Miracle-dz/UniFAR-FTUs huggingface dataset:
Feline microRNAome in ovary and testis: Exploration of in-silico miRNA-mRNA networks involved in gonadal function and cellular stress response

The aim of the study was to perform the first in-depth analysis of miRNAs in ovarian and testicular tissues of the domestic cat, a critical biomedical model. Specifically, potential miRNA involvement was explored in gonadal function, testis development, and cellular stress response to preservation protocols. We performed miRNA-sequencing on 20 ovarian and 20 testicular samples from 15 cats, including different ages and tissue treatments. Using fresh tissues (n = 15), we confirmed gonadal expression of 183 miRNA precursors and discovered additional 52 novel feline candidate precursors. We integrated the mRNA data from our previous study on the same age and treatment groups to create in-silico miRNA-mRNA networks and their functional enrichment, which allows comprehensive exploration into possible miRNA functions in cat gonads. Clusters of miRNAs united by shared differentially expressed mRNA targets are potentially involved in testicular development and spermatogenesis. MicroRNAs could play a significant role in ovarian tissue response to stress from microwave-assisted dehydration, with smaller roles in cellular response to vitrification in both ovary and testis. This new list of miRNAs with potential function in cat gonads is a major step towards understanding the gonadal biology, as well as optimizing fertility preservation protocols.
On-Road Succeeding Vehicle Detection

- A method for the detection of on-road succeeding vehicles using visual characteristic features like horizontal edges, shadow, symmetry and intensity is proposed. The proposed method uses the prominent horizontal edges along with the shadow under the vehicle to generate an initial estimate of the vehicle-road surface contact. Fast symmetry detection, utilizing the edge pixels, is then performed to detect the presence of vertically symmetric object, possibly vehicle, in the region above the initially estimated vehicle-road surface contact. A window defined by the horizontal and the vertical line obtained from above along with local perspective information provides a narrow region for the final search of the vehicle. A bounding box around the vehicle is extracted from the horizontal edges, symmetry histogram and a proposed squared difference of intensity measure. Experiments have been performed on natural traffic scenes obtained from a camera mounted on the side view mirror of a host vehicle demonstrate good and reliable performance of the proposed method
Emotion regulation and delusion-proneness relate to empathetic tendencies in a transdiagnostic sample

Empathetic tendencies (i.e., perspective taking and empathic concern) are a key factor in interpersonal relationships, which may be impacted by emotion regulation (i.e., reappraisal and suppression) and mental health symptoms, such as psychotic-like experiences. However, it is unclear if certain psychotic-like experiences, such as delusion-proneness, are still associated with reduced empathetic tendencies after accounting for emotion regulation style and dimensions of psychopathology that are often comorbid. In the current study, linear models tested these associations in a transdiagnostic community sample (N = 128), using the Interpersonal Reactivity Index (IRI), Emotion Regulation Questionnaire, and the Peter’s Delusion Inventory. Results indicated that perspective taking was positively associated with reappraisal and negatively associated with delusion-proneness, after controlling for age, sex, race, intelligence, and symptoms of anxiety and depression. A significant change in R2 supported the addition of delusion-proneness in this model. Specificity analyses demonstrated perspective taking was also negatively associated with suppression, but this relationship did not remain after accounting for the effects of reappraisal and delusion-proneness. Additional specificity analyses found no association between empathic concern and reappraisal or delusion-proneness but replicated previous findings that empathic concern was negatively associated with suppression. Taken together, delusion-proneness accounts for unique variance in perspective taking, which can inform future experimental research and may have important implications for psychosocial interventions.
Tree-based, two-stage risk factor analysis for postoperative sepsis based on Sepsis-3 criteria in elderly patients: A retrospective cohort study

