Miracle-dz/UniFAR-FTUs huggingface dataset:
A Five-mRNA Expression Signature to Predict Survival in Oral Squamous Cell Carcinoma by Integrated Bioinformatic Analyses

Objectives: This study was designed to identify a messenger RNA (mRNA) expression signature to predict survival in patients with oral squamous cell carcinoma (OSCC). Methods: mRNA expression profiles were integrated with clinical data from 280 samples, including 19 normal tissues and 261 OSCC tissues in The Cancer Genome Atlas. We identified differentially expressed mRNAs (DEmRNAs) between the OSCC and normal tissue samples and developed a novel mRNA-focused expression signature using a Cox regression analysis and other bioinformatic methods. The prognostic value of this signature was evaluated by Kaplan–Meier analysis, multivariable COX regression, and receiver operating characteristic (ROC) curve analysis. Protein–protein interaction (PPI) network, gene ontology, and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were performed to predict the function of the DEmRNAs. Signature-related mRNAs were analyzed by gene set enrichment analyses (GSEA) and validated by quantitative real-time polymerase chain reaction (qRT-PCR) in 20 paired OSCC and adjacent healthy tissues. Results: We identified a novel 5-mRNA expression signature (HOXA1, CELSR3, HIST1H3J, ZFP42, and ASCL4) that could predict patient outcomes in OSCC. The risk score based on the signature was able to separate OSCC patients into high- and low-risk groups that showed significantly different overall survival (p < 0.001, log-rank test). The signature was further validated as an effective independent prognostic predictor of OSCC by multivariate Cox regression analysis (hazard ratio = 3.747, confidence interval: 2.279–5.677, p < 0.001) and ROC curve of the third year (area under the curve = 0.733). Functional analysis demonstrated that the key hub genes in the PPI network were mainly enriched in cell division, cell proliferation, and the p53 signaling pathway. GSEA results showed that the 5 mRNAs were significantly enriched in mismatch repair, DNA replication, and the NOTCH signaling pathway. Finally, qRT-PCR results showed that the 5 mRNAs were upregulated in OSCC tissue in agreement with the predictions from our bioinformatics analysis. Conclusions: We identified a novel 5-mRNA signature that could predict the survival of patients with OSCC and may be a promising biomarker for personalized cancer treatments.
Lignin-based flocculant and dispersant for wastewater treatment

ii Chapter 1: Introduction . 1 1.1 Overview . 1 1.2 Objectives . 5 1.3 References . 6 Chapter 2: Literature review . 9 2.
Measuring quality of life in trials including patients on dialysis: how are transplants and mortality incorporated into the analysis? A systematic review protocol

Introduction It is estimated that 25 000 people in the UK receive dialysis. Dialysis is an intrusive and time-consuming intervention that causes significant reductions in quality of life. When enrolled in a clinical trial, often some patients drop out of the study either because they die, receive a kidney transplant or are lost to follow-up for other reasons. It is unclear how these events are dealt with when analysing quality of life measures within clinical trials. This review will assess current practice for dealing with loss to follow-up in trials including patients on haemodialysis. The methods currently used will be analysed in terms of their adequacy and will form the basis of future work assessing the most appropriate methods to employ under these circumstances. The results of this review will feed into recommendations for future nephrology trials. Methods and analysis A systematic search of electronic databases including MEDLINE and the Cochrane Library will be conducted to find clinical trials enrolling patients on haemodialysis that measure quality of life using either the kidney disease quality of life (KDQoL) or the short form 36 health survey (SF-36) (or any variation of these two measures). Ongoing trials will be identified through a search of trial registers. Articles will be screened against inclusion/exclusion criteria and data will be extracted using a predetermined data extraction form. General information such as the title, location, trial design will be extracted along with more specific information on how the study dealt with patients that died or received a transplant before the end of the follow-up period. Two independent reviewers will perform screening and extraction. Disagreements will be resolved by discussion or by a third independent reviewer. Data synthesis will be performed as a narrative summary. Ethics and dissemination Ethics approval is not required. Dissemination will be by publication in a peer-reviewed journal. PROSPERO registration number CRD42020223869.
Prevalence of food insecurity and association with mental health in an indigenous population in Panamá

