Search Results (64)

The rapid growth of the body of literature on heavy metal hyperaccumulation in plants has created a critical bottleneck in data synthesis. Manual curation is slow, labor-intensive, and not scalable. To address this issue, we developed an artificial intelligence pipeline that automatically transforms unstructured scientific papers, including text, tables, and figures, into a structured knowledge database. Our system recovers numerical data and extracts key experimental parameters, such as plant species, metal types, concentrations, and growing conditions. This enables on-demand dataset generation. We validated our pipeline by replicating a recently published, manually curated dataset that required seven months of expert effort. Our tool achieved comparable accuracy in minutes per article. We implemented a dual-validation strategy combining standard extraction metrics with a qualitative “LLM-as-a-Judge” fact-checking layer to assess contextual correctness. This revealed that high extraction performance does not guarantee factual reliability, underscoring the necessity of semantic validation in scientific knowledge extraction. The resulting open, reproducible framework accelerates evidence synthesis, supports trend analysis (e.g., metal–plant co-occurrence networks), and provides a scalable solution for data-driven environmental research. Full article

Interest in gold nanoclusters (AuNCs) has grown significantly in recent decades. AuNCs, with a core size smaller than 2 nm, represent a unique class of functional nanomaterials. Their distinctive properties enable innovative applications across various interdisciplinary fields. Here, we introduce BioGoldNCDB, a freely available, fully annotated, and manually curated database of mainly about AuNCs and related AuNPs. Despite the rapid growth in biomedical applications of gold nanoclusters (AuNCs), the lack of a centralized and structured data resource hinders comparative analysis and rational design. Researchers face challenges in accessing standardized information on AuNCs’ structures, properties, and biological activities, which limits data-driven development in this emerging field. The database provides essential information, including CAS numbers and PubMed IDs, as well as specific details such as biomedical applications, cell lines used in research, particle size, and excitation/emission wavelengths. It currently covers 247 articles from 104 journals. Designed with a user-friendly and intuitive web interface, BioGoldNCDB is accessible on multiple devices, including phones, tablets, and PCs. Users can refine searches with multiple filters, and a help page is available for guidance. While offering quick insights for newcomers, BioGoldNCDB also serves as a valuable resource for researchers across various fields. Full article

This paper introduces PyBEP, a Python-based tool for the automated and optimized selection of open-circuit potential (OCP) curves and calculation of stoichiometric cycling ranges for lithium-ion battery electrodes based on open-circuit voltage (OCV) measurements. Thereby, it overcomes key challenges in traditional approaches, which are often time-intensive and susceptible to errors due to manual curve digitization, data inconsistency, and coding complexities. The originality of PyBEP arises from the systematic integration of automated electrode chemistry identification, quality-controlled database usage, refinement of the results using incremental capacity methodology, and simultaneous optimization of multiple electrode parameters. The PyBEP database leverages high-quality, curated OCP data and employs differential evolution optimization for precise OCP determination. Validation against literature data and experimental results confirms the robustness and accuracy of PyBEP, consistently achieving precision of 10 mV or better. PyBEP also offers features like electrode chemical composition identification and quality enhancement of measurement data, further extending the battery modeling functionalities without the need for battery disassembly. PyBEP is open-source and accessible on GitHub, providing a streamlined, accurate resource for the battery research community, making PyBEP a unique and directly applicable toolkit for electrochemical researchers and engineers. Full article

This study presents a systematic literature review on the mathematical modeling of resilient and viable supply chains, grounded in the PRISMA methodology and applied to a curated corpus of 235 peer-reviewed scientific articles published between 2011 and 2025. The search strategy was implemented across four major academic databases (Scopus and Web of Science) using Boolean operators to capture intersections among the core concepts of supply chains, resilience, viability, and advanced optimization techniques. The screening process involved a double manual assessment of titles, abstracts, and full texts, based on inclusion criteria centered on the presence of formal mathematical models, computational approaches, and thematic relevance. As a result of the selection process, six thematic categories were identified, clustering the literature according to their analytical objectives and methodological approaches: viability-oriented modeling, resilient supply chain optimization, agile and digitally enabled supply chains, logistics optimization and network configuration, uncertainty modeling, and immune system-inspired approaches. These categories were validated through a bibliometric analysis and a thematic map that visually represents the density and centrality of core research topics. Descriptive analysis revealed a significant increase in scientific output starting in 2020, driven by post-pandemic concerns and the accelerated digitalization of logistics operations. At the methodological level, a high degree of diversity in modeling techniques was observed, with an emphasis on mixed-integer linear programming (MILP), robust optimization, multi-objective modeling, and the increasing use of bio-inspired algorithms, artificial intelligence, and simulation frameworks. The results confirm a paradigm shift toward integrative frameworks that combine robustness, adaptability, and Industry 4.0 technologies, as well as a growing interest in biological metaphors applied to resilient system design. Finally, the review identifies research gaps related to the formal integration of viability under disruptive scenarios, the operationalization of immune-inspired models in logistics environments, and the need for hybrid approaches that jointly address resilience, agility, and sustainability. Full article

