Leveraging FDA Labeling Documents and Large Language Model to Enhance Annotation, Profiling, and Classification of Drug Adverse Events with AskFDALabel.

Background: Drug adverse events (AEs) represent a significant public health concern. US Food and Drug Administration (FDA) drug labeling documents are an essential resource for studying drug safety such as assessing a drug's likelihood to cause certain organ toxicities; however, the manual extraction of AEs is labor-intensive, requires specialized expertise, and is challenging to maintain, due to frequent updates of the labeling documents.

Objective: To automate the extraction of AE data from FDA drug labeling documents, we developed a workflow based on AskFDALabel, a large language model (LLM)-powered framework, and its demonstration in drug safety studies.

Foraging behavior and work patterns of Bombus terrestris (Hymenoptera: Apidae) in response to tomato greenhouse microclimate.

Bumblebees play a significant role as pollinators for many wild plants and cultivated crops, owing to their elongated proboscis, resilience to diverse weather conditions, robustly furred bodies, and their unique capacity for buzz-pollination. To better understand the effect of greenhouse microclimates on bumblebee foraging behavior and working modes, a long-term record of foraging activity for each Bombus terrestris L. (Hymenoptera: Apidae) forager was monitored by the Radio-frequency identification system.

Use of Tox21 screening data to profile PFAS bioactivities on nuclear receptors, cellular stress pathways, and cytochrome p450 enzymes.

Per- and poly-fluoroalkyl substances (PFAS) are synthetic chemicals widely used in commercial products. PFAS are a global concern due to their persistence in the environment and extensive associations with adverse health outcomes. While legacy PFAS have been extensively studied, many non-legacy PFAS lack sufficient toxicity information.

A framework enabling LLMs into regulatory environment for transparency and trustworthiness and its application to drug labeling document.

Regulatory agencies consistently deal with extensive document reviews, ranging from product submissions to both internal and external communications. Large Language Models (LLMs) like ChatGPT can be invaluable tools for these tasks, however present several challenges, particularly the proprietary information, combining customized function with specific review needs, and transparency and explainability of the model's output. Hence, a localized and customized solution is imperative.

A CD25-biased interleukin-2 for autoimmune therapy engineered via a semi-synthetic organism.

Background: Natural cytokines are poorly suited as therapeutics for systemic administration due to suboptimal pharmacological and pharmacokinetic (PK) properties. Recombinant human interleukin-2 (rhIL-2) has shown promise for treatment of autoimmune (AI) disorders yet exhibits short systemic half-life and opposing immune responses that negate an appropriate therapeutic index.

Methods: A semi-synthetic microbial technology platform was used to engineer a site-specifically pegylated form of rhIL-2 with enhanced PK, specificity for induction of immune-suppressive regulatory CD4 + T cells (Tregs), and reduced stimulation of off-target effector T and NK cells.

Generation of a drug-induced renal injury list to facilitate the development of new approach methodologies for nephrotoxicity.

Drug-induced renal injury (DIRI) causes >1.5 million adverse events annually in the USA alone. Although standard biomarkers exist for DIRI, they lack the sensitivity or specificity to detect nephrotoxicity before the significant loss of renal function.

DICTrank: The largest reference list of 1318 human drugs ranked by risk of drug-induced cardiotoxicity using FDA labeling.

Drug-induced cardiotoxicity (DICT) is a leading cause of drug trial failure and discontinuation. Current drug annotations for cardiotoxicity largely focus on individual outcomes or mechanisms. Considering the broad spectrum of adverse cardiac events, we developed Drug-Induced Cardiotoxicity Rank (DICTrank) using FDA labeling and comprehensively classified 1318 human drugs into four categories: Most-DICT-Concern (n = 341), Less-DICT-Concern (n = 528), No-DICT-Concern (n = 343), and Ambiguous-DICT-Concern (n = 106).

Auranofin targets UBA1 and enhances UBA1 activity by facilitating ubiquitin trans-thioesterification to E2 ubiquitin-conjugating enzymes.

UBA1 is the primary E1 ubiquitin-activating enzyme responsible for generation of activated ubiquitin required for ubiquitination, a process that regulates stability and function of numerous proteins. Decreased or insufficient ubiquitination can cause or drive aging and many diseases. Therefore, a small-molecule enhancing UBA1 activity could have broad therapeutic potential.

