bluuebunny/crossref_metadata_2025_split huggingface dataset:
Convergent degeneration of olfactory receptor gene repertoires in marine mammals
Authors: Liu Ake , He Funan , Shen Libing , Liu Ruixiang , Wang Zhijun , Zhou Jingqi 
Published: August 2019

Abstract
Background: Olfactory receptors (ORs) can bind odor molecules and play a crucial role in odor sensation. Due to the frequent gains and losses of genes during evolution, the number of OR members varies greatly among different species. However, whether the extent of gene gains/losses varies between marine mammals and related terrestrial mammals has not been clarified and the factors that might underlie these variations are unknown.
Results: To address these questions, we identified more than 10,000 members of the OR family in 23 mammals and classified them into 830 orthologous gene groups (OGGs) and 281 singletons. Significant differences occurred in the number of OR repertoires and OGGs among different species. We found that all marine mammals had less OR genes than their related terrestrial lineages, with the fewest OR genes found in cetaceans, which may be closely related to olfactory degradation. ORs with more gene duplications or loss events tended to be under weaker purifying selection. The average gain and loss rates of OR genes in terrestrial mammals were higher than those of mammalian gene families, while the average gain and loss rates of OR genes in marine mammals were significantly lower and much higher than those of mammalian gene families, respectively. Additionally, we failed to detect any one-to-one orthologous gene in the focal species, suggesting that OR genes are not well conserved among marine mammals.
Conclusions: Marine mammals have experienced large numbers of OR genes compared with their related terrestrial lineages, which may be related to the weaker purifying selection. Due to their independent degeneration, OR genes present in each lineage are not well conserved among marine mammals. Our study provides a basis for future research on the olfactory receptor function in mammals from the perspective of evolutionary trajectories.
Genome-wide association study reveals new loci for yield-related traits in Sichuan wheat germplasm under stripe rust stress
Authors: Ye Xueling , Li Jian , Cheng Yukun , Yao Fangjie , Long Li , Wang Yuqi , Wu Yu , Li Jing , Wang Jirui , Jiang Qiantao , Kang Houyang , Li Wei , Qi Pengfei , Lan Xiujin , Ma Jian , Liu Yaxi , Jiang Yunfeng , Wei Yuming , Chen Xianming , Liu Chunji , Zheng Youliang , Chen Guoyue 
Published: August 2019

Abstract
Background

As one of the most important food crops in the world, increasing wheat (Triticum aestivum L.) yield is an urgent task for global food security under the continuous threat of stripe rust (caused by Puccinia striiformis f. sp. tritici) in many regions of the world. Molecular marker-assisted breeding is one of the most efficient ways to increase yield. Here, we identified loci associated to multi-environmental yield-related traits under stripe rust stress in 244 wheat accessions from Sichuan Province through genome-wide association study (GWAS) using 44059 polymorphic markers from the 55K single nucleotide polymorphism (SNP) chip.

Results

A total of 13 stable quantitative trait loci (QTLs) were found to be highly associating to yield-related traits, including 6 for spike length (SL), 3 for thousand-kernel weight (TKW), 2 for kernel weight per spike (KWPS), and 2 for both TKW and KWPS, in at least two test environments under stripe rust stress conditions. Of them, ten QTLs were overlapped or very close to the reported QTLs, three QTLs, QSL.sicau-1AL, QTKW.sicau-4AL, and QKWPS.sicau-4AL.1, were potentially novel through the physical location comparison with previous QTLs. Further, twenty-one candidate genes within three potentially novel QTLs were identified, they were mainly involved in the regulation of phytohormone, cell division and proliferation, meristem development, plant or organ development, and carbohydrate transport.

Conclusions

QTLs and candidate genes detected in our study for yield-related traits under stripe rust stress will facilitate elucidating genetic basis of yield-related trait and could be used in marker-assisted selection in wheat yield breeding.
Nutritional status of tuberculosis patients, a comparative cross-sectional study
Authors: Feleke Berhanu Elfu , Feleke Teferi Elfu , Biadglegne Fantahun 
Published: August 2019

Abstract
Background

Each year, more than 13.7 million people became an active case of tuberculosis and more than 1.5 million cases of tuberculosis patient will die. The association between tuberculosis and malnutrition is bi-directional, tuberculosis leads the patient to malnutrition, and malnutrition increases the risk of developing active tuberculosis by 6 to 10 times higher. Improving the nutrition of individual greatly reduces tuberculosis. The objectives of this study were to assess the nutritional status and determinants of tuberculosis patients.

