Miracle-dz/UniFAR-FTUs huggingface dataset:
Cloning, expression analysis and localization of DAZL gene implicated in germ cell development of male Hezuo pig.

Deleted in azoospermia-like (DAZL) is essential for mammalian testicular function and spermatogenesis. To explore the molecular characterization, expression patterns, and cellular localization of the DAZL in Hezuo pig testes, testicular tissue was isolated from Hezuo pig at five development stages including 30 days old (30 d), 90 days old (90 d), 120 days old (120 d), 180 days old (180 d), and 240 days old (240 d). DAZL cDNA was first cloned using the RT-PCR method, and its molecular characterization was analyzed using relevant bioinformatics software. Subsequently, the expression patterns and cellular localization of DAZL were evaluated using quantitative real-time PCR (qRT-PCR), Western blot, and immunohistochemistry. The cloning and sequence analysis showed that the Hezuo pig DAZL cDNA fragment contained 888 bp open reading frame (ORF) capable of encoding 295 amino acid residues and exhibited high identities with some other mammals. The qRT-PCR and Western blot results indicated that DAZL was specifically expressed in Hezuo pig testes, and DAZL levels of both mRNA and protein were expressed at all five reproductive stages of Hezuo pig testes, with extremely significant higher expression levels in 90 d, 120 d, 180 d, and 240 d than those in 30 d (p < 0.01). Additionally, immunohistochemistry results revealed that DAZL protein was mainly localized in gonocytes at 30 d testes, primary spermatocytes, and spermatozoon at other developmental stages, and Leydig cells throughout five development stages. Together, these results suggested that DAZL may play an important role by regulating the proliferation or differentiation of gonocytes, development of primary spermatocytes and spermatozoon, and functional maintenance of Leydig cells in testicular development and spermatogenesis of Hezuo pig. Nevertheless, the specific regulatory mechanisms underlying these phenomena still requires further investigated and verified.
DeepMHCI: an anchor position-aware deep interaction model for accurate MHC-I peptide binding affinity prediction

Abstract Motivation Computationally predicting major histocompatibility complex class I (MHC-I) peptide binding affinity is an important problem in immunological bioinformatics, which is also crucial for the identification of neoantigens for personalized therapeutic cancer vaccines. Recent cutting-edge deep learning-based methods for this problem cannot achieve satisfactory performance, especially for non-9-mer peptides. This is because such methods generate the input by simply concatenating the two given sequences: a peptide and (the pseudo sequence of) an MHC class I molecule, which cannot precisely capture the anchor positions of the MHC binding motif for the peptides with variable lengths. We thus developed an anchor position-aware and high-performance deep model, DeepMHCI, with a position-wise gated layer and a residual binding interaction convolution layer. This allows the model to control the information flow in peptides to be aware of anchor positions and model the interactions between peptides and the MHC pseudo (binding) sequence directly with multiple convolutional kernels. Results The performance of DeepMHCI has been thoroughly validated by extensive experiments on four benchmark datasets under various settings, such as 5-fold cross-validation, validation with the independent testing set, external HPV vaccine identification, and external CD8+ epitope identification. Experimental results with visualization of binding motifs demonstrate that DeepMHCI outperformed all competing methods, especially on non-9-mer peptides binding prediction. Availability and implementation DeepMHCI is publicly available at https://github.com/ZhuLab-Fudan/DeepMHCI.
Dynamics in cardiac surgery: trends in population characteristics and the performance of the EuroSCORE II over time

