Miracle-dz/UniFAR-FTUs huggingface dataset:
Temperate performance and metabolic adaptations following endurance training performed under environmental heat stress

Endurance athletes are frequently exposed to environmental heat stress during training. We investigated whether exposure to 33°C during training would improve endurance performance in temperate conditions and stimulate mitochondrial adaptations. Seventeen endurance‐trained males were randomly assigned to perform a 3‐week training intervention in 18°C (TEMP) or 33°C (HEAT). An incremental test and 30‐min time‐trial preceded by 2‐h low‐intensity cycling were performed in 18°C pre‐ and post‐intervention, along with a resting vastus lateralis microbiopsy. Training was matched for relative cardiovascular demand using heart rates measured at the first and second ventilatory thresholds, along with a weekly “best‐effort” interval session. Perceived training load was similar between‐groups, despite lower power outputs during training in HEAT versus TEMP (p < .05). Time‐trial performance improved to a greater extent in HEAT than TEMP (30 ± 13 vs. 16 ± 5 W, N = 7 vs. N = 6, p = .04), and citrate synthase activity increased in HEAT (fold‐change, 1.25 ± 0.25, p = .03, N = 9) but not TEMP (1.10 ± 0.22, p = .22, N = 7). Training‐induced changes in time‐trial performance and citrate synthase activity were related (r = .51, p = .04). A group × time interaction for peak fat oxidation was observed (Δ 0.05 ± 0.14 vs. −0.09 ± 0.12 g·min−1 in TEMP and HEAT, N = 9 vs. N = 8, p = .05). Our data suggest exposure to moderate environmental heat stress during endurance training may be useful for inducing adaptations relevant to performance in temperate conditions.
The START study: An evaluation to study the impact of a natural experiment in high school start times on adolescent weight and related behaviors

Abstract:Background:Research has shown that early high school start times, which are asynchronous with adolescent biology, are one of the most significant obstacles to youth being able to net sufficient sleep. Given that adolescence is a critical period that sets the stage for long-term obesity risk behavior patterns, there is an need to understand the obesity-related implications of increased sleep as a result of intervention and policy changes.Methods:We evaluated a community-based natural experiment in school start time policy modification when several Minneapolis-St. Paul, MN metro area school districts shifted to later school start times in Fall 2016. We collected data on student weight and related risks (via paper survey, objective weight and height measurement, dietary recall, and sleep actigraphy) before and after two districts (two high schools) shifted their start times later and in a comparison district (three high schools) which kept their start times early (7:30am) through the course of the study. Our specific aims were: 1) Determine how a shift to a later high school start time relates to objectively measured weight change over time. 2) Identify the relationship between school start times and obesity-related behaviors over time.At baseline we had 2,133 returned surveys (93% participation) and 2,037 (86% participation) objective height/weight measurements from 9th grade students (class of 2019) in the five schools. The sample was 87.7% white, 12.8% reported qualifying for free/reduced price lunch (a measure of lower socio-economic status), and the mean age was 15.2 (SD=0.35) years.Discussion:The products of this research will clarify causal connections between sleep and obesity among adolescents as well as provide evidence for whether a school start time policy can minimize unhealthy weight gain.
DetectIS: a pipeline to rapidly detect exogenous DNA integration sites using DNA or RNA paired-end sequencing data

Abstract Motivation Recombinant DNA technology is widely used for different applications in biology, medicine and bio-technology. Viral transduction and plasmid transfection are among the most frequently used techniques to generate recombinant cell lines. Many of these methods result in the random integration of the plasmid into the host genome. Rapid identification of the integration sites is highly desirable in order to characterize these engineered cell lines. Results We developed detectIS: a pipeline specifically designed to identify genomic integration sites of exogenous DNA, either a plasmid containing one or more transgenes or a virus. The pipeline is based on a Nextflow workflow combined with a Singularity image containing all the necessary software, ensuring high reproducibility and scalability of the analysis. We tested it on simulated datasets and RNA-seq data from a human sample infected with Hepatitis B virus. Comparisons with other state of the art tools show that our method can identify the integration site in different recombinant cell lines, with accurate results, lower computational demand and shorter execution times. Availability and implementation The Nextflow workflow, the Singularity image and a test dataset are available at https://github.com/AstraZeneca/detectIS. Supplementary information Supplementary data are available at Bioinformatics online.
Experiences of family caregivers regarding a community-based care- and case-management intervention. A qualitative study.

