Miracle-dz/UniFAR-FTUs huggingface dataset:
Early fish domestication affects methylation of key genes involved in the rapid onset of the farmed phenotype

ABSTRACT Animal domestication is a process of environmental modulation and artificial selection leading to permanent phenotypic modifications. Recent studies showed that phenotypic changes occur very early in domestication, i.e., within the first generation in captivity, which raises the hypothesis that epigenetic mechanisms may play a critical role on the early onset of the domestic phenotype. In this context, we applied reduced representation bisulphite sequencing to compare methylation profiles between wild Nile tilapia females and their offspring reared under farmed conditions. Approximately 700 differentially methylated CpG sites were found, many of them associated not only with genes involved in muscle growth, immunity, autophagy and diet response but also related to epigenetic mechanisms, such as RNA methylation and histone modifications. This bottom-up approach showed that the phenotypic traits often related to domestic animals (e.g., higher growth rate and different immune status) may be regulated epigenetically and prior to artificial selection on gene sequences. Moreover, it revealed the importance of diet in this process, as reflected by differential methylation patterns in genes critical to fat metabolism. Finally, our study highlighted that the TGF-β1 signalling pathway may regulate and be regulated by several differentially methylated CpG-associated genes. This could be an important and multifunctional component in promoting adaptation of fish to a domestic environment while modulating growth and immunity-related traits.
Completing an interdisciplinary outpatient intervention improves patient rehabilitation goals following a mild traumatic brain injury

ABSTRACT Background Individualized and interdisciplinary rehabilitation programs are recommended following a mild traumatic brain injury (mTBI), but often have long waitlists. Accordingly, innovative evidence-based programs are needed. Objectives The first objective of this study was to determine the number and types of rehabilitation goals chosen by individuals completing an interdisciplinary outpatient rehabilitation intervention (BrainEx90) for persisting symptoms following an mTBI. The second objective was to investigate whether completing BrainEx90 or choosing specific types of goals influenced performance and satisfaction ratings of these goals. Methods 217 individuals (44.4 ± 13.5 years old) with persisting symptoms following an mTBI completed BrainEx90, a 16-session interdisciplinary group outpatient rehabilitation intervention at Parkwood Institute between November 2013 and September 2019. Performance and satisfaction ratings of self-identified goals before and after BrainEx90 were assessed using the Canadian Occupational Performance Measure, and changes in ratings were analyzed using a linear mixed effects model. Results 1008 goals were identified and categorized as: productivity (45%); leisure (37%); and self-care (18%). Satisfaction ratings were significantly higher for all goal types following BrainEx90. Satisfaction with self-care goals improved significantly more than leisure [t(151) = 3.24, p < . 01] and productivity [t(144) = 2.97, p < . 01] goals. Performance ratings were also significantly greater following BrainEx90 [2.4, 95% CI [2.27, 2.53], p < . 01)]. Conclusion Performance and satisfaction of self-identified rehabilitation goals significantly improved following BrainEx90. Satisfaction with self-care goals demonstrated the greatest improvements, yet the most identified goal type was productivity.
Title: Risk Factors for the Diagnosis of Colorectal Cancer

