Miracle-dz/UniFAR-FTUs huggingface dataset:
The Bacterial Community in Questing Ticks From Khao Yai National Park in Thailand

Ticks are known vectors for a variety of pathogens including bacteria, viruses, fungi, and parasites. In this study, bacterial communities were investigated in active life stages of three tick genera (Haemaphysalis, Dermacentor, and Amblyomma) collected from Khao Yai National Park in Thailand. Four hundred and thirty-three questing ticks were selected for pathogen detection individually using real-time PCR assays, and 58 of these were subjected to further metagenomics analysis. A total of 62 ticks were found to be infected with pathogenic bacteria, for a 14.3% prevalence rate, with Amblyomma spp. exhibiting the highest infection rate (20.5%), followed by Haemaphysalis spp. (14.5%) and Dermacentor spp. (8.6%). Rickettsia spp. were the most prevalent bacteria (7.9%) found, followed by Ehrlichia spp. (3.2%), and Anaplasma spp. and Borrelia spp. each with a similar prevalence of 1.6%. Co-infection between pathogenic bacteria was only detected in three Haemaphysalis females, and all co-infections were between Rickettsia spp. and Anaplasmataceae (Ehrlichia spp. or Anaplasma spp.), accounting for 4.6% of infected ticks or 0.7% of all examined questing ticks. The prevalence of the Coxiella-like endosymbiont was also investigated. Of ticks tested, 65.8% were positive for the Coxiella-like endosymbiont, with the highest infection rate in nymphs (86.7%), followed by females (83.4%). Among tick genera, Haemaphysalis exhibited the highest prevalence of infection with the Coxiella-like endosymbiont. Ticks harboring the Coxiella-like endosymbiont were more likely to be infected with Ehrlichia spp. or Rickettsia spp. than those without, with statistical significance for Ehrlichia spp. infection in particular (p-values = 0.003 and 0.917 for Ehrlichia spp. and Rickettsia spp., respectively). Profiling the bacterial community in ticks using metagenomics revealed distinct, predominant bacterial taxa in tick genera. Alpha and beta diversities analyses showed that the bacterial community diversity and composition in Haemaphysalis spp. was significantly different from Amblyomma spp. However, when examining bacterial diversity among tick life stages (larva, nymph, and adult) in Haemaphysalis spp. , no significant difference among life stages was detected. These results provide valuable information on the bacterial community composition and co-infection rates in questing ticks in Thailand, with implications for animal and human health.
A review of literature on employability skill needs in engineering

Encouraging skills development is a key part of the UK Government’s strategy. This emphasis on skills has led to changes in Higher Education, where there is an increasing recognition of the need to enhance students’ employability. This paper reviews the data on the type of employer skill needs available in the existing literature with a particular emphasis on those skills required by engineering and manufacturing employers. Statistical data related to skill gaps in engineering and manufacturing in the UK and London/Thames Gateway are presented with the intention to determine whether and how these relate to the employability skills and competences listed by various organisations. The paper arrives at a number of conclusions. In summary, for the ‘engineering and manufacturing workforce skills development’ ethos to become widespread in London (and the UK in general), a lot more needs to be done to understand the needs of industry to be able to develop provision that supports Londoners (and the UK citizens in general) in gaining appropriate skills in engineering. This can only be achieved through cooperative, inclusive, transparent and centrally coordinated approaches to skills assessment, monitoring and development.
Integrated Transcriptome Analysis Reveals the Impact of Photodynamic Therapy on Cerebrovascular Endothelial Cells

