Miracle-dz/UniFAR-FTUs huggingface dataset:
Prenatal thyroid hormone exposure increases growth but not oxidative stress in a wild passerine species

Hormones transferred from mothers to their offspring are thought to be a maternal tool for mothers to prepare their progeny for expected environmental conditions, thus increasing fitness. Thyroid hormones (THs) are crucial across vertebrates for embryonic and post-natal development and metabolism. Nevertheless, the studies that investigated the consequences of maternal hormones have mostly focused on steroid hormones and ignored maternally-derived thyroid hormones. In this study, we experimentally elevated yolk thyroid hormones in a wild population of a migratory passerine, the European Pied flycatcher Ficedula hypoleuca. We injected eggs with a mixture of T4 and T3 within the natural range of the species to assess its effects on hatching success, nestling survival, growth and oxidative status (antioxidant enzyme activity, lipid peroxidation and oxidative balance). We found no effects of yolk THs on egg hatchability or nestling survival. Yolk THs increased nestling growth during the second week post hatching, but this potentially beneficial effect did not incur any costs in terms of oxidative stress. The results should stimulate more research on thyroid hormone mediated maternal effects, further studies into the underlying mechanistic pathways for these effects and how they translate into adulthood and fitness. Summary statement Thyroid hormones have been overlooked in the context of hormone-mediated maternal effects. We found that yolk thyroid hormones in a wild bird species increase growth without incurring oxidative stress.
COVID-19 Status Differentially Affects Olfaction: A Prospective Case-Control Study

Objective The symptoms and long-term sequelae of SARS-CoV-2 infection have yet to be determined, and evaluating possible early signs is critical to determine which patients should be tested and treated. The objective of this ongoing study is to evaluate initial and short-term rhinologic symptoms, olfactory ability, and general quality of life in patients undergoing SARS-CoV-2 testing. Study Design Prospective case-control. Setting Academic institute. Methods Adult patients tested for SARS-CoV-2 were prospectively enrolled and separated into positive and negative groups. Each participant completed 4 validated patient-reported outcome measures. The UPSIT (University of Pennsylvania Smell Identification Test) was distributed to patients who were SARS-CoV-2 positive. Results The positive group reported significantly decreased sense of smell and taste on the 22-item Sinonasal Outcome Test (SNOT-22) as compared with the negative group (mean ± SD: 3.4 ± 1.7 vs 1.2 ± 1.4, P < .001). The positive group had a much higher probability of reporting a decrease in smell/taste as “severe” or “as bad as it can be” (63.3% vs 5.8%) with an odds ratio of 27.6 (95% CI, 5.9-128.8). There were no differences between groups for overall SNOT-22 domain scores, PHQ-4 depression/anxiety (Patient Health Questionnaire−4), and 5-Level EQ-5D quality-of-life scores. Mean Self-MOQ (Self-reported Mini Olfactory Questionnaire) scores were 7.0 ± 5.6 for the positive group and 1.8 ± 4.0 for the negative group (P < .001). The mean UPSIT score was 28.8 ± 7.2 in the positive group. Conclusion Symptomatic patients who are SARS-CoV-2 positive report severe olfactory and gustatory dysfunction via the Self-MOQ and SNOT-22 as compared with symptomatic patients testing negative.
The promise of an intersectoral network in enhancing the response to transgender survivors of sexual assault

