bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome Ortholog Alignment Sequence Tools (TOAST) for Phylogenomic Dataset Assembly
Authors: Wcisel Dustin J. , Howard J. Thomas , Yoder Jeffrey A. , dornburg alex 
Published: March 2020

Abstract
Background

Advances in next-generation sequencing technologies have reduced the cost of whole transcriptome analyses, allowing characterization of non-model species at unprecedented levels. The rapid pace of transcriptomic sequencing has driven the public accumulation of a wealth of data for phylogenomic analyses, however lack of tools aimed towards phylogeneticists to efficiently identify orthologous sequences currently hinders effective harnessing of this resource.

Results

We introduce TOAST, an open source R software package that can utilize the ortholog searches based on the software Benchmarking Universal Single-Copy Orthologs (BUSCO) to assemble multiple sequence alignments of orthologous loci from transcriptomes for any group of organisms. By streamlining search, query, and alignment, TOAST automates the generation of locus and concatenated alignments, and also presents a series of outputs from which users can not only explore missing data patterns across their alignments, but also reassemble alignments based on user-defined acceptable missing data levels for a given research question.

Conclusions

TOAST provides a comprehensive set of tools for assembly of sequence alignments of orthologs for comparative transcriptomic and phylogenomic studies. This software empowers easy assembly of public and novel sequences for any target database of candidate orthologs, and fills a critically needed niche for tools that enable quantification and testing of the impact of missing data. As open-source software, TOAST is fully customizable for integration into existing or novel custom informatic pipelines for phylogenomic inference.
The Development of a Return to Work Intervention Programme for Stroke Survivor (SReTWIP): A Delphi Survey
Authors: Olaoye Olumide Ayoola , Soeker Shaheed Moghammad , Rhoda Anthea 
Published: March 2020

Abstract
Background : Even though clearly defined pathways for vocational re-entry are well recognized for conditions such as mental health, musculoskeletal dysfunction (MSD) and traumatic brain injury (TBI), none has been identified for stroke. There has been a lack of consensus regarding such clear pathways to vocational re-entry and the essential contents of return to work (RTW) interventions for stroke survivors. As part of a larger study aimed to design a RTW programme for stroke survivors, this study describes the concluding process through which Stroke Return to Work Intervention Programme (SReTWIP) was developed.
Methods : Experts in the field of neurorehabilitation and vocational rehabilitation (VR) from 6 countries participated in this 3-round Delphi survey via e-mail. Concept mapping was used to triangulate findings from the Delphi with previous phases of the larger study. Content thematic analysis was conducted on qualitative data while descriptive statistic was used to analyze quantitative data.
Results : Fifteen experts with a mean age and mean duration of practice of 44.73±9.48 years and 18.26±8.71 years respectively participated in this study. The developed RTW programme (SReTWIP) is a 12 week programme that consisted of four interconnected phases of intervention viz: an assessment phase, clinic-based work and non-work specific intervention phase, a work test placement phase and a client full participation in worker role phase. The experts agreed on a set of implementation strategies that included the use of interdisciplinary team, the tailoring of intervention to meet stroke survivor’s need, as well as the use of case management approach.
Conclusion : The SReTWIP is the first step in developing a VR pathway that can ultimately enhance the RTW rates and quick resumption of the worker role of stroke survivors. The stroke survivor can move along the different phases of the SReTWIP after achieving competency in a preceding phase. Future work will include a feasibility study with other key stakeholders involved in RTW such as employers, informal caregivers and stroke survivors before its implementation.
Comparison of videolaryngoscopy and direct laryngoscopy by German paramedics during out-of-hospital cardiopulmonary resuscitation. An observational prospective study.
Authors: Risse Joachim , Volberg Christian , Kratz Thomas , Plöger Birgit , Jerrentrup Andreas , Pabst Dirk , Kill Clemens 
Published: March 2020

