Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessment of HLA-A, HLA-DR, and HLA-DQ alleles in patients with pemphigus vulgaris from eastern of Turkey.

BACKGROUND Pemphigus vulgaris (PV) is a chronic progressive autoimmune bullous disease caused by the interaction of pathogenic factors, genetic, and environmental factors. HLA alleles, which are considered as protective factors against disease or predisposing factors, may be different in various populations and ethnic groups. AIMS The purpose of this study is to examine the HLA-A, HLA-DR, and HLA-DQ alleles in patients that are diagnosed with PV in and around eastern of Turkey and to determine the alleles that create predisposition to disease or protect against the disease. PATIENTS/METHODS Thirty patients diagnosed as PV with clinical, histopathological, and immunofluorescence findings and 30 healthy subjects were included in this study. The HLA-A, HLA-DR, and HLA-DQ typology in the DNA samples that were obtained from the blood samples of the groups was performed by using the PCR-SSP low-resolution gene panels. RESULTS The HLA-A*03 allele was found to be significantly higher in patient group than the control group (P-value: .020). HLA-DRB1*04 and HLA-DRB1*14 alleles in PV patients were found to be significantly higher than the control group (P-value = .000). CONCLUSION It was concluded that the HLA-DRB1*03, HLADQB1*02, and HLA-DQB1*06 alleles in and around eastern of Turkey showed protective effects against pemphigus vulgaris. It was also concluded that the HLA-A*03, HLA-DRB1*04, HLA-DRB1*14, HLA-DRB4, HLA-DQB1*03, and HLA-DQB1*05 alleles could cause predisposition to the disease.
Validation of a Deep Learning System for the Full Automation of Bite and Meal Duration Analysis of Experimental Meal Videos

Eating behavior can have an important effect on, and be correlated with, obesity and eating disorders. Eating behavior is usually estimated through self-reporting measures, despite their limitations in reliability, based on ease of collection and analysis. A better and widely used alternative is the objective analysis of eating during meals based on human annotations of in-meal behavioral events (e.g., bites). However, this methodology is time-consuming and often affected by human error, limiting its scalability and cost-effectiveness for large-scale research. To remedy the latter, a novel “Rapid Automatic Bite Detection” (RABiD) algorithm that extracts and processes skeletal features from videos was trained in a video meal dataset (59 individuals; 85 meals; three different foods) to automatically measure meal duration and bites. In these settings, RABiD achieved near perfect agreement between algorithmic and human annotations (Cohen’s kappa κ = 0.894; F1-score: 0.948). Moreover, RABiD was used to analyze an independent eating behavior experiment (18 female participants; 45 meals; three different foods) and results showed excellent correlation between algorithmic and human annotations. The analyses revealed that, despite the changes in food (hash vs. meatballs), the total meal duration remained the same, while the number of bites were significantly reduced. Finally, a descriptive meal-progress analysis revealed that different types of food affect bite frequency, although overall bite patterns remain similar (the outcomes were the same for RABiD and manual). Subjects took bites more frequently at the beginning and the end of meals but were slower in-between. On a methodological level, RABiD offers a valid, fully automatic alternative to human meal-video annotations for the experimental analysis of human eating behavior, at a fraction of the cost and the required time, without any loss of information and data fidelity.
Activation of endogenous protein phosphatase 1 enhances the calcium sensitivity of the ryanodine receptor type 2 in murine ventricular cardiomyocytes

Increased protein phosphatase 1 (PP‐1) activity has been found in end stage human heart failure. Although PP‐1 has been extensively studied, a detailed understanding of its role in the excitation–contraction coupling mechanism, in normal and diseased hearts, remains elusive. The present study investigates the functional effect of the PP‐1 activity on local Ca2+ release events in ventricular cardiomyocytes, by using an activating peptide (PDP3) for the stimulation of the endogenous PP‐1 protein. We report that acute de‐phosphorylation may increase the sensitivity of RyR2 channels to Ca2+ in situ, and that the RyR2‐serine2808 phosphorylation site may mediate such a process. Our approach unmasks the functional importance of PP‐1 in the regulation of RyR2 activity, suggesting a potential role in the generation of a pathophysiological sarcoplasmic reticulum Ca2+ leak in the diseased heart.
Diabetic ketoacidosis at diagnosis among youth with type 1 and type 2 diabetes: Results from SEARCH (United States) and YDR (India) registries