Methods

A comparative cross-sectional study design was implemented. The sample size was calculated using Epi-info software. The data were collected from July 2015- May 2018. The data were collected by interviewing method, measuring anthropometrics indicators and collecting the stool and blood samples. The data were entered into the computer using Epi-info software and analyzed using SPSS software. Descriptive statistics were used to identify the proportion of malnutrition. Binary logistic regression was used to identify the determinants of malnutrition.

Results

A total of 5045 study participants were included giving the response rate of 93.1%. The prevalence of underweight among tuberculosis patients was 57.17% (95% CI: 54.80% -59.54%) and 88.52% of tuberculosis patients were anemic. The prevalence of malnutrition (underweight) among tuberculosis free residents was 23.37% (95% CI: 21.93-24.80). The nutritional status of tuberculosis patients were determined by site of infection AOR: 0.68[0.49-0.94], sex of the patient AOR: 0.39 [0.25-0.56], residence AOR: 3.84 [2.74-5.54], intestinal parasite infection AOR: 7 [5.2-9.95], alcohol use disorder AOR: 1.52 [1.17-2.13].

Conclusion

High proportion of tuberculosis patients was malnourished. Tuberculosis patients were highly susceptible to malnutrition and even a very distal factor for malnutrition in the community became a proximal factor for tuberculosis patients.
Impaired Fasting Glucose alone or in combination with Hypertension, Dyslipidemia, or both AND Major Adverse Cardiovascular Events among patients without previous cardiovascular disease.
Authors: Madani Nahid Hashemi , Ismail-Beigi Faramarz , Poustchi Hossein , Nalini Mahdi , Sepanlou Sadaf G. , Malek Mojtaba , Abbasi Mohammad Amin , Khajavi Alireza , Khamseh Mohammad Ebrahim , Malekzadeh Reza 
Published: August 2019

Abstract
Background

Whether pre-diabetes in the absence of hypertension (HTN) or dyslipidemia (DLP) is a risk factor for occurrence of major adverse cardiovascular events (MACE) is not fully established. We investigated the effect of impaired fasting glucose (IFG) alone and in combination with HTN, DLP or both on subsequent occurrence of MACE as well as individual MACE components.

Methods

This longitudinal population-based study included 9,831 inhabitants of Northeastern Iran. The participants were free of any cardiovascular disease at baseline and were followed yearly from 2010 to 2017. Cox proportional hazard models were fitted to measure the hazard of IFG alone or in combination with HTN and DLP on occurrence of MACE as the primary endpoint.

Results

297 MACE were recorded during 6.2±0.1 years follow up. IFG alone compared to normal fasting glucose (NFG) was not associated with increased in occurrence of MACE (HR, 1.05; 95% CI, 0.59-1.86; p, 0.8). However, combination of IFG and HTN (HR, 2.75; 95% CI, 1.93-3.90; p, 0.001) or HTN + DLP (HR, 2.85; 95% CI, 1.79-4.54; p, 0.001) significantly increased the hazard of MACE. In contrast, IFG with DLP at baseline did not increase the hazard of MACE compared to normoglycemic- normolipemic individuals (p,0.2). The results also indicated IFG with HTN, DLP, or HTN+DLP were associated with significant higher HRs for some individual components of MACE.

Conclusion

IFG, per se, does not appear to increase hazard of MACE. However, IFG with HTN or HTN + DLP conferred a significant hazard for MACE in an incremental manner.
Exploring undergraduate students achievement emotions during ward round simulation: A mixed-method study
Authors: Behrens Claudia , DOLMANS DIANA H. , GORMLEY GERARD J. , Driessen Erik 
Published: August 2019

Abstract
Background

Simulation based learning (SBL) has increased in its use to best equip students for clinical practice. Simulations that mirror the complex realities of clinical practice have the potential to induce a range of emotions, without a clear understanding of their impact on learning and the learner. Students’ emotional states have important effects on their learning process that can be either positive or negative, and are often difficult to predict. We aimed to determine: (1) To what extent achievement emotions are experienced by medical students during a complex simulation based learning activity, i.e. a ward round simulation (WRS). (2) What their performance scores are and too which extent performance scores do correlate with emotions and 3) how these emotions are perceived to impact learning.

