Miracle-dz/UniFAR-FTUs huggingface dataset:
THE EFFECT OF DAILY PHYSICAL ACTIVITY ON THE ACTIVITY OF INFLAMMATORY BOWEL DISEASES IN THERAPY-FREE PATIENTS

SUMMARY It has been suggested that various environmental factors play a very important role in the etiology of inflammatory bowel diseases (IBDs) and that they have a significant effect on the course of these diseases. The aim of this study was to investigate the effect of daily physical activity on the activity of IBDs in therapy-free patients. This cross-sectional population based study was conducted in eastern Croatia from January to June 2016. The study included 312 patients, mean age 49.9±15.0 years, 53.2% of males and 46.8% of females; there were 63.4% of ulcerative colitis (UC) and 36.6% of Crohn’s disease (CD) patients. Sociodemographic characteristics of patients, data on their daily physical activity and type of therapy taken were collected through a specifically designed and validated questionnaire, while the activity of UC and CD was evaluated using the Mayo index and Harvey-Bradshaw index. The study showed that 24.0% of patients were not taking therapy. Daily physical activity was connected to IBD in study patients when taking both diseases collectively (Fisher exact test; p<0.001), as well as to the inactivity of CD (Fisher exact test; p=0.001) and UC (Fisher exact test; p=0.006), when observing each disease separately. Daily physical activity was connected to the inactivity of IBDs in patients not taking therapy. It is necessary to educate all IBD patients about the importance of physical activity in order to control their disease.
MSC-Derived Exosome Promotes M2 Polarization and Enhances Cutaneous Wound Healing

Mesenchymal stem cell transplantation (MSCT) promotes cutaneous wound healing. Numerous studies have shown that the therapeutic effects of MSCT appear to be mediated by paracrine signaling. However, the cell-cell interaction during MSCT between MSCs and macrophages in the region of cutaneous wound healing is still unknown. In this study, early depletion of macrophages delayed the wound repair with MSC injection, which suggested that MSC-mediated wound healing required macrophages. Moreover, we demonstrated that systemically infused bone marrow MSCs (BMMSCs) and jaw bone marrow MSCs (JMMSCs) could translocate to the wound site, promote macrophages toward M2 polarization, and enhance wound healing. In vitro coculture of MSCs with macrophages enhanced their M2 polarization. Mechanistically, we found that exosomes derived from MSCs induced macrophage polarization and depletion of exosomes of MSCs reduced the M2 phenotype of macrophages. Infusing MSCs without exosomes led to lower number of M2 macrophages at the wound site along with delayed wound repair. We further showed that the miR-223, derived from exosomes of MSCs, regulated macrophage polarization by targeting pknox1. These findings provided the evidence that MSCT elicits M2 polarization of macrophages and may accelerate wound healing by transferring exosome-derived microRNA.
Creating Artificial Human Genomes Using Generative Models

Generative models have shown breakthroughs in a wide spectrum of domains due to recent advancements in machine learning algorithms and increased computational power. Despite these impressive achievements, the ability of generative models to create realistic synthetic data is still under-exploited in genetics and absent from population genetics. Yet a known limitation of this field is the reduced access to many genetic databases due to concerns about violations of individual privacy, although they would provide a rich resource for data mining and integration towards advancing genetic studies. Here we demonstrate that we can train deep generative adversarial networks (GANs) and restricted Boltzmann machines (RBMs) to learn the high dimensional distributions of real genomic datasets and create artificial genomes (AGs). Additionally, we ensure none to little privacy loss while generating high quality AGs. To illustrate the promising outcomes of our method, we show that augmenting reference panels with AGs improves imputation quality for low frequency alleles. In summary, AGs have the potential to become valuable assets in genetic studies by providing high quality anonymous substitutes for private databases.
Can the response of above- and below-ground traits to overgrazing vary between annual and perennial species?

