Miracle-dz/UniFAR-FTUs huggingface dataset:
Hospital-Acquired Bloodstream Infections in Patients Hospitalized With Severe Acute Respiratory Syndrome Coronavirus 2 Infection (Coronavirus Disease 2019): Association With Immunosuppressive Therapies

Abstract Background Immunosuppressive therapies proposed for Coronavirus disease 2019 (COVID-19) management may predispose to secondary infections. We evaluated the association of immunosuppressive therapies with bloodstream-infections (BSIs) in hospitalized COVID-19 patients. Methods This was an institutional review board-approved retrospective, multicenter, cohort study of adults hospitalized with COVID-19 over a 5-month period. We obtained clinical, microbiologic and laboratory data from electronic medical records. Propensity-score-matching helped create balanced exposure groups. Demographic characteristics were compared across outcome groups (BSI/no BSI) using two-sample t-test and Chi-Square test for continuous and categorical variables respectively, while immunosuppressive therapy use was compared using McNemar’s test. Conditional logistic regression helped assess the association between immunosuppressive therapies and BSIs. Results 13,007 patients were originally included, with propensity-score-matching producing a sample of 6,520 patients. 3.74% and 3.97% were diagnosed with clinically significant BSIs in the original and propensity-score-matched populations respectively. COVID-19 patients with BSIs had significantly longer hospitalizations, higher intensive care unit admission and mortality rates compared to those without BSIs. On univariable analysis, combinations of corticosteroids/anakinra [odds-ratio (OR) 2.00, 95% confidence intervals (C.I.) 1.05-3.80, P value.0342] and corticosteroids/tocilizumab [OR 2.13, 95% C.I. 1.16–3.94, P value . 0155] were significantly associated with BSIs. On multivariable analysis (adjusting for confounders), combination corticosteroids/tocilizumab were significantly associated with any BSI [OR 1.97, 95% C.I. 1.04–3.73, P value.0386] and with bacterial BSIs [OR 2.13, 95% C.I. 1.12–4.05, p-value 0.0217]. Conclusions Combination immunosuppressive therapies were significantly associated with BSI occurrence in COVID-19 patients; their use warrants increased BSI surveillance. Further studies are needed to establish their causative role.
Influence of SGLT2 Inhibitor Treatment on Urine Antioxidant Status in Type 2 Diabetic Patients: A Pilot Study

Sodium-glucose cotransporter 2 inhibitors (SGLT2i) have been recognized as potent antioxidant agents. Since SGLT2i are nephroprotective drugs, we aimed to examine the urine antioxidant status in patients with type 2 diabetes mellitus (T2DM). One hundred and one subjects participated in this study, including 37 T2DM patients treated with SGLT2i, 31 T2DM patients not using SGLT2i, and 33 healthy individuals serving as a control group. Total antioxidant capacity (TAC), superoxide dismutase (SOD), manganese superoxide dismutase (MnSOD), free thiol groups (R-SH, sulfhydryl groups), and catalase (CAT) activity, as well as glucose concentration, were assessed in the urine of all participants. Urine SOD and MnSOD activity were significantly higher among T2DM patients treated with SGLT2i than T2DM patients without SGLT2i treatment (p = 0.009 and p = 0.003, respectively) and to the healthy controls (p = 0.002 and p = 0.001, respectively). TAC was significantly lower in patients with T2DM treated with SGLT2i when compared to those not treated and healthy subjects (p = 0.036 and p = 0.019, respectively). It could be hypothesized that the mechanism by which SGLT2i provides nephroprotective effects involves improvement of the SOD antioxidant activity. However, lower TAC might impose higher OS (oxidative stress), and elevation of SOD activity might be a compensatory mechanism.
Central Nervous System Cell-Derived Exosomes in Neurodegenerative Diseases

