Miracle-dz/UniFAR-FTUs huggingface dataset:
A novel immune cell signature for predicting osteosarcoma prognosis and guiding therapy

Dysregulation of immune cell infiltration in the tumor microenvironment contributes to the progression of osteosarcoma (OS). In the present study, we explored genes related to immune cell infiltration and constructed a risk model to predict the prognosis of and guide therapeutic strategies for OS. The gene expression profile of OS was obtained from TARGET and Gene Expression Omnibus, which were set as the discovery and verification cohorts. CIBERSORT and Kaplan survival analyses were used to analyze the effects of immune cells on the overall survival rates of OS in the discovery cohort. Differentially expressed gene (DEG) analysis and protein–protein interaction (PPI) networks were used to analyze genes associated with immune cell infiltration. Cox regression analysis was used to select key genes to construct a risk model that classified OS tissues into high- and low-risk groups. The prognostic value of the risk model for survival and metastasis was analyzed by Kaplan–Meier survival analyses, receiver operating characteristic curves, and immunohistochemical experiments. Immunological characteristics and response effects of immune checkpoint blockade (ICB) therapy in OS tissues were analyzed using the ESTIMATE and Tumor Immune Dysfunction and Exclusion algorithms, while sensitivity for both targeted and chemotherapy drugs was analyzed using the OncoPredict algorithm. It was demonstrated that the high infiltration of resting dendritic cells in OS tissues was associated with poor prognosis. A total of 225 DEGs were found between the high- and low-infiltration groups of OS tissues, while 94 genes interacted with others. Through COX analyses, among these 94 genes, four genes (including AOC3, CDK6, COL22A1, and RNASE6) were used to construct a risk model. This risk model showed a remarkable prognostic value for survival rates and metastasis in both the discovery and verification cohorts. Even though a high microsatellite instability score was observed in the high-risk group, the ICB response in the high-risk group was poor. Furthermore, using OncoPredict, we found that the high-risk group OS tissues were resistant to seven drugs and sensitive to 25 drugs. Therefore, our study indicates that the resting dendritic cell signature constructed by AOC3, CDK6, COL22A1, and RNASE6 may contribute to predicting osteosarcoma prognosis and thus therapy guidance.
Clinical features and surgical outcomes of young patients with lung adenocarcinoma manifesting as ground glass opacity

Background More and more ground glass opacity associated lung adenocarcinoma (GGO-LUAD) have been diagnosed in young patients nowadays. Our study aims to investigate the clinical features and surgical outcomes of young patients with GGO-LUAD. Methods Patients aged ≤ 40 years who were diagnosed as lung adenocarcinoma and who underwent video assisted thoracoscopic surgery (VATS) were retrospectively reviewed from January 2017 to December 2018. According to radiological appearance of the patient’s lesions, they were divided into a solid nodule (SN) group and GGO group. The pathological subtypes, surgical procedures and nodules size were analyzed, and the clinical features and prognosis were evaluated between these patients. Results A total of 165 patients were included, of which 133 were in the GGO group and 32 in the SN group. Both the GGO group and the SN group had a higher proportion of females and non-smokers. Compared with patients (15.63%) in the SN group, there are more patients (27.8%) under the age of 30 in the GGO group. Pathological findings showed 83.5% of lesions were pre-invasive lesions in the GGO group, although 16.5% of lesions were invasive adenocarcinoma, whereas in the SN group, 96.9% were invasive adenocarcinoma. The GGO group had significantly better histological characteristics and prognosis than the SN group. Perioperative complications occurred in only 6 patients, including pneumonia in one patient, pneumothorax in two patients, and prolonged air leak in three patients. No other serious complications or deaths occurred. After a median follow-up time of 41.2 ± 7.2 months (32-56), the 3-year recurrence free survival (RFS) (100%) and overall survival (OS) (100%) of the GGO group were significantly higher than those (93.42% and 96.88%) in the SN group. Conclusions Young patients with GGO-LUAD are mainly non-smokers and female. Most of these patients were early-stage with good prognosis after surgery.
Analysis of S gene characteristic sequences and changes in properties of protein expression in HBV ASCs with low-level HBsAg

