HERB 2.0: an updated database integrating clinical and experimental evidence for traditional Chinese medicine.

Clinical trials and meta-analyses are considered high-level medical evidence with solid credibility. However, such clinical evidence for traditional Chinese medicine (TCM) is scattered, requiring a unified entrance to navigate all available evaluations on TCM therapies under modern standards. Besides, novel experimental evidence has continuously accumulated for TCM since the publication of HERB 1.

Predicting transcriptional responses to novel chemical perturbations using deep generative model for drug discovery.

Understanding transcriptional responses to chemical perturbations is central to drug discovery, but exhaustive experimental screening of disease-compound combinations is unfeasible. To overcome this limitation, here we introduce PRnet, a perturbation-conditioned deep generative model that predicts transcriptional responses to novel chemical perturbations that have never experimentally perturbed at bulk and single-cell levels. Evaluations indicate that PRnet outperforms alternative methods in predicting responses across novel compounds, pathways, and cell lines.

Electrospinning-derived transition metal/carbon nanofiber composites as electrocatalysts for Zn-air batteries.

The sluggish kinetics of the oxygen reduction reaction (ORR) and the oxygen evolution reaction (OER) significantly impede the broader implementation of Zn-air batteries (ZABs), underscoring the necessity for advanced high-efficiency materials to catalyze these electrochemical processes. Recent advancements have highlighted the potential of transition metal/carbon nanofiber (TM/CNF) composite materials, synthesized electrospinning technology, due to their expansive surface area, profusion of active sites, and elevated catalytic efficacy. This review comprehensively examines the structural characteristics of TM/CNFs, with a particular emphasis on the pivotal role of electrospinning technology in fabricating diverse structural configurations.

Structural and compositional analysis of MOF-derived carbon nanomaterials for the oxygen reduction reaction.

The development of low-cost and efficient cathode catalysts is crucial for the advancement of fuel cells, as the oxygen reduction reaction (ORR) on the cathode is constrained by expensive commercial Pt/C catalysts and a significant energy barrier. Metal-organic frameworks (MOFs) are considered excellent precursors for synthesizing carbon nanomaterials due to their simple synthesis, rich structure and composition. MOF-derived carbon nanomaterials (MDCNM) inherit the morphology of their precursors at low dimensional scales, providing abundant edge defects, larger specific surface area, and excellent electron transport paths.

Metal oxide nanomaterials based electrochemical and optical biosensors for biomedical applications: Recent advances and future prospectives.

The amalgamation of nanostructures with modern electrochemical and optical techniques gave rise to interesting devices, so-called biosensors. A biosensor is an analytical tool that incorporates various biomolecules with an appropriate physicochemical transducer. Over the past few years, metal oxide nanomaterials (MONMs) have significantly stimulated biosensing research due to their desired functionalities, versatile chemical stability, and low cost along with their unique optical, catalytic, electrical, and adsorption properties that provide an attractive platform for linking the biomolecules, for example, antibodies, nucleic acids, enzymes, and receptor proteins as sensing elements with the transducer for the detection of signals or signal amplifications.

TREAT: Therapeutic RNAs exploration inspired by artificial intelligence technology.

Recent advances in RNA engineering have enabled the development of RNA-based therapeutics for a broad spectrum of applications. Developing RNA therapeutics start with targeted RNA screening and move to the drug design and optimization. However, existing target screening tools ignore noncoding RNAs and their disease-relevant regulatory relationships.

A review on the toxicity of silver nanoparticles against different biosystems.

Despite significant progress made in the past two decades, silver nanoparticles (AgNPs) have not yet made it to the clinical trials. In addition, they showed both positive and negative effects in their toxicity from unicellular organism to well-developed multi-organ system, for example, rat. Although it is generally accepted that capped (bio)molecules have synergistic bioactivities and diminish the toxicity of metallic Ag core, convincing evidence is completely lacking.

Electrospun Nanofibers of Polycaprolactone/Collagen as a Sustained-Release Drug Delivery System for Artemisinin.

The application of artemisinin (ART) in the treatment of malaria has been restricted to a certain degree due to its inherent limitations, such as short half-life, poor solubility, limited bioavailability, and re-crystallization. Electrospun nanofibers loaded with ART provide an excellent solution to these limitations and yield sustained drug release as well as inhibition of drug re-crystallization. In this study, ART-loaded polycaprolactone (PCL)/collagen (Col) nanofibers with different proportions of polymers were prepared.

KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis.

Gene set enrichment (GSE) analysis plays an essential role in extracting biological insight from genome-scale experiments. ORA (overrepresentation analysis), FCS (functional class scoring), and PT (pathway topology) approaches are three generations of GSE methods along the timeline of development. Previous versions of KOBAS provided services based on just the ORA method.

Electrospun Nanofibers of Natural and Synthetic Polymers as Artificial Extracellular Matrix for Tissue Engineering.

Many types of polymer nanofibers have been introduced as artificial extracellular matrices. Their controllable properties, such as wettability, surface charge, transparency, elasticity, porosity and surface to volume proportion, have attracted much attention. Moreover, functionalizing polymers with other bioactive components could enable the engineering of microenvironments to host cells for regenerative medical applications.

FangNet: Mining herb hidden knowledge from TCM clinical effective formulas using structure network algorithm.

The use of herbs to treat various human diseases has been recorded for thousands of years. In Asia's current medical system, numerous herbal formulas have been repeatedly verified to confirm their effectiveness in different periods, which is a great resource for drug innovation and discovery. Through the mining of these clinical effective formulas by network pharmacology and bioinformatics analysis, important biologically active ingredients derived from these natural products might be discovered.

HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine.

Pharmacotranscriptomics has become a powerful approach for evaluating the therapeutic efficacy of drugs and discovering new drug targets. Recently, studies of traditional Chinese medicine (TCM) have increasingly turned to high-throughput transcriptomic screens for molecular effects of herbs/ingredients. And numerous studies have examined gene targets for herbs/ingredients, and link herbs/ingredients to various modern diseases.

Formulation Strategies for Folate-Targeted Liposomes and Their Biomedical Applications.

The folate receptor (FR) is a tumor-associated antigen that can bind with folic acid (FA) and its conjugates with high affinity and ingests the bound molecules inside the cell via the endocytic mechanism. A wide variety of payloads can be delivered to FR-overexpressed cells using folate as the ligand, ranging from small drug molecules to large DNA-containing macromolecules. A broad range of folate attached liposomes have been proven to be highly effective as the targeted delivery system.

Antibacterial Properties of Graphene-Based Nanomaterials.

Bacteria mediated infections may cause various acute or chronic illnesses and antibiotic resistance in pathogenic bacteria has become a serious health problem around the world due to their excessive use or misuse. Replacement of existing antibacterial agents with a novel and efficient alternative is the immediate demand to alleviate this problem. Graphene-based materials have been exquisitely studied because of their remarkable bactericidal activity on a wide range of bacteria.

Atomic Force Microscopy Based Tip-Enhanced Raman Spectroscopy in Biology.

Most biological phenomena occur at the nanometer scale, which is not accessible by the conventional optical techniques because of the optical diffraction limitation. Tip-enhanced Raman spectroscopy (TERS), one of the burgeoning probing techniques, not only can provide the topography characterization with high resolution, but also can deliver the chemical or molecular information of a sample beyond the optical diffraction limitation. Therefore, it has been widely used in various structural analyses pertaining to materials science, tissue engineering, biological processes and so on.

Ethanol Diffusion on Rutile TiO2(110) Mediated by H Adatoms.

We have studied the diffusion of ethanol on rutile TiO2(110)-(1 × 1) by high-resolution scanning tunneling microscopy (STM) measurements and density functional theory (DFT) calculations. Time-lapsed STM images recorded at ∼200 K revealed the diffusion of ethanol molecules both parallel and perpendicular to the rows of surface Ti atoms. The diffusion of ethanol molecules perpendicular to the rows of surface Ti atoms was found to be mediated by H adatoms in the rows of bridge-bonded O (Obr) atoms similarly to previous results obtained for water monomers.

The importance of bulk Ti3+ defects in the oxygen chemistry on titania surfaces.

The role of bulk defects in the oxygen chemistry on reduced rutile TiO(2)(110)-(1 × 1) has been studied by means of temperature-programmed desorption spectroscopy and scanning tunneling microscopy measurements. Following O(2) adsorption at 130 K, the amount of O(2) desorbing at ∼410 K initially increased with increasing density of surface oxygen vacancies but decreased after further reduction of the TiO(2)(110) crystal. We explain these results by withdrawal of excess charge (Ti(3+)) from the TiO(2)(110) lattice to oxygen species on the surface and by a reaction of Ti interstitials with O adatoms upon heating.