bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis
Authors: Ghoreishifar Seyed Mohammad , Moradi-Shahrbabak Hossein , Fallahi Mohammad Hossein , Sarghale Ali Jalil , Moradi-Shahrbabak Mohammad , Abdollahi-Arpanahi Rostam , Khansefid Majid 
Published: February 2020

Abstract

Background: Consecutive homozygous fragments of a genome inherited by offspring from a common ancestor are known as runs of homozygosity (ROH). ROH can be used to calculate genomic inbreeding and to identify genomic regions that are potentially under historical selection pressure. The dataset of our study consisted of 254 Azeri (AZ) and 115 Khuzestani (KHZ ) river buffalo genotyped for ~65000 SNPs for the following two purposes: 1) to estimate and compare inbreeding calculated using ROH (FROH), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI), and diagonal elements of the genomic relationship matrix (FGRM); 2) to identify frequently occurring ROH (i.e. ROH islands) for our selection signature and gene enrichment studies. Results: In this study, 9102 ROH were identified, with an average number of 21.2±13.1 and 33.2±15.9 segments per animal in AZ and KHZ breeds, respectively. On average in AZ, 4.35% (108.8±120.3 Mb), and in KHZ, 5.96% (149.1±107.7 Mb) of the genome was autozygous. The estimated inbreeding values based on FHOM, FUNI and FGRM were higher in AZ than they were in KHZ, which was in contrast to the FROH estimates. We identified 11 ROH islands (four in AZ and seven in KHZ). In the KHZ breed, the genes located in ROH islands were enriched for multiple Gene Ontology (GO) terms (P≤0.05). The genes located in ROH islands were associated with diverse biological functions and traits such as body size and muscle development (BMP2), immune response (CYP27B1), milk production and components (MARS, ADRA1A, and KCTD16), coat colour and pigmentation (PMEL and MYO1A), reproductive traits (INHBC, INHBE, STAT6 and PCNA), and bone development (SUOX). Conclusion: The calculated FROH was in line with expected higher inbreeding in KHZ than in AZ because of the smaller effective population size of KHZ. Thus, we find that FROH can be used as a robust estimate of genomic inbreeding. Further, the majority of ROH peaks were overlapped with or in close proximity to the previously reported genomic regions with signatures of selection. This tells us that it is likely that the genes in the ROH islands have been subject to artificial or natural selection.
­Transcriptome profiling of non-climacteric ‘Yellow’ melon during ripening: insights on sugar metabolism
Authors: Schemberger Michelle Orane , Stroka Marília Aparecida , Reis Letícia , Los Kamila Karoline de Souza , de Araujo Gillize Aparecida Telles , Sfeir Michelle Zibetti Tadra , Galvão Carolina Weigert , Etto Rafael Mazer , Baptistão Amanda Regina Godoy , Ayub Ricardo Antonio 
Published: February 2020

Abstract
Background: The non-climacteric ‘Yellow’ melon ( Cucumis melo , inodorus group) is an economically important crop and its quality is mainly determined by the sugar content. Thus, knowledge of sugar metabolism and its related pathways can contribute to the development of new field management and post-harvest practices, making it possible to deliver better quality fruits to consumers. Results: The RNA-seq associated with RT-qPCR analyses of four maturation stages were performed to identify important enzymes and pathways that are involved in the ripening profile of non-climacteric ‘Yellow’ melon fruit focusing on sugar metabolism. We identified 895 genes 10 days after pollination (DAP)-biased and 909 genes 40 DAP-biased. The KEGG pathway enrichment analysis of these differentially expressed (DE) genes revealed that ‘hormone signal transduction’, ‘carbon metabolism’, ‘sucrose metabolism’, ‘protein processing in endoplasmic reticulum’ and ‘spliceosome’ were the most differentially regulated processes occurring during melon development. In the sucrose metabolism, five DE genes are up-regulated and twelve are down-regulated during fruit ripening. Conclusions: The results demonstrated important enzymes in the sugar pathway that are responsible for the sucrose content and maturation profile in non-climacteric ‘Yellow’ melon. New DE genes were first detected for melon in this study such as invertase inhibitor LIKE 3 ( CmINH3 ), trehalose phosphate phosphatase ( CmTPP1 ) and trehalose phosphate synthases ( CmTPS5 , CmTPS7 , CmTPS9 ). Furthermore, the results of the protein-protein network interaction demonstrated general characteristics of the transcriptome of young and full-ripe melon and provide new perspectives for the understanding of ripening.
Stigma and discrimination: barriers to the utilisation of a nutritional program in HIV care services in the Tigray region, Ethiopia.
Authors: Tesfay Fisaha , Javanparast Sara , Mwanri Lillian , Ziersch Anna 
Published: February 2020

