Takshan/R1 huggingface dataset:
Systematic review and meta-analysis of diabetes mellitus, cardiovascular and respiratory condition epidemiology in sexual minority women.

OBJECTIVE: Sexual minority women (SMW) experience higher chronic disease risk factors than heterosexual counterparts. However, it was unclear if these risks translate into higher physical condition rates. This systematic review evaluates cardiovascular disease (CVD), hypertension, respiratory disease and diabetes mellitus in SMW. METHODS: A protocol was registered with the Prospero database (CRD42016050299). Included were studies reporting mortality, incidence or prevalence of the above-listed conditions in SMW compared with heterosexual women. Databases (platforms) searched from 2010 to December 2016 were Medline (Ovid), Embase (Elsevier), Cumulative Index to Nursing and Allied Health Literature (Elsevier), PsycINFO (Ovid), Social Policy and Practice (Ovid), Cochrane CENTRAL (Cochrane Library), Science Citation Index (Web of Science), and CAB Abstracts (Ovid). Search terms included Medical Subject Heading (MeSH) terms and text words. Extensive additional searches were conducted in specialist academic journals and websites. Two reviewers checked study eligibility. One independently extracted data and assessed quality, checked by a second reviewer, with disagreements resolved through discussion. The Critical Appraisal Skills Programme cohort checklist was used to assess risk of bias. Meta-analysis was conducted where more than four studies reported the same outcomes, with Comprehensive Meta-Analysis software, using adjusted ORs (AORs) and random-effects models. Heterogeneity was assessed using I2 test. RESULTS: Identified were 23 103 citations, 692 full texts screened and 16 studies included (in 18 papers). One reported mortality (from Denmark), none incidence and 15 prevalence (14 USA, 1 Australia). Same-sex cohabiting women had higher mortality rates compared with opposite-sex cohabiting women in CVD (HR=1.37 (95% CI 1.22 to 1.54)) and respiratory disease (HR=2.10 (95% CI 1.74 to 2.53)). AOR meta-analyses of seven studies showed higher asthma rates in lesbians (OR=1.44 (95% CI 1.27 to 1.64), I2=0%) and bisexual women (OR=1.64 (95% CI 1.41 to 1.89), I2=0%) but no differences for CVD (5 studies), hypertension (5 studies) or diabetes mellitus (7 studies). CONCLUSIONS: These new health estimates require further confirmatory epidemiological studies, and investigation into potential environmental, hormonal, physiological, psychological or genetic causes. This would be supported by routine collection of sexual identity measures in population-level epidemiological surveys.
Plant growth promoting rhizobacteria enhances wheat salt and drought stress tolerance by altering endogenous phytohormone levels and TaCTR1/TaDREB2 expression.

Abiotic stresses such as salt and drought represent adverse environmental conditions that significantly damage plant growth and agricultural productivity. In this study, the mechanism of the plant growth promoting rhizobacteria (PGPR) stimulated tolerance against abiotic stresses has been explored. Results suggest that PGPR strains, Arthrobacter protophormiae (SA3) and Dietzia natronolimnaea (STR1) can facilitate wheat crop in tolerating salt stress while Bacillus subtilis (LDR2) can provide tolerance to wheat crop against drought stress. These PGPR strains enhance photosynthetic efficiency under salt and drought stress conditions. Moreover, all three PGPR strains increase IAA content of wheat under salt and drought stress conditions. The SA3 and LDR2 inoculations counteracted the increase of abscisic acid (ABA) and ACC under both salt and drought stress conditions whereas STR1 had no significant impact on the ABA and ACC content. The impact of PGPR inoculations on these physiological parameters were further confirmed by gene expression analysis as we observed enhanced levels of TaCTR1 gene in SA3, STR1 and LDR2 treated wheat seedlings as compared to un-inoculated drought and salt stressed plants. PGPR inoculations enhanced expression of TaDREB2 gene encoding for a transcription factor which has been shown to be important for improving the tolerance of plants to abiotic stress conditions. Our study suggest that PGPR confer wheat plants abiotic stress tolerance by enhancing IAA content, reducing ABA/ACC content, modulating expression of a regulatory component (CTR1) of ethylene signaling pathway and DREB2 transcription factor.
Prevalence and characteristics of sleep-disordered breathing in familial dysautonomia.

