Variation and evolution analysis of SARS-CoV-2 using self-game sequence optimization.

Introduction: The evolution of SARS-CoV-2 has precipitated the emergence of new mutant strains, some exhibiting enhanced transmissibility and immune evasion capabilities, thus escalating the infection risk and diminishing vaccine efficacy. Given the continuous impact of SARS-CoV-2 mutations on global public health, the economy, and society, a profound comprehension of potential variations is crucial to effectively mitigate the impact of viral evolution. Yet, this task still faces considerable challenges.

MMFSyn: A Multimodal Deep Learning Model for Predicting Anticancer Synergistic Drug Combination Effect.

Combination therapy aims to synergistically enhance efficacy or reduce toxic side effects and has widely been used in clinical practice. However, with the rapid increase in the types of drug combinations, identifying the synergistic relationships between drugs remains a highly challenging task. This paper proposes a novel deep learning model MMFSyn based on multimodal drug data combined with cell line features.

DGCPPISP: a PPI site prediction model based on dynamic graph convolutional network and two-stage transfer learning.

Background: Proteins play a pivotal role in the diverse array of biological processes, making the precise prediction of protein-protein interaction (PPI) sites critical to numerous disciplines including biology, medicine and pharmacy. While deep learning methods have progressively been implemented for the prediction of PPI sites within proteins, the task of enhancing their predictive performance remains an arduous challenge.

Results: In this paper, we propose a novel PPI site prediction model (DGCPPISP) based on a dynamic graph convolutional neural network and a two-stage transfer learning strategy.

A Facile Raman Spectroscopy Method for Online Monitoring of Crystal Plane Orientation of Favipiravir.

The efficiency of pharmacotherapy is significantly influenced by the crystal habit and polymorphic form of the drugs. Especially due to the anisotropy of different facets in crystalline material, crystal habit impacts the physicochemical properties and behaviors of a drug, which has been rarely reported. This paper describes a facile method for online monitoring of crystal plane orientation of favipiravir (T-705) by Raman spectroscopy.

AFTGAN: prediction of multi-type PPI based on attention free transformer and graph attention network.

Motivation: Protein-protein interaction (PPI) networks and transcriptional regulatory networks are critical in regulating cells and their signaling. A thorough understanding of PPIs can provide more insights into cellular physiology at normal and disease states. Although numerous methods have been proposed to predict PPIs, it is still challenging for interaction prediction between unknown proteins.

Identification of Specific Pathogen-Infected sRNA-Mediated Interactions between Turnip Yellows Virus and .

Virus infestation can seriously harm the host plant's growth and development. Turnip yellows virus (TuYV) infestation of host plants can cause symptoms, such as yellowing and curling of leaves and root chlorosis. However, the regulatory mechanisms by which TuYV affects host growth and development are unclear.

Drug Repositioning Based on the Enhanced Message Passing and Hypergraph Convolutional Networks.

Drug repositioning, an important method of drug development, is utilized to discover investigational drugs beyond the originally approved indications, expand the application scope of drugs, and reduce the cost of drug development. With the emergence of increasingly drug-disease-related biological networks, the challenge still remains to effectively fuse biological entity data and accurately achieve drug-disease repositioning. This paper proposes a new drug repositioning method named EMPHCN based on enhanced message passing and hypergraph convolutional networks (HGCN).

A new self-passivating template with the phosphorothioate strategy to effectively improve the detection limit and applicability of exponential amplification reaction.

Exponential amplification reaction (EXPAR) has attracted much attention due to its simple primers and high amplification efficiency, but its applications are hindered by severe non-specificity amplification. Convenient exogenous chemical modification methods modified the entire template while inhibiting both non-specific and specific amplification. In this paper, we proposed a new self-passivating template with the phosphorothioate strategy to effectively improve the detection limit and applicability of EXPAR.

Surface-enhanced Raman spectroscopy integrated with aligner mediated cleavage strategy for ultrasensitive and selective detection of methamphetamine.

New drugs and illicit synthesized mixtures detection at crime scenes is a great challenge for detection method, which requires anti-interference and ultrasensitive methods to detect methamphetamine (METH) in seized street samples and biological fluids. Herein, we constructed a surface-enhanced Raman sensing method based on aligner mediated cleavage (AMC) of nucleic acid for quantitative detection of METH for the first time. This method we proposed relied on AMC to achieve programmable sequence-specific cleavage of METH aptamer linked by gold nanoparticles (METH aptamer-Au NPs), the cleavage product-Au NPs conjugates (cleavage aptamer-Au NPs) would hybridize with complementary DNA (cDNA)-Au NPs, resulting in the aggregation of the Au NPs and concomitant plasmonic coupling effect.

Investigation of Solubility Behavior of Canagliflozin Hydrate Crystals Combining Crystallographic and Hirshfeld Surface Calculations.

Canagliflozin (CG) was a highly effective, selective and reversible inhibitor of sodium-dependent glucose co-transporter 2 developed for the treatment of type 2 diabetes mellitus. The crystal structure of CG monohydrate (CG-HO) was reported for the first time while CG hemihydrate (CG-Hemi) had been reported in our previous research. Solubility and dissolution rate results showed that the solubility of CG-Hemi was 1.

Bioinspired Brochosomes as Broadband and Omnidirectional Surface-Enhanced Raman Scattering Substrates.

Surface-enhanced Raman scattering (SERS) substrates capable of working under laser excitation in a broad wavelength range are highly desirable in diverse application fields. Here, we demonstrate that the bioinspired Ag brochosomes, hollow microscale particles with submicroscale pits, have broadband and omnidirectional SERS performance. The SERS performance of the Ag brochosomes under near-infrared laser excitation makes them promising for applications in biosensing fields, such as the sensitive detection of bacteria and bovine hemoglobin protein.

Circumventing silver oxidation induced performance degradation of silver surface-enhanced Raman scattering substrates.

Surface-enhanced Raman scattering (SERS) has been recognized as a promising sensing technique in biomedical/biosensing applications and analytical chemistry. Silver (Ag) nanostructures have the strongest SERS enhancement, but suffer from severe enhancement degradation induced by oxidation. Here, we introduce electrochemical reduction of silver oxide to produce Ag SERS substrates on request to partially circumvent the SERS enhancement degradation problem of Ag SERS substrates.

Quantitation of polymorphic impurity in entecavir polymorphic mixtures using powder X-ray diffractometry and Raman spectroscopy.

Entecavir was used for the treatment of chronic hepatitis B through inhibiting hepatitis B virus. The anhydrous form of entecavir (ENT-A) often appeared as impurity polymorph in the manufacturing process of entecavir monohydrate (ENT-H) such as granulation, drying and compression. Since different crystal forms might affect drug bioavailability and therapeutic effect, it was vital to control the ENT-A content of the drug product.

Silver Nanoparticle Generators: Silicon Dioxide Microspheres.

A green and simple approach has been developed to synthesize un-coated Ag nanoparticles (AgNPs) in situ on the surface of thiol-group-functionalized silica dioxide microspheres (TSMs) in the aqueous solution. As soon as the Ag ions attach onto the surface of TSMs, nucleation and growth of AgNPs can spontaneously complete within one minute without other reducing agents or capping agents. The main reason is that the self-assembled silane-layer formed by mercaptosilane molecules could reduce the Ag formation energy, transport electrons efficiently, improve the nucleation density, and protect AgNPs against oxidation.