Abstract
Background: In Ethiopia, stigmatising attitudes towards people living with HIV have reduced over time due to improved HIV knowledge and the expansion of services. However, HIV stigma and discrimination remain a key challenge and have negative impacts on access to and utilisation of HIV services including nutritional programs. A small number of studies have examined the experience of stigma related to nutritional programs, but this is limited. This study explored HIV status disclosure and experience of stigma related to a nutritional program in HIV care settings in Ethiopia and impacts on nutritional program utilisation.
Methods: As part of a larger study, qualitative in-depth interviews were conducted with 20 adults living with HIV, 15 caregivers of children living with HIV and 13 program staff working in the nutritional program in three hospitals in the Tigray region of Ethiopia. Framework thematic analysis using NVivo was employed to analyse the data.
Results: The study found varying levels of positive HIV status disclosure, depending on who the target of disclosure was. Disclosing to family members was reported to be less problematic by most participants. Despite reported benefits of the nutritional program in terms of improving weight and overall health status, adults and caregivers of children living with HIV revealed experiences of stigma and discrimination that were amplified by enrolment to the nutritional program. This was due to: a) transporting, consuming and disposing of the nutritional support itself, which is associated with HIV in the broader community; b) required increased frequency of visits to HIV services for those enrolled in the nutritional program and associated.
Conclusion: There was evidence of concerns about HIV-related stigma and discrimination among individuals enrolled in this program and their family members, which in turn negatively affected the utilisation of the nutritional program. Stigma and discrimination are a source of health inequity and undermine access to the nutritional program. Nutritional programs in HIV care should include strategies to take these concerns into account by mainstreaming stigma prevention and mitigation activities. Further research should be done to identify innovative ways of facilitating social inclusion to mitigate stigma and improve utilisation.
Deep learning improves the ability of sgRNA off-target propensity prediction
Authors: Liu Qiaoyue , Cheng Xiang , Liu Gan , Li Bohao , Liu Xiuqin 
Published: February 2020

Abstract
Background
CRISPR/Cas9 system, as the third-generation genome editing technology, has been widely applied in target gene repair and gene expression regulation. Selection of appropriate sgRNA can improve the on-target knockout efficacy of CRISPR/Cas9 system with high sensitivity and specificity. However, when CRISPR/Cas9 system is operating, unexpected cleavage may occur at some sites, known as off-target. Presently, a number of prediction methods have been developed to predict the off-target propensity of sgRNA at specific DNA fragment. Most of them use artificial feature extraction operations and machine learning techniques to obtain off-target scores. With the rapid expansion of off-target data and the rapid development of deep learning theory, the existing prediction methods can no longer satisfy the prediction accuracy at the clinical level.
Results
Here, we propose a prediction method named CnnCrispr to predict the off-target propensity of sgRNA at specific DNA fragments. CnnCrispr automatically trains the sequence features of sgRNA-DNA pairs with GloVe model, and embeds the trained word vector matrix into the deep learning model including biLSTM and CNN with five hidden layers. We conducted performance verification on the data set provided by DeepCrispr, and found that the auROC and auPRC in the "leave-one-sgRNA-out" cross validation could reach 0.957 and 0.429 respectively (the pearson value and spearman value could reach 0.495 and 0.151 respectively under the same settings).
Conclusion
Our results show that CnnCrispr has better classification and regression performance than the existing states-of-art models. The code of CnnCrispr can be freely downloaded from https://github.com/LQYoLH/CnnCrispr.
Sex differences in campylobacteriosis incidence rates at different ages - a seven country, multi-year, meta-analysis. A potential mechanism for the infection.
Authors: Green Manfred S , Schwartz Naama , Peer Victoria 
Published: February 2020

