Miracle-dz/UniFAR-FTUs huggingface dataset:
N6-methyladenosine modulation classes and immune microenvironment regulation in ischemic stroke

N6-methyladenosine (m6A) modifications play an important role in the differentiation and regulation of immune cells. However, research on m6A in ischemic stroke (IS) is still in its infancy, and their role of the immune microenvironment remains unknown. In this study, we systematically assessed the modification classes of m6A regulators in IS based on the GEO database (GSE16561 and GSE22255). We found that in IS patients, IGF2BP2, IGF2BP1, and YTHDF2 expression was significantly upregulated, and ELAVL1, LRPPRC, METTL3, ALKBH5, CBLL1, and METTL14 expression was significantly downregulated. Seven IS-related genes (ELAVL1, IGF2BP2, LRPPRC, YTHDF2, ALKBH5, METTL14, and YTHDC1) were finally screened by logistic and least absolute shrinkage and selection operator (LASSO) regressions, and the AUC of the riskScore was 0.942, which was a good classification. For immune infiltration, there were highly significant differences in memory B cells, CD8 T cells, monocytes, activated dendritic cells, and mast cells between IS and normal samples. The IS samples were grouped into three classes by consistent clustering, and 15 m6A genes were differentially expressed in the different classes. Multiple infiltrating immune cells, immune-associated genes, and HLA-associated genes differed significantly across m6A modification classes, indicating the diversity and complexity of m6A modifications in the immune microenvironment of IS. Finally, 487 genes associated with the m6A modification class were identified, and 227 potential drugs were found. Our findings demonstrated that m6A modification plays a crucial role in the immune regulation of IS.
The role of leadership in collective creativity and innovation: Examining academic research and development environments

Introduction Leadership is pragmatically linked to innovation adoption and implementation at a team level, as managers oversee the strategic decisions and policymaking, control resources, and moderate the scanning and searching of the environment. The paper attempts to provide new concepts and examines theoretical and practical implications to better understand how the leadership role is executed in an R&D environment to foster team creativity and innovation. Methods A quantitative analysis was plausible over qualitative research mainly because the survey was conducted using a single technique, employing a questionnaire that was selected after checking the principal component analysis (PCA) and confirmatory factor analysis (CFA). Results The findings show that the production of ideas positively impacts leadership, leading to growth and competitive advantage for the organization. Also, the PMEG (people, means, effects, goals) framework will positively impact leadership as leaders focus on those factorsthat influence an individual’s attitudes, behaviors, and interactions between groups. Discussion The paper highlights the involvement of R&D organizations and groups in developing innovative products, services, technologies, and processes that further positively impact a team. This study is the first to highlight the role of the PMEG framework with the factors that influence an individual’s attitudes, behaviors, and interactions between groups. The study’s main contribution is to explore creativity as a potential mediator for leadership–organizational innovation.
Identification of Vibrio ponticus as a bacterial pathogen of coral trout Plectropomus leopardus

Vibrio ponticus is a vital pathogen with potential danger for aquaculture animals. Yet V. ponticus pathogenic to the coral trout Plectropomus leopardus is still unknown. In this study, a virulent bacterial strain, temporarily named DX2, was isolated from diseased coral trout suffering liver necrosis with cell vacuolar degeneration, and was identified molecularly and phenotypically as V. ponticus. Besides, the DX2 isolate showed an LD50 value of 6.64×105 CFU mL-1, developed multiple resistances to cephalosporins, macrolides, penicillins, peptides, and sulfonamides antimicrobials, and was highly susceptible to doxycycline and florfenicol in aquaculture use. To the best of our knowledge, this is the first report of the pathogenicity of V. ponticus to the coral trout, and the findings provide a reference for the control of pathogenic V. ponticus in the coral trout.
Fucoidan treatment alleviates chilling injury in cucumber by regulating ROS homeostasis and energy metabolism