Background Sepsis remains the leading cause of postoperative death in elderly patients and is defined as organ dysfunction with proven or suspected infection according to Sepsis-3 criteria. To better avoid potential non-linear associations between the risk factors, we firstly used a tree-based analytic methods to explore the putative risk factors of geriatric sepsis based on the criteria in the study. Methods Data of 7,302 surgical patients aged ≥ 65 years at the Third Affiliated Hospital of Sun Yat-sen University from January 2015 to September 2020 were collected. An analytic method that combined tree-based analysis with the method of Mantel-Haenszel and logistic regression was adopted to assess the association between 17 putative risk factors and postoperative sepsis defined by the Sepsis-3 guideline by controlling 16 potential confounding factors. Results Among the 16 potential covariates, six major confounders were statistically identified by the tree-based model, including cerebrovascular diseases, preoperative infusion of red blood cells, pneumonia, age ≥ 75, malignant tumor and diabetes. Our analysis indicated that emergency surgery increases the risk of postoperative sepsis in elderly patients by more than six times. The type of surgery is also a crucial risk factor for sepsis, particularly transplantation and neurosurgery. Other risk factors were duration of surgery > 120 min, administration of steroids, hypoalbuminemia, elevated creatinine, blood urea nitrogen, hematocrit, platelets, glucose, white blood cell count, abnormal neutrophil-to-lymphocyte ratio and elevated hsCRP-to-albumin ratio. Conclusions Our study uses an effective method to explore some risk factors for postoperative sepsis in elderly by adjusting many potential confounders and it can provide information for intervention design.
Hierarchical and nested associations of suicide with marriage, social support, quality of life, and depression among the elderly in rural China: Machine learning of psychological autopsy data

Objectives To identify mechanisms underpinning the complex relationships between influential factors and suicide risk with psychological autopsy data and machine learning method. Design A case-control study with suicide deaths selected using two-stage stratified cluster sampling method; and 1:1 age-and-gender matched live controls in the same geographic area. Setting Disproportionately high risk of suicide among rural elderly in China. Participants A total of 242 subjects died from suicide and 242 matched live controls, 60 years of age and older. Measurements Suicide death was determined based on the ICD-10 codes. Influential factors were measured using validated instruments and commonly accepted variables. Results Of the total sample, 270 (55.8%) were male with mean age = 74.2 (SD = 8.2) years old. Four CART models were used to select influential factors using the criteria: areas under the curve (AUC) ≥ 0.8, sensitivity ≥ 0.8, and specificity ≥ 0.8. Each model included a lead predictor plus 8–10 hierarchically nested factors. Depression was the first to be selected in Model 1 as the lead predictor; After depression was excluded, quality of life (QOL) was selected in Model 2; After depression and QOL were excluded, social support was selected in Model 3. Finally, after all 3 lead factors were excluded, marital status was selected in Model 4. In addition, CART demonstrated the significance of several influential factors that would not be associated with suicide if the data were analyzed using the conventional logistic regression. Conclusion Associations between the key factors and suicide death for Chinese rural elderly are not linear and parallel but hierarchically nested that could not be effectively detected using conventional statistical methods. Findings of this study provide new and compelling evidence supporting tailored suicide prevention interventions at the familial, clinical and community levels.
Mechanistic target of rapamycin signaling in human nervous system development and disease

Mechanistic target of rapamycin (mTOR) is a highly conserved serine/threonine kinase that regulates fundamental cellular processes including growth control, autophagy and metabolism. mTOR has key functions in nervous system development and mis-regulation of mTOR signaling causes aberrant neurodevelopment and neurological diseases, collectively called mTORopathies. In this mini review we discuss recent studies that have deepened our understanding of the key roles of the mTOR pathway in human nervous system development and disease. Recent advances in single-cell transcriptomics have been exploited to reveal specific roles for mTOR signaling in human cortical development that may have contributed to the evolutionary divergence from our primate ancestors. Cerebral organoid technology has been utilized to show that mTOR signaling is active in and regulates outer radial glial cells (RGCs), a population of neural stem cells that distinguish the human developing cortex. mTOR signaling has a well-established role in hamartoma syndromes such as tuberous sclerosis complex (TSC) and other mTORopathies. New ultra-sensitive techniques for identification of somatic mTOR pathway mutations have shed light on the neurodevelopmental origin and phenotypic heterogeneity seen in mTORopathy patients. These emerging studies suggest that mTOR signaling may facilitate developmental processes specific to human cortical development but also, when mis-regulated, cause cortical malformations and neurological disease.
Non-perturbatively improved clover action for SU(2) gauge + fundamental and adjoint representation fermions