Abstract
Background. There is evidence of an excess of males in the incidence rates of campylobacteriois. The objectives of this study were to determine whether these observations differ between age groups and are consistent over different countries and during different time periods.
Methods. We obtained data on incidence rates of campylobacteriosis by sex and age group over a period of 11-26 years from seven countries. Male to female incidence rate ratios (IRR) were computed by age group, country and time period. For each age group, we used meta-analytic methods to combine the IRRs. Sensitivity analysis was used to test whether the results are robust to differences between countries and time periods. Meta-regression was conducted to estimate the different effects of age, country, and time period on the IRR.
Results. In the age groups <1, 1-4, 5-9, 10-14, 15-44, 45-64 and 65+ years old, the pooled IRRs (with 95% CI) were 1.31 (1.26-1.37), 1.34 (1.31-1.37), 1.35 (1.32-1.38), 1.73 (1.68-1.79), 1.10 (1.08-1.12), 1.19(1.17-1.21) and 1.27 (1.24-1.30), respectively. For each age group, the excess campylobacteriosis incidence rates in males differed at different age groups. However, despite some quantitative differences between countries, the excess was consistently present over long time-periods. In meta-regression analysis, age group was responsible for almost all the variation in the IRRs.
Conclusions. The male predominance in campylobacteriosis incidence rates starts in infancy. This suggests that this is due, at least in part, to physiological or genetic differences and not just behavioural factors. These findings can provide clues to the mechanisms of the infection and could lead to more targeted treatments and vaccine development.
Genome-wide association study (GWAS) reveals genetic loci of lead (Pb) tolerance during seedling establishment in rapeseed (Brassica napus L.)
Authors: Zhang Fugui , Xiao Xin , Xu Kun , Cheng Xi , Xie Ting , Hu Jihong , Wu Xiaoming 
Published: February 2020

Abstract
Background

Lead (Pb) pollution in soil has become one of the major environmental threats to plant growth and human health. Safe utilization of Pb contaminated soil by phytoremediation require Pb tolerant rapeseed ( Brassica napus L.) accessions. However, breeding of new B. napus cultivars tolerance to Pb stress has been restricted by limited knowledge on molecular mechanisms involved in Pb tolerance. This work was carried out to identify genetic loci related to Pb tolerance during seedling establishment in rapeseed.

Results

Pb tolerance, which was assessed by quantifying radicle length (RL) under 0 or 100 mg/L Pb stress condition, shown an extensive variation in 472 worldwide-collected rapeseed accessions. Based on the criterion of relative RL>80%, six Pb tolerant genotypes were selected. Four quantitative trait loci (QTL) associated with Pb tolerance were identified by Genome-wide association study. The expression level of nine promising candidate genes, including GSTUs , BCATs , UBP13 , TBR and HIPP01 , located in these four QTL regions, were significantly higher or induced by Pb in Pb tolerant accessions in comparison to Pb sensitive accessions.

Conclusion

To our knowledge, this is the first study on Pb tolerant germplasms and genomic loci in B. napus . The findings can provide valuable genetic resources for the breeding of Pb tolerant B. napus cultivar and understanding of Pb tolerance mechanism in Brassica species.
Risk Assessment of Heavy Metal in the Surface Sediment at the Drinking Water Source of the Xiangjiang River in South China
Authors: Huang Zhifeng , Liu Chengyou , Zhao Xingru , Dong Jing , Zheng Binghui 
Published: February 2020