Objective We detected the serum HBsAg immune complex (HBsAg-CIC) and sequenced the HBV S gene in these patients to reveal the association between sustained low-level expression of HBsAg and mutated S gene sequence characteristics, protein function changes, and HBsAg immune complex formation. Methods A total of 204 samples were collected and divided into high-level (n = 60, HBsAg level >10 IU/ml) and low-level (n = 144, HBsAg level ≤ 10 IU/ml) HBsAg groups. The clinical and epidemiological data of the two groups were statistically compared. According to different serological patterns and genotypes, the HBsAg-CIC results of the high-level and low-level HBsAg groups were divided into different subgroups, and then the HBsAg-CIC positive rates among different subgroups were compared. We sequenced the S gene of HBV from the two groups and identified the relevant mutations in the MHR of the S gene. In addition, we compared the changes in HBsAg protein properties and functions after hot spot mutation in the MHR of the S gene. Results Comparing the positive rates of HBsAg-CIC under different serological patterns and genotypes in the two groups, the HBsAg-CIC positive rate was higher in the low-level HBsAg group. Moreover, there was weak correlation between HBsAg-CIC and HBsAg or HBV DNA in both groups (r = 0.32, 0.27, 0.41, 0.48; P < 0.05). Sequencing of S gene in the two groups, showed that the hot-spot mutations were T126A, M133L/T/S, and F134L/T/I in MHR of S gene of genotype B, and hot-spot mutations were Q101R and I126S/T in MHR of S gene of genotype C. Additionally, the positive rate of MHR mutation in the S gene from HBsAg-CIC positive patients was higher in the low-level HBsAg group. Conclusion The host immune process of clearing HBV seems to have multiple site mutations in MHR, which changes the physicochemical properties and functions of HBsAg and intensifies the formation of HBsAg-CIC, thus avoiding the effective recognition of HBsAg by the host and resulting in immune tolerance between the host and HBV, which may be one of the formation mechanisms of sustained low-level expression of HBsAg in the serum of HBV-infected persons.
Evolution of the Earth's Ring Current during Geomagnetic Storms

ii Acknowledgments. iii List of Figures . v Introduction . 1 Geomagnetic Storms Driven by Co-rotating Interaction Regions (CIRs) . 7 The 12 July 2008 Event . 7 The 10 August 2008 Event . 13 The 4 September 2008 Event . 18 Geomagnetic Storms Driven by Interplanetary Coronal Mass Ejections (ICMEs) . 27 The 11 March 2011 Event . 27 The 28 May 2011 Event . 32 Discussion . 36 References . 40
Amelioration of dextran sulfate sodium-induced colitis by autoinducer-2-deficient Lactiplantibacillus plantarum is mediated by anti-inflammatory effects and alleviation of dysbiosis of the gut microbiota

Lactic acid bacteria (LAB) attenuate dextran sulfate sodium (DSS)-induced colitis in mice by restoring gut flora homeostasis and modulating the immune response. Because synchronous behavior can be controlled by autoinducer-2 (AI-2)/LuxS-mediated quorum sensing, the Caco-2 cell model and DSS-induced model in C57BL/6 mice were used to explore the unknown effects of these communications involving AI-2 among various intestinal symbiotic species. The results of the cell viability and lactate dehydrogenase leakage assays indicated that the tested strains (the wild-type strains and AI-2-deficient mutants) were characterized by equal cytoprotection from hydrogen peroxide-induced injury independently of AI-2. The results of the assays of multiple indicators and proinflammatory cytokines characteristic for the symptoms of colitis in mice showed that oral administration of AI-2-deficient mutants for 7 days was more effective in ameliorating inflammation than the treatment with the wild-type strains. The treatment with AI-2-deficient mutants enriched potential probiotics (e.g., Lactobacillaceae) and controlled the proliferation of potentially harmful bacteria (e.g., Helicobacteraceae) to achieve the transformation of intestinal flora. These mutants regulated short-chain fatty acids and the intestinal epithelial barrier, thereby promoting the maintenance of relatively favorable intestinal homeostasis. These results demonstrated that the AI-2-deficient mutants provided a more pronounced ameliorative effect on colitis in a mouse model, suggesting that the background of the LAB effect is associated with the alterations in colonic flora induced by AI-2.
Incidence, kinetics, and risk factors for intra- and extracranial cerebral arteriopathies in a newborn sickle cell disease cohort early assessed by transcranial and cervical color Doppler ultrasound

