Miracle-dz/UniFAR-FTUs huggingface dataset:
Clustering Analysis via Deep Generative Models With Mixture Models

Clustering is a fundamental problem that frequently arises in many fields, such as pattern recognition, data mining, and machine learning. Although various clustering algorithms have been developed in the past, traditional clustering algorithms with shallow structures cannot excavate the interdependence of complex data features in latent space. Recently, deep generative models, such as autoencoder (AE), variational AE (VAE), and generative adversarial network (GAN), have achieved remarkable success in many unsupervised applications thanks to their capabilities for learning promising latent representations from original data. In this work, first we propose a novel clustering approach based on both Wasserstein GAN with gradient penalty (WGAN-GP) and VAE with a Gaussian mixture prior. By combining the WGAN-GP with VAE, the generator of WGAN-GP is formulated by drawing samples from the probabilistic decoder of VAE. Moreover, to provide more robust clustering and generation performance when outliers are encountered in data, a variant of the proposed deep generative model is developed based on a Student’s-t mixture prior. The effectiveness of our deep generative models is validated though experiments on both clustering analysis and samples generation. Through the comparison with other state-of-art clustering approaches based on deep generative models, the proposed approach can provide more stable training of the model, improve the accuracy of clustering, and generate realistic samples.
Effect of Low Temperature and Seaweed Extracts on Flowering and Yield of Two Cucumber Cultivars (Cucumis sativus L.)

The experiment was conducted in a plastic house of the vegetable research field Horticulture Department, College of Agriculture, University of Dohuk, Iraq, to study the effect of seaweed extracts (seaforce and seamino) with concentrations (0.0, 1.5ml/L) for both extracts and exposure to low temperature (7±1) ο C for three durations (0, 5 and 10) days on the flowering and yield of two cucumber ( Cucumis sativus L.) cultivars. The extracts were sprayed three times on seven days intervals. Seeds were sown on February 22 th , 2011. The seedlings were exposed to low temperature after expansion of cotyledon leaves. The experiment was arranged in a factorial experiment within split-split plot in a randomized complete block design with four replicates. The results showed that treatment with both extracts significantly enhanced number of female flowers and fruit setting percentage. The dual interaction between factors (seaforce + seamino) + cultivar and (seaforce + seamino) + temperature exposure for (5) days were significant on flowering characters. The triple interaction (seaforce + seamino) + low temperature exposure for (5) days + Karol cultivar increased flowering characters, and for yield characters its showed that (seaforce + seamino) significantly increased cucumber yield (number of fruit per plant, fruit weight, yield per plant, yield.m 2 and total yield).
The hns Gene of Escherichia coli Is Transcriptionally Down-Regulated by (p)ppGpp

Second messenger nucleotides, such as guanosine penta- or tetra-phosphate, commonly referred to as (p)ppGpp, are powerful signaling molecules, used by all bacteria to fine-tune cellular metabolism in response to nutrient availability. Indeed, under nutritional starvation, accumulation of (p)ppGpp reduces cell growth, inhibits stable RNAs synthesis, and selectively up- or down- regulates the expression of a large number of genes. Here, we show that the E. coli hns promoter responds to intracellular level of (p)ppGpp. hns encodes the DNA binding protein H-NS, one of the major components of bacterial nucleoid. Currently, H-NS is viewed as a global regulator of transcription in an environment-dependent mode. Combining results from relA (ppGpp synthetase) and spoT (ppGpp synthetase/hydrolase) null mutants with those from an inducible plasmid encoded RelA system, we have found that hns expression is inversely correlated with the intracellular concentration of (p)ppGpp, particularly in exponential phase of growth. Furthermore, we have reproduced in an in vitro system the observed in vivo (p)ppGpp-mediated transcriptional repression of hns promoter. Electrophoretic mobility shift assays clearly demonstrated that this unusual nucleotide negatively affects the stability of RNA polymerase-hns promoter complex. Hence, these findings demonstrate that the hns promoter is subjected to an RNA polymerase-mediated down-regulation by increased intracellular levels of (p)ppGpp.
The Efficacy and Safety of Roxadustat for Anemia in Patients With Chronic Kidney Disease: A Meta-Analysis

