Miracle-dz/UniFAR-FTUs huggingface dataset:
Long-term warming modulates diversity, vertical structuring of microbial communities, and sulfate reduction in coastal Baltic Sea sediments

Coastal waters such as those found in the Baltic Sea already suffer from anthropogenic related problems including increased algal blooming and hypoxia while ongoing and future climate change will likely worsen these effects. Microbial communities in sediments play a crucial role in the marine energy- and nutrient cycling, and how they are affected by climate change and shape the environment in the future is of great interest. The aims of this study were to investigate potential effects of prolonged warming on microbial community composition and nutrient cycling including sulfate reduction in surface (∼0.5 cm) to deeper sediments (∼ 24 cm). To investigate this, 16S rRNA gene amplicon sequencing was performed, and sulfate concentrations were measured and compared between sediments in a heated bay (which has been used as a cooling water outlet from a nearby nuclear power plant for approximately 50 years) and a nearby but unaffected control bay. The results showed variation in overall microbial diversity according to sediment depth and higher sulfate flux in the heated bay compared to the control bay. A difference in vertical community structure reflected increased relative abundances of sulfur oxidizing- and sulfate reducing bacteria along with a higher proportion of archaea, such as Bathyarchaeota, in the heated compared to the control bay. This was particularly evident closer to the sediment surface, indicating a compression of geochemical zones in the heated bay. These results corroborate findings in previous studies and additionally point to an amplified effect of prolonged warming deeper in the sediment, which could result in elevated concentrations of toxic compounds and greenhouse gases closer to the sediment surface.
Prevalence and Predictors of Combined Body Mass Index and Waist Circumference Among Indian Adults

Objective: To determine the prevalence and predictors of combined BMI-WC disease risk categories among Indian adults. Methods: The study utilizes data from Longitudinal Ageing Study in India (LASI Wave 1) with an eligible sample of 66, 859 individuals. Bivariate analysis was done to get the proportion of individuals in different BMI-WC risk categories. Multinomial logistic regression was used to identify the predictors of BMI-WC risk categories. Results: Poor self-rated health, female sex, urban place of residence, higher educational status, increasing MPCE quintile, and cardio-vascular disease increased with increasing BMI-WC disease risk level while increasing age, tobacco consumption, and engagement in physical activities was negatively associated with BMI-WC disease risk. Conclusion: Elderly persons in India have a considerable higher prevalence of BMI-WC disease risk categories which make them vulnerable to developing several disease. Findings emphasize the need of using combined BMI categories and waist circumference to assess the prevalence of obesity and associated disease risk. Finally, we recommend that intervention programs with an emphasis on urbanites wealthy women and those with a higher BMI-WC risk categories be implemented.
Spatial CT perfusion data helpful in automatically locating vessel occlusions for acute ischemic stroke patients

Introduction Locating a vessel occlusion is important for clinical decision support in stroke healthcare. The advent of endovascular thrombectomy beyond proximal large vessel occlusions spurs alternative approaches to locate vessel occlusions. We explore whether CT perfusion (CTP) data can help to automatically locate vessel occlusions. Methods We composed an atlas with the downstream regions of particular vessel segments. Occlusion of these segments should result in the hypoperfusion of the corresponding downstream region. We differentiated between seven-vessel occlusion locations (ICA, proximal M1, distal M1, M2, M3, ACA, and posterior circulation). We included 596 patients from the DUtch acute STroke (DUST) multicenter study. Each patient CTP data set was processed with perfusion software to determine the hypoperfused region. The downstream region with the highest overlap with the hypoperfused region was considered to indicate the vessel occlusion location. We assessed the indications from CTP against expert annotations from CTA. Results Our atlas-based model had a mean accuracy of 86% and could achieve substantial agreement with the annotations from CTA according to Cohen's kappa coefficient (up to 0.68). In particular, anterior large vessel occlusions and occlusions in the posterior circulation could be located with an accuracy of 80 and 92%, respectively. Conclusion The spatial layout of the hypoperfused region can help to automatically indicate the vessel occlusion location for acute ischemic stroke patients. However, variations in vessel architecture between patients seemed to limit the capacity of CTP data to distinguish between vessel occlusion locations more accurately.
Recent advances in the theoretical studies on the electrocatalytic CO2 reduction based on single and double atoms