There is significant global variation in the prevalence of diabetic ketoacidosis (DKA) at diagnosis among youth with type 1 diabetes (T1D). However, data for youth with type 2 diabetes (T2D) are limited, even in developed countries. We compared the prevalence of DKA at diagnosis among individuals with T1D and T2D from the SEARCH for Diabetes in Youth (SEARCH) and the Registry of Youth Onset Diabetes in India (YDR) registries.
The role of financial strain in college students’ work hours, sleep, and mental health

Abstract Objective To examine poor sleep quality as a potential mediator between college students’ employment hours and depressive symptoms, and to examine if this mediation model might differ across students reporting different levels of financial strain. Participants: The sample was collected through a multi-site study during the Spring of 2019 and included 792 undergraduates (M = 20.1, SD = 1.9) in Upstate New York. Methods: Moderated mediation analyses based on cross-sectional self-report, online questionnaires. Results: Increased work hours predicted greater sleep disturbance, which, in turn, predicted more depressive symptoms. Compared to students in more comfortable financial situations, this mediation model only emerged for students reporting more financial strain and lower family socio-economic status. Conclusions: Student employment hours are a significant predictor of students’ mental well-being when considering their potential impact on their sleep. Furthermore, students reporting higher levels of financial stress are most at risk of being impacted by this process.
Characterization of Ebola Virus Disease (EVD) in Rhesus Monkeys for Development of EVD Therapeutics

Recent Ebola virus (EBOV) outbreaks in West Africa and the Democratic Republic of the Congo have highlighted the urgent need for approval of medical countermeasures for treatment and prevention of EBOV disease (EVD). Until recently, when successes were achieved in characterizing the efficacy of multiple experimental EVD therapeutics in humans, the only feasible way to obtain data regarding potential clinical benefits of candidate therapeutics was by conducting well-controlled animal studies. Nonclinical studies are likely to continue to be important tools for screening and development of new candidates with improved pharmacological properties. Here, we describe a natural history study to characterize the time course and order of progression of the disease manifestations of EVD in rhesus monkeys. In 12 rhesus monkeys exposed by the intramuscular route to 1000 plaque-forming units of EBOV, multiple endpoints were monitored for 28 days following exposure. The disease progressed rapidly with mortality events occurring 7–10 days after exposure. Key disease manifestations observed consistently across the infected animals included, but were not limited to, viremia, fever, systemic inflammation, coagulopathy, lymphocytolysis, renal tubular necrosis with mineralization, and hepatocellular degeneration and necrosis.
Plasma Trimethylamine-N-oxide and impaired glucose regulation: Results from The Oral Infections, Glucose Intolerance and Insulin Resistance Study (ORIGINS)

Trimethylamine-N-oxide (TMAO)–a gut-microbiota metabolite–is a biomarker of cardiometabolic risk. No studies have investigated TMAO as an early biomarker of longitudinal glucose increase or prevalent impaired glucose regulation. In a longitudinal cohort study, 300 diabetes-free men and women (77%) aged 20–55 years (mean = 34±10) were enrolled at baseline and re-examined at 2-years to investigate the association between TMAO and biomarkers of diabetes risk. Plasma TMAO was measured using Ultra Performance Liquid Chromatography-Mass Spectrometry. After an overnight fast, FPG was measured longitudinally, HbA1C and insulin were measured only at baseline. Insulin resistance was defined using HOMA-IR. Multivariable generalized linear models regressed; i) FPG change (year 2 minus baseline) on baseline TMAO tertiles; and ii) HOMA-IR and HbA1c on TMAO tertiles. Multivariable relative risk regressions modeled prevalent prediabetes across TMAO tertiles. Mean values of 2-year longitudinal FPG±SE across tertiles of TMAO were 86.6±0.9, 86.7±0.9, 86.4±0.9 (p = 0.98). Trends were null for FPG, HbA1c, HOMA-IR, cross-sectionally. The prevalence ratio of prediabetes among participants in 2nd and 3rd TMAO tertiles (vs. the 1st) were 1.94 [95%CI 1.09–3.48] and 1.41 [95%CI: 0.76–2.61]. TMAO levels are associated with increased prevalence of prediabetes in a nonlinear fashion but not with insulin resistance or longitudinal FPG change.
Disparities in self-reported eating disorders and academic impairment in sexual and gender minority college students relative to their heterosexual and cisgender peers.