Exosomes are a type of extracellular vesicles secreted by almost all kinds of mammalian cells that shuttle “cargo” from one cell to another, indicative of its role in cell-to-cell transportation. Interestingly, exosomes are known to undergo alterations or serve as a pathway in multiple diseases, including neurodegenerative diseases. In the central nervous system (CNS), exosomes originating from neurons or glia cells contribute to or inhibit the progression of CNS-related diseases in special ways. In lieu of this, the current study investigated the effect of CNS cell-derived exosomes on different neurodegenerative diseases.
Scalable and accurate method for neuronal ensemble detection in spiking neural networks

We propose a novel, scalable, and accurate method for detecting neuronal ensembles from a population of spiking neurons. Our approach offers a simple yet powerful tool to study ensemble activity. It relies on clustering synchronous population activity (population vectors), allows the participation of neurons in different ensembles, has few parameters to tune and is computationally efficient. To validate the performance and generality of our method, we generated synthetic data, where we found that our method accurately detects neuronal ensembles for a wide range of simulation parameters. We found that our method outperforms current alternative methodologies. We used spike trains of retinal ganglion cells obtained from multi-electrode array recordings under a simple ON-OFF light stimulus to test our method. We found a consistent stimuli-evoked ensemble activity intermingled with spontaneously active ensembles and irregular activity. Our results suggest that the early visual system activity could be organized in distinguishable functional ensembles. We provide a Graphic User Interface, which facilitates the use of our method by the scientific community.
Effect of Die Spacer Thickness on the Microshear Bond Strength of CAD/CAM Lithium Disilicate Veneers

Aim The aim of this study was to compare the microshear bond strength of ceramic veneers with digital die spacer settings at 20, 40, and 100 µm. Materials and Methods Eighteen milled lithium disilicate microdiscs (IPS e.max CAD, Ivoclar Vivadent) were divided into three groups (n = 6) according to their digital die spacer settings: group A = 20 µm, group B = 40 µm, and group C = 100 µm. Six randomly selected sound maxillary premolars received three microdiscs each. Each microdisc was 1 mm in diameter and 1 mm in height. The buccal surfaces of the premolars were prepared with a 0.5 mm depth in enamel. After cementation, the specimens were thermocycled for 2,500 cycles between 5 and 55°C. Microshear bond strength testing was performed using a universal testing machine until bonding failure. Failure modes were evaluated using a stereomicroscope. Statistical analyses included one-way ANOVA, Tukey's post hoc test, and chi-square test with a 5% alpha error and 80% study power. Results The mean microshear bond strength values were calculated in MPa for group A = 31.91 ± 12.41, group B = 29.58 ± 5.03, and group C = 13.85 ± 4.12. One-way ANOVA (p ≤ 0.05) showed a statistically significant difference in microshear bond strength among the three groups. Tukey's post hoc test showed significant differences between groups A and C (p=0.004) and between groups B and C (p=0.011). The failure modes were presented as cohesive, adhesive, and mixed failures. Chi-square test indicated that the failure mode distribution was not significantly different among the three groups (p=0.970). Conclusion Higher digital die spacer settings decrease the microshear bond strength of CAD/CAM lithium disilicate veneers.
Photobiomodulation Regulation as One Promising Therapeutic Approach for Myocardial Infarction

Myocardial infarction refers to myocardial necrosis caused by acute or persistent coronary ischemia and hypoxia. It is considered to be one of the significant crises threatening human health in the world. Following myocardial infarction, collagen gradually replaces the original tissue due to the loss of many cardiomyocytes, myocardial contractile function decreases, and myocardial fibrosis eventually leads to heart failure. Phototherapy is a new treatment which has shown superior efficacy on the nerve, skeletal muscle, skin, and other tissues. Likewise, there is growing evidence that phototherapy also has many positive effects on the heart. Therefore, this article introduces the progress of research on phototherapy as a new therapeutic strategy in the treatment of myocardial infarction. The wavelength of photobiomodulation in the treatment of myocardial infarction is specific, and the influence of light source power and light duration on the tissue presents a bell-shaped distribution. Under these conditions, phototherapy can promote ATP synthesis and angiogenesis, inhibit the inflammatory response, improve heart function, reduce infarct size, and protect myocardium. In addition, we summarized the molecular mechanisms of phototherapy. According to the location of photoreceptors, they can be divided into mitochondrial and nonmitochondrial parts.
Updated Review of the Acoustic Modulation of Sleep: Current Perspectives and Emerging Concepts

