Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanism of Action of Natural Compounds in Peripheral Multiorgan Dysfunction and Hippocampal Neuroinflammation Induced by Sepsis

Bacterial sepsis induces the production of excessive pro-inflammatory cytokines and oxidative stress, resulting in tissue injury and hyperinflammation. Patients recovering from sepsis have increased rates of central nervous system (CNS) morbidities, which are linked to long-term cognitive impairment, such as neurodegenerative pathologies. This paper focuses on the tissue injury and hyperinflammation observed in the acute phase of sepsis and on the development of long-term neuroinflammation associated with septicemia. Here we evaluate the effects of Coriolus versicolor administration as a novel approach to treat polymicrobial sepsis. Rats underwent cecal ligation and perforation (CLP), and Coriolus versicolor (200 mg/kg in saline) was administered daily by gavage. Survival was monitored, and tissues from vital organs that easily succumb to infection were harvested after 72 h to evaluate the histological changes. Twenty-eight days after CLP, behavioral analyses were performed, and serum and brain (hippocampus) samples were harvested at four weeks from surgery. Coriolus versicolor increased survival and reduced acute tissue injury. Indeed, it reduced the release of pro-inflammatory cytokines in the bloodstream, leading to a reduced chronic inflammation. In the hippocampus, Coriolus versicolor administration restored tight junction expressions, reduce cytokines accumulation and glia activation. It also reduced toll-like receptor 4 (TLR4) and neuronal nitric oxide synthase (nNOS) and the NLR family pyrin domain containing 3 (NLRP3) inflammasome components expression. Coriolus versicolor showed antioxidant activities, restoring glutathione (GSH) levels and catalase and superoxide dismutase (SOD) activities and reducing lipid peroxidation, nitrite and reactive oxygen species (ROS) levels. Importantly, Coriolus versicolor reduced amyloid precursor protein (APP), phosphorylated-Tau (p-Tau), pathologically phosphorylated tau (PHF1), phosphorylated tau (Ser202 and Thr205) (AT8), interferon-induced transmembrane protein 3 (IFITM3) expression, and β-amyloid accumulation induced by CLP. Indeed, Coriolus versicolor restored synaptic dysfunction and behavioral alterations. This research shows the effects of Coriolus versicolor administration on the long-term development of neuroinflammation and brain dysfunction induced by sepsis. Overall, our results demonstrated that Coriolus versicolor administration was able to counteract the degenerative process triggered by sepsis.
Hybrid Graph Convolutional Network With Online Masked Autoencoder for Robust Multimodal Cancer Survival Prediction

Cancer survival prediction requires exploiting related multimodal information (e.g., pathological, clinical and genomic features, etc.) and it is even more challenging in clinical practices due to the incompleteness of patient’s multimodal data. Furthermore, existing methods lack sufficient intra- and inter-modal interactions, and suffer from significant performance degradation caused by missing modalities. This manuscript proposes a novel hybrid graph convolutional network, entitled HGCN, which is equipped with an online masked autoencoder paradigm for robust multimodal cancer survival prediction. Particularly, we pioneer modeling the patient’s multimodal data into flexible and interpretable multimodal graphs with modality-specific preprocessing. HGCN integrates the advantages of graph convolutional networks (GCNs) and a hypergraph convolutional network (HCN) through node message passing and a hyperedge mixing mechanism to facilitate intra-modal and inter-modal interactions between multimodal graphs. With HGCN, the potential for multimodal data to create more reliable predictions of patient’s survival risk is dramatically increased compared to prior methods. Most importantly, to compensate for missing patient modalities in clinical scenarios, we incorporated an online masked autoencoder paradigm into HGCN, which can effectively capture intrinsic dependence between modalities and seamlessly generate missing hyperedges for model inference. Extensive experiments and analysis on six cancer cohorts from TCGA show that our method significantly outperforms the state-of-the-arts in both complete and missing modal settings. Our codes are made available at https://github.com/lin-lcx/HGCN.
Non-interactive and distributive property of dielectrics in mixture