OBJECTIVE: Familial dysautonomia (FD) is an autosomal recessive disorder characterized by impaired development of sensory and afferent autonomic nerves. Untreated sleep-disordered breathing (SDB) has been reported to increase the risk of sudden unexpected death in FD. We aimed to describe the prevalence and characteristics of SDB in FD. PATIENTS/METHODS: Seventy-five patients with FD (20 adults and 55 children) underwent in-lab polysomnography, including peripheral capillary oxygen saturation (SpO2) and end-tidal capnography (EtCO2) measurements. A t-test and Spearman's correlation analysis were performed to evaluate the impact of age on sleep, occurrence of apneas, SpO2 and EtCO2 levels; and to determine the relationship between apneas and SpO2/EtCO2 measurements during different sleep stages. RESULTS: Overall, 85% of adults and 91% of pediatric patients had some degree of SDB. Obstructive sleep apneas were more severe in adults (8.5 events/h in adults vs. 3.5 events/h in children, p = 0.04), whereas central apneas were more severe (10.8 vs. 2.8 events/h, p = 0.04) and frequent (61.8% vs. 45%, p = 0.017) in children. Overall, a higher apnea-hypopnea index was associated with increased severity of hypoxia and hypoventilation, although in a significant fraction of patients (67% and 46%), hypoxemia and hypoventilation occurred independent of apneas. CONCLUSION: Most adult and pediatric patients with FD suffer from some degree of SDB. There was a differential effect of age in the pattern of SDB observed. In some FD patients, hypoventilation and hypoxia occurred independently of apneas. Therefore, we recommend including EtCO2 monitoring during polysomnography in all patients with FD to detect SDB.
Empirical Evidence for the Outcomes of Therapeutic Video Games for Adolescents With Anxiety Disorders: Systematic Review.

BACKGROUND: Extant evidence suggests that the proportion of adolescents suffering from anxiety disorders (ADs) has increased by up to 70% since the mid-1980s, with experience of anxiety at this stage associated with significant negative short- and long-term life outcomes. The existing therapeutic interventions (eg, cognitive behavioral therapy, CBT; attention bias modification, ABM) have proven to have clinically measurable benefits in reducing anxiety, but their efficacy is often compromised by social and practical barriers. The growing discrepancy between demand for, and access to, clinical interventions for anxiety has led to the development of a range of eHealth (health care practice supported by electronic processes and communication) and mHealth (versions of eHealth using mobile devices) interventions. One such protocol is therapeutic games, which aim to provide clinical frameworks in dynamic, adaptable, and personalized virtual environments. Although some evidence exists to suggest therapeutic games are associated with reductions in subjective anxiety and observed stress reactivity, there is currently, to our knowledge, no systematic review of the adherence to, and effectiveness of, therapeutic games for adolescent anxiety. OBJECTIVE: The aim of this review was to establish the effectiveness of therapeutic games in making clinically measurable reductions in anxiety symptoms in adolescent samples. METHODS: A systematic search of the existing academic literature published between 1990 and July 2017 was conducted using the databases Journal of Medical Internet Research, Journal Storage, Psychology Articles, Psychology Info, ScienceDIRECT, and Scopus. Records linked to empirical papers on therapeutic games for anxiety using adolescent samples were evaluated. RESULTS: A total of 5 studies (N=410 participants) met the inclusion criteria, and 3 gamified anxiety interventions for adolescents were identified. The papers included a mixture of randomized controlled trials, quasi-experimental studies, and usability studies comprising quantitative and qualitative measures, with varying degrees of mixed methods. Extant evidence shows potential for therapeutic games to create clinically measurable reductions in symptoms of anxiety in adolescent samples, though findings are complicated in some cases by a low sample size, and in other cases by research design and methodological complications, including anxiety reductions in control groups caused by a control-game selection. CONCLUSIONS: Although research in this field appears to be extremely limited, as demonstrated by the small number of papers meeting the inclusion criteria for this review, early findings suggest that therapeutic games have potential in helping to engage adolescents with anxiety and lead to clinically measurable reductions in symptoms.
Verbal autopsy in health policy and systems: a literature review.

