bluuebunny/crossref_metadata_2025_split huggingface dataset:
The relationship between headache-attributed disability and lost productivity: 1. A review of the literature
Authors: Kothari Simple Futarmal , Jensen Rigmor Hølland , Steiner Timothy J 
Published: July 2021

AbstractBackgroundHeadache disorders are disabling and have a significant impact on productivity. The relationship between these two consequences is of considerable economic and political interest. We enquired into it through a systematic search of the English-language literature.MethodsWe followed PRISMA guidelines in specifying search terms and syntax and in article selection. We used the term “disability” in the search, accepting any meaning that authors attached to it, but this proved problematic. Accordingly, we adopted the definition used in the Global Burden of Disease study. In article selection, we included only those that purported to measure disability as so defined and lost productivity. We reviewed the full texts of those selected. We included further articles identified from review of the bibliographies of selected articles.ResultsThe literature search found 598 studies, of which 21 warranted further review. Their bibliographies identified another four of possible relevance. On full-text reading of these 25, all were rejected. Ten applied incompatible definitions of disability and/or lost productivity. Two did not measure both. Four reported lost productivity but not disability. Eight studies reported and measured both but did not assess the association between them or provide the means of doing so. One was purely methodological.ConclusionsThe literature is silent on the relationship between headache-attributed disability and lost productivity. In view of its health economic and political importance, empirical studies are required to remedy this. A prerequisite is to clarify what is meant by “disability” in this context.
Classes of childhood adversities and their associations to the mental health of college undergraduates: a nationwide cross-sectional study
Authors: Wang Peigang , Kelifa Mohammedhamid Osman , Yu Bin , Yang Yinmei 
Published: July 2021

Abstract
Background
Childhood adversities pose deleterious consequences on health and well-being, but limited studies explore whether unique patterns of adverse childhood experiences (ACEs) impact the mental health of emerging adults and the mediating role of current stressful events (CSEs). This study examined classes of ACEs and how they relate to CSEs, psychological distress, and subjective well-being among Eritrean College undergraduates.

Methods
Cross-sectional data on ACEs, CSEs, symptoms of psychological distress, and subjective well-being were collected from a national sample of college students (N = 507). We identified ACE patterns using latent class analysis and further examined whether CSEs mediated the effects of ACE classes on psychological distress and subjective well-being.

Results
86.4% of the sample experienced at least one ACE. Collective violence, domestic violence, and physical abuse were the most common ACEs. Three subgroups, low ACEs (66.3%), household violence (19.1%), and multiple ACEs (14.6%) were identified. We found that relative to low ACEs, household violence (β = 0.142, 95% CI 0.046, 0.248) and multiple ACEs (β = 0.501, 95% CI 0.357, 0.666) indirectly influenced psychological distress through CSEs, and CSEs mediated the relationships between household violence (β = −0.096, 95% CI −0.176, −0.033), multiple ACEs (β = −0.338, 95% CI −0.498, −0.210), and subjective well-being. However, there were nonsignificant relative direct effects of ACE patterns on both psychological distress and subjective well-being.

Conclusions
Experiencing multiple ACEs and household violence in conjunction with CSEs significantly predict psychological distress and subjective well-being. Contextual interventions for the early identification of ACEs and the management of CSEs may play a crucial role in the prevention of mental health problems.
Impact of birth season on the years of life lost from respiratory diseases in the elderly related to ambient PM2.5 exposure in Ningbo, China
Authors: Yang Teng , He Tianfeng , Huang Jing , Li Guoxing 
Published: July 2021

Abstract
Background
Ambient fine particle (PM2.5) pollution is an important public health problem in China. Short-term ambient PM2.5 exposure is associated with increased mortality of respiratory diseases. However, few evidence was available on the effect of exposure to ambient PM2.5 on the years of life lost (YLL) from respiratory diseases in the elderly. Furthermore, birth season which is frequently applied as a proxy for environmental exposure in early life may influence the health outcome in the later life. Nevertheless, the modification effect of birth season on the relationship of PM2.5 exposure and respiratory health need to be explored.

