PhosNetVis: A web-based tool for fast kinase-substrate enrichment analysis and interactive 2D/3D network visualizations of phosphoproteomics data.

Protein phosphorylation involves the reversible modification of a protein (substrate) residue by another protein (kinase). Liquid chromatography-mass spectrometry studies are rapidly generating massive protein phosphorylation datasets across multiple conditions. Researchers then must infer kinases responsible for changes in phosphosites of each substrate.

Enhanced antibacterial and genoprotective properties of nanoliposomal L. essential oil.

Nanoliposomes are drug delivery systems that improve bioavailability by encapsulating therapeutic agents. The main objective of this study was to investigate the effects of nanoliposomal (NL) formulation on enhancing the bioavailability of essential oil. The essential oil of (SHO) was encapsulated in nanoliposomes (SHNLs).

Comparison of Candida colonization in intensive care unit patients with and without COVID-19: First prospective cohort study from Turkey.

Candida species are the primary cause of fungal infections in intensive care units (ICUs). Despite the increasing prevalence of Candida-related infections, monitoring the progression of these infections from colonization in COVID-19 ICU patients lacks sufficient information. This study aims prospectively to compare 62 COVID-19 and 60 non-COVID-19 ICU patients from admission to discharge in terms of colonization development, rates, isolated Candida species, risk factors, and Candida infections during hospitalization.

Detection and characterization of the biofilm on the traditionally produced homemade apple vinegar.

yeasts are capable of forming biofilms during vinegar production and causing spoilage in various beverages. In addition, there exists a significant likelihood of encountering yeast contamination which can prevent vinegar production. The present study investigates the detection and characterization of the () biofilm on traditionally produced homemade apple vinegar.

Naples Prognostic Score and Clinical Outcomes in Pulmonary Arterial Hypertension Patients.

Objectives: Pulmonary arterial hypertension (PAH) is a specific form of pulmonary hypertension characterized by an increased mean pulmonary arterial pressure. Risk stratification is crucial in managing PAH, using various clinical, laboratory, and imaging parameters. The Naples prognostic score (NPS), incorporating nutritional and inflammatory markers, has demonstrated prognostic value in other conditions but not in PAH.

Whole-brain resting-state connectivity underlying impaired inhibitory control during early versus longer-term abstinence in cocaine addiction.

Lapses in inhibitory control have been linked to relapse in human drug addiction. Evidence suggests differences in inhibitory control depending on abstinence duration, but the underlying neural mechanisms remain unknown. We hypothesized that early abstinence (2-5 days) would be characterized by the strongest impairments of inhibitory control and most wide-spread deviations in resting-state functional connectivity of brain networks, while longer-term abstinence (>30 days) would be characterized by weaker impairments as compared to healthy controls.

Pulmonary Embolism Severity Index Predicts Adverse Events in Hospitalized COVID-19 Patients: A Retrospective Observational Study.

Objectives: Pulmonary embolism is one of the leading causes of death in patients with COVID-19. Autopsy findings showed that the incidence of thromboembolic events was higher than clinically suspected. In this study, the authors investigated the relationship between pulmonary embolism severity index (PESI) and simplified PESI (sPESI) on admission to the hospital, as well as adverse events in hospitalized COVID-19 patients without clinically documented venous and/or pulmonary embolism.

Acute Coronary Syndrome After Whole-Body Electrical Myostimulation.

Whole body electrical myostimulation (WB-EMS) is an alternative exercise training method. The effects of this exercise program on hemodynamics and coronary circulation have recently been investigated. However acute coronary syndrome associated with WB-EMS has not been reported before.

Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer.

We report a comprehensive proteogenomics analysis, including whole-genome sequencing, RNA sequencing, and proteomics and phosphoproteomics profiling, of 218 tumors across 7 histological types of childhood brain cancer: low-grade glioma (n = 93), ependymoma (32), high-grade glioma (25), medulloblastoma (22), ganglioglioma (18), craniopharyngioma (16), and atypical teratoid rhabdoid tumor (12). Proteomics data identify common biological themes that span histological boundaries, suggesting that treatments used for one histological type may be applied effectively to other tumors sharing similar proteomics features. Immune landscape characterization reveals diverse tumor microenvironments across and within diagnoses.

Synthesis and Anticancer and Antimicrobial Evaluation of Novel Ether-linked Derivatives of Ornidazole.

Objectives: Some novel 1-(2-methyl-5-nitro-1H-imidazol-1-yl)-3-(substituted phenoxy)propan-2-ol derivatives were designed and synthesized.

Materials And Methods: Compounds were obtained by refluxing ornidazole with the corresponding phenolic compounds in the presence of anhydrous KCO in acetonitrile.

Results: Following the structure elucidation, the antimicrobial activity and cytotoxic effects of compounds on K562 leukemia and NIH/3T3 mouse embryonic fibroblast cells were measured.

ProNetView-ccRCC: A Web-Based Portal to Interactively Explore Clear Cell Renal Cell Carcinoma Proteogenomics Networks.