Chronobiotics represent a pharmacologically diverse group of substances, encompassing both experimental compounds and those utilized in clinical practice, which possess the capacity to modulate the parameters of circadian rhythms. These substances influence fluctuations in various physiological and biochemical processes, including the expression of core “clock” genes in model organisms and cell cultures, as well as the expression of clock-controlled genes. Despite their chemical heterogeneity, chronobiotics share the common ability to alter circadian dynamics. The concept of chronobiotic drugs has been recognized for over five decades, dating back to the discovery and detailed clinical characterization of the hormone melatonin. However, the field remains fragmented, lacking a unified classification system for these pharmacological agents. The current categorizations include natural chrononutrients, synthetic targeted circadian rhythm modulators, hypnotics, and chronobiotic hormones, yet no comprehensive repository of knowledge on chronobiotics exists. Addressing this gap, the development of the world’s first curated and continuously updated database of chronobiotic drugs—circadian rhythm modulators—accessible via the global Internet, represents a critical and timely objective for the fields of chronobiology, chronomedicine, and pharmacoinformatics/bioinformatics. The primary objective of this study is to construct a relational database, ChronobioticsDB, utilizing the Django framework and PostGreSQL as the database management system. The database will be accessible through a dedicated web interface and will be filled in with data on chronobiotics extracted and manually annotated from PubMed, Google Scholar, Scopus, and Web of Science articles. Each entry in the database will comprise a detailed compound card, featuring links to primary data sources, a molecular structure image, the compound’s chemical formula in machine-readable SMILES format, and its name according to IUPAC nomenclature. To enhance the depth and accuracy of the information, the database will be synchronized with external repositories such as ChemSpider, DrugBank, Chembl, ChEBI, Engage, UniProt, and PubChem. This integration will ensure the inclusion of up-to-date and comprehensive data on each chronobiotic. Furthermore, the biological and pharmacological relevance of the database will be augmented through synchronization with additional resources, including the FDA. In cases of overlapping data, compound cards will highlight the unique properties of each chronobiotic, thereby providing a robust and multifaceted resource for researchers and practitioners in the field. Full article

With the rapid development of radical initiation technologies such as photocatalysis and electrocatalysis, radical reactions have become an increasingly attractive approach for constructing target molecules. However, designing efficient synthetic routes using radical reactions remains a significant challenge due to the inherent complexity and instability of radical intermediates. While computer-aided synthesis planning (CASP) has advanced retrosynthetic analysis for polar reactions, radical reactions have been largely overlooked in AI-driven approaches. In this study, we introduce RadicalRetro, the first deep learning-based retrosynthesis model specifically tailored for radical reactions. Our work is distinguished by three key contributions: (1) RadicalDB: A novel, manually curated database of 21.6 K radical reactions, focusing on high-impact literature and mechanistic clarity, addressing the critical gap in dedicated radical reaction datasets. (2) Model Innovation: By pretraining Chemformer on ZINC-15 and USPTO datasets followed by fine-tuning with RadicalDB, RadicalRetro achieves a Top-1 accuracy of 69.3% in radical retrosynthesis, surpassing the state-of-the-art models LocalRetro and Mol-Transformer by 23.0% and 25.4%, respectively. (3) Interpretability and Practical Utility: Attention weight analysis and case studies demonstrate that RadicalRetro effectively captures radical reaction patterns (e.g., cascade cyclizations and photocatalytic steps) and proposes synthetically viable routes, such as streamlined pathways for Tamoxifen precursors and glycoside derivatives. RadicalRetro’s performance highlights its potential to transform radical-based synthetic planning, offering chemists a robust tool to leverage the unique advantages of radical chemistry in drug synthesis. Full article