Methods

A mixed methods approach was used in this study. Using an Achievement Emotion Questionnaire, we explored undergraduate medical student’s emotions as they participated in a complex ward round-based simulation. Their performance was rated using an observational ward round assessment tool and correlated with emotions scores. Six focus groups were conducted to provide a deeper understanding of their emotional and learning experiences.

Results

Students experienced a range of emotions during the simulation, they felt proud, enjoyed the simulation and performed well. Students felt proud because they could show in the complex simulation what they had learned so far. Students reported moderate levels of anxiety and low levels of frustration and shame. We found non-significant correlations between achievement emotions and performance during ward round simulation.

Conclusions

Placing undergraduate students in high complex simulations that they can handle raises positive academic achievement emotions which seem to support students’ learning and motivation.
Collaborative Assessment and Management of Suicidality (CAMS) compared to Enhanced Treatment as Usual (E-TAU) for suicidal patients in an inpatient setting: Study protocol for a randomized controlled trial
Authors: Santel Miriam , Driessen Martin , Neuner Frank , Berg Michaela , Hennig-Fast Kristina , Jobes David A. , Beblo Thomas 
Published: August 2019

Abstract
Background: The Collaborative Assessment and Management of Suicidality (CAMS) is a therapeutic framework that has been shown to reduce suicidal ideation and overall symptom distress. CAMS has not been previously evaluated in a standard acute inpatient mental health care setting with only short treatment times for suicidal patients. In this randomized controlled trial (RCT) we investigate, if CAMS is more effective than Enhanced-Treatment as Usual (E-TAU) in reducing suicidal thoughts and behaviors. As secondary outcomes we are also investigating depressive symptoms, symptom relief in general, and quality of the therapeutic relationship. Methods/design: The trial is designed as a single-center, two-armed, parallel group observer-blinded randomized clinical effectiveness trial. We aim to recruit and randomize 60 participants with different diagnoses, who are admitted as inpatients due to acute suicidal thoughts or behavior in the Clinic of Psychiatry and Psychotherapy, Ev. Hospital Bethel in Bielefeld, Germany. The duration of treatment will vary depending on patients’ needs and clinical assessments between 10 and a maximum of 40 days. Patients are assessed at 4 time points (admission, discharge, 1 month, and 5 months after discharge). The primary outcome measure is the Beck Scale for Suicide Ideation. Other outcome measures are included, such as severity of psychiatric symptoms, depression, reasons for living, and the therapeutic relationship. Discussion: This effectiveness study is being conducted on an acute ward in a psychiatric clinic where patients have multiple problems and diagnoses. Treatment times are rather short and therapists have a high workload. The results of this study can be generalized to a typical hospital setting and similar results should be expected if CAMS is implemented in other psychiatric systems.
Genome-wide association mapping revealed syntenic loci QFhb-4AL and QFhb-5DL for Fusarium head blight resistance in common wheat (Triticum aestivum L.)
Authors: Hu Wenjing , Gao Derong , Wu Hongya , Liu Jian , Zhang Chunmei , Wang Junchan , Jiang Zhengning , Liu Yeyu , Li Dongsheng , Zhang Yong , Lu Chenbin 
Published: August 2019