To better understand the molecular basis of cancer, the NCI's Clinical Proteomics Tumor Analysis Consortium (CPTAC) has been performing comprehensive large-scale proteogenomic characterizations of multiple cancer types. Gene and protein regulatory networks are subsequently being derived based on these proteogenomic profiles, which serve as tools to gain systems-level understanding of the molecular regulatory factories underlying these diseases. On the other hand, it remains a challenge to effectively visualize and navigate the resulting network models, which capture higher order structures in the proteogenomic profiles.

Comprehensive Immunoprofiling of Pediatric Zika Reveals Key Role for Monocytes in the Acute Phase and No Effect of Prior Dengue Virus Infection.

Zika virus (ZIKV) is an emerging, mosquito-borne flavivirus responsible for recent epidemics across the Americas, and it is closely related to dengue virus (DENV). Here, we study samples from 46 DENV-naive and 43 DENV-immune patients with RT-PCR-confirmed ZIKV infection at early-acute, late-acute, and convalescent time points from our pediatric cohort study in Nicaragua. We analyze the samples via RNA sequencing (RNA-seq), CyTOF, and multiplex cytokine/chemokine Luminex to generate a comprehensive, innate immune profile during ZIKV infection.

Functional Evaluation of an Ectopic Supernumerary Kidney in Pelvis.

Background: Supernumerary kidney is an accessory organ with its own encapsulated parenchyma, blood vessels and ureters, either separated from the normal kidney or connected to it via fibrous tissue and ectopic kidney is a migration abnormality of the kidney. Here, we have evaluated a rare case of the supernumerary and ectopic kidney with DMSA, MAG3 and also CT fusion of the images.

Methods: The absolute divided renal function was calculated for each kidney by DMSA.

Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma.

To elucidate the deregulated functional modules that drive clear cell renal cell carcinoma (ccRCC), we performed comprehensive genomic, epigenomic, transcriptomic, proteomic, and phosphoproteomic characterization of treatment-naive ccRCC and paired normal adjacent tissue samples. Genomic analyses identified a distinct molecular subgroup associated with genomic instability. Integration of proteogenomic measurements uniquely identified protein dysregulation of cellular mechanisms impacted by genomic alterations, including oxidative phosphorylation-related metabolism, protein translation processes, and phospho-signaling modules.

The effect of hemodialysis adequacy on ventricular repolarization in end-stage kidney disease.

Objective: Ventricular repolarization (VR) markers may predict ventricular arrhythmias and cardiac arrest. The aim of this study was to investigate the acute effects of a hemodialysis (HD) session and HD adequacy on VR markers in HD patients.

Methods: This cross-sectional study was conducted at 2 university hospitals with 83 patients and VR markers were measured before and after an HD session: QT, QTc, QT minimum, QT maximum, dispersion of QT (QTd), T-peak to T-end (Tp-e) interval, and Tp-e/QT.

Effect of Vitamin D and parathyroid hormone levels on the coronary slow-flow phenomenon.

Background: The presence of vitamin D, and parathyroid hormone receptors has been demonstrated in the vascular endothelium. Variations in vitamin D, and parathyroid hormone levels may affect coronary flow and cause the coronary slow-flow phenomenon (CSF).

Methods: We enrolled 93 patients who had undergone coronary angiography and had near-normal coronary arteries.

Propofol with and without Midazolam for Diagnostic Upper Gastrointestinal Endoscopies in Children.

Purpose: Various publications on the use of sedation and anesthesia for diagnostic procedures in children have demonstrated that no ideal agent is available. Although propofol has been widely used for sedation during esophagogastroduodenoscopy in children, adverse events including hypoxia and hypotension, are concerns in propofol-based sedation. Propofol is used in combination with other sedatives in order to reduce potential complications.

Antibacterial and photodynamic effects of some plant extracts for cavity disinfection.

Background: In current dental treatments, with the aim of a preventive approach,it is argued that removing only the infected layer of dentin is sufficient for cavity preparation. However it is impossible to be sure that the infected layer was completely removed. In addition, the cause of secondary caries and post operative sensitivities has been reported as residual bacteria in some studies.

Determination of antimicrobial and antiviral properties of IR3535.

Insect repellent is a substance directly applied to skin or clothing in order to repel flies, mosquitoes, ticks etc. IR3535 or Ethyl butylacetylaminopropionate (EBAAP) is a relatively new repellent which is classified as a biopesticide due to exceptional skin tolerance and overall safety. The repellency against various insect and ticks, and the low toxicity of IR3535 are well acknowledged.

Comprehensive functional genomic resource and integrative model for the human brain.

Despite progress in defining genetic risk for psychiatric disorders, their molecular mechanisms remain elusive. Addressing this, the PsychENCODE Consortium has generated a comprehensive online resource for the adult brain across 1866 individuals. The PsychENCODE resource contains ~79,000 brain-active enhancers, sets of Hi-C linkages, and topologically associating domains; single-cell expression profiles for many cell types; expression quantitative-trait loci (QTLs); and further QTLs associated with chromatin, splicing, and cell-type proportions.