bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic prediction based on selected variants from imputed whole-genome sequence data in Australian sheep populations
Authors: Moghaddar Nasir , Khansefid Majid , van der Werf Julius H. J. , Bolormaa Sunduimijid , Duijvesteijn Naomi , Clark Samuel A. , Swan Andrew A. , Daetwyler Hans D. , MacLeod Iona M. 
Published: December 2019

AbstractBackgroundWhole-genome sequence (WGS) data could contain information on genetic variants at or in high linkage disequilibrium with causative mutations that underlie the genetic variation of polygenic traits. Thus far, genomic prediction accuracy has shown limited increase when using such information in dairy cattle studies, in which one or few breeds with limited diversity predominate. The objective of our study was to evaluate the accuracy of genomic prediction in a multi-breed Australian sheep population of relatively less related target individuals, when using information on imputed WGS genotypes.MethodsBetween 9626 and 26,657 animals with phenotypes were available for nine economically important sheep production traits and all had WGS imputed genotypes. About 30% of the data were used to discover predictive single nucleotide polymorphism (SNPs) based on a genome-wide association study (GWAS) and the remaining data were used for training and validation of genomic prediction. Prediction accuracy using selected variants from imputed sequence data was compared to that using a standard array of 50k SNP genotypes, thereby comparing genomic best linear prediction (GBLUP) and Bayesian methods (BayesR/BayesRC). Accuracy of genomic prediction was evaluated in two independent populations that were each lowly related to the training set, one being purebred Merino and the other crossbred Border Leicester x Merino sheep.ResultsA substantial improvement in prediction accuracy was observed when selected sequence variants were fitted alongside 50k genotypes as a separate variance component in GBLUP (2GBLUP) or in Bayesian analysis as a separate category of SNPs (BayesRC). From an average accuracy of 0.27 in both validation sets for the 50k array, the average absolute increase in accuracy across traits with 2GBLUP was 0.083 and 0.073 for purebred and crossbred animals, respectively, whereas with BayesRC it was 0.102 and 0.087. The average gain in accuracy was smaller when selected sequence variants were treated in the same category as 50k SNPs. Very little improvement over 50k prediction was observed when using all WGS variants.ConclusionsAccuracy of genomic prediction in diverse sheep populations increased substantially by using variants selected from whole-genome sequence data based on an independent multi-breed GWAS, when compared to genomic prediction using standard 50K genotypes.
Identification and characterization of differentially expressed exosomal microRNAs in bovine milk infected with Staphylococcus aureus
Authors: Ma Shaoyang , Tong Chao , Ibeagha-Awemu Eveline M. , Zhao Xin 
Published: December 2019

AbstractBackgroundMicroRNAs (miRNAs) in milk-derived exosomes may reflect pathophysiological changes caused by mastitis. This study profiled miRNAs in exosomes from both normal milk and mastitic milk infected byStaphylococcus aureus(S. aureus). The potential targets for differentially expressed (DE) miRNAs were predicted and the target genes for bta-miR-378 and bta-miR-185 were also validated.ResultsTotal RNA from milk exosomes was collected from healthy cows (n = 3, the control group) andS. aureusinfected cows (n = 6, the SA group). Two hundred ninety miRNAs (221 known and 69 novel ones) were identified. Among them, 22 known and 15 novel miRNAs were differentially expressed. Target genes of DE miRNAs were significantly enriched in intracellular protein transport, endoplasmic reticulum and identical protein binding. The expression of two miRNAs (bta-miR-378 and bta-miR-185) with high read counts and log2fold changes (> 3.5) was significantly higher in mastitic milk infected withS. aureus.One target gene (VAT1L) of bta-miR-378 and five target genes (DYRK1B,MLLT3,HP1BP3,NPR2andPGM1) of bta-miR-185 were validated.ConclusionDE miRNAs in exosomes from normal andS. aureusinfected milk were identified. The predicted targets for two DE miRNAs (bta-miR-378 and bta-miR-185) were further validated. The linkage between the validated target genes and diseases suggested that we should pay particular attention to exosome miRNAs from mastitic milk in terms of milk safety.
Transcriptional profiling of skeletal muscle reveals starvation response and compensatory growth in Spinibarbus hollandi
Authors: Yang Yang , Zhou Huiqiang , Hou Liping , Xing Ke , Shu Hu 
Published: December 2019