Methods
A time-stratified case-crossover design was used to analyze YLL from respiratory diseases in the elderly related to ambient PM2.5 exposure between 2013 and 2016 in Ningbo, China. The modification effect of birth season was explored by subgroup comparisons between different birth seasons.

Results
Each 10 μg/m3 increase in daily ambient PM2.5 was associated with an increment of 1.61 (95% CI 0.12, 3.10) years in YLL from respiratory diseases in the elderly population. Individuals who were born in winter had significantly higher YLL from respiratory diseases associated with ambient PM2.5 exposure than those who were born in other seasons.

Conclusions
Birth season which reflects the early-life PM2.5 exposure level that may influence the lung development has a potential effect on the disease burden of respiratory diseases related to ambient PM2.5 exposure in later life. The results would provide theoretical basis to protect vulnerable population defined by birth season when exploring the adverse effects of ambient PM2.5 in the respiratory health.
Similar improvements in cognitive inhibitory control following low-intensity resistance exercise with slow movement and tonic force generation and high-intensity resistance exercise in healthy young adults: a preliminary study
Authors: Dora Kento , Suga Tadashi , Tomoo Keigo , Sugimoto Takeshi , Mok Ernest , Tsukamoto Hayato , Takada Shingo , Hashimoto Takeshi , Isaka Tadao 
Published: July 2021

AbstractThis study compared the effects of low-intensity resistance exercise with slow movement and tonic force generation (ST-LRE) and high-intensity resistance exercise (HRE) on post-exercise improvements in cognitive inhibitory control (IC). Sixteen young males completed ST-LRE and HRE sessions in a crossover design. Bilateral knee extensor ST-LRE and HRE (8 repetitions/set, 6 sets) were performed with 50% of one-repetition maximum with slow contractile speed and 80% of one-repetition maximum with normal contractile speed, respectively. The IC was assessed using the color–word Stroop task at six time points: baseline, pre-exercise, immediate post-exercise, and every 10 min during the 30-min post-exercise recovery period. The blood lactate response throughout the experimental session did not differ between ST-LRE and HRE (condition × time interaction P = 0.396: e.g., mean ± standard error of the mean; 8.1 ± 0.5 vs. 8.1 ± 0.5 mM, respectively, immediately after exercise, P = 0.983, d = 0.00). Large-sized decreases in the reverse-Stroop interference scores, which represent improved IC, compared to those before exercise (i.e., baseline and pre-exercise) were observed throughout the 30 min post-exercise recovery period for both ST-LRE and HRE (decreasing rate ≥ 38.8 and 41.4%, respectively, all ds ≥ 0.95). The degree of post-exercise IC improvements was similar between the two protocols (condition × time interaction P = 0.998). These findings suggest that despite the application of a lower exercise load, ST-LRE improves post-exercise IC similarly to HRE, which may be due to the equivalent blood lactate response between the two protocols, in healthy young adults.
Accurate plant pathogen effector protein classification ab initio with deepredeff: an ensemble of convolutional neural networks
Authors: Kristianingsih Ruth , MacLean Dan 
Published: July 2021

Abstract
Background
Plant pathogens cause billions of dollars of crop loss every year and are a major threat to global food security. Effector proteins are the tools such pathogens use to infect the cell, predicting effectors de novo from sequence is difficult because of the heterogeneity of the sequences. We hypothesised that deep learning classifiers based on Convolutional Neural Networks would be able to identify effectors and deliver new insights.

Results
We created a training set of manually curated effector sequences from PHI-Base and used these to train a range of model architectures for classifying bacteria, fungal and oomycete sequences. The best performing classifiers had accuracies from 93 to 84%. The models were tested against popular effector detection software on our own test data and data provided with those models. We observed better performance from our models. Specifically our models showed greater accuracy and lower tendencies to call false positives on a secreted protein negative test set and a greater generalisability. We used GRAD-CAM activation map analysis to identify the sequences that activated our CNN-LSTM models and found short but distinct N-terminal regions in each taxon that was indicative of effector sequences. No motifs could be observed in these regions but an analysis of amino acid types indicated differing patterns of enrichment and depletion that varied between taxa.

