GeNeCK: a web server for gene network construction and visualization.

Background: Reverse engineering approaches to infer gene regulatory networks using computational methods are of great importance to annotate gene functionality and identify hub genes. Although various statistical algorithms have been proposed, development of computational tools to integrate results from different methods and user-friendly online tools is still lagging.

Results: We developed a web server that efficiently constructs gene networks from expression data.

Jagged1 is Clinically Prognostic and Promotes Invasion of Glioma-Initiating Cells by Activating NF-κB(p65) Signaling.

Background/aims: Jagged1 is the ligands of the Notch signaling and has been shown to promote glioma-initiating cells (GICs) in glioblastoma. The role of Jagged1 in GICs invasion and underlying molecular mechanisms remain unclear.

Methods: Survival data from R2 genomics analysis, the Cancer Genome Atlas (TCGA), the Chinese Glioma Genome Atlas (CGGA) and visualization platform database were used to evaluate the effects of Jagged1 on overall patient survival.

Transcriptome-based gene expression profiling of diploid radish (Raphanus sativus L.) and the corresponding autotetraploid.

Polyploidy is an important evolutionary factor in most land plant lineages which possess more than two complete sets of chromosomes. Radish (Raphanus sativus L.) is an economically annual/biennial root vegetable crop worldwide.

LCE: an open web portal to explore gene expression and clinical associations in lung cancer.

We constructed a lung cancer-specific database housing expression data and clinical data from over 6700 patients in 56 studies. Expression data from 23 genome-wide platforms were carefully processed and quality controlled, whereas clinical data were standardized and rigorously curated. Empowered by this lung cancer database, we created an open access web resource-the Lung Cancer Explorer (LCE), which enables researchers and clinicians to explore these data and perform analyses.

Use of Hematocrit for Short-Term Prognosis of Patients with Traumatic Brain Injury After Decompressive Craniectomy.

Objective: To discuss the effects of the hematocrit (Hct) in patients with traumatic brain injury after decompressive craniectomy (DC).

Methods: Demographic data, inspection and treatment procedures, and 30-day prognosis were obtained for 158 patients with head injury who underwent unilateral DC in our hospital between January 2013 and June 2018. Uni- and multivariate logistic regression was applied to analyze independent risk factors for 30-day outcome.

Isolation, purification and identification of two new alkaloids metabolites from marine-derived sp. FIM06025.

Chemical investigation of a marine-derived actinomycete strain sp. FIM06025 isolated from a marine sponge sample collected from the East China Sea, resulted in the discovery of two new alkaloids, (2-(hydroxymethyl)-3-(2-(hydroxymethyl)-3-methylaziridin-1-yl) (2-hydroxyphenyl) methanone () and 2-(1-hydroxyethyl)-3,4-dihydrobenzo [] [1,4]oxazepin-5()-one (). The structures of compounds and were determined by the detailed analysis of 1D, 2D NMR and HR-TOF-MS data, along with literature data analysis.

Asymmetric Synthesis of the C15⁻C32 Fragment of Alotamide and Determination of the Relative Stereochemistry.

Alotamide is a cyclic depsipetide isolated from a marine cyanobacterium and possesses a unique activation of calcium influx in murine cerebrocortical neurons (EC 4.18 µM). Due to its limited source, the three stereocenters (C19, C28, and C30) in its polyketide fragment remain undetermined.

Immune dysregulation in cancer patients developing immune-related adverse events.

Background: Up to 40% of cancer patients on immune checkpoint inhibitors develop clinically significant immune-related adverse events (irAEs). The role of host immune status and function in predisposing patients to the development of irAEs remains unknown.

Methods: Sera from 65 patients receiving immune checkpoint inhibitors and 13 healthy controls were evaluated for 40 cytokines at pre-treatment, after 2-3 weeks and after 6 weeks and analysed for correlation with the development of irAEs.

Autophagy suppresses self-renewal ability and tumorigenicity of glioma-initiating cells and promotes Notch1 degradation.

