bluuebunny/crossref_metadata_2025_split huggingface dataset:
X chromosome variants are associated with male fertility traits in two bovine populations
Authors: Fortes Marina R. S. , Porto-Neto Laercio R. , Satake Nana , Nguyen Loan T. , Freitas Ana Claudia , Melo Thaise P. , Scalez Daiane Cristina Becker , Hayes Ben , Raidan Fernanda S. S. , Reverter Antonio , Boe-Hansen Gry B. 
Published: August 2020

Abstract
Background
Twenty-five phenotypes were measured as indicators of bull fertility (1099 Brahman and 1719 Tropical Composite bulls). Measurements included sperm morphology, scrotal circumference, and sperm chromatin phenotypes such as DNA fragmentation and protamine deficiency. We estimated the heritability of these phenotypes and carried out genome-wide association studies (GWAS) within breed, using the bovine high-density chip, to detect quantitative trait loci (QTL).

Results
Our analyses suggested that both sperm DNA fragmentation and sperm protamine deficiency are heritable (h2 from 0.10 to 0.22). To confirm these first estimates of heritability, further studies on sperm chromatin traits, with larger datasets are necessary. Our GWAS identified 12 QTL for bull fertility traits, based on at least five polymorphisms (P < 10−8) for each QTL. Five QTL were identified in Brahman and another seven in Tropical Composite bulls. Most of the significant polymorphisms detected in both breeds and nine of the 12 QTL were on chromosome X. The QTL were breed-specific, but for some traits, a closer inspection of the GWAS results revealed suggestive single nucleotide polymorphism (SNP) associations (P < 10−7) in both breeds. For example, the QTL for inhibin level in Braham could be relevant to Tropical Composites too (many polymorphisms reached P < 10−7 in the same region). The QTL for sperm midpiece morphological abnormalities on chromosome X (QTL peak at 4.92 Mb, P < 10−17) is an example of a breed-specific QTL, supported by 143 significant SNPs (P < 10−8) in Brahman, but absent in Tropical Composites. Our GWAS results add evidence to the mammalian specialization of the X chromosome, which during evolution has accumulated genes linked to spermatogenesis. Some of the polymorphisms on chromosome X were associated to more than one genetically correlated trait (correlations ranged from 0.33 to 0.51). Correlations and shared polymorphism associations support the hypothesis that these phenotypes share the same underlying cause, i.e. defective spermatogenesis.

Conclusions
Genetic improvement for bull fertility is possible through genomic selection, which is likely more accurate if the QTL on chromosome X are considered in the predictions. Polymorphisms associated with male fertility accumulate on this chromosome in cattle, as in humans and mice, suggesting its specialization.
Bias and accuracy of dairy sheep evaluations using BLUP and SSGBLUP with metafounders and unknown parent groups
Authors: Macedo Fernando L. , Christensen Ole F. , Astruc Jean-Michel , Aguilar Ignacio , Masuda Yutaka , Legarra Andrés 
Published: August 2020

Abstract
Background
Bias has been reported in genetic or genomic evaluations of several species. Common biases are systematic differences between averages of estimated and true breeding values, and their over- or under-dispersion. In addition, comparing accuracies of pedigree versus genomic predictions is a difficult task. This work proposes to analyse biases and accuracies in the genetic evaluation of milk yield in Manech Tête Rousse dairy sheep, over several years, by testing five models and using the estimators of the linear regression method. We tested models with and without genomic information [best linear unbiased prediction (BLUP) and single-step genomic BLUP (SSGBLUP)] and using three strategies to handle missing pedigree [unknown parent groups (UPG), UPG with QP transformation in the $${\mathbf{H}}$$
H
matrix (EUPG) and metafounders (MF)].

Methods
We compared estimated breeding values (EBV) of selected rams at birth with the EBV of the same rams obtained each year from the first daughters with phenotypes up to 2017. We compared within and across models. Finally, we compared EBV at birth of the rams with and without genomic information.