The research of strongly coupled beyond-the-standard-model theories has generated significant interest in non-abelian gauge field theories with different number of fermions in different representations. Motivated by the increased interest to vario us technicolor scenarios, we study the non-perturbative improvement of the Wilson-clover action with SU(2) gauge fields and 2 flavors of fermions in the fundamental and adjoint representations. The Sheikholeslami-Wohlert coefficients are fixed using Schrodinger functional boundar y conditions. The adjoint representation theory is a candidate for a "minimal technicolor" theory, already studied on the lattice using unimproved Wilson fermions.
Association between interindividual variability in training volume and strength gain

This study aimed to examine the association between interindividual variability in strength changes and in training volume. A total of 26 untrained men completed 4-weeks of isometric knee extension (KE group, n = 12) and hip flexion (HF group, n = 14) training. Each training session comprised four sets of ten isometric contractions, 3-s contractions every 20 s. Training volume, which was defined as impulse during contractions, and maximal voluntary contraction (MVC) torque during KE and HF were evaluated. Based on the magnitude of MVC torque changes, the participants were divided into the high and low responders (n = 13; KE = 6 and HF = 7 per responders). The MVC torque changes (KE, 20.8%; HF, 22.4%) and total training volume did not significantly differ between the two groups. A higher training volume was demonstrated in the low responders than the high responders. The total training volume was positively associated with the MVC torque changes in low responders (r = 0.869%, 95% confidence interval [0.610, 0.960], p < 0.001), but not in high responders [r = 0.229, 95% confidence interval (−0.368, 0.693), p = 0.451], KE or HF group. Results showed that training volume was an important factor in determining the magnitude of strength gains in low responders, and MVC torque could improve by approximately 20% with the use of the study protocol regardless of joint actions involved during training.
Human gut microbiota in health and disease: Unveiling the relationship

The human gut possesses millions of microbes that define a complex microbial community. The gut microbiota has been characterized as a vital organ forming its multidirectional connecting axis with other organs. This gut microbiota axis is responsible for host-microbe interactions and works by communicating with the neural, endocrinal, humoral, immunological, and metabolic pathways. The human gut microorganisms (mostly non-pathogenic) have symbiotic host relationships and are usually associated with the host’s immunity to defend against pathogenic invasion. The dysbiosis of the gut microbiota is therefore linked to various human diseases, such as anxiety, depression, hypertension, cardiovascular diseases, obesity, diabetes, inflammatory bowel disease, and cancer. The mechanism leading to the disease development has a crucial correlation with gut microbiota, metabolic products, and host immune response in humans. The understanding of mechanisms over gut microbiota exerts its positive or harmful impacts remains largely undefined. However, many recent clinical studies conducted worldwide are demonstrating the relation of specific microbial species and eubiosis in health and disease. A comprehensive understanding of gut microbiota interactions, its role in health and disease, and recent updates on the subject are the striking topics of the current review. We have also addressed the daunting challenges that must be brought under control to maintain health and treat diseases.
Small-diameter bacterial cellulose-based vascular grafts for coronary artery bypass grafting in a pig model