Excess of carbon dioxide (CO2) in the atmosphere poses a significant threat to the global climate. Therefore, the electrocatalytic carbon dioxide reduction reaction (CO2RR) is important to reduce the burden on the environment and provide possibilities for developing new energy sources. However, highly active and selective catalysts are needed to effectively catalyze product synthesis with high adhesion value. Single-atom catalysts (SACs) and double-atom catalysts (DACs) have attracted much attention in the field of electrocatalysis due to their high activity, strong selectivity, and high atomic utilization. This review summarized the research progress of electrocatalytic CO2RR related to different types of SACs and DACs. The emphasis was laid on the catalytic reaction mechanism of SACs and DACs using the theoretical calculation method. Furthermore, the influences of solvation and electrode potential were studied to simulate the real electrochemical environment to bridge the gap between experiments and computations. Finally, the current challenges and future development prospects were summarized and prospected for CO2RR to lay the foundation for the theoretical research of SACs and DACs in other aspects.
Single-cell genetic models to evaluate orphan gene function: The case of QQS regulating carbon and nitrogen allocation

We demonstrate two synthetic single-cell systems that can be used to better understand how the acquisition of an orphan gene can affect complex phenotypes. The Arabidopsis orphan gene, Qua-Quine Starch (QQS) has been identified as a regulator of carbon (C) and nitrogen (N) partitioning across multiple plant species. QQS modulates this important biotechnological trait by replacing NF-YB (Nuclear Factor Y, subunit B) in its interaction with NF-YC. In this study, we expand on these prior findings by developing Chlamydomonas reinhardtii and Saccharomyces cerevisiae strains, to refactor the functional interactions between QQS and NF-Y subunits to affect modulations in C and N allocation. Expression of QQS in C. reinhardtii modulates C (i.e., starch) and N (i.e., protein) allocation by affecting interactions between NF-YC and NF-YB subunits. Studies in S. cerevisiae revealed similar functional interactions between QQS and the NF-YC homolog (HAP5), modulating C (i.e., glycogen) and N (i.e., protein) allocation. However, in S. cerevisiae both the NF-YA (HAP2) and NF-YB (HAP3) homologs appear to have redundant functions to enable QQS and HAP5 to affect C and N allocation. The genetically tractable systems that developed herein exhibit the plasticity to modulate highly complex phenotypes.
Editorial: AI for tackling STEM education challenges

COPYRIGHT © 2023 Zhai, Neumann and Krajcik. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Editorial: AI for tackling STEM education challenges
Deciphering the role of QPCTL in glioma progression and cancer immunotherapy

Background Glioma is the most lethal and most aggressive brain cancer, and currently there is no effective treatment. Cancer immunotherapy is an advanced therapy by manipulating immune cells to attack cancer cells and it has been studied a lot in glioma treatment. Targeting the immune checkpoint CD47 or blocking the CD47-SIRPα axis can effectively eliminate glioma cancer cells but also brings side effects such as anemia. Glutaminyl-peptide cyclotransferase-like protein (QPCTL) catalyzes the pyroglutamylation of CD47 and is crucial for the binding between CD47 and SIRPα. Further study found that loss of intracellular QPCTL limits chemokine function and reshapes myeloid infiltration to augment tumor immunity. However, the role of QPCTL in glioma and the relationship between its expression and clinical outcomes remains unclear. Deciphering the role of QPCTL in glioma will provide a promising therapy for glioma cancer immunotherapy. Methods QPCTL expression in glioma tissues and normal adjacent tissues was primarily analyzed in The Cancer Genome Atlas (TCGA) database, and further validated in another independent cohort from the Gene Expression Omnibus (GEO) database, Chinese Glioma Genome Atlas (CGGA), and Human Protein Atlas (HPA). The relationships between QPCTL expression and clinicopathologic parameters and overall survival (OS) were assessed using multivariate methods and Kaplan-Meier survival curves. And the proteins network with which QPCTL interacted was built using the online STRING website. Meanwhile, we use Tumor Immune Estimation Resource (TIMER) and Gene Expression Profiling Interactive Analysis (GEPIA) databases to investigate the relationships between QPCTL expression and infiltrated immune cells and their corresponding gene marker sets. We analyzed the Differentially Expressed Genes (DEGs) including GO/KEGG and Gene Set Enrichment Analysis (GSEA) based on QPCTL-high and -low expression tumors. Results In contrast to normal tissue, QPCTL expression was higher in glioma tumor tissue (p < 0.05). Higher QPCTL expression was closely associated with high-grade malignancy and advanced tumor stage. Univariate and multivariate analysis indicated the overall survival of glioma patients with higher QPCTL expression is shorter than those with lower QPCTL expression (p < 0.05). Glioma with QPCTL deficiency presented the paucity of infiltrated immune cells and their matching marker sets. Moreover, QPCTL is essential for glioma cell proliferation and tumor growth and is a positive correlation with glioma cell stemness. Conclusion High QPCTL expression predicts high grades of gliomas and poor prognosis with impaired infiltration of adaptive immune cells in the tumor microenvironment as well as higher cancer stemness. Moreover, targeting QPCTL will be a promising immunotherapy in glioma cancer treatment.
Interactions between animal temperament and exposure to endophytic tall fescue: Effects on cell-mediated and humoral immunity in beef heifers

