bluuebunny/crossref_metadata_2025_split huggingface dataset:
Landscape and evolution of cis- and trans-regulatory divergence in chicken genome between two contrasted breeds analyzed in three tissues at one day age
Authors: Wang Qiong , Jia Yaxiong , Wang Yuan , Jiang Zhihua , Zhou Xiang , Zhang Zebin , Nie Changsheng , Li Junying , Yang Ning , Qu Lujiang 
Published: October 2019

Abstract
Background: Gene expression variation is an important mechanism underlying phenotypic variation, and can occur via cis- and trans-regulation. In order to understand the role of cis- and trans-regulatory variation on population divergence of chicken, we developed reciprocal crosses of two chicken breeds, White Leghorn and Cornish Game, with major differences in body size and reproductive traits, and used them to identify the degree of cis versus trans variation in brain, liver and muscle of both male and female samples at 1 day age.
Results: We provided a landscape about how the transcriptomes are regulated in the hybrid progenies of two contrasted breeds by allele specific expression analysis. Our results showed that compared with the cis-regulatory divergence, trans-acted genes existed more extensively in the chicken genome. Furthermore, a widespread tendency of compensatory regulation exists in chicken genome. Most importantly, we found the evidence of stronger purifying selection on genes regulated by trans variations than the cis elements.
Conclusions: We demonstrated a pipeline to explore the allele-specific expression in the hybrid progenies of inbred lines without specific reference genome. Our research performed the first study to describe the regulatory divergence between two contrasted breeds. The results suggested that artificial selection associated with domestication in chicken may have more often acted on trans-regulatory divergence than cis.
­­Assessment of Viral RNA in Idiopathic Pulmonary Fibrosis Using RNA-seq
Authors: Yin Qinyan , Strong Michael J , Zhuang Yan , Flemington Erik K , Kaminski Naftali , de Andrade Joao AM , Lasky Joseph A 
Published: October 2019

Abstract
Background Numerous publications suggest an association between herpes virus infection and idiopathic pulmonary fibrosis (IPF). These reports have employed immunohistochemistry, in situ hybridization and/or PCR, which are susceptible to specificity artifacts. Methods We investigated the possible association between IPF and viral RNA expression using next-generation sequencing, which has the potential to provide a high degree of both sensitivity and specificity. We quantified viral RNA expression for 740 viruses in 28 IPF patient lung biopsy samples and 20 age-matched controls. Key RNA-seq results were confirmed using Real-time RT-PCR for select viruses (EBV, HCV, herpesvirus saimiri and HERV-K). Results We identified sporadic low-level evidence of viral infections in our lung tissue specimens, but did not find a statistical difference for expression of any virus, including EBV, herpesvirus saimiri and HERV-K, between IPF and control lungs. Conclusions To the best of our knowledge, this is the first publication that employs RNA-seq to assess whether viral infections are linked to the pathogenesis of IPF. Our results do not address the role of viral infection in acute exacerbations of IPF, however, this analysis patently did not support an association between herpes virus detection and IPF.
De novo transcriptome assembly reveals putative biosynthetic genes involved in the biosyntheses of isoflavones and miroestrol in Pueraria candollei var. mirifica
Authors: Suntichaikamolkul Nithiwat , Tantisuwanichkul Kittiya , Prombutara Pinidphon , Kobtrakul Khwanlada , Zumsteg Julie , Wannachart Siriporn , Schaller Hubert , Yamazaki Mami , Saito Kazuki , De-eknamkul Wanchai , Vimolmangkang Sornkanok , Sirikantaramas Supaart 
Published: October 2019

