Miracle-dz/UniFAR-FTUs huggingface dataset:
Substrate Utilization and Competitive Interactions Among Soil Bacteria Vary With Life-History Strategies

Microorganisms have evolved various life-history strategies to survive fluctuating resource conditions in soils. However, it remains elusive how the life-history strategies of microorganisms influence their processing of organic carbon, which may affect microbial interactions and carbon cycling in soils. Here, we characterized the genomic traits, exometabolite profiles, and interactions of soil bacteria representing copiotrophic and oligotrophic strategists. Isolates were selected based on differences in ribosomal RNA operon (rrn) copy number, as a proxy for life-history strategies, with pairs of “high” and “low” rrn copy number isolates represented within the Micrococcales, Corynebacteriales, and Bacillales. We found that high rrn isolates consumed a greater diversity and amount of substrates than low rrn isolates in a defined growth medium containing common soil metabolites. We estimated overlap in substrate utilization profiles to predict the potential for resource competition and found that high rrn isolates tended to have a greater potential for competitive interactions. The predicted interactions positively correlated with the measured interactions that were dominated by negative interactions as determined through sequential growth experiments. This suggests that resource competition was a major force governing interactions among isolates, while cross-feeding of metabolic secretion likely contributed to the relatively rare positive interactions observed. By connecting bacterial life-history strategies, genomic features, and metabolism, our study advances the understanding of the links between bacterial community composition and the transformation of carbon in soils.
Blood Inflammatory Cytokines as Predictors of Depression in Patients With Glioma

Background Depression commonly develops as a comorbid disorder related to glioma, which affects the patients’ physical function and prognosis. Circulating inflammatory cytokines are potential predictors of depression in disparate cancers. However, less research has specifically investigated this aspect within the context of glioma. Study objectives The objective of this study was to investigate the occurrence of depression in patients with glioma and draw a comparison of the ability to predict it through diverse inflammatory cytokines. Methods A total of 203 patients with stage I–IV glioma were enrolled in this study. Depression was evaluated according to the Hamilton Depression Scale, and the plasma inflammatory cytokines levels were simultaneously measured. We performed the receiver operating characteristic (ROC) analysis to confirm the abilities of identified inflammatory cytokines to predict depression. Results Among the 203 patients with glioma, 135 (66.5%) showed obvious depressive symptoms. Proinflammatory cytokines, including interleukin (IL)-6 (area under the curve (AUC) = 0.76) and tumor necrosis factor (TNF)-α (AUC = 0.75), showed good performance in accurately predicting depression in patients with glioma. These inflammatory cytokines indicated great potential to be depression biomarkers regardless of the patients’ disparate treatment experience. Conclusion With their relatively simple and time-saving measurement procedures, inflammatory cytokines should be seriously considered effective clinical screening and diagnostic tools, as well as potential biomarkers for depression in patients with glioma.
Development and Validation of a Clinical Prediction Model for Complicated Appendicitis in the Elderly

Background For elderly patients with mild clinical symptoms of uncomplicated appendicitis(UA), non-surgical treatment has been shown to be feasible, whereas emergency surgical treatment is recommended in elderly patients with complicated appendicitis(CA), but it is still challenging to accurately distinguish CA and UA before treatment. This study aimed to develop a predictive model to assist clinicians to quickly determine the type of acute appendicitis. Methods We retrospectively studied the clinical data of elderly patients with acute appendicitis who visited the First Affiliated Hospital of Anhui University of Traditional Chinese Medicine from January 2012 to January 2022. The patients were divided into UA group and CA group, and the general conditions, medical history, physical examination, laboratory examination and imaging examination were compared between the two groups, and SPSS 26.0 and R 4.0. 2 software were used to establish CA clinic. Predict the model, and validate it internally. Results The clinical data of 441 elderly patients with acute appendicitis were collected, 119 patients were excluded due to incomplete clinical data or other diseases. Finally, 332 patients were included in the study and divided into UA group (n = 229) and CA group (n = 103). By analyzing the clinical data of the two groups of patients, the duration of abdominal pain [OR = 1.094, 95% CI (1.056–1.134)], peritonitis [OR = 8.486, 95% CI (2.017–35.703))] and total bilirubin [OR = 1.987, 95% CI (1.627–2.426)] were independent predictors of CA (all p < 0.01). The model's Area Under Curve(AUC) = 0.985 (95% CI, 0.975–0.994). After internal verification by Bootstrap method, the model still has high discriminative ability (AUC = 0.983), and its predicted CA curve is still in good agreement with the actual clinical CA curve. Conclusion We found that a clinical prediction model based on abdominal pain duration, peritonitis, and total bilirubin can help clinicians quickly and effectively identify UA or CA before treatment of acute appendicitis in the elderly, so as to make more scientific clinical decisions.
Assessment of Milk Quality and Food Safety Challenges in the Complex Nairobi Dairy Value Chain