Conclusions
Small training sets can be used effectively to train highly accurate and sensitive deep learning models without need for the operator to know anything other than sequence and without arbitrary decisions made about what sequence features or physico-chemical properties are important. Biological insight on subsequences important for classification can be achieved by examining the activations in the model
Post-genotyping optimization of dataset formation could affect genetic diversity parameters: an example of analyses with alpine goat breeds
Authors: Pogorevc Neža , Simčič Mojca , Khayatzadeh Negar , Sölkner Johann , Berger Beate , Bojkovski Danijela , Zorc Minja , Dovč Peter , Medugorac Ivica , Horvat Simon 
Published: July 2021

Abstract
Background
Local breeds retained unique genetic variability important for adaptive potential especially in light of challenges related to climate change. Our first objective was to perform, for the first time, a genome-wide diversity characterization using Illumina GoatSNP50 BeadChip of autochthonous Drežnica goat breed from Slovenia, and five and one local breeds from neighboring Austria and Italy, respectively. For optimal conservation and breeding programs of endangered local breeds, it is important to detect past admixture events and strive for preservation of purebred representatives of each breed with low or without admixture. In the second objective, we hence investigated the effect of inclusion or exclusion of outliers from datasets on genetic diversity and population structure parameters.

Results
Distinct genetic origin of the Drežnica goat was demonstrated as having closest nodes to Austrian and Italian breeds. A phylogenetic study of these breeds with other goat breeds having SNP data available in the DRYAD repository positioned them in the alpine, European and global context. Swiss breeds clustered with cosmopolitan alpine breeds and were closer to French and Spanish breeds. On the other hand, the Drežnica goat, Austrian and Italian breeds were closer to Turkish breeds. Datasets where outliers were excluded affected estimates of genetic diversity parameters within the breed and increased the pairwise genetic distances between most of the breeds. Alpine breeds, including Drežnica, Austrian and Italian goats analyzed here, still exhibit relatively high levels of genetic variability, homogeneous genetic structure and strong geographical partitioning.

Conclusions
Genetic diversity analyses revealed that the Slovenian Drežnica goat has a distinct genetic identity and is closely related to the neighboring Austrian and Italian alpine breeds. These results expand our knowledge on phylogeny of goat breeds from easternmost part of the European Alps. The here employed outlier test and datasets optimization approaches provided an objective and statistically powerful tool for removal of admixed outliers. Importance of this test in selecting the representatives of each breed is warranted to obtain more objective diversity parameters and phylogenetic analysis. Such parameters are often the basis of breeding and management programs and are therefore important for preserving genetic variability and uniqueness of local rare breeds.
ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw
Authors: Milosavljevic Stefan , Kuo Tony , Decarli Samuele , Mohn Lucas , Sese Jun , Shimizu Kentaro K. , Shimizu-Inatsugi Rie , Robinson Mark D. 
Published: July 2021

Abstract
Background
Whole genome duplication (WGD) events are common in the evolutionary history of many living organisms. For decades, researchers have been trying to understand the genetic and epigenetic impact of WGD and its underlying molecular mechanisms. Particular attention was given to allopolyploid study systems, species resulting from an hybridization event accompanied by WGD. Investigating the mechanisms behind the survival of a newly formed allopolyploid highlighted the key role of DNA methylation. With the improvement of high-throughput methods, such as whole genome bisulfite sequencing (WGBS), an opportunity opened to further understand the role of DNA methylation at a larger scale and higher resolution. However, only a few studies have applied WGBS to allopolyploids, which might be due to lack of genomic resources combined with a burdensome data analysis process. To overcome these problems, we developed the Automated Reproducible Polyploid EpiGenetic GuIdance workflOw (ARPEGGIO): the first workflow for the analysis of epigenetic data in polyploids. This workflow analyzes WGBS data from allopolyploid species via the genome assemblies of the allopolyploid’s parent species. ARPEGGIO utilizes an updated read classification algorithm (EAGLE-RC), to tackle the challenge of sequence similarity amongst parental genomes. ARPEGGIO offers automation, but more importantly, a complete set of analyses including spot checks starting from raw WGBS data: quality checks, trimming, alignment, methylation extraction, statistical analyses and downstream analyses. A full run of ARPEGGIO outputs a list of genes showing differential methylation. ARPEGGIO was made simple to set up, run and interpret, and its implementation ensures reproducibility by including both package management and containerization.