Abstract
Background: Pueraria candollei var. mirifica , a Thai medicinal plant used traditionally as a rejuvenating herb, is known as a rich source of phytoestrogens, including isoflavonoids and the highly estrogenic miroestrol and deoxymiroestrol. Although these active constituents in P. candollei var. mirifica have been known for some time, actual knowledge regarding their biosynthetic genes remains unknown.
Results: A de novo transcriptome analysis was conducted using combined P. candollei var. mirifica tissues of young leaves, mature leaves, tuberous cortices, and cortex-excised tubers.A total of 166,923 contigs was assembled for functional annotation using protein databases and as a library for identification of genes that are potentially involved in the biosynthesis of isoflavonoids and miroestrol. Twenty-one differentially expressed genes from four separate libraries were identified as candidatesinvolved in these biosyntheticpathways, and their respective expressions were validated by quantitative real-time reverse transcription polymerase chain reaction. Notably, isoflavonoid profiling generated by LC-MS/MS was positively correlated with expression levels of isoflavonoid biosynthetic genes across the four types of tissues. Moreover, we identified R2R3 MYB transcription factors that may be involved in the regulation of isoflavonoid biosynthesis in P. candollei var. mirifica . To confirm the function of a key-isoflavone biosynthetic gene, P. candollei var. mirifica isoflavone synthase identified in our library was transiently co-expressed with an Arabidopsis MYB12 transcription factor ( At MYB12) in Nicotiana benthamiana leaves. Remarkably, the combined expression of these proteins ledto the production of the isoflavone genistein.
Conclusions: Our results provide compelling evidence regarding the integration of transcriptome and metabolome as a powerful tool for unraveling biosynthetic pathways in plants.
Female sex workers perspectives and concerns regarding HIV self-testing: An exploratory study in Tanzania
Authors: Nnko Soori , Nyato Daniel , Kuringe Evodius , Casalini Caterina , Shao Amani , Komba Albert , Changalucha John , Wambura Mwita 
Published: October 2019

Abstract
Background: HIV testing is a gateway to HIV care and treatment for those testing positive and can link those with negative results to HIV preventive services. Despite the importance of HIV testing services (HTS) in HIV control, uptake of HTS among female sex workers (FSWs) across sub-Saharan Africa (SSA) remains sub optimal. Concerns about stigma associated with sex work and fear of loss of livelihood if HIV status becomes known, are some of the restrictions for FSWs to utilize HTS offered through health care facilities. Introduction of HIV self-testing (HIVST) may mitigate some of the barriers for the uptake of HTS. This study explored perspectives of FSWs towards HIVST in Tanzania.
Methods:We conducted an exploratory study employing in-depth interviews (IDI) and participatory group discussions (PGD) with FSWs in selected regions of Tanzania. Study participants were recruited through snowball sampling. Data were thematically analysed by two analysts using NVivo software. Emerging themes were explored in the tradition of Grounded Theory. The analysis was informed by the social ecological model and focused on factors associated with the feasibility of scaling up HIVST.
Results:A total of 23 PGD sessions were conducted involving 227 FSWs. Data from PGDs were complemented by 21 IDI. FSWs were enthusiastic toward HIVST. Convenience (time and cost saved), and belief that HIVST will increase privacy and confidentiality motivated participants’ support for the self-testing approach. Participants did express concerns about their ability to interpret and trust the results of the test. Participants also expressed concern that HIVST could cause personal harm, including severe distress and self-harm for individuals with reactive test. This was linked to the study participants’ perception that HIVST would be provided only through unassisted modality.
Conclusions: FSWs demonstrated high enthusiasm to use the HIVST once it becomes available. Increased confidentiality, reduced opportunity costs, and increased autonomy were among the key factors for the intended use of HIVST. Major concerns included fear of HIV reactive test and not trusting self-diagnoses. Our findings underscore the importance of providing adequate access to counselling and referral services in conjunction with HIVST.
Voluntary Medical Male Circumcision and Sexual Practices among Sexually Active Circumcised Men in Mzuzu, Malawi: A Cross-Sectional Study
Authors: Chatsika Zimveka Jones , Kumitawa Andrew , Samuel Vincent , Azizi Steven Chifundo , Jumbe Vincent C 
Published: October 2019