Food networks present varying food safety concerns because of the complexity of interactions, production, and handling practices. We investigated total bacteria counts (TBCs) and total coliform counts (TCCs) in various nodes of a Nairobi dairy value chain and identified practices that influence food safety. A value chain analysis framework facilitated qualitative data collection through 23 key informant interviews and 20 focus group discussions. Content thematic analysis identified food safety challenges. Cow milk products (N = 290) were collected from farms (N = 63), collection centers (N = 5), shops/kiosks (N = 37), milk bars (N = 17), roadside vendors (N = 14), restaurants (N = 3), milk vending machines (N = 2), mobile traders (N = 2) and a supermarket (N = 1). Mean values of colony-forming units for TBC and TCC were referenced to East African Standards (EAS). Logistic regression analysis assessed differences in milk acceptability based on EAS. The raw milk from farms and collection centers was relatively within acceptable EAS limits in terms of TBC (3.5 × 105 and 1.4 × 106 respectively) but TCC in the milk from farms was 3 times higher than EAS limits (1.5 × 105). Compared to farms, the odds ratio of milk acceptability based on TBC was lower on milk bars (0.02), restaurants (0.02), roadside vendors (0.03), shops/kiosks (0.07), and supermarkets (0.17). For TCC, the odds that milk samples from collection centers, milk bars, restaurants, roadside vendors, and shops/kiosks were acceptable was less than the odds of samples collected from farms (0.18, 0.03, 0.06, 0.02, and 0.12, respectively). Comparison of raw milk across the nodes showed that the odds of milk samples from restaurants, roadside vendors, and shops/kiosks being acceptable were less than the odds of samples collected the farm for TBC (0.03, 0.04, and 0.04, respectively). For TCC, the odds of raw milk from collection centers, restaurants, roadside vendors, milk bars, and shops/kiosks being acceptable were lower than the odds of acceptability for the farm samples (0.18, 0.12, 0.02, 0.04, and 0.05, respectively). Practices with possible influence on milk bacterial quality included muddy cowsheds, unconventional animal feed sources, re-use of spoilt raw milk, milk adulteration, acceptance of low-quality milk for processing, and lack of cold chain. Therefore, milk contamination occurs at various points, and the designing of interventions should focus on every node.
Promoter Specific Methylation of SSTR4 is Associated With Alcohol Dependence in Han Chinese Males

Alcohol dependence (AD), a disease can be affected by environmental factors with epigenetic modification like DNA methylation changes, is one of the most serious and complex public health problems in China and worldwide. Previous findings from our laboratory using the Illumina Infinium Human Methylation450 BeadChip suggested that methylation at the promoter of SSTR4 was one of the major form of DNA modification in alcohol-dependent populations. To investigate whether DNA methylation levels of the SSTR4 promoter influence alcohol-dependent behaviors, genomic DNA was extracted from the peripheral blood sample of 63 subjects with AD and 65 healthy controls, and pyrosequencing was used to verify the results of BeadChip array. Linear regression was used to analyze the correlation between the methylation levels of SSTR4 promoter and the scores of alcohol dependence scales. Gene expression of SSTR4 in brain tissue was obtained from the Genotype-Tissue Expression (GTEx) project and Human Brain Transcriptome database (HBT). We found the methylation levels of SSTR4 in AD group were significantly lower than healthy controls (two-tailed t-test, t = 14.723, p < 0.001). In addition, only weak to moderate correlations between the methylation levels of the SSTR4 promoter region and scale scores of Alcohol Use Disorders Identification Test (AUDIT), Life Events Scale (LES) and Wheatley Stress Profile (WSS) based on linear regression analyses (AUDIT: R 2 = 0.35, p < 0.001; LES: R 2 = 0.27, p < 0.001; WSS: R 2 = 0.49, p < 0.001). The hypomethylated status of SSTR4 may involve in the development of AD and increase the risk of AD persistence in Han Chinese males.
Gut Microbiota Ecology and Inferred Functions in Children With ASD Compared to Neurotypical Subjects