Family caregivers play an essential role in healthcare for elderly people in primary care settings. The complexity of geriatric patients as well as the fragmentation of healthcare systems can lead to a burden for family caregivers, which can affect their physical and psychological health as well as social relationships, economic productivity and quality of caregiving. Care- and case-management offers a possibility to support, empower and navigate family caregivers through healthcare systems in order to reduce their own burden. The project RubiN (Continuous care in a regional network) was developed to provide regional care- and case-management for outpatient care of the elderly (age >70 years) in a primary care setting in Germany. The aim of this qualitative study was to explore experiences and attitudes of family caregivers of geriatric patients regarding the community-based care- and case-management intervention RubiN. Telephone interviews with a purposeful sample of 21 family caregivers enlisted in all RubiN networks were conducted between March and May 2020 and were followed by qualitative content analysis. The main categories, which emerged were namely: (1) current healthcare situation and (2) experiences with RubiN. Main findings suggest that participants in this study valued the provided support and experienced a sense of relief. However, some participants were disappointed with RubiN and the included support by care- and case-managers. A care- and case-management affected caregiving per se as well as the patient's and family caregiver's well-being. Important aspects contributing to these findings were a continuous relationship, training and expertise of the care- and case-managers. Establishing networks between the patients, family caregivers, care- and case-managers and healthcare providers were key components as well as a good explanation about RubiN itself for family caregivers. Therefore, a community-based care- and case-management can play an important role in detecting, facilitating and preventing family caregiver burden.
Noncovalent microarrays from synthetic amino-terminating glycans: Implications in expanding glycan microarray diversity and platform comparison

Abstract Glycan microarrays have played important roles in detection and specificity assignment of glycan recognition by proteins. However, the size and diversity of glycan libraries in current microarray systems are small compared to estimated glycomes, and these may lead to missed detection or incomplete assignment. For microarray construction, covalent and noncovalent immobilization are the two types of methods used, but a direct comparison of results from the two platforms is required. Here we develop a chemical strategy to prepare lipid-linked probes from both naturally derived aldehyde-terminating and synthetic amino-terminating glycans that addresses the two aspects: expansion of sequence-defined glycan libraries and comparison of the two platforms. We demonstrate the specific recognition by plant and mammalian lectins, carbohydrate-binding modules and antibodies and the overall similarities from the two platforms. Our results provide new knowledge on unique glycan-binding specificities for the immune receptor Dectin-1 toward β-glucans and the interaction of rotavirus P[19] adhesive protein with mucin O-glycan cores.
Effortless retaliation: the neural dynamics of interpersonal intentions in the Chicken Game using brain–computer interface

Abstract The desire for retaliation is a common response across a majority of human societies. However, the neural mechanisms underlying aggression and retaliation remain unclear. Previous studies on social intentions are confounded by a low-level response-related brain activity. Using an Electroencephalogram (EEG)-based brain–computer interface combined with the Chicken Game, our study examined the neural dynamics of aggression and retaliation after controlling for nonessential response-related neural signals. Our results show that aggression is associated with reduced alpha event-related desynchronization (alpha-ERD), indicating reduced mental effort. Moreover, retaliation and tit-for-tat strategy use are also linked with smaller alpha-ERD. Our study provides a novel method to minimize motor confounds and demonstrates that choosing aggression and retaliation is less effortful in social conflicts.
High-quality genome assembly of Pseudopestalotiopsis theae, the pathogenic fungus of tea grey blight.