OBJECTIVE The purpose of the current study was threefold: (a) compare rates of self-reported anorexia nervosa (AN), self-reported bulimia nervosa (BN), and eating pathology-specific academic impairment (EAI) by gender identity (cisgender men, cisgender women, transgender or genderqueer) and sexual orientation (gay or lesbian, bisexual, unsure, other), (b) examine associations between gender identity, sexual orientation, and eating outcomes, and (c) identify for whom rates of eating disorder diagnosis and impairment is greatest. METHOD The study includes a sample of Minnesota students (n = 13,906) who participated in the College Student Health Survey from 2015 to 2018. Chi-square tests with bootstrapping examined differences in eating pathology rates between groups. Adjusted logistic regressions tested the association between gender identity, sexual orientation, and self-reported eating outcomes. RESULTS Chi-square results revealed heightened rates of self-reported AN, self-reported BN, and EAI in cisgender women, transgender or genderqueer, and sexual minority (e.g., lesbian or bisexual) students. Logistic regression analyses in cisgender men and cisgender women revealed higher odds of self-reported AN, self-reported BN, and EAI in sexual minority students relative their heterosexual peers. Chi-square analyses indicated that bisexual cisgender women reported heightened rates of all three eating pathology measures relative to other sexual and/or gender (e.g., transgender) minority students. DISCUSSION Individuals with marginalized gender and/or sexual orientation identities report heightened rates of eating pathology, with cisgender bisexual women reporting the poorest outcomes relative to individuals from other marginalized identities. Preventive efforts and more research are needed to understand the mechanisms driving this disparity and to reduce prevalence among marginalized groups.
Bacterial Community Diversity Dynamics Highlight Degrees of Nestedness and Turnover Patterns

Bacterial communities change their structure rapidly due to short generation times of their members. How bacteria assemble to certain structures provides insight into ecological mechanisms that shape a bacterial community. Microbial community flow cytometry was used to create community fingerprints based on subcommunity distributions and to visualize the dynamic variations of 10 independently grown communities under equal conditions. Inventory diversity values were recorded by α‐ and γ‐diversity whereas the degree of subsistence of subcommunities (nestedness) and the degree of gain or loss of subcommunities (turnover) was calculated as multi‐sites ß‐diversity terms ßNES and ßSIM. Numbers of unique subcommunities of pairwise samples were determined by intra‐ and inter‐community ß‐diversity values. Although all communities were exposed to niche‐differentiating conditions they assembled to disparate structures. In our study, the turnover coefficients were high (> 0.6), while the nestedness coefficients were complementary low in the separate 10 bioreactors. Intra‐ and inter‐community ß‐diversity values indicated fast community shifts. Microbial community flow cytometry straightforwardly identifies the dominance and subsistence of subsets of cells in a community or the degree of their replacement. The calculation of either turnover or nestedness patterns might have implications in medical, biotechnological, or environmental research. © 2020 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.
Longitudinal Associations Between Perceptions of Peer Group Drinking Norms and Students' Alcohol Use Frequency Within College Sport Teams.