Background Colorectal cancer defined as cancer of the colon or rectum, is the third most frequently diagnosed cancer in men and the second in women, and, according to the World Health Organization database GLOBOCAN, it accounts for nearly 1.4 million new cases annually worldwide. The occurrence of colorectal cancer is associated with nonmodifiable risk factors, including age and hereditary factors, as well as with modifiable environmental and lifestyle factors. Methods The study included 800 patients, 400 diagnosed with colorectal cancer and 400 within the control group, who gave their written informed consent to participate in the study. Patients with cancer other than colorectal cancer were randomly selected for control group I, and patients with no cancer diagnosis were selected for control group II. The method used was a case-control study – an observational and analytical study with a control group, conducted among patients of the Clinical Oncology Centre and the Provincial Hospital in the years 2019–2020. The study comparing the exposure was carried out in a group of people who developed the endpoint, that is colorectal cancer, with the exposure in a well-matched group of controls who did not reach the endpoint. Assessment of activity and BMI was used according to WHO recommendations, as well as the expert system. The data were tested for the distribution and the homogeneity of variance was validated before applying the parameter tests. Comparison of quantitative variables between groups was performed using ANOVA. Results The mean age of the patients was 64.53 ± 8.86 years, of the control group I – 59.64 ± 9.33 and the control group II – 57.5 (7.83). There was a strong positive association between the incidence of ulcerative colitis and the risk of colorectal cancer (P < .01). Among obese subjects, the risk of developing colorectal cancer was 1.27 (95% CI, 1.06–1.53) compared with nonobese subjects. A strong positive relationship was found between low physical activity converted to metabolic equivalent of MET effort per week and the risk of colorectal cancer (P < .001). The relative risk for current smokers was 2.17 (95% CI 1.79–2.66). There was an association between higher fat consumption and higher red meat consumption and the risk of developing colorectal cancer (P < .01). Conclusions Obesity, low physical activity, active and passive smoking and high salt and red meat consumption have been associated with an increased risk of colorectal cancer. These findings provide further evidence of the importance of maintaining a healthy lifestyle.
Thermal Storage System for Electric Vehicle Cabin Heating - Component and System Analysis

Cabin heating of current electric vehicle (EV) designs is typically provided using electrical energy from the traction battery, since waste heat is not available from an engine as in the case of a conventional automobile. In very cold climatic conditions, the power required for space heating of an EV can be of a similar magnitude to that required for propulsion of the vehicle. As a result, its driving range can be reduced very significantly during the winter season, which limits consumer acceptance of EVs and results in increased battery costs to achieve a minimum range while ensuring comfort to the EV driver. To minimize the range penalty associated with EV cabin heating, a novel climate control system that includes thermal energy storage from an advanced phase change material (PCM) has been designed for use in EVs and plug-in hybrid electric vehicles (PHEVs). The present paper focuses on the modeling and analysis of this electrical PCM-Assisted Thermal Heating System (ePATHS) and is a companion to the paper Design and Testing of a Thermal Storage System for Electric Vehicle Cabin Heating. A detailed heat transfer model was developed to simulate the PCM heat exchanger that is at the heart of the ePATHSmore » and was subsequently used to analyze and optimize its design. The results from this analysis were integrated into a MATLAB Simulink system model to simulate the fluid flow, pressure drop and heat transfer in all components of the ePATHS. The system model was then used to predict the performance of the climate control system in the vehicle and to evaluate control strategies needed to achieve the desired temperature control in the cabin. The analysis performed to design the ePATHS is described in detail and the system s predicted performance in a vehicle HVAC system is presented. « less
Knee symptoms do not affect walking biomechanics among women 6 months after anterior cruciate ligament reconstruction

Women with anterior cruciate ligament reconstruction report worse pain and knee‐related symptoms, and also exhibit biomechanical changes that may be related to knee osteoarthritis (OA) development. This is particularly concerning as symptom state has been previously associated with knee OA development. The purpose of this study was to compare lower extremity walking biomechanics between women (age: 21.40 ± 8.54 years) experiencing clinically significant knee‐related symptoms and women with acceptable symptoms 6 months following surgery. Twenty‐eight women with history of primary, unilateral anterior cruciate ligament reconstruction who completed a lower extremity walking biomechanics assessment 6 months following surgery were included in this analysis. Women were dichotomized as experiencing acceptable or clinically significant knee symptoms according to Knee injury and OA Outcomes Score cut‐offs described by Englund et al. Walking biomechanics were compared between women with clinically significant and acceptable symptoms using one‐way analysis of covariances for involved limb biomechanics. Biomechanical variables of interest were: peak vertical ground reaction forces (vGRFs), vGRF loading rates, knee flexion angles, knee extension moments, knee adduction angles, and knee adduction moments, and gait speed. Nearly 60% of women reported clinically significant knee symptoms 6 months postoperative. There were no statistically significant differences between symptom groups for walking biomechanics and gait speed outcomes. These findings suggest patient reported knee symptoms may not be a primary influence on walking biomechanics 6 months following anterior cruciate ligament reconstruction. Though, longitudinal assessment of changes in symptom state and walking biomechanics may be warranted as poorer walking biomechanics and symptoms are indicators of knee OA.
Clinical Reliability of Genomic Data Obtained from Spinal Metastatic Tumor Samples.