Abstract
Background:Fusarium head blight (FHB), primarily caused by Fusarium graminearum, is a major threat to wheat production and food security worldwide. Breeding stably and durably resistant cultivars is the most effective approach for managing and controlling the disease. The success of FHB resistance breeding relies on identification of an effective resistant germplasm. We performed a genome-wide association study (GWAS) using the high-density wheat 90K single nucleotide polymorphism (SNP) assays to better understand the genetic basis of FHB resistance in natural population and identify associated molecular markers.
Results:The resistance to FHB fungal spread along the rachis (Type II resistance) was evaluated on 171 wheat cultivars in the 2016-2017 and 2017-2018 growing seasons. Using Illumina Infinum iSelect 90K SNP genotyping data, a genome-wide association study (GWAS) identified 26 loci(88 marker-trait associations), which explained 6.65-14.18% of the phenotypic variances. The associated loci distributed across all chromosomes except 2D, 6A, 6D and 7D, with those on chromosomes 1B, 4A, 5D and 7A being detected in both years. New loci for Type II resistance were found on syntenic genomic regions of chromsome 4AL (QFhb-4AL, 621.85 - 622.24 Mb) and chromosome 5DL (QFhb-5DL, 546.09 - 547.27 Mb) which showed highly collinarity in gene content and order. SNP markers wsnp_JD_c4438_5568170 and wsnp_CAP11_c209_198467 of 5D, reported previously linked to a soil-borne wheat mosaic virus (SBWMV) resistance gene, were also associated with FHB resistance in this study.
Conclusion:The syntenic FHB resistant loci and associated SNP markers identified in this study are valuable for FHB resistance breeding via marker-assisted selection.
Prevalence of accelerometer-measured physical activity in adolescents. The Tromsø Study: Fit Futures
Authors: Beldo Sigurd Klemetsen , Morseth Bente , Christoffersen Tore , Halvorsen Peder Andreas , Hansen Bjørge Herman , Furberg Anne-Sofie , Ekelund Ulf , Horsch Alexander 
Published: August 2019

Abstract
Background: Previous studies show large variations in physical activity (PA) levels among adolescents. However, the number of studies is limited and even fewer studies have assessed PA in adolescents by accelerometer devices. This study aimed to describe accelerometer-measured PA levels in adolescents in a population-based cohort in Northern Norway.
Methods: In 611 students aged 16-17 years attending the Fit Futures Study, PA was measured by Actigraph GT3X for seven consecutive days. PA was expressed as total PA volume (counts per minute, CPM), time spent in intensity zones, steps per day, and fulfilment of WHO recommendation (i.e. accumulation of 60 minutes or more of at least moderate intensity PA per day). Potential correlates of PA such as sex, socioeconomic status, study program, self-perceived health, and PA variations by weekday versus weekend were also examined.
Results: 16% of the girls and 25% of the boys fulfilled current WHO-recommendations. Total PA volume (CPM) was higher in boys than in girls (353 (SD 130) versus 326 (SD 114) CPM, p<0.05). PA levels differed with study program and increased with better self-perceived health, but were not associated with socioeconomic status. Both boys and girls were more active on weekdays than weekends (altogether; 350 (SD 124) versus 299 (SD 178) CPM, p<0.05).
Conclusions: In this cohort of adolescents, less than 25 % of 16-17-year-old boys and girls fulfilled the WHO recommendations. The levels of physical activity in 16-17-year-old adolescents are similar to previous data reported in adults.
Measles Outbreak Amplified in a Pediatric Ward: Lyantonde District, Uganda, August 2017
Authors: Biribawa Claire , Atuhairwe Joselyn Annet , Bulage Lilian , Okethwangu Denis Othuba , Kwesiga Benon , Ario Alex Riolexus , Zhu Bao-Ping 
Published: August 2019

Abstract
Background

Measles is a highly infectious viral disease. In August 2017, Lyantonde District, Uganda reported a measles outbreak to Uganda Ministry of Health. We investigated to assess the outbreak scope, factors facilitating transmission, and recommend control measures.

Methods

We defined a probable case as sudden onset of fever and generalized rash in a resident of Lyantonde, Lwengo, or Rakai Districts from 1 June-30 September 2017, plus ≥1 of the following: coryza, conjunctivitis, or cough. A confirmed case was a probable case with serum positivity of measles-specific IgM. We conducted a neighborhood- and age-matched case-control study to identified exposure factors, and used conditional logistic regression to analyze the data. We estimated vaccine effectiveness and vaccination coverage.

Findings

We identified 81 cases (75 probable, 6 confirmed); 4 patients (4.9%) died. In the case-control study, 47% of case-patients and 2.3% of controls were hospitalized at Lyantonde Hospital pediatric department for non-measles conditions 7-21 days before case-patient’s onset (ORadj=34, 95%CI: 5.1-225). Estimated vaccine effectiveness was 95% (95%CI: 75-99%) and vaccination coverage was 76% (95%CI: 68-82%). During the outbreak, an “isolation” ward was established inside the pediatric ward. Measles and non-measles patients were mixed in regular pediatric wards.