Abstract
Background: Videolaryngoscopy (VL) has become a popular method of intubation (ETI). Although VL may facilitate ETI in less-experienced rescuers there are limited data available concerning ETI performed by paramedics during CPR. The goal was to evaluate the impact VL compared with DL on intubation success and glottic view during CPR performed by German paramedics. We investigated in an observational prospective study the superiority of VL by paramedics during CPR compared with direct laryngoscopy (DL).
Methods: In a single Emergency Medical Service (EMS) in Germanywith in total 32 ambulances paramedics underwent an initial instruction from in endotracheal intubation (ETI) with GlideScope ® (GVL) during resuscitation. The primary endpoint was good visibility of the glottis (Cormack-Lehane grading 1/2), and the secondary endpoint was successful intubation comparing GVL and DL.
Results: In total n = 97 patients were included, n = 69 with DL (n = 85 intubation attempts) and n = 28 VL (n = 37 intubation attempts). Videolaryngoscopy resulted in a significantly improved visualization of the larynx compared with DL. In the group using GVL, 82% rated visualization of the glottis as CL 1&2 versus 55% in the DL group (p = 0.02). Despite better visualization of the larynx, there was no statistically significant difference in successful ETI between GVL and DL (GVL 75% vs. DL 68.1%, p = 0.63).
Conclusions:
We found no difference in Overall and First Pass Success (FPS) between GVL and DL during CPR by German paramedics despite better glottic visualization with GVL. Therefore, we conclude that education in VL should also focus on insertion of the endotracheal tube, considering the different procedures of GVL.
Indoor residual spraying for malaria control in Sub-Saharan Africa 1997 to 2017; an adjusted retrospective analysis
Authors: Tangena Julie-Anne , Hendriks Chantal M.J. , Devine Maria , Tammaro Meghan , Trett Anna E. , Williams Ignatius , DePina Adilson José , Sisay Achamylesh , Herizo Ramandimbiarijaona , Kafy Hmooda Toto , Chizema Elizabeth , Were Allan , Rozier Jennifer , Coleman Michael , Moyes Catherine L. 
Published: March 2020

Abstract
Background: Indoor residual spraying (IRS) is a key tool for controlling and eliminating malaria by targeting vectors. To support the development of effective intervention strategies it is important to understand the impact of vector control tools on malaria incidence and on the spread of insecticide resistance. In 2006, the World Health Organization (WHO) stated that countries should report on coverage and impact of IRS, yet IRS coverage data are still sparse and unspecific. Here we estimated the subnational coverage of IRS across sub-Saharan Africa for the four main insecticide classes from 1997 to 2017.
Methods: Data on IRS deployment were collated from a variety of sources, including the President’s Malaria Initiative spray reports and National Malaria Control program reports, for all 46 malaria-endemic countries in Sub-Saharan Africa from 1997 to 2017. The data were mapped to the applicable administrative divisions and the proportion of households sprayed for each of the four main insecticide classes; carbamates, organochlorines, organophosphates and pyrethroids was calculated.
Results: We found that the number of countries implementing IRS increased considerably over time, although the focal nature of deployment means the number of people protected remains low. From 1997 to 2010, DDT and pyrethroids were commonly used, then partly replaced by carbamates from 2011 and by organophosphates from 2013. IRS deployment since the publication of resistance management guidelines has typically avoided overlap between pyrethroid IRS and ITN use. However, annual rotations of insecticide classes with differing modes of action are not routinely used.
Conclusion: This study highlights the gaps between policy and practice, emphasizing the continuing potential of IRS to drive resistance. The data presented here can improve studies on the impact of IRS on malaria incidence and help to guide future malaria control efforts.
Analyzing Big Tobacco’s global youth marketing strategies and factors influencing smoking initiation by Nigeria youths using the theory of triadic influence
Authors: Isip Ukoabasi , Calvert John Robert 
Published: March 2020