Results
We evaluated ARPEGGIO in two ways. First, we tested EAGLE-RC’s performance with publicly available datasets given a ground truth, and we show that EAGLE-RC decreases the error rate by 3 to 4 times compared to standard approaches. Second, using the same initial dataset, we show agreement between ARPEGGIO’s output and published results. Compared to other similar workflows, ARPEGGIO is the only one supporting polyploid data.

Conclusions
The goal of ARPEGGIO is to promote, support and improve polyploid research with a reproducible and automated set of analyses in a convenient implementation. ARPEGGIO is available at https://github.com/supermaxiste/ARPEGGIO.
Deploying new generation sequencing for the study of flesh color depletion in Atlantic Salmon (Salmo salar)
Authors: Vo Thu Thi Minh , Nguyen Tuan Viet , Amoroso Gianluca , Ventura Tomer , Elizur Abigail 
Published: July 2021

Abstract
Background
The flesh pigmentation of farmed Atlantic salmon is formed by accumulation of carotenoids derived from commercial diets. In the salmon gastrointestinal system, the hindgut is considered critical in the processes of carotenoids uptake and metabolism. In Tasmania, flesh color depletion can noticeably affect farmed Atlantic salmon at different levels of severity following extremely hot summers. In this study, RNA sequencing (RNA-Seq) was performed to investigate the reduction in flesh pigmentation. Library preparation is a key step that significantly impacts the effectiveness of RNA sequencing (RNA-Seq) experiments. Besides the commonly used whole transcript RNA-Seq method, the 3’ mRNA-Seq method is being applied widely, owing to its reduced cost, enabling more repeats to be sequenced at the expense of lower resolution. Therefore, the output of the Illumina TruSeq kit (whole transcript RNA-Seq) and the Lexogen QuantSeq kit (3’ mRNA-Seq) was analyzed to identify genes in the Atlantic salmon hindgut that are differentially expressed (DEGs) between two flesh color phenotypes.

Results
In both methods, DEGs between the two color phenotypes were associated with metal ion transport, oxidation-reduction processes, and immune responses. We also found DEGs related to lipid metabolism in the QuantSeq method. In the TruSeq method, a missense mutation was detected in DEGs in different flesh color traits. The number of DEGs found in the TruSeq libraries was much higher than the QuantSeq; however, the trend of DEGs in both library methods was similar and validated by qPCR.

Conclusions
Flesh coloration in Atlantic salmon is related to lipid metabolism in which apolipoproteins, serum albumin and fatty acid-binding protein genes are hypothesized to be linked to the absorption, transport and deposition of carotenoids. Our findings suggest that Grp could inhibit the feeding behavior of low color-banded fish, resulting in the dietary carotenoid shortage. Several SNPs in genes involving in carotenoid-binding cholesterol and oxidative stress were detected in both flesh color phenotypes. Regarding the choice of the library preparation method, the selection criteria depend on the research design and purpose. The 3’ mRNA-Seq method is ideal for targeted identification of highly expressed genes, while the whole RNA-Seq method is recommended for identification of unknown genes, enabling the identification of splice variants and trait-associated SNPs, as we have found for duox2 and duoxa1.
Detection of Legionella species, the influence of precipitation on the amount of Legionella DNA, and bacterial microbiome in aerosols from outdoor sites near asphalt roads in Toyama Prefecture, Japan
Authors: Kanatani Jun-ichi , Watahiki Masanori , Kimata Keiko , Kato Tomoko , Uchida Kaoru , Kura Fumiaki , Amemura-Maekawa Junko , Isobe Junko 
Published: July 2021

