Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional near-infrared spectroscopy of medical students answering various item types

Background Traditionally, the effect of assessment item types including true/false questions (TFQs), multiple-choice questions (MCQs), short answer questions (SAQs), and case scenario questions (CSQs) is examined through psychometric qualities or student interviews. However, brain activity while answering such questions or items remains unknown. Functional near-infrared spectroscopy (fNIRS) can be used to safely measure cerebral cortex hemodynamic response during various tasks. Hence, this fNIRS study aimed to determine differences in frontotemporal cortex activity as medical students answered TFQs, MCQs, SAQs, and CSQs. Methods In total, 24 medical students (13 males and 11 females) were recruited in this study during their mid-psychiatry posting. Oxy-hemoglobin and deoxy-hemoglobin levels in the frontal and temporal regions were measured with a 52-channel fNIRS system. Participants answered 9–18 trials under each of the four types of tasks that were based on their psychiatry curriculum during fNIRS measurements. The area under the oxy-hemoglobin curve (AUC) for each participant and each item type was derived. Repeated measures ANOVA with post-hoc Bonferroni-corrected pairwise comparisons were used to determine differences in oxy-hemoglobin AUC between TFQs, MCQs, SAQs, and CSQs. Results Oxy-hemoglobin AUC was highest during the CSQs, followed by SAQs, MCQs, and TFQs in both the frontal and temporal regions. Statistically significant differences between different types of items were observed in oxy-hemoglobin AUC of the frontal region (p ≤ 0.001). Oxy-hemoglobin AUC in the frontal region was significantly higher during the CSQs than TFQ (p = 0.005) and during the SAQ than TFQ (p = 0.025). Although the percentage of correct responses was significantly lower in MCQ than in the other item types, there was no correlation between the percentage of correct response and oxy-hemoglobin AUC in both regions for all four item types (p > 0.05). Conclusion CSQs and SAQs elicited greater hemodynamic response than MCQs and TFQs in the prefrontal cortex of medical students. This suggests that more cognitive skills may be required to answer CSQs and SAQs.
Habitual physical activity improves outcomes among patients with myocardial infarction

Purpose This study evaluates the association between habitual physical activity (HPA) and the outcomes of patients with myocardial infarction (MI). Methods Patients newly diagnosed with MI were divided into two groups based on whether they engaged in HPA, defined as an aerobic activity with a duration of no less than 150 min/week, before the index admission. The primary outcomes included major adverse cardiovascular events (MACEs), cardiovascular (CV) mortality, and cardiac readmission rate 1 year following the index date of admission. A binary logistic regression model was applied to analyze whether HPA was independently associated with 1-year MACEs, 1-year CV mortality, and 1-year cardiac readmission rate. Results Among the 1,266 patients (mean age 63.4 years, 72% male), 571 (45%) engaged in HPA, and 695 (55%) did not engage in HPA before MI. Patients who participated in HPA were independently associated with a lower Killip class upon admission (OR = 0.48: 95% CI, 0.32–0.71, p < 0.001) and a lower prevalence of 1-year MACEs (OR = 0.74: 95% CI, 0.56–0.98, p = 0.038) and 1-year CV mortality (OR = 0.50: 95% CI, 0.28–0.88, p = 0.017) than those who did not participate in HPA. HPA was not associated with cardiac-related readmission (OR = 0.87: 95% CI, 0.64–1.17, p = 0.35). Conclusions HPA before MI was independently associated with a lower Killip class upon admission, 1-year MACEs, and 1-year CV mortality rate.
AMSR2 all-sky radiance assimilation and its impact on the analysis and forecast of Hurricane Sandy with a limited-area data assimilation system