Introduction: Estimates suggest that one in two deaths go unrecorded globally every year in terms of medical causes, with the majority occurring in low and middle-income countries (LMICs). This can be related to low investment in civil registration and vital statistics (CRVS) systems. Verbal autopsy (VA) is a method that enables identification of cause of death where no other routine systems are in place and where many people die at home. Considering the utility of VA as a pragmatic, interim solution to the lack of functional CRVS, this review aimed to examine the use of VA to inform health policy and systems improvements. Methods: A literature review was conducted including papers published between 2010 and 2017 according to a systematic search strategy. Inclusion of papers and data extraction were assessed by three reviewers. Thereafter, thematic analysis and narrative synthesis were conducted in which evidence was critically examined and key themes were identified. Results: Twenty-six papers applying VA to inform health policy and systems developments were selected, including studies in 15 LMICs in Africa, Asia, the Middle East and South America. The majority of studies applied VA in surveillance sites or programmes actively engaging with decision makers and governments in different ways and to different degrees. In the papers reviewed, the value of continuous collection of cause of death data, supplemented by social and community-based investigations and underpinned by electronic data innovations, to establish a robust and reliable evidence base for health policies and programmes was clearly recognised. Conclusion: VA has considerable potential to inform policy, planning and measurement of progress towards goals and targets. Working collaboratively at sub-national, national and international levels facilitates data collection, aggregation and dissemination linked to routine information systems. When used in partnerships between researchers and authorities, VA can help to close critical information gaps and guide policy development, implementation, evaluation and investment in health systems.
Do people with multiple sclerosis want to know their prognosis? A UK nationwide study.

BACKGROUND: Multiple sclerosis (MS) has a varied and uncertain trajectory. The recent development of analytical processing tools that draw on large longitudinal patient databases facilitates personalised long-term prognosis estimates. This has the potential to improve both shared treatment decision-making and psychological adjustment. However, there is limited research on how people with MS feel about prognosis communication and forecasting. This study investigated the prognosis communication experiences and preferences of people with MS and explored whether clinical, demographic and psychological factors are associated with prognosis information preferences. METHODS: 3175 UK MS Register members (59% of those with active accounts) completed an online survey containing 17 questions about prognosis communication experiences, attitudes and preferences. Participants also completed validated questionnaires measuring coping strategies, tendencies to seek out ('monitor') or avoid ('blunt') information in threatening situations, and MS risk perceptions and reported their clinical and sociodemographic characteristics. Data already held on the MS Register about participants' quality of life, anxiety and depression symptoms and MS impact were obtained and linked to the survey data. RESULTS: 53.1% of participants had never discussed long-term prognosis with healthcare professionals. 54.2% lacked clarity about their long-term prognosis. 76% had strong preferences for receiving long-term prognosis information. 92.8% were interested in using tools that generate personalised predictions. Most participants considered prognostication useful for decision-making. Participants were more receptive to receiving prognosis information at later time-points, versus at diagnosis. A comprehensive set of sociodemographic, clinical and psychological variables predicted only 7.9% variance in prognosis information preferences. CONCLUSIONS: People with MS have an appetite for individualised long-term prognosis forecasting and their need for information is frequently unmet. Clinical studies deploying and evaluating interventions to support prognostication in MS are now needed. This study indicates suitable contexts and patient preferences for initial trials of long-term prognosis tools in clinical settings.
A systematic review of the cost and economic outcomes of home enteral nutrition.