AbstractBackgroundLegionellosis is caused by the inhalation of aerosolized water contaminated withLegionellabacteria. In this study, we investigated the prevalence ofLegionellaspecies in aerosols collected from outdoor sites near asphalt roads, bathrooms in public bath facilities, and other indoor sites, such as buildings and private homes, using amoebic co-culture, quantitative PCR, and 16S rRNA gene amplicon sequencing.ResultsLegionellaspecies were not detected by amoebic co-culture. However,LegionellaDNA was detected in 114/151 (75.5%) air samples collected near roads (geometric mean ± standard deviation: 1.80 ± 0.52 log10copies/m3), which was comparable to the numbers collected from bathrooms [15/21 (71.4%), 1.82 ± 0.50] but higher than those collected from other indoor sites [11/30 (36.7%), 0.88 ± 0.56] (P < 0.05). The amount ofLegionellaDNA was correlated with the monthly total precipitation (r = 0.56,P < 0.01). It was also directly and inversely correlated with the daily total precipitation for seven days (r = 0.21,P = 0.01) and one day (r = − 0.29,P < 0.01) before the sampling day, respectively. 16S rRNA gene amplicon sequencing revealed thatLegionellaspecies were detected in 9/30 samples collected near roads (mean proportion of reads, 0.11%). At the species level,L. pneumophilawas detected in 2/30 samples collected near roads (the proportion of reads, 0.09 and 0.11% of the total reads number in each positive sample). The three most abundant bacterial genera in the samples collected near roads wereSphingomonas,Streptococcus, andMethylobacterium(mean proportion of reads; 21.1%, 14.6%, and 1.6%, respectively). In addition, the bacterial diversity in outdoor environment was comparable to that in indoor environment which contains aerosol-generating features and higher than that in indoor environment without the features.ConclusionsDNA fromLegionellaspecies was widely present in aerosols collected from outdoor sites near asphalt roads, especially during the rainy season. Our findings suggest that there may be a risk of exposure toLegionellaspecies not only in bathrooms but also in the areas surrounding asphalt roads. Therefore, the possibility of contracting legionellosis in daily life should be considered.
TCM-Blast for traditional Chinese medicine genome alignment with integrated resources
Authors: Chen Zhao , Li Jing , Hou Ning , Zhang Yanling , Qiao Yanjiang 
Published: July 2021

AbstractThe traditional Chinese medicine (TCM) genome project aims to reveal the genetic information and regulatory network of herbal medicines, and to clarify their molecular mechanisms in the prevention and treatment of human diseases. Moreover, the TCM genome could provide the basis for the discovery of the functional genes of active ingredients in TCM, and for the breeding and improvement of TCM. The traditional Chinese Medicine Basic Local Alignment Search Tool (TCM-Blast) is a web interface for TCM protein and DNA sequence similarity searches. It contains approximately 40G of genome data on TCMs, including protein and DNA sequence for 36 TCMs with high medical value.The development of a publicly accessible TCM genome alignment database hosted on the TCM-Blast website (http://viroblast.pungentdb.org.cn/TCM-Blast/viroblast.php) has expanded to query multiple sequence databases to obtain TCM genome data, and provide user-friendly output for easy analysis and browsing of BLAST results. The genome sequencing of TCMs helps to elucidate the biosynthetic pathways of important secondary metabolites and provides an essential resource for gene discovery studies and molecular breeding. The TCMs genome provides a valuable resource for the investigation of novel bioactive compounds and drugs from these TCMs under the guidance of TCM clinical practice. Our database could be expanded to other TCMs after the determination of their genome data.