Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi-omics subtyping pipeline for chronic obstructive pulmonary disease

Chronic Obstructive Pulmonary Disease (COPD) is the third leading cause of mortality in the United States; however, COPD has heterogeneous clinical phenotypes. This is the first large scale attempt which uses transcriptomics, proteomics, and metabolomics (multi-omics) to determine whether there are molecularly defined clusters with distinct clinical phenotypes that may underlie the clinical heterogeneity. Subjects included 3,278 subjects from the COPDGene cohort with at least one of the following profiles: whole blood transcriptomes (2,650 subjects); plasma proteomes (1,013 subjects); and plasma metabolomes (1,136 subjects). 489 subjects had all three contemporaneous -omics profiles. Autoencoder embeddings were performed individually for each -omics dataset. Embeddings underwent subspace clustering using MineClus, either individually by -omics or combined, followed by recursive feature selection based on Support Vector Machines. Clusters were tested for associations with clinical variables. Optimal single -omics clustering typically resulted in two clusters. Although there was overlap for individual -omics cluster membership, each -omics cluster tended to be defined by unique molecular pathways. For example, prominent molecular features of the metabolome-based clustering included sphingomyelin, while key molecular features of the transcriptome-based clusters were related to immune and bacterial responses. We also found that when we integrated the -omics data at a later stage, we identified subtypes that varied based on age, severity of disease, in addition to diffusing capacity of the lungs for carbon monoxide, and precent on atrial fibrillation. In contrast, when we integrated the -omics data at an earlier stage by treating all data sets equally, there were no clinical differences between subtypes. Similar to clinical clustering, which has revealed multiple heterogenous clinical phenotypes, we show that transcriptomics, proteomics, and metabolomics tend to define clusters of COPD patients with different clinical characteristics. Thus, integrating these different -omics data sets affords additional insight into the molecular nature of COPD and its heterogeneity.
Patients’ knowledge of diabetes foot complications and self-management practices in Ghana: A phenomenological study

Background The prevalence of diabetes is increasing in low and middle-income countries (LMICs) and over two-thirds of these are not diagnosed. Consequently, diabetes complications usually exist at the time of diagnosis. Foot ulcers is a leading cause of disability and mortality among diabetes patients. Purpose To assess the knowledge and experiences of adult patients with Diabetes on diabetes complications and self-management practices with emphasis on foot care. Methodology This applied phenomenological study design. Twenty patients attending Diabetes clinics were purposively sampled from two hospitals in Ghana. Face-to-face semi-structured interviews were conducted to evaluate patient’s understanding of diabetes and self-management practices. The interviews were audio-taped, transcribed, and analysed to generate themes using the constant comparison method. Results Three-quarters of the participants in the study correctly defined diabetes as high blood glucose levels, but few knew the risk factors and complications of diabetes. Stroke and Hypertension were the most popular complications known, whiles diabetes foot complications were the least known. Almost all participants showed awareness of dietary self-management practices, but few had limited knowledge in foot care practices. Conclusion Diabetes education in LMICs should promote self-management practices, especially foot care and clear dietary guidelines. There is also opportunity to invest in specialist diabetes training for healthcare providers and increase community-based care for people living with diabetes in Ghana.
Posterior Reversible Encephalopathy Occurring During Treatment With Palbociclib

Palbociclib (Ibrance™) has been marketed since 2015 for patients with metastatic hormone-receptor-positive breast cancer. We report here the case of a patient who presented with a posterior reversible encephalopathy syndrome (PRES) during treatment with this new targeted therapy. The 67-year-old woman presented prodromal headaches followed by occurrences of two episodes of generalized convulsive seizures. The brain MRI revealed a bilateral, globally symmetrical, sub-cortical parietooccipital fluid-attenuated inversion recovery (FLAIR) hypersignal of the white matter. The patient recovered after palbociclib discontinuation with no further neurological signs. A follow-up MRI performed one month upon palbociclib discontinuation showed a decrease in the FLAIR signal abnormalities. Altogether, the clinical presentation was consistent with PRES. This case report aims to encourage physicians whom patients are treated with cyclin-dependent kinase 4/6 inhibitors to cautiously monitor symptoms suggesting PRES in contexts known to promote its occurrence such as that of arterial hypertension, immunosuppression, and/or autoimmune disease. PRES should be considered in the event of seizure, headache, and/or visual disturbances.
Comparison Prophylactic Effects of Gargling Different Doses of Ketamine on Attenuating Postoperative Sore Throat: A Single-Blind Randomized Controlled Trial

