Search Results (1,926)

Background/Objectives: An impediment to successful drug discovery is the potential for off-target liabilities to eliminate otherwise promising candidates. As the drug discovery process is time-consuming and expensive, the use of artificial intelligence (AI) methods such as machine learning (ML) has drastically increased. It is invaluable to generate models that can quickly differentiate between successful and unsuccessful small-molecule drug candidates. Previous efforts established that molecular similarity could be used with other metrics to inform predictions of potential activity against a protein target. Similar methods were pursued here to combine similarity and machine learning for a collection of models called OPLE. Methods: Models were trained with proprietary and publicly available data to predict the likelihood of a given compound to be active against targets present in existing experimental SafetyScreen panels 18 and 44. Two-dimensional (2D) Tanimoto similarity from extended-connectivity fingerprints (ECFPs) and trained ML models were combined to obtain predictions. Results: Using all training data, a relationship between similarity and activity was established by fitting a probability assignment curve. Calibrated ML label assignment likelihoods were joined with the predictions from ECFP Tanimoto similarity to known active compounds using the belief theory formula, which maintains that activity prediction increases when both pieces of evidence support it. When assessing the performance of OPLE models for SafetyScreen 18 and 44 targets with external data from ChEMBL, more than 80% of the models had recall values greater than 0.8. This indicated favorable predictive ability to identify active molecules while limiting false negative predictions. Conclusions: Predicting and experimentally verifying safety liabilities is insightful at every stage of small-molecule drug discovery. This early detection tool can help project teams save resources that could be better deployed on series with no predicted or measured off-target liabilities. Full article

Kidney transplantation remains the ultimate treatment option for patients with end-stage renal disease. However, the global shortage in donor kidneys, exacerbated by challenges such as ischemia–reperfusion injury (IRI), reduces renal graft viability and negatively impacts post-transplant outcomes. Static cold storage, the gold standard of organ preservation, reduces metabolic demand but increases the risk of cold-induced mitochondrial dysfunction and IRI, especially in marginal kidneys. The introduction of machine perfusion techniques allows renal grafts and other solid organ grafts to be preserved at a wider range of temperatures. Organ preservation temperatures play an important role in determining post-transplant outcomes in the transplantation of the kidney and other transplantable solid organs. Therefore, determining the optimal preservation temperature may help increase organ utilization by avoiding unnecessary graft discards and increasing the safe use of marginal organs. This review discusses the impact of various preservation temperatures and methods of preservation on post-transplant outcomes in renal grafts and other organ grafts. Drawing from preclinical, clinical, and meta-analytic studies, we compare hypothermic (0–4 °C), moderate hypothermic (10 °C), subnormothermic (20–32 °C), normothermic (35–37 °C), and subzero preservation strategies, and cellular and molecular changes that occur in renal grafts and other solid organ grafts during preservation at these temperatures. Overall, temperature-controlled machine perfusion outperforms static preservation of renal grafts and other solid organ grafts from marginal and deceased donors, potentially expanding donor pools and improving long-term graft survival, and suggests the need for future research to determine optimal preservation temperature for renal grafts and other solid organ grafts to improve viability and post-transplant outcomes. Full article

Plant immunity research is being reshaped by integrative multi-omics approaches that connect transcriptomic, proteomic, and interactomic data to build systems-level views of plant–pathogen interactions. This review outlines the scope and methodological landscape of these approaches, with particular emphasis on how transcriptomic and proteomic insights converge through network-based analyses to elucidate defense regulation. Transcriptomics captures infection-induced transcriptional reprogramming, while proteomics reveals protein abundance changes, post-translational modifications, and signaling dynamics essential for immune activation. Network-driven computational frameworks including iOmicsPASS, WGCNA, and DIABLO enable the identification of regulatory modules, hub genes, and concordant or discordant molecular patterns that structure plant defense responses. Interactomic techniques such as yeast two-hybrid screening and affinity purification–mass spectrometry further map host–pathogen protein–protein interactions, highlighting key immune nodes such as receptor-like kinases, R proteins, and effector-targeted complexes. Recent advances in machine learning and gene regulatory network modeling enhance the predictive interpretation of transcription–translation relationships, especially under combined or fluctuating stress conditions. By synthesizing these developments, this review clarifies how integrative multi-omics and network-based frameworks deepen understanding of the architecture and coordination of plant immune networks and support the identification of molecular targets for engineering durable pathogen resistance. Full article