Accurate segmentation of brain tumors in magnetic resonance imaging (MRI) remains a challenging task due to heterogeneous tumor structures, varying intensities across modalities, and limited annotated data. Deep learning has significantly advanced segmentation accuracy; however, it often suffers from sensitivity to hyperparameter settings and limited generalization. To overcome these challenges, bio-inspired metaheuristic algorithms have been increasingly employed to optimize various stages of the deep learning pipeline—including hyperparameter tuning, preprocessing, architectural design, and attention modulation. This review systematically examines developments from 2015 to 2025, focusing on the integration of nature-inspired optimization methods such as Particle Swarm Optimization (PSO), Genetic Algorithm (GA), Differential Evolution (DE), Grey Wolf Optimizer (GWO), Whale Optimization Algorithm (WOA), and novel hybrids including CJHBA and BioSwarmNet into deep learning-based brain tumor segmentation frameworks. A structured multi-query search strategy was executed using Publish or Perish across Google Scholar and Scopus databases. Following PRISMA guidelines, 3895 records were screened through automated filtering and manual eligibility checks, yielding a curated set of 106 primary studies. Through bibliometric mapping, methodological synthesis, and performance analysis, we highlight trends in algorithm usage, application domains (e.g., preprocessing, architecture search), and segmentation outcomes measured by metrics such as Dice Similarity Coefficient (DSC), Jaccard Index (JI), Hausdorff Distance (HD), and ASSD. Our findings demonstrate that bio-inspired optimization significantly enhances segmentation accuracy and robustness, particularly in multimodal settings involving FLAIR and T1CE modalities. The review concludes by identifying emerging research directions in hybrid optimization, real-time clinical applicability, and explainable AI, providing a roadmap for future exploration in this interdisciplinary domain. Full article

Dietary l-carnitine produces γ-butylbetaine (γBB) in a gut-microbiota-dependent manner in humans, and has been proven to be an intermediate product possibly associated with incident cardiovascular diseases or major adverse events. Eliminating or reducing the production of microbiota-dependent γBB may contribute to adjuvant therapy for cardiovascular diseases. However, to date, our understanding of the γBB metabolic gene clusters (MGCs) and associated microorganisms remains limited. To solve this problem, we constructed a manually curated γBB metabolic gene cluster database (γBMGC) based on Hidden Markov Models (HMMs). It comprised 171,510 allelic genes from 85 species and 20 genera, which could effectively provide high-resolution analysis at the strain level. For simulated gene datasets, with a 50% identity cutoff, we achieved an annotation accuracy, PPV, specificity, F1-score, and NPV of 99.4%, 97.97%, 99.16%, 98.97%, and 100%, respectively, which significantly outperformed existing databases such as KEGG at similar thresholds. The γBMGC database is more accurate, comprehensive, and faster for profiling cardiovascular disease (CVD)-associated genes at the species or strain level, offering a higher resolution in identifying strain-specific γBB metabolic pathways compared to existing databases like KEGG or COG. Meanwhile, we validated the excellent performance of γBMGC in gene abundance analysis and bacterial species distinction. γBMGC is a powerful database for enhancing our understanding of the microbial l-carnitine pathway in the human gut, enabling rapid and high-accuracy analyses of the associated cardiovascular disease processes. Full article

The range of chemical databases available has dramatically increased in recent years, but the reliability and quality of their data are often negatively affected by human-error fidelity. The size of chemical databases can make manual data curation/checking of such sets time consuming; thus, automated tools to help this process are highly desirable. Herein, we propose the use of Graph Neural Networks (GNNs) to identifying potential stereochemical misassignments in the primary asymmetric catalysis literature. Our method relies on the use of an ensemble of GNN models to predict the expected stereoselectivity of exemplars for a particular asymmetric reaction. When the majority of these models do not correlate to the reported outcome, the point is labeled as a possible stereochemical misassignment. Such identified cases are few in number and more easily investigated for their cause. We demonstrate the use of this approach to spot potential literature stereochemical misassignments in the ketone products resulting from catalytic asymmetric 1,4-addition of organoboron nucleophiles to Michael acceptors in two different databases, each one using a different family of chiral ligands (bisphosphine and diene ligands). Our results demonstrate that this methodology is useful for curation of medium-sized databases, speeding this process significantly compared to complete manual curation/checking. In the datasets investigated, human expert checking was reduced to 2.2% and 3.5% of the total data exemplars. Full article

