Miracle-dz/UniFAR-FTUs huggingface dataset:
Mental and Substance Use Disorders Prevalence Study: Background and Methods

Abstract Objective The Mental and Substance Use Disorders Prevalence Study (MDPS) builds upon previous epidemiologic studies to provide estimates of prevalence and treatment rates of mental and substance use disorders among adults aged 18–65 in the U.S. The study background and methods are described. Method The MDPS employed novel techniques such as the inclusion of household, prison, homeless and state psychiatric hospital populations, a semi‐structured clinical interview administered by trained clinical interviewers to assess disorders, the assessment of both past year and lifetime schizophrenia spectrum disorder (SSD) using full Diagnostic and Statistical Manual 5 criteria, as well as other mental and substance use disorders, and video‐based interviewing. Population specific and combined sample weights were developed to estimate nationally representative prevalence and treatment rates. Results Data collection was conducted between October 2020 and October 2022 resulting in 5679 clinical interviews. The statistical weighting and analytic plan are described. Weighted response rates and reasons for non‐response are provided for each study population. Conclusions The MDPS successfully developed and employed novel techniques to estimate the prevalence and treatment rates of mental and substance use disorders in both household and non‐household populations, including some of the most impairing disorders such as SSD.
ncRNAs-mediated TIMELESS overexpression in lung adenocarcinoma correlates with reduced tumor immune cell infiltration and poor prognosis

Lung adenocarcinoma (LUAD) has a poor prognosis. Circadian genes such as TIMELESS have been associated with several pathologies, including cancer. The expression of TIMELESS and the relationship between TIMELESS, infiltration of tumors and prognosis in LUAD requires further investigation. In this study, we investigated the expression of TIMELESS and its association with survival across several types of human cancer using data from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression Program. Noncoding RNAs (ncRNAs) regulating overexpression of TIMELESS in lung adenocarcinoma (LUAD) were explored with expression, correlation, and survival analyses. Immune cell infiltration and biomarkers were analyzed between different TIMELESS expression levels. The relationship between TIMELESS expression and immunophenoscores, which were used to predict response to immunotherapy, was evaluated. TIMELESS was identified as a potential oncogene in LUAD. NcRNA analysis showed MIR4435-2HG/hsa-miR-1-3p may interact with TIMELESS in a competitive endogenous RNA network in LUAD tumor tissues. Most immune cells were significantly decreased in TCGA LUAD tumor tissues with high TIMELESS expression except for CD4+T cells and Th2 cells. TIMELESS expression in LUAD tumor tissues was significantly negatively correlated with neutrophil biomarkers, dendritic cell biomarkers (HLA-DPB1, HLA-DQB1, HLA-DRA, HLA-DPA1, CD1C) and an immunophenoscore that predicted outcomes associated with the use of immune checkpoint inhibitors. These findings imply that ncRNAs-mediated TIMELESS overexpression in LUAD tumor tissues correlated with poor prognosis, reduced immune cell infiltration in the tumor microenvironment, and poor response to immune checkpoint inhibitors.
Vancomycin-variable enterococci in sheep and cattle isolates and whole-genome sequencing analysis of isolates harboring vanM and vanB genes

Background: Vancomycin resistance encoded by the vanA/B/M genes in enterococci is clinically important because of the transmission of these genes between bacteria. While vancomycin resistance is determined by detecting only vanA and vanB genes by routine analyses, failure to detect vanM resistance causes vancomycin resistance to be overlooked, and clinically appropriate treatment cannot be provided. Aims: The study aimed to examine the presence of vanM-positive enterococcal isolates in Ankara, Turkey, and to have detailed information about them with sequence analyses. Methods: Caecal samples were collected from sheep and cattle during slaughter at different slaughterhouses in Ankara, Turkey. Enterococci isolates were identified, confirmed, and analyzed for the presence of vanA/B/M genes. Antibiotic resistance profiles of isolates were determined by the broth microdilution method. A whole genome sequence analysis of the isolates harboring the vanM and vanB genes was performed. Results: 13.7% of enterococcal isolates were determined as Enterococcus faecium and Enterococcus faecalis. 15% of these isolates contained vanB, and 40% were vanM-positive. S98b and C32 isolates were determined to contain 16 CRISPR-Cas elements. 80% of the enterococci isolates were resistant to nitrofurantoin and 15% to ciprofloxacin. The first vanM-positive vancomycin-variable enterococci (VVE) isolates from food-producing animals were identified, and the S98b strain has been assigned to Genbank with the accession number CP104083.1. Conclusion: Therefore, new studies are needed to facilitate the identification of vanM-resistant enterococci and VVE strains.
Molecular epidemiology, associated risk factors, and phylogeny of Theileria annulata infecting buffaloes and cattle from different agro-climatic regions of Punjab, Pakistan