Introduction Chilling injury is a major hindrance to cucumber fruit quality during cold storage. Methods and Results In this study, we evaluated the effects of fucoidan on fruit quality, reactive oxygen species homeostasis, and energy metabolism in cucumbers during cold storage. The results showed that, compared with the control cucumber fruit, fucoidan-treated cucumber fruit exhibited a lower chilling injury index and less weight loss, as well as reduced electrolyte leakage and malondialdehyde content. The most pronounced effects were observed following treatment with fucoidan at 15 g/L, which resulted in increased 1,1-diphenyl-2-picrylhydrazyl and hydroxyl radical scavenging rates and reduced superoxide anion production rate and hydrogen peroxide content. The expression and activity levels of peroxidase, catalase, and superoxide dismutase were enhanced by fucoidan treatment. Further, fucoidan treatment maintained high levels of ascorbic acid and glutathione, and high ratios of ascorbic acid/dehydroascorbate and glutathione/oxidized glutathione. Moreover, fucoidan treatment increased the activities of ascorbate peroxidase, monodehydroascorbate reductase, dehydroascorbate reductase, and glutathione reductase and their gene expression. Fucoidan treatment significantly delayed the decrease in ATP and ADP, while preventing an increase in AMP content. Finally, fucoidan treatment delayed the decrease of energy charge and the activities and gene expression of H+-ATPase, Ca2+-ATPase, cytochrome c oxidase, and succinate dehydrogenase in cucumber fruits. Conclusion Altogether, our findings indicate that fucoidan can effectively enhance antioxidant capacity and maintain energy metabolism, thereby improving cucumber cold resistance during cold storage.
A diagnostic accuracy study comparing RNA LAMP, direct LAMP, and rapid antigen testing from nasopharyngeal swabs

Introduction During the coronavirus disease 2019 (COVID-19) pandemic, the early detection and isolation of individuals infected with severe acute respiratory syndrome coronavirus disease 2 (SARS-CoV-2) through mass testing can effectively prevent disease transmission. SARS-CoV-2 nucleic acid rapid detection based on loop-mediated isothermal amplification (LAMP) may be appropriate to include in testing procedures. Methods We used 860 nasopharyngeal specimens from healthcare workers of Huashan Hospital and COVID-19 patients collected from April 7th to 21st, 2022, to assess the clinical diagnostic performance of the LAMP assay marketed by Shanghai GeneSc Biotech and compared it to the result of a rapid antigen test (RAT) head-to-head. Results Overall, the diagnostic performance of LAMP assay and RAT were as follows. The LAMP assay represented higher sensitivity and specificity than RAT, especially in the extracted RNA samples. The sensitivity was 70.92% and 92.91% for direct LAMP and RNA-LAMP assay, respectively, while the specificity was 99.86% and 98.33%. The LAMP assay had overall better diagnostic performance on the specimens with relatively lower Ct values or collected in the early phase (≤7 days) of COVID-19. The combination of LAMP assay and RAT improved diagnostic efficiency, providing new strategies for rapidly detecting SARS-CoV-2. Conclusion The LAMP assay are suitable for mass screenings of SARS-CoV-2 infections in the general population.
TRPC1 channels underlie stretch-modulated sarcoplasmic reticulum calcium leak in cardiomyocytes