Understanding functional traits that capture species response to grazing is crucial for uncovering mechanisms underlying the grazing-induced alterations in vegetation composition. Currently, the majority of studies ignore the effects of life form on the response of above- and below-ground traits to grazing. In this study we quantified i) whether below-ground traits exhibit similar response to overgrazing as do above-ground traits; and ii) whether the response of above- and below-ground traits to overgrazing varied with life form (annual versus perennial species). To testify the generality of these two questions, we compared common grassland species between an undisturbed and an over grazed meadow at each of four elevations ranging from 3000m to 3600m on the Qinghai Tibetan Plateau. We found both above-ground and below-ground traits exhibited similar resource conservation vs. resource acquisition trade-off for responding to overgrazing. Moreover, perennial species but not annual species determine the response of above- and below-ground traits to overgrazing. This work bridges the gap in the literature for the influence of land-use (in the absence and presence of overgrazing) and life forms (annual and perennial species) on species-specific response at both above-, and below-ground level.
Farmers’ awareness regarding deforestation at Jalma union of Batiaghata upazila under Khulna district of Bangladesh

Deforestation causes environmental degradation. Awareness of the people might have influence on reduction of deforestation. The main purposes of the study were to determine the farmers’ awareness regarding deforestation and to explore relationship between the selected characteristics of the farmers and their awareness. The study was conducted to only one village namely Raingamari (The project village of Khulna University) of Jalma union under Batiaghata upazila of Khulna district. Data were collected from 53 family heads of the village on their 10 selected characteristics such as age, educational qualification, farming experience, family size, farm size, family income, organizational participation, cosmopoliteness, extension media contact, training exposure. Data were also collected on farmers’ awareness regarding deforestation. Data were collected from the respondents during April to July 2017 through personal interview using a pretested interview schedule. Most of the respondents were highly aware of deforestation. The respondents showed highest level of awareness regarding “deforestation causes greenhouse effect which consequently increase the average temperature of the earth” while they were less aware regarding “deforestation threatens the livelihoods and cultural integrity of people that depend on forest”. Among the 10 selected characteristics of the respondents, educational qualification, organizational participation, extension media contact showed positive significant relationships with their awareness regarding deforestation while only the annual income had the negative significant relationship with their awareness regarding deforestation. Res. Agric. , Livest. Fish.6(2): 193-202, August 2019
CARDIOTOXIC EFFECTS OF ANABOLIC-ANDROGENIC STEROIDS GENERAL SPECIFICATIONS OF ALGAE AND THEIR IMPORTANCE ON PHARMACY

Anabolik androjenik streoidler (AAS) testosteronun sentetik turevleri olup, iskelet kasinin buyumesini ve (anabolik etki) erkek seks karakterlerinin gelismesini (androjenik etki) saglarlar. Illegal olarak, bu ilaclar halterciler ve vucut gelistiriciler tarafindan sportif performansi artirma amaciyla kullanilmaktadirlar. AAS suistimali birtakim kardiyovaskuler yan etkilerle iliskilidir. Vaka raporlarinda, akut miyokard infarktusu en sik gorulen yan etki olarak bildirilse de, sol ventrikul hipertrofisi, azalmis sol ventrikul kontraktil fonksiyonu, hipertansiyon, arteriyel tromboz, pulmoner embolizm, endotel disfonksiyonu, lipid metabolizmasinda degisiklikler hayati tehdit eden aritmiler ve ani kardiyak olum gibi yan etkiler de gorulebilir. Ancak bugune kadar AAS suiistimalinin uzun sureli kardiyovaskuler etkilerini gosteren prospektif, randomize calisma yapilmamistir. Bu derlemede, AAS ile induklenen kardiyotoksisiteye iliskin guncel literaturu ve kendi deneysel calismalarimizi da ozetlemeye calistik. Buna ek olarak bu yan etkinin olasi mekanizmalarini da tartisacagiz
Cd, Cu, Pb and Zn in terraced soil on flysch deposits of Kaštela Bay coastal area, Croatia