Results
Within models, bias and over-dispersion were small (bias: 0.20 to 0.40 genetic standard deviations; slope of the dispersion: 0.95 to 0.99) except for model SSGBLUP-EUPG that presented an important over-dispersion (0.87). The estimates of accuracies confirm that the addition of genomic information increases the accuracy of EBV in young rams. The smallest bias was observed with BLUP-MF and SSGBLUP-MF. When we estimated dispersion by comparing a model with no markers to models with markers, SSGBLUP-MF showed a value close to 1, indicating that there was no problem in dispersion, whereas SSGBLUP-EUPG and SSGBLUP-UPG showed a significant under-dispersion. Another important observation was the heterogeneous behaviour of the estimates over time, which suggests that a single check could be insufficient to make a good analysis of genetic/genomic evaluations.

Conclusions
The addition of genomic information increases the accuracy of EBV of young rams in Manech Tête Rousse. In this population that has missing pedigrees, the use of UPG and EUPG in SSGBLUP produced bias, whereas MF yielded unbiased estimates, and we recommend its use. We also recommend assessing biases and accuracies using multiple truncation points, since these statistics are subject to random variation across years.
Phenotypic and molecular marker analysis uncovers the genetic diversity of the grass Stenotaphrum secundatum
Authors: Luo Ying , Zhang Xiujie , Xu Jiahong , Zheng Yao , Pu Shouqin , Duan Zhizhen , Li Zhihao , Liu Guodao , Chen Jinhui , Wang Zhiyong 
Published: August 2020

Abstract
Background
Stenotaphrum secundatum is an important grass with a rich variety of accessions and great potential for development as an economically valuable crop. However, little is known about the genetic diversity of S. secundatum, limiting its application and development as a crop. Here, to provide a theoretical basis for further conservation, utilization, and classification of S. secundatum germplasm resources, we used phenotypic and molecular markers (single-nucleotide polymorphisms, SNPs; sequence-related amplified polymorphism, SRAP; inter-simple sequence repeat, ISSR) to analyze the genetic diversity of 49 S. secundatum accessions.

Results
Based on seven types of phenotypic data, the 49 S. secundatum accessions could be divided into three classes with great variation. We identified 1,280,873 SNPs in the 49 accessions, among which 66.22% were transition SNPs and 33.78% were transversion SNPs. Among these, C/T was the most common (19.12%) and G/C the least common (3.68%). Using 28 SRAP primers, 267 polymorphic bands were detected from the 273 bands amplified. In addition, 27 ISSR markers generated 527 amplification bands, all of which were polymorphic. Both marker types revealed a high level of genetic diversity, with ISSR markers showing a higher percentage of polymorphic loci (100%) than SRAP markers (97.8%). The genetic diversity of the accessions based on SRAP markers (h = 0.47, I = 0.66) and ISSR markers (h = 0.45, I = 0.64) supports the notion that the S. secundatum accessions are highly diverse. S. secundatum could be divided into three classes based on the evaluated molecular markers.

Conclusions
Phenotypic and molecular marker analysis using SNP, SRAP, and ISSR markers revealed great genetic variation among S. secundatum accessions, which were consistently divided into three classes. Our findings provide a theoretical basis for the genetic diversity and classification of S. secundatum. Our results indicate that SNP, SRAP and ISSR markers are reliable and effective for analyzing genetic diversity in S. secundatum. The SNPs identified in this study could be used to distinguish S. secundatum accessions.
Population analysis of the Korean native duck using whole-genome sequencing data
Authors: Lee Daehwan , Lee Jongin , Heo Kang-Neung , Kwon Kisang , Moon Youngbeen , Lim Dajeong , Lee Kyung-Tai , Kim Jaebum 
Published: August 2020

