Unusual Hydrophobic Property of Blue Fluorescent Amino Acid 4-Cyanotryptophan.

It is a common belief that the negative heat capacity change (Δ) associated with protein folding, which is a manifestation of the hydrophobic effect, results from a decrease in the solvent accessible hydrophobic surface area. Herein, we investigate the conformational energy landscape and dynamics of a tetrapeptide composed of two glycine and two 4-cyanotryptophan residues using time-resolved fluorescence spectroscopy, molecular dynamics simulations, and density functional theory calculations and find that, contrary to this expectation, the hydrophobic association of two 4-cyanotryptophan side chains leads to a positive Δ (approximately 543 J K mol). Furthermore, we find that promoting one of the 4-cyanotryptophans to its excited electronic state strengthens this self-association.

Function of unconventional T cells in oral lichen planus revealed by single-cell RNA sequencing.

Objective: We intended to map the single-cell profile of OLP, explore the molecular characteristics of unconventional T cells in OLP tissues.

Methods: Buccal mucosa samples from OLP patients and healthy individuals were used to prepare single-cell suspension. Single-cell RNA sequencing was used to analyze the proportion of all the cells, and the molecular characteristics of unconventional T cells.

Recent Progress in Janus Nano-Objects with Asymmetric Polymer Brushes.

Over the past few decades, Janus materials have drawn much interest owing to the combination of two different functionalities on the opposite sides. Janus nano-objects (JNOs) with asymmetric polymer brushes are one unique material of them, which consist of a polymeric or inorganic core and asymmetric polymer chains coated on the core. Combining the properties of nanomaterials, asymmetric structures and flexible polymer brushes, hairy JNOs have shown great potential in interfacial compatibilization, interfacial catalysis, oil-water separation and drug delivery.

A comparative study on laparoscopic and open surgical approaches for perforated peptic ulcer repair: efficacy and outcomes analysis.

Purpose: This study aimed to compare the clinical outcomes of the clinical outcomes of laparoscopic and open sutures for peptic ulcer perforation (PPU).

Materials And Methods: PubMed, EMBASE, and Cochrane Library databases were searched for eligible studies from inception to March 31, 2023. Odds ratios (OR) and 95% confidence intervals (Cl) were also calculated.

Impact of preoperative type 2 diabetes mellitus on the outcomes of patients with gastric cancer following gastrectomy: Analysis of 834 patients using propensity score matching.

The purpose of the current study was to compare the outcomes of patients with gastric cancer (GC) between the type 2 diabetes mellitus (T2DM) group and the non-T2DM group. The PubMed, Embase and Cochrane Library databases were searched from inception to March 8, 2022, to identify propensity score matching (PSM) studies that analyzed the effect of T2DM on the outcomes of patients with GC. Total complications, overall survival (OS), disease-free survival (DFS) and cancer-specific survival (CSS) were compared between the T2DM group and the non-T2DM group.

MACC: a visual interactive knowledgebase of metabolite-associated cell communications.

Metabolite-associated cell communications play critical roles in maintaining the normal biological function of human through coordinating cells, organs and physiological systems. Though substantial information of MACCs has been continuously reported, no relevant database has become available so far. To address this gap, we here developed the first knowledgebase (MACC), to comprehensively describe human metabolite-associated cell communications through curation of experimental literatures.

SEPPA-mAb: spatial epitope prediction of protein antigens for mAbs.

Identifying the exact epitope positions for a monoclonal antibody (mAb) is of critical importance yet highly challenging to the Ab design of biomedical research. Based on previous versions of SEPPA 3.0, we present SEPPA-mAb for the above purpose with high accuracy and low false positive rate (FPR), suitable for both experimental and modelled structures.

Function of normal oral mucosa revealed by single-cell RNA sequencing.

The functions of oral mucosa include barrier, sensation, and secretion. The barrier protection function is particularly important, which includes physical barrier and immunological barrier. Few studies have revealed the function of oral mucosa by displaying the map of normal oral mucosal cells from the perspective of single cells.

MetNC: Predicting Metabolites for Natural Compounds.