Blood vessels in the brain tissue form a compact vessel structure and play an essential role in maintaining the homeostasis of the neurovascular system. The low dosage of photodynamic intervention (PDT) significantly affects the expression of cellular biomarkers. To understand the impact of photodynamic interventions on cerebrovascular endothelial cells, we evaluated the dosage-dependent impact of porfimer sodium-mediated PDT on B.END3 cells using flow cytometer, comet assay, RNA sequencing, and bioinformatics analysis. To examine whether PDT can induce disorder of intracellular organelles, we did not observe any significance damage of DNA and cellular skeleton. Moreover, expression levels of cellular transporters-related genes were significantly altered, implying the drawbacks of PDT on cerebrovascular functions. To address the potential molecular mechanisms of these phenotypes, RNA sequencing and bioinformatics analysis were employed to identify critical genes and pathways among these processes. The gene ontology (GO) analysis and protein-protein interaction (PPI) identified 15 hub genes, highly associated with cellular mitosis process (CDK1, CDC20, MCM5, MCM7, MCM4, CCNA2, AURKB, KIF2C, ESPL1, BUB1B) and DNA replication (POLE2, PLOE, CDC45, CDC6). Gene set enrichment analysis (GSEA) reveals that TNF-α/NF-κB and KRAS pathways may play a critical role in regulating expression levels of transporter-related genes. To further perform qRT-PCR assays, we find that TNF-α/NF-κB and KRAS pathways were substantially up-regulated, consistent with GSEA analysis. The current findings suggested that a low dosage of PDT intervention may be detrimental to the homeostasis of blood-brain barrier (BBB) by inducing the inflammatory response and affecting the expression of surface biomarkers.
High Expression of C1ORF112 Predicts a Poor Outcome: A Potential Target for the Treatment of Low-Grade Gliomas

Background: Glioma is the most common primary tumor of the central nervous system and is associated with poor overall survival, creating an urgent need to identify survival-associated biomarkers. C1ORF112, an alpha-helical protein, is overexpressed in some cancers; however, its prognostic role has not yet been explored in gliomas. Thus, in this study, we attempted to address this by determining the prognostic value and potential function of C1ORF112 in low-grade gliomas (LGGs). Methods: The expression of C1ORF112 in normal and tumor tissues was analyzed using data from The Cancer Genome Atlas (TCGA), Chinese Glioma Genome Atlas (CGGA), Oncomine, and Rembrandt databases. The genetic changes of C1ORF112 in LGG were analyzed using cBioPortal. Survival analysis was used to evaluate the relationship between C1ORF112 expression and survival in patients with LGG. Correlation between immune infiltration and C1ORF112 expression was determined using Timer software. Additionally, data from three online platforms were integrated to identify the co-expressed genes of C1ORF112. The potential biological functions of C1ORF112 were investigated by enrichment analysis. Results: C1ORF112 mRNA was highly expressed in LGGs (p < 0.01). Area under the ROC curve (AUC) showed that the expression of C1ORF112 in LGG was 0.673 (95% confidence interval [CI] = 0.618–0.728). Kaplan-Meier survival analysis showed that patients with high C1ORF112 expression had lower OS than patients with low C1ORF112 expression (p < 0.05). Multivariate analysis showed that high expression of C1ORF112 was an independent prognostic factor for the overall survival in patients from TCGA and CGGA databases. C1ORF112 expression was positively correlated with six immunoinfiltrating cells (all p < 0.001). The enrichment analysis suggested the enrichment of C1ORF112 and co-expressed genes in cell cycle and DNA replication. Conclusion: This study suggested that C1ORF112 may be a prognostic biomarker and a potential immunotherapeutic target for LGG.
Tetrandrine Modulates Rheb-mTOR Signaling-Mediated Selective Autophagy and Protects Pulmonary Fibrosis

Idiopathic pulmonary fibrosis is a progressive fatal disease characterized by interstitial remodeling, with high lethality and a lack of effective medical therapies. Tetrandrine has been proposed to present anti-fibrotic effects, but the efficacy and mechanisms have not been systematically evaluated. We sought to study the potential therapeutic effects and mechanisms of tetrandrine against lung fibrosis. The anti-fibrotic effects of tetrandrine were evaluated in bleomycin-induced mouse models and TGF-β1-stimulated murine lung fibroblasts. We performed Chromatin Immunoprecipitation (ChIP), Immunoprecipitation (IP), and mRFP-GFP-MAP1LC3B adenovirus construct to investigate the novel mechanisms of tetrandrine-induced autophagy. Tetrandrine decreased TGF-β1-induced expression of α-smooth muscle actin, fibronectin, vimentin, and type 1 collagen and proliferation in fibroblasts. Tetrandrine restored TGF-β1-induced impaired autophagy flux, accompanied by enhanced interaction of SQSTM1 and MAP1LC3-Ⅱ. ChIP studies revealed that tetrandrine induced autophagy via increasing binding of NRF2 and SQSTM1 promoter. Furthermore, tetrandrine inhibited TGF-β1-induced phosphorylation of mTOR by reducing activation of Rheb. In vivo tetrandrine suppressed the bleomycin-induced expression of fibrotic markers and improved pulmonary function. Our data suggest that protective effect of tetrandrine against lung fibrosis might be through promoting Rheb-mTOR and NRF2-SQSTM1 mediated autophagy. Tetrandrine may thus be potentially employed as a novel therapeutic medicine against IPF.
Gut-Evolved Candida albicans Induces Metabolic Changes in Neutrophils

