bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence and factors associated with tobacco use among men in India: findings from a nationally representative data
Authors: Islam Md Shariful , Saif-Ur-Rahman K. M. , Bulbul Md. Mofijul Islam , Singh Deepak 
Published: October 2020

Abstract
Background
Tobacco consumption causes almost 638,000 premature deaths per year in India. This study sought to examine the prevalence and determinants of tobacco use among men in India.

Methods
We analyzed data from the fourth round of the National Family Health Survey in India. These nationally representative cross-sectional sample data were collected from January 20, 2015, to December 4, 2016. A total of 112,122 men aged 15–54 years were included in this study. Primary outcomes were tobacco use categorized into smoking, smokeless, any tobacco, and both smoked and smokeless tobacco use. Complex survey design and sampling weights were applied in both the descriptive analyses and logistic regression models. We present the findings using odds ratios.

Results
The prevalence of tobacco use among men in India for the studied period was 45.5% (95% CI 44.9–46.1), smoking was 24.6% (95% CI 24.1–25.1), smokeless tobacco use was 29.1% (95% CI 28.6–29.6), and both smoked and smokeless tobacco use was 8.4% (95% CI 8.1–8.7). The prevalence of tobacco use among men was higher among the elderly, separated/divorced/widowed individuals, those with lower education and wealth status, alcohol consumers, manual workers, and residents of the northeast region. Multivariate analysis showed that age, lower education, occupation, region, alcohol consumption, separated/divorced/widowed status, and economic status were substantially associated with tobacco use among Indian men.

Conclusions
Innovative and cost-effective strategies targeting high-risk groups are crucial to curbing the tobacco epidemic in India. Anti-smoking campaigns should also focus on mitigating alcohol abuse. Reducing tobacco marketing and implementing formal education about the dangers of tobacco use, progressive taxing, packaging, and labeling of tobacco products and price strategies should be harmonized in legal provisions.
Regional difference in semen quality of young men: a review on the implication of environmental and lifestyle factors during fetal life and adulthood
Authors: Rahban Rita , Nef Serge 
Published: October 2020

AbstractThe prevalence of low semen quality and the incidence of testicular cancer have been steadily increasing over the past decades in different parts of the World. Although these conditions may have a genetic or epigenetic origin, there is growing evidence that multiple environmental and lifestyle factors can act alone or in combination to induce adverse effects. Exposure to these factors may occur as early as during fetal life, via the mother, and directly throughout adulthood after full spermatogenic capacity is reached. This review aims at providing an overview of past and current trends in semen quality and its relevance to fertility as well as a barometer of men’s general health. The focus will be on recent epidemiological studies of young men from the general population highlighting geographic variations in Europe. The impact of some lifestyle and environmental factors will be discussed with their role in both fetal life and adulthood. These factors include smoking, alcohol consumption, psychological stress, exposure to electromagnetic radiation, and Endocrine Disrupting Chemicals (EDCs). Finally, the challenges in investigating the influence of environmental factors on semen quality in a fast changing world are presented.
Why breed disease-resilient livestock, and how?
Authors: Knap Pieter W. , Doeschl-Wilson Andrea 
Published: October 2020

