P2-TYPE PURINERGIC RECEPTOR 2(P2K2) gene. Interestingly, the P2K2 allele from Landsbergerectais conserved amongBrassicaceae. P2K2 has been implicated in pathogen tolerance and sensing extracellular ATP. The constitutive activation of defense responses inold12results in improved resistance againstPseudomonas syringae pv. tomato DC3000.ConclusionWe demonstrate thatold12is an auto-immune mutant and that allelic variation ofP2K2contributes to diversity in Arabidopsis immune responses.
Weighted gene coexpression correlation network analysis reveals the potential molecular regulatory mechanism of citrate and anthocyanin accumulation between postharvest ‘Bingtangcheng’ and ‘Tarocco’ blood orange fruit
Authors: Jin Yan , Liao Manyu , Li Na , Ma Xiaoqian , Zhang Huimin , Han Jian , Li Dazhi , Yang Junfeng , Lu Xiaopeng , Long Guiyou , Deng Ziniu , Sheng Ling 
Published: June 2023

Abstract
Background
Organic acids and anthocyanins are the most important compounds for the flavor and nutritional quality of citrus fruit. However, there are few reports on the involvement of co-regulation of citrate and anthocyanin metabolism. Here, we performed a comparative transcriptome analysis to elucidate the genes and pathways involved in both citrate and anthocyanin accumulation in postharvest citrus fruit with ‘Tarocco’ blood orange (TBO; high accumulation) and ‘Bingtangcheng’ sweet orange (BTSO; low accumulation).

Results
A robust core set of 825 DEGs were found to be temporally associated with citrate and anthocyanin accumulation throughout the storage period through transcriptome analysis. Further according to the results of weighted gene coexpression correlation network analysis (WGCNA), the turquoise and brown module was highly positively correlated with both of the content of citrate and anthocyanin, and p-type ATPase (PH8), phosphoenolpyruvate carboxylase kinase (PEPCK), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavonoid 3’-hydroxylase (F3’H) and glutathione S transferase (GST) were considered key structural genes. Moreover, MYB family transcription factor (PH4), Zinc finger PHD-type transcription factor (CHR4, HAC12), Zinc finger SWIM-type transcription factor (FAR1) and Zinc finger C3H1-type transcription factor (ATC3H64) were considered hub genes related to these structural genes. Further qRT-PCR analysis verified that these transcription factors were highly expressed in TBO fruit and their expression profiles were significantly positively correlated with the structural genes of citrate and anthocyanin metabolism as well as the content of citrate and anthocyanin content.

Conclusions
The findings suggest that the CHR4, FAR1, ATC3H64 and HAC12 may be the new transcription regulators participate in controlling the level of citrate and anthocyanin in postharvest TBO fruit in addition to PH4. These results may providing new insight into the regulation mechanism of citrate and anthocyanin accumulation in citrus fruit.
Iva xanthiifolia leaf extract reduced the diversity of indigenous plant rhizosphere bacteria
Authors: Wu Jia-wen , Li Feng-lan , Yao Shu-kuan , Zhao Zi-yi , Feng Xu , Chen Rong-ze , Xu Yong-qing 
Published: June 2023

Abstract
Background
Iva xanthiifolia, native to North America, is now widely distributed in northeastern China and has become a vicious invasive plant. This article aims to probe the role of leaf extract in the invasion of I. xanthiifolia.

Methods
We collected the rhizosphere soil of Amaranthus tricolor and Setaria viridis in the invasive zone, the noninvasive zone and the noninvasive zone treated with extract from I. xanthiifolia leaf, and obtained I. xanthiifolia rhizosphere soil in the invasive zone. All wild plants were identified by Xu Yongqing. I. xanthiifolia (collection number: RQSB04100), A. tricolor (collection number: 831,030) and S. viridis (collection number: CF-0002-034) are all included in Chinese Virtual Herbarium (https://www.cvh.ac.cn/index.php). The soil bacterial diversity was analyzed based on the Illumina HiSeq sequencing platform. Subsequently, taxonomic analysis and Faprotax functional prediction were performed.

Results
The results showed that the leaf extract significantly reduced the diversity of indigenous plant rhizosphere bacteria. A. tricolor and S. viridis rhizobacterial phylum and genus abundances were significantly reduced under the influence of I. xanthiifolia or its leaf extract. The results of functional prediction showed that bacterial abundance changes induced by leaf extracts could potentially hinder nutrient cycling in native plants and increased bacterial abundance in the A. tricolor rhizosphere related to aromatic compound degradation. In addition, the greatest number of sensitive Operational Taxonomic Units (OTUs) appeared in the rhizosphere when S. viridis was in response to the invasion of I. xanthiifolia. It can be seen that A. tricolor and S. viridis have different mechanisms in response to the invasion of I. xanthiifolia.