Objectives This study explores the promise of an intersectoral network in enhancing the response to transgender (trans) survivors of sexual assault. Methods One hundred and three representatives of healthcare and community organizations across Ontario, Canada were invited to participate in a survey. Respondents were asked to: 1) identify systemic challenges to supporting trans survivors, 2) determine barriers to collaborating across sectors, and 3) indicate how an intersectoral network might address these challenges and barriers. Descriptive statistics were used to summarize quantitative data and qualitative data were collated thematically. Results Sixty-seven representatives responded to the survey, for a response rate of 65%. Several themes capturing the challenges organizations face in supporting trans survivors were identified: Lack of knowledge and training among providers, Inadequate resources across organizations and institutions, and Limited access to and availability of appropriate services. Barriers to collaborating across sectors considered important by the overwhelming majority of respondents were: Lack of trans-positive service professionals (e.g., a paucity of sensitivity training), lack of resources (e.g., staff, staff time and workload, spaces to meet), and Institutional structures (e.g., oppressive policies, funding mandates). Four ways in which a network could address these challenges and barriers emerged from the data: Center the voices of trans communities in advocacy; Support competence of professionals to provide trans-affirming care; Provide the platform, strategies, and tools to aid in organizational change; and Create space for organizations to share ideas, goals, and resources. Conclusion Our findings deepen our understanding of important impediments to enhancing the response to trans survivors of sexual assault and the role networks of healthcare and community organizations can play in comprehensively responding to complex health and social problems.
Genome-Wide Characterization of OFP Family Genes in Wheat (Triticum aestivum L.) Reveals That TaOPF29a-A Promotes Drought Tolerance

OVATE family proteins (OFPs) are plant-specific transcription factors that play important roles in plant development. Although common wheat (Triticum aestivum L.) is a major staple food worldwide, OFPs have not been systematically analyzed in this important crop. Here, we performed a genome-wide survey of OFP genes in wheat and identified 100 genes belonging to 34 homoeologous groups. Arabidopsis thaliana, rice (Oryza sativa), and wheat OFP genes were divided into four subgroups based on their phylogenetic relationships. Structural analysis indicated that only four TaOFPs contain introns. We mapped the TaOFP genes onto the wheat chromosomes and determined that TaOFP17 was duplicated in this crop. A survey of cis-acting elements along the promoter regions of TaOFP genes suggested that subfunctionalization of homoeologous genes might have occurred during evolution. The TaOFPs were highly expressed in wheat, with tissue- or organ-specific expression patterns. In addition, these genes were induced by various hormone and stress treatments. For instance, TaOPF29a-A was highly expressed in roots in response to drought stress. Wheat plants overexpressing TaOPF29a-A had longer roots and higher dry weights than nontransgenic plants under drought conditions, suggesting that this gene improves drought tolerance. Our findings provide a starting point for further functional analysis of this important transcription factor family and highlight the potential of using TaOPF29a-A to genetically engineer drought-tolerant crops.
Fragile heroes. The psychological impact of the COVID-19 pandemic on health-care workers in Italy

This survey-based study aimed to explore the mental health status and psychological care needs of 933 health-care workers in Italy during the COVID-19 outbreak. Sociodemographic data, exposure to COVID-19, perception of psychological care needs, depression, anxiety, somatization, and post-traumatic symptoms were concurrently assessed. The majority of the sample (71%) suffered from somatization and 55% of distress. Female care workers experienced higher levels of anxiety (d = 0.50) and somatization symptoms (d = 0.82) and stated they needed psychological care more than men (p < .001). Younger participants (aged <40 years-old) reported higher levels of somatization, depression, anxiety, and post-traumatic symptoms (effects size range from d = 0.22 to d = 0.31). Working in a high infected area (red-zones) and directly with COVID-19 patients (front-line) affected the psychological health of participants to a smaller degree. Health-care workers who lost one of their patients reported higher levels of depression (d = 0.22), anxiety (d = 0.19), post-traumatic symptoms (d = 0.30), and psychological care needs than those who did not have the same experience (p < .01). Health-care workers who perceived the need for psychological support scored above the clinical alarming level (cut-off scores) in all the psychological scales, ranging from 76% to 88%. Psychological distress (p < .01), anxiety (p < .05), depression (p < .05), and being women (p < .01) contribute to explain the need for psychological care and accounted for 32% of the variance in this sample. These findings point out the importance to consider the psychological impact of COVID-19 on Italian health-care workers and strongly suggest establishing psychological support services for providing adequate professional care.
Pain Experiences and Their Relation to Opioid Misuse Risk and Emotion Dysregulation