A new property of dielectrics in mixtures which is non-interactive and distributive has been defined. The Taylor expansion of this new property and subsequent use of the Pade approximation has generated the parametric expression for the new property which has been used to develop a dielectric mixture model that works better than some alternatives.
Who Gets Believed? Trust and Investor Reaction to Earnings Announcements in Sharīʿah-Compliant vs. Sharīʿah Non-Compliant Firms

Purpose ‒ Considering the proclamations of trustworthiness within the Islamic financial system and the positive relationship between stock market reaction and earnings announcement of the trustworthy firm, this paper aims to empirically test the presence of trust in Sharīʿah-compliant listed firms in Pakistan. Design/Methodology/Approach ‒ The research question has been addressed by investigating firms listed on the Pakistan Stock Exchange (PSX) from 1 July 2019 to 30 June 2020. Event study method has been used by taking Abnormal Return Variance (ARV) and Abnormal Trading Volume (ATV) as proxies to measure the investors’ reaction following earnings announcements. Findings ‒ The results suggest that stock price variations around earnings announcements are negatively related to trustworthy firms compared to less-trusted firms (i.e., Sharīʿah non-compliant firms). For ATV, it was found that traders react to annual earnings announcements for both types of firms in a similar way. Originality/Value ‒ This research is an attempt to evaluate the Islamic financial system from its trustworthiness perspective. Sufficient literature has already documented that being trustworthy is obligatory for Sharīʿah-compliant firms. This study contributes to the literature by examining whether the market/investors trust such firms or not. Research Limitations/Implications ‒ This research is based on a single-country analysis with a research span of one year. Cross-country analysis with a broader time horizon may give further clarity. Practical Implications ‒ This paper has made a valuable contribution to the literature by providing the guideline on how investors’ reactions to Sharīʿah-compliant firms differ from their reactions to Sharīʿah non-compliant firms. It also indicates how religious elements may subdue other social factors such as trust. This paper has also explored the market reaction by assessing both the liquidity and volatility of the stock market in Pakistan.
Pharmacogenetic association of the NR1H3 promoter variant with antihypertensive response among patients with hypertension: A longitudinal study

Background: The genetic factors in assessing therapeutic efficacy and predicting antihypertensive drug response are unclear. Therefore, this study aims to identify the associations between variants and antihypertensive drug response. Methods: A longitudinal study including 1837 hypertensive patients was conducted in Northern China and followed up for a median 2.24 years. The associations of 11 candidate variants with blood pressure changes in response to antihypertensive drugs and with the risk of cardiovascular events during the follow-up were examined. The dual-luciferase assay was carried out to assess the effect of genetic variants on gene transcriptional activity. Results: The variant rs11039149A>G in the promoter of nuclear receptor subfamily 1 group H member 3 (NR1H3) was associated with the change in systolic blood pressure (ΔSBP) in response to calcium channel blockers (CCBs) monotherapy. Patients carrying rs11039149AG genotype showed a significant increase of systolic blood pressure (SBP) at follow-up compared with AA carriers, and the difference of ΔSBP between AG and AA carriers was 5.94 mm Hg (95%CI: 2.09–9.78, p = 0.002). In 1,184 patients with CCBs therapy, SBP levels decreased in AA carriers, but increased in AG carriers, the difference of ΔSBP between AG and AA carriers was 8.04 mm Hg (95%CI: 3.28–12.81, p = 0.001). Further analysis in 359 patients with CCBs monotherapy, the difference of ΔSBP between AG and AA carriers was 15.25 mm Hg (95%CI: 6.48–24.02, p = 0.001). However, there was no significant difference in ΔSBP between AG and AA carriers with CCBs multitherapy. The rs11039149A>G was not associated with the cardiovascular events incidence during the follow-up. Additionally, transcriptional factor forkhead box C1 (FOXC1) bound to the NR1H3 promoter containing rs11039149A and significantly increased the transcriptional activity, while rs11039149 A to G change led to a loss-of-function and disabled FOXC1 binding. For the other 10 variants, associations with blood pressure changes or risk of cardiovascular events were not observed. Conclusion: Hypertensive patients with rs11039149AG genotype in the NR1H3 gene have a significant worse SBP control in response to CCBs monotherapy compared with AA carriers. Our findings suggest that the NR1H3 gene might act as a promising genetic factor to affect individual sensitivity to antihypertensive drugs.
Analysis of MIR27A (rs11671784) Variant Association with Systemic Lupus Erythematous