Conclusion
I. xanthiifolia leaves material has potential role in invasion by altering indigenous plant rhizosphere bacteria.
Radiomics for therapy-specific head and neck squamous cell carcinoma survival prognostication (part I)
Authors: Bernatz Simon , Böth Ines , Ackermann Jörg , Burck Iris , Mahmoudi Scherwin , Lenga Lukas , Martin Simon S. , Scholtz Jan-Erik , Koch Vitali , Grünewald Leon D. , Koch Ina , Stöver Timo , Wild Peter J. , Winkelmann Ria , Vogl Thomas J. , dos Santos Daniel Pinto 
Published: June 2023

Abstract
Background
Treatment plans for squamous cell carcinoma of the head and neck (SCCHN) are individually decided in tumor board meetings but some treatment decision-steps lack objective prognostic estimates. Our purpose was to explore the potential of radiomics for SCCHN therapy-specific survival prognostication and to increase the models’ interpretability by ranking the features based on their predictive importance.

Methods
We included 157 SCCHN patients (male, 119; female, 38; mean age, 64.39 ± 10.71 years) with baseline head and neck CT between 09/2014 and 08/2020 in this retrospective study. Patients were stratified according to their treatment. Using independent training and test datasets with cross-validation and 100 iterations, we identified, ranked and inter-correlated prognostic signatures using elastic net (EN) and random survival forest (RSF). We benchmarked the models against clinical parameters. Inter-reader variation was analyzed using intraclass-correlation coefficients (ICC).

Results
EN and RSF achieved top prognostication performances of AUC = 0.795 (95% CI 0.767–0.822) and AUC = 0.811 (95% CI 0.782–0.839). RSF prognostication slightly outperformed the EN for the complete (ΔAUC 0.035, p = 0.002) and radiochemotherapy (ΔAUC 0.092, p < 0.001) cohort. RSF was superior to most clinical benchmarking (p ≤ 0.006). The inter-reader correlation was moderate or high for all features classes (ICC ≥ 0.77 (± 0.19)). Shape features had the highest prognostic importance, followed by texture features.

Conclusions
EN and RSF built on radiomics features may be used for survival prognostication. The prognostically leading features may vary between treatment subgroups. This warrants further validation to potentially aid clinical treatment decision making in the future.
Predicting insulin use among women with gestational diabetes diagnosed in oral glucose tolerance test
Authors: Zaccara Tatiana A , Mikami Fernanda C F , Paganoti Cristiane F , Francisco Rossana P V , Costa Rafaela A 
Published: June 2023

Abstract
Background
Gestational diabetes mellitus (GDM) is one of the most common complications affecting pregnant women. While most women will achieve adequate glycemic levels with diet and exercise, some will require pharmacological treatment to reach and maintain glucose levels between the desired thresholds. Identifying these patients early in pregnancy could help direct resources and interventions.

Methods
This retrospective cohort of women with GDM diagnosed with an abnormal 75g-OGTT presents data from 869 patients (724 in the diet group and 145 in the insulin group). Univariate logistic regression was used to compare the groups, and multivariable logistic regression was used to identify independent factors associated with the need for insulin. A log-linear function was used to estimate the probability of requiring pharmacological treatment.

Results
Women in the insulin group had higher pre-pregnancy BMI index (29.8 vs 27.8 kg/m2, odds ratio [OR] 1.06, 95% confidence interval [CI] 1.03–1.09), more frequent history of previous GDM (19.4% vs. 7.8%, OR 2.84, 95% CI 1.59–5.05), were more likely to have chronic hypertension (31.7% vs. 23.2%, OR 1.54, 95% CI 1.04–2.27), and had higher glucose levels at all three OGTT points. Multivariable logistic regression final model included age, BMI, previous GDM status, and the three OGTT values as predictors of insulin requirement.

Conclusions
We can use regularly collected data from patients (age, BMI, previous GDM status, and the three OGTT values) to calculate the risk of a woman with GDM diagnosed in OGTT needing insulin. Identifying patients with a greater risk of requiring pharmacological treatment could help healthcare services to better allocate resources and offer closer follow-up to high-risk patients.
Intracardiac thrombosis after congenital heart disease surgeries in neonates: a report of two cases
Authors: Yang Yanlin , Lv Jing , Li Yajiao , Gan Changping , Ji Peng 
Published: June 2023

AbstractBackgroundIntracardiac thrombosis (ICT) is a rare complication after the cardiopulmonary surgery for interrupted aortic arch (IAA) or total anomalous pulmonary venous connection (TAPVC) without previous records. There are still no general guidelines regarding as the mechanism or management of postoperative ICT in neonates and younger infants.Case presentationWe reported the conservative and surgical therapies in two neonates with intra-ventricular and intra-atrial thrombosis after the anatomical repair for IAA and TAPVC, respectively. There were no risk factors for ICT in both patients, except for the use of blood product and prothrombin complex concentrate. The surgery was indicated after TAPVC correction due to the worsening respiratory status and rapidly decreased mixed venous saturation. Anticoagulation combined with antiplatelet therapies was adopted in another patient. These two were both finally recovered, and three-month, six-month, and one-year follow-up echocardiography revealed no abnormality.ConclusionsICT is uncommon in pediatric population after the surgery for congenital heart disease. Single ventricle palliation, heart transplantation, longer central line use, post-extracorporeal membrane oxygenation, and massive blood product use are major risk factors for postcardiotomy thrombosis. The causes of postoperative ICT are multifactorial, and the immaturity of thrombolytic and fibrinolytic system in neonates may serve as a prothrombotic factor. However, no consensus reached regarding as the therapies for postoperative ICT, and the large-scale prospective cohort study or randomized clinical trial is needed.