Background and Objective: Colorectal cancer (CRC) liver metastasis (CRLM) represents a major clinical challenge, and acquired resistance to radiotherapy (RT) significantly limits therapeutic efficacy. A deep and comprehensive understanding of the cellular and molecular mechanisms driving RT resistance is urgently required to develop effective combination strategies. Here, we aimed to dissect the dynamic cellular landscape of the tumor microenvironment (TME) and identify key epigenetic regulators mediating radioresistance in CRLM by integrating cutting-edge single-cell and spatial omics technologies. Methods and Results: We performed integrated single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) on matched pre- and post-radiotherapy tumor tissues collected from three distinct CRLM patients. Employing a robust machine-learning framework on the multi-omics data, we successfully identified MORF4L1 (Mortality Factor 4 Like 1), an epigenetic reader, as a critical epigenetic mediator of acquired radioresistance. High-resolution scRNA-seq analysis of the tumor cell compartment revealed that the MORF4L1-high subpopulation exhibited significant enrichment in DNA damage repair (DDR) pathways, heightened activity of multiple pro-survival metabolic pathways, and robust signatures of immune evasion. Pseudotime trajectory analysis further confirmed that RT exposure drives tumor cells toward a highly resistant state, marked by a distinct increase in MORF4L1 expression. Furthermore, cell–cell communication inference demonstrated a pronounced, systemic upregulation of various immunosuppressive signaling axes within the TME following RT. Crucially, high-resolution ST confirmed these molecular and cellular interactions in their native context, revealing a significant spatial co-localization of MORF4L1-expressing tumor foci with multiple immunosuppressive immune cell types, including regulatory T cells (Tregs) and tumor-associated macrophages (TAMs), thereby underscoring its role in TME-mediated resistance. Conclusions: Our comprehensive spatial and single-cell profiling establishes MORF4L1 as a pivotal epigenetic regulator underlying acquired radioresistance in CRLM. These findings provide a compelling mechanistic rationale for combining radiotherapy with the targeted inhibition of MORF4L1, presenting a promising new therapeutic avenue to overcome treatment failure and improve patient outcomes in CRLM. Full article

The microstructure of the Ti-Al binary system is an area of great interest, as it affects material properties and plasticity. Phase transformations induce microstructural changes; therefore, accurately modeling the phase transformations of the Ti-Al system is necessary to describe plasticity. Interatomic potentials can be a powerful tool to model how materials behave; however, existing potentials lack accuracy in certain aspects. While classical potentials like the Modified Embedded Atom Method (MEAM) perform adequately for modeling a dilute Al solute within Ti’s $\alpha$ phase, they struggle with accurately predicting plasticity. In particular, they struggle with stacking fault energies in intermetallics and to some extent elastic properties. This hinders their effectiveness in investigating the plastic behavior of formed intermetallics in Ti-Al alloys. Classical potentials also fail to predict the $\alpha$-to-$\beta$ phase boundary. Existing machine learning (ML) potentials reproduce the properties of formed intermetallics with density functional theory (DFT) but do not accurately capture the $\alpha$-to-$\beta$ or $\alpha$-to-D0₁₉ phase boundaries. This work uses a rapid artificial neural network (RANN) framework to produce a neural network potential for the Ti-Al binary system. This potential is capable of reproducing the Ti-Al binary phase diagram up to 30% Al concentration. The present interatomic potential ensures stability and allows results near the accuracy of DFT. Using Monte Carlo simulations, the RANN potential accurately predicts the $\alpha$-to-$\beta$ and $\alpha$-to-D0₁₉ phase transitions. The current potential also exhibits accurate elastic constants and stacking fault energies for the L1₀ and D0₁₉ phases. Full article