Tea grey blight is one of the most serious foliar diseases of tea tree caused by the plant pathogenic fungus Pseudopestalotiopsis theae which can affect production and quality of tea worldwide. We generated a highly contiguous, 50.41Mbp genome assembly (N50 1.30 Mbp) of P. theae strain CYF27 by combining PacBio long-read and Illumina short-read sequencing technologies. We identified a total of 15,626 gene models, of which 1,038 genes encode putative secreted proteins. The high-quality genome assembly and annotation resource reported here will be useful for the study of fungal infection mechanisms and pathogen-host interaction.
Associations between beta-blocker use and psychological distress in bereaved adults with cardiovascular conditions.

The death of a close other is a major life stressor that disrupts mental and physical health. Beta-blocker medications are indicated treatments for cardiovascular conditions that may also mitigate psychological distress in the context of stressors by reducing adrenergic activity. We sought to examine observational links between beta-blocker medication use and psychological distress during bereavement. Using publicly-available data from the Midlife in the United States Refresher study, we examined associations between beta-blocker use and general distress, depressive symptoms, and anxiety symptoms (as measured by the Mood and Anxiety Symptom Questionnaire) among bereaved adults with cardiovascular conditions (n=161) using t-tests and regression models. Beta-blocker users reported lower levels- of anxiety-related general distress (b= -2.49, SE=0.88, p=.005) and depression-related general distress than non-users (b= -2.39, SE=1.14, p=.039) in multivariate linear regression models adjusting for demographic characteristics, mental health treatments, time since loss, and comorbid health conditions. These observed links between beta-blockers and lower psychological distress in bereavement warrant further investigation in prospective and randomized studies, as beta-blockers could be a scalable intervention for mitigating distress following loss. This article is protected by copyright. All rights reserved.
BiPella: Mini Review on a Novel Method to Treat Cardiogenic Shock Patients.

Despite medical advancements in treatment of cardiogenic shock, it still remains as a condition with highmorbidity and mortality. There are many treatment modalities to help the heart’s pumping function and perfusion in compromised states, such as inotrope & vasopressor application, intra-aortic balloon pump (IABP) counterpulsation, percutaneous left ventricular assist devices, which are Tandem Heart and Impella (Abiomed, MA, USA); and lastly, surgically placed left ventricular assist devices (LVAD). 1-7 In severe cases where pharmacologic treatment and percutaneous options are not enough to stabilize hemodynamic status and where surgery is not applicable, novel approaches should be applied. Benefits of Impella devices in supporting left ventricle (LV) in cardiogenic shock are well established, 1,2,5,8,9
Antimicrobial activities of Bacillus velezensis strains isolated from stingless bee products against methicillin-resistant Staphylococcus aureus

Infections caused by methicillin-resistant Staphylococcus aureus (MRSA) have reached epidemic proportions globally. Therefore, there is an urgent need for a continuous supply of antibiotics to combat the problem. In this study, bacteria initially identified as species belonging to the Bacillus amyloliquefaciens operational group were re-identified based on the housekeeping gene, gyrB. Cell-free supernatants (CFS) from the strains were used for antimicrobial tests using the agar well diffusion assay against MRSA and various types of pathogenic bacteria. The minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC) and physicochemical characteristics of the CFS were determined. Based on gyrB sequence analysis, five strains (PD9, B7, PU1, BP1 and L9) were identified as Bacillus velezensis. The CFS of all B. velezensis strains showed broad inhibitory activities against Gram-negative and -positive as well as MRSA strains. Strain PD9 against MRSA ATCC 33742 was chosen for further analysis as it showed the biggest zone of inhibition (21.0 ± 0.4 mm). The MIC and MBC values obtained were 125 μl/ml. The crude antimicrobial extract showed bactericidal activity and was stable at various temperatures (40–80°C), pH (4–12), surfactants (Tween 20, Tween 80, SDS and Triton X-100) and metal ions (MgCI2, NaCI2, ZnNO3 and CuSO4) when tested. However, the crude extract was not stable when treated with proteinase K. All these properties resembled the characteristics of peptides. The antimicrobial compound from the selected strain was purified by using solvent extraction method and silica gel column chromatography. The purified compound was subjected to High Performance Liquid Chromatography which resulted in a single peak of the anti-MRSA compound being detected. The molecular weight of the anti-MRSA compound was determined by using SDS-PAGE and zymogram. The size of the purified antimicrobial peptide was approximately ~ 5 kDa. The antimicrobial peptide produced from B. velezensis strain PD9 is a promising alternative to combat the spread of MRSA infections in the future.
Study quality and efficacy of psychological interventions for posttraumatic stress disorder: a meta-analysis of randomized controlled trials