Abstract
Background: Major transnational tobacco companies (TTCs) have identified Nigeria, the seventh most populous country in the world, as a market with a significant revenue potential, given its high youth population and growing gross domestic product (GDP). This research analyses tobacco industry-related strategies and activities targeting youth (aged 15 to 24 years) in Nigeria involving existing, but most importantly, future tobacco users. Nigeria is the focus of this study because the tobacco industry has viewed it as a major emerging market since the 1990s. Successful marketing in Nigeria could provide the industry with a template for similar initiatives in other emerging markets in low- and middle-income countries.Methods: The research began with a systematic review of secondary literature to determine how the tobacco industry has targeted youth globally and factors contributing to youth smoking initiation. It then used the theory of triadic influence as a heuristic framework to categorize the various factors influencing youth smoking initiation and industry strategies related to increasing tobacco use among youths. Quotations from internal tobacco industry documents were organized into the three streams of the theory of triadic influence: biology/personality, social and cultural/environmental streams. A total of 12 interviews were conducted with 6 policymakers and governmental officials, 2 civil society organization representatives, a high school principal, a journalist and 2 researchers to investigate how the tobacco industry had targeted youth in Nigeria. Results: The findings indicate that TTCs have actively targeted youth in Nigeria since the 1990s, focusing on changing behaviour through the biology/personality, social and environmental/ cultural streams. Conclusion: The study suggests that Nigeria implement and vigorously enforce its 2015 National Tobacco Control Bill as well as a package of other measures to prevent tobacco companies targeting youth.
Genetic and phenotypic associations between root architecture, arbuscular mycorrhizal fungi colonisation and low phosphate tolerance in strawberry (Fragaria× ananassa)
Authors: Cockerton Helen Maria , Li Bo , Stavridou Eleftheria , Johnson Abigail , Karlström Amanda , Armitage Andrew Douglas , Martinez-Crucis Ana , Arjona Lorena Galiano , Harrison Nicola , Barber-Pérez Nuria , Cobo-Medina Magdalena , Harrison Richard Jonathan 
Published: March 2020

Abstract
Background
Phosphate is an essential plant macronutrient required to achieve maximum crop yield. Roots are able to uptake soil phosphate from the immediate root area, thus creating a nutrient depletion zone. Many plants are able to exploit phosphate from beyond this root nutrient depletion zone through symbiotic association with Arbuscular Mycorrhizal Fungi (AMF). Here we characterise the relationship between root architecture, AMF association and low phosphate tolerance in strawberries. The contrasting root architecture in the parental strawberry cultivars ‘Redgauntlet’ and ‘Hapil’ was studied through a mapping population of 168 progeny. Low phosphate tolerance and AMF association was quantified for each genotype to allow assessment of the phenotypic and genotypic relationships between traits.

Results
A “phosphate scavenging” root phenotype where individuals exhibit a high proportion of surface lateral roots was associated with a reduction in root system size across genotypes. A genetic correlation between “root system size” traits was observed with a network of pleiotropic QTL were found to represent five “root system size” traits. By contrast, average root diameter and the distribution of roots appeared to be under two discrete methods of genetic control. A total of 18 QTL were associated with plant traits, 4 of which were associated with solidity that explained 46 % of the observed variation. Investigations into the relationship between AMF association and root architecture found that a higher root density was associated with greater AMF colonisation across genotypes. However, no phenotypic correlation or genotypic association was found between low phosphate tolerance and the propensity for AMF association, nor root architectural traits when plants are grown under optimal nutrient conditions.

Conclusions
Understanding the genetic relationships underpinning phosphate capture can inform the breeding of strawberry varieties with better nutrient use efficiency. Solid root systems were associated with greater AMF colonisation. However, low P-tolerance was not phenotypically or genotypically associated with root architecture traits in strawberry plants. Furthermore, a trade-off was observed between root system size and root architecture type, highlighting the energetic costs associated with a “phosphate scavenging” root architecture.
Distribution of Parkinson’s disease associated RAB39B in mouse brain tissue
Authors: Gao Yujing , Wilson Gabrielle R. , Stephenson Sarah E.M. , Oulad-Abdelghani Mustapha , Charlet-Berguerand Nicolas , Bozaoglu Kiymet , McLean Catriona A. , Thomas Paul Q. , Finkelstein David I. , Lockhart Paul 
Published: March 2020