Abstract
Background: Voluntary Medical Male Circumcision (VMMC) is one of the strategies being promoted to prevent sexual heterosexual transmission of HIV. It has been adopted by 14 countries with high HIV prevalence and low circumcision rates. The 60% protective efficacy of VMMC has come with misconceptions in some societies in Malawi, hence VMMC clients may opt for risky sexual practices owing to its perceived protective effect. The study estimated proportion of circumcised men engaging in risky sexual behaviors post-VMMC, assessed knowledge on VMMC protective effect and identified socio-demographic factors associated with risky sexual practices.
Method: A cross sectional study was conducted at two sites of Mzuzu city. Systematic random sampling was used to select 322 participants aged 18-49 who had undergone VMMC. The independent variables included age, location, occupation, religion, marital status and education. Outcome variables were non condom use, having multiple sexual partners and engaging in transactional sex. Data from questionnaires was analyzed using Pearson’s chi square test and logistic regression.
Results: Out of 322 respondents, 84.8% (273) understood the partial protection offered by VMMC in HIV prevention. Ninety-six percent of the participants self-reported continued use of condoms post VMMC. Overall 23.7% - 38.3% participants self-reported engaging in risky sexual practices post VMMC, 23.7% (76) had more than one sexual partner; 29.2% (94) paid for sex while 39.9% (n=187) did not use a condom. Residing in high density areas was associated with non-condom use, (p = 0.043). Being single (p <0.001), and residing in low density areas (p = 0.004) was associated with engaging in transactional sex.
Conclusion: Risky sexual practices are evident among participants that have undergone VMMC. Messages on safer sexual practices and limitations of VMMC need to be emphasized to clients, especially unmarried or single and those residing in low density areas.
Service provision for depressed children and youth: a survey of the scope and nature of services in Ontario.
Authors: Watson Priya , Mehra Kamna , Hawke Lisa D , Henderson Joanna 
Published: October 2019

Abstract
Background The worldwide prevalence of depressive disorders among children and youth has been reported in ranges from just under 3% to over 10%. In Canada, 7% of youth report past year depression, which is higher than any other age demographic. Yet, many of these youth do not receive evidence based interventions, increasing their risk for serious lifetime consequences. To better understand low service use, it is crucial to map and evaluate current services. This study aimed to determine the scope and nature of services available to depressed children and youth, and compare services to best evidence treatment guidelines. Methods Several government and non-government resources were utilized to develop a new multi-sectoral database of depression services for children and youth across Ontario. An online survey was sent to program managers serving children/youth with depression, examining agency characteristics, populations served, services provided, patterns of service use, evaluation activities, and research priorities. Results 413 agencies with 869 program managers participated, representing mental health, addictions and other sectors. Age groups served included children up to 12 years of age (31%), adolescents aged 13-17 (70%) and transition aged youth (18-25 years) (81%). Over half of respondents worked in the mental health (43.4%) or mental health and addiction (24.4%) sectors. The most frequently provided services were assessment, psychotherapy, case management, and psychoeducation; the most common types of psychotherapy provided included cognitive behavioral therapy, social skills training, and solution-focused therapy. Psychotherapies are offered in widely varying formats, frequencies and durations. Discontinuation rates varied, with higher discontinuation among transition aged youth as compared to children. Respondents identified effective treatment, improving access, and reducing service gaps as top future research priorities. Conclusions This study provides important new data on service provision and uptake for depressed children and youth. Comparing these results with best-evidence practice guidelines raises significant concerns about the services most commonly offered and their delivery formats. In addition, high early discontinuation rates raise questions about the service experiences of children, youth and their families. Other factors which may contribute to ongoing treatment engagement challenges include access barriers, service or client characteristics, and unintentional treatment impacts.
Identification of bacterial pathogens in cultured fish using Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)
Authors: Piamsomboon Patharapol , Jaresitthikunchai Janthima , Hung Tran Quang , Roytrakul Sittiruk , Wongtavatchai Janenuj 
Published: October 2019

Abstract
Background Majority of infectious diseases of cultured fish is caused by bacteria. Rapid identification of bacterial pathogen is necessary for immediate management. The present study developed Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for a fast identification of fish bacterial pathogens. Streptococcus agalactiae, S. iniae, Aeromonas hydrophila, A. veronii, and Edwardsiella tarda obtained from diseased fish were used as representative bacterial pathogens in this study. Bacterial peptides were extracted to create the Main Spectra Profile (MSP), and the MSP of each bacterial species was added into the MALDI Biotyper database. Ten additional field isolates of each bacterial species were tested to validate the technique.Results The MSP of all field isolates were clearly distinguishable, and the MSPs of the same species were clustered together. However, the species identification when matching with the public MALDI Biotyper library (Bruker MALDI Biotyper) showed unreliable result at the species level. The accurate identification only obtained when the custom-made database was used, giving a 100% matching result.Conclusion This study demonstrates a newly developed technique for the effective identification of fish bacterial pathogens. Further applications require a broad, well-established database to accommodate the prudent identification of many fish bacterial pathogens by MALDI-TOF MS.
Training needs for Ugandan primary care health workers in management of respiratory diseases: a cross sectional survey
Authors: Nantanda Rebecca , Kayingo Gerald , Jones Rupert , Gemert Frederik van , Kirenga Bruce 
Published: October 2019