Background: Chronic kidney disease (CKD) is a global public health problem, and anemia is a common complication in CKD patients. Roxadustat (FG-4592) is an oral hypoxia-inducible factor (HIF) stabilizer. Roxadustat has been shown in studies to keep up with and increase hemoglobin better than placebo or erythropoietin. The purpose of this meta-analysis was to assess the efficacy and safety of roxadustat. Methods: We searched CBM, CNKI, VIP, Wanfang Database, PubMed, Cochrane Library, Embase, and Web of Science for randomized controlled trials of roxadustat for the treatment of anemia in CKD patients. The papers were screened using rigorous criteria and their quality was assessed using the Cochrane 5.1. 0 assessment manual for randomized controlled trials (RCTs). RevMan 5.3 was used to extract and synthesize data for meta-analysis. Results: There were 8 RCTs (7 articles) in all, and 1,364 patients with chronic kidney disease anemia were involved. The overall quality of the studies included was satisfactory. The meta-analysis findings revealed that roxadustat can considerably enhance hemoglobin, transferrin, and total iron binding capacity (TIBC) in both dialysis-dependent (DD) and non-dialysis-dependent (NDD) patients: Hemoglobin (Hb): DD: [SMD = 0.23, 95% CI (0.01, 0.44), p = 0.04], NDD: [SMD = 2.08, 95% CI (1.23, 2.93) p < 0.000001]; transferrin: DD: [SMD = 0.78, 95% CI (0.24, 1.32), p = 0.004], NDD: [SMD = 1.37, 95% CI (0.76, 1.98), p < 0.0001]; TIBC: DD [SMD = 0.97, 95% CI (0.64, 1.29), p < 0.00001], NDD [SMD = 1.34, 95% CI (0.9, 1.78), p < 0.00001]. After roxadustat therapy, patients’ serum iron levels were considerably higher in the dialysis group than in the control group, but there was no significant change in the NDD group [SMD = 0.42, 95% CI (0.27, 0.57), p < 0.00001]. In the NDD group, hepcidin, ferritin, and transferrin saturation (TSAT) were significantly reduced after roxadustat treatment: Hepcidin [SMD = −1.59, 95% CI (−2.69, −0.49), p = 0.005], ferritin [SMD = −0.51, 95% CI (−0.72, 0.3) p < 0.00001], TSAT [SMD = −0.41, 95% CI (−0.62, 0.2), p < 0.0001]. In terms of safety, adverse events (AE) [SMD = 1.08, 95% CI (0.98, 1.18) p = 0.11] and serious adverse events (SAE) [SMD = 1.32, 95% CI (0.97, 1.9) p = 0.08] were not significantly different between the two groups. Conclusion: Roxadustat can improve anemia in NDD patients with chronic kidney disease, and its short-term safety was comparable to that of the comparison group.
Epigenetic Mechanisms of Plant Adaptation to Biotic and Abiotic Stresses

Unlike animals, plants are immobile and could not actively escape the effects of aggressive environmental factors, such as pathogenic microorganisms, insect pests, parasitic plants, extreme temperatures, drought, and many others. To counteract these unfavorable encounters, plants have evolved very high phenotypic plasticity. In a rapidly changing environment, adaptive phenotypic changes often occur in time frames that are too short for the natural selection of adaptive mutations. Probably, some kind of epigenetic variability underlines environmental adaptation in these cases. Indeed, isogenic plants often have quite variable phenotypes in different habitats. There are examples of successful “invasions” of relatively small and genetically homogenous plant populations into entirely new habitats. The unique capability of quick environmental adaptation appears to be due to a high tendency to transmit epigenetic changes between plant generations. Multiple studies show that epigenetic memory serves as a mechanism of plant adaptation to a rapidly changing environment and, in particular, to aggressive biotic and abiotic stresses. In wild nature, this mechanism underlies, to a very significant extent, plant capability to live in different habitats and endure drastic environmental changes. In agriculture, a deep understanding of this mechanism could serve to elaborate more effective and safe approaches to plant protection.
Processing of Polyester-Urethane Filament and Characterization of FFF 3D Printed Elastic Porous Structures with Potential in Cancellous Bone Tissue Engineering