Abstract
Pathogenic variants in the gene encoding the small GTPase Ras analogue in Brain 39b (RAB39B) are associated with early-onset parkinsonism. In this study we investigated the expression and localization of RAB39B (RNA and protein) in mouse brain tissue to gain a better understanding of its normal physiological function(s) and role in disease.We developed novel resources, including monoclonal antibodies directed against RAB39B and mice with Rab39b knockout, and performed real-time PCR and western blot analysis on whole brain lysates. To determine the spatial localization of Rab39b RNA and protein, we performed in-situ hybridization and immunohistochemistry on fresh frozen and fixed brain tissue. Our results show that RAB39B is localized throughout the cortex, hippocampus and substantia nigra of mice throughout postnatal life. We found high levels of RAB39B within MAP2 positive cortical and hippocampal neurons, and TH positive dopaminergic neurons in the substantia nigra pars compacta.Our studies support and extend current knowledge of the localization of RAB39B. We validate RAB39B as a neuron-enriched protein and demonstrate that it is present throughout the mouse cortex and hippocampus. Further, we observe high levels in the substantia nigra pars compacta, the brain region most affected in Parkinson’s disease pathology. The distribution of Rab39b is consistent with human disease associations with parkinsonism and cognitive impairment. We also describe and validate novel resources, including monoclonal antibodies directed against RAB39B and mice with Rab39b knockout, both of which are valuable tools for future studies of the molecular function of RAB39B.
Full-length transcriptome sequencing and comparative transcriptomic analysis to uncover genes involved in early gametogenesis in the gonads of Amur sturgeon (Acipenser schrenckii)
Authors: Zhang Xiujuan , Zhou Jiabin , Li Linmiao , Huang Wenzhong , Ahmad Hafiz Ishfaq , Li Huiming , Jiang Haiying , Chen Jinping 
Published: March 2020

Abstract
Background: Sturgeons (Acipenseriformes) are polyploid chondrostean fish that constitute an important model species for studying development and evolution in vertebrates. To better understand the mechanisms of reproduction regulation in sturgeon, this study combined PacBio isoform sequencing (Iso-Seq) with Illumina short-read RNA-seq methods to discover full-length genes involved in early gametogenesis of the Amur sturgeon, Acipenser schrenckii .
Results: A total of 50.04 G subread bases were generated from two SMRT cells, and herein 164,618 nonredundant full-length transcripts (unigenes) were produced with an average length of 2,782 bp from gonad tissues (three testes and four ovaries) from seven 3-year-old A. schrenckii individuals. The number of ovary-specific expressed unigenes was greater than those of testis (19,716 vs. 3,028), and completely different KEGG pathways were significantly enriched between the ovary-biased and testis-biased DEUs. Importantly, 60 early gametogenesis-related genes (involving 755 unigenes) were successfully identified, and exactly 50 percent (30/60) genes of those showed significantly differential expression in testes and ovaries. Among these, the Amh and Gsdf with testis-biased expression, and the Foxl2 and Cyp19a with ovary-biased expression strongly suggested the important regulatory roles in spermatogenesis and oogenesis of A. schrenckii , respectively. We also found the four novel Sox9 transcript variants, which increase the numbers of regulatory genes and imply function complexity in early gametogenesis. Finally, a total of 236,672 AS events (involving 36,522 unigenes) were detected, and 10,556 putative long noncoding RNAs (lncRNAs) and 4,339 predicted transcript factors (TFs) were also respectively identified, which were all significantly associated with the early gametogenesis of A. schrenckii .
Conclusions: Overall, our results provide new genetic resources of full-length transcription data and information as a genomic-level reference for sturgeon. Crucially, we explored the comprehensive genetic characteristics that differ between the testes and ovaries of A. schrenckii in the early gametogenesis stage, which could provide candidate genes and theoretical basis for further the mechanisms of reproduction regulation of sturgeon.
Health inequalities in workers from fifteen countries of Latin America and the Caribbean
Authors: Silva-Peñaherrera Michael , Lopez-Ruiz María , Merino-Salazar Pamela , Gómez-García Antonio Ramón , Benavides Fernando G. 
Published: March 2020

Abstract
Background: Latin America and the Caribbean (LAC) is the world’s most inequitable region in terms of wealth distribution. The full scale of social inequalities in health has been hidden by the lack of reliable data. This study aimed to measure and compare health inequalities in the working population within and between 15 countries of LAC.
Methods: A sample of 180 163 workers ages 18 years and older was drawn from the most recent national surveys of working conditions or health in 15 LAC countries. Poor self-perceived health (P-SPH) was used as a health indicator, and age, education level, and occupational category as inequality stratifiers. We calculated four measures: absolute and relative population-attributable risks, the Kuznets and weighted Keppel indexes.