Multiple microRNAs (miRs) are associated with systemic autoimmune disease susceptibility/phenotype, including systemic lupus erythematosus (SLE). With this work, we aimed to unravel the association of the miR-27a gene (MIR27A) rs11671784G/A variant with SLE risk/severity. One-hundred sixty-three adult patients with SLE and matched controls were included. A TaqMan allelic discrimination assay was applied for MIR27A genotyping. Logistic regression models were run to test the association with SLE susceptibility/risk. Genotyping of 326 participants revealed that the heterozygote form was the most common genotype among the study cohort, accounting for 72% of the population (n = 234), while A/A and G/G represented 15% (n = 49) and 13% (n = 43), respectively. Similarly, the most prevalent genotype among cases was the A/G genotype, which was present in approximately 93.3% of cases (n = 152). In contrast, only eight and three patients had A/A and G/G genotypes, respectively. The MIR27A rs11671784 variant conferred protection against the development of SLE in several genetic models, including heterozygous (G/A vs. A/A; OR = 0.10, 95% CI = 0.05–0.23), dominant (G/A + G/G vs. AA; OR = 0.15, 95% CI = 0.07–0.34), and overdominant (G/A vs. A/A + G/G; OR = 0.07, 95% CI = 0.04–0.14) models. However, the G/G genotype was associated with increased SLE risk in the recessive model (G/G vs. A/A+ G/G; OR = 17.34, 95% CI = 5.24–57.38). Furthermore, the variant showed significant associations with musculoskeletal and mucocutaneous manifestations in the patient cohort (p = 0.035 and 0.009, respectively) and platelet and white blood cell counts (p = 0.034 and 0.049, respectively). In conclusion, the MIR27A rs11671784 variant showed a potentially significant association with SLE susceptibility/risk in the studied population. Larger-scale studies on multiethnic populations are recommended to verify the results.
Tissue vs. Fecal-Derived Bacterial Dysbiosis in Precancerous Colorectal Lesions: A Systematic Review

Simple Summary Although alterations of intestinal bacterial microbiota have been admitted as playing one of the most important roles in colorectal carcinogenesis, the links between microbiota compositional changes and premalignant colorectal polyps have still not been fully examined. Furthermore, there is a lack of knowledge in terms of defining the precise differences and the correct interpretation of tissue-derived and stool-based bacterial dysbiosis in patients with precancerous colorectal lesions. Thus, this systematic review aims, firstly, to assess whether and how the tissue-derived intestinal microbiota structure differs from the bacterial dysbiosis in fecal samples of patients with simple, advanced colorectal adenoma and carcinoma in situ, and, secondly, to propose the correct selection of each matrix in order to increase sampling accuracy and applicability in future microbiota studies and clinical practice. Abstract Alterations in gut microbiota play a pivotal role in the adenoma-carcinoma sequence. However, there is still a notable lack of the correct implementation of tissue and fecal sampling in the setting of human gut microbiota examination. This study aimed to review the literature and to consolidate the current evidence on the use of mucosa and a stool-based matrix investigating human gut microbiota changes in precancerous colorectal lesions. A systematic review of papers from 2012 until November 2022 published on the PubMed and Web of Science databases was conducted. The majority of the included studies have significantly associated gut microbial dysbiosis with premalignant polyps in the colorectum. Although methodological differences hampered the precise fecal and tissue-derived dysbiosis comparison, the analysis revealed several common characteristics in stool-based and fecal-derived gut microbiota structures in patients with colorectal polyps: simple or advanced adenomas, serrated lesions, and carcinomas in situ. The mucosal samples considered were more relevant for the evaluation of microbiota’s pathophysiological involvement in CR carcinogenesis, while non-invasive stool sampling could be beneficial for early CRC detection strategies in the future. Further studies are required to identify and validate mucosa-associated and luminal colorectal microbial patterns and their role in CRC carcinogenesis, as well as in the clinical setting of human microbiota studies.
Weighted Gene Co-Expression Network Analysis of Oxymatrine in Psoriasis Treatment