Epilepsy remains an active and important area of research due to its complex etiology, significant global burden, and variable response to treatment. Current knowledge has provided valuable insights into the underlying molecular mechanisms of the disease and continues to guide the development of novel therapeutic strategies. This review presents a comprehensive overview of the etiologies of epilepsy, as well as traditional and modern medical and surgical treatment approaches, while highlighting future research directions. Peer-reviewed articles retrieved from PubMed and Google Scholar were analyzed and synthesized to produce this review. The etiological complexity of epilepsy arises from genetic, metabolic, structural, and inflammatory mechanisms, which often coexist rather than act independently. A wide range of anti-seizure drugs (ASDs) is currently available, with many new agents targeting novel mechanisms under development. Surgical approaches, including resection, disconnection, corpus callosotomy, and neuromodulation, are widely used for patients with drug-resistant epilepsy and result in variable seizure outcomes. In addition, minimally invasive techniques such as laser interstitial thermal therapy (LITT), stereoelectroencephalography-guided radiofrequency thermocoagulation, gamma knife radiosurgery, and high-intensity focused ultrasound have gained clinical relevance and continue to be explored. Emerging technologies, including artificial intelligence, machine learning, and precision medicine, offer promising directions for future research. Although several potential biomarkers have been identified, none are yet established for routine clinical use. Continued investigation is essential to improve understanding of epileptogenesis and to develop safer, more effective therapies. Full article

Sepsis is a life-threatening syndrome characterized by marked clinical heterogeneity and complex host–pathogen interactions. Although traditional mechanistic studies have identified key molecular pathways, they remain insufficient to capture the highly dynamic, multifactorial, and systems-level nature of this condition. The advent of high-throughput omics technologies—particularly integrative multi-omics approaches encompassing genomics, transcriptomics, proteomics, and metabolomics—has profoundly reshaped sepsis research by enabling comprehensive profiling of molecular perturbations across biological layers. However, the unprecedented scale, dimensionality, and heterogeneity of multi-omics datasets exceed the analytical capacity of conventional statistical methods, necessitating more advanced computational strategies to derive biologically meaningful and clinically actionable insights. In this context, artificial intelligence (AI) has emerged as a powerful paradigm for decoding the complexity of sepsis. By leveraging machine learning and deep learning algorithms, AI can efficiently process ultra-high-dimensional and heterogeneous multi-omics data, uncover latent molecular patterns, and integrate multilayered biological information into unified predictive frameworks. These capabilities have driven substantial advances in early sepsis detection, molecular subtyping, prognosis prediction, and therapeutic target identification, thereby narrowing the gap between molecular mechanisms and clinical application. As a result, the convergence of AI and multi-omics is redefining sepsis research, shifting the field from descriptive analyses toward predictive, mechanistic, and precision-oriented medicine. Despite these advances, the clinical translation of AI-driven multi-omics approaches in sepsis remains constrained by several challenges, including limited data availability, cohort heterogeneity, restricted interpretability and causal inference, high computational demands, difficulties in integrating static molecular profiles with dynamic clinical data, ethical and governance concerns, and limited generalizability across populations and platforms. Addressing these barriers will require the establishment of standardized, multicenter datasets, the development of explainable and robust AI frameworks, and sustained interdisciplinary collaboration between computational scientists and clinicians. Through these efforts, AI-enabled multi-omics research may progress toward reproducible, interpretable, and equitable clinical implementation. Ultimately, the synergy between artificial intelligence and multi-omics heralds a new era of intelligent discovery and precision medicine in sepsis, with the potential to transform both research paradigms and bedside practice. Full article