PURPOSE The role of tumor genomic profiling is rapidly growing as it results in targeted, personalized, cancer therapy. Though routinely used in clinical practice, there are no data exploring the reliability of genomic data obtained from spine metastases samples often leading to multiple biopsies in clinical practice. This study compares the genomic tumor landscape between spinal metastases and the corresponding primary tumors as well as between spinal metastases and visceral metastases. PATIENTS AND METHODS Spine tumor samples, obtained for routine clinical care from 2013 to 2019, were analyzed using MSK-IMPACT, a next generation sequencing assay. These samples were matched to primary or metastatic tumors from the corresponding patients. A concordance rate for genomic alterations was calculated for matching sample pairs within patients for the primary and spinal metastatic tumor samples as well as for the matching sample pairs within patients for the spinal and visceral metastases. For a more robust and clinically relevant estimate of concordance, a subgroup analyses of previously established driver mutations specific to the main primary tumor histologies was performed. RESULTS Eighty-four patients contributed next generation sequencing from a spinal metastasis and at least one other site of disease: 54 from the primary tumor, 39 had genomic tumor data from another, non-spinal metastasis, 12 patients participated in both subsets. For the cohort of matched primary tumors and spinal metastases (n = 54) comprised of mixed histologies, we found an average concordance rate of 96.97% for all genetic events, 97.17% for mutations, 100% for fusions, 89.81% for deletions, and 97.01% for amplifications across all matched samples. Notably, >25% of patients harbored at least one genetic variant between samples tested, though not specifically for known driver mutations. The average concordance rate of driver mutations was 96.99% for prostate cancer, 95.69% (p = 0.0004513) for lung cancer and 96.43% for breast cancer. An average concordance of 99.02% was calculated for all genetic events between spine metastases and non-spinal metastases (n=41) and, more specifically, a concordance rate of 98.91% was calculated between spine metastases and liver metastases (n=12) which was the largest represented group of non-spine metastases. CONCLUSION Sequencing data performed on spine tumor samples demonstrate a high concordance rate for genetic alterations between the primary tumor and spinal metastasis as well as between spinal metastases and other, visceral metastases, particularly for driver mutations. Spine tumor samples may be reliably used for genomic based decision making in cancer care, particularly for prostate, NSCLC and breast cancer.
The reliability, validity and sensitivity of an individualised sub-maximal fitness test in elite rugby league athletes

ABSTRACT We aimed to examine the reliability, validity and sensitivity of an individualised sub-maximal fitness test (SMFTIFT60). Nineteen elite rugby league players performed a one-week test-retest of SMFTIFT60. Typical Errors and ICCs were: small (<3.5%) and extremely high (>0.90) for accelerometer-derived variables; moderate (<2.5% points) and moderate to very high (0.71–0.89) for exercise and recovery heart rate (HRex and HRR, respectively). Convergent validity correlations with the 10-week pre-season change in 30–15 Intermittent Fitness Test performance were large for changes in SMFTIFT60 HRex (r = −0.57) and HRR (0.60), and very large for changes in accelerometer measures (range: −0.71 to −0.79). For sensitivity, within-player dose–response relationships between SMFTIFT60 HRex and prior 3-day training loads were negative and ranged from moderate (session ratings of perceived exertion [sRPE-TL], r = −0.34), to large (high-speed running distance, −0.51; acceleration load, −0.73) and very large (heart rate Training Impulse [TRIMP], −0.83). All other relationships were unclear or trivial to small. Physiological and accelerometer-derived measures from the SMFTIFT60 are reliable and valid for the assessment of fitness in rugby league players. Only HRex appears sensitive to acute changes in training load. The SMFTIFT60 could be a useful monitoring tool in team sports
Dual inoculation of dark septate endophytes and Trichoderma viride drives plant performance and rhizosphere microbiome adaptations of Astragalus mongholicus to drought

