Miracle-dz/UniFAR-FTUs huggingface dataset:
Risk Factors for and Frequency of CT Scans, Steroid Use, and Repeat Visits in Inflammatory Bowel Disease Patients Seen at a Single-Center Emergency Department: A Retrospective Cohort Study

Patients with inflammatory bowel disease often present to the emergency department due to the chronic relapsing nature of the disease. Previous studies have shown younger patients to have an increased frequency of emergency department visits, resulting in repeated exposure to imaging studies and steroids, both of which are associated with risks. We performed a retrospective cohort analysis of inflammatory bowel disease patients seen at Houston Methodist Hospital’s emergency department from January 2014 to December 2017 using ICD codes to identify patients with Crohn’s disease, ulcerative colitis, or indeterminate colitis from the electronic medical record. Data were collected on demographics, medications, and imaging. Five hundred and fifty-nine patients were randomly selected for inclusion. Older age was associated with decreased risk of CT scan or steroid use. Patients with ulcerative colitis compared to Crohn’s had decreased risk of CT scan, while there was an increased risk of CT in patients on a biologic, immunomodulator, or when steroids were given. Steroid use was also more common in those with inflammatory bowel disease as the primary reason for the visit. Patients in our study frequently received steroids and had CT scans performed. The increased risk of CT in those on a biologic, immunomodulator, or steroids suggests more severe disease may contribute. Guidelines are needed to reduce any unnecessary corticosteroid use and limit repeat CT scans in young inflammatory bowel disease patients to decrease the risk of radiation-associated malignancy over their lifetime.
Digestion-Specific Acupuncture Effect on Feeding Intolerance in Critically Ill Post-Operative Oral and Hypopharyngeal Cancer Patients: A Single-Blind Randomized Control Trial

Malnourishment is prevalent in patients suffering from head and neck cancer. The postoperative period is crucial in terms of nutritional support, especially after composite resection and reconstruction surgery. These patients present with a number of risk factors that aggravate feeding intolerance, including postoperative status, prolonged immobility, decreased head elevation, mechanical ventilation, and applied sedative agents. Routine management protocols for feeding intolerance include prokinetic drug use and post-pyloric tube insertion, which could be both limited and accompanied by detrimental adverse events. This single-blind clinical trial aimed to investigate the effects of acupuncture in postoperative feeding intolerance in critically ill oral and hypopharyngeal cancer patients. Twenty-eight patients were randomized into two groups: Intervention group and Control group. Interventions were administered daily over three consecutive postoperative days. The primary outcome revealed that the intervention group reached 70% and 80% of target energy expenditure (EE) significantly earlier than the control group (4.00 ± 1.22 versus 6.69 ± 3.50 days, p = 0.012), accompanied by higher total calorie intake within the first postoperative week (10263.62 ± 1086.11 kcals versus 8384.69 ± 2120.05 kcals, p = 0.004). Furthermore, the intervention group also needed less of the prokinetic drug (Metoclopramide, 20.77 ± 48.73 mg versus 68.46 ± 66.56 mg, p = 0.010). In conclusion, digestion-specific acupuncture facilitated reduced postoperative feeding intolerance in oral and hypopharyngeal cancer patients.
Coffee Disease Visualization and Classification

Deep learning architectures are widely used in state-of-the-art image classification tasks. Deep learning has enhanced the ability to automatically detect and classify plant diseases. However, in practice, disease classification problems are treated as black-box methods. Thus, it is difficult to trust the model that it truly identifies the region of the disease in the image; it may simply use unrelated surroundings for classification. Visualization techniques can help determine important areas for the model by highlighting the region responsible for the classification. In this study, we present a methodology for visualizing coffee diseases using different visualization approaches. Our goal is to visualize aspects of a coffee disease to obtain insight into what the model “sees” as it learns to classify healthy and non-healthy images. In addition, visualization helped us identify misclassifications and led us to propose a guided approach for coffee disease classification. The guided approach achieved a classification accuracy of 98% compared to the 77% of naïve approach on the Robusta coffee leaf image dataset. The visualization methods considered in this study were Grad-CAM, Grad-CAM++, and Score-CAM. We also provided a visual comparison of the visualization methods.
Chemokine/Cytokine Levels Correlate with Organ Involvement in PR3-ANCA-Associated Vasculitis