OBJECTIVES: Studies are lacking in the health economic implications of home enteral nutrition (HEN) in home-residing and long-term care/institutionalized patients. The aims of this review were to determine the total costs, the cost-effectiveness and other economic outcomes for HEN. DESIGN: A systematic search of randomized trials and observational studies available from January 2000 to April 2016 was performed using standard literature and electronic databases. Inclusion criteria were adults receiving HEN with economic outcomes in the long-term care or home settings. There was no restriction to the control groups used in the studies. RESULTS: A total of 10 studies met the inclusion criteria. The majority of the studies were not specifically designed for economic evaluation. Cost per QALY was lower in residents residing in home compared to long-term care facilities, and HEN appeared to be cost-effective for those with pressure ulcers. Higher costs were incurred for patients with dementia on HEN. Lower hospitalization costs and infection rates were reported for patients who switched to commercial feeds from blenderized food. The availability of nutritional support teams may decrease overall costs but these studies were of poor study quality. CONCLUSIONS: The lack of good quality economic evaluation studies affected the ability to conclude the overall cost-effectiveness of HEN. There is a trend for cost-saving and improved clinical outcomes in some populations. HEN is unlikely beneficial for patients with dementia. The availability of a nutrition support team may lead to cost savings and improved clinical outcomes for HEN.
The use of a specialised amino acid mixture for pressure ulcers: a placebo-controlled trial.

OBJECTIVE: To compare pressure ulcer healing rates in patients supplemented with a specialised amino acid mixture containing (beta)-hydroxy (beta)-methylbutyrate (HMB), arginine and glutamine, and standard oral nutritional supplements versus patients supplemented with oral nutritional supplements and a placebo mixture. METHOD: Twenty-three inpatients with stage II, III or IV pressure ulcers in an acute care hospital were randomised to recieve (A) a HMB, arginine and glutamine mixture twice daily alongside oral nutritional supplements (n=11) or (B) standard nutritional care alongside oral nutritional supplements (n=12) for 2 weeks. Pressure ulcers were measured weekly for area, depth and Pressure Ulcer Scale for Healing (PUSH) scores. The proportion of viable tissue was determined based on area of wound tracing. Weekly laboratory tests were performed to measure C-reactive protein and pre-albumin levels. This trial is registered at http://ClinicalTrials.gov under NCT01090076. RESULTS: There was no difference between anthropometrical measurements, biochemical parameters and nutritional intake pre- and post- study. Wound area did not decrease significantly in the short term for both groups. The proportion of viable tissues increased within 2 weeks on HMB, arginine and glutamine supplementation (p=0.02). PUSH scores showed significant improvement within 1 week of supplementation for the experimental group (p=0.013). CONCLUSION: The use of specialised amino acid does not appear to reduce wound size and PUSH scores but may improve tissue viability after 2 weeks. Further confirmation on a larger scale is required to determine the benefits of supplementing additional HMB, arginine and glutamine in patients with pressure ulcers.
Ensemble of rankers for efficient gene signature extraction in smoke exposure classification.

BACKGROUND: System toxicology aims at understanding the mechanisms used by biological systems to respond to toxicants. Such understanding can be leveraged to assess the risk of chemicals, drugs, and consumer products in living organisms. In system toxicology, machine learning techniques and methodologies are applied to develop prediction models for classification of toxicant exposure of biological systems. Gene expression data (RNA/DNA microarray) are often used to develop such prediction models. RESULTS: The outcome of the present work is an experimental methodology to develop prediction models, based on robust gene signatures, for the classification of cigarette smoke exposure and cessation in humans. It is a result of the participation in the recent sbv IMPROVER SysTox Computational Challenge. By merging different gene selection techniques, we obtain robust gene signatures and we investigate prediction capabilities of different off-the-shelf machine learning techniques, such as artificial neural networks, linear models and support vector machines. We also predict six novel genes in our signature, and firmly believe these genes have to be further investigated as biomarkers for tobacco smoking exposure. CONCLUSIONS: The proposed methodology provides gene signatures with top-ranked performances in the prediction of the investigated classification methods, as well as new discoveries in genetic signatures for bio-markers of the smoke exposure of humans.
Identification, characterization and heparin binding capacity of a spore-wall, virulence protein from the shrimp microsporidian, Enterocytozoon hepatopenaei (EHP).