Summary Rhizosphere microbiome adapts their structural compositions to water scarcity and have the potential to mitigate drought stress of plants. To unlock this potential, it is crucial to understand community responses to drought in the interplay between soil properties, water management and exogenous microbes interference. Inoculation with dark septate endophytes (DSE) (Acrocalymma vagum, Paraboeremia putaminum) and Trichoderma viride on Astragalus mongholicus grown in the non‐sterile soil was exposed to drought. Rhizosphere microbiome were assessed by Illumina MiSeq sequencing of the 16S and ITS2 rRNA genes. Inoculation positively affected plant growth depending on DSE species and water regime. Ascomycota, Proteobacteria, Actinobacteria, Chloroflexi and Firmicutes were the dominant phyla. The effects of dual inoculation on bacterial community were greater than those on fungal community, and combination of P. putaminum and T. viride exerted a stronger impact on the microbiome under drought stress. The observed changes in soil factors caused by inoculation could be explained by the variations in microbiome composition. Rhizosphere microbiome mediated by inoculation exhibited distinct preferences for various growth parameters. These findings suggest that dual inoculation of DSE and T. viride enriched beneficial microbiota, altered soil nutrient status and might contribute to enhance the cultivation of medicinal plants in dryland agriculture.
Nicaraven mitigates radiation-induced lung injury by downregulating the NF-κB and TGF-β/Smad pathways to suppress the inflammatory response

Abstract Radiation-induced lung injury (RILI) is commonly observed in patients receiving radiotherapy, and clinical prevention and treatment remain difficult. We investigated the effect and mechanism of nicaraven for mitigating RILI. C57BL/6 N mice (12-week-old) were treated daily with 6 Gy X-ray thoracic radiation for 5 days in sequences (cumulative dose of 30 Gy), and nicaraven (50 mg/kg) or placebo was injected intraperitoneally in 10 min after each radiation exposure. Mice were sacrificed and lung tissues were collected for experimental assessments at the next day (acute phase) or 100 days (chronic phase) after the last radiation exposure. Of the acute phase, immunohistochemical analysis of lung tissues showed that radiation significantly induced DNA damage of the lung cells, increased the number of Sca-1+ stem cells, and induced the recruitment of CD11c+, F4/80+ and CD206+ inflammatory cells. However, all these changes in the irradiated lungs were effectively mitigated by nicaraven administration. Western blot analysis showed that nicaraven administration effectively attenuated the radiation-induced upregulation of NF-κB, TGF-β, and pSmad2 in lungs. Of the chronic phase, nicaraven administration effectively attenuated the radiation-induced enhancement of α-SMA expression and collagen deposition in lungs. In conclusion we find that nicaraven can effectively mitigate RILI by downregulating NF-κB and TGF-β/pSmad2 pathways to suppress the inflammatory response in the irradiated lungs.
Benefits and challenges of using logistic regression to assess neuropsychological performance validity: Evidence from a simulation study