Abstract
Background Acute and chronic respiratory diseases are among the leading causes of morbidity and mortality in Uganda, but there is little attention to chronic respiratory diseases in the health programmes. This survey assessed the gaps in knowledge and skills, among healthcare workers in managing respiratory illnesses. Methods A mixed methods study was conducted among primary care health workers, physicians and healthcare planners to assess gaps in knowledge and skills, and training needs in managing respiratory illnesses. The perspectives of patients with respiratory diseases were also sought. Data were collected using questionnaires, patient panel discussions and review of pre-service training curricula for clinicians, nurses and midwives. Survey Monkey was used to collect survey data. Descriptive analysis was undertaken for quantitative data and content analysis for qualitative data. Results A total of 104 respondents participated in the survey and of these, 76.9% (80/104) were primary care health workers, 16.3% (17/104) specialist clinicians and 6.7% (7/104) healthcare planners. Over 90% of the respondents indicated that more than half of the patients in their clinics presented with respiratory symptoms. More than half (52%) of the primary care health workers were not comfortable in diagnosing and managing chronic respiratory diseases like asthma and COPD. Only 4% of them were comfortable performing procedures like pulse oximetry, nebulization, and interpreting x-rays. Majority (75%) of the primary care health workers had received in-service training but only 4% of the sessions focused on respiratory diseases. The clinicians indicated that the pre-service training curricula included a wide scope of respiratory diseases, but the actual training had not sufficiently prepared them to manage respiratory diseases. The patients were unsatisfied with the care in primary care facilities and reported that they were often treated for the wrong illnesses. Conclusions Respiratory illnesses contribute significantly to the burden of diseases in primary care facilities in Uganda. Management of patients with respiratory diseases remains a challenge partially because of inadequate knowledge and skills of the primary care health workers. A training programme to improve the competences of health workers in respiratory medicine is highly recommended.
The effect of a whole grain diet on reducing cardiovascular risks in obese/overweight adults: a systematic review and meta-analysis
Authors: Wang Weihao , Li Jianan , Chen Xiaoxi , Yu Miao , Pan Qi , Guo Lixin 
Published: October 2019

Abstract
Background: Cardiovascular disease (CVD) remains the leading cause of mortality worldwide. Overweight, hypertension, and dyslipidemia are clinically recognized as the most significant cardiovascular risk conditions. Studies have shown that whole grains are beneficial to affect glucose metabolism, obesity, blood pressure, lipids and inflammatory markers. Methods: We did a research in PubMed, Embase and Cochrane for randomized controlled trials (RCTs) and selected the study according to the eligibility criteria and data extraction. Then we evaluate the effectiveness of whole grain foods on body weight (primary outcome) and other CVD risk factor indicators, including plasma low-density lipoprotein-cholesterol level, insulin resistance index, blood pressure, BMI, waist circumference (secondary outcome) in overweight/obese adults. Results: Our results showed that there are significant decrease of weight (P<0.0001, mean difference -0.5, 95% CI[-0.74, -0.25], I 2 =35%), LDL-C (P=0.05, mean difference -0.08, 95% CI[-0.16, 0.00], I 2 =27%), CRP (P<0.0001, mean difference -0.36, 95% CI[-0.54, -0.18], I 2 =69%) in whole grain group compared with control group (Fig 2-4). There are no significant difference in waist circumference (P=0.76, mean difference -0.12, 95% CI[-0.92,0.68], I 2 =44%), systolic blood pressure (P=0.88, mean difference -0.11, 95% CI[-1.55, 1.33], I 2 =3%), diastolic blood pressure (P=0.39, mean difference -0.44, 95% CI[-1.44, 0.57], I 2 =15%), fasting glucose (P=0.11, mean difference -0.05, 95% CI[-0.12, 0.01], I 2 =31%) between two groups. Conclusion: This study suggests whole grain food has only a moderate effect on reducing body weight, LDL-C and CRP in obese population, which is obviously showed in patients combined with other chronic metabolic disorders.
Another piece on the Zika puzzle: assessing the associated factors to microcephaly in a systematic review and meta-analysis.
Authors: Gallo Luciana Guerra , Martinez-Cajas Jorge L , Peixoto Henry Maia , Pereira Ana Carolina Esteves da Silva , Carter Jillian E , McKeown Sandra , Shaub Bruno , Ventura Camila V. , de França Giovanny Vinicius Araújo , Pomar Leo , Ventura Liana O. , Nerurkar Vivek R. , de Araújo Wildo Navegantes , Velez Maria P. 
Published: October 2019