Background: ANCA-associated vasculitis (AAV) is a rare small vessel disease characterized by multi-organ involvement. Biomarkers that can measure specific organ involvement are missing. Here, we ask whether certain circulating cytokines and chemokines correlate with renal involvement and if distinct cytokine/chemokine patterns can differentiate between renal, ear/nose/throat, joints, and lung involvement of AAV. Methods: Thirty-two sets of Birmingham vasculitis activity score (BVAS), PR3-ANCA titers, laboratory marker, and different cytokines were obtained from 17 different patients with AAV. BVAS, PR3-ANCA titers, laboratory marker, and cytokine concentrations were correlated to different organ involvements in active AAV. Results: Among patients with active PR3-AAV (BVAS > 0) and kidney involvement we found significant higher concentrations of chemokine ligand (CCL)-1, interleukin (IL)-6, IL21, IL23, IL-28A, IL33, monocyte chemoattractant protein 2 (MCP2), stem cell factor (SCF), thymic stromal lymphopoietin (TSLP), and thrombopoietin (TPO) compared to patients without PR3-ANCA-associated glomerulonephritis. Patients with ear, nose, and throat involvement expressed higher concentrations of MCP2 and of the (C-X-C motif) ligand-12 (CXCL-12) compared to patients with active AAV and no involvement of these organs. Conclusion: We identified distinct cytokine patterns for renal manifestation and for ear, nose and throat involvement of PR3-AAV. Distinct plasma cytokines might be used as non-invasive biomarkers of organ involvement in AAV.
Retention Forces of Monolithic CAD/CAM Crowns Adhesively Cemented to Titanium Base Abutments—Effect of Saliva Contamination Followed by Cleaning of the Titanium Bond Surface

The aim of this study was to investigate the effects of saliva contamination and the cleaning of the bond surface of titanium base (ti-base) abutments on the bonding stability and retention force values. The bond surface of the ti-base abutments was treated with airborne-particle abrasion. After contamination, the ti-base abutments underwent different cleaning protocols: water spray (H2O); alcohol (ALC); suspension of zirconium particles (SZP); reapplied airborne-particle abrasion (APA); and a control condition without contamination and cleaning (CTR). All lithium disilicate crowns were bonded to the ti-base abutments using a primer and a self-curing composite. Bonded specimens underwent thermo-mechanical aging. Bond failure analysis and pull-off testing were performed. Bond failure occurred more frequently in groups H2O, ALC, SZP, and APA (p < 0.05). Significant differences in retention force values were only found between CTR and ALC (p < 0.05). Specimens which did not show bond failure after ageing had higher retention force values than the specimens that showed bond failure (p < 0.05). Saliva contamination with cleaning can degrade the bonding properties to titanium. For the retention force values, only the protocol with alcohol after contamination could not restore the values.
Increase in Phloem Area in the Tomato hawaiian skirt Mutant Is Associated with Enhanced Sugar Transport

The HAWAIIAN SKIRT (HWS) gene has been described in Arabidopsis, rice, tomato and poplar where it seems to perform distinct functions with relatively little overlap. In tomato, alteration of the gene function confers facultative parthenocarpy, thought to be a consequence of changes in the microRNA metabolism. In the rice mutant, improvement in panicle architecture is associated with an increase in grain yield. Knowing that hws tomato fruits show a higher Brix level, it was suspected that vascular bundles might also be altered in this species, in a similar fashion to the rice phenotype. The pedicel structure of the hws-1 line was therefore examined under the microscope and sugar concentrations from phloem exudate were determined in an enzymatic assay. A distinct increase in the phloem area was observed as well as a higher sugar content in mutant phloem exudates, which is hypothesized to contribute to the high Brix level in the mutant fruits. Furthermore, the described phenotype in this study bridges the gap between Arabidopsis and rice phenotypes, suggesting that the modulation of the microRNA metabolism by HWS influences traits of agricultural interest across several species.
Pro-Oxidative Effect of KIO3 and Protective Effect of Melatonin in the Thyroid—Comparison to Other Tissues