Pain is a complex, multidimensional experience but often is measured as a unidimensional experience. This study aimed to separately assess the sensory and affective components of pain and identify their relations to important pain-related outcomes, particularly in terms of opioid misuse risk and emotion dysregulation among patients with chronic pain receiving treatment in Appalachia. Two hundred and twelve patients presenting to a multidisciplinary pain center completed the Difficulties in Emotion Regulation Scale (DERS-18), Screener and Opioid Assessment for Patients with Pain—Revised (SOAPP-R), and short-form McGill Pain Questionnaire (SF-MPQ). The sensory experience of pain was unrelated to emotion dysregulation (r = 0.06, p = 0.57) and weakly related to opioid misuse risk (r = 0.182, p < 0.05). In contrast, the affective experience of pain was moderately related to emotion dysregulation (r = 0.217, p < 0.05) and strongly related to opioid misuse risk (r = 0.37, p < 0.01). In addition, emotion dysregulation predicted variance in opioid misuse risk above and beyond the affective and sensory experiences of pain ((b = 0.693, p < 0.001). The results suggest patients with a strong affective experience versus sensory experience of pain and challenges with emotion regulation may require a more comprehensive intervention to address these underlying components in order to reduce their risk of misusing opioid medications.
The acute effect of wearable resistance load and placement upon change of direction performance in soccer players

The aim of the study was to examine the acute effect of different lower limb wearable resistance on placement (shank vs thigh) and various loads (1−5% of body mass) upon change of direction (COD) ability. Twelve male soccer players (age: 23.3 ± 2.5 years; height: 179.2 ± 7.4 cm; body mass: 78.3 ± 7.1 kg) performed a change of direction test with different additional loads fixed on either the shank or thigh. Measurement consisted of total time, 90° and 45° split times. large effects of the different wearable resistance placement (p<0.05) and load (p<0.001) were found for total and split change of direction time performance. Change of direction times were higher with shank loading compared with thigh loading. It was concluded that lower limb wearable resistance loading with different loads had an acute effect upon change of direction performance in male soccer players. Furthermore, that distal placement (shank vs thigh) with similar body mass load had a larger effect upon COD performance.
The complete chloroplast genome sequence of Cremastra appendiculata (Orchidaceae) revealed by next-generation sequencing and phylogenetic implication

Abstract The complete chloroplast genome sequence of Cremastra appendiculata, a rare and endangered species of China, was determined by Illumina pair-end sequencing. The results showed that the complete plastid genome was 160,494 bp in length, containing a large single copy (LSC) of 88,249 bp and a small single copy (SSC) of 21,457 bp, which were separated by a pair of 25,394 bp inverted repeats (IRs). A total of 132 unique genes were annotated, including 86 protein coding genes, 38 tRNA genes, and 8 rRNA genes. Among these genes, 18 genes contained one or two introns. The overall GC contents of the plastid genome were 36.9%, and in the IR regions, LSC and SSC were 43.8, 34.4 and 30.9%, respectively. Maximum likelihood analysis revealed that the new sequenced species C. appendiculata was closer to the species in Cattleya and formed one clade with a high bootstrap value at the middle of the phylogenetic tree of Orchidaceae.
The structural complexity of the Gammaproteobacteria flagellar motor is related to the type of its torque-generating stators

The bacterial flagellar motor is a cell-envelope-embedded macromolecular machine that functions as a propeller to move the cell. Rather than being an invariant machine, the flagellar motor exhibits significant variability between species, allowing bacteria to adapt to, and thrive in, a wide range of environments. For instance, different torque-generating stator modules allow motors to operate in conditions with different pH and sodium concentrations and some motors are adapted to drive motility in high-viscosity environments. How such diversity evolved is unknown. Here we use electron cryo-tomography to determine the in situ macromolecular structures of the flagellar motors of three Gammaproteobacteria species: Legionella pneumophila, Pseudomonas aeruginosa, and Shewanella oneidensis MR-1, providing the first views of intact motors with dual stator systems. Complementing our imaging with bioinformatics analysis, we find a correlation between the stator system of the motor and its structural complexity. Motors with a single H+-driven stator system have only the core P- and L-rings in their periplasm; those with dual H+-driven stator systems have an extra component elaborating their P-ring; and motors with Na+- (or dual Na+-H+)- driven stator systems have additional rings surrounding both their P- and L-rings. Our results suggest an evolution of structural complexity that may have enabled pathogenic bacteria like L. pneumophila and P. aeruginosa to colonize higher-viscosity environments in animal hosts.
Bryophytes in fir waves: Forest canopy indicator species and functional diversity decline in canopy gaps

