Miracle-dz/UniFAR-FTUs huggingface dataset:
Breathomics profiling of metabolic pathways affected by major depression: Possibilities and limitations

Background Major depressive disorder (MDD) is one of the most common psychiatric disorders with multifactorial etiologies. Metabolomics has recently emerged as a particularly potential quantitative tool that provides a multi-parametric signature specific to several mechanisms underlying the heterogeneous pathophysiology of MDD. The main purpose of the present study was to investigate possibilities and limitations of breath-based metabolomics, breathomics patterns to discriminate MDD patients from healthy controls (HCs) and identify the altered metabolic pathways in MDD. Methods Breath samples were collected in Tedlar bags at awakening, 30 and 60 min after awakening from 26 patients with MDD and 25 HCs. The non-targeted breathomics analysis was carried out by proton transfer reaction mass spectrometry. The univariate analysis was first performed by T-test to rank potential biomarkers. The metabolomic pathway analysis and hierarchical clustering analysis (HCA) were performed to group the significant metabolites involved in the same metabolic pathways or networks. Moreover, a support vector machine (SVM) predictive model was built to identify the potential metabolites in the altered pathways and clusters. The accuracy of the SVM model was evaluated by receiver operating characteristics (ROC) analysis. Results A total of 23 differential exhaled breath metabolites were significantly altered in patients with MDD compared with HCs and mapped in five significant metabolic pathways including aminoacyl-tRNA biosynthesis (p = 0.0055), branched chain amino acids valine, leucine and isoleucine biosynthesis (p = 0.0060), glycolysis and gluconeogenesis (p = 0.0067), nicotinate and nicotinamide metabolism (p = 0.0213) and pyruvate metabolism (p = 0.0440). Moreover, the SVM predictive model showed that butylamine (p = 0.0005, pFDR=0.0006), 3-methylpyridine (p = 0.0002, pFDR = 0.0012), endogenous aliphatic ethanol isotope (p = 0.0073, pFDR = 0.0174), valeric acid (p = 0.005, pFDR = 0.0162) and isoprene (p = 0.038, pFDR = 0.045) were potential metabolites within identified clusters with HCA and altered pathways, and discriminated between patients with MDD and non-depressed ones with high sensitivity (0.88), specificity (0.96) and area under curve of ROC (0.96). Conclusion According to the results of this study, the non-targeted breathomics analysis with high-throughput sensitive analytical technologies coupled to advanced computational tools approaches offer completely new insights into peripheral biochemical changes in MDD.
Associations between repetitive negative thinking and resting-state network segregation among healthy middle-aged adults

Background Repetitive Negative Thinking (RNT) includes negative thoughts about the future and past, and is a risk factor for depression and anxiety. Prefrontal and anterior cingulate cortices have been linked to RNT but several regions within large-scale networks are also involved, the efficiency of which depends on their ability to remain segregated. Methods Associations between RNT and system segregation (SyS) of the Anterior Salience Network (ASN), Default Mode Network (DMN) and Executive Control Network (ECN) were explored in healthy middle-aged adults (N = 341), after undergoing resting-state functional magnetic resonance imaging. Regression analyses were conducted with RNT as outcome variable. Explanatory variables were: SyS, depression, emotional stability, cognitive complaints, age and sex. Results Analyses indicated that RNT was associated with depression, emotional stability, cognitive complaints, age and segregation of the left ECN (LECN) and ASN. Further, the ventral DMN (vDMN) presented higher connectivity with the ASN and decreased connectivity with the LECN, as a function of RNT. Conclusion Higher levels of perseverative thinking were related to increased segregation of the LECN and decreased segregation of the ASN. The dissociative connectivity of these networks with the vDMN may partially account for poorer cognitive control and increased self-referential processes characteristic of RNT.
Evidence for reproductive senescence across ray-finned fishes: A review