A method to assimilate all-sky radiances from the Advanced Microwave Scanning Radiometer 2 (AMSR2) was developed within the Weather Research and Forecasting (WRF) model's data assimilation (WRFDA) system. The four essential elements are: (1) extending the community radiative transform model's (CRTM) interface to include hydrometeor profiles; (2) using total water Qt as the moisture control variable; (3) using a warm-rain physics scheme for partitioning the Qt increment into individual increments of water vapour, cloud liquid water and rain; and (4) adopting a symmetric observation error model for all-sky radiance assimilation. Compared to a benchmark experiment with no AMSR2 data, the impact of assimilating clear-sky or all-sky AMSR2 radiances on the analysis and forecast of Hurricane Sandy (2012) was assessed through analysis/forecast cycling experiments using WRF and WRFDA's three-dimensional variational (3DVAR) data assimilation scheme. With more cloud/precipitation-affected data being assimilated around tropical cyclone (TC) core areas in the all-sky AMSR2 assimilation experiment, better analyses were obtained in terms of the TC's central sea level pressure (CSLP), warm-core structure and cloud distribution. Substantial (>20 %) error reduction in track and CSLP forecasts was achieved from both clear-sky and all-sky AMSR2 assimilation experiments, and this improvement was consistent from the analysis time to 72-h forecasts. Moreover, the all-sky assimilation experiment consistently yielded better track and CSLP forecasts than the clear-sky did for all forecast lead times, due to a better analysis in the TC core areas. Positive forecast impact from assimilating AMSR2 radiances is also seen when verified against the European Center for Medium-Range Weather Forecasts (ECMWF) analysis and the Stage IV precipitation analysis, with an overall larger positive impact from the all-sky assimilation experiment.
Constructing a cancer stem cell related prognostic model for predicting immune landscape and drug sensitivity in colorectal cancer

Background: Colorectal cancer (CRC) ranks the second malignancy with high incidence and mortality worldwide. Cancer stem cells (CSCs) function critically in cancer progression and metastasis via the interplay with immune cells in tumor microenvironment. This study aimed to identify important CSC marker genes and parsed the role of these marker genes in CRC. Materials and methods: CRC samples’ single-cell RNA sequencing data and bulk transcriptome data were utilized. Seurat R package annotated CSCs and identified CSC marker genes. Consensus clustering subtyped CRC samples based on CSC marker genes. Immune microenvironment, pathway and oxidative stress analysis was performed using ESTIMATE, MCP-counter analysis and ssGSEA analysis. A prognostic model was established by Lasso and stepAIC. Sensitivity to chemotherapeutic drugs was determined by the biochemical half maximal inhibitory concentration with pRRophetic R package. Results: We identified a total of 29 CSC marker genes related to disease-specific survival (DSS). Two clusters (CSC1 and CSC2) were determined, and CSC2 showed shorter DSS, a larger proportion of late-stage samples, and higher oxidative stress response. Two clusters exhibited differential activation of biological pathways associated with immune response and oncogenic signaling. Drug sensitivity analysis showed that 44 chemotherapy drugs were more sensitive to CSC2 that those in CSC1. We constructed a seven-gene prognostic model (DRD4, DPP7, UCN, INHBA, SFTA2, SYNPO2, and NXPH4) that was effectively to distinguish high-risk and low-risk patients. 14 chemotherapy drugs were more sensitive to high-risk group and 13 chemotherapy drugs were more sensitive to low-risk group. Combination of higher oxidative stress and risk score indicated dismal prognosis. Conclusion: The CSC marker genes we identified may help to further decipher the role of CSCs in CRC development and progression. The seven-gene prognostic model could serve as an indicator for predicting the response to immunotherapy and chemotherapy as well as prognosis of CRC patients.
Connectomes: from a sparsity of networks to large-scale databases

The analysis of whole brain networks started in the 1980s when only a handful of connectomes were available. In these early days, information about the human connectome was absent and one could only dream about having information about connectivity in a single human subject. Thanks to non-invasive methods such as diffusion imaging, we now know about connectivity in many species and, for some species, in many individuals. To illustrate the rapid change in availability of connectome data, the UK Biobank is on track to record structural and functional connectivity in 100,000 human subjects. Moreover, connectome data from a range of species is now available: from Caenorhabditis elegans and the fruit fly to pigeons, rodents, cats, non-human primates, and humans. This review will give a brief overview of what structural connectivity data is now available, how connectomes are organized, and how their organization shows common features across species. Finally, I will outline some of the current challenges and potential future work in making use of connectome information.
Editorial: Composites and surface and interface engineering (CSIE): preparation and modification of biomaterials and their anti-biofouling ability and surface wettability