Abstract Objective: Logistic regression (LR) is recognized as a promising method for making decisions about neuropsychological performance validity by integrating information across multiple measures. However, this method has yet to be widely adopted in clinical practice, likely because several open questions remain about its utility relative to simpler methods, its effectiveness across different clinical contexts, and its feasibility at sample sizes common in the field. The current study addresses these questions by assessing classification performance of logistic regression and alternative methods across an array of simulated data sets. Methods: We simulated scores of valid and invalid performers on 6 tests designed to mimic the psychometric and distributional properties of real performance validity measures. Out-of-sample predictive performance of LR and a commonly used alternative (“vote counting”) was assessed across different base rates, validity measure properties, and sample sizes. Results: LR improved classification accuracy by 2%–12% across simulation conditions, primarily by improving sensitivity. False positives and negatives can be further reduced when LR predictions are interpreted as continuous, rather than binary. LR made robust predictions at sample sizes feasible for neuropsychology research (N = 307) and when as few as 2 tests with good psychometric properties were used. Conclusions: Although training and test data sets of at least several hundred individuals may be required to develop and evaluate LR models for use in clinical practice, LR promises to be an efficient and powerful tool for improving judgements about performance validity. We offer several recommendations for model development and LR interpretation in a clinical setting.
Recovery of Male Reproductive Function After Ceasing Prolonged Testosterone Undecanoate Injections.

CONTEXT The time course of male reproductive hormone recovery after stopping injectable testosterone undecanoate (TU) treatment is not known. OBJECTIVE To investigate rate, extent, and determinants of reproductive hormone recovery over 12 months after stopping TU injections. METHODS Men (n=303) with glucose intolerance but without pathologic hypogonadism who completed a 2-year placebo(P)-controlled randomized clinical trial of TU treatment were recruited for a further 12 months while remaining blinded to treatment. Sex steroids (T, DHT, E2, E1) by LCMS, LH, FSH and SHBG by immunoassays and sexual function questionnaires (Psychosexual Diary Questionnaire (PDQ), International Index of Erectile Function (IIEF), SF-12) were measured at entry (three months after last injection) and 6, 12, 18, 24, 40 and 52 weeks later. RESULTS In the nested cohort of TU-treated men, serum T was initially higher but declined to 12 weeks remaining stable thereafter with serum T and SHBG 11% and 13%, respectively, lower than P-treated men. Similarly, both questionnaires showed initial carryover higher scores in T-treated men, but after weeks 18 showed no difference between T and P treated men. Initially fully suppressed serum LH and FSH recovered slowly towards the participant's own pre-treatment baseline over 12 months since last injection. CONCLUSIONS After stopping 2 years of 1000 mg injectable TU treatment, full reproductive hormone recovery is slow and progressive over 15 months since last testosterone injection but may take longer than 12 months to be complete. Persistent proportionate reduction in serum SHBG and T reflects lasting exogenous T effects on hepatic SHBG secretion rather than androgen deficiency.
Composite dietary antioxidant index and the risk of colorectal cancer: Findings from the Singapore Chinese Health Study

Colorectal cancer (CRC) is a major contributor to cancer death globally. Several studies showed some protections by certain individual dietary antioxidants against CRC development. Epidemiologic data on the composite dietary antioxidant index (CDAI) in relation to CRC risk are sparse. Using the Singapore Chinese Health Study, an ongoing prospective cohort consisting of 61 321 cancer‐free participants aged 45 to 74 years at baseline, a food‐based CDAI was calculated according to a previously established and validated method that included six food‐sourced antioxidants including vitamins A, C and E, manganese, selenium and zinc. Cox proportional hazard regression method was used to estimate the hazard ratios (HRs) and their 95% confidence intervals (CIs) for CRC associated with various levels of CDAI with adjustment for multiple potential confounders. After an average of 17.5 years of follow‐up, 2140 participants developed CRC. HRs (95% CIs) of CRC for quartiles 2, 3 and 4 of CDAI were 0.94 (0.83‐1.07), 0.86 (0.75‐1.00) and 0.80 (0.66‐0.98), respectively, compared to the lowest quartile (Ptrend = .02). This inverse association between CDAI and CRC risk was more apparent in women or those without a history of diabetes, without family history of CRC, never smokers or overweight/obese individuals. However, none of the heterogeneity tests for the CDAI‐CRC risk association reached statistical significance. Our findings suggest that food‐based antioxidants may be beneficial for reducing the risk of CRC in the general population.