Transient receptor potential canonical 1 (TRPC1) channels are Ca2+-permeable ion channels expressed in cardiomyocytes. An involvement of TRPC1 channels in cardiac diseases is widely established. However, the physiological role of TRPC1 channels and the mechanisms through which they contribute to disease development are still under investigation. Our prior work suggested that TRPC1 forms Ca2+ leak channels located in the sarcoplasmic reticulum (SR) membrane. Prior studies suggested that TRPC1 channels in the cell membrane are mechanosensitive, but this was not yet investigated in cardiomyocytes or for SR localized TRPC1 channels. We applied adenoviral transfection to overexpress or suppress TRPC1 expression in neonatal rat ventricular myocytes (NRVMs). Transfections were evaluated with RT-qPCR, western blot, and fluorescent imaging. Single-molecule localization microscopy revealed high colocalization of exogenously expressed TRPC1 and the sarco/endoplasmic reticulum Ca2+ ATPase (SERCA2). To test our hypothesis that TRPC1 channels contribute to mechanosensitive Ca2+ SR leak, we directly measured SR Ca2+ concentration ([Ca2+]SR) using adenoviral transfection with a novel ratiometric genetically encoded SR-targeting Ca2+ sensor. We performed fluorescence imaging to quantitatively assess [Ca2+]SR and leak through TRPC1 channels of NRVMs cultured on stretchable silicone membranes. [Ca2+]SR was increased in cells with suppressed TRPC1 expression vs. control and Transient receptor potential canonical 1-overexpressing cells. We also detected a significant reduction in [Ca2+]SR in cells with Transient receptor potential canonical 1 overexpression when 10% uniaxial stretch was applied. These findings indicate that TRPC1 channels underlie the mechanosensitive modulation of [Ca2+]SR. Our findings are critical for understanding the physiological role of TRPC1 channels and support the development of pharmacological therapies for cardiac diseases.
Differences in retinal microvasculature between large artery atherosclerosis and small artery disease: an optical coherence tomography angiography study

Purpose: Recent reports suggest retinal microvasculature mirror cerebral microcirculation. Using optical coherence tomography angiography (OCTA), we investigated the retinal microvasculature differences between ischemic stroke patients with large artery atherosclerosis (LAA) and small artery disease (SAD). Methods: All patients underwent MR imaging and were classified as SAD and LAA; LAA was subdivided into anterior LAS and posterior LAS depending on the location. Swept-source OCTA (SS-OCTA) was used to image and segment the retina into the superficial vascular complex (SVC) and deep vascular complex (DVC) in a 6 × 6 mm area around the fovea. A deep learning algorithm was used to assess the vessel area density (VAD, %) in the retinal microvasculature. Results: Fifty-eight (mean age = 60.26 ± 10.88 years; 81.03% males) were LAA while 64 (mean age = 55.58 ± 10.34 years; 85.94% males) were SAD. LAS patients had significantly reduced VAD in the DVC (P = 0.022) compared to SAD patients; the VAD in the SVC did not show any significant difference between the two groups (P = 0.580). Anterior LAA ischemic stroke showed significantly lower VAD (P = 0.002) in the SVC compared with posterior LAS patients. There was no significant difference in the DVC between the two groups (P = 0.376). Conclusions: We found LAA patients had significantly reduced DVC density compared with SAD; we also showed anterior LAA patients had significantly reduced SVC density compared with posterior LAA. These findings suggest retinal imaging has the potential to be used to detect microvasculature changes in subtypes of ischemic stroke.
Frequent somatic mosaicism in T lymphocyte subsets in individuals with and without multiple sclerosis

Background Somatic variants are variations in an individual’s genome acquired after the zygotic stadium and result from mitotic errors or not (fully) repaired DNA damage. Objectives To investigate whether somatic mosaicism in T lymphocyte subsets is enriched early in multiple sclerosis (MS). Methods We identified somatic variants with variant allele fractions ≥1% across the whole exome in CD4+ and CD8+ T lymphocytes of 21 treatment-naive MS patients with <5 years of disease duration and 16 partially age-matched healthy controls. We investigated the known somatic STAT3 variant p.Y640F in peripheral blood in a larger cohort of 446 MS patients and 259 controls. Results All subjects carried 1-142 variants in CD4+ or CD8+ T lymphocytes. Variants were more common, more abundant, and increased with age in CD8+ T lymphocytes. Somatic variants were common in the genes DNMT3A and especially STAT3. Overall, the presence or abundance of somatic variants, including the STAT3 p.Y640F variant, did not differ between MS patients and controls. Conclusions Somatic variation in T lymphocyte subsets is widespread in both control individuals and MS patients. Somatic mosaicism in T lymphocyte subsets is not enriched in early MS and thus unlikely to contribute to MS risk, but future research needs to address whether a subset of variants influences disease susceptibility.
Pectin-based bioinks for 3D models of neural tissue produced by a pH-controlled kinetics