Background: Tropical theileriosis is the most prevalent hemoprotozoan disease in Pakistan. Aims: The study aimed to investigate the epidemiology and evolutionary relationship of Theileria annulata in bovines in diverse agro-climatic regions of Punjab, Pakistan. Methods: 800 blood specimens were collected from asymptomatic cattle (n=480) and buffaloes (n=320) using a multistage sampling method from Sargodha (n=400) and Multan (n=400) districts. The samples were assessed for blood smear microscopy and cytochrome b gene based PCR. Twenty samples were collected from each union council of each district. Results: The overall prevalence of T. annulata infection in bovines was 9% and 17.13% as determined by blood smear analysis and PCR, respectively. The disease positivity in cattle and buffaloes was respectively 10.21% and 20.42% by blood smear screening and 7.19%, 12.19% by PCR. The overall PCR based prevalence in the Sargodha and Multan districts was 19% and 15.25%, respectively. Absence of rural poultry, tick infestation, and a history of tick-borne diseases had significant effect in cattle. Tick infestation and age were the main statistically significant disease determinants in buffaloes. The evolutionary analysis of the cytochrome b gene showed that the Pakistani isolate infecting buffalo was related to those from Iran, India, Egypt, and Sudan. The isolate from cattle was genetically close to those from Pakistan, India, Iran, Iraq, and Turkey. Conclusion: It can be concluded that biotic and abiotic factors contribute to disease occurrence. The current study will help to devise control strategies to prevent substantial economic losses.
Sleep and fatigue management strategies: How nurses, midwives and paramedics cope with their shift work schedules—a qualitative study

Abstract Aims To understand the benefits and challenges of shift work, and the coping strategies used by nurses, midwives and paramedics to manage the impact of shift work on sleep and fatigue from shift work. Design A single case study with embedded units. Methods Twenty‐seven participants were interviewed exploring their shift work experiences, coping strategies used to improve sleep, and what their recommendations are for improving shift work management. Interviews were completed between November and December 2022. Results Participants enjoyed the lifestyle, flexibility and financial rewards offered by working shift work. However, fatigue and sleep deprivation undermined these benefits, as it impacted their ability to enjoy social and family events. There were also concerns of long‐term health consequences of shift work and delivery of care. Changes to rostering practices and sleep and shift work education were common recommendations. Conclusion This study provides insights on how healthcare professionals manage sleep and fatigue due to shift work and the inadequate support. There is absence of adequate policies, processes and training at an organizational, academic and personal level on how to best manage sleep and fatigue when working shift work. Future research is needed to explore how to equip healthcare shift workers with the skills to successfully manage their schedules to mitigate the negative impact that poor sleep and fatigue has on the health and safety of themselves and their patients. Implications for the Profession and/or Patient Care Understanding the specific challenges of shift work and how workers manage their shift work schedules is critical for improving the health and safety of themselves and their patients. This study identified that there is insufficient training regarding sleep and shift work management strategies, potentially leading to occupational health and safety concerns. Further education and training to equip staff with the necessary information, training and guidance to staff on how to reduce fatigue risk is required. Patient or Public Contribution This study involved healthcare shift workers in semi‐structured interviews. Data gathered from a previous survey that participants were involved in helped shape the interview topics and the study design.
Energy, water, and protein folding: A molecular dynamics‐based quantitative inventory of molecular interactions and forces that make proteins stable