Hormesis and insects: Effects and interactions in agroecosystems.

Insects in agroecosystems contend with many stressors - e.g., chemicals, heat, nutrient deprivation - that are often encountered at low levels.

Thrombospondin-1 Restricts Interleukin-36γ-Mediated Neutrophilic Inflammation during Pseudomonas aeruginosa Pulmonary Infection.

Interleukin-36γ (IL-36γ), a member of the IL-1 cytokine superfamily, amplifies lung inflammation and impairs host defense during acute pulmonary infection. To be fully active, IL-36γ is cleaved at its N-terminal region by proteases such as neutrophil elastase (NE) and cathepsin S (CatS). However, it remains unclear whether limiting extracellular proteolysis restrains the inflammatory cascade triggered by IL-36γ during infection.

Untargeted metabolomic and molecular network approaches to reveal tomato root secondary metabolites.

Introduction: The tomato plant, Solanum lycopersicum L. (Solanaceae), is one of the most widely consumed vegetables in the world and plays an important role in human diet. Tomato cultivars are hosts for diverse types of pests, implying diverse chemical defence strategies.

Sublethal effects of beta-cypermethrin modulate interspecific interactions between specialist and generalist aphid species on soybean.

In agroecosystems, plant-pest interactions are at the basis of complex food webs, which can be affected by both biotic and abiotic factors. In the present study, we evaluated the impact of the insecticide beta-cypermethrin on interspecific interactions between the specialist aphid Aphis glycines and the generalist aphid Aulacorthum solani on soybean. Aphis glycines showed higher fecundity than A.

Electricity-free amplification and visual detection of Cronobacter species in powdered infant formula.

Due to the lack of electricity and thermostatic instruments in certain settings for convenient detection of Cronobacter species in powdered infant formula (PIF), a novel investigation was conducted to establish an electricity-free visual detection system for rapid detection of Cronobacter species in PIF. This system included a portable electricity-free heater that could use the exothermic reaction of calcium oxide and water and 3 kinds of phase change materials to supply 3 constant temperatures for immunomagnetic separation, DNA extraction, and loop-mediated isothermal amplification assay. Meanwhile, the amplified reaction combined with hydroxynaphthol blue could achieve rapid visual detection.

Quantitative capillary zone electrophoresis-mass spectrometry reveals the N-glycome developmental plan during vertebrate embryogenesis.

Glycans are known to be involved in many biological processes, while little is known about the expression of N-glycans during vertebrate development. We now report the first quantitative studies of both the expression of N-linked glycans at six early development stages and the expression of N-glycosylated peptides at two early development stages in Xenopus laevis, the African clawed frog. N-Glycans were labeled with isobaric tandem mass tags, pooled, separated by capillary electrophoresis, and characterized using tandem mass spectrometry.

Downregulation of serum exosomal miR-150-5p is associated with poor prognosis in patients with colorectal cancer.

Growing evidence have revealed the serum exosomal miRNAs emerged as biomarkers for various cancer types, including colorectal cancer (CRC). Here, we sought to explore the potential clinical significance of serum exosomal miR-150-5p in CRC. A total of 133 CRC patients and 60 healthy volunteers as control group were recruited in this study.

MicroRNA-221 promotes cisplatin resistance in osteosarcoma cells by targeting PPP2R2A.

Osteosarcoma (OS), the most common malignant bone tumor, is the main cause of cancer-related deaths in children and young adults. Despite the combination of surgery and multi-agent chemotherapy, patients with OS who develop resistance to chemotherapy or experience recurrence have a dismal prognosis. MicroRNAs (miRNAs) are a class of small noncoding RNAs that repress their targets by binding to the 3'-UTR and/or coding sequences, leading to the inhibition of gene expression.

Platelets inhibit apoptotic lung epithelial cell death and protect mice against infection-induced lung injury.

Thrombocytopenia is associated with worse outcomes in patients with acute respiratory distress syndrome, which is most commonly caused by infection and marked by alveolar-capillary barrier disruption. However, the mechanisms by which platelets protect the lung alveolar-capillary barrier during infectious injury remain unclear. We found that natively thrombocytopenic mice deficient in the thrombopoietin receptor sustain severe lung injury marked by alveolar barrier disruption and hemorrhagic pneumonia with early mortality following acute intrapulmonary (PA) infection; barrier disruption was attenuated by platelet reconstitution.

