bluuebunny/crossref_metadata_2025 huggingface dataset:
d-Pinitol protects against endoplasmic reticulum stress and apoptosis in hepatic ischemia-reperfusion injury via modulation of AFT4-CHOP/GRP78 and caspase-3 signaling pathways
Authors: Yan Lei , Luo Heng , Li Xingsheng , Li Yongyong
Published: July 2021

Hepatic ischemia-reperfusion injury (IRI) is a major unavoidable clinical problem often accompanying various liver surgery and transplantation. d-Pinitol, a cyclic polyol, exhibits hepatoprotective efficacy. The objective of this study is to determine the possible mechanism of action of pinitol against endoplasmic reticulum (ER) stress regulation-mediated hepatic IRI and compare its effects with thymoquinone (TQ) in experimental rats. Male Sprague Dawley rats were pre-treated orally with either vehicle (DMSO) or d-Pinitol (5, 10, and 20 mg/kg) or TQ (30 mg/kg) for 21 days and subjected to 60 min of partial hepatic ischemia followed by 24 h of reperfusion. Pre-treatment with pinitol (10 and 20 mg/kg) effectively ( P  < 0.05) protected against IRI-induced hepatic damage reflected by attenuation of elevated oxidative stress and pro-inflammatory cytokines. Additionally, western blot and ELISA analyses suggested that pinitol significantly ( P  < 0.05) down-regulated expression of endoplasmic reticulum stress apoptotic markers, namely glucose-regulated protein (GRP)-78, CCAAT/enhancer-binding protein homologous protein (CHOP), activating transcription factor (AFT)-4 and -6α, X-box binding protein-1, and caspase-3, 9, and 12. Additionally, pinitol pre-treatment effectively ( P  < 0.05) improved mitochondrial function and phosphorylation of Extracellular signal-regulated kinase (ERK)-1/2 and p38. Pinitol markedly ( P  < 0.05) protected hepatic apoptosis determined by flow cytometry. Further, pinitol provided effective ( P  < 0.05) protection against hepatic histological and ultrastructural aberrations induced by IRI. TQ showed more pronounced protective effect against attenuation of IRI-induced hepatic injury as compared to d-Pinitol. Pinitol offered protection against endoplasmic reticulum stress-mediated phosphorylation of ERK1/2 and p38, thereby inhibiting AFT4-CHOP/GRP78 signaling response and caspase-3 induced hepatocellular apoptosis during hepatic ischemia-reperfusion insults. Thus, Pinitol can be considered as a viable option for the management of hepatic IRI.
Improving Visual Working Memory With Training on a Tactile Orientation Sequence Task in Humans
Authors: Guo Ting , Ren Yanna , Yu Yinghua , Yu Yiyang , Hasegawa Yuuki , Wu Qiong , Yang Jiajia , Takahashi Satoshi , Ejima Yoshimichi , Wu Jinglong
Published: July 2021

Working memory refers to the cognitive capacity to temporarily store and manipulate information from multiple sensory domains. Recent studies have shown that cognitive training can improve performance in both visual working memory and tactile working memory tasks. However, it is still unclear whether the effects of training can be transferred from one sensory modality to another. The current study assessed whether the training effect of the tactile orientation sequence task could transfer to visual orientation sequence and visuospatial working memory tasks. The results showed that participants’ accuracy in the tactile orientation sequence task was significantly increased after 9 days of training compared with that before training. Remarkably, participants’ accuracy in both the visual orientation sequence task and the visuospatial task was significantly improved after 9 days of training. These results suggest that it is possible to improve visual working memory through a transfer effect from tactile task training without practice in the visual domain, which opens a wide range of applications for tactile orientation sequence tasks.
The Validity and Reliability Study of the Basic Motor Movement, Social Skill Observation, and Evaluation Scale for Basic Movement Education
Authors: Esen H. Tolga , Eraslan Meriç , Altınkök Mustafa , Eravşar Hakan , Demir Bahadır , Özküçük Sinem , Şeran Buket
Published: July 2021