AbstractBackgroundAdvances in next-generation sequencing technologies have provided an opportunity to perform population-level comparative genomic analysis to discover unique genomic characteristics of domesticated animals. Duck is one of the most popular domesticated waterfowls, which is economically important as a source of meat, eggs, and feathers. The objective of this study is to perform population and functional analyses of Korean native duck, which has a distinct meat flavor and texture phenotype, using whole-genome sequencing data. To study the distinct genomic features of Korean native duck, we conducted population-level genomic analysis of 20 Korean native ducks together with 15 other duck breeds.ResultsA total of 15.56 million single nucleotide polymorphisms were detected in Korean native duck. Based on the unique existence of non-synonymous single nucleotide polymorphisms in Korean native duck, a total of 103 genes related to the unique genomic characteristics of Korean native duck were identified in comparison with 15 other duck breeds, and their functions were investigated. The nucleotide diversity and population structures among the used duck breeds were then compared, and their phylogenetic relationship was analyzed. Finally, highly differentiated genomic regions among Korean native duck and other duck breeds were identified, and functions of genes in those regions were examined.ConclusionsThis is the first study to compare the population of Korean native duck with those of other duck breeds by using whole-genome sequencing data. Our findings can be used to expand our knowledge of genomic characteristics of Korean native duck, and broaden our understanding of duck breeds.
S-layer associated proteins contribute to the adhesive and immunomodulatory properties of Lactobacillus acidophilus NCFM
Authors: Klotz Courtney , Goh Yong Jun , O’Flaherty Sarah , Barrangou Rodolphe 
Published: August 2020

AbstractBackgroundSurface layers (S-layers) are two-dimensional crystalline arrays of repeating proteinaceous subunits that form the outermost layer of many bacterial cell envelopes. Within theLactobacillusgenus, S-layer presence is frequently associated with probiotic-relevant properties such as improved adherence to host epithelial cells and modulation of the immune response. However, recent studies have demonstrated that certain S-layer functions may be supplemented by a novel subset of proteins embedded within its lattice, termed S-layer associated proteins (SLAPs). In the following study, fourLactobacillus acidophilusNCFM SLAPs (LBA0046, LBA0864, LBA1426, and LBA1539) were selected for in silico and phenotypic assessment.ResultsDespite lacking any sequence similarity or catalytic domains that may indicate function, the genes encoding the four proteins of interest were shown to be unique to S-layer-forming, host-adapted lactobacilli species. Likewise, their corresponding deletion mutants exhibited broad, host-relevant phenotypes including decreased inflammatory profiles and reduced adherence to Caco-2 intestinal cells, extracellular matrices, and mucin in vitro.ConclusionsOverall, the data presented in this study collectively links several previously uncharacterized extracellular proteins to roles in the underlying host adaptive mechanisms ofL. acidophilus.
Differences between predicted outer membrane proteins of genotype 1 and 2 Mannheimia haemolytica
Authors: Clawson Michael L. , Schuller Gennie , Dickey Aaron M. , Bono James L. , Murray Robert W. , Sweeney Michael T. , Apley Michael D. , DeDonder Keith D. , Capik Sarah F. , Larson Robert L. , Lubbers Brian V. , White Brad J. , Blom Jochen , Chitko-McKown Carol G. , Brichta-Harhay Dayna M. , Smith Timothy P. L. 
Published: August 2020

Abstract
Background
Mannheimia haemolytica strains isolated from North American cattle have been classified into two genotypes (1 and 2). Although members of both genotypes have been isolated from the upper and lower respiratory tracts of cattle with or without bovine respiratory disease (BRD), genotype 2 strains are much more frequently isolated from diseased lungs than genotype 1 strains. The mechanisms behind the increased association of genotype 2 M. haemolytica with BRD are not fully understood. To address that, and to search for interventions against genotype 2 M. haemolytica, complete, closed chromosome assemblies for 35 genotype 1 and 34 genotype 2 strains were generated and compared. Searches were conducted for the pan genome, core genes shared between the genotypes, and for genes specific to either genotype. Additionally, genes encoding outer membrane proteins (OMPs) specific to genotype 2 M. haemolytica were identified, and the diversity of their protein isoforms was characterized with predominantly unassembled, short-read genomic sequences for up to 1075 additional strains.

Results
The pan genome of the 69 sequenced M. haemolytica strains consisted of 3111 genes, of which 1880 comprised a shared core between the genotypes. A core of 112 and 179 genes or gene variants were specific to genotype 1 and 2, respectively. Seven genes encoding predicted OMPs; a peptidase S6, a ligand-gated channel, an autotransporter outer membrane beta-barrel domain-containing protein (AOMB-BD-CP), a porin, and three different trimeric autotransporter adhesins were specific to genotype 2 as their genotype 1 homologs were either pseudogenes, or not detected. The AOMB-BD-CP gene, however, appeared to be truncated across all examined genotype 2 strains and to likely encode dysfunctional protein. Homologous gene sequences from additional M. haemolytica strains confirmed the specificity of the remaining six genotype 2 OMP genes and revealed they encoded low isoform diversity at the population level.