Two experiments (n=12 Angus heifers/experiment) investigated influences of animal temperament, as indicated by exit velocity (EV; determined at weaning) and consumption of toxic endophyte-infected tall fescue seed on peripheral lymphocyte production of interferon-γ. Heifers were selected from calves born on the University of Kentucky’s C. Oran Little Research Center. In experiment 1, calves were randomly selected from 50 heifers within a single calf crop. In experiment 2, calves with the 6 fastest and 6 slowest EV in the subsequent year’s calf crop were selected. In both experiments, heifers were assigned to either high or low EV treatments based on relative ranking, and endophyte treatments (toxic endophyte-infected, E+, or endophyte-free, E-, fescue seed) were balanced by body weight. Rations were restricted to 1.8 x NEm and common diet was top-dressed with fescue seed each morning. Experiment 1 had four phases (pre-endophyte treatment/thermoneutral, increased room temperature, increased room temperature/endophyte treatment, and post-endophyte/thermoneutral) and experiment 2 had two phases (increased room temperature/endophyte treatment and thermoneutral). During endophyte treatment phases, heifers were fed their respective treatment seed. During all other phases, all heifers received E- seed. In experiment 1, proportions of lymphocytes producing interferon-γ were decreased in E+ heifers during the heat/endophyte phase (P=0.03) whereas during the subsequent thermoneutral period this response was greater in high, compared with low, EV heifers on E- treatment, with no difference observed among E+ heifers (interaction P=0.08). Also during the recovery phase, average lymphocyte production of interferon-γ was higher in E+ heifers (P=0.01). Consistent with experiment 1 findings, during the recovery period of experiment 2, endophyte exposure increased the per cell production of interferon-γ (P<0.01). In this experiment, the difference was of sufficient magnitude to result in a concomitant increase (P=0.03) in total interferon-γ production during that period. These results indicate peripheral lymphocyte production of interferon-γ can be influenced by both EV and endophyte exposure following periods of increased ambient temperature humidity indices, though there was minimal indication of interactions between temperament and alkaloid exposure. This may imply that cattle with high exit velocities and those previously exposed to toxic endophyte-infected tall fescue are better poised against cell-mediated challenges.
Global, regional, and national burden of 10 digestive diseases in 204 countries and territories from 1990 to 2019

Background Digestive diseases are very common worldwide and account for considerable health care use and expenditures. However, there are no global population-based estimates of the disease burden and temporal trend of digestive diseases. Methods Annual case numbers, age-standardized rates of prevalence, incidence, death, and disability-adjusted life-years (DALYs), and their estimated annual percentage changes (EAPCs) for digestive diseases between 1990 and 2019 were derived from the Global Burden of Disease, Injuries, and Risk Factors Study (GBD) 2019. The association between digestive disease burden and the sociodemographic index (SDI) was investigated. We also calculated DALYs attributable to risk factors that had evidence of causation with digestive diseases. Results Globally, in 2019, there were 88.99 million DALYs due to digestive diseases (3.51% of global DALYs). Digestive diseases were the 13th leading cause of DALYs globally in 2019. Global digestive disease DALYs were highest in the middle SDI quintile and in South Asia and were higher in males than females in 2019. Cirrhosis and other chronic liver diseases constituted the highest proportion of categorized digestive disease DALY burdens globally. From 1990 to 2019, the global age-standardized DALY rate of digestive diseases decreased from 1570.35 in 1990 to 1096.99 in 2019 per 1,00,000 population, with the EAPC being −1.32 (95% confidence interval [CI] −1.36 to −1.27). In 2019, the largest contributor to digestive disease DALYs at the global level, for both sexes, was alcohol use. Conclusion The results of this systematic analysis suggest that the global burden of digestive diseases is substantial and varies markedly according to age, sex, SDI, and geographical region. These results provide comprehensive and comparable estimates that can potentially inform efforts toward digestive disease control worldwide.
Impact of localized fine tuning in the performance of segmentation and classification of lung nodules from computed tomography scans using deep learning