This paper addresses the potential of self-made polyester-urethane filament as a candidate for Fused Filament Fabrication (FFF)-based 3D printing (3DP) in medical applications. Since the industry does not provide many ready-made solutions of medical-grade polyurethane filaments, we undertook research aimed at presenting the process of thermoplastic polyurethane (TPU) filament formation, detailed characteristics, and 3DP of specially designed elastic porous structures as candidates in cancellous tissue engineering. Additionally, we examined whether 3D printing affects the structure and thermal stability of the filament. According to the obtained results, the processing parameters leading to the formation of high-quality TPU filament (TPU_F) were captured. The results showed that TPU_F remains stable under the FFF 3DP conditions. The series of in vitro studies involving long- and short-term degradation (0.1 M phosphate-buffered saline (PBS); 5 M sodium hydroxide (NaOH)), cytotoxicity (ISO 10993:5) and bioactivity (simulated body fluid (SBF) incubation), showed that TPU printouts possessing degradability of long-term degradable tissue constructs, are biocompatible and susceptible to mineralization in terms of hydroxyapatite (HAp) formation during SBF exposure. The formation of HAp on the surface of the specially designed porous tissue structures (PTS) was confirmed by scanning electron microscope (SEM) and energy-dispersive X-ray spectroscopy (EDS) studies. The compression test of PTS showed that the samples were strengthened due to SBF exposure and deposited HAp on their surface. Moreover, the determined values of the tensile strength (~30 MPa), Young’s modulus (~0.2 GPa), and compression strength (~1.1 MPa) allowed pre-consideration of TPU_F for FFF 3DP of cancellous bone tissue structures.
Neutrophil/Lymphocyte Ratio as Predictor of Anastomotic Leak after Gastric Cancer Surgery

Introduction. Neutrophil/lymphocyte ratio (NLR) is known as a prognostic for the outcome of the patients with gastric cancer. As no definite risk marker for anastomotic leakage after gastric resection was identified, we investigated the possible role of NLR. Methods. Peripheral blood count for neutrophils and lymphocytes was done at the patient’s admission. We retrospectively evaluated 204 gastric cancer patients, who underwent gastric resection, comparing the values of NLR between the group of patients with anastomotic leakage and those without complications. Results. Using the ROC curve, we found the cutoff value of NLR, which permitted the comparison of the group with low NLR, presenting increased NLR. The cutoff value for NLR was 3.54. Between the two groups, we could observe statistically significant differences in developing fistula (p < 0.01) and complications leading to death (p < 0.025). The odds ratio for patients with NLR greater than 3.54 to develop anastomotic leak was 17.62, compared to those with lower NLR. Conclusion. Peripheral blood NLR proved to be a predictor for anastomotic leakage.
Combination of D-dimer and simplified pulmonary embolism severity index to improve prediction of hospital death in patients with acute pulmonary embolism

Objective To investigate whether the combination of D-dimer and simplified pulmonary embolism severity index (sPESI) could improve prediction of in-hospital death from pulmonary embolism (PE). Methods Patients with PE (n = 272) were divided into a surviving group (n = 249) and an in-hospital death group (n = 23). Results Compared with surviving patients, patients who died in hospital had significantly higher rates of hypotension and tachycardia, reduced SaO2 levels, elevated D-dimer and troponin T levels, higher sPESI scores, and were more likely to be classified as high risk. Elevated D-dimer levels and high sPESI scores were significantly associated with in-hospital death. Using thresholds for D-dimer and sPESI of 3.175 ng/mL and 1.5, respectively, the specificity for prediction of in-hospital death was 0.357 and 0.414, respectively, and the area under the receiver operating characteristic curve (AUC) was 0.665 and 0.668, respectively. When D-dimer and sPESI were considered together, the specificity for prediction of in-hospital death increased to 0.838 and the AUC increased to 0.74. Conclusions D-dimer and sPESI were associated with in-hospital death from PE. Considering D-dimer levels together with sPESI can significantly improve the specificity of predicting in-hospital death for patients with PE.
Effect of Different Enological Tannins on Oxygen Consumption, Phenolic Compounds, Color and Astringency Evolution of Aglianico Wine