The risk of stroke in children with sickle cell disease (SCD) is detected by abnormal intracranial arterial time-averaged mean of maximum velocities (TAMVs ≥200 cm/s). Recently, extracranial internal carotid artery (eICA) arteriopathy has been reported, and a cross-sectional study showed that eICA-TAMVs ≥160 cm/s are significantly associated with eICA kinkings and stenosis. The cumulative incidence of and predictive risk factors for intracranial arteriopathy are well described in sickle cell anemia (SCA=SS/Sβ0) but are lacking for SC/Sβ+ children, as is the cumulative incidence of eICA arteriopathy. We report a prospective longitudinal cohort study including 493 children with SCD (398 SCA, 95 SC/Sβ+), all assessed by transcranial and cervical color Doppler ultrasound. Cerebral MRI/MRA data were available in 375 children with SCD and neck MRA in 365 children. eICA kinkings were defined as eICA tortuosities on neck MRA, with an internal acute angle between the two adjacent segments <90°. The median follow-up was 10.6 years. The cumulative incidence of kinkings was significantly lower in SC/Sβ+ children than in children with SCA, and no SC/Sβ+ child developed intra- or extracranial stenotic arteriopathy. The 10-year KM estimate of cumulative incidence (95% CI) for eICA-TAMVs ≥160 cm/s revealed its development in the 2nd year of life in children with SCA, reaching a plateau of 17.4% (13.2–21.6%) by about 10 years of age, while the plateau for eICA stenosis was 12.3% (8.3–16.3%). eICA assessment identified 13.5% (9.3–17.7%) patients at risk of stroke who were not detected by transcranial color Doppler ultrasound. We also show, for the first time, that in addition to a congenital origin, eICA kinkings sin patients with SCD can develop progressively with aging as a function of eICA-TAMVs, themselves related to anemia severity. Ongoing hydroxyurea treatment was significantly associated with a lower risk of abnormal intracranial arteriopathy and eICA kinkings. After adjustment with hydroxyurea, baseline low hemoglobin, high reticulocyte, and WBC counts remained independent risk factors for intracranial arteriopathy, while low hemoglobin and SEN β-haplotype number were independent risk factors for extracranial arteriopathy. The association between extracranial arteriopathy and SEN β-haplotype number suggested a genetic link between the ethnic origin and incidence of eICA kinkings. This prospective cohort study shows the importance of systematically assessing the eICA and of recording biological parameters during the 2nd year of life before any intensive therapy to predict the risk of cerebral arteriopathy and treat patients with severe baseline anemia.
Commentary: Pandemic exposure, post-traumatic stress disorder, conflict behaviors, and online aggressive behaviors among college students during the COVID-19 pandemic: Examining the moderating role of gender

COPYRIGHT © 2022 Feizi, Elgar, Lonergan, Eisenberg, Rahmouni and Brunet. 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. Commentary: Pandemic exposure, post-traumatic stress disorder, conflict behaviors, and online aggressive behaviors among college students during the COVID-19 pandemic: Examining the moderating role of gender
Mesenchymal stromal cells induced regulatory B cells are enriched in extracellular matrix genes and IL-10 independent modulators

Regulatory B cells (Breg) are essential players in tolerance and immune homeostasis. However, lack of specific Breg markers limit their potential in clinical settings. Mesenchymal stromal cells (MSC) modulate B cell responses and are described to induce Breg in vitro. The aim of this work was to characterize MSC induced Breg (iBreg) and identify specific Breg biomarkers by RNAseq. After 7-day coculture with adipose tissue-derived MSC, B cells were enriched in transitional B cell populations, with increased expression and secretion of IL-10 and no TNFα. In addition, iBreg showed potential to modulate T cell proliferation at 2 to 1 cell ratios and their phenotype remained stable for 72h. RNAseq analysis of sorted IL-10 positive and negative iBreg populations identified over 1500 differentially expressed genes (DEG) among both populations. Analysis of biological processes of DEG highlighted an enrichment of immune regulation and extracellular matrix genes in IL-10- iBreg populations, while IL-10+ iBreg DEG were mostly associated with cell activation. This was supported by T cells modulation assays performed in the presence of anti-IL-10 neutralizing antibodies showing the non-essential role of IL-10 in the immunomodulatory capacity of iBregs on T cells. However, based on RNAseq results we explored the role of TGF-β and found out that it plays a major role on iBreg induction and iBreg immunomodulatory properties. Therefore, we report that MSC induce B cell populations characterized by the generation of extracellular matrix and immune modulation independently of IL-10.
Development of a nomogram prediction model for depression in patients with systemic lupus erythematosus

Systemic lupus erythematosus (SLE) is an inflammatory autoimmune disease with depression as one of its most common symptoms. The aim of this study is to establish a nomogram prediction model to assess the occurrence of depression in patients with SLE. Based on the Hospital Anxiety and Depression Scale cutoff of 8, 341 patients with SLE, recruited between June 2017 and December 2019, were divided into depressive and non-depressive groups. Data on socio-demographic characteristics, medical history, sociopsychological factors, and other risk factors were collected. Between-group differences in clinical characteristics were assessed with depression as the dependent variable and the variables selected by logistic multiple regression as predictors. The model was established using R language. Marital status, education, social support, coping, and anxiety predicted depression (p < 0.05). The nomogram prediction model showed that the risk rate was from 0.01 to 0.80, and the receiver operating characteristic curve analysis showed that the area under the curve was 0.891 (p < 0.001). The calibration curve can intuitively show that the probability of depression predicted by the nomogram model is consistent with the actual comparison. The designed nomogram provides a highly predictive assessment of depression in patients with SLE, facilitating more comprehensive depression evaluation in usual clinical care.
Trichoderma – genomes and genomics as treasure troves for research towards biology, biotechnology and agriculture