Abstract
Background: Although it is known that Zika virus (ZIKV) infection during pregnancy may lead to microcephaly in the foetus, the risk factors associated to this tragic disorder remain unclear. We conducted a systematic review and meta-analysis toto assess risk factors associated with the incidence of microcephaly in congenital ZIKV infection. Methods: We conducted a comprehensive search in Ovid MEDLINE, Ovid MEDLINE (R) Epub ahead of print, Embase, Embase Classic, Web of Science, CINAHL, Cochrane CENTRAL, LILACS and various thesis databases to identify human studies reporting microcephaly associated with congenital ZIKV infection. We requested primary data from authors of the studies included in this review to calculate summary estimates and conduct meta-analysis of the most prevalent factors. Results: We screened 4,106 titles and abstracts, and identified 12 studies for inclusion in the systematic review. The assessment of ZIKV infection and the definition of microcephaly varied among studies. A total of 6,154 children/foetuses were enrolled; of those, 1,120 (18.20%) had a diagnostic of ZIKV infection, of which 509 (45.45%) were diagnosed with microcephaly. Nine studies addressed the link between congenital ZIKV infection and neurological findings in foetuses/ children. Half of the studies provided primary data. Two out of eleven factors of interest were associated with microcephaly: infant’s sex – males presented a higher risk of microcephaly compared to females (RR 1.30, 95% CI 1.14, 1.49); and the stage of pregnancy when infection occurred - infection in the first trimester of pregnancy had a higher risk of microcephaly (RR 1.41, 95% CI 1.09 to 1.82), compared to infection at other stages of pregnancy. Conclusion: Our findings support the female-biased resistance hypothesis and reinforce the risk associated with the stage of pregnancy when Zika virus infection occurs. Continued surveillance of ZIKV during pregnancy is needed to identify additional factors that could contribute to developing microcephaly in affected foetuses.
Genomic Nucleotide-Based Distance Analysis for Delimiting Old World Monkey Derived Herpes Simplex Viruses Species.
Authors: Kolb Aaron W , Brandt Curtis R 
Published: October 2019

Abstract
Herpes simplex viruses form a genus within the alphaherpesvirus subfamily, with three identified viral species isolated from Old World monkeys (OWM); Macacine alphaherpesvirus 1 (herpes B), Cercopithecine alphaherpesvirus 2 (SA8), and Papiine alphaherpesvirus 2 (PaHV-2; herpes papio). Herpes B is endemic to macaques, while PaHV-2 and SA8 appear endemic to baboons. All three viruses are genetically and antigenically similar, with SA8 and PaHV-2 thought to be avirulent in humans, while herpes B is a biosafety level 4 pathogen. Recently, next-generation sequencing (NGS) has resulted in an increased number of published OWM herpes simplex genomes, allowing an encompassing phylogenetic analysis. In this study, phylogenetic networks, in conjunction with a genome-based genetic distance cutoff method were used to examine 27 OWM monkey herpes simplex isolates. Genome-based genetic distances were calculated, resulting in distances between Lion and Pig-tailed simplex viruses themselves, and versus herpes B core strains that were higher than those between PaHV-2 and SA8 (approximately 14% and 10% respectively). The species distance cutoff was determined to be 8.94%, with the method recovering separate species status for PaHV-2 and SA8 and showed that Lion and Pig-tailed simplex viruses (vs core herpes B strains) were well over the distance species cutoff. In conclusion, we propose designating Lion and Pig-tailed simplex viruses as separate, individual viral species, and that this may be the first identification of viral cryptic species.