Conclusion
Genotype 2 M. haemolytica possess genes encoding conserved OMPs not found intact in more commensally prone genotype 1 strains. Some of the genotype 2 specific genes identified in this study are likely to have important biological roles in the pathogenicity of genotype 2 M. haemolytica, which is the primary bacterial cause of BRD.
Development and evaluation of an up-converting phosphor technology-based lateral flow assay for rapid and quantitative detection of Coxiella burnetii phase I strains
Authors: Zhang Pingping , Jiao Jun , Zhao Yong , Fu Mengjiao , Wang Jin , Song Yajun , Zhou Dongsheng , Wang Yongqiang , Wen Bohai , Yang Ruifu , Xiong Xiaolu 
Published: August 2020

AbstractBackgroundCoxiella burnetiiis an obligate intracellular Gram-negative bacterium that causes a zoonotic disease commonly called Q fever globally. In this study, an up-converting phosphor technology-based lateral flow (UPT-LF) assay was established for the rapid and specific detection of phase I strains ofC. burnetii.ResultsSpecific monoclonal antibodies (10B5 and 10G7) againstC. burnetiiphase I strains were prepared and selected for use in the UPT-LF assay by the double-antibody-sandwich method. The detection sensitivity of theCoxiella-UPT-LF was 5 × 104GE/ml for a purifiedC. burnetiiphase I strain and 10 ng/ml for LPS ofC. burnetiiNine Mile phase I (NMI). Good linearity was observed forC. burnetiiphase I and NMI LPS quantification (R2 ≥ 0.989). The UPT-LF assay also exhibited a high specificity toC. burnetii, without false-positive results even at 108GE/ml of non-specific bacteria, and good inclusivity for detecting different phase I strains ofC. burnetii. Moreover, the performance of theCoxiella-UPT-LF assay was further confirmed using experimentally and naturally infected samples.ConclusionsOur results indicate thatCoxiella-UPT-LF is a sensitive and reliable method for rapid screening ofC. burnetii,suitable for on-site detection in the field.
Evaluation of approaches for multiple imputation of three-level data
Authors: Wijesuriya Rushani , Moreno-Betancur Margarita , Carlin John B. , Lee Katherine J. 
Published: August 2020

AbstractBackgroundThree-level data arising from repeated measures on individuals who are clustered within larger units are common in health research studies. Missing data are prominent in such longitudinal studies and multiple imputation (MI) is a popular approach for handling missing data. Extensions of joint modelling and fully conditional specification MI approaches based on multilevel models have been developed for imputing three-level data. Alternatively, it is possible to extend single- and two-level MI methods to impute three-level data using dummy indicators and/or by analysing repeated measures in wide format. However, most implementations, evaluations and applications of these approaches focus on the context of incomplete two-level data. It is currently unclear which approach is preferable for imputing three-level data.MethodsIn this study, we investigated the performance of various MI methods for imputing three-level incomplete data when the target analysis model is a three-level random effects model with a random intercept for each level. The MI methods were evaluated via simulations and illustrated using empirical data, based on a case study from the Childhood to Adolescence Transition Study, a longitudinal cohort collecting repeated measures on students who were clustered within schools. In our simulations we considered a number of different scenarios covering a range of different missing data mechanisms, missing data proportions and strengths of level-2 and level-3 intra-cluster correlations.ResultsWe found that all of the approaches considered produced valid inferences about both the regression coefficient corresponding to the exposure of interest and the variance components under the various scenarios within the simulation study. In the case study, all approaches led to similar results.ConclusionResearchers may use extensions to the single- and two-level approaches, or the three-level approaches, to adequately handle incomplete three-level data. The two-level MI approaches with dummy indicator extension or the MI approaches based on three-level models will be required in certain circumstances such as when there are longitudinal data measured at irregular time intervals. However, the single- and two-level approaches with the DI extension should be used with caution as the DI approach has been shown to produce biased parameter estimates in certain scenarios.
Prevention of infection in asplenic adult patients by general practitioners in France between 2013 and 2016
Authors: Quéffélec Charlotte , Billet Louis , Duffau Pierre , Lazaro Estibaliz , Machelart Irène , Greib Carine , Viallard Jean-François , Pellegrin Jean-Luc , Rivière Etienne 
Published: August 2020