Artificial intelligence (AI), particularly machine learning and deep learning architectures, has been widely applied to support thyroid cancer diagnosis, but existing evidence on its performance and limitations remains scattered across techniques, tasks, and data types. This systematic review synthesizes recent work on knowledge extraction from heterogeneous imaging and clinical data for thyroid cancer diagnosis and detection published between 2021 and 2025. We searched eight major databases, applied predefined inclusion and exclusion criteria, and assessed study quality using the Newcastle–Ottawa Scale. A total of 150 primary studies were included and analyzed with respect to AI techniques, diagnostic tasks, imaging and non-imaging modalities, model generalization, explainable AI, and recommended future directions. We found that deep learning, particularly convolutional neural networks, U-Net variants, and transformer-based models, dominated recent work, mainly for ultrasound-based benign–malignant classification, nodule detection, and segmentation, while classical machine learning, ensembles, and advanced paradigms remained important in specific structured-data settings. Ultrasound was the primary modality, complemented by cytology, histopathology, cross-sectional imaging, molecular data, and multimodal combinations. Key limitations included diagnostic ambiguity, small and imbalanced datasets, limited external validation, gaps in model generalization, and the use of largely non-interpretable black-box models with only partial use of explainable AI techniques. This review provides a structured, machine learning-oriented evidence map that highlights opportunities for more robust representation learning, workflow-ready automation, and trustworthy AI systems for thyroid oncology. Full article

Wee1-like protein kinase 2 (WEE2) is an oocyte-specific kinase that regulates meiotic arrest and fertilization. Its largely restricted expression in female germ cells and absence in somatic tissues make it a highly selective target for reproductive health interventions. Despite its central role in human fertility, no clinically approved WEE2 modulator is available. In this study, we employed an integrated in silico approach that combines structure-based virtual screening, molecular dynamics (MD) simulations, and MM-PBSA free-energy calculations to identify repurposed drug candidates with potential WEE2 inhibitory activity. Screening of ~3800 DrugBank compounds against the WEE2 catalytic domain yielded ten high-affinity hits, from which Midostaurin and Nilotinib emerged as the most mechanistically relevant based on kinase-targeting properties and pharmacological profiles. Docking analyses revealed strong binding affinities (−11.5 and −11.3 kcal/mol) and interaction fingerprints highly similar to the reference inhibitor MK1775, including key contacts with hinge-region residues Val220, Tyr291, and Cys292. All-atom MD simulations for 300 ns demonstrated that both compounds induce stable protein–ligand complexes with minimal conformational drift, decreased residual flexibility, preserved compactness, and stable intramolecular hydrogen-bond networks. Principal component and free-energy landscape analyses further indicate restricted conformational sampling of WEE2 upon ligand binding, supporting ligand-induced stabilization of the catalytic domain. MM-PBSA calculations confirmed favorable binding free energies for Midostaurin (−18.78 ± 2.23 kJ/mol) and Nilotinib (−17.47 ± 2.95 kJ/mol), exceeding that of MK1775. To increase the translational prioritization of candidate hits, we place our structure-based pipeline in the context of modern machine learning (ML) and deep learning (DL)-enabled virtual screening workflows. ML/DL rescoring and graph-based molecular property predictors can rapidly re-rank docking hits and estimate absorption, distribution, metabolism, excretion, and toxicity (ADMET) liabilities before in vitro evaluation. Full article

Background: No Fourier transform infrared (FTIR) spectroscopy studies have directly evaluated adrenalectomy vessels, the technique’s established ability to probe collagen/elastin-associated spectral features and lipid peroxidation-related signatures, and protein structural damage. Stable gastric pentadecapeptide BPC 157 therapy was found to maintain the vascular function under severe stress, as FTIR spectroscopy recently demonstrated rapid peptide-induced molecular changes in healthy rat blood vessels, particularly in lipid content and protein secondary structure. Methods: To extend these findings and highlight the BPC 157 vascular background in the special circumstances of the course following unilateral adrenalectomy, abdominal aortas were collected at 15 min, 5 h, and 24 h after unilateral adrenalectomy for the FTIR spectroscopy assessment. Results: FTIR spectra were acquired, preprocessed, and analyzed using principal component analysis (PCA), support vector machine discriminant analysis (SVMDA), and band-specific statistics. BPC 157 (10 ng/kg intragatrically immediately after unilateral adrenalectomy) produced a clear, reproducible separation of aortic spectra from control samples at all time points. The main discriminatory spectral signatures were observed in three regions, including amide I and amide II (protein-related bands, consistent with collagen/elastin contributions) and lipid C–H stretching bands. These spectral signatures are consistent with early extracellular matrix reinforcement and membrane preservation in the vascular wall and align with the recovering effect on the lesions in counteraction of the severe vascular and multiorgan failure, attenuation/elimination of thrombosis and blood pressure disturbances in various occlusion/occlusion-like syndromes. Conclusions: Together, after unilateral adrenalectomy, the FTIR data provide molecular-level spectral signatures consistent with rapid remodeling of the aortic wall toward a more structurally stable and functionally favorable state. Full article