Abstract Objective: Understanding food insecurity and its health consequences is important for identifying strategies to best target support for individuals and communities. Given the limited information that exists for indigenous groups in Latin America, this study aimed to understand the association between food insecurity and mental health in an indigenous population in Panama. Design: Cross-sectional data were collected using a survey conducted with Kuna Indians residing off the coast of Panama. Data sources included measures from the Panamanian prevalence of risk factors associated with CVD survey, and validated measures for psychosocial factors and standardised health outcome measures. Regression models with each of the mental health outcomes (depression, serious psychological distress, perceived stress) were used to examine the association between food insecurity and mental health outcomes. Setting: Indigenous Kuna community residing on the San Blas Islands of Panama. Participants: Two-hundred nine adults. Results: Food insecurity was reported by 83 % of the participants. Across demographic categories, the only significant difference was by age with higher prevalence in younger ages. After adjusting for demographics, higher food insecurity was significantly associated with higher number of depressive symptoms and more serious psychological distress, but not with levels of perceived stress. Conclusions: Based on these findings, treatment for mental health in the Kuna community may need to account for social determinants of health and be tailored to meet the needs of younger age groups in this population. In addition, interventions designed to decrease food insecurity should be considered as a possible means for improving mental health.
Cellular Protein HuR Regulates the Switching of Genomic RNA Templates for Differential Functions during the Coxsackievirus B3 Life Cycle

A positive-strand RNA virus must balance the availability of its genomic template for different viral processes at different stages of its life cycle. A few host proteins are shown to be important to help the virus in switching the usage of a template between these processes. ABSTRACT Coxsackievirus B3 (CVB3) is an enterovirus belonging to the family Picornaviridae. Its 5′ untranslated region (UTR) contains a cloverleaf structure followed by an internal ribosome entry site (IRES). The cloverleaf forms an RNA-protein complex known to regulate virus replication, translation, and stability of the genome, and the IRES regulates virus RNA translation. For positive-strand RNA-containing viruses, such as members of the flaviviruses or enteroviruses, the genomic RNA is used for translation, replication, and encapsidation. Only a few regulatory mechanisms which govern the accessibility of genomic RNA templates for translation or replication have been reported. Here, we report the role of human antigen R (HuR) in regulating the fate of CVB3 positive-strand RNA into the replication cycle or translation cycle. We have observed that synthesis of HuR is induced during CVB3 infection, and it suppresses viral replication by displacing PCBP-2 (a positive regulator of virus replication) at the cloverleaf RNA. Silencing of HuR increases viral RNA replication and consequently reduces viral RNA translation in a replication-dependent manner. Furthermore, we have shown that HuR level is upregulated upon CVB3 infection. Moreover, HuR limits virus replication and can coordinate the availability of genomic RNA templates for translation, replication, or encapsidation. Our study highlights the fact that the relative abundance of translation factors and replication factors in the cell decides the outcome of viral infection. IMPORTANCE A positive-strand RNA virus must balance the availability of its genomic template for different viral processes at different stages of its life cycle. A few host proteins are shown to be important to help the virus in switching the usage of a template between these processes. These proteins inhibit translation either by displacing a stimulator of translation or by binding to an alternative site. Both mechanisms lead to ribosome clearance and availability of the genomic strand for replication. We have shown that HuR also helps in maintaining this balance by inhibiting replication and subsequently promoting translation and packaging.
Enhanced catalytic properties of Pt-based electrode by doped Cu and Ce

Novel PtCuCeOx composite membrane electrode materials were fabricated on the surface of graphite fibrous cloth by ion beam sputtering (IBS). The cyclic voltammetry (CV) and linear sweep voltammetry (LSV) were used to analyze the influence of doped Cu and Ce on the membrane electrocatalysis performance in a tri-electrode system. The phase composition, surface structure, interfacial structure and catalytic performance of PtCuCeOx membrane were studied by x-ray diffraction (XRD) and high resolution transmission electron microscope (HR-TEM&STEM). The results indicate that surface particles of membrane electrode are made up of PtCu alloy grains and a few CeOx grains, and the interface structure of oxide metal is formed between them. The crystal plane spacing between PtCu alloy grain is reduced by about 1.11% after the corrosion, which helps increase the electron density on Pt atom. As a result, the catalysis capability of PtCu alloy is enhanced. When the content of Ce is less than or equal to 0.28 wt. %, CeOx exists in the form of amorphous. It is exciting to demonstrate that the existence of CeOx enhances the dispersion of PtCuCeOx catalyst particles. The experimental results reveal that the synthesized material possesses the best electrochemical activity surface area (ESA) and exchange current density (i0). Compared to pure Pt catalyst, this PtCuCeOx catalyst contains much less Pt content (only 42% of Pt catalyst). However, the electrochemical performance is enhanced by 71.8% compared with pure Pt.
Leveraging Fecal Microbial Markers to Improve the Diagnostic Accuracy of the Fecal Immunochemical Test for Advanced Colorectal Adenoma