Context: Postoperative sore throat (POST) is a common annoying problem following endotracheal (ET) intubation. Aims: Comparing the impact of low and high doses of ketamine gargle on lowering POST incidence and severity. Settings and Design: 96 patients selected for septoplasty surgery under general anesthesia were investigated through a single-blind randomized controlled trial. Methods: This study was performed on three equal groups. Group K and G gargled 50 and 100 mg ketamine, respectively, solved in normal saline and group C gargled pure normal saline for 30 s at 5 min before tracheal intubation. POST severity measured immediately after the entrance to the postanesthetic care unit (PACU) and then 2 h, 4 h, 8 h, and 24 h after operation. Statistical Analysis Used: Collected data were analyzed by the Chi-square test, Mann-Whitney test, Kruskal-Wallis test, one-way analysis of variance (ANOVA) and Friedman test using SPSS version 20. Results: POST incidence and severity in group C were significantly higher than both K and G groups at all times. Although significant differences between low and high doses of ketamine were acknowledged at 8 h post-operation, 100 mg ketamine could attenuate POST severity further than 50 mg at all times. Conclusions: It seems that 100 mg outperformed 50 mg ketamine without rising complications and dissatisfaction for subjects. So, it gives us a powerful reason to suggest gargling 100 mg ketamine for lessening POST incidence and severity.
Amniotic membrane conditioned medium (AMCM) reduces inflammatory response on human limbal myofibroblast, and the potential role of lumican

Purpose Viral infections such as herpetic keratitis (HSK) activate the innate immune response in the cornea triggering opacity and loss of vision. This condition is performed mainly by myofibroblasts that exacerbate secretion of inflammatory cytokines. Amniotic membrane transplantation (AMT) reduces ocular opacity and scarring inhibiting secretion of inflammatory cytokines and proliferation of myofibroblasts. We previously reported that the amniotic membrane (AM) favors an anti-inflammatory microenvironment inhibiting the secretion of inflammatory cytokines, expression of innate immune receptors, and translocation of nuclear NF-κB on human limbal myofibroblasts (HLMs). The aim of the present study was to determine whether the soluble factors of the AM decrease the immune response of HLMs stimulated with polyinosinic-polycytidylic acid sodium salt (poly I:C). Methods The AM was incubated in Dulbecco's modified eagle medium (DMEM)/F12, and the supernatant was collected to obtain amniotic membrane conditioned medium (AMCM). HLMs were isolated from cadaveric sclera-corneal rims. HLMs were cultured in DMEM/F12 or AMCM and stimulated or not with poly I:C (10 µg/ml) for 12 h to analyze synthesis of CCL2, CCL5, CXCL10, MDA5, RIG-1, and TLR3 or for 2 h to analyze translocation of nuclear NF-kB, IRF3, and IRF7. The proteins contained on AMCM were analyzed by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), and the acquired peptide ions were analyzed with the Mascot program using both National Center for Biotechnology Information (NCBI) and expressed sequence tag (EST) databases. Results AMCM downregulated the mRNA levels of CCL2, CCL5, CXCL10, MDA5, RIG-1, and TLR3. In addition, AMCM decreased secretion of CCL2, CCL5, and CXCL10 and translocation of nuclear NF-κB. Interestingly, AMCM increased translocation of nuclear IRF3 and synthesis and secretion of type I IFN-β. We also identified small leucine-rich proteoglycan lumican in the AMCM. The administration of rh-lumican to poly I:C–stimulated HLMs reduced the mRNA levels of CCL2, CCL5, and CXCL10. Conclusions These results suggest that the AM can trigger an anti-inflammatory response on HLMs through soluble factors, and that lumican could play an important role in these effects.
Icariin, an Up-and-Coming Bioactive Compound Against Neurological Diseases: Network Pharmacology-Based Study and Literature Review