Natural compounds (NCs) undergo complicated biotransformation to produce diverse forms of metabolites dynamically, many of which are of high medicinal value. Predicting the profiles of chemical products may help to narrow down possible candidates, yet current computational methods for predicting biotransformation largely focus on synthetic compounds. Here, we proposed a method of MetNC, a tailor-made method for NC biotransformation prediction, after exploring the overall patterns of NC metabolism.

HIT 2.0: an enhanced platform for Herbal Ingredients' Targets.

Literature-described targets of herbal ingredients have been explored to facilitate the mechanistic study of herbs, as well as the new drug discovery. Though several databases provided similar information, the majority of them are limited to literatures before 2010 and need to be updated urgently. HIT 2.

Probing Synergistic Targets by Natural Compounds for Hepatocellular Carcinoma.

Background: Designing combination drugs for malignant cancers has been restricted due to the scarcity of synergy-medicated targets, while some natural compounds have demonstrated potential to enhance anticancer effects.

Methods: We here explored the feasibility of probing synergy-mediated targets by Berberine (BER) and Evodiamine (EVO) in hepatocellular carcinoma (HCC). Using the genomics-derived HCC signaling networks of compound treatment, NF-κB and c-JUN were inferred as key responding elements with transcriptional activity coinhibited during the synergistic cytotoxicity induction in BEL-7402 cells.

Rank-in: enabling integrative analysis across microarray and RNA-seq for cancer.

Though transcriptomics technologies evolve rapidly in the past decades, integrative analysis of mixed data between microarray and RNA-seq remains challenging due to the inherent variability difference between them. Here, Rank-In was proposed to correct the nonbiological effects across the two technologies, enabling freely blended data for consolidated analysis. Rank-In was rigorously validated via the public cell and tissue samples tested by both technologies.

H-RACS: a handy tool to rank anti-cancer synergistic drugs.

Though promising, identifying synergistic combinations from a large pool of candidate drugs remains challenging for cancer treatment. Due to unclear mechanism and limited confirmed cases, only a few computational algorithms are able to predict drug synergy. Yet they normally require the drug-cell treatment results as an essential input, thus exclude the possibility to pre-screen those unexplored drugs without cell treatment profiling.

Detecting Prognosis Risk Biomarkers for Colon Cancer Through Multi-Omics-Based Prognostic Analysis and Target Regulation Simulation Modeling.

Background: Colon cancer is one of the most common health threats for humans since its high morbidity and mortality. Detecting potential prognosis risk biomarkers (PRBs) is essential for the improvement of therapeutic strategies and drug development. Currently, although an integrated prognostic analysis of multi-omics for colon cancer is insufficient, it has been reported to be valuable for improving PRBs' detection in other cancer types.

Reveal the Regulation Patterns of Prognosis-Related miRNAs and lncRNAs Across Solid Tumors in the Cancer Genome Atlas.

Background: The dysregulation of non-coding RNAs (ncRNAs) such as miRNAs and lncRNAs are associated with the pathogenesis and progression in multiple cancers including solid tumors. Comprehensive investigations of prognosis-related ncRNA markers could promote the development of therapeutic strategies for solid tumors, but rarely reported.

Methods: By taking advantage of The Cancer Genome Atlas (TCGA), pan-cancer prognosis analysis (PCPA) models were firstly constructed based on miRNA and lncRNA expression profiles of 8,450 samples in 19 solid tumors.

Comparative Network Pharmacology Analysis of Classical TCM Prescriptions for Chronic Liver Disease.

Chronic liver disease (CLD) has become a major global health problem while herb prescriptions are clinically observed with significant efficacy. Three classical Traditional Chinese Medicine (TCM) formulae, Yinchenhao Decoction (YCHT), Huangqi Decoction (HQT), and Yiguanjian (YGJ) have been widely applied in China to treat CLD, but no systematic study has yet been published to investigate their common and different mechanism of action (MOA). Partial limitation may own to deficiency of effective bioinformatics methods.

Study of Anti-Insomnia Mechanism for Suanzaoren Prescription.