Background: Training of machine learning algorithms on dish images collected in other countries requires possible sources of systematic discrepancies, including country-specific food composition databases (FCDBs), to be tackled. The US Nutrition5k project provides for ~5000 dish images and related dish- and ingredient-level information on mass, energy, and macronutrients from the US FCDB. The aim of this study is to (1) identify challenges/solutions in linking the nutritional composition of Italian foods with food images from Nutrition5k and (2) assess potential differences in nutrient content estimated across the Italian and US FCDBs and their determinants. Methods: After food matching, expert data curation, and handling of missing values, dish-level ingredients from Nutrition5k were integrated with the Italian-FCDB-specific nutritional composition (86 components); dish-specific nutrient content was calculated by summing the corresponding ingredient-specific nutritional values. Measures of agreement/difference were calculated between Italian- and US-FCDB-specific content of energy and macronutrients. Potential determinants of identified differences were investigated with multiple robust regression models. Results: Dishes showed a median mass of 145 g and included three ingredients in median. Energy, proteins, fats, and carbohydrates showed moderate-to-strong agreement between Italian- and US-FCDB-specific content; carbohydrates showed the worst performance, with the Italian FCDB providing smaller median values (median raw difference between the Italian and US FCDBs: −2.10 g). Regression models on dishes suggested a role for mass, number of ingredients, and presence of recreated recipes, alone or jointly with differential use of raw/cooked ingredients across the two FCDBs. Conclusions: In the era of machine learning approaches for food image recognition, manual data curation in the alignment of FCDBs is worth the effort. Full article

Bone health is ensured by the coordinated action of two types of cells—the osteoblasts that build up bone structure and the osteoclasts that resorb the bone. The loss of balance in their action results in pathological conditions such as osteoporosis. Central to this study is a class of RNA-binding proteins (RBPs) that regulates the biogenesis of miRNAs. In turn, miRNAs represent a critical level of regulation of gene expression and thus control multiple cellular and biological processes. The impact of miRNAs on the pathobiology of various multifactorial diseases, including osteoporosis, has been demonstrated. However, the role of RBPs in bone remodeling is yet to be elucidated. The aim of this study is to dissect the transcriptional landscape of genes encoding the compendium of 180 RBPs in bone cells. We developed and applied a multi-modular integrative analysis algorithm. The core methodology is gene expression analysis using the GENEVESTIGATOR platform, which is a database and analysis tool for manually curated and publicly available transcriptomic data sets, and gene network reconstruction using the Ingenuity Pathway Analysis platform. In this work, comparative insights into gene expression patterns of RBPs in osteoblasts and osteoclasts were obtained, resulting in the identification of 24 differentially expressed genes. Furthermore, the regulation patterns upon different treatment conditions revealed 20 genes as being significantly up- or down-regulated. Next, novel gene–gene associations were dissected and gene networks were reconstructed. Additively, a set of osteoblast- and osteoclast-specific gene signatures were identified. The consolidation of data and information gained from each individual analytical module allowed nominating novel promising candidate genes encoding RBPs in osteoblasts and osteoclasts and will significantly enhance the understanding of potential regulatory mechanisms directing intracellular processes in the course of (patho)physiological bone turnover. Full article

Probiotics are live microorganisms that, when consumed in adequate amounts, exert health benefits on the host by regulating intestinal and extraintestinal homeostasis. Common probiotic microorganisms include lactic acid bacteria (LAB), yeasts, and Bacillus species. Here, we present Probio-ichnos, the first manually curated, literature-based database that collects and comprehensively presents information on the microbial strains exhibiting in vitro probiotic characteristics (i.e., resistance to acid and bile, attachment to host epithelia, as well as antimicrobial, immunomodulatory, antiproliferative, and antioxidant activity), derived from human, animal or plant microbiota, fermented dairy or non-dairy food products, and environmental sources. Employing a rigorous methodology, we conducted a systematic search of the PubMed database utilizing the keyword ‘probiotic’ within the abstracts or titles, resulting in a total of 27,715 studies. Upon further manual filtering, 2207 studies presenting in vitro experiments and elucidating strain-specific probiotic attributes were collected and used for data extraction. The Probio-ichnos database consists of 12,993 entries on the in vitro probiotic characteristics of 11,202 distinct strains belonging to 470 species and 143 genera. Data are presented using a binary categorization approach for the presence of probiotic attributes according to the authors’ conclusions. Additionally, information about the availability of the whole-genome sequence (WGS) of strains is included in the database. Overall, the Probio-ichnos database aims to streamline the navigation of the available literature to facilitate targeted validation and comparative investigation of the probiotic properties of the microbial strains. Full article