Abstract Protein folding energetics can be determined experimentally on a case‐by‐case basis but it is not understood in sufficient detail to provide deep control in protein design. The fundamentals of protein stability have been outlined by calorimetry, protein engineering, and biophysical modeling, but these approaches still face great difficulty in elucidating the specific contributions of the intervening molecules and physical interactions. Recently, we have shown that the enthalpy and heat capacity changes associated to the protein folding reaction can be calculated within experimental error using molecular dynamics simulations of native protein structures and their corresponding unfolded ensembles. Analyzing in depth molecular dynamics simulations of four model proteins (CI2, barnase, SNase, and apoflavodoxin), we dissect here the energy contributions to ΔH (a key component of protein stability) made by the molecular players (polypeptide and solvent molecules) and physical interactions (electrostatic, van der Waals, and bonded) involved. Although the proteins analyzed differ in length, isoelectric point and fold class, their folding energetics is governed by the same quantitative pattern. Relative to the unfolded ensemble, the native conformations are enthalpically stabilized by comparable contributions from protein–protein and solvent–solvent interactions, and almost equally destabilized by interactions between protein and solvent molecules. The native protein surface seems to interact better with water than the unfolded one, but this is outweighed by the unfolded surface being larger. From the perspective of physical interactions, the native conformations are stabilized by van de Waals and Coulomb interactions and destabilized by conformational strain arising from bonded interactions. Also common to the four proteins, the sign of the heat capacity change is set by interactions between protein and solvent molecules or, from the alternative perspective, by Coulomb interactions.
A protocol for systematic review and meta-analysis

Background:Numerous studies have reported that transcranial magnetic stimulation (TMS) and fluoxetine is used in the treatment of postpartum depression (PPD). Currently, no study has systematically investigated the efficacy and safety of TMS and fluoxetine for the treatment of patients with PPD. Thus, this study will assess the efficacy and safety of TMS and fluoxetine for treating PPD. Methods: Relevant studies involving TMS and fluoxetine for the treatment of patients with PPD will be comprehensively searched from the electronic databases from inception to the February 1, 2020: Cochrane Library, EMBASE, MEDILINE, CINAHL, AMED, WANGFANG, VIP, and CNKI databases. No language and publication time restrictions will be applied. RevMan 5.3 software will be utilized for data pooling, data analysis, and risk of bias evaluation. If necessary, we will also assess reporting bias using funnel plot and Egger test. Results: This study will comprehensively summarize the existing evidence to assess the efficacy and safety of TMS and fluoxetine for treating PPD. Conclusion: The findings of this study may help to establish a better approach to treat PPD using TMS and fluoxetine. Dissemination and ethics: This study will be disseminated through a peer-reviewed journal. This study does not need ethical approval as no primary patient data will be used. Systematic review registration: INPLASY202040017. Abbreviations: PPD = postpartum depression, TMS = transcranial magnetic stimulation.
Preservation of ancient impact ages on the R chondrite parent body: 40Ar/39Ar age of hornblende‐bearing R chondrite LAP 04840

The hornblende‐ and biotite‐bearing R chondrite LAP 04840 is a rare kind of meteorite possibly containing outer solar system water stored during metamorphism or postshock annealing deep within an asteroid. Because little is known regarding its age and origin, we determined 40Ar/39Ar ages on hornblende‐rich separates of the meteorite, and obtained plateau ages of 4340(±40) to 4380(±30) Ma. These well‐defined plateau ages, coupled with evidence for postshock annealing, indicate this meteorite records an ancient shock event and subsequent annealing. The age of 4340–4380 Ma (or 4.34–4.38 Ga) for this and other previously dated R chondrites is much older than most impact events recorded by ordinary chondrites and points to an ancient event or events that predated the late heavy bombardment that is recorded in so many meteorites and lunar samples.
Association between Processed Meat Protein Consumption and Incident Osteoporosis in Adults Aged 50 Years and Older: A Prospective Cohort Study Based on Korean Genome and Epidemiology Study Data (2005-2020).

