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PubChem ( https://pubchem.ncbi.nlm.nih.gov ) is a public chemical information resource containing more than 100 million unique chemical structures. One of the most requested tasks in PubChem and other chemical databases is to search chemicals by name (also commonly called a "chemical synonym"). PubChem performs this task by looking up chemical synonym-structure associations provided by individual depositors to PubChem. In addition, these synonyms are used for many purposes, including creating links between chemicals and PubMed articles (using Medical Subject Headings (MeSH) terms). However, these depositor-provided name-structure associations are subject to substantial discrepancies within and between depositors, making it difficult to unambiguously map a chemical name to a specific chemical structure. The present paper describes PubChem's crowdsourcing-based synonym filtering strategy, which resolves inter- and intra-depositor discrepancies in synonym-structure associations as well as in the chemical-MeSH associations. The PubChem synonym filtering process was developed based on the analysis of four crowd-voting strategies, which differ in the consistency threshold value employed (60% vs 70%) and how to resolve intra-depositor discrepancies (a single vote vs. multiple votes per depositor) prior to inter-depositor crowd-voting. The agreement of voting was determined at six levels of chemical equivalency, which considers varying isotopic composition, stereochemistry, and connectivity of chemical structures and their primary components. While all four strategies showed comparable results, Strategy I (one vote per depositor with a 60% consistency threshold) resulted in the most synonyms assigned to a single chemical structure as well as the most synonym-structure associations disambiguated at the six chemical equivalency contexts. Based on the results of this study, Strategy I was implemented in PubChem's filtering process that cleans up synonym-structure associations as well as chemical-MeSH associations. This consistency-based filtering process is designed to look for a consensus in name-structure associations but cannot attest to their correctness. As a result, it can fail to recognize correct name-structure associations (or incorrect ones), for example, when a synonym is provided by only one depositor or when many contributors are incorrect. However, this filtering process is an important starting point for quality control in name-structure associations in large chemical databases like PubChem.
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http://dx.doi.org/10.1186/s13321-024-00868-3 | DOI Listing |
Int J Psychophysiol
March 2025
Department of Psychology, University of Utah, 380 S 1530 E BEH S 502, Salt Lake City, UT 84112, United States.
EEG mid-frontal theta-band activity (MFT; 4-8 Hz) is of considerable interest as a possible biomarker in translational research on cognitive control. However, because most of the MFT literature has focused on experimental within-subjects effects, the impact of particular data processing choices on individual difference analyses is not well understood. This study aimed to reduce that gap by examining the psychometric properties of different pipelines for measuring individual differences in MFT power and latency.
View Article and Find Full Text PDFSci Rep
March 2025
School of Computing, Gachon University, Seongnam, 13120, Republic of Korea.
Denoising is one of the most important processes in digital image processing to recover visual quality and structural integrity in images. Traditional methods often suffer from limitations like computational complexity, over-smoothing, and the inability to preserve critical details, particularly edges. This paper introduces a hybrid denoising algorithm combining Adaptive Median Filter (AMF) and Modified Decision-Based Median Filter (MDBMF) to address these challenges.
View Article and Find Full Text PDFSLAS Technol
March 2025
Discovery Research, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States. Electronic address:
The adoption of mass spectrometry for high-throughput screening in drug discovery has become increasingly prevalent and has enabled label-free screening against diverse targets. Cellular assays for phenotypic screening, however, are primarily conducted by microscopy as there remain many challenges associated with conducting phenotypic screens via ultra-high throughput mass spectrometry. Following a simple on-plate extraction, infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) was employed to directly sample the cell lysate at a speed of one sample per second with high mass resolution.
View Article and Find Full Text PDFMol Ecol
March 2025
CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China.
Hot spring microbial mats represent intricate biofilms that establish self-sustaining ecosystems, hosting diverse microbial communities which facilitate a range of biochemical processes and contribute to the structural and functional complexity of these systems. While community structuring across mat depth has received substantial attention, mechanisms shaping horizontal spatial composition and functional structure of these communities remain understudied. Here, we explored the contributions of species source, local environment and species interaction to microbial community assembly processes in six microbial mat regions following a flow direction with a temperature decreasing from 73.
View Article and Find Full Text PDFJ Neuroeng Rehabil
March 2025
State Key Laboratory of Mechanical System and Vibration, School of Mechanical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
Objective: Surface electromyography (EMG) decomposition is crucial for identifying motor neuron activities by analyzing muscle-generated electrical signals. This study aims to develop and validate a novel motor unit action potential (MUAP)-based method for surface EMG decomposition, addressing the limitations of traditional blind source separation (BSS)-based techniques in computation complexity and motor unit (MU) tracking.
Methods: Within the framework of the convolution kernel compensation algorithm, we developed a MUAP-based decomposition algorithm by reconstructing the MU filters from MUAPs and evaluated its performance using both simulated and experimental datasets.
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