Not only iodine deficiency, but also its excess may contribute to thyroid cancer. Potassium iodate (KIO3), which is broadly used in the salt iodization program, can increase oxidative damage to membrane lipids (lipid peroxidation, LPO) under experimental conditions, with the strongest damaging effect at KIO3 concentration of ~10 mM (corresponding to physiological iodine concentration in the thyroid). Melatonin is an effective antioxidant, which protects against KIO3-induced LPO in the thyroid. This study aimed to compare the protective effects of melatonin, used in the highest achievable in vitro concentration, against KIO3-induced oxidative damage to membrane lipids in various porcine tissues (thyroid, ovary, liver, kidney, brain, spleen, and small intestine). Homogenates were incubated in the presence of KIO3 (20; 15; 10; 7.5; 5.0; 0.0 mM) without/with melatonin (5 mM). The malondialdehyde + 4-hydroxyalkenals (MDA + 4-HDA) concentration (LPO index) was measured spectrophotometrically. KIO3 increased the LPO in all examined tissues; in the thyroid, the damaging effect of KIO3 (10; and 7.5 mM) was lower than in other tissues and was not observed for the lowest concentration of 5 mM. Melatonin reduced LPO induced by KIO3 (10, 7.5, and 5 mM) in all tissues, and in the thyroid it was also protective against as high a concentration of KIO3 as 15 mM; the LPO level resulting from KIO3 + melatonin treatment was lower in the thyroid than in other tissues. In conclusion, the thyroid is less sensitive tothe pro-oxidative effects of KIO3 compared to other tissues. The strongest protective effect of melatonin was observed in the thyroid, but beneficial effects were significant also in other tissues. Melatonin should be considered to avoid the potential damaging effects of iodine compounds applied in iodine prophylaxis.
Predictors of COVID-19-Related Perceived Improvements in Dietary Health: Results from a US Cross-Sectional Study

The COVID-19 pandemic resulted in substantial lifestyle changes. No US study has identified predictors of perceived dietary healthfulness changes during the pandemic period. This study included analyses of lifestyle and dietary healthfulness changes using 958 survey responses from US primary household food purchasers. Information was collected related to demographics, COVID-19-related household changes, and health-related habits before and during the pandemic. Binary logistic regression identified predictors of perceived increase in dietary healthfulness during the pandemic period. Overall, 59.8%, 16.4%, and 23.4% of participants reported that their eating habits likely changed, may have changed, and likely did not change, respectively. Of the participants whose dietary habits likely or may have changed, 64.1%, 16.8%, and 19% reported healthier, neither healthier nor less healthy, and less healthy eating habits, respectively. COVID-19-related income loss, more meals consumed with household members in front of the television, an increase in food advertisement exposure, increased perceived stress, and better perceived current health were significant predictors of a perceived increase in dietary healthfulness. Overall, dietary habits were perceived to become healthier during the pandemic. The predictors of perceived improvement in dietary healthfulness were surprising and indicate the need for further study of these factors in crisis and noncrisis situations.
Improvement of Glucose Tolerance by Food Factors Having Glucagon-Like Peptide-1 Releasing Activity

Glucagon-like peptide-1 (GLP-1) is a gastrointestinal hormone released from enteroendocrine L cells in response to meal ingestion. GLP-1 receptor agonists and GLP-1 enhancers have been clinically employed to treat diabetes owing to their glucose-dependent insulin-releasing activity. The release of GLP-1 is primarily stimulated by macronutrients such as glucose and fatty acids, which are nutritionally indispensable; however, excessive intake of sugar and fat is responsible for the development of obesity and diabetes. Therefore, GLP-1 releasing food factors, such as dietary peptides and non-nutrients, are deemed desirable for improving glucose tolerance. Human and animal studies have revealed that dietary proteins/peptides have a potent effect on stimulating GLP-1 secretion. Studies in enteroendocrine cell models have shown that dietary peptides, amino acids, and phytochemicals, such as quercetin, can directly stimulate GLP-1 secretion. In our animal experiments, these food factors improved glucose metabolism and increased GLP-1 secretion. Furthermore, some dietary peptides not only stimulated GLP-1 secretion but also reduced plasma peptidase activity, which is responsible for GLP-1 inactivation. Herein, we review the relationship between GLP-1 and food factors, especially dietary peptides and flavonoids. Accordingly, utilization of food factors with GLP-1-releasing/enhancing activity is a promising strategy for preventing and treating obesity and diabetes.
Investigation of Long COVID Prevalence and Its Relationship to Epstein-Barr Virus Reactivation