Autism spectrum disorders (ASDs) is a multifactorial neurodevelopmental disorder. The communication between the gastrointestinal (GI) tract and the central nervous system seems driven by gut microbiota (GM). Herein, we provide GM profiling, considering GI functional symptoms, neurological impairment, and dietary habits. Forty-one and 35 fecal samples collected from ASD and neurotypical children (CTRLs), respectively, (age range, 3–15 years) were analyzed by 16S targeted-metagenomics (the V3–V4 region) and inflammation and permeability markers (i.e., sIgA, zonulin lysozyme), and then correlated with subjects’ metadata. Our ASD cohort was characterized as follows: 30/41 (73%) with GI functional symptoms; 24/41 (58%) picky eaters (PEs), with one or more dietary needs, including 10/41 (24%) with food selectivity (FS); 36/41 (88%) presenting high and medium autism severity symptoms (HMASSs). Among the cohort with GI symptoms, 28/30 (93%) showed HMASSs, 17/30 (57%) were picky eaters and only 8/30 (27%) with food selectivity. The remaining 11/41 (27%) ASDs without GI symptoms that were characterized by HMASS for 8/11 (72%) and 7/11 (63%) were picky eaters. GM ecology was investigated for the overall ASD cohort versus CTRLs; ASDs with GI and without GI, respectively, versus CTRLs; ASD with GI versus ASD without GI; ASDs with HMASS versus low ASSs; PEs versus no-PEs; and FS versus absence of FS. In particular, the GM of ASDs, compared to CTRLs, was characterized by the increase of Proteobacteria, Bacteroidetes, Rikenellaceae, Pasteurellaceae, Klebsiella, Bacteroides, Roseburia, Lactobacillus, Prevotella, Sutterella, Staphylococcus, and Haemophilus. Moreover, Sutterella, Roseburia and Fusobacterium were associated to ASD with GI symptoms compared to CTRLs. Interestingly, ASD with GI symptoms showed higher value of zonulin and lower levels of lysozyme, which were also characterized by differentially expressed predicted functional pathways. Multiple machine learning models classified correctly 80% overall ASDs, compared with CTRLs, based on Bacteroides, Lactobacillus, Prevotella, Staphylococcus, Sutterella, and Haemophilus features. In conclusion, in our patient cohort, regardless of the evaluation of many factors potentially modulating the GM profile, the major phenotypic determinant affecting the GM was represented by GI hallmarks and patients’ age.
The Past, Present, and Future of Non-Viral CAR T Cells

Adoptive transfer of chimeric antigen receptor (CAR) T lymphocytes is a powerful technology that has revolutionized the way we conceive immunotherapy. The impressive clinical results of complete and prolonged response in refractory and relapsed diseases have shifted the landscape of treatment for hematological malignancies, particularly those of lymphoid origin, and opens up new possibilities for the treatment of solid neoplasms. However, the widening use of cell therapy is hampered by the accessibility to viral vectors that are commonly used for T cell transfection. In the era of messenger RNA (mRNA) vaccines and CRISPR/Cas (clustered regularly interspaced short palindromic repeat–CRISPR-associated) precise genome editing, novel and virus-free methods for T cell engineering are emerging as a more versatile, flexible, and sustainable alternative for next-generation CAR T cell manufacturing. Here, we discuss how the use of non-viral vectors can address some of the limitations of the viral methods of gene transfer and allow us to deliver genetic information in a stable, effective and straightforward manner. In particular, we address the main transposon systems such as Sleeping Beauty (SB) and piggyBac (PB), the utilization of mRNA, and innovative approaches of nanotechnology like Lipid-based and Polymer-based DNA nanocarriers and nanovectors. We also describe the most relevant preclinical data that have recently led to the use of non-viral gene therapy in emerging clinical trials, and the related safety and efficacy aspects. We will also provide practical considerations for future trials to enable successful and safe cell therapy with non-viral methods for CAR T cell generation.
A Bibliometric Analysis on Motivation Between 2016 and 2020 of Physical Education in Scopus Database

