TheMarker: a comprehensive database of therapeutic biomarkers.

Distinct from the traditional diagnostic/prognostic biomarker (adopted as the indicator of disease state/process), the therapeutic biomarker (ThMAR) has emerged to be very crucial in the clinical development and clinical practice of all therapies. There are five types of ThMAR that have been found to play indispensable roles in various stages of drug discovery, such as: Pharmacodynamic Biomarker essential for guaranteeing the pharmacological effects of a therapy, Safety Biomarker critical for assessing the extent or likelihood of therapy-induced toxicity, Monitoring Biomarker indispensable for guiding clinical management by serially measuring patients' status, Predictive Biomarker crucial for maximizing the clinical outcome of a therapy for specific individuals, and Surrogate Endpoint fundamental for accelerating the approval of a therapy. However, these data of ThMARs has not been comprehensively described by any of the existing databases. Herein, a database, named 'TheMarker', was therefore constructed to (a) systematically offer all five types of ThMAR used at different stages of drug development, (b) comprehensively describe ThMAR information for the largest number of drugs among available databases, (c) extensively cover the widest disease classes by not just focusing on anticancer therapies. These data in TheMarker are expected to have great implication and significant impact on drug discovery and clinical practice, and it is freely accessible without any login requirement at: https://idrblab.org/themarker.

EMNPD: a comprehensive endophytic microorganism natural products database for prompt the discovery of new bioactive substances.

The discovery and utilization of natural products derived from endophytic microorganisms have garnered significant attention in pharmaceutical research. While remarkable progress has been made in this field each year, the absence of dedicated open-access databases for endophytic microorganism natural products research is evident. To address the increasing demand for mining and sharing of data resources related to endophytic microorganism natural products, this study introduces EMNPD, a comprehensive endophytic microorganism natural products database comprising manually curated data. Currently, EMNPD offers 6632 natural products from 1017 endophytic microorganisms, targeting 1286 entities (including 94 proteins, 282 cell lines, and 910 species) with 91 diverse bioactivities. It encompasses the physico-chemical properties of natural products, ADMET information, quantitative activity data with their potency, natural products contents with diverse fermentation conditions, systematic taxonomy, and links to various well-established databases. EMNPD aims to function as an open-access knowledge repository for the study of endophytic microorganisms and their natural products, thereby facilitating drug discovery research and exploration of bioactive substances. The database can be accessed at http://emnpd.idrblab.cn/ without the need for registration, enabling researchers to freely download the data. EMNPD is expected to become a valuable resource in the field of endophytic microorganism natural products and contribute to future drug development endeavors.

Systematic Description of the Content Variation of Natural Products (NPs): To Prompt the Yield of High-Value NPs and the Discovery of New Therapeutics.

Natural products (NPs) have long been associated with human production and play a key role in the survival of species. Significant variations in NP content may severely affect the "return on investment" of NP-based industries and render ecological systems vulnerable. Thus, it is crucial to construct a platform that relates variations in NP content to their corresponding mechanisms. In this study, a publicly accessible online platform, NPcVar (http://npcvar.idrblab.net/), was developed, which systematically described the variations of NP contents and their corresponding mechanisms. The platform comprises 2201 NPs and 694 biological resources, including plants, bacteria, and fungi, curated using 126 diverse factors with 26,425 records. Each record contains information about the species, NP, and factors involved, as well as NP content data, parts of the plant that produce NPs, the location of the experiment, and reference information. All factors were manually curated and categorized into 42 classes which belong to four mechanisms (molecular regulation, species factor, environmental condition, and combined factor). Additionally, the cross-links of species and NP to well-established databases and the visualization of NP content under various experimental conditions were provided. In conclusion, NPcVar is a valuable resource for understanding the relationship between species, factors, and NP contents and is anticipated to serve as a promising tool for improving the yield of high-value NPs and facilitating the development of new therapeutics.

A systematic review of state-of-the-art strategies for machine learning-based protein function prediction.

New drug discovery is inseparable from the discovery of drug targets, and the vast majority of the known targets are proteins. At the same time, proteins are essential structural and functional elements of living cells necessary for the maintenance of all forms of life. Therefore, protein functions have become the focus of many pharmacological and biological studies. Traditional experimental techniques are no longer adequate for rapidly growing annotation of protein sequences, and approaches to protein function prediction using computational methods have emerged and flourished. A significant trend has been to use machine learning to achieve this goal. In this review, approaches to protein function prediction based on the sequence, structure, protein-protein interaction (PPI) networks, and fusion of multi-information sources are discussed. The current status of research on protein function prediction using machine learning is considered, and existing challenges and prominent breakthroughs are discussed to provide ideas and methods for future studies.

A systematic review on the state-of-the-art strategies for protein representation.

The study of drug-target protein interaction is a key step in drug research. In recent years, machine learning techniques have become attractive for research, including drug research, due to their automated nature, predictive power, and expected efficiency. Protein representation is a key step in the study of drug-target protein interaction by machine learning, which plays a fundamental role in the ultimate accomplishment of accurate research. With the progress of machine learning, protein representation methods have gradually attracted attention and have consequently developed rapidly. Therefore, in this review, we systematically classify current protein representation methods, comprehensively review them, and discuss the latest advances of interest. According to the information extraction methods and information sources, these representation methods are generally divided into structure and sequence-based representation methods. Each primary class can be further divided into specific subcategories. As for the particular representation methods involve both traditional and the latest approaches. This review contains a comprehensive assessment of the various methods which researchers can use as a reference for their specific protein-related research requirements, including drug research.

Kirkendall Effect Boosts Phosphorylated nZVI for Efficient Heavy Metal Wastewater Treatment.

Removal of non-biodegradable heavy metals has been the top priority in wastewater treatment and the development of green technologies remains a significant challenge. We demonstrate that phosphorylated nanoscale zero-valent iron (nZVI) is promising for removal of heavy metals (NiII , CuII , CrVI , HgII ) via a boosted Kirkendall effect. Phosphorylation confines tensile hoop stress on the nZVI particles and "breaks" the structurally dense spherical nZVI to produce numerous radial nanocracks. Exemplified by NiII removal, the radial nanocracks favor the facile inward diffusion of NiII and the rapid outward transport of electrons and ferrous ions through the oxide shell for surface (NiII /electron) and boundary (NiII /Fe0 ) galvanic exchange. Accompanied by a pronounced hollowing phenomenon, phosphorylated nZVI can instantly reduce and immobilize NiII throughout the oxide shell with a high capacity (258 mg Ni g-1 Fe). For real electroplating factory wastewater treatment, this novel nZVI performs simultaneous NiII and CuII removal, producing effluent of stable quality that meets local discharge regulations.

A prediction model of MF radiation in environmental assessment.

OBJECTIVE: To predict the impact of MF radiation on human health. METHODS: The vertical distribution of field intensity was estimated by analogism on the basis of measured values from simulation measurement. RESULTS: A kind of analogism on the basis of geometric proportion decay pattern is put forward in the essay. It showed that with increasing of height the field intensity increased according to geometric proportion law. CONCLUSION: This geometric proportion prediction model can be used to estimate the impact of MF radiation on inhabited environment, and can act as a reference pattern in predicting the environmental impact level of MF radiation.

Study on model of indoor air pollution forecast for decoration under natural ventilation condition.

OBJECTIVE: To establish the model of indoor air pollution forecast for decoration. METHODS: The model was based on the balance model for diffusing mass. RESULTS: The data between testing concentration and estimating concentration were compared. The maximal error was less than 30% and average error was 14.6%. CONCLUSION: The model can easily predict whether the pollution for decoration exceeds the standard and how long the room is decorated.