Abstract With growing interest in the use of acoustic stimuli in sleep research and acoustic interventions used therapeutically for sleep enhancement, there is a need for an overview of the current lines of research. This paper summarizes the various ways to use acoustic input before sleep or stimulation during sleep. It thereby focuses on the respective methodological requirements, advantages, disadvantages, potentials and difficulties of acoustic sleep modulation. It highlights differences in subjective and objective outcome measures, immediate and whole night effects and short versus long term effects. This recognizes the fact that not all outcome parameters are relevant in every research field. The same applies to conclusions drawn from other outcome dimensions, consideration of mediating factors, levels of stimulation processing and the impact of inter-individual differences. In addition to the deliberate influences of acoustic input on sleep, one paragraph describes adverse environmental acoustic influences. Finally, the possibilities for clinical and basic research-related applications are discussed, and emerging opportunities are presented. This overview is not a systematic review but aims to present the current perspective and hence summarizes the most up-to-date research results and reviews. This is the first review providing a summary of the broad spectrum of possibilities to acoustically influence sleep.
J Point and ST Elevation Resembling Brugada: A Marker of Mortality in Methanol Toxicity

Objective J point and coved ST elevation in right precordial leads (not produced by coronary artery disease) are still a matter of challenge, especially when resembling Brugada patients. This clinical entity, among asymptomatic individuals with no family history of sudden cardiac death, would be reported in some severely ill patients before ventricular fibrillation. This study investigated the relationship between the electrocardiograms with demographic and laboratory data and also analyzed their association with mortality rate among patients with methanol poisoning. Methods The sample consisted of 356 patients who were hospitalized with a diagnosis of methanol poisoning in Faghihi and Namazi Hospitals in Shiraz, Southern Iran, in March and April 2020. In this period, a major outbreak of methanol poisoning had occurred in this area. Furthermore, the study used the data on any recorded complications or mortality during hospital course. Results The ECG (BrP) was observed in a total of 20 (5.6%) patients. Its presence was associated with increased mortality, Glasgow coma scale score <3, and blood sugar levels and was inversely associated with PH, O2 saturation, and calcium levels (P < 0.05). Conclusions This study found that certain ECG patterns and laboratory data can be used as prognostic factors of morbidity and mortality in patients with methanol intoxication. Electrocardiography machines are widely available tools, which can be easily used for risk stratification based on the presence of Brugada approximating electrocardiograms among patients with methanol intoxication.
Fasting Glucose of 6.1 mmol/L as a Possible Optimal Target for Type 2 Diabetic Patients with Insulin Glargine: A Randomized Clinical Trial

To observe whether different insulin glargine titration algorithms based on fasting blood glucose (FBG) levels lead to different glycaemic variations (GVs) in type 2 diabetes (T2D) patients, a prospective, randomized, single-centre, comparative, three-arm parallel-group, open-label, treat-to-target, 24-week study was performed. A total of 71 uncontrolled T2D patients were recruited and randomized 1 : 3 : 3 into Groups 1, 2, and 3 (insulin titration goals of FBG ≤ 5.6, ≤6.1, and ≤7.0) for this study. The initiated insulin glargine dose was recommended at 0.2 U/kg/day and was then titrated following the FBG target. Patients were subjected to two 3-day continuous glucose monitoring (CGM) at baseline and the endpoint, wherein the CGM data were analysed, and the study's primary endpoint was the difference in 24 hrs mean amplitude of glycaemic excursion (MAGE) among the three groups. We observed that patients in the three groups had similar MAGE levels at the endpoint; however, Group 2 achieved a significant decrease in the MAGE level from baseline to the endpoint as compared to Groups 1 and 3 (all p < 0.05). We also observed that these patients had significant glycated haemoglobin A1c (HbA1c) value improvements as compared to the other two groups (all p < 0.05). Therefore, choosing an FBG level of 6.1 mmol/L as an insulin titration target provided significant GVs and HbA1c value improvements in T2D patients. Moreover, our data indicated that an FBG of 6.1 mmol/L could possibly be an insulin glargine titration target in T2D patients.
National and Subnational Cancer Incidence for 22 Cancer Groups, 2000 to 2016: A Study Based on Cancer Registration Data of Iran