AbstractBackgroundFighting and controlling epidemic and endemic diseases represents a considerable cost to livestock production. Much research is dedicated to breeding disease resilient livestock, but this is not yet a common objective in practical breeding programs. In this paper, we investigate how future breeding programs may benefit from recent research on disease resilience.Main bodyWe define disease resilience in terms of its component traits resistance (R: the ability of a host animal to limit within-host pathogen load (PL)) and tolerance (T: the ability of an infected host to limit the damage caused by a given PL), and model the host's production performance as a reaction norm on PL, depending on R and T. Based on this, we derive equations for the economic values of resilience and its component traits. A case study on porcine respiratory and reproductive syndrome (PRRS) in pigs illustrates that the economic value of increasing production in infectious conditions through selection for R and T can be more than three times higher than by selection for production in disease-free conditions. Although this reaction norm model of resilience is helpful for quantifying its relationship to its component traits, its parameters are difficult and expensive to quantify. We consider the consequences of ignoring R and T in breeding programs that measure resilience as production in infectious conditions with unknown PL—particularly, the risk that the genetic correlation between R and T is unfavourable (antagonistic) and that a trade-off between them neutralizes the resilience improvement. We describe four approaches to avoid such antagonisms: (1) by producing sufficient PL records to estimate this correlation and check for antagonisms—if found, continue routine PL recording, and if not found, shift to cheaper proxies for PL; (2) by selection on quantitative trait loci (QTL) known to influence both R and T in favourable ways; (3) by rapidly modifying towards near-complete resistance or tolerance, (4) by re-defining resilience as the animal's capacity to resist (or recover from) the perturbation caused by an infection, measured as temporal deviations of production traits in within-host longitudinal data series.ConclusionsAll four alternatives offer promising options for genetic improvement of disease resilience, and most rely on technological and methodological developments and innovation in automated data generation.
MCCMF: collaborative matrix factorization based on matrix completion for predicting miRNA-disease associations
Authors: Wu Tian-Ru , Yin Meng-Meng , Jiao Cui-Na , Gao Ying-Lian , Kong Xiang-Zhen , Liu Jin-Xing 
Published: October 2020

AbstractBackgroundMicroRNAs (miRNAs) are non-coding RNAs with regulatory functions. Many studies have shown that miRNAs are closely associated with human diseases. Among the methods to explore the relationship between the miRNA and the disease, traditional methods are time-consuming and the accuracy needs to be improved. In view of the shortcoming of previous models, a method, collaborative matrix factorization based on matrix completion (MCCMF) is proposed to predict the unknown miRNA-disease associations.ResultsThe complete matrix of the miRNA and the disease is obtained by matrix completion. Moreover, Gaussian Interaction Profile kernel is added to the miRNA functional similarity matrix and the disease semantic similarity matrix. Then the Weight K Nearest Known Neighbors method is used to pretreat the association matrix, so the model is close to the reality. Finally, collaborative matrix factorization method is applied to obtain the prediction results. Therefore, the MCCMF obtains a satisfactory result in the fivefold cross-validation, with an AUC of 0.9569 (0.0005).ConclusionsThe AUC value of MCCMF is higher than other advanced methods in the fivefold cross validation experiment. In order to comprehensively evaluate the performance of MCCMF, accuracy, precision, recall and f-measure are also added. The final experimental results demonstrate that MCCMF outperforms other methods in predicting miRNA-disease associations. In the end, the effectiveness and practicability of MCCMF are further verified by researching three specific diseases.
Assessment and molecular characterization of Bacillus cereus isolated from edible fungi in China
Authors: Liu Chengcheng , Yu Pengfei , Yu Shubo , Wang Juan , Guo Hui , Zhang Ying , Zhang Junhui , Liao Xiyu , Li Chun , Wu Shi , Gu Qihui , Zeng Haiyan , Zhang Youxiong , Wei Xianhu , Zhang Jumei , Wu Qingping , Ding Yu 
Published: October 2020

Abstract
Background
Bacillus cereus is a foodborne pathogen commonly found in nature and food and can cause food spoilage and health issues. Although the prevalence of B. cereus in foods has been reported worldwide, the extent of contamination in edible fungi, which has become increasingly popular as traditional or functional food, is largely unknown. Here we investigated the prevalence, toxin genes’ distribution, antibiotic resistance, and genetic diversity of B. cereus isolated from edible fungi in China.

Results
Six hundred and ninety-nine edible fungi samples were collected across China, with 198 (28.3%) samples found to be contaminated by B. cereus, with an average contamination level of 55.4 most probable number (MPN)/g. Two hundred and forty-seven B. cereus strains were isolated from the contaminated samples. Seven enterotoxin genes and one cereulide synthetase gene were detected. The detection frequencies of all enterotoxin genes were ≥ 80%, whereas the positive rate of the cesB gene in B. cereus was 3%. Most isolates were resistant to penicillins, β-lactam/β-lactamase inhibitor combinations, cephems, and ansamycins, but were susceptible to penems, aminoglycosides, macrolides, ketolide, glycopeptides, quinolones, phenylpropanol, tetracyclines, lincosamides, streptogramins, and nitrofurans. Meanwhile, 99.6% of all isolates displayed multiple antimicrobial resistance to three or more classes of antimicrobials. Using genetic diversity analysis, all isolates were defined in 171 sequence types (STs), of which 83 isolates were assigned to 78 new STs.