Serial passaging of the human fungal pathogen Candida albicans in the gastrointestinal tract of antibiotics-treated mice selects for virulence-attenuated strains. These gut-evolved strains protect the host from infection by a wide range of pathogens via trained immunity. Here, we further investigated the molecular and cellular mechanisms underlying this innate immune memory. Both Dectin-1 (the main receptor for β-glucan; a well-described immune training molecule in the fungal cell wall) and Nod2 (a receptor described to mediate BCG-induced trained immunity), were redundant for the protection induced by gut-evolved C. albicans against a virulent C. albicans strain, suggesting that gut-evolved C. albicans strains induce trained immunity via other pathways. Cytometry by time of flight (CyTOF) analysis of mouse splenocytes revealed that immunization with gut-evolved C. albicans resulted in an expansion of neutrophils and a reduction in natural killer (NK) cells, but no significant numeric changes in monocytes, macrophages or dendritic cell populations. Systemic depletion of phagocytes or neutrophils, but not of macrophages or NK cells, reduced protection mediated by gut-evolved C. albicans. Splenocytes and bone marrow cells of mice immunized with gut-evolved C. albicans demonstrated metabolic changes. In particular, splenic neutrophils displayed significantly elevated glycolytic and respiratory activity in comparison to those from mock-immunized mice. Although further investigation is required for fully deciphering the trained immunity mechanism induced by gut-evolved C. albicans strains, this data is consistent with the existence of several mechanisms of trained immunity, triggered by different training stimuli and involving different immune molecules and cell types.
HSP90 and HSP70 Families in Lateolabrax maculatus: Genome-Wide Identification, Molecular Characterization, and Expression Profiles in Response to Various Environmental Stressors

Heat shock proteins (HSPs) are a large class of highly conserved chaperons, which play important roles in response to elevated temperature and other environmental stressors. In the present study, 5 HSP90 genes and 17 HSP70 genes were systematically characterized in spotted seabass (Lateolabrax maculatus). The evolutionary footprint of HSP genes was revealed via the analysis of phylogeny, chromosome location, and gene copy numbers. In addition, the gene structure features and the putative distribution of heat shock elements (HSEs) and hypoxia response elements (HREs) in the promoter regions were analyzed. The protein-protein interaction (PPI) network analyses results indicated the potential transcriptional regulation between the heat shock factor 1 (HSF1) and HSPs and a wide range of interactions among HSPs. Furthermore, quantitative (q)PCR was performed to detect the expression profiles of HSP90 and HSP70 genes in gill, liver, and muscle tissues after heat stress, meanwhile, the expression patterns in gills under alkalinity and hypoxia stresses were determined by analyzing RNA-Seq datasets. Results showed that after heat stress, most of the examined HSP genes were significantly upregulated in a tissue-specific and time-dependent manners, and hsp90aa1.1, hsp90aa1.2, hsp70.1, and hsp70.2 were the most intense responsive genes in all three tissues. In response to alkalinity stress, 11 out of 13 significantly regulated HSP genes exhibited suppressed expression patterns. Alternatively, among the 12 hypoxia-responsive-expressed HSP genes, 7 genes showed induced expressions, while hsp90aa1.2, hsp70.1, and hsp70.2 had more significant upregulated changes after hypoxic challenge. Our findings provide the essential basis for further functional studies of HSP genes in response to abiotic stresses in spotted seabass.
Conservation and Divergence of the CONSTANS-Like (COL) Genes Related to Flowering and Circadian Rhythm in Brassica napus