The aims of this study were: (i) to determine concentrations of heavy metals (HMs): Cd, Cu, Pb and Zn in terraced soils on flysch deposits of Kastela Bay coastal area, Croatia, (ii) to highlight their possible sources and (iii) to compare concentrations of HMs among olive groves, vineyards and abandoned agricultural land (grassland). In a total of 26 topsoil samples (0-25 cm) were analyzed for pH, carbonates, organic carbon, K2O, P2O5, texture and concentrations of the HMs. The elements were extracted with aqua regia and determined by inductively coupled plasma - optical emission spectrometry (ICP-OES). The following mean values of Cd, Cu, Pb and Zn concentrations were 0.39, 46.54, 15.82 and 51.39 mg*kg-1, respectively. The principal component analysis (PCA) and the correlation matrix (CM) revealed weak relationships HMs with soil properties and strong similarity among Cd, Pb and Zn concentrations indicating its common origin, controlled by different anthropogenic activity. The Cu poorly correlated with all other metals that point to its different origin - application of copper-based fungicide. The mean concentrations of Cd, Pb and Zn in vineyards, olive groves and grasslands were not statistically significant difference. The Cu concentrations in vineyards were significantly higher compared to other land use types
Identification of Reference Genes for Quantitative Gene Expression Studies in Pinus massoniana and Its Introgression Hybrid

qRT-PCR is a powerful molecular research tool to study the regulation of gene expression. However, to accurately calculate gene expression levels, an experiment should include proper reference genes that show no changes in their expression level. Pinus massoniana, P. hwangshanensis, and their introgression hybrid in Mountain Lushan, China, are an ideal model for studying introgression and speciation. Although some research on reference gene selection for P. massoniana has been reported before, no studies on this subject have been performed where P. massoniana and its introgression hybrid were evaluated simultaneously. Here, we investigated ten genes (upLOC, SDH, ACT, EF, TOC75, DMWD, FBOX, PGK1, UBQ, and CL2417C7) identified from transcriptome data of these two taxa for reference gene potential. These ten genes were then screened across multiple tissues such as cone, young and mature stems, and young needles according to qRT-PCR thermal cycling and dissociation. Correlation coefficient, amplification efficiency, and cycle threshold value (Ct) range were applied to evaluate the reliability of each gene. The stability of candidate reference gene expression was calculated using three algorithms: geNorm, NormFinder, and BestKeeper. Base on the reliability and stability, we then offered a list of genes of recommended and not recommended for seven different tissue type and species. Our results demonstrated that different sample lines require different genes as reference to evaluate.
Exons, Introns, and UCEs Reveal Conflicting Phylogenomic Signals in a Rapid Radiation of Frogs (Ranidae: Hylarana)

Numerous types of genomic markers have been used to resolve recalcitrant nodes, yet their relative performance and congruence have rarely been compared directly. Using target-capture sequencing, we obtained more than 12,000 highly informative exons and introns, including ∼600 UCEs to address long-standing systematic problems in Southeast Asian Golden-backed frogs of the genus complex Hylarana. To reduce gene tree estimation errors, we filtered the data using different thresholds of taxon completeness and parsimony informative sites (PIS) in addition to using the best-fit models of DNA evolution to estimate individual single-locus gene trees. We then estimated species trees using concatenation (IQ-TREE), summary coalescent (ASTRAL), and distance-based methods (ASTRID). Topological incongruence among these methods and variation in nodal support were examined in detail using a suite of different measures including quartet frequencies, bootstrap, local posterior probabilities, gene concordance factors, and quartet scores. Results showed that high levels of incongruence were present along the backbone of the phylogeny, specifically surrounding short internodes. We also demonstrated that filtering data by PIS was more efficacious at improving congruence compared to filtering by missing data, and that exons were more sensitive to data filtering than introns and UCEs. Despite utilizing more than 6.9 million characters and 2.7 million PIS, analyses failed to converge on a single concordant topology. Instead, exons, introns, and UCEs produced genuinely strongly-supported yet conflicting phylogenetic signals, which affected our phylogeny estimates at different scales/levels—indicating a general, potentially alarming challenge for phylogenomics inference employing many of todays massive datasets. Additionally, bootstrap values were consistently high despite low levels of congruence and high proportions of gene trees that support conflicting topologies, indicating that traditional bootstraps are likely poor measures of congruence or branch support in large phylogenomic datasets, especially during instances of rapid diversification. Although low bootstrap values do ostensibly reflect low heuristic support, we recommend that high bootstrap support obtained from large genomic datasets be interpreted with caution. Additional complimentary measures such quartet frequencies, gene concordance factors, quartet scores, and posterior probabilities can be useful to provide a more robust and accurate representation of bipartition certainty and ultimately, evolutionary history of incompletely resolved or poorly-understood clades.
Effects of Resistance Training Frequency on Muscle Function Adaptations Using a Multiple-Joint Eccentric Training Model