Results: P-SPH prevalence ranged from 9% in men from Uruguay to 50% in women from Nicaragua. It was higher in women than in men in most countries. A clear gradient was shown, in which young people in non-manual skilled jobs and high education had the lowest prevalence. Nearly 45% of cases that reported P-SPH among men and 35% among women could be avoided if all the groups received a higher level of education. Also, approximately 42% of P-SPH reported by men and 31% by women could be avoided if they all shared the working and employment conditions of non-manual skilled jobs.
Conclusions: Wide health inequalities were found between occupational and educational groups in LAC. However, country borders appear to be an even more important stratifier in the production of health inequalities. Urgent intervention is needed in countries where prevalence of poor self-perceived health is high. Monitoring of occupational health inequity is essential to inform public policies.
Key words: Health inequalities, occupational health; self-perceived health, inequity
Transplantation of neural stem cells encapsulated in hydrogels improve functional recovery in a cauda equina lesion model
Authors: Fu Zhiyi , Wang Huidong , Wu Yujie , Zhu Tong 
Published: March 2020

Abstract
Background

This study explored the therapeutic effects of transplantation of neural stem cells (NSCs) encapsulated in hydrogels in a cauda equina lesion model.

Methods

NSCs were isolated from neonatal dorsal root ganglion (DRG) and cultured in three-dimensional porous hydrogel scaffolds. Immunohistochemistry, transmission electron microscopy, Luxol fast blue staining, TUNEL assay were performed to detect the differentiation capability, ultrastructural and pathological changes, and apoptosis of NSCs. Furthermore, the functional recovery of sensorimotor reflexes was determined using the tail-flick test.

Results

NSCs derived from DRG were able to proliferate to form neurospheres and mainly differentiate into oligodendrocytes in the three-dimensional hydrogel culture system. After transplantation of NSCs encapsulated in hydrogels, NSCs differentiated into oligodendrocytes, neurons or astrocytes in vivo . Moreover, NSCs engrafted on the hydrogels decreased apoptosis and alleviated the ultrastructural and pathological changes of injured cauda equina. Behavioral analysis showed that transplanted hydrogel-encapsulated NSCs decreased the tail-flick latency and showed a neuroprotective role on injured cauda equina.

Conclusions

Our results indicate transplantation of hydrogel-encapsulated NSCs promotes stem cell differentiation into oligodendrocytes, neurons or astrocytes and contributes to the functional recovery of injured cauda equina, suggesting that NSCs encapsulated in hydrogels may be applied for the treatment of cauda equina injury.
Anxiety and Depression in Patients Who Undergo a Cerebrovascular Procedure
Authors: Lombardo Lauren , Shaw Richard , Sayles Kathleen , Altschul Dorothea 
Published: March 2020

Abstract
Background: Observe the relationship of anxiety and depression on quality of life outcomes after open and endovascular cerebrovascular procedures.

Methods: We retrospectively analyzed 349 patients who underwent a procedure for aneurysm, arteriovenous malformation, intraparenchymal hemorrhage, carotid stenosis, acute stroke, and conventional catheter angiogram over three years at a community hospital. We correlated pre-procedural anxiety and depression with Global Physical Health, Global Mental Health, and Modified Rankin Scale scores. We performed univariate and multivariate linear and logistic regression analyses adjusting for past medical history and sociodemographic factors.
Results: Anxiety or depression occurred in eighteen percent of patients. Patients with anxiety or depression were more likely to be female (81% vs 60.8%; p=0.002) and younger (54 vs. 59 years old; p=0.025). The groups did not differ in type or urgency of procedure, smoking or history of diabetes, or cardiovascular disease. Patients with anxiety or depression reported lower mental health scores at 30 days (45.1 vs 48.2; p=0.002) post-procedure. In multivariate analyses, anxious or depressed patients had worse mental health scores at 30 days (t=-2.893; p=0.008) than those who did not have a history of anxiety or depression. There was no difference between groups in length of stay, mortality, physical health t-scores, functionality scores, or six month quality of life outcomes.
Conclusions: Patients undergoing cerebrovascular procedures who self-reported anxiety or depression showed a significant difference in mental health outcomes at 30 days, but six month mental health and other medical and functional outcomes measures were similar to patients without these diagnoses.