Institute for Advanced Study, Research Center of Composites and Surface and Interface Engineering, Chengdu University, Chengdu, China, Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia, School of Engineering, Macquarie University, Sydney, NSW, Australia, College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials and Engineering, Sichuan University, Chengdu, China, Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, Hong Kong SAR, China, College of Biomass Science and Engineering, Sichuan University, Chengdu, China, Institute of Biomedical Engineering, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
Editorial: Photosynthesis under fluctuating light

COPYRIGHT © 2023 Longoni, Grieco, Santabarbara and Harbinson. 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. TYPE Editorial PUBLISHED 09 June 2023 DOI 10.3389/fpls.2023. 1220360
Diagnostic efficacy of a combination of the Chinese thyroid imaging reporting and data system and shear wave elastography in detecting category 4a and 4b thyroid nodules

Objectives Differential diagnosis of benign and malignant thyroid imaging reporting and data system (TIRADS) category 4a and 4b nodules can be difficult using conventional ultrasonography (US). The objective of this study was to evaluate the diagnostic efficacy of a combination of the Chinese-TIRADS (C-TIRADS) and shear wave elastography (SWE) in detecting malignant nodules among category 4a and 4b thyroid nodules. Methods Among 409 thyroid nodules in 332 patients that we included in this study, 106 thyroid nodules were diagnosed as category 4a and 4b using C-TIRADS. We used SWE to measure the maximum Young’s modulus (Emax) values of category 4a and 4b thyroid nodules. We calculated the diagnostic efficacy of only the C-TIRADS, only SWE, and a combination of C-TIRADS with SWE, and compared these, while taking the pathology results as the gold standard. Results The area under the ROC curve (AUC), sensitivity, and accuracy values of the combination of C-TIRADS and SWE (0.870, 83.3%, and 84.0%, respectively) were all higher when compared with the values of only the C-TIRADS (0.785, 68.5%, and 78.3%, respectively) or only SWE (0.775, 68.5%, and 77.4%, respectively) in the diagnosis of category 4a and 4b thyroid nodules. Conclusion In this study, we found that the combination of C-TIRADS and SWE significantly improved the diagnostic efficacy in detecting malignant nodules among category 4a and 4b thyroid nodules, and this could provide a reference for further use of this combination by clinicians for diagnosis and treatment.
Risk factors for colonization with multidrug-resistant Gram-negative bacteria and Clostridioides difficile in Long Term Care Facilities (LTCFs) residents: the evidence from 27 facilities in a high endemic setting

Introduction Residency in LTCFs increases the likelihood of colonization with multidrug resistant Gram-negative bacteria (MDR-GNB). We assessed the prevalence and risk factors for enteric colonization by III-generation cephalosporins-resistant and carbapenem-resistant (CR) GNB in a large group of LTCFs in a high endemic setting. We also assessed the prevalence and risk factors for C. difficile colonization. Methods A point prevalence survey with rectal screening (RS) was conducted in 27 LTCFs in north Italy. Epidemiological and clinical variables on the survey day, history of hospitalization and surgery within one year, and antibiotics within three months, were collected. The presence of III-generation cephalosporin resistant and CR GNB was assessed using a selective culture on chromogenic medium and PCR for carbapenemase detection. The presence of C. difficile was assessed using ELISA for GDH and RT-PCR to identify toxigenic strains. Multi-variable analyses were performed using two-level logistic regression models. Results In the study period 1947 RSs were performed. The prevalence of colonization by at least one GNB resistant to III-generation cephalosporin was 51% (E. coli 65%, K. pneumoniae 14% of isolates). The prevalence of colonization by CR GNB was 6%. 6% of all isolates (1150 strains) resulted in a carbapenem-resistant K. pneumoniae, and 3% in a carbapenem-resistant E. coli. KPC was the most frequent carbapenemase (73%) identified by PCR, followed by VIM (23%). The prevalence of colonization by C. difficile was 11.7%. The presence of a medical device (OR 2.67) and previous antibiotic use (OR 1.48) were significantly associated with III-generation cephalosporin resistant GNB colonization. The presence of a medical device (OR 2.67) and previous hospitalization (OR 1.80) were significantly associated with CR GNB. The presence of a medical device (OR 2.30) was significantly associated with C. difficile colonization. Main previously used antibiotic classes were fluoroquinolones (32% of previously treated subjects), III-generation cephalosporins (21%), and penicillins (19%). Conclusion Antimicrobial stewardship in LTCFs is a critical issue, being previous antibiotic treatment a risk factor for colonization by MDR-GNB. The prevalence of colonization by III-generation cephalosporin and CR GNB among LTCF residents also underlines the importance to adhere to hand hygiene indications, infection prevention and control measures, and environmental hygiene protocols, more achievable than rigorous contact precautions in this type of social setting.
The diversity and abundance of bacterial and fungal communities in the rhizosphere of Cathaya argyrophylla are affected by soil physicochemical properties