Introduction: In the view of 3D-bioprinting with cell models representative of neural cells, we produced inks to mimic the basic viscoelastic properties of brain tissue. Moving from the concept that rheology provides useful information to predict ink printability, this study improves and expands the potential of the previously published 3D-reactive printing approach by introducing pH as a key parameter to be controlled, together with printing time. Methods: The viscoelastic properties, printability, and microstructure of pectin gels crosslinked with CaCO3 were investigated and their composition was optimized (i.e., by including cell culture medium, HEPES buffer, and collagen). Different cell models representative of the major brain cell populations (i.e., neurons, astrocytes, microglial cells, and oligodendrocytes) were considered. Results and Discussion: The outcomes of this study propose a highly controllable method to optimize the printability of internally crosslinked polysaccharides, without the need for additives or post-printing treatments. By introducing pH as a further parameter to be controlled, it is possible to have multiple (pH-dependent) crosslinking kinetics, without varying hydrogel composition. In addition, the results indicate that not only cells survive and proliferate following 3D-bioprinting, but they can also interact and reorganize hydrogel microstructure. Taken together, the results suggest that pectin-based hydrogels could be successfully applied for neural cell culture.
Health condition and mycobiome diversity in Mediterranean tree species

Introduction Mediterranean forests are currently facing a surge in abiotic stressors such as droughts and massive fires as a result of climate crisis and human pressure. Susceptibility to biotic stressors has also increased, including a variety of pests and pathogens capable of weakening and potentially killing forest flora. Biodiversity of microbiome protects forests against declines as it increases trees’ resilience and adaptability. Objectives With the objective of analyzing the relationship between health status and fungal diversity, in the present work the mycobiota of declined and healthy specimens of keystone Mediterranean tree species is described and compared. Methods To this end, bark and wood from declining Spanish forests of Castanea sativa (chestnut), Quercus ilex (holm oak), Quercus suber (cork oak), and Quercus pyrenaica (pyrenean oak) were sampled and the Internal Transcribed Spacer (ITS1) genomic region was sequenced. Results Results showed a predominance of Ascomycota, Basidiomycota, and Mucoromycota in all samples. Alpha diversity at genus level was not affected by health status and was characterized by uneven, poorly distributed fungal communities dominated by a few genera. Differentially abundant (DA) genera between healthy and declined samples were found in chestnut (15), holm oak (6), and pyrenean oak (4) trees, but not in cork oak. Some genera known for their plant protection potential, such as Trichoderma, were found exclusively in healthy trees. Functional profiles revealed a predominance of phytopathogens and saprobes in all tree species, irrespective of their health status. Discussion This study emphasizes the importance of Mediterranean forests as biodiversity refuges and highlights the value of above-ground tissues as a valid approach to assess shifts in forests’ microbiome diversity in response to biotic and abiotic stressors.
Preferred structures in large‐scale circulation and the effect of doubling greenhouse gas concentration in HadCM3

Preferred structures in the surface pressure variability are investigated in and compared between two 100‐year simulations of the Hadley Centre climate model HadCM3. In the first (control) simulation, the model is forced with pre‐industrial carbon dioxide concentration (1 × CO2) and in the second simulation the model is forced with doubled CO2 concentration (2 × CO2). Daily winter (December–January–February) surface pressures over the Northern Hemisphere are analysed. The identification of preferred patterns is addressed using multivariate mixture models. For the control simulation, two significant flow regimes are obtained at 5% and 2.5% significance levels within the state space spanned by the leading two principal components. They show a high pressure centre over the North Pacific/Aleutian Islands associated with a low pressure centre over the North Atlantic, and its reverse. For the 2 × CO2 simulation, no such behaviour is obtained. At higher‐dimensional state space, flow patterns are obtained from both simulations. They are found to be significant at the 1% level for the control simulation and at the 2.5% level for the 2 × CO2 simulation. Hence under CO2 doubling, regime behaviour in the large‐scale wave dynamics weakens. Doubling greenhouse gas concentration affects both the frequency of occurrence of regimes and also the pattern structures. The less frequent regime becomes amplified and the more frequent regime weakens. The largest change is observed over the Pacific where a significant deepening of the Aleutian low is obtained under CO2 doubling. Copyright © 2008 Royal Meteorological Society
An assessment of seasonal predictability using atmospheric general circulation models