To enhance the screening efficiency of bioactive peptides, an AI-driven approach was employed to screen DPP-IV inhibitory peptides from goat blood proteins by an integrated in silico, in vitro, and machine learning strategy. Furthermore, the inhibitory mechanism of DPP-IV inhibitory peptides was elucidated by kinetics, molecular docking and simulation. Additionally, their in vitro digestive stability was assessed. In silico results revealed that goat blood proteins were promising precursors of DPP-IV inhibitory peptides, while bromelain was the optimal protease. Their peptide sequences were further identified by peptidomics and predicted by self-developed machine learning models (LightGBM) to identify the potent DPP-IV inhibitory peptides. Two novel DPP-IV inhibitory peptides were identified (FPL and FPHFDL). Enzyme kinetics, molecular docking and molecular simulation data indicated that FPL served as a competitive inhibitor, whereas FPHFDL was a non-competitive inhibitor. Overall, the integrative in silico and in vitro strategy is feasible for rapid screening of DPP-IV inhibitory peptides from goat blood proteins. Full article

Background: Rhodopseudomonas palustris is a metabolically versatile bacterium with significant biotechnological potential, including the ability to catabolize lignin and its heterogeneous breakdown products. Understanding the molecular determinants of growth on lignin-derived compounds is essential for advancing lignin valorization strategies under both aerobic and anaerobic conditions. Methods: R. palustris was cultivated on multiple lignin breakdown products (LBPs), including p-coumaryl alcohol, coniferyl alcohol, sinapyl alcohol, p-coumarate, sodium ferulate, and kraft lignin. Condition-specific transcriptomics and proteomics datasets were generated and used as input features to train machine-learning models, with experimentally measured growth rates as the prediction target. Artificial Neural Networks (ANNs), Random Forest (RF), and Support Vector Machine (SVM) models were evaluated and compared. Permutation feature importance analysis was applied to identify genes and proteins most influential for growth. Results: Among the tested models, ANNs achieved the highest predictive performance, with accuracies of 94% for transcriptomics-based models and 96% for proteomics-based models. Feature importance analysis identified the top twenty growth-associated genes and proteins for each omics layer. Integrating transcriptomic and proteomic results revealed eight key transport proteins that consistently influenced growth across LBP conditions. Re-training ANN models using only these eight transport proteins maintained high predictive accuracy, achieving 86% for proteomics and 76% for transcriptomics. Conclusions: This study demonstrates the effectiveness of ANN-based models for predicting growth-associated genes and proteins in R. palustris. The identification of a small set of key transport proteins provides mechanistic insight into lignin catabolism and highlights promising targets for metabolic engineering aimed at improving lignin utilization. Full article