Coronavirus disease 2019 (COVID-19) patients sometimes experience long-term symptoms following resolution of acute disease, including fatigue, brain fog, and rashes. Collectively these have become known as long COVID. Our aim was to first determine long COVID prevalence in 185 randomly surveyed COVID-19 patients and, subsequently, to determine if there was an association between occurrence of long COVID symptoms and reactivation of Epstein–Barr virus (EBV) in 68 COVID-19 patients recruited from those surveyed. We found the prevalence of long COVID symptoms to be 30.3% (56/185), which included 4 initially asymptomatic COVID-19 patients who later developed long COVID symptoms. Next, we found that 66.7% (20/30) of long COVID subjects versus 10% (2/20) of control subjects in our primary study group were positive for EBV reactivation based on positive titers for EBV early antigen-diffuse (EA-D) IgG or EBV viral capsid antigen (VCA) IgM. The difference was significant (p < 0.001, Fisher’s exact test). A similar ratio was observed in a secondary group of 18 subjects 21–90 days after testing positive for COVID-19, indicating reactivation may occur soon after or concurrently with COVID-19 infection. These findings suggest that many long COVID symptoms may not be a direct result of the SARS-CoV-2 virus but may be the result of COVID-19 inflammation-induced EBV reactivation.
Comparative Genomics of Prophages Sato and Sole Expands the Genetic Diversity Found in the Genus Betatectivirus

Tectiviruses infecting the Bacillus cereus group represent part of the bacterial “plasmid repertoire” as they behave as linear plasmids during their lysogenic cycle. Several novel tectiviruses have been recently found infecting diverse strains belonging the B. cereus lineage. Here, we report and analyze the complete genome sequences of phages Sato and Sole. The linear dsDNA genome of Sato spans 14,852 bp with 32 coding DNA sequences (CDSs), whereas the one of Sole has 14,444 bp comprising 30 CDSs. Both phage genomes contain inverted terminal repeats and no tRNAs. Genomic comparisons and phylogenetic analyses placed these two phages within the genus Betatectivirus in the family Tectiviridae. Additional comparative genomic analyses indicated that the “gene regulation-genome replication” module of phages Sato and Sole is more diverse than previously observed among other fully sequenced betatectiviruses, displaying very low sequence similarities and containing some ORFans. Interestingly, the ssDNA binding protein encoded in this genomic module in phages Sato and Sole has very little amino acid similarity with those of reference betatectiviruses. Phylogenetic analyses showed that both Sato and Sole represent novel tectivirus species, thus we propose to include them as two novel species in the genus Betatectivirus.
The Divergent Immunomodulatory Effects of Short Chain Fatty Acids and Medium Chain Fatty Acids

Fatty acids are derived from diet and fermentative processes by the intestinal flora. Two to five carbon chain fatty acids, termed short chain fatty acids (SCFA) are increasingly recognized to play a role in intestinal homeostasis. However, the characteristics of slightly longer 6 to 10 carbon, medium chain fatty acids (MCFA), derived primarily from diet, are less understood. Here, we demonstrated that SCFA and MCFA have divergent immunomodulatory propensities. SCFA down-attenuated host pro-inflammatory IL-1β, IL-6, and TNFα response predominantly through the TLR4 pathway, whereas MCFA augmented inflammation through TLR2. Butyric (C4) and decanoic (C10) acid displayed most potent modulatory effects within the SCFA and MCFA, respectively. Reduction in TRAF3, IRF3 and TRAF6 expression were observed with butyric acid. Decanoic acid induced up-regulation of GPR84 and PPARγ and altered HIF-1α/HIF-2α ratio. These variant immune characteristics of the fatty acids which differ by just several carbon atoms may be attributable to their origins, with SCFA being primarily endogenous and playing a physiological role, and MCFA exogenously from the diet.
Mitochondrial Function Are Disturbed in the Presence of the Anticancer Drug, 3-Bromopyruvate

3-bromopuryvate (3-BP) is a compound with unique antitumor activity. It has a selective action against tumor cells that exhibit the Warburg effect. It has been proven that the action of 3-BP is pleiotropic: it acts on proteins, glycolytic enzymes, reduces the amount of ATP, induces the formation of ROS (reactive oxygen species), and induces nuclear DNA damage. Mitochondria are important organelles for the proper functioning of the cell. The production of cellular energy (ATP), the proper functioning of the respiratory chain, or participation in the production of amino acids are one of the many functions of mitochondria. Here, for the first time, we show on the yeast model that 3-BP acts in the eukaryotic cell also by influence on mitochondria and that agents inhibiting mitochondrial function can potentially be used in cancer therapy with 3-BP. We show that cells with functional mitochondria are more resistant to 3-BP than rho0 cells. Using an MTT assay (a colorimetric assay for assessing cell metabolic activity), we demonstrated that 3-BP decreased mitochondrial activity in yeast in a dose-dependent manner. 3-BP induces mitochondrial-dependent ROS generation which results in ∆sod2, ∆por1, or ∆gpx1 mutant sensitivity to 3-BP. Probably due to ROS mtDNA lesions rise during 3-BP treatment. Our findings may have a significant impact on the therapy with 3-BP.
Microbiological and physicochemical characteristics of Van herby cheese, a traditional Turkish dairy product