Background: In the wine industry, in addition to condensed tannins of grape origin, other commercial tannins are commonly used. However, the influence of oxygen uptake related to different tannin additions during the post fermentative phase in wine has not been completely investigated. In this study, we evaluated the influence of four different commercial tannins (namely, condensed tannins, gallotannins, ellagitannins and tea tannins) during four saturation cycles. Method: Wine samples were added with four different tannin classes (30 g/hL) as to have 5 different experimental samples: control, gallotannins (GT), condensed tannins (CT), ellagitannins (ET), and tea tannins (TT). The chemical composition of the four commercially available tannin mixtures was defined by means of NMR and high-resolution mass spectrometry. After the addition of tannins, each wine sample was oxidized by air over four cycles of saturation. During the experiment oxygen consumption rate (OCR), sulfur dioxide consumption, acetaldehyde production, phenolic compounds, chromatic characteristics, astringency measured by the reactivity towards saliva proteins and astringency subqualities were evaluated. Results: The experiment lasted 52 days. The addition of tannins influenced the oxygen consumption on the 1st day of the saturation cycles and, in the case of TT, a higher total consumption of oxygen was also detected. Acetaldehyde increased during the experiment while the native anthocyanins decreased throughout the oxidation process. Conclusion: Wines added with tannins featured improved color intensities with respect to the control; the addition of TT, GT and ET slightly promoted the formation of short polymeric pigments; the astringency, determined before and at the end of the experiment, decreased in all the samples, including the control wine, and mostly in the ET and GT samples.
House Dust Mite Exposure Causes Increased Susceptibility of Nasal Epithelial Cells to Adenovirus Infection

Adenovirus (AdV) infections in the respiratory tract may cause asthma exacerbation and allergic predisposition, and the house dust mite (HDM) may aggravate virus-induced asthma exacerbations. However, the underlying mechanisms of whether and how AdV affects asthmatic patients remains unclear. To address this question, we investigated nasal epithelial cells (NAEPCs) derived from a pediatric exacerbation study cohort for experimental analyses. We analyzed twenty-one different green-fluorescent protein- and luciferase-tagged AdV types in submerged 2D and organotypic 3D cell culture models. Transduction experiments revealed robust transduction of AdV type 5 (AdV5) in NAEPCs, which was associated with an increased uptake of AdV5 in the presence of HDM. In healthy and asthmatic NAEPCs exposed to HDM before infection, we observed a time- and dose-dependent increase of AdV5 uptake associated with upregulation of entry receptors for AdV5. Furthermore, electron microscopic and histologic analyses of 3D cell cultures revealed an impairment of the respiratory cilia after HDM exposition. This ex vivo pilot study shows the impact of AdV infection and HDM exposition in a primary cell culture model for asthma.
LncRNA HOTAIRM1 promotes MDSC expansion and suppressive functions through up-regulating HOXA1 expression during latent HIV infection.

OBJECTIVE Myeloid-derived suppressor cells (MDSCs) contribute to HIV progression by impairing antiviral immunity; however, the mechanisms responsible for MDSC development during HIV infection are incompletely understood. HOX antisense intergenic RNA myeloid 1 (HOTAIRM1) is a long noncoding RNA (lncRNA) that plays a pivotal role in regulating myeloid cell development via targeting HOXA1. The role of HOTAIRM1-HOXA1 in the differentiation and functions of MDSCs during HIV infection remains unclear. METHODS In this study, we measured MDSC induction and suppressive functions by flow cytometry, RT-PCR, and co-culture experiments using CD33 myeloid cells derived from people living with HIV (PLHIV) on antiretroviral therapy (ART). We also manipulated the HOTAIRM1-HOXA1 axis in myeloid cells using knockdown and overexpression approaches. RESULTS We demonstrate that HOTAIRM1 and HOXA1 expressions are reciprocally upregulated and are responsible for increased levels of immunosuppressive molecules, such as arginase 1 (Arg1), inducible nitric oxide synthase (iNOS), signal transducer and activator of transcription 3 (STAT3), and reactive oxygen species (ROS), in CD33 myeloid cells derived from PLHIV on ART. We found that overexpression of HOTAIRM1 or HOXA1 in CD33 cells isolated from healthy individuals promoted the differentiation and suppressive functions of MDSCs, whereas silencing of HOTAIRM1 or HOXA1 expression in MDSCs derived from PLHIV significantly inhibited the frequency of MDSCs and expressions of the immunosuppressive molecules and reduced their immunosuppressive effects on T cells. CONCLUSION These results indicate that the HOTAIRM1-HOXA1 axis enhances differentiation and suppressive functions of MDSCs and could be a potential therapeutic target for immunomodulation during latent HIV infection.
Evaluation of Financial Conflicts of Interests Among Congress of Neurological Surgeon Guideline Authors.