Background Osteoporosis is one of the inevitable diseases affecting an aging society, substantially impacting the quality of life of its population. Protein intake has been shown to be beneficial in reducing the incidence of osteoporosis, and the effects of both animal and vegetable proteins have been studied. However, the relationship between processed meat consumption and osteoporosis has not been studied in Korea. Therefore, we aimed to analyze the correlation between processed meat consumption and incident osteoporosis in adults. Methods Our analysis included 1,260 adults aged 50 years and older from the Korean Genome and Epidemiology Study (KoGES), recruited between 2005 and 2020. Participants were categorized into two groups according to their processed meat intake, assessed using a semi-quantitative 103-food item food frequency questionnaire. Diagnosis of osteoporosis was based on questionnaire answers. Multiple Cox hazard regression analyses were conducted to examine the association between processed meat intake and incident osteoporosis. Results During an average follow-up period of 8.8 years, 230 participants developed osteoporosis. According to the Cox proportional regression models, the hazard ratio (95% confidence interval) of incident osteoporosis in the high intake group was 0.62 (0.41-0.94), compared to the low intake group after adjusting for confounding variables. Conclusion These findings reveal that processed meat protein intake is inversely related to the incidence of osteoporosis in adults aged 50 years and older. This in turn suggests that processed meat intake can be proposed as an additional strategy to prevent osteoporosis.
Simulating Marine Ice Sheets with the Community Ice Sheet Model

We have applied CISM to several test problems of the Marine Ice Sheet Model Intercomparison Project (MISMIP) and the Marine Ice Sheet–Ocean Model Intercomparison Project (MISOMIP). Here we show results for MISMIP3d (part of MISMIP) and MISMIP+ (the icesheet component of MISOMIP). Using a subgrid grounding-line parameterization (GLP), simulations at moderate resolution (~1 km) agree well with published benchmarks. For flow on a downward-sloping bed, SSA results are in good agreement with the boundary-layer solution of Schoof (2007). For cases with basal-sliding perturbations, CISM successfully simulates reversible migration of curved grounding lines. Without a GLP, much higher resolution is needed for similar accuracy. These results suggest that a resolution of ~1 km may be sufficient for accurate simulation of whole marine ice sheets.
The Coriolis effect on mass wasting during the Rheasilvia impact on asteroid Vesta

We investigate the influence of the Coriolis force on mass motion related to the Rheasilvia impact on asteroid Vesta. Observations by the NASA Dawn mission revealed a pattern of curved radial ridges, which are related to Coriolis‐deflected mass‐wasting during the initial modification stage of the crater. Utilizing the projected curvature of the mass‐wasting trajectories, we developed a method that enabled investigation of the initial mass wasting of the Rheasilvia impact by observational means. We demonstrate that the Coriolis force can strongly affect the crater formation processes on rapidly rotating objects, and we derive the material's velocities (28.9 ± 22.5 m/s), viscosities (1.5–9.0 × 106 Pa s) and coefficients of friction (0.02–0.81) during the impact modification stage. The duration of the impact modification stage could be estimated to (1.1 ± 0.5) h. By analyzing the velocity distribution with respect to the topography, we deduce that the Rheasilvia impactor hit a heterogeneous target and that the initial crater walls were significantly steeper during the modification stage.
Remote measurement methods for 3-D modeling purposes using BAE Systems’ Software

Effi cient, accurate data collection from imagery is the key to an economical generation of useful geospatial products. Incremental developments of traditional geospatial data collection and the arrival of new image data sources cause new software packages to be created and existing ones to be adjusted to enable such data to be processed. In the past, BAE Systems’ digital photogrammetric workstation, SOCET SET®, met fi n de siècle expectations in data processing and feature extraction. Its successor, SOCET GXP®, addresses today’s photogrammetric requirements and new data sources. SOCET GXP is an advanced workstation for mapping and photogrammetric tasks, with automated functionality for triangulation, Digital Elevation Model (DEM) extraction, orthorectifi cation and mosaicking, feature extraction and creation of 3-D models with texturing. BAE Systems continues to add sensor models to accommodate new image sources, in response to customer demand. New capabilities added in the latest version of SOCET GXP facilitate modeling, visualization and analysis of 3-D features.
Functional genetic characterization of stress tolerance and biofilm formation in Nakaseomyces (Candida) glabrata via a novel CRISPR activation system