Purpose Psoriasis is a common, chronic, inflammatory, recurrent, immune-mediated skin disease. Oxymatrine is effective for treating moderate and severe psoriasis. Here, transcriptional changes in skin lesions before and after oxymatrine treatment of patients with psoriasis were identified using full-length transcriptome analysis and then compared with those of normal skin tissues. Patients and Methods Co-expression modules were constructed by combining the psoriasis area and severity index (PASI) score with weighted gene co-expression network analysis to explore the action mechanism of oxymatrine in improving clinical PASI. The expression of selected genes was verified using immunohistochemistry, quantitative real-time PCR, and Western blotting. Results Kyoto Encyclopedia of Gene and Genome pathway analysis revealed that oxymatrine treatment reversed the abnormal pathways, with an improvement in lesions and a reduction in PASI scores. Gene Ontology (GO) analysis revealed that oxymatrine treatment led to altered GO terms being regulated with a decrease in the PASI score in patients. Therefore, oxymatrine treatment may improve the skin barrier, differentiation of keratinocytes, and alleviate abnormality of organelles such as desmosomes. Protein-protein interaction network interaction analysis revealed that the top five hub genes among many interrelated genes were CNFN, S100A8, SPRR2A, SPRR2D, and SPRR2E, associated with the epidermal differentiation complex (EDC). EDC regulates keratinocyte differentiation. This result indicates that oxymatrine treatment can restore keratinocyte differentiation by regulating the expression of EDC-related genes. Conclusion Oxymatrine can improve erythema, scales, and other clinical symptoms of patients with psoriasis by regulating EDC-related genes and multiple pathways, thereby promoting the repair of epithelial tissue and maintaining the dynamic balance of skin keratosis.
Explicit Solutions for Survival Probabilities in the Classical Risk Model

The purpose of this paper is to show that, for the classical risk model, explicit expressions for survival probabilities in a finite time horizon can be obtained through the inversion of the double Laplace transform of the distribution of time to ruin. To do this, we consider Gerber and Shiu (1998) and a particular value for their penalty function. Although other methods to address the problem exist, we find this approach, perhaps, more direct and simple. For the analytic inversion, we have applied twice, after some algebra, the Laplace complex inversion formula.
A new hybrid turbulence modelling strategy for industrial CFD

This paper presents a new strategy for turbulence model employment with emphasis on the model's applicability for industrial computational fluid dynamics (CFD). In the hybrid modelling strategy proposed here, the Reynolds stress and mean rate of strain tensors are coupled via Boussinesq's formula as in the standard k–εmodel. However, the turbulent kinetic energy is calculated as the sum of the normal Reynolds‐stress components, representing the solutions of the appropriate transport equations. The equations governing the Reynolds‐stress tensor and dissipation rate have been solved in the framework of a ‘background’ second‐moment closure model. Furthermore, the structure parameter C‐µ has been re‐calculated from a newly proposed functional dependency $f(\overline{u_{i}u_{j}},\partial U_{i}/\partial x_{j})$ rather than kept constant. This new definition of C‐µ has been assessed by using direct numerical simulation (DNS) results of several generic flow configurations featuring different phenomena such as separation, reattachment and rotation. Comparisons show a large departure of C‐µ from the commonly used value of 0.09. The model proposed is computationally validated in a number of well‐proven fluid flow benchmarks, e.g. backward‐facing step, 180° turn‐around duct, rotating pipe, impinging jet and three‐dimensional (3D) Ahmed body. The obtained results confirm that the present hybrid model delivers a robust solution procedure while preserving most of the physical advantages of the Reynolds‐stress model over simple k–εmodels. A low Reynolds number version of the hybrid model is also proposed and discussed. Copyright © 2003 John Wiley & Sons, Ltd.
Population genetics of zig-zag eel (Mastacembelus armatus) uncover gene flow between an isolated island and the mainland China