The origin, incidence, and consequences of reproductive senescence vary greatly across the tree of life. In vertebrates, research on reproductive senescence has been mainly focused on mammals and birds, demonstrating that its variation is largely linked to critical life history traits, such as growth patterns, juvenile, and adult mortality, and reproductive strategy. Fishes represent half of the vertebrate taxonomic diversity and display remarkable variation in life history. Based on a thorough literature review, we summarize current evidence on reproductive senescence in ray-finned fishes (Actinopterygii). While survival and physiological senescence are acknowledged in fish, their potential age-related reproductive decline has often been disregarded due to the prevalence of indeterminate growth. We demonstrate that age-related reproductive decline is reported across fish phylogeny, environments, and traits. An important point of our review is that the incidence of reproductive senescence in a species depends on both the number of studies for that species and the coverage of its maximum lifespan by the study. Reproductive senescence was documented for one-third of the studied fish species, with females suffering an age-related decline in reproductive traits less often than males or both parents combined. Neither parental care nor migratory strategy corresponded with the occurrence of reproductive senescence in fish. The traits that were affected by reproductive senescence most often were sex-specific, with pre-mating and mating categories of traits declining in females and sperm quality and quantity in males. We also demonstrate that reproductive senescence can be buffered by indeterminate growth. We provide rich evidence of reproductive senescence across ray-finned fishes, but we highlight the need for better data on age-related reproduction in fishes.
Critical-Field Curve of Superconducting Lead

The critical field of pure monocrystalline lead has been measured throughout its range. A vibrating phase-boundary technique was used, permitting continuous observation of the boundary between the normal and superconducting phases within the sample. Because of the co-existence of both phases at all times, supercooling and superheating effects are avoided. Departures from thermodynamic equilibrium are small, as is indicated by the very weak hysteresis (as low as several parts in 10 000). The deviation curve is strongly positive, as expected for strong-coupling superconductors. The measured values of the usual superconductive parameters are ${T}_{c}=(7.195\ifmmode\pm\else\textpm\fi{}0.006)$ \ifmmode^\circ\else\textdegree\fi{}K, ${H}_{0}=803.4\ifmmode\pm\else\textpm\fi{}0.3$ Oe, ${\frac{d{H}_{c}}{\mathrm{dT}}|}_{{T}_{c}}=237.3\ifmmode\pm\else\textpm\fi{}1.1$ Oe/\ifmmode^\circ\else\textdegree\fi{}K.
Adversarial Robustness of Deep Inverse Reinforcement Learning

Reinforcement learning research experienced substantial jumps in its progress after the ﬁrst achievement on utilizing deep neural networks to approximate the state-action value function in high-dimensional states. While deep reinforcement learning algorithms are currently being employed in many different tasks from industrial control to biomedical applications, the fact that an MDP has to provide a clear reward function limits the tasks that can be achieved via reinforcement learning. In this line of research, some studies proposed to directly learn a policy from observing expert trajectories (i.e. imitation learning), and others proposed to learn a reward function from expert demonstrations (i.e. inverse reinforcement learning). In this paper we will focus on robustness and vulnerabilities of deep imitation learning and deep inverse reinforcement learning policies. Furthermore, we will layout non-robust features learnt by the deep inverse reinforcement learning policies. We conduct experiments in the Arcade Learning Environment (ALE), and compare the non-robust features learnt by the deep inverse reinforcement learning algorithms to vanilla trained deep reinforcement learning policies. We hope that our study can provide a basis for the future discussions on the robustness of both deep inverse reinforcement learning and deep reinforcement learning.
Methane Production of Pistia Stratiotes as a Single Substrate and as a Co-Substrate with Dairy Cow Manure

Mono anaerobic digestion (AD) of dairy cow manure (DCM) is constrained by high moisture, ash and crude fibre content. Anaerobic co-digestion DCM and other biomass is one of the methods to overcome this drawback. This study aimed to evaluate: methane production from different parts of Pistia stratiotes (PS), methane production from the mixed substrate of PS and DCM in different proportions of PS in terms of volatile solids (VS) (0%, 7.99%, 14.91%, and 20.94%) using continuous digesters, and the potency of biogas yield from the digested slurry. Methane production from the whole plant, shoot system, and root of PS was 405.68, 416.82, and 326.42 L/kg VS, respectively. The highest methane production was obtained from the shoot system because that part contained higher crude protein and hemicellulose contents. Utilization of PS as a co-substrate for AD of the DCM can increase methane production by 28.65–56.98% compared to the control digester. No effect on pH, total ammonia nitrogen and total volatile fatty acid indicated that PS was suitable as a co-substrate of DCM and can significantly increase methane yield of the mixed substrate. AD of digested slurries showed that to recover the biogas production from the mixed substrate, the post-digestion treatment should be applied before the slurries are used as organic fertilizer.
Structural Equation Models