Abstract
Background: The Xiangjiang River is an important drinking water resource for the Hunan province of China. It is crucial to ascertain the pollution status, influencing factors, ecological risks, and possible sources of heavy metals in the sediments of the Xiangjiang River. Sediment is both a source and a sink of heavy metals in aquatic ecosystems. In this study, surface sediment was collected from the Zhuzhou Reach of the Xiangjiang River and eight heavy metals were investigated. Results: In all sediment samples, all eight heavy metals were detected and their average concentration fell in the order of Zn > Pb > As > Cu > Cr > Ni > Cd > Co. Assessment shows extremely serious Cd pollution and a very high potential ecological risk from Cd. According to correlation analysis and principle component analysis (PCA), As, Cu, Ni, Pb, and Zn originate from industrial wastewater and mineral smelting activities, whereas Co, Cr, and Ni come from natural sources. Redundancy analysis (RDA) reveals that the organic matter content and the particle size of the sediment have some influence on the enrichment of heavy metals. Conclusion: Among all eight examined heavy metals in the surveyed area, the content of Zn, Pb, and As is the highest, and that of Cd and Co is the lowest. Despite a low level of absolute content, the Cd in sediment already renders a high ecological risk and thus calls for urgent attention. Anthropogenic activities are the main source of heavy metals in the sediment. The distribution of heavy metals is also influenced by sediment properties. The results provide guidance for controlling heavy metal pollution and protecting drinking water sources in the Xiangjiang River.
Validity, reliability and feasibility of assessment of cilinical reasoning of medical students by observation versus post encounter assessment in a clinical practice setting.
Authors: Haring Catharina Maria , Klaarwater Claudia , Bouwmans Geert , Cools Bernadette , Gurp Petra van , Meer Jos van der , Postma Cornelis 
Published: February 2020

Abstract
Background The assessment of clinical reasoning by medical students in clinical practice is very difficult. Partly this is because the fundamental mechanisms of clinical reasoning are difficult to uncover and when known, hard to observe and interpret. Methods We developed an observation tool to assess the clinical reasoning ability of medical students during clinical practice. The observation tool consists of an 11-item observation rating form. The validity, reliability and feasibility of this tool were verified among medical students during the internal medicine clerkship and compared to an existing post-encounter rating tool. Results Six raters assessed each, the same 15 student-patient encounters. The internal consistency (Cronbach’s alfa) for the observation rating tool (ORT) was 0.87 (0.71-0.84) and the 5-item post encounter rating tool (PERT) was 0.81 (0.71-0.87). The intraclass-correlation coefficient for single measurements was poor for both the ORT; 0.32 (p<0.001) as well as the PERT; 0.36 (p<0.001). The generalizability study (G-study) and decision study (D-study) showed that 6 raters are required to achieve a G-coefficient of > 0.7 for the ORT and 7 raters for the PERT. The largest sources of variance are the interaction between raters and students. There was a correlation between the ORT and PERT of 0.53 (p=0.04) Conclusions The ORT and PERT are both feasible, valid and reliable instruments to assess students’ clinical reasoning skills in clinical practice.
Effect of community active case-finding strategies for detection of tuberculosis in Cambodia: study protocol for a pragmatic cluster randomized controlled trial
Authors: Teo Alvin Kuo Jing , Prem Kiesha , Evdokimov Konstantin , Ork Chetra , Eng Sothearith , Tuot Sovannary , Chry Monyrath , Mao Tan Eang , Hsu Li Yang , Yi Siyan 
Published: February 2020