Abstract OBJECTIVES The aim of this study was to investigate the performance of the EuroSCORE II over time and dynamics in values of predictors included in the model. METHODS A cohort study was performed using data from the Netherlands Heart Registration. All cardiothoracic surgical procedures performed between 1 January 2013 and 31 December 2019 were included for analysis. Performance of the EuroSCORE II was assessed across 3-month intervals in terms of calibration and discrimination. For subgroups of major surgical procedures, performance of the EuroSCORE II was assessed across 12-month time intervals. Changes in values of individual EuroSCORE II predictors over time were assessed graphically. RESULTS A total of 103 404 cardiothoracic surgical procedures were included. Observed mortality risk ranged between 1.9% [95% confidence interval (CI) 1.6–2.4] and 3.6% (95% CI 2.6–4.4) across 3-month intervals, while the mean predicted mortality risk ranged between 3.4% (95% CI 3.3–3.6) and 4.2% (95% CI 3.9–4.6). The corresponding observed:expected ratios ranged from 0.50 (95% CI 0.46–0.61) to 0.95 (95% CI 0.74–1.16). Discriminative performance in terms of the c-statistic ranged between 0.82 (95% CI 0.78–0.89) and 0.89 (95% CI 0.87–0.93). The EuroSCORE II consistently overestimated mortality compared to observed mortality. This finding was consistent across all major cardiothoracic surgical procedures. Distributions of values of individual predictors varied broadly across predictors over time. Most notable trends were a decrease in elective surgery from 75% to 54% and a rise in patients with no or New York Heart Association I class heart failure from 27% to 33%. CONCLUSIONS The EuroSCORE II shows good discriminative performance, but consistently overestimates mortality risks of all types of major cardiothoracic surgical procedures in the Netherlands.
Le temps des cépages. Du terroir au système-monde//Local or global stratégies for wine-growing

The consumption and production of wine reflect the evolution of markets between local and global Due to the increase in wine consumption in new countries, many wines are not marketed under geographic names but under grape names : Chardonnay, Cabernet, for example. Major wine groups, knowing this trend, invest where it is possible to produce good quality wines at interesting prices
Disrupted Lives: Caregivers' Experiences of In‐Hospital Cardiac Arrest Survivors' Recovery 5 Years Later

Background Survivors of in‐hospital cardiac arrest (IHCA) experience ongoing physical and cognitive impairments, often requiring support from a caregiver at home afterwards. Caregivers are important in the survivor's recovery, yet there is little research specifically focused on their experiences once the survivor is discharged home. In this study, we highlight how caregivers for veteran IHCA survivors described and experienced their caregiver role, the strategies they used to fulfill their role, and the additional needs they still have years after the IHCA event. Methods and Results Between March and July 2019, semistructured telephone interviews were conducted with 12 caregivers for veteran IHCA survivors. Interviews were transcribed, and content analysis was performed. Patterns within the data were further analyzed and grouped into themes. A predominant theme of “disruption” was identified across 3 different domains including the following: (1) disruption in caregiver's life, (2) disruption in caregiver–patient relationship, and (3) disruption in caregiver's well‐being. Disruption was associated with both positive and negative caregiver experiences. Strategies caregivers used and resources they felt would have helped them adjust to their caregiver role were also identified. Conclusions Caregivers for veteran IHCA survivors experienced a disruption in many facets of their lives. Caregivers felt the veterans' IHCA impacted various aspects of their lives, and they continued to need additional support in order to care for the IHCA survivor and themselves. Although some were able to procure coping strategies, such as counseling and engaging in stress‐relieving activities, most indicated additional help and resources were still needed.
Comparative Studies of Different Preservation Methods and Relative Freeze-Drying Formulations for Extracellular Vesicle Pharmaceutical Applications

Extracellular vesicles (EVs) have been studied for years for their role as effectors and mediators of cell-to-cell communication and their potential application to develop new and increasingly performing nanotechnological systems for the diagnosis and/or treatment of many diseases. Given all the EVs applications as just isolated, functionalized, or even engineered cellular-derived pharmaceuticals, the standardization of reliable and reproducible methods for their preservation is urgently needed. In this study, we isolated EVs from a healthy blood cell line, B lymphocytes, and compared the effectiveness of different storage methods and relative freeze-drying formulations to preserve some of the most important EVs’ key features, i.e., concentration, mean size, protein content, and surface antigen’s expression. To develop a preservation method that minimally affects the EVs’ integrity and functionality, we applied the freeze-drying process in combination with different excipients. Since EVs are isolated not only from body fluids but also from culture media conditioned by the cells growing there, we decided to test both the effects of the traditional pharmaceutical excipient and of biological media to develop EVs solidified products with desirable appearance and performance properties. Results showed that some of the tested excipients, i.e., sugars in combination with dextran and glycine, successfully maintained the stability and integrity of EVs upon lyophilization. In addition, to evaluate the preservation of the EVs’ biological activity, we assessed the cytotoxicity and internalization ability of the reconstituted EVs in healthy (B lymphocytes) and tumoral (Burkitt’s lymphoma) cells. Reconstituted EVs demonstrated toxicity only toward the cancerous cells, opening new therapeutic opportunities for the oncological field. Furthermore, our study showed how some biological or cellular-conditioned fluids, commonly used in the field of cell cultures, can act not only as cryoprotectants but also as active pharmaceutical ingredients, significantly tuning the therapeutic effect of EVs, even increasing their cellular internalization.
Effects of Sport Stacking on Cognition in Patients With Mild Alzheimer’s Disease and MCI: Preliminary Findings of Randomized Controlled Trial