The genus Trichoderma is among the best studied groups of filamentous fungi, largely because of its high relevance in applications from agriculture to enzyme biosynthesis to biofuel production. However, the physiological competences of these fungi, that led to these beneficial applications are intriguing also from a scientific and ecological point of view. This review therefore summarizes recent developments in studies of fungal genomes, updates on previously started genome annotation efforts and novel discoveries as well as efforts towards bioprospecting for enzymes and bioactive compounds such as cellulases, enzymes degrading xenobiotics and metabolites with potential pharmaceutical value. Thereby insights are provided into genomes, mitochondrial genomes and genomes of mycoviruses of Trichoderma strains relevant for enzyme production, biocontrol and mycoremediation. In several cases, production of bioactive compounds could be associated with responsible genes or clusters and bioremediation capabilities could be supported or predicted using genome information. Insights into evolution of the genus Trichoderma revealed large scale horizontal gene transfer, predominantly of CAZyme genes, but also secondary metabolite clusters. Investigation of sexual development showed that Trichoderma species are competent of repeat induced point mutation (RIP) and in some cases, segmental aneuploidy was observed. Some random mutants finally gave away their crucial mutations like T. reesei QM9978 and QM9136 and the fertility defect of QM6a was traced back to its gene defect. The Trichoderma core genome was narrowed down to 7000 genes and gene clustering was investigated in the genomes of multiple species. Finally, recent developments in application of CRISPR/Cas9 in Trichoderma, cloning and expression strategies for the workhorse T. reesei as well as the use genome mining tools for bioprospecting Trichoderma are highlighted. The intriguing new findings on evolution, genomics and physiology highlight emerging trends and illustrate worthwhile perspectives in diverse fields of research with Trichoderma.
Do Chinese children need parental supervision to manage their out-of-school visual art activities and academic work time?

Unlike in Western countries, scholars and the Chinese government pay less attention to the role of extracurricular activities (ECAs) in fostering children’s cognitive and non-cognitive well-being. Accordingly, essential ECAs such as visual arts programs are serviced by expensive privately owned schools, creating social injustice. The primary aim of the current study is to examine whether children benefit from ECAs if parental support and guidance for managing time spent on ECAs and academics exist based on the threshold model. The study comprised over 2,400 primary school students in one Chinese province and considered the SES of the area. Surprisingly, the present study’s findings illustrate that contemporary Chinese parents differ from traditionally aggressive and overbearing parents who do not value their children’s interests. However, the current study finding suggested that children’s participation in out-of-school visual art activities doesn’t have a substantial value in promoting children’s academic performance in the face of genuine interest and supportive parenting, which negates the threshold model.
Best Nursing Intervention Practices to Prevent Non-Communicable Disease: A Systematic Review

Objectives: To explore nursing health education interventions for non-communicable disease patients. Methods: The design was a systematic review of research work published between 2008 and 2018. The data sources included the Web of Science, PubMed, Scopus, COCHRANE, and LILACS. The studies that met the inclusion were assessed, and the analysis for methodological quality through the recommended tools CASPe, and JADAD. Results: Fifteen original studies from eight counties were included in the review; Findings revealed 13 studies with randomized samples and six used power analysis. Nurses’ interventions included house calls, home care, and individual and group health education. Conclusion: Nursing interventions showed 76.4% the effectiveness of results in patient outcomes to promote and improve healthier lifestyles and quality of life of non-communicable disease patients. This review discloses the significant impact of nursing health education interventions. Nursing leadership and political decision-makers should consider providing programs to enhance health education knowledge and abilities. All of this can favor the sustainability of the global economy by changing the life style of thousands of people worldwide. Systematic Review Registration: https://www.crd. york.ac. uk/prospero/, identifier CRD42020208809.
Acceptability of virtual therapy for postpartum women during COVID-19: A national mixed methods study

Background Postpartum depression (PPD) affects one in eight women in the U.S., with rates increasing due to the COVID-19 pandemic. Given the unique circumstances of COVID-19, virtual therapy might be a unique way to overcome barriers to mental health services. The study sought to explore the acceptability of virtual therapy among women in the postpartum period. Methods Using an online recruitment mixed methods approach, we collected data from a U.S. national cross-sectional sample of women (N = 479) who gave birth in the last 12 months. Findings Results show that 66% of women endorsed items consistent with possible depression during the COVID-19 pandemic. Only 27% accessed therapy services during the postpartum period. While 88% were open to engaging in virtual therapy services, 12% identified several major concerns with virtual therapy, namely: (1) preference for in-person therapy (2) no perceived need for therapy (3) uncomfortable with virtual therapy, and (4) lack of privacy. Of note, 36% more Latinas reported dissatisfaction with quality of care received during virtual therapy compared to non-Latina participants. Despite a major shift to virtual care with COVID-19, future work is needed to make virtual mental health services more accessible for women with PPD.