Abstract
Background
Spinibarbus hollandi is an economically important fish species in southern China. This fish is known to have nutritional and medicinal properties; however, its farming is limited by its slow growth rate. In the present study, we observed that a compensatory growth phenomenon could be induced by adequate refeeding following 7 days of fasting in S. hollandi. To understand the starvation response and compensatory growth mechanisms in this fish, the muscle transcriptomes of S. hollandi under control, fasting, and refeeding conditions were profiled using next-generation sequencing (NGS) techniques.

Results
More than 4.45 × 108 quality-filtered 150-base-pair Illumina reads were obtained from all nine muscle samples. De novo assemblies yielded a total of 156,735 unigenes, among which 142,918 (91.18%) could be annotated in at least one available database. After 7 days of fasting, 2422 differentially expressed genes were detected, including 1510 up-regulated genes and 912 down-regulated genes. Genes involved in fat, protein, and carbohydrate metabolism were significantly up-regulated, and genes associated with the cell cycle, DNA replication, and immune and cellular structures were inhibited during fasting. After refeeding, 84 up-regulated genes and 16 down-regulated genes were identified. Many genes encoding the components of myofibers were significantly up-regulated. Histological analysis of muscle verified the important role of muscle hypertrophy in compensatory growth.

Conclusion
In the present work, we reported the transcriptome profiles of S. hollandi muscle under different conditions. During fasting, the genes involved in the mobilization of stored energy were up-regulated, while the genes associated with growth were down-regulated. After refeeding, muscle hypertrophy contributed to the recovery of growth. The results of this study may help to elucidate the mechanisms underlying the starvation response and compensatory growth.
Characterization of genome-wide genetic variations between two varieties of tea plant (Camellia sinensis) and development of InDel markers for genetic research
Authors: Liu Shengrui , An Yanlin , Tong Wei , Qin Xiuju , Samarina Lidia , Guo Rui , Xia Xiaobo , Wei Chaoling 
Published: December 2019

AbstractBackgroundSingle nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the major genetic variations and are distributed extensively across the whole plant genome. However, few studies of these variations have been conducted in the long-lived perennial tea plant.ResultsIn this study, we investigated the genome-wide genetic variations betweenCamellia sinensis var. sinensis‘Shuchazao’ andCamellia sinensis var. assamica‘Yunkang 10’, identified 7,511,731 SNPs and 255,218 InDels based on their whole genome sequences, and we subsequently analyzed their distinct types and distribution patterns. A total of 48 InDel markers that yielded polymorphic and unambiguous fragments were developed when screening six tea cultivars. These markers were further deployed on 46 tea cultivars for transferability and genetic diversity analysis, exhibiting information with an average 4.02 of the number of alleles (Na) and 0.457 of polymorphism information content (PIC). The dendrogram showed that the phylogenetic relationships among these tea cultivars are highly consistent with their genetic backgrounds or original places. Interestingly, we observed that the catechin/caffeine contents between ‘Shuchazao’ and ‘Yunkang 10’ were significantly different, and a large number of SNPs/InDels were identified within catechin/caffeine biosynthesis-related genes.ConclusionThe identified genome-wide genetic variations and newly-developed InDel markers will provide a valuable resource for tea plant genetic and genomic studies, especially the SNPs/InDels within catechin/caffeine biosynthesis-related genes, which may serve as pivotal candidates for elucidating the molecular mechanism governing catechin/caffeine biosynthesis.
Needs assessment of emergency medical and rescue services in Abuja/Nigeria and environs
Authors: Mac Peter Asaga , Kroeger Axel , Airiohuodion Philomena Ehi 
Published: December 2019

Abstract
Background
Nigeria is ranked second highest in the rate of road accidents and other emergencies (Deaths, disabilities) among 193 countries of the world. There is therefore the need for analyzing Emergency Medical Rescue Services (EMRS) in the country to identify options for improvement.

Method
The study was conducted from February, 2016 to March, 2017 in three EMRS organizations (FRSC, NEMA and MAITAMA Hospital) located in Abuja. The structure, resources, process of EMRS activities and outcome (delay times, case fatality as well as victims and service-providers satisfaction with services) were assessed through observation, time measurements and interviews.