Production of Over 27 000 Peptide and Nearly 4400 Protein Identifications by Single-Shot Capillary-Zone Electrophoresis-Mass Spectrometry via Combination of a Very-Low-Electroosmosis Coated Capillary, a Third-Generation Electrokinetically-Pumped Sheath-Flow Nanospray Interface, an Orbitrap Fusion Lumos Tribrid Mass Spectrometer, and an Advanced-Peak-Determination Algorithm.

We show that capillary-zone electrophoresis-electrospray ionization-tandem mass spectrometry (CZE-ESI-MS/MS) generates very large numbers of peptide and protein identifications (IDs) by combining four technologies: a separation capillary coated to generate very low electroosmosis, an electrokinetically pumped sheath-flow nanoelectrospray interface to produce high-sensitivity ionization, an Orbitrap Fusion Lumos Tribrid platform to provide high-speed analysis, and an advanced-peak-determination (APD) algorithm to take advantage of the mass spectrometer's data-acquisition speed. The use of the APD algorithm resulted in 2 times more identifications than the standard peak algorithm. We also investigated the effect of the isolation window, injection time, and loading amount.

Label-free Neutrophil Enrichment from Patient-derived Airway Secretion Using Closed-loop Inertial Microfluidics.

Airway secretions contain a large number of immune-related cells, e.g., neutrophils, macrophages, and lymphocytes, which can be used as a major resource to evaluate a variety of pulmonary diseases, both for research and clinical purposes.

Asymmetric distribution of biomolecules of maternal origin in the Xenopus laevis egg and their impact on the developmental plan.

Asymmetric cell division is a ubiquitous feature during the development of higher organisms. Asymmetry is achieved by differential localization or activities of biological molecules such as proteins, and coding and non-coding RNAs. Here, we present subcellular transcriptomic and proteomic analyses along the animal-vegetal axis of Xenopus laevis eggs.

Thrombospondin-1 protects against pathogen-induced lung injury by limiting extracellular matrix proteolysis.

Acute lung injury is characterized by excessive extracellular matrix proteolysis and neutrophilic inflammation. A major risk factor for lung injury is bacterial pneumonia. However, host factors that protect against pathogen-induced and host-sustained proteolytic injury following infection are poorly understood.

Sensitive and fast characterization of site-specific protein glycosylation with capillary electrophoresis coupled to mass spectrometry.

Glycoproteomic analysis requires efficient separation and sensitive detection to enable the comprehensive characterization of glycan heterogeneity. Here, we report the use of capillary zone electrophoresis-electrospray ionization-mass spectrometry (CZE-ESI-MS) with an electrokinetically-pumped nanospray interface for the study of protein glycosylation microheterogeneity. A fast separation was developed that resolved intact glycopeptides generated from standard proteins within ~9min.

Site-Specific Glycan Heterogeneity Characterization by Hydrophilic Interaction Liquid Chromatography Solid-Phase Extraction, Reversed-Phase Liquid Chromatography Fractionation, and Capillary Zone Electrophoresis-Electrospray Ionization-Tandem Mass Spectrometry.

Reversed-phase chromatographic separation of glycopeptides tends to be dominated by the peptide composition. In contrast, capillary zone electrophoresis separation of glycopeptides is particularly sensitive to the sialic acid composition of the glycan. In this paper, we combine the two techniques to achieve superior N-glycopeptide analysis.

A -Specific TCR-Transgenic Mouse Demonstrates Th1 Polyfunctionality with Enhanced Effector Function.

is responsible for millions of new infections annually, and current efforts focus on understanding cellular immunity for targeted vaccine development. The -specific CD4 T cell response is characterized by the production of IFN-γ, and polyfunctional Th1 responses are associated with enhanced protection. A major limitation in studying these responses is the paucity of tools available for detection, quantification, and characterization of polyfunctional Ag-specific T cells.

Sublethal and hormesis effects of beta-cypermethrin on the biology, life table parameters and reproductive potential of soybean aphid Aphis glycines.

Beta-cypermethrin has long been recommended as an effective pesticide to control the soybean aphid, Aphis glycines Matsumura, a serious pest in soybean crops. Besides acute toxicity, it leads to changes in life history traits of A. glycines, notably its reproductive potential.