Conclusions
This study provides large-scale insight into the prevalence and potential risk of B. cereus in edible fungi in China. Approximately one-third of the samples were contaminated with B. cereus, and almost all isolates showed multiple antimicrobial resistance. Detection frequencies of all seven enterotoxin genes were equal to or more than 80%. These new findings may indicate a need for proper pre-/post-processing of edible fungi to eliminate B. cereus, thereby preventing the potential risk to public health.
Molecular cytological analysis of alien introgressions in common wheat lines derived from the cross of TRITICUM AESTIVUM with T. kiharae
Authors: Orlovskaya Оlga , Dubovets Nadezhda , Solovey Lylia , Leonova Irina 
Published: October 2020

Abstract
Background
Triticum kiharae (AtAtGGDD, 2n = 42) is of interest for the improvement of bread wheat as a source of high grain protein and gluten content, as well as resistance to many diseases. The use of T. kiharae for the improvement of T. aestivum L. is complicated by the fact that the homology degree of their genomes is low and this leads to an unbalanced set of chromosomes in the gametes of its first generations and the elimination of some genotypes. The aim of this study was to analyze the nature of alien introgressions and their effect on the cytological stability of hybrids obtained from crossing of bread wheat varieties with T. kiharae.

Results
Using C-banding, the presence of entire chromosomes of T. kiharae in the karyotypes of hybrid lines (intergenomic substitution 2G/2B), chromosome arms (centric translocation Т2AtS:2AL) and large inserts in the form of terminal translocations involving chromosomes of 1st, 3rd and 5th homoeologous groups of B- and G-genomes were found. Molecular markers revealed short introgression of T. kiharae into the genome of common wheat varieties. The highest introgression frequency was shown for 1A, 1B, 2A, 5B, and 6A chromosomes, while no foreign chromatin was detected in 4A and 4B chromosomes. A high level of cytological stability (a meiotic index of 88.18–93.0%) was noted for the majority of introgression lines. An exception was found for the lines containing the structural reorganization of chromosome 5B, affecting the main genes of chromosome synapsis in terms of their functioning.

Conclusions
During the stabilization of hybrid karyotypes, the introgression of genetic material from T. kiharae into the genome of T. aestivum occurs in the form of short fragments detectable only by molecular markers and in the form of whole chromosomes (intergenomic substitution) and their large fragments (centric and terminal translocations). The level of cytological stability achieved in F10 by the majority of introgression lines ensures the formation of functional gametes sufficient for the successful reproduction of the obtained hybrids.
Genetic diversity of SAD and FAD genes responsible for the fatty acid composition in flax cultivars and lines
Authors: Dmitriev Alexey A. , Kezimana Parfait , Rozhmina Tatiana A. , Zhuchenko Alexander A. , Povkhova Liubov V. , Pushkova Elena N. , Novakovskiy Roman O. , Pavelek Martin , Vladimirov Gleb N. , Nikolaev Evgeny N. , Kovaleva Oxana A. , Kostyukevich Yury I. , Chagovets Vitaliy V. , Romanova Elena V. , Snezhkina Anastasiya V. , Kudryavtseva Anna V. , Krasnov George S. , Melnikova Nataliya V. 
Published: October 2020

Abstract
Background
Flax (Linum usitatissimum L.) is grown for fiber and seed in many countries. Flax cultivars differ in the oil composition and, depending on the ratio of fatty acids, are used in pharmaceutical, food, or paint industries. It is known that genes of SAD (stearoyl-ACP desaturase) and FAD (fatty acid desaturase) families play a key role in the synthesis of fatty acids, and some alleles of these genes are associated with a certain composition of flax oil. However, data on genetic polymorphism of these genes are still insufficient.