ABSTRACT The overexpression of genes frequently arises in Nakaseomyces (formerly Candida) glabrata via gain-of-function mutations, gene duplication, or aneuploidies, with important consequences on pathogenesis traits and antifungal drug resistance. This highlights the need to develop specific genetic tools to mimic and study genetic amplification in this important fungal pathogen. Here, we report the development, validation, and applications of the first clustered regularly interspaced short palindromic repeats (CRISPR) activation (CRISPRa) system in N. glabrata for targeted genetic overexpression. Using this system, we demonstrate the ability of CRISPRa to drive high levels of gene expression in N. glabrata, and further assess optimal guide RNA targeting for robust overexpression. We demonstrate the applications of CRISPRa to overexpress genes involved in fungal pathogenesis and drug resistance and detect corresponding phenotypic alterations in these key traits, including the characterization of novel phenotypes. Finally, we capture strain variation using our CRISPRa system in two commonly used N. glabrata genetic backgrounds. Together, this tool will expand our capacity for functional genetic overexpression in this pathogen, with numerous possibilities for future applications. IMPORTANCE Nakaseomyces (formerly Candida) glabrata is an important fungal pathogen that is now the second leading cause of candidiasis infections. A common strategy that this pathogen employs to resist antifungal treatment is through the upregulation of gene expression, but we have limited tools available to study this phenomenon. Here, we develop, optimize, and apply the use of CRISPRa as a means to overexpress genes in N. glabrata. We demonstrate the utility of this system to overexpress key genes involved in antifungal susceptibility, stress tolerance, and biofilm growth. This tool will be an important contribution to our ability to study the biology of this important fungal pathogen.
Investigation of the Effect of Swelling on the Diffusion Properties of Polyethylene Glycol Hydrogel for Wound Healing Applications

The present research work aims to comprehensively analyze the effect of swelling of polyethylene glycol (PEG) hydrogel on its diffusion properties for wound healing applications. For this study, a computational model based on three fundamental theories namely, equilibrium swelling theory, rubber elasticity theory and free volume theory has been implemented to determine the diffusion parameters of PEG hydrogel having a molecular weight of 20,000 g/mol. The diffusion of two plant metabolites with inherent antimicrobial activity namely, Cinnamaldehyde and Curcumin and two synthetic antimicrobial drugs namely, Amphotericin B and Vancomycin has been simulated. The results demonstrate that the proposed theoretical framework is capable of predicting the alterations occurring in the diffusion characteristics due to the swelling of PEG hydrogel. The diffusion coefficient of the solute is found to increase with the volumetric swelling ratio (Qv), owing to the wider mesh size of the hydrogel matrix. The diffusion time of the therapeutic compounds is observed to be in the range of 2.40 - 8.30 h.Clinical Relevance— The modelling approach employed in this study will be clinically relevant for designing hydrogel drug delivery systems capable of accelerating the treatment of the infected wounds.
RNA methylation in inflammatory bowel disease

Abstract RNA modifications, including the renowned m6A, have recently garnered significant attention. This chemical alteration, present in mRNA, exerts a profound influence on protein expression levels by affecting splicing, nuclear export, stability, translation, and other critical processes. Although the role of RNA methylation in the pathogenesis and progression of IBD and colorectal cancer has been reported, many aspects remain unresolved. In this comprehensive review, we present recent studies on RNA methylation in IBD and colorectal cancer, with a particular focus on m6A and its regulators. We highlight the pivotal role of m6A in the pathogenesis of IBD and colorectal cancer and explore the potential applications of m6A modifications in the diagnosis and treatment of these diseases.