Although there are more and more women in universities in the areas of science, technology, engineering and mathematics (STEM), in terms of representativeness they are still far from equaling men. Gender stereotypes and segregation of STEM careers are obstacles for female students, as they generate exclusionary practices and hostile environments. The objective of this article was to propose a model for measuring the phenomenon of STEM women that considers latent variables related to male beliefs, inspirations, coping strategies, the labor market, school and a taste for mathematics. For this, an instrument was built that measures the perception of STEM women in university students. 1826 questionnaires were applied to students from two higher education schools of the Instituto Politécnico Nacional. The exploratory and confirmatory factor analysis was carried out, later the structural equations model was worked and finally six hypotheses generated from the latent variables were established. It was found that coping contributes to explain the School variable, in addition to male beliefs explaining the School and Labor Market constructs. It is concluded that it is necessary for schools to work to develop respectful and challenging environments for women, coupled with the fact that the labor sector has to support to close the gaps and eliminate gender discrimination.
MiSim: A Simulator for Resilience Assessment of Microservice-Based Architectures

Increased resilience compared to monolithic architectures is both one of the key promises of microservice-based architectures and a big challenge, e.g., due to the systems’ distributed nature. Resilience assessment through simulation requires fewer resources than the measurement-based techniques used in practice. However, there is no existing simulation approach that is suitable for a holistic resilience assessment of microservices comprised of (i) representative fault injections, (ii) common resilience mechanisms, and (iii) time-varying workloads. This paper presents MiSim — an extensible simulator for resilience assessment of microservice-based architectures. It overcomes the stated limitations of related work. MiSim fits resilience engineering practices by supporting scenario-based experiments and requiring only lightweight input models. We demonstrate how MiSim simulates (1) common resilience mechanisms — i.e., circuit breaker, connection limiter, retry, load balancer, and autoscaler — and (2) fault injections — i.e., instance/service killing and latency injections. In addition, we use TeaStore, a reference microservice-based architecture, aiming to reproduce scaling behavior from an experiment by using simulation. Our results show that MiSim allows for quantitative insights into microservice-based systems’ complex transient behavior by providing up to 25 metrics.
Prognostic value of metformin in cancers: An updated meta-analysis based on 80 cohort studies

Background: Experiments have shown that metformin can inhibit cancer cell growth, but clinical observations have been inconsistent, so we pooled the currently available data to evaluate the impact of metformin on cancer survival and progression. Methods: PubMed, web of science, Embase, and Cochrane databases were searched. Pooled hazard ratios (HRs) were identified using a random-effects model to estimate the strength of the association between metformin and survival and progression in cancer patients. Results: We incorporated 80 articles published from all databases which satisfied the inclusion criterion. It showed that metformin was associated with better overall survival (hazard ratio [HR] = 0. 81; 95% confidence interval [CI]: [0.77–0.85]) and cancer-specific survival (HR = 0.79; 95% CI: [0.73–0.86]), and metformin was associated with progression-free survival (HR = 0.76; 95% CI: [0.66–0.87]). In patients with diabetes mellitus, the HR of overall survival was 0.79(95% CI: [0.75–0.83]), progression-free survival was 0.72(95% CI: [0.60–0.85]), and the cancer-specific survival was 0.76(95% CI: [0.68–0.86]). It was proposed that metformin can improve the prognosis of cancer patients with diabetes mellitus. Conclusion: Based on cohort studies, metformin therapy has potential survival benefits for patients with malignancy, especially with the greatest benefits seen in breast cancer on overall survival, progression-free survival, and cancer-specific survival. And metformin also showed potential benefits in cancer-specific survival in colorectal and prostate cancer.
Efficacy of acupuncture for generalized anxiety disorder: A PRISMA-compliant systematic review and meta-analysis