Co-ordinating Editor: Tohru Nakashizuka Abstract Aims: Bryophytes can cover three quarters of the ground surface, play key ecological functions, and increase biodiversity in mesic highelevation conifer forests of the temperate zone. Forest gaps affect species coexistence (and ecosystem functions) as suggested by the gap and gapsize partitioning hypotheses (GPH, GSPH). Here we test these hypotheses in the context of highelevation forest bryophyte communities and their functional attributes. Study Site: Spruce–fir forests on Whiteface Mountain, NY, USA. Methods: We characterized canopy openness, microclimate, forest floor substrates, vascular vegetation cover, and moss layer (cover, common species, and functional attributes) in three canopy openness environments (gap, gap edge, forest canopy) across 20 gaps (fir waves) (n = 60); the functional attributes were based on 16 morphologic, reproductive, and ecological bryophyte plant functional traits (PFTs). We tested GPH and GSPH relative to bryophyte community metrics (cover, composition), traits, and trait functional sensitivity (functional dispersion; FDis) using indicator species analysis, ordination, and regression. Results: Canopy openness drove gradients in groundlevel temperature, substrate abundance and heterogeneity (beta diversity), and understory vascular vegetation cover. The GPH was consistent with (a) the abundance patterns of forest canopy indicator species (Dicranum fuscescens, Hypnum imponens, and Tetraphis pellucida), and (b) FDis based on three PFTs (growth form, fertility, and acidity), both increasing with canopy cover. We did not find support for GPH in the remaining species or traits, or for GSPH in general; gap width (12–44 m) was not related to environmental or bryophyte community gradients. Conclusions: The observed lack of variation in most bryophyte metrics across canopy environments suggests high resistance of the bryophyte layer to natural canopy gaps in highelevation forests. However, responses of forest canopy indicator species suggest that canopy mortality, potentially increased by changing climate or insect pests, may cause declines in some forest canopy species and consequently in the functional diversity of bryophyte communities.
The Therapeutic Properties of Plants Used Traditionally to Treat Gastrointestinal Disorders on Groote Eylandt, Australia

The First Australians had well-developed healing systems. Groote Eylandt inhabitants used a variety of plant species to treat diarrhoea and other gastrointestinal illnesses. This study was undertaken to test, identify, and evaluate traditional medicines to treat these conditions against gastrointestinal bacterial, protozoal, and viral pathogens, as well as against cancer cell proliferation. Six plant species (Buchanania obovata Engl., Casuarina equisetifolia L., Eucalyptus tetrodonta F. Muell., Planchonia careya (F. Muell.) R. Knuth, Terminalia carpentariae C. T. White, and Vigna vexillata (L.) A. Rich. ) were selected from a survey of a panel of elders from the Warnindhilyagwa tribe and compared with the published literature. Decoctions prepared according to traditional methods were screened for growth inhibitory activity of a panel of diarrhoea-causing bacterial pathogens by disc diffusion and liquid dilution MIC assays. Inhibitory activity against the gastrointestinal protozoal parasite Giardia duodenalis and antiproliferative activity against human colorectal (Caco2) and cervical (HeLa) cancer cell lines were evaluated using MTS-based colorimetric cell proliferation assays. Preliminary antiviral screening was accomplished using an MS2 bacteriophage plaque reduction assay. Toxicity was evaluated using Artemia franciscana nauplii mortality and HDF cell viability bioassays. All traditional medicines tested inhibited bacterial growth, often with MIC values substantially <1000 μg/mL. T. carpentariae was particularly noteworthy, with MIC values of 230–350 μg/mL against Citrobacter freundii, Salmonella newport, Shigella sonnei, Staphylococcus aureus, and Staphylococcus epidermidis. This species also had MICs 450–950 μg/mL against all other bacterial pathogens. B. obovata Engl. and E. tetrodonta were also good inhibitors of bacterial growth, albeit with substantially higher MIC values than determined for T. carpentariae. The T. carpentariae decoction was also the best inhibitor of MS2 phage replication (IC50 = 427 μg/mL) and Caco2 and HeLa proliferation (IC50 values of 885 and 85 μg/mL, respectively). None of the extracts were particularly strong inhibitors of Giardia duodenalis growth. All decoctions were nontoxic in the Artemia nauplii and HDF cell viability bioassays, indicating their suitability for therapeutic use.
Lack of correlation between number of neurons and behavioral performance in Swiss mice

