Role of long non-coding RNA in inflammatory bowel disease.

Inflammatory bowel disease (IBD) is a group of recurrent chronic inflammatory diseases, including Crohn's disease (CD) and ulcerative colitis (UC). Although IBD has been extensively studied for decades, its cause and pathogenesis remain unclear. Existing research suggests that IBD may be the result of an interaction between genetic factors, environmental factors and the gut microbiome. IBD is closely related to non-coding RNAs (ncRNAs). NcRNAs are composed of microRNA(miRNA), long non-coding RNA(lnc RNA) and circular RNA(circ RNA). Compared with miRNA, the role of lnc RNA in IBD has been little studied. Lnc RNA is an RNA molecule that regulates gene expression and regulates a variety of molecular pathways involved in the pathbiology of IBD. Targeting IBD-associated lnc RNAs may promote personalized treatment of IBD and have therapeutic value for IBD patients. Therefore, this review summarized the effects of lnc RNA on the intestinal epithelial barrier, inflammatory response and immune homeostasis in IBD, and summarized the potential of lnc RNA as a biomarker of IBD and as a predictor of therapeutic response to IBD in the future.

Resolving the dynamic properties of entangled linear polymers in non-equilibrium coarse grain simulation with a priori scaling factors.

The molecular weight of polymers can influence the material properties, but the molecular weight at the experiment level sometimes can be a huge burden for property prediction with full-atomic simulations. The traditional bottom-up coarse grain (CG) simulation can reduce the computation cost. However, the dynamic properties predicted by the CG simulation can deviate from the full-atomic simulation result. Usually, in CG simulations, the diffusion is faster and the viscosity and modulus are much lower. The fast dynamics in CG are usually solved by a posteriori scaling on time, temperature, or potential modifications, which usually have poor transferability to other non-fitted physical properties because of a lack of fundamental physics. In this work, a priori scaling factors were calculated by the loss of degrees of freedom and implemented in the iterative Boltzmann inversion. According to the simulation results on 3 different CG levels at different temperatures and loading rates, such a priori scaling factors can help in reproducing some dynamic properties of polycaprolactone in CG simulation more accurately, such as heat capacity, Young's modulus, and viscosity, while maintaining the accuracy in the structural distribution prediction. The transferability of entropy-enthalpy compensation and a dissipative particle dynamics thermostat is also presented for comparison. The proposed method reveals the huge potential for developing customized CG thermostats and offers a simple way to rebuild multiphysics CG models for polymers with good transferability.

Analysis of the vibrational characteristics of diamane nanosheet based on the Kirchhoff plate model and atomistic simulations.

Single layer diamond-diamane, has been reported with excellent mechanical properties. In this work, molecular dynamics (MD) simulation and Kirchhoff plate model are utilized to investigate the vibrational characteristics of diamane sheets. The mechanical parameters of diamane sheets, including bending stiffness, Young's modulus, Poisson's ratio and coefficient of thermal expansion, are calibrated by using MD simulations. The natural frequencies and corresponding modal shapes of the diamane sheets predicted by the Kirchhoff plate model agree well with that obtained from the MD simulations. It is found that the edges exert marginal effect on the modal shapes when free boundary conditions are applied. Additionally, the Kirchhoff plate model considering the thermal expansion provides reasonable prediction for the natural frequencies of the diamane sheets with all boundary clamped under varying temperatures. This study offers valuable insights into the vibrational properties of diamane sheets, from both a simulation and theoretical standpoint. The findings would be beneficial for the design of nanoscale mechanical resonators utilizing these novel carbon materials.

Trastuzumab resistance in HER2-positive breast cancer: Mechanisms, emerging biomarkers and targeting agents.

Trastuzumab is a standard molecular targeted therapy for human epidermal growth factor receptor 2(HER2) -positive breast cancer, which can significantly improve the survival of patients with this molecular subtype of breast cancer. However, the clinical problem of onset or secondary resistance to trastuzumab has limited its efficacy. Therefore, it is very important to explore the mechanism of trastuzumab resistance and formulate countermeasures. Our study described the underlying molecular mechanism of trastuzumab resistance including ERBB2 mutations and nuclear localization, transcriptional and post-translational alterations of ERBB2, over-activation of bypass signaling pathways activation and so on. Then summarize the potential emerging predicting biomarkers and therapeutic strategies for trastuzumab resistance, in order to provide research direction for reversing trastuzumab resistance.

Performing Data Mining And Integrative Analysis Of Biomarker in Breast Cancer Using Multiple Publicly Accessible Databases.

In recent years, emerging databases were designed to lower the barriers for approaching the intricate cancer genomic datasets, thereby, facilitating investigators to analyze and interpret genes, samples and clinical data across different types of cancer. Herein, we describe a practical operation procedure, taking ID1 (Inhibitor of DNA binding proteins 1) as an example, to characterize the expression patterns of biomarker and survival predictors of breast cancer based on pooled clinical datasets derived from online accessible databases, including ONCOMINE, bcGenExMiner v4.0 (Breast cancer gene-expression miner v4.0), GOBO (Gene expression-based Outcome for Breast cancer Online), HPA (The human protein atlas), and Kaplan-Meier plotter. The analysis began with querying the expression pattern of the gene of interest (e.g., ID1) in cancerous samples vs. normal samples. Then, the correlation analysis between ID1 and clinicopathological characteristics in breast cancer was performed. Next, the expression profiles of ID1 was stratified according to different subgroups. Finally, the association between ID1 expression and survival outcome was analyzed. The operation procedure simplifies the concept to integrate multidimensional data types at the gene level from different databases and test hypotheses regarding recurrence and genomic context of gene alteration events in breast cancer. This method can improve the credibility and representativeness of the conclusions, thereby, present informative perspective on a gene of interest.

General existence of flexural mode doublets in nanowires targeting vectorial sensing applications.

Nanowires (NWs) are one of the fundamental building blocks for nanoscale devices, and have been frequently utilized as mechanical resonators. Earlier studies show that ultra-sensitive vectorial sensing toolkits can be fabricated by changing the flexural mode of NWs to oscillation doublets along two orthogonal directions. Based on in silico studies and the Timoshenko beam theory, this work finds that the dual orthogonal flexural mode of NWs can be effectively controlled through the proper selection of their growth direction. It is found that metallic NWs with a directional-independent shear modulus possess a single flexural mode. However, NWs with a directional-dependent shear modulus naturally exhibit flexural mode doublets, which do not disappear even with increasing slenderness ratio. Further studies show that such a feature generally exists in other NWs, such as Si NWs. Mimicking a pendulum configuration as used in NW-based scanning force microscopy, the cantilevered 110 Si NW demonstrates zeptogram mass resolution and a force sensitivity down to the order of 10-24 N Hz-1/2 (yN Hz-1/2) in both transverse directions. The findings in this work open up a new and facile avenue to fabricate 2D vectorial force sensors, which could enable ultra-sensitive and novel detection devices/systems for 2D effects, such as the anisotropy strength of atomic bonds.

The synthesis of quaternary ammonium salts from ammonium salts and dialkyl carbonate.

Quaternary ammonium salts were synthesized from ammonium salts and dialkyl carbonates over an ionic liquid catalyst 1-ethyl-3-methylimidazolium bromide.