Eccentric resistance training has been shown to be beneficial for improving multiple performance and health metrics. However, recommendations on eccentric training frequency have not been established. PURPOSE: To investigate the effects of volume-matched resistance training frequency comparing one versus three training days per week of isokinetic multiple-joint eccentric training on strength and lower body function adaptations during a 4-week training period. METHODS: Thirty recreationally-trained men and women were randomly assigned to either a high frequency (HF), three times per week, or low frequency (LF), once per week, training group for four weeks. A motor-driven isokinetic eccentric dynamometer was used for the training and testing. Eccentric strength and vertical jump (VJ) measures were taken at Pre, Mid (two weeks), and Post (four weeks) intervention. Soreness and ratings of perceived exertion (RPE) were taken throughout the training period. RESULTS: There was no significant group × trial interaction for eccentric strength or VJ. For eccentric strength, all trials were significantly different from each other. For VJ, there was a main effect for trial such that VJ increased from Pre to Post and Mid to Post but was not different between Pre and Mid. The HF reported significantly lower RPE and soreness compared to the LF condition. CONCLUSIONS: Both HF and LF protocols elicited large and rapid neuromuscular strength adaptations. Eccentric-based workload may be dispersed across the week to allow for reduced soreness and exertion levels without compromising neuromuscular adaptations. Some transfer to functional (VJ) task may also be observed, independent of training frequency.
Impact Of Fdaaa On Registration, Results Reporting, And Publication Of Clinical Trials Evaluating New Neuropsychiatric Drugs Approved Between 2005 And 2014

IMPACT OF FDAAA ON REGISTRATION, RESULTS REPORTING, AND PUBLICATION OF CLINICAL TRIALS EVALUATING NEW NEUROPSYCHIATRIC DRUGS APPROVED BETWEEN 2005 AND 2014 Constance X. Zou, Jessica E. Becker, Adam T. Phillips, James M. Garritano, Harlan M. Krumholz, Jennifer E. Miller, Joseph S. Ross Center for Outcome Research and Evaluation, Department of Medicine, Yale University School of Medicine and Yale-New Haven Hospital, New Haven, Connecticut Evidence-based medicine (EBM) promotes the use of randomized controlled trials (RCTs) published in peer reviewed medical journals as the “gold standard”. However, up to 50% of the completed clinical trials are never published and trials with results in favor of studied interventions are 2-4 times more likely to have been published then those with non favorable results. Publication bias seems to be a particularly severe problem for RCTs evaluating newly approved brand-name neuropsychiatric drugs. Mandatory trial registration, and later results reporting, were proposed to mitigate selective clinical trial publication and outcome reporting. Congress enacted the FDA Amendments Act (FDAAA) on September 27, 2007 requiring the registration of all non-phase I clinical trials involving FDA-regulated medical interventions and results reporting for FDA approved drugs. It’s been 10 years since FDAAA enactment, the impact of FDAAA on the selective publication of clinical trials has not been studied. Our objective is to determine whether FDAAA enactment is associated with improvements in trial
Mechanical Roles of Vinculin/β-catenin interaction in Adherens Junction