Background Algorithm malfunction may occur when there is a performance mismatch between the dataset with which it was developed and the dataset on which it was deployed. Methods A baseline segmentation algorithm and a baseline classification algorithm were developed using public dataset of Lung Image Database Consortium to detect benign and malignant nodules, and two additional external datasets (i.e., HB and XZ) including 542 cases and 486 cases were involved for the independent validation of these two algorithms. To explore the impact of localized fine tuning on the individual segmentation and classification process, the baseline algorithms were fine tuned with CT scans of HB and XZ datasets, respectively, and the performance of the fine tuned algorithms was tested to compare with the baseline algorithms. Results The proposed baseline algorithms of both segmentation and classification experienced a drop when directly deployed in external HB and XZ datasets. Comparing with the baseline validation results in nodule segmentation, the fine tuned segmentation algorithm obtained better performance in Dice coefficient, Intersection over Union, and Average Surface Distance in HB dataset (0.593 vs. 0.444; 0.450 vs. 0.348; 0.283 vs. 0.304) and XZ dataset (0.601 vs. 0.486; 0.482 vs. 0.378; 0.225 vs. 0.358). Similarly, comparing with the baseline validation results in benign and malignant nodule classification, the fine tuned classification algorithm had improved area under the receiver operating characteristic curve value, accuracy, and F1 score in HB dataset (0.851 vs. 0.812; 0.813 vs. 0.769; 0.852 vs. 0.822) and XZ dataset (0.724 vs. 0.668; 0.696 vs. 0.617; 0.737 vs. 0.668). Conclusions The external validation performance of localized fine tuned algorithms outperformed the baseline algorithms in both segmentation process and classification process, which showed that localized fine tuning may be an effective way to enable a baseline algorithm generalize to site-specific use.
Non-coding RNAs derived from the foot-and-mouth disease virus genome trigger broad antiviral activity against coronaviruses

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of a potentially severe respiratory disease, the coronavirus disease 2019 (COVID-19), an ongoing pandemic with limited therapeutic options. Here, we assessed the anti-coronavirus activity of synthetic RNAs mimicking specific domains in the non-coding regions of the foot-and-mouth disease virus (FMDV) genome (ncRNAs). These molecules are known to exert broad-spectrum antiviral activity in cell culture, mice and pigs effectively triggering the host innate immune response. The ncRNAs showed potent antiviral activity against SARS-CoV-2 after transfection in human intestinal Caco-2 and lung epithelium Calu-3 2B4 cells. When the in vivo efficacy of the FMDV ncRNAs was assessed in K18-hACE2 mice, administration of naked ncRNA before intranasal SARS-CoV-2 infection significantly decreased the viral load and the levels of pro-inflammatory cytokines in the lungs compared with untreated infected mice. The ncRNAs were also highly efficacious when assayed against common human HCoV-229E and porcine transmissible gastroenteritis virus (TGEV) in hepatocyte-derived Huh-7 and swine testis ST cells, respectively. These results are a proof of concept of the pan-coronavirus antiviral activity of the FMDV ncRNAs including human and animal divergent coronaviruses and potentially enhance our ability to fight future emerging variants.
Impact of COVID-19 stress on the psychological health of sexual & gender minority individuals: A systematic review

Introduction The differential effect of the Covid-19 pandemic on the mental health of the population around the globe is well documented. Social isolation, loss of job, financial crisis, and fear of infection due to the pandemic have widely affected people across countries, and the sexual and gender minority (SGM) group is no exception. However, the additional stressors like stigma, discrimination, rejection, non-acceptance, and violence associated with diverse sexual orientation complicated the situation for the SGM group in the context of the Covid-19 pandemic. Method The present study conducted a systematic review of research (n = 16) investigating the impact of Covid-19 stress on the psychological health of SGM individuals. The review had two objectives: (a) to explore the effect of the stress associated with the pandemic on the psychological health of the SGM individuals; and (b) to identify potential stressors associated with the Covid-19 pandemic affecting the mental health of SGM individuals. Studies were selected following a PRISMA protocol and several inclusion criteria. Results The review provided new insights into the mental health issues of the SGM individual in the Covid-19 context. The outcome of the review focused on five aspects: (a) depression and anxiety symptoms related to Covid-19 symptoms; (b) perceived social support and Covid-19 stress; (c) family support and psychological distress related to Covid-19; (d) Covid-19 stress and disordered eating, and (e) problem drinking and substance abuse associated with Covid-19 stress. Discussion The present review indicated a negative association between Covid-19 stress and psychological distress among sexual and gender minority individuals. The findings have important implications for psychologists and social workers working with this population and policymakers around the globe.
Generating Uniformly Distributed Random Numbers without Floating Point Operations

We present a fast algorithm for random numbers distributed uniformly on (0,1). In contrast to most other generators, it uses no floating point operations. Instead, the internal bit representation of the numbers is generated directly from a random bit source. It can easily be implemented in high-level languages like Modula-2 and shows good empirical behavior.