Autophagy is a vital process that involves degradation of long-lived proteins and dysfunctional organelles and contributes to cellular metabolism. Glioma-initiating cells (GICs) have the ability to self-renew, differentiate into heterogeneous types of tumor cells, and sustain tumorigenicity; thus, GICs lead to tumor recurrence. Accumulating evidence indicates that autophagy can induce stem cell differentiation and increase the lethality of temozolomide against GICs.

Phase 1 study of ARQ 761, a β-lapachone analogue that promotes NQO1-mediated programmed cancer cell necrosis.

Background: NAD(P)H:quinone oxidoreductase 1 (NQO1) is a two-electron oxidoreductase expressed in multiple tumour types. ARQ 761 is a β-lapachone (β-lap) analogue that exploits the unique elevation of NQO1 found in solid tumours to cause tumour-specific cell death.

Methods: We performed a 3+3 dose escalation study of 3 schedules (weekly, every other week, 2/3 weeks) of ARQ 761 in patients with refractory advanced solid tumours.

Comparative proteomic analysis provides insight into a complex regulatory network of taproot formation in radish ( L.).

The fleshy taproot of radish is an important storage organ determining its yield and quality. Taproot thickening is a complex developmental process in radish. However, the molecular mechanisms governing this process remain unclear at the proteome level.

DIGREM: an integrated web-based platform for detecting effective multi-drug combinations.

Motivation: Synergistic drug combinations are a promising approach to achieve a desirable therapeutic effect in complex diseases through the multi-target mechanism. However, in vivo screening of all possible multi-drug combinations remains cost-prohibitive. An effective and robust computational model to predict drug synergy in silico will greatly facilitate this process.

Validation of the 12-gene Predictive Signature for Adjuvant Chemotherapy Response in Lung Cancer.

Purpose: Response to adjuvant chemotherapy after tumor resection varies widely among patients with non-small cell lung cancer (NSCLC); therefore, it is of clinical importance to prospectively predict who will benefit from adjuvant chemotherapy before starting the treatment. The goal of this study is to validate a 12-gene adjuvant chemotherapy predictive signature developed from a previous study using a clinical-grade assay.

Experimental Design: We developed a clinical-grade assay for formalin-fixed, paraffin-embedded (FFPE) samples using the NanoString nCounter platform to measure the mRNA expression of the previously published 12-gene set.

Anti-inflammatory furostanol saponins from the rhizomes of Smilax china L.

Seven new furostanol saponins (1-7), chongrenosides A-G, were isolated from the rhizomes of Smilax china L., together with nine known furostanol saponins (8-16). The structures of the new furostanol saponins (1-7) were elucidated by extensive spectroscopic data analyses (1D and 2D NMR, HRESIMS) and chemical evidence.

A Bayesian hierarchical model for analyzing methylated RNA immunoprecipitation sequencing data.

Background: The recently emerged technology of methylated RNA immunoprecipitation sequencing (MeRIP-seq) sheds light on the study of RNA epigenetics. This new bioinformatics question calls for effective and robust peaking calling algorithms to detect mRNA methylation sites from MeRIP-seq data.

Methods: We propose a Bayesian hierarchical model to detect methylation sites from MeRIP-seq data.

NKCC1 promotes EMT-like process in GBM via RhoA and Rac1 signaling pathways.

Glioblastoma is the most common and lethal primary intracranial tumor. As the key regulator of tumor cell volume, sodium-potassium-chloride cotransporter 1 (NKCC1) expression increases along with the malignancy of the glioma, and NKCC1 has been implicated in glioblastoma invasion. However, little is known about the role of NKCC1 in the epithelial-mesenchymal transition-like process in gliomas.

Kub5-Hera Deficiency Promotes "BRCAness" and Vulnerability to PARP Inhibition in BRCA-proficient Breast Cancers.

Purpose: Identification of novel strategies to expand the use of PARP inhibitors beyond BRCA deficiency is of great interest in personalized medicine. Here, we investigated the unannotated role of Kub5-Hera (K-H) in homologous recombination (HR) repair and its potential clinical significance in targeted cancer therapy.