Abstract Icariin is a biologically active substance in Epimedii herba that is used for the treatment of neurologic disorders. However, a comprehensive analysis of the molecular mechanisms of icariin is lacking. In this review, we present a brief history of the use of icariin for medicinal purposes; describe the active chemical components of Epimedii herba; and examine the evidence from experimental studies that have uncovered molecular targets of icariin in different diseases. We also constructed a protein–protein interaction network and carried out Gene Ontology and Kyoto Encyclopedia of Genes and Genomes functional enrichment analyses to predict the therapeutic actions of icariin in nervous system diseases including Alzheimer disease, Parkinson disease, ischemic stroke, depressive disorder, multiple sclerosis, glioblastoma, and hereditary spastic paraplegias. The results of our analyses can guide future studies on the application of icariin to the treatment of neurologic disorders.
Functional Status of Pancreatic α and β Cells in Type 2 Diabetes Mellitus Patients with Different Plasma Triglyceride Levels: A Retrospective Analysis

Objective To investigate the functional status of pancreatic α and β cells in Type 2 diabetes mellitus (T2DM) patients with different plasma triglyceride (TG) levels. TG levels can be prognostic markers for T2DM. Methods A total of 328 patients with T2DM were divided into three groups according to different TG levels: the TGL group: TG < 1.7 mmol/L; TGM group: 1.7 mmol/L ≤ TG < 2.3 mmol/L; and TGH group: TG ≥ 2.3 mmol/L. An oral glucose tolerance test (OGTT), insulin release test, and glucagon release test were performed in each patient. The changes of glucagon, glucagon/insulin ratio, early insulin secretion index (ΔI30/ΔG30), and area under the insulin curve (AUCI) were compared among each group. Also, the correlations between glucagon and pancreatic β-cell function, glycosylated hemoglobin (HbA1c), and other indices were analyzed. Results With the increase of TG, the fasting and postprandial glucagon levels, the glucagon/insulin ratio, and the area under the glucagon curve (AUCG) presented an increasing trend. The homeostasis model assessment of insulin resistance (HOMA–IR) of the TGH group was significantly increased compared to the TGL and TGM groups. In addition to the increase in TG levels, the insulin sensitivity index (ISI), homeostasis model assessment for β-cell function index (HOMA-β), ΔI30/ΔG30, and AUCI displayed a reducing trend. Glucagon was negatively correlated with ΔI30/ΔG30, high-density lipoprotein (HDL), HOMA-β, body mass index (BMI), ISI, and AUCI (P < 0.05) and positively correlated with fasting blood glucose (FPG), AUCG, HOMA-IR, HbA1c, duration, TG, low-density lipoprotein (LDL), and total cholesterol (TC) (P < 0.05). Conclusion Hypertriglyceridemia aggravated the dysfunction of pancreatic α and β cells. A reasonable control of the TG level makes it easier for blood glucose to reach the standard.
Dietary inclusion of glucose oxidase supplementation to corn-wheat-based diet enhance growth performance, nutrient digestibility, blood profile of lactating sows

Abstract The objective of this study is to investigate the effect of dietary glucose oxidase (GOx) supplementation on the reproductive performance, litter performance, total tract digestibility, and blood profile of lactating sows fed corn-wheat-based diet. A total of twenty multiparous sows (Landrace × Yorkshire) were allocated into one of four treatments with five replicates per treatment. The dietary treatments were as follows: CON (Basal diet), GO1 (basal diet + 200 U GOx/kg), GO2 (basal diet + 300 U GOx/kg), GO3 (basal diet + 400 U Gox/kg). Dietary GOx supplementation did not affect lactating sow’s reproduction performance as well as body weight, backfat thickness, and body condition score during pre and post farrowing, and at weaning (p > 0.05). However, after farrowing to weaning period lactating sow’s fed GOx supplement has linearly (p = 0.0196) decreased the bodyweight loss. While, there were no effects (p > 0.05) observed on sows backfat thickness loss, average daily feed intake, and estrus interval among treatment groups. Dietary supplementation of GOx has linearly improved the body weight gain (p = 0.049) and average daily gain (p = 0.040) of suckling piglets. The total tract digestibility of dry matter and nitrogen was linearly increased with the graded level of GOx supplement. Also, a linear effect was observed on the glucose and superoxide dismutase of blood profile with the dietary inclusion of GOx. In summary, our finding indicates that the dietary inclusion of GOx supplement with corn-wheat-based diet had a beneficial effect on the nutrient digestibility and blood profile of lactating sows and improved the growth performance of suckling piglets.
Short-Term Effects of a Novel Eye Mask Producing Heat and Vibration for the Treatment of Meibomian Gland Dysfunction: A Pilot Study