Phytoplasmas are small, intracellular bacteria that infect a vast range of plant species, causing significant economic losses and impacting agriculture and farmers’ livelihoods. Early and rapid diagnosis of phytoplasma infections is crucial for preventing the spread of these diseases, particularly through early symptom recognition in the field by farmers and growers. A symptom database for phytoplasma infections can assist in recognizing the symptoms and enhance early detection and management. In this study, nearly 35,000 phytoplasma sequence entries were retrieved from the NCBI nucleotide database using the keyword “phytoplasma” and information on phytoplasma disease-associated plant hosts and symptoms was gathered. A total of 945 plant species were identified to be associated with phytoplasma infections. Subsequently, links to symptomatic images of these known susceptible plant species were manually curated, and the Phytoplasma Disease Symptom Database (iPhyDSDB) was established and implemented on a web-based interface using the MySQL Server and PHP programming language. One of the key features of iPhyDSDB is the curated collection of links to symptomatic images representing various phytoplasma-infected plant species, allowing users to easily access the original source of the collected images and detailed disease information. Furthermore, images and descriptive definitions of typical symptoms induced by phytoplasmas were included in iPhyDSDB. The newly developed database and web interface, equipped with advanced search functionality, will help farmers, growers, researchers, and educators to efficiently query the database based on specific categories such as plant host and symptom type. This resource will aid the users in comparing, identifying, and diagnosing phytoplasma-related diseases, enhancing the understanding and management of these infections. Full article

The vast array of omics data in microbiology presents significant opportunities for studying bacterial pathogenesis and creating computational tools for predicting pathogenic potential. However, the field lacks a comprehensive, curated resource that catalogs bacterial strains and their ability to cause human infections. Current methods for identifying pathogenicity determinants often introduce biases and miss critical aspects of bacterial pathogenesis. In response to this gap, we introduce BacSPaD (Bacterial Strains’ Pathogenicity Database), a thoroughly curated database focusing on pathogenicity annotations for a wide range of high-quality, complete bacterial genomes. Our rule-based annotation workflow combines metadata from trusted sources with automated keyword matching, extensive manual curation, and detailed literature review. Our analysis classified 5502 genomes as pathogenic to humans (HP) and 490 as non-pathogenic to humans (NHP), encompassing 532 species, 193 genera, and 96 families. Statistical analysis demonstrated a significant but moderate correlation between virulence factors and HP classification, highlighting the complexity of bacterial pathogenicity and the need for ongoing research. This resource is poised to enhance our understanding of bacterial pathogenicity mechanisms and aid in the development of predictive models. To improve accessibility and provide key visualization statistics, we developed a user-friendly web interface. Full article

Most of the studied MADS box members are linked to flowering and fruit traits. However, higher volumes of studies on type II of the two types so far suggest that the florigenic effect of the gene members could just be the tip of the iceberg. In the current study, we used a systematic approach to obtain a general overview of the MADS box members’ cross-trait and multifactor associations, and their pleiotropic potentials, based on a manually curated local reference database. While doing so, we screened for the co-occurrence of terms of interest within the title or abstract of each reference, with a threshold of three hits. The analysis results showed that our approach can retrieve multi-faceted information on the subject of study (MADS box gene members in the current case), which could otherwise have been skewed depending on the authors’ expertise and/or volume of the literature reference base. Overall, our study discusses the roles of MADS box members in association with plant organs and trait-linked factors among plant species. Our assessment showed that plants with most of the MADS box member studies included tomato, apple, and rice after Arabidopsis. Furthermore, based on the degree of their multi-trait associations, FLC, SVP, and SOC1 are suggested to have relatively higher pleiotropic potential among others in plant growth, development, and flowering processes. The approach devised in this study is expected to be applicable for a basic understanding of any study subject of interest, regardless of the depth of prior knowledge. Full article