Background Cancer is an increasing public health concern, and detailed knowledge of the cancer incidence is required for developing effective cancer control plans. The objective of this study is to present the cancer incidence of 22 cancer groups in Iran and all 31 provinces of the country from 2000 to 2016, for both sexes across different age groups. Method To study the national and provincial cancer incidence in Iran, we extracted data from the Cancer Project, which collects the Iranian cancer registry data and visualizes it in the VIZIT data visualization system. The methodology and statistical analysis that is used in this study follow the cancer project study protocol. Joinpoint analysis was performed to calculate the average annual percent change of the crude rates and age-standardized rates from 2000 to 2016. Results Cancer incidence was 126,982 patients in 2016, and the crude rate (CR) of cancer in both sexes and all ages was 155 per 100,000 people. Cancer incidence approximately doubled between 2000 and 2016; however, the age-standardized rate (ASR) had a less drastic increase. The most incident cancers in 2016 were breast, skin, and colorectal cancers; however, the ranking of cancer groups by incidence was different in different age and sex groups and provinces. Some cancers exhibited a unique distribution pattern in the country with high-incidence local areas. Discussion. The study showed that cancer incidence, crude rate, and age-standardized rate (ASR) in Iran had increased in 2000-2016 with vast heterogeneity by cancer type, province, and sex. Moreover, it was shown that the crude rate of cancer in Iran was much less than the global cancer crude rate. Providing such data helps to allocate resources and develop effective national cancer control plans appropriately.
L. Cucurbita pepo Alleviates Chronic Unpredictable Mild Stress via Modulation of Apoptosis, Neurogenesis, and Gliosis in Rat Hippocampus

Pumpkin has received significant attention due to its nutritional compounds that have antioxidant, antifatigue, and anti-inflammatory effects. This study is aimed at assessing the antidepressant-like effect of L. Cucurbita pepo, sweet pumpkin, in an animal model of chronic unpredictable mild stress (CUMS) and investigating its effect on the histological structure of hippocampus compared to fluoxetine. Forty male albino rats assigned into the negative control, positive control (CUMS), and Flu-treated and pumpkin-treated groups (n = 10) were utilized in this study. Exposing rats to CUMS continued for 28 days, and treatments used were applied during the last 14 days of exposure. Behavioral, biochemical, and histopathological changes were assessed after 28 days. In this study, pumpkin significantly reduced the immobility time (p = 0.02), corticosterone (p < 0.001), TNF-α, IL-6 (p < 0.001), and malondialdehyde (p = 0.003), whereas it significantly increased the level of superoxide dismutase (SOD), catalase, and glutathione peroxidase (GPX) in the serum of rats exposed to CUMS. Pumpkin markedly relieved the degenerative and atrophic changes observed in the CA3 region and the dentate gyrus of the hippocampus. It significantly reduced caspase-3 and increased glial fibrillary acidic protein (GFAP) immunoexpression in the CA3 and DG. In conclusion, administration of pumpkin extract improved the behavioral, biochemical, and hippocampal pathological alternations induced in rats after exposure to CUMS in a comparable pattern to fluoxetine. This study highlighted the potential efficacy of pumpkin in alleviating depression disorder either alone or in conjugation with conventional antidepressant therapy.
Correlation between Family RB1 Gene Pathogenic Variant with Clinical Features and Prognosis of Retinoblastoma under 5 Years Old