Surgical revascularization is the gold standard in most cases of complex coronary artery disease. For coronary artery bypass grafting, autologous grafts are state-of-the-art due to their long-term patency. A non-negligible amount of patients lack suitable bypass material as a result of concomitant diseases or previous interventions. As a promising alternative, tissue-engineered vascular grafts made of biomaterials such as bacterial cellulose (BC) are gaining more and more attention. However, the production of small-diameter grafts (inner diameter < 6 mm) of application-oriented length (> 5 cm) and their in vivo long-term patency remain challenging. In this study, grafts of 20 cm in length with an inner diameter of 3 mm were generated in a custom-made bioreactor. To potentially improve graft compliance and, therefore in vivo patency, BC was combined with an embedded cobalt–chromium mesh. The grafts were designed for in vivo endothelialization and specific surgical properties and implanted as an aortocoronary bypass in a left anterior descending occluded pig model (n = 8). Coronary angiography showed complete patency postoperatively at 4 weeks. Following 4 weeks in vivo, the grafts were explanted revealing a three-layered wall structure. Grafts were colonized by smooth muscle cells and a luminal layer of endothelial cells with early formation of vasa privata indicating functional remodeling. These encouraging findings in a large animal model reveal the great potential of small-diameter BC grafts for coronary and peripheral bypass grafting.
Occurrence of Nine Antibiotics in Different Kinds of Sewage Sludge, Soils, Corn and Grapes After Sludge Spreading

The huge worldwide use of antibiotics triggers the accumulation of these substances in sludge from wastewater treatment plants (WWTP) and the possible contamination of soils amended with it, as well as of crops growing in these soils. In this work we analyzed the presence of the antibiotics amoxicillin (AMO), cefuroxime (CEF), ciprofloxacin (CIP), clarithromycin (CLA), levofloxacin (LEV), lincomycin (LIN), norfloxacin (NOR), sulfadiazine (SUL), and trimethoprim (TRI), in sludge from different WWTPs in Galicia (NW Spain), as well as in sludge technically treated by waste-managers, in soils where treated sludge was applied, and in crops (corn and vineyard) growing in the amended areas. The antibiotics were quantified by means of high resolution HPLC-mass-chromatography. The results indicate that almost all the sludge samples contained antibiotics, being ciprofloxacin and levofloxacin the most abundant reaching maximum values of 623 and 893 ng/g, respectively. The sludge treatment significantly reduced the number and the concentrations of antibiotics. In 12% of the soil samples where sludge was applied, some antibiotics were detected, but always in small concentrations. Regarding the crops, no antibiotic was detected in the roots, stalk, leaves and grain of corn, neither in grapes sampled in vineyards. It can be concluded that the treatments currently applied in the WWTPs under study are not totally effective in removing antibiotics from the sludge, although the findings of this research suggest that the additional specific treatment of the sludge derived from these WWTPs is effective in reducing the risk of environmental pollution due to a variety of antibiotics, and specifically in the case of soils amended with these organic materials and crops growing on it.
Revealing phosphorylation regulatory networks during embryogenesis of honey bee worker and drone (Apis mellifera)

Protein phosphorylation is known to regulate a comprehensive scenario of critical cellular processes. However, phosphorylation-mediated regulatory networks in honey bee embryogenesis are mainly unknown. We identified 6342 phosphosites from 2438 phosphoproteins and predicted 168 kinases in the honey bee embryo. Generally, the worker and drone develop similar phosphoproteome architectures and major phosphorylation events during embryogenesis. In 24 h embryos, protein kinases A play vital roles in regulating cell proliferation and blastoderm formation. At 48–72 h, kinase subfamily dual-specificity tyrosine-regulated kinase, cyclin-dependent kinase (CDK), and induced pathways related to protein synthesis and morphogenesis suggest the centrality to enhance the germ layer development, organogenesis, and dorsal closure. Notably, workers and drones formulated distinct phosphoproteome signatures. For 24 h embryos, the highly phosphorylated serine/threonine-protein kinase minibrain, microtubule-associated serine/threonine-protein kinase 2 (MAST2), and phosphorylation of mitogen-activated protein kinase 3 (MAPK3) at Thr564 in workers, are likely to regulate the late onset of cell proliferation; in contrast, drone embryos enhanced the expression of CDK12, MAPK3, and MAST2 to promote the massive synthesis of proteins and cytoskeleton. In 48 h, the induced serine/threonine-protein kinase and CDK12 in worker embryos signify their roles in the construction of embryonic tissues and organs; however, the highly activated kinases CDK1, raf homolog serine/threonine-protein kinase, and MAST2 in drone embryos may drive the large-scale establishment of tissues and organs. In 72 h, the activated pathways and kinases associated with cell growth and tissue differentiation in worker embryos may promote the configuration of rudimentary organs. However, kinases implicated in cytoskeleton organization in drone embryos may drive the blastokinesis and dorsal closure. Our hitherto most comprehensive phosphoproteome offers a valuable resource for signaling research on phosphorylation dynamics in honey bee embryos.
An indigenous inland genotype of the black yeast Hortaea werneckii inhabiting the great pyramid of Giza, Egypt