Purpose In the field of physical education (PE), which encompasses a wide range of variables, the question of motivation has become increasingly important. The bibliometric methods can help researchers and educators understand the related research of motivation. The purpose of this study was to explore the bibliometric characteristics of motivation in the field of PE from 2016 to 2020 that try to discover the related research context and topics. Methods By using the keywords “motivation” and “physical education,” the bibliographic records and references have been retrieved from the Scopus databases (date of search: September 7, 2021). The Vosviewer software tool and Bibliometrix R package were used for information analysis and visualization. The themes include the annual publication, countries/regions, journals, authors, co-occurrences, and theme trends. Finally, it is presented with the characteristics of the big picture of bibliometrics. Results From the analysis of the above theme, this study showed that there were 623 studies published over the 5 years, with the number gradually increasing in 2017 and peaking in 2020. The number of citations was the highest in 2016. In terms of total publications, Spain, the United States, and Australia are the top three countries/regions. Most of the articles were published in sport pedagogy and public health relevant journals. The four main research directions were identified: Education, activity, health, and self-determination theory. Conclusion This study helped us to comprehend the consistent publishing and rapid development of motivation in PE research. Via the bibliometric analysis, we can also incorporate previous research and predicted trends. All these works can help us to understand the basic psychological needs, leadership styles, and teacher support of PE teachers, and the intrinsic and extrinsic motivations of students at different ages. It is suggested that the in-depth study could be conducted on a single variable or emerging issues for future investigation. Researchers can keep tracking and reviewing motivation-related models.
Factors Contributing to English as a Foreign Language Learners’ Academic Burnout: An Investigation Through the Lens of Cultural Historical Activity Theory

During the shift from face-to-face to online emergency classes due to the COVID-19 pandemic, learners of English as a Foreign Language (EFL) were under constant pressure to familiarize themselves with the once-in-many-generations learning context. Based on the cultural-historical activity theory (CHAT), this qualitative study investigated factors contributing to EFL learners’ academic burnout at Open University, Vietnam. The interviewees were seven students, two teachers, and two administrators recruited using a theoretical-based sampling technique. The data consisted of iterative rounds of interviews which lasted approximately 60 min each until the data saturation point was reached. The content analysis revealed six factors that impacted EFL learners’ physical and psychological exhaustion, including prolonged online learning time, privacy concerns and cyber-bullying, teachers’ role, institution’s role, and support community outside the classroom. Also, teachers’ insufficient preparation for online teaching and students’ academic misconduct during exams were factors that created EFL learners’ academic cynicism. Finally, participation in social networking sites’ extracurricular activities, participation checking, and cheating in exams affected the last dimension of academic burnout, the sense of academic achievement. Based on this study, the authority, administrators, and teachers can take a more proactive role in supporting students in curbing their academic burnout during this unprecedented pandemic. The authors also hope that this study can lay the foundation for further humanistic research into the EFL learner’s psychological world in online classes, particularly when each student’s social and cultural background is considered.
Physical Process Controlling the Surface Bacterial Community Composition in the Ulleung Basin of East Sea