Seasonal predictability is investigated using a 15‐year set of 4‐month range, 9‐member ensemble integrations from atmospheric general circulation models (AGCMs) involved in the European PROVOST project (PRediction Of climate Variations On Seasonal to interannual Time‐scales). The integrations were performed using prescribed ideal (observed) sea surface temperatures (SSTs), therefore skill attained (referred to as ‘potential’ skill) represents an estimated upper bound on skill achievable with current models using predicted SSTs. Most analysis is presented for The Met. Office Unified Model (UM), the European Centre for Medium‐Range Weather Forecasts (ECMWF) T63 model (T63) and an 18‐member multiple‐model ensemble (JT2) constructed from these individual models. The benefits of higher‐order multiple models (employing all four participating PROVOST AGCMs) are also investigated. Evaluation is focused on four assessment regions: the tropics; the northern extratropics; Europe; and North America. Probabilistic skill is assessed for the basic events: 3‐month mean 850 hPa temperature above/below normal; 3‐month mean precipitation accumulation above/below normal. Deterministic (ensemble mean) skill is also assessed. A summary of the main results is provided below.
4. Bayesian data analysis (2nd edn). Andrew Gelman, John B. Carlin, Hal S. Stern and Donald B. Rubin (eds), Chapman & Hall/CRC, Boca Raton, 2003. No. of pages: xxv + 668. Price: $59.95. ISBN 1‐58488‐388‐X

3401 regression structure may be the primary focus. The marginalized latent variable models allow a exible choice between modelling the marginal means or the conditional means. The marginalized transition models separate the dependence on the exposure variables from the dependence on previous response values. Orthogonality properties between the mean and the dependence parameters in a marginalized model secure robustness for the marginal means. Marginalized models further allow for simple procedures to determine a suitable dependence model for the data. Chapter 12 on time-dependent covariates is also new. The temporal order between key exposure and response events is emphasized and exogenous and endogenous covariates are formally deÿned. When covariates are endogenous, then meaningful targets for inference need to be formulated as well as valid methods of estimation. A longitudinal study on maternal stress, child illness and maternal employment illustrates concepts. The scientiÿc questions include (i) Is there an association between maternal employment and stress? (ii) Is there an association between maternal employment and child illness? (iii) Do the data provide evidence that maternal stress causes child illness? Since stress may be in the causal pathway that leads from employment to illness no adjustment is made for the daily stress indicators when evaluating the dependence of illness on employment. Similarly no adjustment is made for illness in the analysis of employment and stress. Question (iii) raises issues such as 'does illness at day t depend on prior stress measured at day (t − k)' and 'does illness on day (t − k) predict stress on day t'. A covariate which is both a predictor for the response and is predicted by earlier responses is endogenous. No standard regression methods are available to obtain causal statements when dealing with endogenous covari-ates. Targets for inference are discussed in terms of counterfactual outcomes. Causal eeects refer to interventions in the entire population rather than among possibly select, observed subgroups. Focus is on an average response after assignment of the covariate value rather than the average response in subgroups after simply observing the covariate status. The g-computation algorithm of Robins is presented as well as estimation using inverse probability of treatment weighting (IPTW). Chapter 13 discusses approaches to dealing with incomplete data in longitudinal studies, with emphasis on random and informative missing data mechanism. Likelihood inference and generalized estimating equations when data are missing at random are dealt with. Selection models and pattern mixture models are …
Analysis of the motivations and barriers to the use of Airbnb from the belgian guest perspective

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