Results
FRSC and NEMA offers (Road Traffic Injury) RTI and Disaster services, the ambulances consist of Intensive Care Unit(ICU) buses, Helicopters, Speed boats, motorbikes and other specialized vehicles. Mortality and morbidity recorded for 2016 was 1.1 and 2% respectively. MAITAMA is a specialist centre that offers general medical services. A total number 1227(88.8%) lives were saved during the observational period by three organizations, 60(4.9%) deaths, 132 (9.6%) disabilities, 793 (57.2%) NCDs and 593(42.8%) RTI.

Conclusion
Non-communicable diseases (NCDs) cause many deaths and morbidities in the developing world compared to infectious diseases. There is need for total revamping and education of EMRS institutions in Nigeria and Low- Middle Income Countries (LMICs). Abuja and its surroundings suffers from delays in rapid emergency services, lack of adequate awareness, functional ambulances, minimal specialists and inadequate consumables lead to the loss of many lives.
Healthy ageing and the prediction of mortality and incidence dependence in low- and middle- income countries: a 10/66 population-based cohort study
Authors: Daskalopoulou Christina , Prince Martin , Koukounari Artemis , Haro Josep Maria , Panagiotakos Demosthenes B. , Prina A. Matthew 
Published: December 2019

Abstract
Background
In the absence of a consensus on definition and measurement of healthy ageing, we created a healthy ageing index tallying with the functional ability framework provided by the World Health Organization. To create this index, we employed items of functional ability and intrinsic capacity. The current study aims to establish the predictive validity and discrimination properties of this healthy ageing index in settings in Latin American, part of the 10/66 cohort.

Methods
Population-based cohort studies including 12,865 people ≥65 years old in catchment areas of Cuba, Dominican Republic, Venezuela, Mexico and Peru. We employed latent variable modelling to estimate the healthy ageing scores of each participant. We grouped participants according to the quintiles of the healthy ageing score distribution. Cox’s proportional hazard models for mortality and sub-hazard (competing risks) models for incident dependence (i.e. needing care) were calculated per area after a median of 3.9 years and 3.7 years, respectively. Results were pooled together via fixed-effects meta-analysis. Our findings were compared with those obtained from self-rated health.

Results
Participants with lowest levels, compared to participants with highest level of healthy ageing, had increased risk of mortality and incident dependence, even after adjusting for sociodemographic and health conditions (HR: 3.25, 95%CI: 2.63–4.02; sub-HR: 5.21, 95%CI: 4.02–6.75). Healthy ageing scores compared to self-rated health had higher population attributable fractions (PAFs) for mortality (43.6% vs 19.3%) and incident dependence (58.6% vs 17.0%), and better discriminative power (Harrell’s c-statistic: mortality 0.74 vs 0.72; incident dependence 0.76 vs 0.70).

Conclusion
These results provide evidence that our healthy ageing index could be a valuable tool for prevention strategies as it demonstrated predictive and discriminative properties. Further research in other cultural settings will assist moving from a theoretical conceptualisation of healthy ageing to a more practical one.
Privacy-protecting estimation of adjusted risk ratios using modified Poisson regression in multi-center studies
Authors: Shu Di , Young Jessica G. , Toh Sengwee 
Published: December 2019

Abstract
Background
Multi-center studies can generate robust and generalizable evidence, but privacy considerations and legal restrictions often make it challenging or impossible to pool individual-level data across data-contributing sites. With binary outcomes, privacy-protecting distributed algorithms to conduct logistic regression analyses have been developed. However, the risk ratio often provides a more transparent interpretation of the exposure-outcome association than the odds ratio. Modified Poisson regression has been proposed to directly estimate adjusted risk ratios and produce confidence intervals with the correct nominal coverage when individual-level data are available. There are currently no distributed regression algorithms to estimate adjusted risk ratios while avoiding pooling of individual-level data in multi-center studies.

Methods
By leveraging the Newton-Raphson procedure, we adapted the modified Poisson regression method to estimate multivariable-adjusted risk ratios using only summary-level information in multi-center studies. We developed and tested the proposed method using both simulated and real-world data examples. We compared its results with the results from the corresponding pooled individual-level data analysis.