Congress of Neurological Surgeon Guideline Authors Most professional medical societies sponsor clinical practice guidelines (CPGs) relevant to their clinical specialty. Previous studies report that physicians selected to serve as CPG authors have considerable industry relationships.1,2 In the field of neurosurgery, where evidence suggests that industryfunded neurosurgery trials are more likely to produce favorable results than non–industry-funded trials,3 the extent of financial conflict of interest (FCOI) among guideline authors remains unknown. In this investigation, we examined payments from medical device and pharmaceutical companies compiled in the Open Payments Database (OPD) to physicianauthors of the Congress of Neurological Surgery’s (CNS) internally produced and endorsed CPGs a year before and after the CPG publication date. We also identified the portion of undisclosed payments made to authors for medications and devices relevant to CPGs.
Therapeutic Implications for PDE2 and cGMP/cAMP Mediated Crosstalk in Cardiovascular Diseases

Phosphodiesterases (PDEs) are the principal superfamily of enzymes responsible for degrading the secondary messengers 3′,5′-cyclic nucleotides cAMP and cGMP. Their refined subcellular localization and substrate specificity contribute to finely regulate cAMP/cGMP gradients in various cellular microdomains. Redistribution of multiple signal compartmentalization components is often perceived under pathological conditions. Thereby PDEs have long been pursued as therapeutic targets in diverse disease conditions including neurological, metabolic, cancer and autoimmune disorders in addition to numerous cardiovascular diseases (CVDs). PDE2 is a unique member of the broad family of PDEs. In addition to its capability to hydrolyze both cAMP and cGMP, PDE2 is the sole isoform that may be allosterically activated by cGMP increasing its cAMP hydrolyzing activity. Within the cardiovascular system, PDE2 serves as an integral regulator for the crosstalk between cAMP/cGMP pathways and thereby may couple chronically adverse augmented cAMP signaling with cardioprotective cGMP signaling. This review provides a comprehensive overview of PDE2 regulatory functions in multiple cellular components within the cardiovascular system and also within various subcellular microdomains. Implications for PDE2- mediated crosstalk mechanisms in diverse cardiovascular pathologies are discussed highlighting the prospective use of PDE2 as a potential therapeutic target in cardiovascular disorders.
Rituximab as the treatment of pemphigus vulgaris in the COVID‐19 pandemic era: A narrative review

Pemphigus vulgaris (PV), an autoimmune blistering disease is treated with immunosuppressive medications. As the immunosuppressive effect of rituximab, the first‐line therapy of PV, lasts more than 6 months, many concerns have raised due to the ongoing novel coronavirus disease (COVID‐19) pandemic. With this background, our objective was to review the currently available literature as well as important websites for the evidence related to rituximab, PV and COVID‐19, adverse effects associated with drugs, and relevant guidelines. “PubMed” and “Google Scholar” database were systematically searched for retrieving all articles related to anti‐CD20 therapy in pemphigus vulgaris and COVID‐19 published up to 14 July 2020. A total of seven clinical studies are performed with anti‐CD20 therapy in COVID‐19, three of which are performed on pemphigus patients, and have shown concerns employing rituximab in patients with COVID‐19. Evidence for treating PV patients with rituximab in COVID‐19 pandemic is limited. Until sufficient evidence or guideline for pemphigus and COVID‐19 treatment is available, we advocate caution commencing rituximab in patients with pemphigus, due to the reported adverse outcomes.
NMR-Based Metabolomic Analysis and Microbial Composition of Soil Supporting Burkea africana Growth

Burkea africana is a leguminous tree used for medicinal purposes, growing in clusters, on soils impoverished from most nutrients. The study aimed to determine the factors responsible for successful reproduction and establishment of the B. africana trees in nature, as all efforts for commercial production has been proven unsuccessful. An investigation was carried out to determine the metabolomic profile, chemical composition, and microbial composition of the soils where B. africana grows (Burkea soil) versus the soil where it does not grow (non-Burkea soil). 1H-NMR metabolomic analysis showed different metabolites in the respective soils. Trehalose and betaine, as well as a choline-like and carnitine-like compound, were found to be in higher concentration in Burkea soils, whereas, acetate, lactate, and formate were concentrated in non-Burkea soils. Liquid Chromatography-Mass Spectrometry analysis revealed the presence of numerous amino acids such as aspartic acid and glutamine to be higher in Burkea soils. Since it was previously suggested that the soil microbial diversity is the major driver for establishment and survival of seedlings in nature, Deoxyribonucleic acid (DNA) was extracted and a BLAST analysis conducted for species identification. Penicillium species was found to be highly prevalent and discriminant between the two soils, associated with the Burkea soils. No differences in the bacterial composition of Burkea and non-Burkea soils were observed. The variances in fungal composition suggests that species supremacy play a role in development of B. africana trees and is responsible for creating a supporting environment for natural establishment and survival of seedlings.