Insomnia is a common and widespread sleeping disorder caused by various risk factors. Though beneficial, conventional treatments of insomnia have significant limitations. As an alternative treatment, Chinese herbal formula Suanzaoren prescription (SZRP), composed of Suanzaoren [seeds of var.

SEPPA 3.0-enhanced spatial epitope prediction enabling glycoprotein antigens.

B-cell epitope information is critical to immune therapy and vaccine design. Protein epitopes can be significantly affected by glycosylation, while no methods have considered this till now. Based on previous versions of Spatial Epitope Prediction of Protein Antigens (SEPPA), we here present an enhanced tool SEPPA 3.

DSab-origin: a novel IGHD sensitive VDJ mapping method and its application on antibody response after influenza vaccination.

Background: Functional antibody genes are often assembled by VDJ recombination and then diversified by somatic hypermutation. Identifying the combination of sourcing germline genes is critical to understand the process of antibody maturation, which may facilitate the diagnostics and rapid generation of human monoclonal antibodies in therapeutics. Despite of successful efforts in V and J fragment assignment, method in D segment tracing remains weak for immunoglobulin heavy diversity (IGHD).

Exploring the Mechanism of Flavonoids Through Systematic Bioinformatics Analysis.

Flavonoids are the largest class of plant polyphenols, with common structure of diphenylpropanes, consisting of two aromatic rings linked through three carbons and are abundant in both daily diets and medicinal plants. Fueled by the recognition of consuming flavonoids to get better health, researchers became interested in deciphering how flavonoids alter the functions of human body. Here, systematic studies were performed on 679 flavonoid compounds and 481 corresponding targets through bioinformatics analysis.

CE-BLAST makes it possible to compute antigenic similarity for newly emerging pathogens.

Major challenges in vaccine development include rapidly selecting or designing immunogens for raising cross-protective immunity against different intra- or inter-subtypic pathogens, especially for the newly emerging varieties. Here we propose a computational method, Conformational Epitope (CE)-BLAST, for calculating the antigenic similarity among different pathogens with stable and high performance, which is independent of the prior binding-assay information, unlike the currently available models that heavily rely on the historical experimental data. Tool validation incorporates influenza-related experimental data sufficient for stability and reliability determination.

Advances in computational approaches in identifying synergistic drug combinations.

Accumulated empirical clinical experience, supported by animal or cell line models, has initiated efforts of predicting synergistic combinatorial drugs with more-than-additive effect compared with the sum of the individual agents. Aiming to construct better computational models, this review started from the latest updated data resources of combinatorial drugs, then summarized the reported mechanism of the known synergistic combinations from aspects of drug molecular and pharmacological patterns, target network properties and compound functional annotation. Based on above, we focused on the main in silico strategies recently published, covering methods of molecular modeling, mathematical simulation, optimization of combinatorial targets and pattern-based statistical/learning model.

Diagnostic accuracy of transient elastography (FibroScan) in detection of esophageal varices in patients with cirrhosis: A meta-analysis.

Aim: To investigate the diagnostic accuracy of FibroScan (FS) in detecting esophageal varices (EV) in cirrhotic patients.

Methods: Through a systemic literature search of multiple databases, we reviewed 15 studies using endoscopy as a reference standard, with the data necessary to calculate pooled sensitivity (SEN) and specificity (SPE), positive and negative LR, diagnostic odds ratio (DOR) and area under receiver operating characteristics (AUROC). The quality of the studies was rated by the Quality Assessment of Diagnostic Accuracy studies-2 tool.

[Application of Bishop-Koop stoma in refractory congenital intestinal atresia].

Objective: To explore the feasibility and safety of Bishop-Koop stoma procedure in the treatment of neonates with refractory congenital intestinal atresia.

Methods: Clinical and follow-up data of 25 neonates with refractory congenital intestinal atresia undergoing Bishop-Koop stoma procedure in our center from January 2011 to December 2014 were retrospectively analyzed. Of 25 neonates, 13 (52%) were male, 12(48%) were female, the birth weight was 1600-3800 g (mean 2920 g), the age of admission was 10 hours to 20 days, and the age of operation was 1-58 d (mean 7 d).