It is aimed to develop a measurement tool which is a basic motor movement, social skill, attitude observation and evaluation scale for Basic Movement Education. In the study, the natural observation from qualitative research methods is used. The scale outline with 40 items is formed as a result of literature review and negotiations. To determine the content validity of the scale draft, the opinions of six field experts (lecturers), two preschool teachers, two physical education (PE) teachers, and two language experts were analyzed using the Lashwe technique. By analyzing the experts’ opinions according to Lashwe technique, four items are removed since their content validity rate (CVR) assets are less than 0.75. CVR shows that the scale provides 4-point Likert-type construct validity and consists of two subdimensions with 36 items (the basic motor movement skill dimension is 16 items and social skill dimension is 20 items). Total points of the Spearman correlation coefficient are checked among the observers. While the correlation coefficient of the basic motor movement skill dimension is .71 ( p = .000), the correlation coefficient of social skill dimension is .82 ( p = .002). The correlation coefficient among the total points is more than .70, and the results ( p < .01) are meaningful. This shows that the measurement tool is reliable, and the scale provides reliability with 4-point Likert-type gradation.
Do not (Just) Think, But (Also) Feel!: Empirical Corroboration of Emotion-Involved Processing Hypothesis on Foreign Language Lexical Retention
Authors: Kanazawa Yu
Published: July 2021

Emotion plays important roles in learning, memory, and other cognitive processes; it does so not only in the form of macro-level emotion (e.g., salient affective states and self-reportable motivational currents) but also in the form of micro-level emotion (e.g., subtle feelings and linguistic attributes that are usually processed subconsciously without special attention). According to the Emotion-Involved Processing Hypothesis (EIPH), processing that draws attention to emotional aspects (EmInvProc+) is postulated as a deeper version of semantic processing which has cognitive advantage to facilitate linguistic processing and retention more than non-emotional semantic processing (EmInvProc−). This study empirically investigated whether the EIPH can be experimentally corroborated for learners of a distant foreign language (viz., Japanese learners of English). In the experiment, participants processed visually presented English words that were either positively or negatively valenced under different conditions, followed by the test session in which they engaged in memory tests. Two processing modes were compared (EmInvProc+ vs. EmInvProc−). The dependent variables were correct recall frequency, correct recognition frequency, and correct recognition reaction time. It was revealed that EmInvProc+ was more cognitively facilitatory in making stronger foreign language lexical memory traces than EmInvProc− for all the measures employed in the experiment, regarding both accuracy (correct response frequency) and fluency (correct response reaction time). Therefore, it is implied that EmInvProc+ can be regarded as a sui generis deeper level of processing that is qualitatively distinguishable from mere semantic processing, supporting the Emotion-Involved Processing Hypothesis.
Mixed-Reality Learning Environments in Teacher Education: An Analysis of TeachLivE™ Research
Authors: Ersozlu Zara , Ledger Susan , Ersozlu Alpay , Mayne Fiona , Wildy Helen
Published: July 2021

TeachLivE™, a mixed-reality simulated classroom technology, has been used in initial teacher education programs to provide repeatable experiential learning opportunities for students now for more than a decade and in more than 80 universities worldwide. However, no broad scale investigation has been conducted into how the platform has been used or what research has been generated as a result. The aim of this study is to provide insight into the types of TeachLivE™ research carried out since its inception and to identify trends and potential gaps in this research. Peer-reviewed academic primary research publications—journal articles (23), conference proceedings (12), and thesis dissertations (20)—were reviewed for participants, research methods, analysis, research design, data collection tools, and design approaches. Of the 102 articles identified as relevant, “instructional skills development” and “integration of TeachLivE™ in teacher education” were the most commonly researched topics. Findings indicate that preservice teachers were the most commonly studied group of participants, research methods were predominately qualitative, single-subject experimental research design was employed most often, and the most used data collection tools were surveys and observation. These findings highlight that the range of topics is increasing, with studies on in-service teachers in school-based contexts beginning to emerge as a new area of interest. This systematic review has implications for researchers and the developers of TeachLivE™. It provides valuable insight and recommendations for future studies in this emerging teacher education field, where technology is not simply used “in the classroom” but rather “as the classroom.”
An Investigation of Factors Influencing Chinese Young Women’s Intention for Mammography Screening
Authors: Li Li , Li Jinhui
Published: July 2021