Results
Our proposed method produced the same adjusted risk ratio estimates and standard errors as the corresponding pooled individual-level data analysis without pooling individual-level data across data-contributing sites.

Conclusions
We developed and validated a distributed modified Poisson regression algorithm for valid and privacy-protecting estimation of adjusted risk ratios and confidence intervals in multi-center studies. This method allows computation of a more interpretable measure of association for binary outcomes, along with valid construction of confidence intervals, without sharing of individual-level data.
Maternal characteristics and outcomes affected by hypothyroidism during pregnancy (maternal hypothyroidism on pregnancy outcomes, MHPO-1)
Authors: Kiran Zareen , Sheikh Aisha , Malik Sarwar , Meraj Areeba , Masood Maha , Ismail Safana , Rashid Muhammad Owais , Shaikh Quratulain , Majeed Numan , Sheikh Luman , Islam Najmul 
Published: December 2019

Abstract
Background
Hypothyroidism in pregnancy is an arena of ongoing research, with international conflicts regarding screening, management, and outcomes. Various studies have described the outcomes depending on geographical and international diagnostic criteria. No study has been conducted in this regard from the region of Pakistan. Therefore, we aim to report the clinical features and maternal outcomes of hypothyroid pregnancies and compare the maternal outcomes between uncontrolled and controlled TSH levels in the preconception as well as the gestational period.

Methods
We conducted a cross-sectional retrospective study on 718 cases in the Aga Khan University Hospital after ethical approval. We collected information on pregnant females who have diagnosed hypothyroidism before conception or during their antenatal period. We noted the maternal characteristics and maternal comorbidities. Laboratory data were recorded for thyroid stimulating hormone levels before conception and during gestation. We recorded maternal outcomes as pregnancy loss (including miscarriage, stillbirth/intrauterine death, medical termination of pregnancy and ectopic pregnancy), gestational hypertension, pre-eclampsia, postpartum hemorrhage, placental abruption, and modalities of delivery. Data analysis was performed on Statistical Package for the Social Sciences version 20.0.

Results
Among 708 hypothyroid women 638 had live births. Postpartum hemorrhage was the most frequent maternal outcome (38.8%). The emergency cesarean section occurred in 23.4% of cases. We determined TSH levels in 53.2, 56.7, 61.7 and 66.6% of cases in preconception, 1st, 2nd, and 3rd trimester periods. A significant association existed between cesarean section and preconception thyrotropin levels > 2.5 mIU/L, whereas postpartum hemorrhage was significantly associated with thyrotropin levels > 2.5 mIU/L in the preconception and third trimester.

Conclusion
Successful live births in our patients were complicated by maternal postpartum hemorrhage and a frequent number of emergency cesarean section.
Serum metallome in pregnant women and the relationship with congenital malformations of the central nervous system: a case-control study
Authors: Troisi Jacopo , Giugliano Luigi , Sarno Laura , Landolfi Annamaria , Richards Sean , Symes Steven , Colucci Angelo , Maruotti Giuseppe , Adair David , Guida Marco , Martinelli Pasquale , Guida Maurizio 
Published: December 2019

Abstract
Background
Congenital malformations of the central nervous system (CNS) consist of a wide range of birth defects of multifactorial origin.

Methods
Concentrations of 44 metals were determined by Inductively Coupled Plasma Mass Spectrometry in serum of 111 mothers in the second trimester of pregnancy who carried a malformed fetus and compared them with serum concentrations of the same metals in 90 mothers with a normally developed fetus at the same week of pregnancy.
Data are reported as means ± standard deviations.

Results
We found a direct relationship between congenital defects of the CNS and maternal serum concentration of aluminum: it was statistically higher in women carrying a fetus with this class of malformation, compared both to mothers carrying a fetus with another class of malformation (6.45 ± 15.15 μg/L Vs 1.44 ± 4.21 μg/L, p < 0.0006) and to Controls (i.e. mothers carrying a normally-developed fetus) (6.45 ± 15.15 μg/L Vs 0.11 ± 0.51 μg/L, p < 0.0006). Moreover, Aluminum abundances were below the limit of detection in the majority of control samples.