Background: Generalized anxiety disorder (GAD) tightly traps modern people. Its incidence shows an increased peak during the 2019 novel coronavirus (COVID-19) epidemic. Acupuncture is regarded as an effective way to relieve anxiety symptoms. However, there are still controversies. This study aimed to systematically evaluate the clinical efficacy of acupuncture in patients with GAD. Methods: Four English and 3 Chinese databases were searched from their inception to January 2022. Only randomized controlled trials (RCTs) in which acupuncture was the main intervention were included. The literature was independently screened and extracted by two investigators. The Cochrane Bias Risk Assessment Tool was used for quality evaluation. Analyses were conducted by RevMan 5.3. 0 and STATA 15.0 software. The primary outcome was the Hamilton Anxiety Scale (HAMA). The secondary indicators were the total effective rate, the Self-Rating Anxiety Scale (SAS), and the Treatment Emergent Symptom Scale (TESS). Results: Twenty-seven studies were included with a total of 1782 participants. The risk of performance bias or reporting bias for most of the included trials was unclear. Combined results showed the acupuncture group had better outcomes in the HAMA score [MD = −0.78, 95%CI (−1.09, −0.46)], the total effective rate [RR = 1.14, 95%CI (1.09, 1.19)], the SAS score [MD = −2.55, 95%CI (−3.31, −1.80)] compared with the control group. Regarding the number of adverse events, the acupuncture group was safer than the control group and scored less grade in the TESS score [MD = −1.54, 95%CI (−1.92, −1.17)]. Conclusions: Acupuncture can effectively relieve the anxiety symptoms of generalized anxiety disorder patients with fewer side effects, but randomized controlled trials with large sample size and high quality are also required to support the result.
The effects of curcumin supplementation on high-sensitivity C-reactive protein, serum adiponectin, and lipid profile in patients with type 2 diabetes: A protocol for systematic review and meta-analysis

Background: Type 2 diabetes mellitus (T2DM) is an ensemble of metabolic diseases that has reached pandemic dimensions all over the world. There is a lack of evidence on the contribution of curcumin in the treatment of T2DM. We conducted a protocol for systematic review and meta-analysis to evaluate whether curcumin supplementation is effective and safe in T2DM patients. Methods: The systematic review will follow the guidelines of Preferred Reporting Items for Systematic Reviews and Meta-analyses Protocols (PRISMA-P). We will obtain studies through PubMed, Cochrane Library, Embase, Web of Science, and Medline databases. In addition, we will also collect 4 databases of China: China National Knowledge Infrastructure, China Biomedical Literature Database, China Science Journal Database, and Wan-fang Database. Eligible study conference abstracts and reference lists of manuscripts will be searched. The data collection and analysis will be conducted independently by 2 reviewers. Meta-analysis will be performed using Review Manager software, version 5.3 (Update Software Ltd, Oxford, Oxon, UK). Results: The results of this systematic review and meta-analysis will be published in a peer-reviewed journal. Conclusion: The findings of this systematic review may encourage supplementation of curcumin and its preparation specifically in T2DM patients. Nevertheless, the application of curcumin supplementation in clinical practice should be taken with individual’s contributing factors.
Comparative efficacy and safety of JAK inhibitors and leflunomide in rheumatoid arthritis: A protocol for systematic review and meta-analysis