Cathaya argyrophylla is an ancient Pinaceae species endemic to China that is listed on the IUCN Red List. Although C. argyrophylla is an ectomycorrhizal plant, the relationship between its rhizospheric soil microbial community and soil properties related to the natural habitat remains unknown. High-throughput sequencing of bacterial 16S rRNA genes and fungal ITS region sequences was used to survey the C. argyrophylla soil community at four natural spatially distributed points in Hunan Province, China, and functional profiles were predicted using PICRUSt2 and FUNGuild. The dominant bacterial phyla included Proteobacteria, Acidobacteria, Actinobacteria, and Chloroflexi, and the dominant genus was Acidothermus. The dominant fungal phyla were Basidiomycota and Ascomycota, while Russula was the dominant genus. Soil properties were the main factors leading to changes in rhizosphere soil bacterial and fungal communities, with nitrogen being the main driver of changes in soil microbial communities. The metabolic capacities of the microbial communities were predicted to identify differences in their functional profiles, including amino acid transport and metabolism, energy production and conversion, and the presence of fungi, including saprotrophs and symbiotrophs. These findings illuminate the soil microbial ecology of C. argyrophylla, and provide a scientific basis for screening rhizosphere microorganisms that are suitable for vegetation restoration and reconstruction for this important threatened species.
Exploring the prospect of intrinsic wave propagation in evaluating myocardial stiffness among patients with type 2 diabetes

Background Diabetes predisposes affected individuals to impaired myocardial perfusion and ischemia, leading to cardiac dysfunction. Increased myocardial stiffness is an independent and significant risk factor in diastolic dysfunction. This study sought to estimate myocardial stiffness in Type 2 diabetes (T2DM) patients using the intrinsic wave velocity propagation (IVP) along the longitudinal wall motion during late diastole and evaluate the value of IVP in assessing cardiac function and structure. Methods 87 and 53 participants with and without T2DM (control group) were enrolled. Of the 87 T2DM patients (DM group), 43 were complicated with hypertension (DM + H group), and 44 were not (DM-H group). Ultrasound parameters were measured and analyzed, including color M-mode flow propagation velocity, global longitudinal systolic strain (GLS), and IVP. Results IVP was higher in the DM group than in the control group (1.62 ± 0.25 m/s and 1.40 ± 0.19 m/s, P < 0.001). After stratification for hypertension, IVP in both DM + H (1.71 ± 0.25 m/s) and DM-H (1.53 ± 0.20 m/s) groups were found to be significantly higher than that in the control group (1.40 ± 0.19 m/s); also, the difference of IVP between DM + H and DM-H group reached statistical significance. Moreover, IVP was significantly correlated with flow propagation velocity during early diastole (Pve) (r = −0.580, P < 0.001), flow propagation velocity during late diastole (Pva) (r = 0.271, P < 0.001), GLS (r = 0.330, P < 0.001), interventricular septal thickness at end-diastole (IVSd) (r = 0.321, P < 0.001), blood glucose (r = 0.246, P < 0.003), systolic blood pressure (r = 0.370, P < 0.001) and diastolic blood pressure (r = 0.389, P < 0.001). Conclusions The results indicated the application potential of IVP in assessing the early detection of cardiac function changes noninvasively and sensitively. The correlation with myocardial stiffness warrants further studies to substantiate its potential clinical utility.
EZH1/2 dual inhibitors suppress HTLV-1-infected cell proliferation and hyperimmune response in HTLV-1-associated myelopathy