Abstract Background Research indicates that higher study quality may be associated with smaller treatment effects. Yet, knowledge about the association between study quality and treatment efficacy for posttraumatic stress disorder (PTSD) is limited. We aimed at evaluating the efficacy of psychological interventions for adult PTSD and the association between study quality and treatment effects. Methods We conducted a systematic search to identify randomized controlled trials (RCTs) that examined the efficacy of psychological interventions for chronic PTSD symptoms in adult samples with at least 70% of patients being diagnosed with PTSD by means of a structured interview. We assessed study quality using the following eight criteria from prior research: N ⩾ 50, all patients met criteria for PTSD, a treatment manual was used, therapists were trained, treatment integrity was checked, intent-to-treat analyses were applied, randomization was conducted by an independent party, and treatment outcome was conducted by blind assessors. Results The search resulted in 136 RCTs with 8978 patients. Active treatment conditions were largely effective in reducing PTSD symptoms at posttreatment and follow-up (Hedges' g = 1.09 and 0.81, respectively) when compared to passive control conditions. The comparison to active control conditions at posttreatment and follow-up resulted in medium effect sizes. A total of 14 trials met all study quality criteria and these trials produced large effect sizes when compared to passive control conditions at posttreatment and follow-up. Conclusions Overall, study quality was not significantly associated with effect size. The findings indicate that psychological interventions can effectively reduce PTSD symptoms irrespective of study quality.
A Ran-binding protein facilitates nuclear import of human papillomavirus type 16

Human papillomaviruses (HPVs) utilize an atypical mode of nuclear import during cell entry. Residing in the Golgi apparatus until mitosis onset, a subviral complex composed of the minor capsid protein L2 and viral DNA (L2/vDNA) is imported into the nucleus after nuclear envelope breakdown by associating with mitotic chromatin. In this complex, L2 plays a crucial role in the interactions with cellular factors that enable delivery and ultimately tethering of the viral genome to mitotic chromatin. To date, the cellular proteins facilitating these steps remain unknown. Here, we addressed which cellular proteins may be required for this process. Using label-free mass spectrometry, biochemical assays, microscopy, and functional virological assays, we discovered that L2 engages a hitherto unknown protein complex of Ran-binding protein 10 (RanBP10), karyopherin alpha2 (KPNA2), and dynein light chain DYNLT3 to facilitate transport towards mitotic chromatin. Thus, our study not only identifies novel cellular interactors and mechanism that facilitate a poorly understood step in HPV entry, but also a novel cellular transport complex.
Efficacy and Safety of Platinum-Based Chemotherapy as First-Line Therapy for Metastatic Triple-Negative Breast Cancer: A Meta-Analysis of Randomized Controlled Trials