Results
On the basis of the collection of the Institute for Flax (Torzhok, Russia), we formed a representative set of 84 cultivars and lines reflecting the diversity of fatty acid composition of flax oil. An approach for the determination of full-length sequences of SAD1, SAD2, FAD2A, FAD2B, FAD3A, and FAD3B genes using the Illumina platform was developed and deep sequencing of the 6 genes in 84 flax samples was performed on MiSeq. The obtained high coverage (about 400x on average) enabled accurate assessment of polymorphisms in SAD1, SAD2, FAD2A, FAD2B, FAD3A, and FAD3B genes and evaluation of cultivar/line heterogeneity. The highest level of genetic diversity was observed for FAD3A and FAD3B genes – 91 and 62 polymorphisms respectively. Correlation analysis revealed associations between particular variants in SAD and FAD genes and predominantly those fatty acids whose conversion they catalyze: SAD – stearic and oleic acids, FAD2 – oleic and linoleic acids, FAD3 – linoleic and linolenic acids. All except one low-linolenic flax cultivars/lines contained both the substitution of tryptophan to stop codon in the FAD3A gene and histidine to tyrosine substitution in the FAD3B gene, while samples with only one of these polymorphisms had medium content of linolenic acid and cultivars/lines without them were high-linolenic.

Conclusions
Genetic polymorphism of SAD and FAD genes was evaluated in the collection of flax cultivars and lines with diverse oil composition, and associations between particular polymorphisms and the ratio of fatty acids were revealed. The achieved results are the basis for the development of marker-assisted selection and DNA-based certification of flax cultivars.
Effects of Rht17 in combination with Vrn-B1 and Ppd-D1 alleles on agronomic traits in wheat in black earth and non-black earth regions
Authors: Kroupin Pavel Yu. , Karlov Gennady I. , Bespalova Ludmila A. , Salina Elena A. , Chernook Anastasiya G. , Watanabe Nobuyoshi , Bazhenov Mikhail S. , Panchenko Vladimir V. , Nazarova Lubov A. , Kovtunenko Victor Ya. , Divashuk Mikhail G. 
Published: October 2020

Abstract
Background
Plant height is an important wheat trait that is regulated by multiple genes, among which Rht is of the utmost value. In wheat, Rht-B1p (=Rht17) is a mutant allele of the Rht gene that encodes for a DELLA-protein and results in the development of gibberellin-insensitive plants with a dwarfing phenotype. The pleiotropic effects of dwarfing genes on yield are highly dependent on both the genetic background and the environmental conditions. In Russia, the Central Non-Black Earth Region and Krasnodar Krai are two economically important regions that require differing management for sustainable wheat production for food, feed and industry. The purpose of our study was to compare the pleiotropic effects of Rht-B1p on the main valuable agronomic traits in the F3:4 families of the spring bread wheat Chris Mutant/Novosibirskaya 67 in the genetic background of Vrn-B1a/vrn-B1 (spring/winter phenotype) and Ppd-D1a/Ppd-D1b (insensitivity/sensitivity to photoperiod) alleles in a field experiment in Moscow and Krasnodar Krai.

Results
Plant height was reduced on average by 21 cm (28%) and 25 cm (30%), respectively; Ppd-D1a slightly strengthened the dwarfing effect in Moscow and mitigated it in Krasnodar Krai. Grain weight of the main spike was reduced by Rht-B1p in Moscow and to lesser extent in Krasnodar; Ppd-D1a and Vrn-B1a tended to partially compensate for this loss in Krasnodar Krai. Thousand grain weight was reduced on average by 5.3 g (16%) and 2.9 g (10%) in Moscow and Krasnodar Krai, respectively, but was partially compensated for by Ppd-D1a in Krasnodar Krai. Harvest index was increased due to Rht-B1p by 6 and 10% in Moscow and Krasnodar Krai, respectively. Rht-B1p resulted in a delay of heading by 1–2 days in Moscow. Ppd-D1a accelerated heading by 1 day and 6 days in Moscow and in Krasnodar Krai, respectively.