Objective This mixed-method pilot study aims to investigate the feasibility and preliminary effects of sport stacking on cognitive function in individuals with mild Alzheimer's disease (AD) and those with mild cognitive impairment (MCI). Methods Twenty-four community-dwelling subjects with confirmed mild AD or MCI were evenly randomly assigned to either the 12-week sport stacking intervention group (n = 12) or clinic routine management control group (n = 12). Outcome evaluation included the Auditory Verbal Learning Test (AVLT), Alzheimer's Disease Cooperative Study–Activities of Daily Living scale (ADCS-ADL), and plasma brain-derived neurotrophic factor (BDNF). A qualitative descriptive study was conducted to explore the overall perception and experience of the sport stacking from the subjects’ perspective. Results Twenty-two subjects completed the trial. At 12 weeks post-intervention, compared to the control group, the sport stacking group had significantly greater improvements in AVLT immediate recall (P < .001, Cohen d = .66) and an increase in plasma BDNF (P < .001, Cohen d = .64). Subgroup analysis indicated that subjects with MCI had significantly greater increases in AVLT immediate recall (P = .005, Cohen d = .72), ADCS-ADL (P = .130, Cohen d = .42) and plasma BDNF (P = .024, Cohen d = .83). Twelve subjects participating in the post-intervention interviews expressed the benefits (e.g., hand-eye coordination and faster reaction) from sport stacking and their enjoyment of it. Conclusion To the best of our knowledge, this is the first study indicating that sport stacking is feasible among individuals with MCI and mild AD. The preliminary effect on episodic memory is encouraging, possibly via upregulation of BDNF.
The effects of conjugated linoleic acid supplementation on anthropometrics and body composition indices in adults: a systematic review and dose–response meta-analysis

Abstract Prior meta-analytic investigations over a decade ago rather inconclusively indicated that conjugated linoleic acid (CLA) supplementation could improve anthropometric and body composition indices in the general adult population. More recent investigations have emerged, and an up-to-date systematic review and meta-analysis on this topic must be improved. Therefore, this investigation provides a comprehensive systematic review and meta-analysis of randomised controlled trials (RCT) on the impact of CLA supplementation on anthropometric and body composition (body mass (BM), BMI, waist circumference (WC), fat mass (FM), body fat percentage (BFP) and fat-free mass (FFM)) markers in adults. Online databases search, including PubMed, Scopus, the Cochrane Library and Web of Science up to March 2022, were utilised to retrieve RCT examining the effect of CLA supplementation on anthropometric and body composition markers in adults. Meta-analysis was carried out using a random-effects model. The I 2 index was used as an index of statistical heterogeneity of RCT. Among the initial 8351 studies identified from electronic databases search, seventy RCT with ninety-six effect sizes involving 4159 participants were included for data analyses. The results of random-effects modelling demonstrated that CLA supplementation significantly reduced BM (weighted mean difference (WMD): −0·35, 95 % CI (−0·54, −0·15), P < 0·001), BMI (WMD: −0·15, 95 % CI (−0·24, −0·06), P = 0·001), WC (WMD: −0·62, 95% CI (−1·04, −0·20), P = 0·004), FM (WMD: −0·44, 95 % CI (−0·66, −0·23), P < 0·001), BFP (WMD: −0·77 %, 95 % CI (−1·09, −0·45), P < 0·001) and increased FFM (WMD: 0·27, 95 % CI (0·09, 0·45), P = 0·003). The high-quality subgroup showed that CLA supplementation fails to change FM and BFP. However, according to high-quality studies, CLA intake resulted in small but significant increases in FFM and decreases in BM and BMI. This meta-analysis study suggests that CLA supplementation may result in a small but significant improvement in anthropometric and body composition markers in an adult population. However, data from high-quality studies failed to show CLA’s body fat-lowering properties. Moreover, it should be noted that the weight-loss properties of CLA were small and may not reach clinical importance.
Characterizing the phenotypic and genetic structure of psychopathology in UK Biobank