Herby cheese, made from sheep and/or cow milk and mixture of some herbs namely wild species of garlic, thyme, Ferula sp. , mint, etc., is a traditional Turkish cheese. In this research, 15 different herby cheeses were examined for microbiological, physicochemical and organoleptic properties. The mean log counts/g of the herby cheese for total aerobic mesophilic bacteria, psychrotrophs , lipolytic bacteria , enterobacteriaceae , coliforms , proteolytic organisms, Staphylococcus aureus, enterococci and yeasts and moulds were analysed. The means of lactic acid bacteria (LAB) counts obtained from MRS and M17 agar plates were 5.17′2.07 and 4.72′2.01, respectively. Isolates of LAB were identified as Lactobacillus plantarum, L. caseissp. casei, L. brevis, Pediococcus pentosaceus, P. acidilactic, Entemcoccus faecalis and E. faecium. L. plantarum, L. casei and P. pentosaceus were the most frequently found. The means of total solid (TS)%, pH value, acidity%, fat%, fat/TS%, total nitrogen (TN)%, TN/TS%, protein%, water-soluble nitrogen (WSN)%, WSN/TS%, WSN/TN%, NaCl%, NaCl/TS%, ripening index% and herbs% were determined, and the α s -casein, β-casein and other casein levels were analyzed.
Contemporary Analysis of Electronic Frailty Measurement in Older Adults with Multiple Myeloma Treated in the National US Veterans Affairs Healthcare System

Simple Summary Geriatric and frailty assessment are recommended for all older adults with cancer undergoing systemic therapy, but assessments remain difficult to scale. The aim of this study was to use an electronic frailty index based on data from administrative claims and electronic health records—the Veterans Affairs Frailty Index (VA-FI-10)—to estimate frailty and its impact on older United States (US) military veterans treated for multiple myeloma (MM) throughout the national VA Healthcare System. We found frailty to be prevalent and strongly associated with mortality and hospitalizations—independently of age, race, and MM stage. We also showed that changing the way in which the VA-FI-10 is measured affects its classification of frailty for individual veterans but not its association with mortality. These findings support the VA-FI-10’s use in research investigating outcomes in frail veterans treated with contemporary MM therapies. We provide further insights into the VA-FI-10’s potential use in clinical practice. Abstract Electronic frailty indices based on data from administrative claims and electronic health records can be used to estimate frailty in large populations of older adults with cancer where direct frailty measures are lacking. The objective of this study was to use the electronic Veterans Affairs Frailty Index (VA-FI-10)—developed and validated to measure frailty in the national United States (US) VA Healthcare System—to estimate the prevalence and impact of frailty in older US veterans newly treated for multiple myeloma (MM) with contemporary therapies. We designed a retrospective cohort study of 4924 transplant-ineligible veterans aged ≥ 65 years initiating MM therapy within VA from 2004 to 2017. Initial MM therapy was measured using inpatient and outpatient treatment codes from pharmacy data in the VA Corporate Data Warehouse. In total, 3477 veterans (70.6%) were classified as frail (VA-FI-10 > 0.2), with 1510 (30.7%) mildly frail (VA-FI-10 > 0.2–0.3), 1105 (22.4%) moderately frail (VA-FI-10 > 0.3–0.4), and 862 (17.5%) severely frail (VA-FI-10 > 0.4). Survival and time to hospitalization decreased with increasing VA-FI-10 severity (log-rank p-value < 0.001); the VA-FI-10 predicted mortality and hospitalizations independently of age, sociodemographic variables, and measures of disease risk. Varying data sources and assessment periods reclassified frailty severity for a substantial portion of veterans but did not substantially affect VA-FI-10’s association with mortality. Our study supports use of the VA-FI-10 in future research involving older veterans with MM and provides insights into its potential use in identifying frailty in clinical practice.