Abstract
• Background: Cambodia has made notable progress in the fight against tuberculosis (TB). However, these gains are impeded by a significant proportion of undiagnosed cases. To effectively reach people with TB, active case finding (ACF) strategies have been adopted by countries affected by the epidemic, including Cambodia, alongside passive case finding (PCF). Despite increased efforts to improve case detection, approximately 40% of TB cases in Cambodia remained undiagnosed in 2018. In Cambodia, several community-based TB ACF modalities have been implemented, but their effectiveness has yet to be systematically assessed.• Methods: This pragmatic cluster randomized controlled trial will be conducted between December 2019 and June 2021. We will randomize eight operational districts (cluster) in seven provinces (Kampong Cham, Kampong Thom, Prey Veng, Thbong Khmum, Kampong Chhnang, Kandal, and Kampong Speu) to either the control group (PCF) or the intervention groups (ACF using a seed-and-recruit model, ACF targeting household and neighborhood contacts, and ACF targeting persons aged ≥55 using mobile screening units). The primary endpoints will be TB case notification rates, additionality, and cumulative yield of TB cases. The secondary endpoints include treatment outcomes, the number needed to screen to find one TB case, and cost-effectiveness outcome measures. We will analyze the primary and secondary endpoints by intention-to-treat. We will compare cluster and individual-level characteristics using student’s t-test and hierarchical or mixed-effect models to estimate the ratio of these means. Incremental cost-effectiveness ratio per disability-adjusted life year averted will also be considered as a benchmark to determine if the interventions are cost-effective.• Discussion: This study will build an evidence base to inform future scale-up, implementation, and sustainability of ACF strategies in Cambodia and other similar settings. Implementation of this study will also complement TB control strategies in Cambodia by conducting ACF in operational districts without active interventions to find TB cases currently. Those who are ill and might have TB will be promptly screened, diagnosed, and linked to care. Early diagnosis and treatment initiation will also benefit their community by interrupting transmission and prevent further infections. The experience gained from this project will inform future attempts in conducting pragmatic trials in low-resource settings.• Trial registration: This trial is registered at ClinicalTrials.gov, NCT04094350. Registered 18 September 2019.
Correlation between UGT1A1 gene polymorphism and irinotecan chemotherapy in metastatic colorectal cancer：a study from Guangxi Zhuang
Authors: Chen Shaojun , Hua Li , Feng Chenjun , Mo Qia , Wei Mengzhuan , Shen Yongqi , Lin Zhan , Li Guisheng , Xu Junyi , Guo Chengxian , huang haixin 
Published: February 2020

Abstract
Background: UGTlA1 gene polymorphism has different distribution in different ethnicities, geographical regions and ethnic groups, which may lead to different toxicity and efficacy of irinotecan. The study aimed to explore the correlation of UGT1A1 gene polymorphism of Guangxi Zhuang metastatic colorectal cancer (mCRC) with irinotecan -based chemotherapy, in order to develop an individualized irinotecan regimen for mCRC patients of Guangxi Zhuang. Methods: From June 2013 and June 2015, a total of 406 patients of Guangxi who were histologically diagnosed as metastatic colorectal cancer with 102 patients of this cohort with three generations of Zhuang, and 86 patients that conformed to inclusion and exclusion criteria were competitively enrolled . The distribution of UGT1A1 gene polymorphism was analyzed-retrospectively in all patients. Pyrosequencing method was used to detect the UGT1A1 * 28 and * 6 gene polymorphism in the 86 Guangxi Zhuang mCRC patients. After first-line chemotherapy with FOLFIRI regimen, the relationship between gene polymorphism of UGT1A1 and adverse reactions, and efficacy of Irinotecan were analyzed with χ2 test and Kaplan-Meier method.Results: UGT1A1 * 28 wild-type (TA6 / 6), heterozygous mutant (TA6 /7) and homozygous mutant (TA7 / 7) accounted for 69.8%, 30.2% and 0%, respectively. UGT1A1 * 6 wild type (G / G), heterozygous mutation type (G / A) and homozygous mutant (A / A) accounted for 76.7%，20.9% and 2.3%，respectively.UGT1A1 * 28 TA6 / 7 type could increase the risk of grade 3-4 diarrhea (P=0.027), which did not increase the risk of grade 3-4 neutropenia (P=0.092). UGT1A1 * 6 G / A and A / A type could increase the risk of grade 3-4 diarrhea and neutropenia (P=0.001; P=0.017). After chemotherapy with FOLFIRI, there was no significant difference in response rate (RR) (P=0.729; P=0.745) or in median progression-free survival (mPFS) between the wild-type, mutant treatment of UGT1A1 * 28 and UGT1A1 * 6 (7.0 m vs 7.4 m, P=0.427; 6.9 m vs 7.0m P=0.408).Conclusions: The distribution of UGT1A1*28 and UGT1A1* 6 gene polymorphism in Guangxi Zhuang patients were differed from the existing reported of European people and Chinese Han population. The UGT1A1 gene polymorphism with irinotecan chemotherapy-associated diarrhea and neutropenia were closely related. There was no significant association between UGT1A1 gene polymorphism and therapeutic efficacy of irinotecan.