Conclusions
Rht-B1p could be introduced into wheat breeding along with dwarfing genes such as Rht-B1b and Rht-D1b. Special attention should be paid to its combination with Ppd-D1a and Vrn-B1a as regulators of developmental rates, compensators of adverse effects of Rht-B1p on productivity and enhancers of positive effect of Rht-B1p on harvest index.
Two divergent chloroplast genome sequence clades captured in the domesticated rice gene pool may have significance for rice production
Authors: Moner Ali Mohammad , Furtado Agnelo , Henry Robert J. 
Published: October 2020

Abstract
Background
The whole chloroplast genomes of 3018 rice genotypes were assembled from available sequence data by alignment with a reference rice chloroplast genome sequence, providing high quality chloroplast genomes for analysis of diversity on a much larger scale than in any previous plant study.

Results
Updated annotation of the chloroplast genome identified 13 more tRNA genes and 30 more introns and defined the function of more of the genes. Domesticated rice had chloroplast genomes that were distinct from those in wild relatives. Analysis confirms an Australian chloroplast clade as a sister to the domesticated clade. All domesticated rice genotypes could be assigned to one of two main clades suggesting the domestication of two distinct maternal genome clades that diverged long before domestication. These clades were very distinct having 4 polymorphisms between all 1486 accession in clade A and all 1532 accessions in clade B. These would result in expression of 3 proteins with altered amino acid sequences and a tRNA with an altered sequence and may be associated with adaptive evolution of the two chloroplast types. Diversity within these pools may have been captured during domestication with subclades enriched in specific groups such as basmati, tropical japonica and temperate japonica. However the phylogenies of the chloroplast and nuclear genomes differed possibly due to modern rice breeding and reticulate evolution prior to domestication. Indica and aus genotypes were common in both chloroplast clades while japonica genotypes were more likely to be found in the same clade (cladeB).

Conclusions
The different evolutionary paths of the cytoplasmic and nuclear genomes of rice have resulted in the presence of apparently functional chloroplast genome diversity and the implications for rice crop performance require further investigation.
Cardiac symptom attribution and knowledge of the symptoms of acute myocardial infarction: a systematic review
Authors: Birnbach Benedikt , Höpner Jens , Mikolajczyk Rafael 
Published: October 2020

AbstractBackgroundSince the knowledge of the symptoms of acute myocardial infarction (AMI) may reduce the decision time for patients to seek help in case of an AMI, we aimed to summarize evidence on the knowledge of the AMI symptoms and the symptom attribution in case of an acute coronary syndrome (ACS).MethodsTherefore, we systematically searched the databases PubMed, CINAHL, Embase, and Cochrane Library for relevant studies published between January 1, 2008 and 2019 (last search August 1, 2019).ResultsA total of 86 studies were included, with a composite sample size of 354,497 participants. The weighted mean of the knowledge scores for the symptoms of AMI of 14,420 participants from the general population, was 42.1% (when maximum score was considered 100%) and 69.5% for 7642 cardiac patients. There was a substantially better level of knowledge for six symptoms (‘chest pain or discomfort’, ‘shortness of breath’, ‘pain or discomfort in arms or shoulders’, ‘feeling weak, lightheaded, or faint’, ‘pain or discomfort in the jaw, neck, or back’, and ‘sweating’) (49.8–88.5%) compared to the four less obvious/atypical symptoms ‘stomach or abdominal discomfort’, ‘nausea or vomiting’, ‘headache’, and ‘feeling of anxiety’ (8.7–36.7%). Only 45.1% of 14,843 patients, who experienced ACS, have correctly attributed their symptoms to a cardiac cause.ConclusionIn conclusion, we found a moderate to good knowledge of “classic” and insufficient knowledge of less obvious symptoms of AMI. This might suggest that increasing knowledge about less obvious symptoms of AMI could be beneficial. It appears also important to address cardiac attribution of symptoms.