Conclusion
CAluminum may play a role in the onset of central nervous system malformations, although the exact Aluminum species and related specific type of malformation needs further elucidation.
Family dissolution and children’s social well-being at school: a historic cohort study
Authors: Laursen Line Lund , Madsen Kathrine Bang , Obel Carsten , Hohwü Lena 
Published: December 2019

Abstract
Background
Family dissolution has become more common and one third of the child population in most Western countries now experience family dissolution. Studies show that children from dissolved families have lower levels of social well-being than children from intact families, but only few studies have examined the impact on social well-being specifically in the school setting. We investigated the association between family dissolution and children’s social well-being at school, including the possible influence of the child’s age at the time of the family dissolution.

Methods
We defined a historic cohort study of 219,226 children and adolescents aged 9–16 years and combined demographic registry data of family structure with questionnaire data on social well-being based on the Danish National Well-being Questionnaire completed in 2015. The definition of social well-being was constructed on the children’s perception of sense of belonging in the school setting, in the class and the school community, as well as perceptions on safety, loneliness and bullying. We examined low social well-being according to family dissolution and used multiple logistic regression analyses to adjust for parental educational level, ethnicity and siblings and further stratified for gender and age.

Results
A total of 5% of the children had a low social well-being at school. Among the 31% who lived in dissolved families, we found more children with a low level of social well-being at school (adjusted OR 1.41, 95% CI 1.36;1.47) than those in intact families; especially among those who at the time of family dissolution were in the preschool age (1.55, 95% CI 1.47;1.64).

Conclusion
Children from dissolved families had higher odds for low social well-being at school compared with children from intact families, especially those who experienced family dissolution in the preschool age. The school may be an important setting for identifying and providing help and support in children experiencing family dissolution.
Participatory development and pilot testing of the Makasi intervention: a community-based outreach intervention to improve sub-Saharan and Caribbean immigrants’ empowerment in sexual health
Authors:   for the MAKASI Study Group, Gosselin Anne , Carillon Séverine , Coulibaly Karna , Ridde Valéry , Taéron Corinne , Kohou Veroska , Zouménou Iris , Mbiribindi Romain , Derche Nicolas , Desgrées du Loû Annabel 
Published: December 2019

AbstractBackgroundSub-Saharan and Caribbean immigrants are particularly affected by HIV in Europe, and recent evidence shows that a large portion of them acquired HIV after arrival. There is a need for efficient interventions that can reduce immigrants’ exposure to HIV. We describe the pilot phase of a community-based empowerment outreach intervention among sub-Saharan and Caribbean immigrants in the greater Paris area aimed at 1) constructing the intervention, 2) assessing its feasibility, and 3) assessing the feasibility of its evaluation based on a stepped-wedge approach.Methods1) To develop the intervention, a literature review was conducted on existing interventions and participatory approaches developed, including the constitution of peer groups. 2) To assess the intervention’s feasibility, a pilot was conducted between April 2018 and December 2018. A daily register was used to collect data on sociodemographic characteristics of all persons who visited the mobile team to assess eligibility and acceptability. 3) To assess the feasibility of performing a stepped-wedge trial to evaluate the intervention, we compared eligibility, enrolment and retention at 3 months in two arms (immediate vs deferred). Chi-squared tests were used to compare reach and retention between the two arms.ResultsIntervention development.The Makasi intervention was designed as an outreach intervention that starts with the persons’ capacities and helps them appropriate existing resources and information and obtain knowledge about sexual health,based upon motivational interviewing techniques.Intervention Feasibility.Between April 2018 and December 2018, a total of 485 persons were identified as eligible. Participation in the intervention was proposed to 79% of eligible persons. When proposed, the persons enrolled in the intervention with a response rate of 69%. Some were lost to follow-up, and 188 persons were finally included.Evaluation Feasibility.The proportions of eligible (45 and 42%) individuals and of enrolled individuals (65 and 74%) were similar and not significantly different in the immediate and deferred arms, respectively.ConclusionsA community-based outreach intervention aimed at improving sub-Saharan and Caribbean immigrants’ empowerment in sexual health is feasible. The pilot phase was key to identifying challenges, designing a relevant intervention and validating the stepped-wedge protocol for evaluation.