Mechanical force transmission through the adherens junctions (AJs) are highly regulated processes essential for multicellular organization of tissues. AJ proteins such as E-cadherin, α-catenin, and vinculin have been shown to be sensing or bearing mechanical forces being transmitted between the actin cytoskeleton and the intercellular contacts. However, the molecular organization and connectivity of these components remains not well understood. Using a super-resolution microscopy approach, we report that vinculin, once activated, could form a direct structural connection with β-catenin, which can bypass α-catenin, one of the main mechanotransducers in AJs. Direct vinculin/β-catenin interaction is capable of supporting mechanical tension and contributes to the stabilization of the cadherin-catenin complexes. These findings suggest a multi-step model for the force-dependent reinforcement of AJs whereby α-catenin may serve as the initial catalytic activator of vinculin, followed by vinculin translocation to form a direct link between E-cadherin-bound β-catenin and the actin cytoskeleton.
Nuptial feeding and genital coupling of Neopanorpa scorpionflies (Insecta: Mecoptera: Panorpidae) with notal organs of various lengths

Neopanorpa, the second largest genus in Panorpidae, is mainly characterized by the well-developed notal organ on male tergum III. However, it remains largely unknown how the length of the notal organ influences the nuptial feeding behaviour of Neopanorpa. Here, we investigated the nuptial feeding by comparing the morphology of mating-related structures and the genital coupling of a) Neopanorpa lui Chou & Ran, 1981 with a weakly-developed notal organ, b) N. carpenteri Cheng, 1957 with a medium-sized notal organ, and c) N. longiprocessa Hua & Chou, 1997 with an extremely elongated notal organ. The couples of N. lui and N. carpenteri maintain an intermittent mouth-to-mouth mode but do not exchange any edible food. After that the males secrete a salivary mass onto the surface as a nuptial gift, which is distinctly larger in N. carpenteri than in N. lui. Correspondingly, the male salivary glands are more developed in N. carpenteri than in N. lui. Males of N. longiprocessa bear very short salivary glands corresponding to a coercive mating tactic. The genital couplings are similar among the three species of Neopanorpa. The paired hypovalves of males are used to control the cerci of females. The prominent basal processes of male gonostyli grasp the posterior portion of the female medigynium across the intersegmental membrane. The male aedeagus physically couples with the female medigynium to ensure the male phallotreme to connect to the female copulatory pore. The influence of the notal organ length on the nuptial feeding behaviour of Neopanorpa is briefly discussed.
Bryophyte diversity on a tropical continental island (Hainan, China): potential vulnerable species and environmental indicators

ABSTRACT Introduction. Tropical bryophyte diversity is threatened by habitat loss and climate change. Methods. We reinvestigated the bryophyte biodiversity of Hainan Island, a continental island off the south China coast, with an extensive literature survey focusing on specimen information, and additional field collections. Endemic and threatened species, as well as biodiversity hotspots were identified using latest available information. Key results. Eight endemic species were proposed as potentially vulnerable species; their conservation status needs further investigation. Regional species richness identified the central mountain range as the bryological hotspot on Hainan Island. Environmental heterogeneity-diversity analyses employing Ordinary Least Squares demonstrated that percentage area of nature reserves within each region, range of precipitation, and range of temperature had strong correlations with regional species richness variation. Precipitation variables had more significant correlation with species richness variation than temperature variables. Water availability was the most important climatic predictor for bryophytes. Within bryophyte groups, liverworts and mosses occupied slightly different ecological niches. Conclusions. Our results support tropical bryophytes as sensitive indicators to drastic climate changes. Their ability to respond to climatic changes will contribute greatly to comprehensive conservation strategies.