The CONSTANS-LIKE (COL) genes are important signaling component in the photoperiod pathway and flowering regulation pathway. However, people still know little about their role in Brassica napus. To achieve a better understanding of the members of the BnaCOL gene family, reveal their evolutionary relationship and related functions involved in photoperiod regulation, we systematically analyzed the BnaCOL family members in B. napus genome. A total of 33 BnaCOL genes distributed unevenly on 16 chromosomes were identified in B. napus and could be classified into three subfamilies. The same subfamilies have relatively conservative gene structures, three-dimensional protein structures and promoter motifs such as light-responsive cis-elements. The collinearity analysis detected 37 pairs of repetitive genes in B. napus genome. A 67.7% of the BnaCOL genes were lost after B. napus genome polyploidization. In addition, the BnaCOL genes showed different tissue-specific expression patterns. A 81.8% of the BnaCOL genes were mainly expressed in leaves, indicating that they may play a conservative role in leaves. Subsequently, we tested the circadian expression profiles of nine homologous genes that regulate flowering in Arabidopsis. Most BnaCOL genes exhibit several types of circadian rhythms, indicating that these BnaCOL genes are involved in the photoperiod pathway. As such, our research has laid the foundation for understanding the exact role of the BnaCOL family in the growth and development of rapeseed, especially in flowering.
Linear Modeling of Neurophysiological Responses to Speech and Other Continuous Stimuli: Methodological Considerations for Applied Research

Cognitive neuroscience, in particular research on speech and language, has seen an increase in the use of linear modeling techniques for studying the processing of natural, environmental stimuli. The availability of such computational tools has prompted similar investigations in many clinical domains, facilitating the study of cognitive and sensory deficits under more naturalistic conditions. However, studying clinical (and often highly heterogeneous) cohorts introduces an added layer of complexity to such modeling procedures, potentially leading to instability of such techniques and, as a result, inconsistent findings. Here, we outline some key methodological considerations for applied research, referring to a hypothetical clinical experiment involving speech processing and worked examples of simulated electrophysiological (EEG) data. In particular, we focus on experimental design, data preprocessing, stimulus feature extraction, model design, model training and evaluation, and interpretation of model weights. Throughout the paper, we demonstrate the implementation of each step in MATLAB using the mTRF-Toolbox and discuss how to address issues that could arise in applied research. In doing so, we hope to provide better intuition on these more technical points and provide a resource for applied and clinical researchers investigating sensory and cognitive processing using ecologically rich stimuli.
Prognostic Enigma of Pancreatic Solid Pseudopapillary Neoplasm: A Single-Center Experience of 63 Patients

Background: Studies investigating prognostic factors of solid pseudopapillary neoplasm (SPN) have been published with conflicting findings. Methods: Retrospective analysis of 63 consecutive cases of SPN in our institution from January 2010 to December 2019 was carried out. The clinicopathological features, treatment practices along with survival associations were collected and analyzed. Results: Fifteen patients (23.8%) were male, and 48 (76.2%) were female, with a median age of 34.0 ± 14.5 years. The larger tumor size was correlated with the more mixed components (p = 0.000) and the higher Ki-67 index (p = 0.042). No recurrence was found in the nine patients whose tumors fulfilled the WHO criteria for malignancy due to the presence of at least perineural invasion (6.4%), angiovascular invasion (2.3%), and/or adjacent organ invasion (6.4%). Microscopic infiltrative growth was detected in 9 (14.3%) tumors, which was correlated significantly with the WHO criteria (p = 0.002), capsule invasion (p = 0.005), and pancreatic parenchyma invasion (p = 0.001), but not with disease-free survival (p = 0.13). CD99 was found to be positively expressed in 88.9% (40/45) of tumors and more likely to have depressed Ki-67 index (p = 0.016). After a median follow-up of 58 months, only two patients (3.2%) had a recurrence after their first operation outside of our hospital. No patient died due to tumor progression. Conclusions: Although survival is favorable with aggressive surgery, it is actually difficult to assess the prognostic factors of resected SPNs. Future investigations into the role of clinicopathological evaluation will unveil the prognostic enigma of pancreatic SPN after resection.
Supporting Delay-Sensitive Applications with Multipath QUIC and Forward Erasure Correction