Background: Rheumatoid arthritis is the most prevalent systemic autoimmune disease among the rheumatic inflammatory musculoskeletal diseases. Currently, there is no reliable evidence regarding the comparisons of anti-rheumatic effects between leflunomide and Janus kinase inhibitors. We performed a protocol for systematic review and meta-analysis to compare the efficacy and safety of Janus kinase inhibitors and leflunomide in rheumatoid arthritis. Methods: This review has been reported following the preferred reporting items for systematic reviews and meta-analyses protocol. We will search 7 electronic databases to identify relevant studies from inception to November, 2022, which includes PubMed, MEDLINE, Embase, Cochrane Clinical Trials Database, Web of Science, China National Knowledge Infrastructure, and Chinese Biomedical Literature Database. Risk of bias will be assessed according to the Cochrane Risk of Bias Tool. The Grading of Recommendations Assessment, Development and Evaluation system will be used to judge the overall quality of evidence supporting outcomes in this work. Data analysis was performed using Reviewer Manager 5.4. Results: The results of this systematic review will be published in a peer-reviewed journal. Conclusion: This systematic review will provide evidence to judge whether Janus kinase inhibitors is superior to leflunomide in patients with in rheumatoid arthritis.
Efficacy and safety of Xinmai’an tablet in treatment of premature ventricular contractions due to coronary heart disease: A protocol for systematic review and meta-analysis

Background: Coronary heart disease (CHD) is the leading cause of human death in the world and a public health problem of global concern. As a common arrhythmia in CHD, premature ventricular contractions are very likely to progress to fatal arrhythmias, resulting in serious adverse consequences. At present, the treatment of premature ventricular contractions due to CHD mainly focuses on catheter ablation, beta-blockers and antiarrhythmics. Both require ongoing monitoring because relapses may lead to redevelopment of cardiomyopathy, and there are varying degrees of indications and side effects. Several clinical studies have shown that Xinmai’an can effectively control the occurrence of premature ventricular contractions and reduce the risk of recurrence. However, there is currently no systematic review evaluating its effectiveness. Therefore, the purpose of this study is to provide strong evidence-based medical evidence for Xinmai’an tablet in the treatment of premature ventricular contractions due to CHD. Methods: We will search the main Chinese and English databases from inception to June 5, 2022. And identified as the randomized controlled trials. In addition, a reference list of studies meeting the inclusion criteria will be retrieved. Two researchers will conduct literature screening and quality evaluation. And we will conduct bias risk assessment and sensitivity analysis. The analysis software uses RevMan 5.3. Results: Mainly by observing the number of ventricular premature beat attacks (24-hour holter monitoring electrocardiogram), electrocardiogram efficacy (ST segment and T wave changes) and echocardiogram assesses the structure and function of the left and right ventricular, left ventricular ejection fraction, etc. To evaluate the clinical effect of Xinmai’an on premature ventricular contractions due to CHD. Conclusion: The results of this study will provide a basis for the selection of treatment options for premature ventricular contractions due to CHD.
Structural basis of histone H2A lysine 119 deubiquitination by Polycomb Repressive Deubiquitinase BAP1/ASXL1

The maintenance of gene expression patterns during metazoan development is achieved by the actions of Polycomb group (PcG) complexes. An essential modification marking silenced genes is monoubiquitination of histone H2A lysine 119 (H2AK119Ub) deposited by the E3 ubiquitin ligase activity of the non-canonical Polycomb Repressive Complex 1. The Polycomb Repressive Deubiquitinase (PR-DUB) complex cleaves monoubiquitin from histone H2A lysine 119 (H2AK119Ub) to restrict focal H2AK119Ub at Polycomb target sites and to protect active genes from aberrant silencing. BAP1 and ASXL1, subunits that form active PR-DUB, are among the most frequently mutated epigenetic factors in human cancers, underscoring their biological importance. How PR-DUB achieves specificity for H2AK119Ub to regulate Polycomb silencing is unknown, and the mechanisms of most of the mutations in BAP1 and ASXL1 found in cancer have not been established. Here we determine a cryo-EM structure of human BAP1 bound to the ASXL1 DEUBAD domain in complex with a H2AK119Ub nucleosome. Our structural, biochemical, and cellular data reveal the molecular interactions of BAP1 and ASXL1 with histones and DNA that are critical for remodeling the nucleosome and thus establishing specificity for H2AK119Ub. These results further provide a molecular explanation for how >50 mutations in BAP1 and ASXL1 found in cancer can dysregulate H2AK119Ub deubiquitination, providing new insight into understanding cancer etiology. One Sentence Summary We reveal the molecular mechanism of nucleosomal H2AK119Ub deubiquitination by human BAP1/ASXL1.