China has witnessed a dramatic increase in breast cancer incidence over the past few decades. Clear evidence has proven the effectiveness of mammography screening in reducing the number of breast cancer–related deaths. The study aims to extend the theory of planned behavior (TPB) with two additional components, personality traits and attention to media, to investigate the factors related to young Chinese women’s intention for mammography screening. A cross-sectional web survey was conducted among female students ( n = 1,002) in a large public university in southwest China. Hierarchical regression analysis showed that the three original TPB variables (attitudes, subjective norms and perceived behavioral control) have the strongest relationship with women’s intention to engage in mammography screening. Moreover, extraversion and attention to new media are positively associated with intention for mammography screening. The study contributes to existing health communication literature by showing how the original TPB model cooperated with psychological and communication factors that are related to women’s intention for mammography screening. The findings can be used to assist government and health professionals in developing a more effective strategies to promote mammography screening in the context of China.
Family Choices on Welfare and Territorial Disadvantages: The Perception of the Child Care Services Approach in Urban and Rural Areas
Authors: Bucaite-Vilke Jurga
Published: July 2021

Although the research on social-economic and demographic inequities of parents and their approach to formal child care (early childhood education and care [ECEC] system) is increasing, the territorial effects on child care remain underresearched. In Lithuania, the importance of the accessibility and availability of formal child care services are highlighted by the political agenda. However, the residential location is not considered enough to explain the differences in parental approach to child care in rural and urban regions. The article seeks to analyze how families’ child care choices and family welfare priorities are related to parental socioeconomic backgrounds, territorial dimension (residential location of parents), and general life satisfaction. The article uses the subsample of representative population survey data of the working-age generation cohort (34–48 years old cohort), focusing on respondents who have children below 4 years old and benefit from formal child care services in Lithuania. The main results contribute to explaining parental preferences to benefits-in-cash or services-in-kind (child care) family welfare priorities and their socioeconomic backgrounds, including residential location. The less is the residential location size (rural areas), the more likely respondents would support the benefits-in-cash system rather than formal child care services.
Competition and Financial Stability in the European Listed Banks
Authors: López-Penabad Maria Celia , Iglesias-Casal Ana , Neto José Fernando Silva
Published: July 2021

The analysis of the relationship between bank competition and financial stability remains a controversial issue and widely discussed in the academic and political community. Using a sample of 117 listed banks in 16 European countries for the years 2011 to 2018, the article explores the impact of market power, measured by the Lerner index, on the bank stability, measured by distance-to-default and Z score. Our results show that for the overall sample, higher market power in banking decreases the risky behavior of banks, confirming the “competition-fragility” view. We do not find any support for a U-shaped relationship between competition and bank risk-taking. However, our findings differ from previous studies pointing out that the relationship between bank competition and risk-taking is differentiated depending on whether the bank is based in a country with a more stable banking system or a less stable one. In countries with a less financially stable banking system, increased competition leads to increased bank risk-taking. In countries with a more stable banking system, market power seems not to influence banks’ financial stability. Public policies must guarantee banking competition but limiting excessive bank risk-taking, especially in countries with less financially sound banking systems. The consolidation of European banking can be a key element for achieving these policies.
Prejudice Nation: Hypersexualization and Abuse in Jude Dibia’s Unbridled
Authors: Amonyeze Chinenye , Okoye-Ugwu Stella
Published: July 2021

With the global #Metoo movement yet to arrive in Nigeria, Jude Dibia’s Unbridled reflects an emblematic moment for the underrepresented to occupy their stories and make their voices heard. The study analyzes patriarchy’s complicated relationship with the Nigerian girl child, significantly reviewing the inherent prejudices in patriarchy’s power hierarchies and how radical narratives explore taboo topics like incest and sexual violence. Contextualizing the concepts of hypersexualization and implicit bias to put in perspective how women, expected to be the gatekeepers of sex, are forced to navigate competing allegiances while remaining submissive and voiceless, the article probes the struggles of sexual victims and how hierarchies in a patriarchal society exacerbate their affliction through a culture of silence. Arguing that Dibia’s Unbridled confronts the narrative of silence in Nigerian fiction, the article explores ways the author empowers gender by challenging social values and traditional gender roles, underscoring gender dynamics and the problematic nature of prevalent bias against the feminine gender in Nigeria.
Career Advancement in the Hotel Industry in Timor-Leste: Study of Individual, Organizational, and Gender Differences
Authors: Brites da Silva Helio , Yukongdi Vimolwan , Kusakabe Kyoko , Zimmermann Willi
Published: July 2021