BACKGROUND Students' alcohol use behaviors are shaped by the attitudes and behaviors of others, especially the peers within students' proximal social groups. Explaining the association between perceived drinking norms and alcohol use, researchers propose contradicting pathways that focus on conformity (i.e., social norms predict alcohol use) and projection (i.e., alcohol use predicts perceived norms). The current study examined the extent to which conformity and projection processes were evident in the association between college student alcohol use and the perceived alcohol use norms for students' club sport teams. METHODS The sample comprised 1,054 college students (61% female) nested in 35 intact same-sex club sport teams. On 3 separate occasions during a single school year (3-month lag), participants reported drinking frequency and perceptions of descriptive and injunctive group drinking norms. We employed random intercepts cross-lagged panel modeling to estimate prospective within-person associations separately from stable trait-like between-person associations. RESULTS Descriptive and injunctive group drinking norms were both positively related to students' alcohol use frequency at the between-person level. Individuals nevertheless demonstrated variability at the within-person level. Results revealed a strong contemporaneous association between descriptive norms and alcohol use frequency within each timepoint, but no prospective associations. Models including perceptions of injunctive drinking norms demonstrated similar contemporaneous associations with alcohol use frequency, but also identified significant prospective associations signifying conformity. CONCLUSIONS Findings align with previous research reporting a strong and positive association between student's self-reported alcohol use and subjective peer alcohol use norms. After disentangling within- and between-person effects to probe for conformity and projection processes, the current findings are somewhat contrary to previous research that has reported reciprocal relationships between social norms and alcohol use behavior. Further investigation of the potential conformity and projection mechanisms of social norms is critical to advance norm-based strategies to reduce harm.
Aptamer-Conjugated Tb(III)-Doped Silica Nanoparticles for Luminescent Detection of Leukemia Cells

DNA aptamers have many benefits for cell imaging, such as high affinity and specificity, easiness of chemical functionalization, and low cost of production. Among known aptamers, Sgc8-aptamer was selected against acute lymphoblastic leukemia cells with a dissociation constant in a nanomolar range. The aptamer was previously used for the covalent coupling with fluorescent and magnetic nanoparticles, as well as for the fabrication of aptamer-based biosensors. Among commonly used fluorescent tags, lanthanide nanoparticles offer stable luminescence with narrow, well-resolved emission peaks and the absence of photoblinking. In other words, lanthanide nanoparticles could serve as luminescence reporters and be used in biosensing. In our study, we conjugated amino- and carboxyl-modified silica-coated terbium (III) thiacalix[4]arenesulfonate luminescent nanoparticles with Sgc8-aptamer and showed the ability of the aptamer-conjugated nanoparticles to detect leukemia cells using fluorescence microscopy. In addition, we conducted a cell viability assay and confirmed that the nanoparticles do not induce spontaneous cell apoptosis or necrosis and could be potentially used for bioimaging applications.
Growth Mode and Physiological State of Cells Prior to Biofilm Formation Affect Immune Evasion and Persistence of Staphylococcus aureus

The present study investigated Staphylococcus aureus ATCC25923 surfaceomes (cell surface proteins) during prolonged growth by subjecting planktonic and biofilm cultures (initiated from exponential or stationary cells) to label-free quantitative surfaceomics and phenotypic confirmations. The abundance of adhesion, autolytic, hemolytic, and lipolytic proteins decreased over time in both growth modes, while an opposite trend was detected for many tricarboxylic acid (TCA) cycle, reactive oxygen species (ROS) scavenging, Fe-S repair, and peptidolytic moonlighters. In planktonic cells, these changes were accompanied by decreasing and increasing adherence to hydrophobic surface and fibronectin, respectively. Specific RNA/DNA binding (cold-shock protein CspD and ribosomal proteins) and the immune evasion (SpA, ClfA, and IsaB) proteins were notably more abundant on fully mature biofilms initiated with stationary-phase cells (SDBF) compared to biofilms derived from exponential cells (EDBF) or equivalent planktonic cells. The fully matured SDBF cells demonstrated higher viability in THP-1 monocyte/macrophage cells compared to the EDBF cells. Peptidoglycan strengthening, specific urea-cycle, and detoxification enzymes were more abundant on planktonic than biofilm cells, indicating the activation of growth-mode specific pathways during prolonged cultivation. Thus, we show that S. aureus shapes its surfaceome in a growth mode-dependent manner to reach high levofloxacin tolerance (>200-times the minimum biofilm inhibitory concentration). This study also demonstrates that the phenotypic state of the cells prior to biofilm formation affects the immune-evasion and persistence-related traits of S. aureus.
Modelling the effects of alcohol pricing policies on alcohol consumption in subpopulations in Australia.