Experimental Design: Functional characterization of K-H alterations on HR repair of double-strand breaks (DSB) were assessed by targeted gene silencing, plasmid reporter assays, immunofluorescence, and Western blots.

An Effective Capillary Valve Based on Micro-hole Array for Microfluidic Systems.

With the development of microfluidic systems for portable devices where the capillary force as the driving force drove the liquid in a microchannel. An effective capillary microvalve based on a micro-hole array is proposed in this paper for the purpose of good performance, and programmable control, and easy-to-fabricate. The Wenzel model was used to slow down the velocity of fluid flow.

NIR-II nanoprobes in-vivo assembly to improve image-guided surgery for metastatic ovarian cancer.

Local recurrence is a common cause of treatment failure for patients with solid tumors. Tumor-specific intraoperative fluorescence imaging may improve staging and debulking efforts in cytoreductive surgery and, thereby improve prognosis. Here, we report in vivo assembly of the second near-infrared window (NIR-II) emitting downconversion nanoparticles (DCNPs) modified with DNA and targeting peptides to improve the image-guided surgery for metastatic ovarian cancer.

Segmental Characteristics of Main Thoracic Curves in Patients with Severe Adolescent Idiopathic Scoliosis.

Objective: Segmental flexibility in adolescent idiopathic scoliosis is crucial for the development of nonfusion and osteotomy technology. However, only global curve flexibility has been assessed in previous studies. Knowledge about segmental characteristics is absent.

Glucocorticoid-induced CREB activation and myostatin expression in C2C12 myotubes involves phosphodiesterase-3/4 signaling.

Muscle atrophy in metabolic conditions like chronic kidney disease (CKD) and diabetes are associated with glucocorticoid production, dysfunctional insulin/Akt/FoxO3 signaling and increased myostatin expression. We recently found that CREB, a transcription factor proposed to regulate myostatin expression, is highly phosphorylated in some wasting conditions. Based on a novel Akt-PDE3/4 signaling paradigm, we hypothesized that reduced Akt signaling contributes to CREB activation and myostatin expression.

Simultaneous Determination of Inorganic Cations and Anions in Microchip Electrophoresis Using High-voltage Relays.

A new and simple method for the simultaneous determination of cations and anions by microchip electrophoresis with capacitively coupled contactless conductivity detection (ME-CD) is described. The best analytical performance was found by applying a sinusoidal wave with 800 kHz frequency and 20 V amplitude. An optimized background electrolyte (BGE) composed of 20 mM His/MES and 0.

Comprehensive analysis of lung cancer pathology images to discover tumor shape and boundary features that predict survival outcome.

Pathology images capture tumor histomorphological details in high resolution. However, manual detection and characterization of tumor regions in pathology images is labor intensive and subjective. Using a deep convolutional neural network (CNN), we developed an automated tumor region recognition system for lung cancer pathology images.

Co-benefits of climate mitigation on air quality and human health in Asian countries.

Climate change mitigation involves reducing fossil fuel consumption and greenhouse gas emissions, which is expensive, particularly under stringent mitigation targets. The co-benefits of reducing air pollutants and improving human health are often ignored, but can play significant roles in decision-making. In this study, we quantified the co-benefits of climate change mitigation on ambient air quality and human health in both physical and monetary terms with a particular focus on Asia, where air quality will likely be degraded in the next few decades if mitigation measures are not undertaken.

Tuning the Photoinduced Electron Transfer in a Zr-MOF: Toward Solid-State Fluorescent Molecular Switch and Turn-On Sensor.

The immobilization of fluorescent photoinduced electron transfer (PET) switches/sensors into solid state, which usually cannot maintain their identical properties in solution, has remained a big challenge. Herein, a water-stable anthracene and maleimide appended zirconium-based-metal-organic framework (Zr-MOF; UiO-68-An/Ma) is reported. Unlike the regular intramolecular "fluorophore-spacer-receptor" format, the separated immobilization of fluorescent (anthracene) and acceptor (maleimide) groups into the framework of a multivariate MOF can also favor a pseudo-intramolecular fluorescent PET process, resulting in UiO-68-An/Ma with very weak fluorescence.