The hotel industry in Timor-Leste is female-dominated, but women are under-represented in management and senior executive positions. The objective of this study is to examine gender differences in the relative importance of individual and organizational factors and their effects on career advancement in the hotel industry in Dili. A survey of hotel employees in Dili was undertaken, yielding a total of 385 respondents. Data were analyzed using structural equation modeling. The hypothesized model predicted that individual factors of personality traits, education, work experience, and organizational variables of opportunities for promotion and corporate training and development would have a positive effect on career advancement. The results found that for both genders, education and work experience were two common factors with a direct effect on career advancement. However, for male employees, conscientiousness directly predicted career growth, while corporate training and development mediated the effect of harmonious passion for work on career advancement. On the other hand, among female employees, corporate training and development directly influenced career progression and mediated the effect of openness to experience and opportunity for promotion on career advancement. This study is the first to examine the factors facilitating the career advancement of hotel employees in Timor-Leste and the extent to which their path to advancement differed for males and females. We present the theoretical and practical implications of the role of individual and organizational factors on career advancement and possible ways to mitigate gender inequality in organizations.
The Impact of Company Characteristics on Human Resource Disclosure Index: A Study on Service Sector Companies in India
Authors: Aggarwal Kirti
Published: July 2021

The main purpose of the study is to know the impact of company characteristics on Human Resource Disclosure Index (HRDI) in service sector companies in India. The sample consists of 22 service sector companies listed on the NSE-500 Index. The data of dependent variable are collected from annual reports using the content analysis approach, and the data of independent variables are collected from CMIE Prowess Database and annual reports of the sample companies. The time period of the study ranges from 2012–13 to 2017–18. For analysis, descriptive statistics, Pearson’s correlation matrix and One-way Least-Square Dummy Variable (LSDV) regression model are used. The findings of the study show that the mean percentage of HRDI is 34.26. It represents the low level of HR disclosure. Further, the results of the LSDV regression model demonstrate that net fixed assets, market capitalization, return on total assets, quick ratio and pages of an annual report have significant positive and net sales, profit after tax, current ratio and type of auditor have significant negative influence on the HRDI. Overall, it can be said that the HRDI used in the present study is a first step towards evaluating the voluntary HR disclosure practices of listed companies in India from the stakeholder perspective and voluntary disclosure of HR information help to rebuild the trust of stakeholders in an accounting system.
Labour-use Efficiency of Assam Gramin Vikash Bank: Branch- and District-level Analysis
Authors: Purkayastha Mohuya Deb , Deb Joyeeta , Sinha Ram Pratap
Published: July 2021

The present study estimated labour-use efficiency of 48 branches of Assam Gramin Vikash Bank at its branch level, covering three districts of Barak Valley, which falls under Silchar region of the bank for the time period from 2010–2011 to 2017–2018. The study applied data envelopment analysis for estimating labour-use efficiency. In the second stage, the study applied censored Tobit regression for determining the impact of several contextual variables on efficiency. The study reveals that the mean labour-use efficiency score of the selected branches is 76% when averaged for the in-sample branches over the observation period. Results of the Tobit regression identified cluster 2 and total business of the branches as the significant factors for determining efficiency and the number of employees as a significant variable influencing inefficiency.

JEL Classifications: G2, G20, G21, J3
Can ‘Territoriality’ be Social? Interrogating the ‘Political’ of Dalit Social Inclusion in India
Authors: Ram Ronki
Published: July 2021

Social exclusion of Dalits in India is often understood in terms of discriminatory social structures embedded in oppressive cultural domains of pure versus polluted. Territorial demarcation of Dalits from upper/dominant castes is yet another way of perpetuating and sustaining social exclusion while segregating them in separate neighbourhoods built on the Varna principle of graded social inequality. However, over the last few years, Dalits have gathered some strength to say no to social exclusion while re-territorializing their segregated living spaces into radical sites of social contestation. Dalit counterculture and alternative Dalit heritage are what provided the necessary material for the re-territorialization of Dalit segregated neighbourhoods. The central concern of this study is to unravel what led to transformation of separate Dalit neighbourhoods into social territoriality of contestation.
Crafting Words and Creating Dalit Histories
Authors: Menon Shailaja
Published: July 2021

Many communities are not privileged enough to possess histories which also reflects their precarious position in the sociocultural hierarchy. As Trouillot observed, ‘History is the fruit of power, but power itself is never so transparent that its analysis become superfluous. The ultimate mark of power may be its invisibility, the ultimate challenge, the exposition of its roots’. (Trouillot, 1995, p. 19) Thus, the possession of history scripted or otherwise is a privilege seldom granted equally. For millennia, many groups and communities like African Americans, women, tribals, and the former untouchables in India did not exist in history. The semantics of cultural and ideological domination ensured that such people were invisibilized and silenced. Is it possible to recover or reconstruct the histories of the silenced people? This article argues that the genre of autobiography is a vital source to represent the peoples without histories.
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

Background

Headache 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.