Within the context of cultural heritage conservation, the biological study of tangible archeological sites is an important task to extend their existence and strengthen the transmission of their cultural value to future generations. In Egypt, a hyper-arid region, a microcolonial fungus with inky black growth was observed on a stone surface in the royal corridor of the Great Pyramid of Giza (King Khufu’s pyramid). The isolate was studied and characterized by microscopic morphometric measurements, evaluation of enzymatic activities, and genotyping techniques. The isolate was identified as Hortaea werneckii, a pleomorphic black yeast that naturally inhabits hypersaline environments and infects human skin. It has been reported from humid temperate, subtropical, and tropical zones, mainly from marine habitats and adjacent areas, and is associated with marine life. Since it was observed in an unusual habitat, it raises the question of its type and origin, whether environmental or clinical. The Egyptian Hortaea werneckii GPS5 isolate was profiled and characterized by adaptive extremophilic tolerance to arid salt stress, low portability to infect human skin, and the capability of solubilizing calcite; besides it was phylogenetically clustered with previous recorded environmental accessions. A profile that matches the biodeterioration fungal agents known as rock-inhabiting fungi, a potential threat to cultural heritage sites that requires attention and prevention plans.
Association between antibiotics and dementia risk: A retrospective cohort study

Background: The possible relation between antibiotic exposure and the alteration of gut microbiota, which may affect dementia risk, has been revealed. However, the association between antibiotics and dementia incidence has rarely been studied. We aimed to determine the association between antibiotic exposure and the risk of dementia. Methods: This population-based retrospective cohort study used data from the National Health Insurance Service-Health Screening Cohort (NHIS-HEALS) in South Korea. Exposure was the cumulative days of antibiotic prescription from 2002 to 2005. Newly diagnosed overall dementia, Alzheimer’s disease (AD), and vascular dementia (VD) were identified based on diagnostic codes and prescriptions for dementia-related drugs. The follow-up investigation was carried out from 1 January 2006 to 31 December 2013. The Cox proportional hazards regression was used to assess the association between cumulative antibiotic prescription days and dementia incidence. Results: A total of 313,161 participants were analyzed in this study. Compared to antibiotic non-users, the participants who used antibiotics for 91 or more days had an increased risk of overall dementia [adjusted hazard ratio (aHR), 1.44; 95% confidence interval (CI), 1.19–1.74], AD (aHR, 1.46; 95% CI, 1.17–1.81), and VD (aHR, 1.38; 95% CI, 0.83–2.30). Those who used five or more antibiotic classes had higher risks of overall dementia (aHR, 1.28; 95% CI, 1.00–1.66) and AD (aHR, 1.34; 95% CI, 1.00–1.78) than antibiotic non-users. Conclusion: Antibiotic exposure may increase the risk of dementia in a cumulative duration-dependent manner among adult participants. Future studies are needed to assess the causality between the long-term prescription of antibiotics and dementia risk.