Retinoblastoma (RB) is the most common primary intraocular malignant tumor in infants and the prototype of human hereditary tumors. Its occurrence and development are closely related to the pathogenic variant of tumor suppressor RB1 gene. We aim to analyze the characteristics of RB1 gene pathogenic variant and clinical phenotype in retinoblastoma patients and their relatives. Children with RB were recruited from August 2007 to November 2017. QT-PCR, probing, and gene sequencing were used to analyze the sequence of RB1 gene in RB children, their parents, or grandparents with a clear history of illness. The SPSS20.0 software was used to analyze the correlation between polymorphisms of RB1 gene and the incidence and prognosis of the enrolled children and relatives. 40 RB children (20 males and 20 females) were recruited, unilateral RB accounted for 52.5% (21/40), bilateral RB accounted for 42.5% (17/40), and trilateral RB accounted for 5.0% (2/40). 6 patients had a clear family history (15.0%, 6/40). It had been verified that 19 probands (47.5%) have RB1 gene pathogenic variants (11 frameshift and 8 missense pathogenic variants), of which germline inheritance accounted for 47.4% (9/19) and nongermline heredity accounted for 52.6% (10/19). Pathogenic variants of 10 nucleic acid sites without reported were found, among which c.2455C>G (p.L819V) was confirmed to have heterozygous pathogenic variants in both a bilateral RB patient and his mother with unilateral RB. Family genetic high-risk factors, bilateral/trilateral RB, >12-month-onset RB have a higher proportion of RB1 gene pathogenic variant than children with no family history, unilateral RB, and ≤12-month (P = 0.021, 0.001,0.034). The proportion of pedigree inheritance of infantile retinoblastoma with bilateral disease is high. There was a certain proportion of RB1 gene pathogenic variant in 3-5-year-old children with bilateral RB, even if they had no family genetic history. Therefore, the detection of RB1 gene pathogenic variant should not only focus on infants but also on the phenotype of RB1 gene pathogenic variant in children over 3 years old with bilateral eye disease.
Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae

Premise Custom probe design for target enrichment in phylogenetics is tedious and often hinders broader phylogenetic synthesis. The universal angiosperm probe set Angiosperms353 may be the solution. Here, we test the relative performance of Angiosperms353 on the Rosaceae subtribe Malinae in comparison with custom probes that we specifically designed for this clade. We then address the impact of bioinformatically altering the performance of Angiosperms353 by replacing the original probe sequences with orthologs extracted from the Malus domestica genome. Methods To evaluate the relative performance of these probe sets, we compared the enrichment efficiency, locus recovery, alignment length, proportion of parsimony‐informative sites, proportion of potential paralogs, the topology and support of the resulting species trees, and the gene tree discordance. Results Locus recovery was highest for our custom Malinae probe set, and replacing the original Angiosperms353 sequences with a Malus representative improved the locus recovery relative to Angiosperms353. The proportion of parsimony‐informative sites was similar between all probe sets, while the gene tree discordance was lower in the case of the custom probes. Discussion A custom probe set benefits from data completeness and can be tailored toward the specificities of the project of choice; however, Angiosperms353 was equally as phylogenetically informative as the custom probes. We therefore recommend using both a custom probe set and Angiosperms353 to facilitate large‐scale systematic studies, where financially possible.
Applicability and implementation of the collagen-induced arthritis mouse model, including protocols (Review)

Animal models of rheumatoid arthritis (RA) are essential for studying the pathogenesis of RA in vivo and determining the efficacy of anti-RA drugs. During the past decades, numerous rodent models of arthritis have been evaluated as potential models and the modeling methods are relatively well-developed. Among these models, the collagen-induced arthritis (CIA) mouse model is the first choice and the most widely used because it may be generated rapidly and inexpensively and is relatively similar in pathogenesis to human RA. To date, there have been numerous classic studies and reviews discussing related pathogeneses and modeling methods. Based on this knowledge, combined with the latest convenient and effective methods for CIA model construction, the present review aims to introduce the model to beginners and clarify important details regarding its use. Information on the origin and pathogenesis of the CIA model, the protocol for establishing it, the rate of successful arthritis induction and the methods used to evaluate the severity of arthritis are briefly summarized. With this information, it is expected that researchers who have recently entered the field or are not familiar with this information will be able to start quickly, avoid unnecessary errors and obtain reliable results.