Gut microbiota is a potential therapeutic target for type 2 diabetes (T2D), but its role remains unclear. Investigating causal associations between them could further our understanding of their biological and clinical significance. A two-sample Mendelian randomization (MR) analysis was conducted to assess the causal relationship between gut microbiota and T2D. Key genes and mechanisms were identified through the integration of Genome-Wide Association Studies (GWAS) and cis-expression quantitative trait loci (cis-eQTL) data. Network pharmacology was applied to identify potential drugs and targets. Additionally, gut microbiota community analysis and machine learning models were used to construct a diagnostic model for T2D. MR analysis identified 17 gut microbiota taxa associated with T2D, with three showing significant associations: Actinomyces (odds ratio [OR] = 1.106; 95% confidence interval [CI]: 1.06–1.15; p < 0.01; adjusted p-value [p_adj] = 0.0003), Ruminococcaceae (UCG010 group) (OR = 0.897; 95% CI: 0.85–0.95; p < 0.01; p_adj = 0.018), and Deltaproteobacteria (OR = 1.072; 95% CI: 1.03–1.12; p < 0.01; p_adj = 0.029). Ten key genes, such as EXOC4 and IGF1R, were linked to T2D risk. Network pharmacology identified INSR and ESR1 as target driver genes, with drugs like Dienestrol showing promise. Gut microbiota analysis revealed reduced α-diversity in T2D patients (p < 0.05), and β-diversity showed microbial community differences (R² = 0.012, p = 0.001). Furthermore, molecular docking confirmed the binding affinity of potential therapeutic agents to their targets. Finally, we developed a class-weight optimized Extreme Gradient Boosting (XGBoost) diagnostic model, which achieved an area under the curve (AUC) of 0.84 with balanced sensitivity (95.1%) and specificity (83.8%). Integrating machine learning predictions with MR causal inference highlighted Bacteroides as a key biomarker. Our findings elucidate the gut microbiota-T2D causal axis, identify therapeutic targets, and provide a robust tool for precision diagnosis. Full article

Anti-N-methyl-D-aspartate receptor (anti-NMDAR) encephalitis is an immune-mediated neurological disorder driven by dysregulated neuroimmune interactions, yet the molecular architecture linking tumor-associated immune activation, peripheral immunity, and neuronal dysfunction remains insufficiently understood. In this study, we established an integrative computational framework that combines multi-tissue transcriptomic profiling, weighted gene co-expression network analysis, immune deconvolution, and machine learning-based feature prioritization to systematically characterize the regulatory landscape of the disease. Joint analysis of three independent GEO datasets spanning ovarian teratoma tissue and peripheral blood transcriptomes identified 2001 consistently dysregulated mRNAs, defining a shared tumor–immune–neural transcriptional axis. Across multiple feature selection algorithms, ACVR2B and MX1 were reproducibly prioritized as immune-associated candidate genes and were consistently downregulated in anti-NMDAR encephalitis samples, showing negative correlations with neutrophil infiltration. Reconstruction of an integrated mRNA-miRNA-lncRNA regulatory network further highlighted a putative core axis (ENSG00000262580–hsa-miR-22-3p–ACVR2B), proposed as a hypothesis-generating regulatory module linking non-coding RNA regulation to immune-neuronal signaling. Pathway and immune profiling analyses demonstrated convergence of canonical immune signaling pathways, including JAK-STAT and PI3K-Akt, with neuronal communication modules, accompanied by enhanced innate immune signatures. Although limited by reliance on public datasets and small sample size, these findings delineate a systems-level neuroimmune regulatory program in anti-NMDAR encephalitis and provide a scalable, network-based multi-omics framework for investigating immune-mediated neurological and autoimmune disorders and for guiding future experimental validation. Full article

Eutrophication of water bodies and the bloom of toxin-producing cyanoprokaryotes raise health concerns. Various cyanoprokaryotes species, including Microcystis, Raphidiopsis, Nodularia, and Chrysosporum, release toxins into the aquatic environment, which can reach concentrations toxic to humans and animals. Rising temperatures and human activities are primary drivers behind the increasing frequency of toxic cyanobacterial blooms. The Word Health Organization (WHO) has established provisional guideline values for cyanotoxins in drinking water and water used for other purposes in daily human activities, and has published guidance for identifying hazards and managing risks posed by cyanobacteria and their toxins. There are currently no acceptable limit values for cyanotoxins. To address monitoring needs, contemporary strategies now incorporate molecular genetics, immunoassays, biochemical profiling, and emerging machine-learning frameworks. This paper reviews current early detection methods for harmful cyanobacterial blooms, highlighting their practical advantages and drawbacks. Full article