Background Human T-cell leukemia virus type 1 (HTLV-1) causes HTLV-1-associated myelopathy (HAM), adult T-cell leukemia/lymphoma (ATL), HTLV-1-associated uveitis, and pulmonary diseases. Although both HAM and ATL show proliferation of infected cells, their pathogeneses are quite different. In particular, the pathogenesis of HAM is characterized by hyperimmune responses to HTLV-1-infected cells. Recently, we demonstrated the overexpression of histone methyltransferase EZH2 in ATL cells and the cytotoxic effects of EZH2 inhibitors and EZH1/2 dual inhibitors on these cells. However, these phenomena have never been studied in HAM. Furthermore, what effect these agents have on the hyperimmune response seen in HAM is completely unknown. Methods In this study, we investigated histone methyltransferase expression levels in infected cell populations (CD4+ and CD4+CCR4+ cells) from patients with HAM using microarray and RT-qPCR analyses. Next, using an assay system that utilizes the spontaneous proliferation characteristic of peripheral blood mononuclear cells derived from patients with HAM (HAM-PBMCs), we investigated the effects of EZH2 selective inhibitors (GSK126 and tazemetostat) and EZH1/2 dual inhibitors (OR-S1 and valemetostat, also known as DS-3201), particularly on cell proliferation rate, cytokine production, and HTLV-1 proviral load. We also examined the effect of EZH1/2 inhibitors on the proliferation of HTLV-1-infected cell lines (HCT-4 and HCT-5) derived from patients with HAM. Results We found elevated expression of EZH2 in CD4+ and CD4+CCR4+ cells from patients with HAM. EZH2 selective inhibitors and EZH1/2 inhibitors significantly inhibited spontaneous proliferation of HAM-PBMC in a concentration-dependent manner. The effect was greater with EZH1/2 inhibitors. EZH1/2 inhibitors also reduced the frequencies of Ki67+ CD4+ T cells and Ki67+ CD8+ T cells. Furthermore, they reduced HTLV-1 proviral loads and increased IL-10 levels in culture supernatants but did not alter IFN-γ and TNF-α levels. These agents also caused a concentration-dependent inhibition of the proliferation of HTLV-1-infected cell lines derived from patients with HAM and increased annexin-V(+)7-aminoactinomycin D(−) early apoptotic cells. Conclusion This study showed that EZH1/2 inhibitors suppress HTLV-1-infected cell proliferation through apoptosis and the hyperimmune response in HAM. This indicates that EZH1/2 inhibitors may be effective in treating HAM.
Transport of nitrite from large arteries modulates regional blood flow during stress and exercise

Background Acute cardiovascular stress increases systemic wall shear stress (WSS)–a frictional force exerted by the flow of blood on vessel walls–which raises plasma nitrite concentration due to enhanced endothelial nitric oxide synthase (eNOS) activity. Upstream eNOS inhibition modulates distal perfusion, and autonomic stress increases both the consumption and vasodilatory effects of endogenous nitrite. Plasma nitrite maintains vascular homeostasis during exercise and disruption of nitrite bioavailability can lead to intermittent claudication. Hypothesis During acute cardiovascular stress or strenuous exercise, we hypothesize enhanced production of nitric oxide (NO) by vascular endothelial cells raises nitrite concentrations in near-wall layers of flowing blood, resulting in cumulative NO concentrations in downstream arterioles sufficient for vasodilation. Confirmation and implications Utilizing a multiscale model of nitrite transport in bifurcating arteries, we tested the hypothesis for femoral artery flow under resting and exercised states of cardiovascular stress. Results indicate intravascular transport of nitrite from upstream endothelium could result in vasodilator-active levels of nitrite in downstream resistance vessels. The hypothesis could be confirmed utilizing artery-on-a-chip technology to measure NO production rates directly and help validate numerical model predictions. Further characterization of this mechanism may improve our understanding of symptomatic peripheral artery occlusive disease and exercise physiology.