INTRODUCTION: Fecal immunochemical tests (FITs) detect colorectal adenoma inefficiently. The gut microbiota participates in colorectal cancer development. We aimed to explore fecal microbial signatures for advanced adenomas and evaluate their diagnostic value and complementary capacity to FIT. METHODS: Using 16S rRNA sequencing, we studied gut microbiota in feces from 1,546 subjects in a screening setting, including 268 patients with advanced adenomas, 490 patients with nonadvanced adenomas, and 788 healthy subjects. Feature selections were performed using linear discriminant analysis effect size, multivariate association with linear models, and least absolute shrinkage and selection operator. The diagnostic performance of microbial signatures and their auxiliary role to FITs and the added value of the Asia-Pacific Colorectal Screening score were evaluated. We applied 0.632+ bootstrapping to adjust the potential overfitting. RESULTS: We identified 13 microbial signatures to show the joint diagnostic value for advanced adenoma, with genus Tyzzerella 4 demonstrating the highest adjusted area under the curve (AUC) of 0.545 (95% confidence interval [CI], 0.520–0.610). The 13-bacteria increased the adjusted AUC to 0.607 (95% CI, 0.548–0.660). Compared with individual FIT (adjusted AUC = 0.527; 95% CI, 0.519–0.571), 13-bacteria and FITs collectively reached an adjusted AUC of 0.641 (95% CI, 0.579–0.691). At cutoff values yielding specificities of 90% and 80%, the adjusted sensitivities were 28.4% (95% CI, 19.3–36.8) and 41.1% (95% CI, 29.9–49.4), respectively. The Asia-Pacific Colorectal Screening score further boosted the adjusted AUC to 0.706 (95% CI, 0.648–0.750). DISCUSSION: In this study using fecal samples from a screening setting, the identified microbial signatures could complement FITs for detecting advanced adenomas. Gut microbiota can act as a promising tool to optimize the current colorectal cancer screening modalities.
Draft Genomic Sequences of Bacillus amyloliquefaciens CBMAI 1301 and Bacillus subtilis CBMAI 1302, Strains with Potential for the Biocontrol of Phytopathogens

Here, we report the draft genomic sequences of Bacillus amyloliquefaciens strain CBMAI 1301, isolated from soybean seeds, and Bacillus subtilis strain CBMAI 1302, isolated from soil. These strains have potential applications for the biological control of phytopathogens, and the sequencing of these two genomes could greatly benefit soybean cultivation. ABSTRACT Here, we report the draft genomic sequences of Bacillus amyloliquefaciens strain CBMAI 1301, isolated from soybean seeds, and Bacillus subtilis strain CBMAI 1302, isolated from soil. These strains have potential applications for the biological control of phytopathogens, and the sequencing of these two genomes could greatly benefit soybean cultivation.
Endocrine‐disrupting chemicals and obesity risk: A review of recommendations for obesity prevention policies

Emerging evidence indicates that industrially produced endocrine‐disrupting chemicals (EDCs) may be as obesogenic as poor dietary patterns and should be considered in obesity prevention policies. The authors conducted two reviews: (a) a systematic search of four electronic databases for papers published since January 2010 to identify the policy recommendations contained in scientific reviews of EDC exposure and obesity risk and (b) a narrative review of obesity policy documents published since January 2012 to identify the recommendations of national and international agencies. A search of four electronic databases found 63 scientific reviews with policy recommendations, of which 26 suggested individual responsibility to avoid exposure, 11 suggested medical interventions to counter the effects of exposure, and 42 suggested regulatory control of hazardous chemicals. Of sixty policy documents examined, six mentioned pollutants as a possible risk factor for obesity, and only one made explicit reference to strategies for reducing exposure to EDCs. The UN Sustainable Development Goals include targets to prevent ill health from hazardous chemicals (Targets 3.9 and 12.4) and to remove unsafe industrial chemicals from the environment (Targets 6.3, 11.6, 12.4, and 14.1). The authors suggest these should be explicitly linked to World Health Assembly targets to halt the rise in obesity.
Self-diffusion mechanisms based defect complexes in MoSi2

MoSi2 is widely concerned due to excellent electrical conductivity, oxidation resistance as a typical transition metal silicide. The high-temperature diffusion behavior is one of the important factors for the degradation of MoSi2 coatings. However, the diffusion mechanism in MoSi2 is still unclear. Prior theoretical work mostly focused on defect formation energy, but these are not consistent with the self-diffusion experiments because the migration behaviors were not considered. Therefore, the purpose of this work was to investigate the microscopic diffusion mechanisms of Mo and Si atoms in MoSi2 using density functional theory and the CI-NEB method. We confirmed that the temperature-dependent vibrational contribution has a significant impact on the defect formation free energy. The isolated point defects in MoSi2 will tend to aggregate to form defect complexes, which participate in the atomic diffusion as mediators. The defect migration behaviors of atoms for vacancy mediated, vacancy complex mediated, and antisite assisted jumps were obtained based on electronic structures analysis. The results show that Si diffusion is mediated by intrasublattice jumps of the nearest neighbor Si vacancies. Moreover, the destroyed covalent Mo–Si bonds by Si vacancies and the non-directional weak metal bonds formed by the Mo antisites and Mo atoms could improve the mobility of the Mo atom which results in the low migration barrier. The agreement between our calculations and the reported experimental results indicates that the dominant diffusion mechanism for Mo atoms is mediated by vacancy complex mediated jumps and antisite assisted jumps. It is concluded that the Si vacancy-based defect complexes are likely the diffusion mediators for Mo atom self-diffusion in MoSi2. This work provides a deeper insight into the connection between the atomic mechanism and the macroscopic behavior for the diffusion in the MoSi2, and establishes the basis for further optimizing high-temperature coating materials.
Dimensional stability of acrylic denture base material after poly vinyl pyrrolidone addition