Methods

We 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.

Results

The 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.

Conclusions

The 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

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

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

This 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

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

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

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

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

Background

Legionellosis 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.

Results

Legionellaspecies 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.

Conclusions

DNA 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

The 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.
Interventions to prevent aspiration in older adults with dysphagia living in nursing homes: a scoping review
Authors: Chen Shen , Kent Bridie , Cui Yan
Published: July 2021

Background

Dysphagia is highly prevalent condition in older adults living in nursing homes. There is also evidence indicating that aspiration is one of the major health risks for these older adults, which is more likely to result in respiratory infections, aspiration pneumonia and sudden bolus death. Evidence syntheses have demonstrated the effectiveness of interventions for prevention of aspiration among hospitalized older people. The aim of this scoping review is to describe the current spread of interventions to prevent or reduce aspiration in older adults with dysphagia with a specific focus on those who reside in nursing homes.

Methods

The Joanna Briggs Institute methods and PRISMA-ScR guidelines were used to inform this review. MEDLINE, CINAHL, EMBASE, Cochrane Library, Joanna Briggs Institute EBP Database and Web of Science were searched for related articles from 2010 to 2020 as well as Chinese databases (CNKI, WANFANG DATA and VIP) and databases for unpublished material. A three-step search strategy was utilized, including the use of citation software to manage search results and de-duplication, abstract review and full-text review by two reviewers. Details of included studies were then extracted using a prepared data extraction tool. The resulting map was displayed in tabular form along with a narrative summary.

Results

Although 637 articles were located, 19 papers were included in the final analysis. Interventions to prevent aspiration in older adults with dysphagia living in nursing homes included: more bedside evaluation, modification of dietary, creating an appropriate environment for swallowing, providing appropriate feeding assistance, appropriate posture or maneuver for swallowing, appropriate rehabilitation program, medication treatment, and stimulation treatment.

Conclusion

Nursing homes, particularly those in developing countries, require more support for staff training and necessary equipment. Professional interventions provided by speech and language therapists are still limited in the setting of nursing homes. Modification of dietary was the most frequently used intervention to prevent or reduce aspiration. Multi-disciplinary interventions had the best results for aspiration management, but for many nursing homes, access to such teams is limited. Nursing home residents respond well to person-centered interventions that have a comprehensive consideration of their degree of aspiration risk, health condition, individual feelings and cognitive state.
A retrospective cohort study using a national surveillance questionnaire to investigate the characteristics of maternal venous thromboembolism in Japan in 2018
Authors: Morikawa Mamoru , Adachi Tomoko , Itakura Atsuo , Nii Masafumi , Nakabayashi Yasushi , Kobayashi Takao
Published: July 2021

Background

In Japan, the numbers of deliveries by women of older maternal age and women with overweight or obesity have recently increased. Since 2008, the guidelines and practices to prevent the maternal venous thromboembolism (VTE) have been recommended antepartum and postpartum thromboprophylaxis for each risk level of VTE. This study aimed to clarify the incidence and characteristics (type of VTE and thromboprophylaxis) of VTE in pregnant women in Japan to reduce the rate of mortality from VTE

Methods

Of 2299 institutions sent the surveillance questionnaire, 666 (29.0%) responded, and data from 295,961 women who gave birth in those institutions in 2018 were analyzed. We calculated the incidence and characteristics of VTE before and after the deliveries.

Results

At the responding institutions, 243 women (0.082%) had VTE in 2018. In 2018, deep vein thrombosis was significantly more common (0.0053%) than pulmonary thromboembolism (0.0019%; p < 0.0001). The incidence of antepartum VTE (0.0055%) was significantly higher than that of postpartum VTE (0.0026%; p < 0.0001). The incidence of VTE after cesarean Sect. (0.0074%) was significantly higher than that after vaginal delivery (0.0012%; p < 0.0001). Of the women with VTE, 4 (1.6%) died.

Conclusions

Among the women thought to have a low risk of VTE during the antepartum period, and especially women who had a vaginal delivery, the actual incidence of VTE might have increased in Japan.