Although environmental drivers are known to shape the abundance and distribution of bacterial communities in the East Sea, the effects of physical processes have not been directly studied. Here, we aimed to examine the influences of water mass mixing (summer) and eddy circulation (winter) on the surface bacterial communities of the Ulleung Basin (UB), East Sea, based on the metagenomic approach. Overall, 490,087 operational taxonomic units (OTUs) were identified from five stations, and prokaryotic abundance was dominant at all stations in both seasons. Among the prokaryotes, most OTUs were affiliated with Proteobacteria, Cyanobacteria, Flavobacteria, and Actinobacteria during summer and winter. Bacterial communities were found to differ with water masses (Changjiang, Tsushima, and North Korea surface water) and eddy circulation, and were strongly correlated with environmental variables, suggesting specific bacterial community responses with specific seasonal physicochemical parameters. Our investigation indicates that together with distance and environment, advection shapes the UB bacterial community composition, helping us better understand the physical cues related to biological composition in the East Sea. However, further studies are needed to ascertain the role of microbial functional genes along with the advection of oceanographic processes in the East Sea to better understand the regional biogeochemical processes.
The Role of the NLRP3 Inflammasome in Mediating Glomerular and Tubular Injury in Diabetic Nephropathy

The NOD-like receptor protein 3 (NLRP3) inflammasome is a multi-protein signalling complex integral to the chronic inflammatory response, activated in response to sterile and non-sterile cellular damage. The assembly and activation of the NLRP3 inflammasome comprise a two-step process involving nuclear factor kappa B (NFkB)-mediated priming, followed by canonical, non-canonical or alternative signalling pathways. These result in the maturation and release of inflammatory cytokines interleukin 1 beta (IL1ß) and interleukin-18 (IL18), which are associated with chronic inflammatory conditions including diabetic kidney disease. Diabetic nephropathy is a condition affecting ∼40% of people with diabetes, the key underlying pathology of which is tubulointerstitial inflammation and fibrosis. There is growing evidence to suggest the involvement of the NLRP3 inflammasome in this chronic inflammation. Early deterioration of kidney function begins in the glomerulus, with tubular inflammation dictating the progression of late-stage disease. Priming and activation of the NLRP3 inflammasome have been linked to several clinical markers of nephropathy including proteinuria and albuminuria, in addition to morphological changes including mesangial expansion. Treatment options for diabetic nephropathy are limited, and research that examines the impact of directly targeting the NLRP3 inflammasome, or associated downstream components are beginning to gain favour, with several agents currently in clinical trials. This review will explore a role for NLRP3 inflammasome activation and signalling in mediating inflammation in diabetic nephropathy, specifically in the glomerulus and proximal tubule, before briefly describing the current position of therapeutic research in this field.
Seroprevalence of Anti-S1-RBD Antibodies in Pre-pandemic and Pandemic Subjects From Hail Region, KSA

Background Two years into the pandemic, yet the threat of new SARS-CoV-2 variants continues to loom large. Sustained efforts are required to fully understand the infection in asymptomatic individuals and those with complications. Identification, containment, care, and preventative strategies rely on understanding the varied humoral immune responses. Methods An in-house ELISA was developed and standardized to screen for serum IgG antibodies against the SARS-CoV-2 S1-RBD protein as an antigen. This study aims to investigate the seroprevalence of serum antibodies against S1-RBD antigen in pre-pandemic (n = 120) and during the early pandemic period (n = 120) in subjects from the Hail region, KSA and to correlate it with clinical and demographic factors. Results Samples collected from both male (n = 60) and female (n = 60) subjects during the pandemic in the age groups of 20–40 (0.31 ± 0.029 and 0.29 ± 0.024, respectively) and 41–60 years (0.35 ± 0.026 and 0.30 ± 0.025, respectively) showed significantly higher levels of serum antibodies against S-RBD antigen than the age-matched pre-pandemic samples [male (n = 60) and female (n = 60)]. Pandemic subjects exhibited significantly (p < 0.01) higher inhibition (80–88%) than age-matched pre-pandemic subjects (32–39%). Antibodies against S1-RBD antigen were detected in approximately 10% of the total pre-pandemic population (males and females). However, subjects > 60 years did not show antibodies. Conclusion Antibody levels increased in samples collected during the pandemic, even though these subjects were not clinically COVID-19 positive. A small number of pre-pandemic subjects showed serum antibodies, suggesting prior exposure to other coronaviruses in the region. With dwindling neutralizing antibody levels and reduced vaccine efficacy against newer variants, it remains crucial to develop better assays for surveillance, management, and future research.