AIMS To model the effects of a range of alcohol pricing policies on alcohol consumption in subpopulation groups (e.g. alcohol consumption pattern, and age and income groups) in Australia. DESIGN We used estimated price elasticities to model the effects of proposed pricing policies on consumption for 11 beverage categories among subpopulation groups. SETTING Australia. PARTICIPANTS A total of 1789 adults (16+ years) who reported they purchased and consumed alcohol in the 2013 Australian International Alcohol Control Study, an adult population survey. MEASUREMENTS Mean and percentage changes in alcohol consumption were estimated for each scenario across subgroups. The policy scenarios evaluated included: (1) increasing the excise rate 10% for all off-premise beverages; (2) replacing the wine equalization tax with a volumetric excise rate equal to the current spirits tax rate; (3) applying a uniform excise tax rate to all beverages equal to the current sprits tax rate and a 10 or 20% increase in it; and(4) introducing a minimum unit price (MUP) on all beverages categories at $1.00, 1.30 or 1.50. FINDINGS The effects of different tax and MUP policies varied greatly across different subgroups. The effects of the MUP policy on alcohol consumption increased rapidly in the range from $1.00 to $1.50. Applying a uniform tax rate across all beverages equal to current spirits tax rate, or a 10 or 20% increase beyond that, could generate large reductions in overall alcohol consumption in Australia. Compared with the uniform tax rate with or without further tax increase, introducing a MUP at $1.30 or $1.50 could reduce consumption particularly among harmful drinkers and lower-income drinkers, with comparatively smaller impacts on moderate and higher-income drinkers. CONCLUSIONS Both uniform excise tax and minimum unit price policies are predicted to reduce alcohol consumption in Australia. Minimum unit price policies are predicted to have a greater impact on drinking among harmful drinkers than moderate drinkers.
Predictive and prognostic value of L-lactate, D-dimer, leukocyte, C-reactive protein and neutrophil/lymphocyte ratio in patients with acute mesenteric ischemia.

BACKGROUND Acute mesenteric ischemia (AMI) is a disease that causes an ischemia in the intestines due to the obstruction of the mesenteric vessels feeding the intestines, with a mortality rate reaching up to 80%. The overall incidence of AMI is 0.63 per 100,000 people. Early diagnosis and treatment are very important for survival. There is no ideal biomarker that can reflect different types and stages of AMI. This study investigated the predictive and prognostic value of L-lactate, D-dimer, leukocyte, C reactive protein (CRP) and neutrophil/lymphocyte ratio (NLR) in the preoperative period were investigated in patients operated for AMI. METHODS A total of 44 patients operated for AMI between 2015 and 2019 were evaluated in this study. Demographic, clinical, radiological, laboratory and surgical findings of the patients included in this study were recorded. The patients were divided into groups according to the etiological type of AMI. L-lactate, D-dimer, CRP, leukocyte, and NLR levels of these patients were determined. Statistical analysis was performed according to AMI groups. RESULTS The mean age of the 44 patients included in this study was 67.7 years and the female to male ratio was 0.76. According to tomography results, 31.8% (n=14) of the patients had mesenteric artery embolism, 29.5% (n=13) had mesenteric artery thrombus, 25% (n=11) had mesenteric vein thrombus and 13.6% (n=6) had non-occlusive mesenteric ischemia. When AMI types were compared, D-dimer and CRP levels were found to be significantly different from other markers. The total length of stay in the hospital was found to be significantly correlated with the L-lactate (p=0.047) and CRP (p=0.045) levels. In the analyses, CRP was determined to be the common biomarker that could be used in the diagnosis of mesenteric ischemia in all AMI types. CONCLUSION Particularly, the CRP level can be used effectively in the preoperative period to diagnose AMI and to determine its subtype and clinical course. However, L-lactate, D-dimer, leukocyte and NLR are markers that have no predictive value in the diagnosis of all AMI subtypes.