Mental conditions exhibit a higher-order transdiagnostic factor structure which helps to explain the widespread comorbidity observed in psychopathology. However, the phenotypic and genetic structures of psychopathology may differ, raising questions about the validity and utility of these factors. Here, we study the phenotypic and genetic factor structures of ten psychiatric conditions using UK Biobank and public genomic data. Although the factor structure of psychopathology was generally genetically and phenotypically consistent, conditions related to externalizing (e.g., alcohol use disorder) and compulsivity (e.g., eating disorders) exhibited cross-level disparities in their relationships with other conditions, plausibly due to environmental influences. Domain-level factors, especially thought disorder and internalizing factors, were more informative than a general psychopathology factor in genome-wide association and polygenic index analyses. Collectively, our findings enhance the understanding of comorbidity and shared etiology, highlight the intricate interplay between genes and environment, and offer guidance for psychiatric research using polygenic indices.
Clinical and microbiological aspects of periodontal disease in horses in South-East Queensland, Australia

The study of periodontal disease as part of equine dentistry is one of the overlooked fields of study, which truly needs more study and research to clearly understand the nature of the disease, the most appropriate diagnostic technique and prevention or treatment to provide for a good quality of life for horses. The abattoir survey of the oral cavity and dentition of 400 horses from SouthEast Queensland, Australia, showed that the most common dental abnormality was sharp enamel points (55.3% prevalence). Several types of dental abnormalities were strongly associated with age. The highest frequency of dental abnormalities (97.5%) were observed in senior horses (11-15 years old) and this included periodontal disease that increased to almost fifty percent in senior horses. The findings also confirmed that all horses, not just young horses, should have regular complete dental examinations as early as possible which should limit the development of more severe dental pathologies later in life. The equine oral microbiome found in dental plaque can cause oral disease which involves the some of the endogenous oral microbiota becoming opportunistic pathogens. The conventional method of oral microbiology based on culture dependent techniques usually overestimates the significance of species that are easily grown and overlooks microbial community diversity. Recently, the culture independent techniques using the next generation sequencing (NGS) method can determine the whole bacterial microbiota. The results from culture dependent and NGS method of analysis of healthy gingiva and periodontitis samples showed that the most common Genera isolated were Prevotella and Porphyromonas without a statistical significance in bacterial diversity, between the control and periodontitis groups. In conclusion, equine bacterial diversity between the healthy and periodontitis groups were similar which is different from other animals and this may be due to factors such as dentition, feed type and husbandry. The standard approach for diagnosis of equine periodontal disease (EPD) is based on clinical dental examination but to evaluate the current stage of disease and for further treatment planning, auxiliary aids such radiography are required. Equine dental radiography has been largely restricted to extraoral techniques by the standard equine radiography technology and the complexity of equine head anatomy. In
Nomogram for predicting overall survival in patients with large (>5 cm) hepatocellular carcinoma based on real-world practice