Recent developments in the Internet infrastructure have enabled new classes of real-time applications that strictly require low end-to-end data delivery latency. While many radio technologies offer millisecond-grade transmission latency, guaranteeing sub-second application-level delays is still a challenging goal. Conventional delay-sensitive applications do not use reliable network transport protocols to avoid packet loss recovery delay, especially in loss-prone environments such as wireless networks. QUIC is a UDP-based transport protocol with many TCP-like features, designed to reduce connection and transport latency. With the additional support of multipath transmission and packet-level Forward Erasure Correction (FEC), QUIC has the potential to provide reliable connections for latency-sensitive applications. In this work, we introduce DIOD (\underlineD elay-based \underlineI n-\underlineO rder \underlineD ecode) --- a multipath scheduler designed to work alongside FEC to minimize MPQUIC's application-level latency. An FEC adaptation scheme is also proposed to support the schedulers in dynamic environments. Our solution is evaluated with a synthetic traffic generator and a live video streaming application in emulated networks with correlated and uncorrelated loss models. Our experimental results show its significant latency reduction, especially when the traffic pattern is similar to that of real-time applications.
An Integrated, Probabilistic Modeling Approach to Assess the Evolution of Barrier-Island Systems Over the Twenty-First Century

Barrier-island systems, spanning ∼7% of the world’s coastlines, are of great importance to society because not only they provide attractive, liveable space for coastal communities but also act as the first line of defense from coastal storms. As many of these unique coastal systems are affected by both oceanic and terrestrial processes, it is necessary to consider the holistic behavior of applicable terrestrial and coastal processes when investigating their evolution under plausible future scenarios for climate change, population growth and human activities. Such holistic assessments, also accounting for uncertainties, can readily be achieved via reduced-complexity modeling techniques, owing to their much faster simulation times compared to sophisticated process-based models. Here, we develop and demonstrate a novel probabilistic modeling framework to obtain stochastic projections of barrier-island evolution over the twenty-first century while accounting for relevant oceanic and terrestrial processes under climate change impacts and anthropogenic activities. The model is here demonstrated at the Chandeleur islands (Louisiana, United States) under the four Intergovernmental Panel on Climate Change (IPCC) greenhouse gas emission scenarios (i.e., Representative Concentration Pathways 2.6, 4.5, 6.0, and 8.5) with results indicating that there are significant uncertainties in projected end-century barrier-island migration distance and available barrier freeboard under the high emission scenario RCP 8.5. The range of uncertainties in these projections underscores the value of stochastic projections in supporting the development of effective adaptation strategies for these fragile coastal systems.
The Dietary Inflammatory Index Is Not Associated With Gut Permeability or Biomarkers of Systemic Inflammation in HIV Immunologic Non-responders

Immunologic non-responders (INRs) are a subset of individuals living with HIV who have suboptimal blood CD4+ T cell recovery despite effective antiretroviral therapy (ART). They are at an increased risk of serious non-AIDS co-morbidities and death, and demonstrate enhanced systemic immune activation. In other populations diet has been correlated with markers of systemic inflammation through the Diet Inflammatory Index (DII), but this association has not been studied in persons living with HIV (PLWH). Blood was collected from 28 INR PLWH with a blood CD4+ T cell count <350/μL despite ≥2 years of effective ART. Participants completed a Canadian Diet History Questionnaire, and their responses were used to calculate the DII. Plasma inflammatory markers (IFNγ, TNF, IL-6, sVCAM, D-dimer, sCD14 and CRP) were assayed by ELISA, cellular immune activation (HLA-DR and CD38 on CD4+ and CD8+ T cells) was quantified using flow cytometry, and small bowel permeability assessed by calculation of the urine LacMan ratio after drinking a mix of lactulose and mannitol. Participants were a median age of 57 years, had been on effective ART for 15 years, and the median DII was −1.91 (range of −3.78 to +2.23). No correlation was observed between DII and plasma markers of inflammation, levels of T cell activation, gut permeability, or the biomarker of bacterial translocation sCD14. Self-reported alcohol intake, a potential confounder of the relationship between diet and inflammatory biomarkers, was also not associated with systemic inflammation or gut permeability. Our findings suggest that other mechanisms, rather than diet, are likely to be the major driver of systemic inflammation in INR individuals.