Purpose To investigate the short-term effects on tear film parameters and ocular symptoms of a novel eye mask producing heat and vibration developed for the treatment of dry eye disease owing to meibomian gland dysfunction (MGD). Methods This is a pilot study including the first 20 consecutive patients (6 males, 14 females; mean age 52.4 ± 16.8 years) who were treated with a novel eye mask producing heat (42°) and vibration (up to 20 Hz) (Activa, SBS Sistemi, Turin, Italy) for 15 minutes. The treatment incorporates 2 phases in the following chronological order: 5 minutes of heating (phase I); 10 minutes of combination of heating and vibration (phase II). Noninvasive ocular surface examination was carried out before (T0) and 30 minutes after the mask session (T1) by means of Idra (SBS Sistemi, Turin, Italy) for the measurement of noninvasive break-up time (NIBUT) and lipid layer thickness (LLT). Patients' satisfaction after treatment was ascertained by asking the patients whether they perceived improvement from their baseline symptoms according to a 5-grade scale: none = 0; trace = 1; mild = 2; moderate = 3; high = 4. Results All patients completed regularly the mask session and no device-related adverse events were noted. NIBUT improved significantly from T0 to T1 (from 7.2 ± 1.8 s to 8.1 ± 2.1; P = 0.014). In parallel, also LLT improved from from T0 to T1 (72.5 ± 13.9 nm to 83.1 ± 16.1; P = 0.016). Seven patients (35% of the total) had a moderate satisfaction (grade 3) while 13 patients (65%) had a high satisfaction (grade 4) with treatment. Conclusions This eye mask represents a novel well tolerated tool in the armamentarium of MGD treatments. Thirty minutes after the session, NIBUT and LLT increased significantly; furthermore, all patients reported an improvement of discomfort symptoms with a moderate to high satisfaction with treatment.
Kimchi cabbage (Brassica rapa L.) by-products treated with calcium oxide and alkaline hydrogen peroxide as feed ingredient for Holstein steers

Abstract This study aimed to investigate the effects of Kimchi cabbage by-products either treated or untreated with calcium oxide (CaO) and alkaline hydrogen peroxide (AHP) as substitutional ingredient of total mixed ration (TMR) on in vitro fermentation, in situ disappearance and growth performance of Holstein steers. Cannulated Holstein (600 ± 47 kg) was used for both the in vitro and in situ experiments. The treatments used were TMR only (CON), TMR + 30% Kimchi cabbage by-products fresh matter (FM) basis (TC), TMR + 30% Kimchi cabbage by-products FM basis + 5% CaO FM basis (TCC), and TMR + 30% Kimchi cabbage by-products FM basis + 5% CaO FM basis + 3.22% AHP FM basis (TCCA). For in vivo experiment, thirty-four Holstein steers (273 ± 45 kg) were subjected to a 150-day feeding trial, divided into two groups: CON and TC. In the in vitro experiment, pH of TCCA was greatest (p < 0.05) among other treatments at all incubation times. Ammonia nitrogen and volatile fatty acid concentrations were not significantly different for each treatment. However, butyrate was greater (p < 0.05) in TCC and CON than in both TC and TCCA. During in situ experiment, the dry matter (DM) disappearance was greatest (p < 0.05) in TCCA among other treatments. Also, disappearance of neutral detergent fiber (NDF) and acid detergent fiber (ADF) were observed greatest (p > 0.05) in TCCA treatment. In the in vivo experiment, average daily gain (ADG) did not differ between CON and TC. In blood profile analysis, alanine aminotransferase, aspartate aminotransferase, glucose, total cholesterol, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and total protein concentration were not significantly different between treatments. But, creatinine concentration was greater (p < 0.05) in TC than in CON. Overall results suggest that Kimchi cabbage by-products either treated or untreated with CaO and AHP can be used as substitutional ingredient in TMR for Holstein steers.
Twenty years review of probiotic meta-analyses articles: Effects on disease prevention and treatment