BACKGROUND: The microsporidian Enterocytozoon hepatopenaei (EHP) is a spore-forming, intracellular parasite that causes an economically debilitating disease (hepatopancreatic microsporidiosis or HPM) in cultured shrimp. HPM is characterized by growth retardation and wide size variation that can result in economic loss for shrimp farmers. Currently, the infection mechanism of EHP in shrimp is poorly understood, especially at the level of host-parasite interaction. In other microsporidia, spore wall proteins have been reported to be involved in host cell recognition. For the host, heparin, a glycosaminoglycan (GAG) molecule found on cell surfaces, has been shown to be recognized by many parasites such as Plasmodium spp. and Leishmania spp. RESULTS: We identified and characterized the first spore wall protein of EHP (EhSWP1). EhSWP1 contains three heparin binding motifs (HBMs) at its N-terminus and a Bin-amphiphysin-Rvs-2 (BAR2) domain at its C-terminus. A phylogenetic analysis revealed that EhSWP1 is similar to an uncharacterized spore wall protein from Enterospora canceri. In a cohabitation bioassay using EHP-infected shrimp with naïve shrimp, the expression of EhSWP1 was detected by RT-PCR in the naïve test shrimp at 20 days after the start of cohabitation. Immunofluorescence analysis confirmed that EhSWP1 was localized in the walls of purified, mature spores. Subcellular localization by an immunoelectron assay revealed that EhSWP1 was distributed in both the endospore and exospore layers. An in vitro binding assay, a competition assay and mutagenesis studies revealed that EhSWP1 is a bona fide heparin binding protein. CONCLUSIONS: Based on our results, we hypothesize that EhSWP1 is an important host-parasite interaction protein involved in tethering spores to host-cell-surface heparin during the process of infection.
Expression analysis of the PMP22 gene in glioma and osteogenic sarcoma cell lines.

Previously we reported the amplification of the peripheral myelin protein 22 (PMP22) gene in cell lines of human osteogenic and glioma tumors. PMP22 normally is expressed at high levels in Schwann cells of the peripheral nervous system and is suggested to function as a structural protein of the myelin sheath. One of the most common inherited peripheral neuropathies, Charcot-Marie-Tooth Type 1A (CMT1A), is associated with a duplication of a 1.5-Mb DNA region on chromosome 17p11.2 - p12 containing PMP22. On the other hand, PMP22 is identical to gas3, whose expression is induced in growth-arresting NIH3T3-fibroblasts and is thought to play a role in cell proliferation. The precise role of gas3/PMP22 remains to be determined. Here we show that in the tumor cell lines RH30 and SF763 the amplified region including PMP22 comprises the whole 1.5-Mb CMT1A region. We could prove expression of PMP22 by reverse transcriptase-polymerase chain reaction (RT-PCR) and discovered an unusual PMP22 transcript in these tumor cell lines. Western blot analyses resulted in detection of a 22-kDa protein by the PMP22-specific antibody 558/2 and in exclusion of myelin protein zero (MPZ) expression in these cell lines.
Zoo-FISH with region-specific paints for mink chromosome 5q: delineation of inter- and intrachromosomal rearrangements in human, pig, and fox.

Comparison of evolutionarily conserved mammalian chromosomes homologous to human chromosome 17, performed with microdissected painting probes, revealed rearrangements inside these chromosomes in mink and pig and a disruption of this conserved region in the fox. Detection of a homologous region on an Iberian shrew chromosome showed the efficiency of microdissected painting probes for delineation of homologous chromosome regions in species belonging to orders that diverged at least 100 million years ago.
Genetic imbalances in 26 cases of penile squamous cell carcinoma.

To obtain more information on chromosomal changes in the up-to-now poorly studied tumor class of penile squamous cell carcinoma (SCC), we performed a comparative genomic hybridization study of 26 cases of this rare tumor. DNA sequence copy number alterations (CNAs) very similar to those detected in other SCC types, such as oral and esophageal SCC, were noted. The most common copy number gains were found in 8q24, 16p11-12, 20q11-13, 22q, 19q13, and 5p15, and the most common deletions were detected in 13q21-22, 4q21-32, and along the X chromosome. Classifying the patients according to the number of CNAs showed a possible correlation with clinical outcome.