Abstract
Background
Guidelines that detail preventive measures against Streptococcus pneumoniae, Neisseria meningitidis, Haemophilus influenzae type b, and influenza are published annually in France to decrease the risk of severe infections in immunocompromised patients. We aimed at describing adherence to these guidelines by GPs in the management of their asplenic patients in France between 2013 and 2016.

Method
We conducted a multicenter retrospective study between January 2013 and December 2016 in three French hospitals: asplenic adults were identified and their GPs were questioned. A descriptive analysis was performed to identify the immunization coverage, type and length of antibiotic prophylaxis, number of infectious episodes, and education of patients.

Results
103 patients were finally included in this study: only 57% were adequately vaccinated against Streptococcus pneumoniae or Neisseria meningitidis, 74% against Haemophilus influenzae type b, and 59% against influenza. Only 24% of patients received a combination of all four vaccinations. Two-thirds of patients received prophylactic antibiotics for at least 2 years. Overall, this study found that 50% of splenectomized patients experienced at least one pulmonary or otorhinolaryngological infection, or contracted influenza.

Conclusions
These data match those reported in other countries, including Australia and the United Kingdom, meaning a still insufficient coverage of preventive measures in asplenic patients. Improved medical data sharing strategies between healthcare professionals, along with educational measures to keep patients and physicians up to date in the prevention of infections after splenectomy would improve health outcomes of asplenic patients.
Validation of a new prognostic model to predict short and medium-term survival in patients with liver cirrhosis
Authors: Dziodzio Tomasz , Öllinger Robert , Schöning Wenzel , Rothkäppel Antonia , Nikolov Radoslav , Juraszek Andrzej , Ritschl Paul V. , Stockmann Martin , Pratschke Johann , Jara Maximilian 
Published: August 2020

Abstract
Background
MELD score and MELD score derivates are used to objectify and grade the risk of liver-related death in patients with liver cirrhosis. We recently proposed a new predictive model that combines serum creatinine levels and maximum liver function capacity (LiMAx®), namely the CreLiMAx risk score. In this validation study we have aimed to reproduce its diagnostic accuracy in patients with end-stage liver disease.

Methods
Liver function of 113 patients with liver cirrhosis was prospectively investigated. Primary end-point of the study was liver-related death within 12 months of follow-up.

Results
Alcoholic liver disease was the main cause of liver disease (n = 51; 45%). Within 12 months of follow-up 11 patients (9.7%) underwent liver transplantation and 17 (15.1%) died (13 deaths were related to liver disease, two not). Measures of diagnostic accuracy were comparable for MELD, MELD-Na and the CreLiMAx risk score as to power in predicting short and medium-term mortality risk in the overall cohort: AUROCS for liver related risk of death were for MELD [6 months 0.89 (95% CI 0.80–0.98) p < 0.001; 12 months 0.89 (95% CI 0.81–0.96) p < 0.001]; MELD-Na [6 months 0.93 (95% CI 0.85–1.00) p < 0.001 and 12 months 0.89 (95% CI 0.80–0.98) p < 0.001]; CPS 6 months 0.91 (95% CI 0.85–0.97) p < 0.01 and 12 months 0.88 (95% CI 0.80–0.96) p < 0.001] and CreLiMAx score [6 months 0.80 (95% CI 0.67–0.96) p < 0.01 and 12 months 0.79 (95% CI 0.64–0.94) p = 0.001]. In a subgroup analysis of patients with Child-Pugh Class B cirrhosis, the CreLiMAx risk score remained the only parameter significantly differing in non-survivors and survivors. Furthermore, in these patients the proposed score had a good predictive performance.

Conclusion
The CreLiMAx risk score appears to be a competitive and valid tool for estimating not only short- but also medium-term survival of patients with end-stage liver disease. Particularly in patients with Child-Pugh Class B cirrhosis the new score showed a good ability to identify patients not at risk of death.