Introduction Mastacembelus armatus is a commercially valuable fish, normally distributed in southern China and Southeast Asia. The natural population size of M. armatus is shrinking in recent years because of overfishing and habitat loss. In order to clarify the genetic diversity and differentiation of M. armatus populations, we collected 114 samples from eight populations in southern China and Vietnam and analyzed their population structure using nuclear ribosomal DNA sequences, the concatenated 18S and ITS2 regions. Methods Genomic DNA from the fin clip was extracted and sequenced on an Illumina novaseq 6000 (Illumina, USA) high-throughput sequencing platform in accordance with the manufacturer’s instructions. After assembly and annotation, haplotype diversity, TCS network analysis, AMOVA analysis, population pairwise genetic distances, and UPGMA tree construction were conducted based on the concatenated sequences of 18S and ITS2. Results and discussion In total, eleven nrDNA haplotypes were detected based on the concatenated sequences of 18S and ITS2. Amongst, three haplotypes were the main haplotypes, as representatives of three corresponding Clusters. There were two major Clusters in China, however, the Cluster in Vietnam was significantly divergent from the other two in China, likely due to the lack of river connection between China and Vietnam. Interestingly, based on low FST value, we found that gene flow occurred between the isolated island, Hainan Province, and the mainland China of Guangxi Province, probably as a result of exposed continental shelf connected them during glacial periods. In general, combing our data and literature data, genetic diversity and differentiation of M. armatus populations are relatively high regardless of spatial scale, although their natural population size is declining. This suggests that it is not too late to adopt measures to protect M. armatus, which benefits not only species itself but also the whole ecosystem.
MoS2-Carbon Nanodots as a New Electrochemiluminescence Platform for Breast Cancer Biomarker Detection

In this work, we present the combination of two different types of nanomaterials, 2D molybdenum disulfide nanosheets (MoS2-NS) and zero-dimensional carbon nanodots (CDs), for the development of a new electrochemiluminescence (ECL) platform for the early detection and quantification of the biomarker human epidermal growth factor receptor 2 (HER2), whose overexpression is associated with breast cancer. MoS2-NS are used as an immobilization platform for the thiolated aptamer, which can recognize the HER2 epitope peptide with high affinity, and CDs act as coreactants of the anodic oxidation of the luminophore [Ru(bpy)3]2+. The HER2 biomarker is detected by changes in the ECL signal of the [Ru(bpy)3]2+/CD system, with a low detection limit of 1.84 fg/mL and a wide linear range. The proposed method has been successfully applied to detect the HER2 biomarker in human serum samples.
Low Frequency Sound Scattering from Rough Bubbly Ocean Surface: Small Perturbation Theory Based on the Reformed Helmholtz-Kirchhoff-Fresnel Method

Through the use of perturbation theory, Kuo has previously introduced a joint surface roughness/volumetric model in order to characterize bubbly sea surface reverberation based on volumetric wave spectra, surface roughness wave spectrum, and correlation of volumetric wave spectrum and surface roughness wave spectrum. Due to the lack of undetermined volumetric scattered wave number Kv, Kuo obtained backscattering strengths using only Pierson-Moskwitz wave spectrum. In this paper, the reformed integral equation of authentic Helmholtz-Kirchhoff-Fresnel is discussed in which volumetric scattering is involved. By applying the reformed Helmholtz-Kirchhoff-Fresnel, volumetric scattered acoustic pressure field Pv is obtained. Using Helmholtz wave equation and the obtained pressure field Pv, the wave number vector of volumetric scattered field Kv is calculated, and this used to compute the volumetric wave spectrum and the joint surface roughness/volumetric wave spectrum. The obtained spectra are then used to compute scattering strengths. Comparison of the obtained results against the results of experimental Critical Sea Tests shows good agreement. Finally, a parametric study is conducted to examine the effects of wind speeds, grazing angles, and frequencies on the scattering strengths.