Conclusion

This outbreak was amplified by nosocomial transmission and facilitated by low vaccination coverage. We recommended moving the isolation ward outside of the building, supplemental vaccination, and vaccinating pediatric patients during measles outbreaks.
Genome-wide characterization of copy number variations in genetic resistance to Marek’s disease using next generation sequencing
Authors: Bai Hao , He Yanghua , Ding Yi , Zhang Huanmin , Chen Jilan , Song Jiuzhou 
Published: August 2019

Abstract
Background: Marek’s disease (MD) is a highly neoplastic disease primarily affecting chickens, and remains as a chronic infectious disease that threatens the poultry industry. Copy number variation (CNV) has been examined in many species and is recognized as a major source of genetic variation that directly contributes to phenotypic variation such as resistance to infectious diseases. Two highly inbred chicken lines 63 (MD-resistant) and 72 (MD-susceptible), as well as their F1 generation and six recombinant congenic strains (RCSs) with varied susceptibility to MD, are considered as ideal models to identify the complex mechanisms of genetic and molecular resistance to MD.
Results: In the present study, to unravel the potential genetic mechanisms underlying MD, we performed a genome-wide CNV detection using next generation sequencing on the inbred chicken lines with the assistance of CNVnator. As a result, a total of 1,649 CNV regions (CNVRs) were successfully identified after merging all the nine datasets, of which 90 CNVRs were overlapped across all the chicken lines. Within these shared regions, 1,360 harbored genes were identified. In addition, 55 and 44 CNVRs with 62 and 57 harbored genes were specifically identified in line 63 and 72, respectively. Bioinformatics analysis showed that the nearby genes were significantly enriched in 36 GO terms and 6 KEGG pathways including JAK/STAT signaling pathway. Ten CNVRs (nine deletions and one duplication) involved in 10 disease-related genes were selected for validation by using qRT-PCR, all of which were successfully confirmed. Finally, qRT-PCR was also used to validate two deletion events in line 72 that were definitely normal in line 63. One high-confidence gene, IRF2 was identified as the most promising candidate gene underlying MD in view of its function and overlaps with previous study.
Conclusions: Our findings provide valuable insights for understanding the genetic mechanism of resistance to MD and the identified gene and pathway could be considered as the subject of further functional characterization.
Genetic Diversity of Kedah Kelantan Cattle Breed and Its Crossbred types in Malaysia Based on Microsatellite Markers
Authors: Abdelwahid Haytham Hago , Panandam Jothi M , Sharma Reuben S K , Yaakub Halimatun 
Published: August 2019

Abstract
Background

The Kedah Kelantan (KK) is the indigenous cattle breed of Malaysia and is mainly kept by small farmers for meat production because of its small and compact body, and low maintenance requirement. This breed faces risk of germplasm dilution due to extensive crossbreeding and breeds replacement practices in the country. The population size of purebred KK is fast decreasing and most of the commercial populations are actually crossbreds. There is a lack of information on the genetic characteristics of KK. The genetic relationships between the KK, the synthetic breeds developed using the KK as the maternal line, as well as the non-descriptive KK crossbred types are also unknown. It is with these in mind that the present study was conducted. The objective of the study was to evaluate the genetic variability within and among the indigenous KK cattle and its crossbred types in Malaysia using 30 microsatellites loci.

Results

All the 30 microsatellites loci used were polymorphic in all populations. Heterozygosity values observed were moderate and lower than the expected values. The inbreeding was present in all populations and could lead to loss of genetic diversity if not addressed. In general, the genetic differentiation measures were moderate, with a mean FST of 0.054. The structure analysis grouped the populations into three clusters. Analysis of zebu and taurine diagnostic alleles showed that all population had high proportion of Indian zebu alleles and very low proportions of African taurine and European taurine diagnostic alleles.

Conclusions

It may be concluded that there is still some genetic variation present in the KK. However, this genetic diversity is at risk of being lost if no appropriate breeding practices are implemented.