The study of the probiotic effect in the prevention or treatment of diseases has long attracted the attention of many researchers. Here, we collected close to 300 meta-analysis articles for 20 years, investigating the effect of probiotics in the prevention and treatment of diseases. The goal of this study is to provide an overview of all meta-analysis articles of the effects of probiotics on various human diseases. For this purpose, different online databases, Pubmed, ScienceDirect, and Google Scholar, were searched with the keywords "probiotics" + "disease" + "meta-analysis" in the title, abstract, and keywords. Papers studied and categorized and investigated in order to present valuable insights for researchers in the field. Some of main categories are based on publication year, publishing journals, gender, age, effect type, disease type, contradicting reports and etc. According to the results, most meta-analyses indicated probiotics were 79% effective in preventing or treating the diseases. Some articles have also reported no positive effects, but there is not any paper in our study confirming the detrimental influence of probiotic effect on human health. For the future works, Cochrane reviews, meta-analysis including dozens of articles (as e.g. for NEC and AAD) may be investigated.
Associations between dietary fatty acid patterns and cognitive function in the Hispanic Community Health Study/Study of Latinos

Abstract Our objective was to quantify the cross-sectional associations between dietary fatty acid (DFA) patterns and cognitive function among Hispanic/Latino adults. This study included data from 8942 participants of the Hispanic Community Health Study/Study of Latinos, a population-based cohort study (weighted age 56·2 years and proportion female 55·2 %). The National Cancer Institute method was used to estimate dietary intake from two 24-h recalls. We derived DFA patterns using principal component analysis with twenty-six fatty acid and total plant and animal MUFA input variables. Global cognitive function was calculated as the average z-score of four neurocognitive tests. Survey linear regression models included multiple potential confounders such as age, sex, education, depressive symptoms, physical activity, energy intake and CVD. DFA patterns were characterised by the consumption of long-chain SFA, animal-based MUFA and trans-fatty acids (factor 1); short to medium-chain SFA (factor 2); very-long-chain n-3 PUFA (factor 3); very-long-chain SFA and plant-based MUFA and PUFA (factor 4). Factor 2 was associated with greater scores for global cognitive function (β = 0·037 (sd 0·012)) and the Digit Symbol Substitution (DSS) (β = 0·56 (sd 0·17)), Brief Spanish English Verbal Learning-Sum (B-SEVLT) (β = 0·23 (sd 0·11)) and B-SEVLT-Recall (β = 0·11 (sd 0·05)) tests (P < 0·05 for all). Factors 1 (β = 0·04 (sd 0·01)) and 4 (β = 0·70 (sd 0·18)) were associated with the DSS test (P < 0·05 for all). The consumption of short to medium-chain SFA may be associated with higher cognitive function among US-residing Hispanic/Latino adults. Prospective studies are necessary to confirm these findings.
Transcriptomics and Metabolomics Analyses Provide Novel Insights into Glucose-Induced Trophic Transition of the Marine Diatom Nitzschia laevis

Diatoms have important ecological roles and are natural sources of bioactive compounds. Nitzschia laevis is a member of marine diatoms that accumulates high-value products including fucoxanthin and eicosapentaenoic acid (EPA). In this study, physiological data showed that comparing to autotrophic growth, mixotrophic cultivation with glucose supplementation led to a decrease of chlorophyll and fucoxanthin content in N. laevis, and an increase of biomass density and EPA yield. To further examine the metabolic barriers for fucoxanthin and EPA biosynthesis, comparative transcriptomic and metabolome analyses were conducted, with a focus on the genes related to carotenoids biosynthesis and fatty acid metabolism. The results indicated that phytoene desaturase (PDS) and zeta-carotene isomerase (ZISO) could be the rate-limiting enzymes in carotenoid biosynthesis. The transcription regulation of 3-ketoacyl-CoA synthase (KCS) and elongation of very long chain fatty acids protein (EVOVL) are important contributors associated with polyunsaturated fatty acids (PUFAs) accumulation. Furthermore, we also investigated the glucose-associated regulatory genes using weighted gene co-expression network analysis, and identified potential hub genes linked with cell cycle, carbohydrate metabolism, purine biosynthesis, and lipid metabolism. This study offers a high-quality transcriptome resource for N. laevis and provides a molecular framework for further metabolic engineering studies on fucoxanthin and EPA production.