Background: Triple-negative breast cancer constitutes approximately 12%-17% of all breast cancer cases, and >33% of patients develop distant metastases. Systemic cytotoxic chemotherapy is the primary treatment for patients with metastatic triple-negative breast cancer; however, the role of first-line platinum-based chemotherapy in these patients remains controversial. This meta-analysis evaluated the efficacy and safety of platinum-based first-line chemotherapy for patients with metastatic triple-negative breast cancer. Methods: We systematically searched the PubMed, Embase, Cochrane, and Clinical Trials registry databases up to June 1, 2020 to identify randomized controlled trials that investigated platinum-based vs. first-line platinum-free chemotherapy in patients with metastatic triple-negative breast cancer. We used fixed and random effects models to calculate pooled hazard ratios and odds ratios with 95% confidence intervals for progression-free and overall survival, objective response rates, and grade 3 and 4 adverse events. Results: Four randomized controlled trials (N = 590 patients) were included. Platinum-based chemotherapy significantly increased the objective response rates from 43.1% to 62.7% (odds ratio 2.34, 95% confidence interval 1.66-3.28, P < 0.001). Three randomized controlled trials (N = 414 patients) reported survival outcomes. Patients administered platinum-based regimens showed significantly longer progression-free survival (hazard ratio 0.55, 95% confidence interval 0.37-0.82, P = 0.004) and a nonsignificant trend toward improved overall survival (hazard ratio 0.76, 95% confidence interval 0.57-1.00, P = 0.05). Only 2 studies reported the rates of grade 3 and 4 adverse events; grade 3-4 thrombocytopenia was more commonly associated with platinum-based chemotherapy (odds ratio 7.54, 95% confidence interval 1.37-41.60, P = 0.02) and grade 3-4 fatigue with platinum-free chemotherapy (odds ratio 0.23, 95% confidence interval 0.08-0.68, P = 0.008). Conclusions: First-line platinum-based chemotherapy was associated with significantly increased objective response rates, longer progression-free survival, and a nonsignificant trend toward improved overall survival in patients with metastatic triple-negative breast cancer at the high risk of grade 3-4 thrombocytopenia.
Low amounts of heavy water increase the phase separation propensity of a fragment of the androgen receptor activation domain

The phase equilibria of intrinsically disordered proteins are exquisitely sensitive to changes in solution conditions and this can be used to investigate the driving forces of phase separation in vitro as well as the biological roles of phase transitions in live cells. Here we investigate how using D2O as co‐solvent in an aqueous buffer changes the phase equilibrium of a fragment of the activation domain of the androgen receptor, a transcription factor that plays a role in the development of the male phenotype and is a therapeutic target for castration resistant prostate cancer. We show how replacing even small fractions of H2O with D2O increases the propensity of this fragment to undergo liquid–liquid phase separation, likely reflecting a stabilization of the hydrophobic interactions that drive condensation. Our results indicate that it is necessary to take this effect into consideration when studying phase separation phenomena with biophysical methods that require using D2O as a co‐solvent. In addition, they suggest that additions of D2O may be used to enhance phase separation phenomena in cells, facilitating their observation.
Psychometric properties of the Food Environment Assessment Survey Tool (FEAST) in people with mobility impairment

Abstract Objective: Approximately one in ten adults under the age of 65 in the USA has a mobility impairing disability. People with mobility impairment generally have poorer dietary habits contributing to obesity and related negative health outcomes. This article presents the psychometric properties of the Food Environment Assessment Survey Tool (FEAST) instrument that measures barriers to accessing healthy food from the perspective of people with mobility impairment (PMI). Design: The current study presents cross-sectional data from two sequential independent surveys. Setting: Surveys were administered online to a national sample of PMI. Participants: Participants represented PMI living throughout the USA. The pilot FEAST survey involved 681 participants and was used to shape the final instrument; 25 % completed a retest survey. After following empirically and theoretically guided item reduction strategies, the final FEAST instrument was administered to a separate sample of 304 PMI. Results: The final twenty-seven-item FEAST instrument includes items measuring Neighbourhood Environment, Home Environment, Personal Control and Access to Support (Having Help, Food Delivery Services, Parking/Transportation). The final four scales had acceptable intra-class correlations, indicating that the scales could be used as reliable measures of the hypothesised constructs in future studies. Conclusions: The FEAST instrument is the first of its kind developed to assess the food environment from the perspective of PMI themselves. Future studies would benefit from using this measure in research and practice to help guide the development of policy aimed at improving access to healthy food and promoting healthy eating in community-dwelling PMI.