Problem Denture base dimensional changes were found with commercial theremocured acrylic resins. The dimensional stability of acrylic resin denture base is the main necessity effects the retention and stability of the denture. This study was conducted to measure the dimensional accuracy of experimental prepared material in comparison with control material before and after thermo cycling cured by water bath and microwave. In this stady the total (40) specimens of heat cure acrylic resin lower denture base were cured by water bath and microwave after addition poly vinyl pyrrolidone (PVP). (Experimental). Preparation of modified heat cured denture base acrylic resin was carried out by preparing of (PMMA) (80%) and poly vinyl pyrrolidone (PVP) (20%) and the liquid part composed of methyl methacrylate (MMA) monomer. Evaluation was made by measuring dimensional stability and accuracy. Distances were measured between (3) points marked on denture bases "AB, AC and BC" before and after thermo cycling for both control and experimental groups. The result of this study showed that there was no significant differences (p>0.05) between control and experimental groups at three point "AB, AC and BC" before and after thremocycling. Dimensional stability and accuracy was not influenced by addition of PVP to acrylic denture base resin before and after thermo cycling in both heat and microwave treatment.
What you say and what I hear—Investigating differences in the perception of the severity of psychological and physical violence in intimate partner relationships

The correct communication of the severity of violence is essential in the context of legal trials, custody cases, support of victims, etc., for providing fair treatment. A narrator that communicates their experiences of interpersonal violence may rate the seriousness of the incident differently than a rater reading the narrator’s text, suggesting that there exist perceptual differences (PD) in severity ratings between the narrator and the rater. We propose that these perceptual differences may depend on whether the narrative is based on physical or psychological violence, and on gender differences. Physical violence may be evaluated as more serious by the receiver of the narrative than by the narrator (Calibration PD), whereas the seriousness of psychological violence may be difficult to convey, leading to a discrepancy in the seriousness ratings between the narrator and the rater (Accuracy PD). In addition, gender stereotypes may influence the seriousness rating (Gender PD), resulting in violence against women being perceived as more serious than the same violence against men. These perceptual differences were investigated in 3 phases using a new experimental procedure. In Phase 1, 113 narrators provided descriptions and seriousness ratings of self-experienced physical and psychological violence in relationships. In Phase 2, 340 independent raters rated the seriousness of 10 randomly selected narrations from Phase 1. In Phase 3, the genders in the narrations were changed to the opposite gender, and seriousness ratings were collected from 340 different raters. Our results confirmed the hypothesized perceptual differences. Violence to male victims was considerably more likely to be seen as severe when the raters were misled to believe the victim was a woman. We propose that these data provide practical guidelines for how to deal with misinformation in the communication of violence. The data also show that mean values and the confidence of such severity ratings need to be adjusted for several factors, such as whether it is self-experienced or communicated, the type of violence, and the gender of the victims and raters.
Genome Sequence of Lymphocystis Disease Virus 2 LCDV-JP_Oita_2018, Isolated from a Diseased Japanese Flounder (Paralichthys olivaceus) in Japan

Here, we present the genome sequence of lymphocystis disease virus 2 LCDV-JP_Oita_2018 (genus Lymphocystivirus, family Iridoviridae), which was isolated from a diseased Japanese flounder (Paralichthys olivaceus) in Japan. The LCDV-JP_Oita_2018 genome was assembled into a circular contig of 186,627 bp, with 140 predicted protein-coding genes and a GC content of 27%. ABSTRACT Here, we present the genome sequence of lymphocystis disease virus 2 LCDV-JP_Oita_2018 (genus Lymphocystivirus, family Iridoviridae), which was isolated from a diseased Japanese flounder (Paralichthys olivaceus) in Japan. The LCDV-JP_Oita_2018 genome was assembled into a circular contig of 186,627 bp, with 140 predicted protein-coding genes and a GC content of 27%.