Neuronal number varies by several orders of magnitude across species, and has been proposed to predict cognitive capability across species. Remarkably, numbers of neurons vary across individual mice by a factor of 2 or more. We directly addressed the question of whether there is a relationship between performance in behavioral tests and the number of neurons in functionally relevant structures in the mouse brain. Naive Swiss mice went through a battery of behavioral tasks designed to measure cognitive, motor and olfactory skills. We estimated the number of neurons in different brain regions (cerebral cortex, hippocampus, olfactory bulb, cerebellum and remaining areas) and crossed the two datasets to test the a priori hypothesis of correlation between cognitive abilities and numbers of neurons. As previous evidence indicates that environmental enrichment may increase neurogenesis and improve neuronal survival, we added a control group that did not undergo cognitive testing to rule out the possibility that our test battery could alter the neuronal number. We found that behavioral testing did not change numbers of neurons in the cerebral cortex and in the hippocampus. Surprisingly, performance in the behavioral tasks did not correlate strongly with number of neurons in any of the brain regions studied. Our results show that whereas neuronal number is a good predictor of cognitive skills across species, it is not a predictor of cognitive, sensory or motor ability across individuals within a species, which suggests that other factors are more relevant for explaining cognitive differences between individuals of the same species.
Analysis of patient derived xenograft studies in Oncology drug development: impact on design and interpretation of future studies

Background Preclinical Oncology drug development is heavily reliant on xenograft studies to assess the anti-tumour effect of new compounds. Patient derived xenograft (PDX) have become popular as they may better represent the clinical disease, however variability is greater than in cell-line derived xenografts. The typical approach of analysing these studies involves performing an un-paired t-test on the mean tumour volumes between the treated and control group at the end of the study. This approach ignores the time-series and may result in false conclusions, especially when considering the increased variability of PDX studies. Aim To test the hypothesis that a model-based analysis provides increased power than analysis of final day volumes and to provide insights into more efficient PDX study designs. Methods Data was extracted from tumour xenograft time-series data from a large publicly available PDX drug treatment database released by Novartis. For all 2-arm studies the percent tumour growth inhibition (TGI) at two time-points, day 10 and day 14 was calculated. For each study, the effect of treatment was calculated using an un-paired t-test and also a model-based analysis using the likelihood ratio-test. In addition a simulation study was also performed to assess the difference in power between the two data-analysis approaches for different levels of TGI for PDX or standard cell-line derived xenografts (CDX). Results The model-based analysis had greater statistical power than the un-paired t-test approach within the PDX data-set. The model-based approach was able to detect TGI values as low as 25 percent whereas the un-paired t-test approach required at least 50 percent TGI. These findings were confirmed within the simulation study performed which also highlighted that CDX studies require less animals than PDX studies which show the equivalent level of TGI. Conclusion The analysis of 59 2-arm PDX studies highlighted that taking a model-based approach gave increased statistical power over simply performing an un-paired t-test on the final study day. Importantly the model-based approach was able to detect smaller size of effect compared to the un-paired t-test approach is which maybe common of such studies. These findings were confirmed within simulated studies which also highlighted the same sample size used for CDX studies would lead to inadequately powered PDX studies. Application of a model-based analysis should allow studies to use less animals and run experiments for a shorter period thus providing effective insight into compound anti-tumour activity