Background/Aim Patients with large (>5 cm) hepatocellular carcinoma (HCC) have limited treatment options, thus necessitating the identification of prognostic factors and the development of predictive tools. This study aimed to identify prognostic factors and to construct a nomogram to predict survival outcomes in patients with large HCC. Methods A cohort of 438 patients, who were diagnosed with large HCC at a tertiary hospital between 2015 and 2018, was analyzed. Cox proportional hazards models were used to identify key prognosticators of overall survival (OS), and an independent set of prognostic factors was used to develop a nomogram. The discrimination and calibration abilities of the nomogram were assessed and internal validation was performed using cross-validation and bootstrapping methods. Results During a median follow-up of 9.3 months, the median OS was 9.9 months, and the 1-year OS rate was 43.9%. Multivariable Cox regression analysis revealed that performance status, modified albumin-bilirubin grade, tumor size, extent of portal vein tumor thrombosis, and initial treatment significantly affected OS. The newly developed nomogram incorporating these variables demonstrated favorable accuracy (Harrell’s concordance index, 0.807). Conclusions The newly developed nomogram facilitated the estimation of individual survival outcomes in patients with large HCC, providing an acceptable level of accuracy.
Spatial Ecology of Wolverines in Scandinavia

1. Conservation of carnivores in an increasingly changing environment is much enhanced by understanding the decision-making processes underlying habitat patch choice. In a fluctuating environment incorporation of spatio-temporal activity patterns and home range use in resource selection models enhances the biological meaning of behavioural choices animals make along their path. Especially for central place foragers, such as the wolverine Gulo gulo L. , the nature and strength of the trade-off between central place foraging and optimal foraging are likely to influence both spatio-temporal movement patterns and patch choice. 2. We investigated the spatio-temporal ranging behaviour of seven reproductive female wolverines in south-central Norway, based on GPS data collected in 2002-2005. The study was conducted using autoregressive models and discrete choice models, which incorporated individual preferences. Travel speed, home range use and selection for elevation were analysed in relation to spatial and temporal covariates (time-of-day and date). 3. Wolverines were more active during the night and in the home range periphery. The stronger selection for higher elevations towards the periphery of the wolverines’ home ranges may be explained in two ways: (1) the location of the optimal central place lies in the “centre of gravity” of the food distribution, or (2) peripheral locations represent ranging movements for the purpose of transportation from patch to patch or central place. Over the summer, travel speed decreased and preference for lower-lying patches at day time increased, indicating a diminishing central place foraging movement pattern. At night wolverines selected similar patches at lower elevations all through the summer, enabling them to forage in the forest–alpine tundra ecotone; likely to be the patch with the highest expected profitability. May et al. – Spatio-temporal ranging behaviour in wolverines 3/36 4. The elevation preferences throughout the summer clearly showed a change from central place foraging to optimal foraging in wolverines with dependent cubs. Whereas in the beginning of the summer cubs are placed at rendezvous sites, towards the end of the summer cubs grow more mobile and independent. Apparently, female wolverines are faced with a continuous, but diminishing, trade-off between providing food and shelter for their offspring throughout the summer.
Drag Reduction in Flows Past 2D and 3D Circular Cylinders Through Deep Reinforcement Learning

We investigate drag reduction mechanisms in flows past two- and three-dimensional cylinders controlled by surface actuators using deep reinforcement learning. We investigate 2D and 3D flows at Reynolds numbers up to 8,000 and 4,000, respectively. The learning agents are trained in planar flows at various Reynolds numbers, with constraints on the available actuation energy. The discovered actuation policies exhibit intriguing generalization capabilities, enabling open-loop control even for Reynolds numbers beyond their training range. Remarkably, the discovered two-dimensional controls, inducing delayed separation, are transferable to three-dimensional cylinder flows. We examine the trade-offs between drag reduction and energy input while discussing the associated mechanisms. The present work paves the way for control of unsteady separated flows via interpretable control strategies discovered through deep reinforcement learning.
MLC at Feigenbaum points

We prove a priori bounds for Feigenbaum quadratic polynomials, i.e., infinitely renormalizable polynomials $f_c: z\mapsto z^2+c$ of bounded type. It implies local connectivity of the corresponding Julia sets $J(f_c)$ and MLC (local connectivity of the Mandelbrot set) at the corresponding parameters $c$. It also yields the scaling Universality, dynamical and parameter, for the corresponding combinatorics. The MLC Conjecture was open for the most classical period-doubling Feigenbaum parameter as well as for the complex tripling renormalizations. Universality for the latter was conjectured by Goldberg-Khanin-Sinai in the early 1980s.