Comparative Toxicogenomics Database's 20th anniversary: update 2025.

For 20 years, the Comparative Toxicogenomics Database (CTD; https://ctdbase.org) has provided high-quality, literature-based curated content describing how environmental chemicals affect human health. Today, CTD includes over 94 million toxicogenomic connections relating chemicals, genes/proteins, phenotypes, anatomical terms, diseases, comparative species, pathways and exposures.

Transforming environmental health datasets from the comparative toxicogenomics database into chord diagrams to visualize molecular mechanisms.

In environmental health, the specific molecular mechanisms connecting a chemical exposure to an adverse endpoint are often unknown, reflecting knowledge gaps. At the public Comparative Toxicogenomics Database (CTD; https://ctdbase.org/), we integrate manually curated, literature-based interactions from CTD to compute four-unit blocks of information organized as a potential step-wise molecular mechanism, known as "CGPD-tetramers," wherein a chemical interacts with a gene product to trigger a phenotype which can be linked to a disease.

More management, less damage? With increasing population size, economic costs of managing geese to minimize yield losses may outweigh benefits.

Conflicts between farmers and geese are intensifying; yet, it remains unclear how interactions between goose population size and management regimes affect yield loss and economic costs. We investigate the cost-effectiveness of accommodation and scaring areas in relation to barnacle goose (Branta leucopsis) population size. We use an existing individual-based model of barnacle geese foraging in nature, accommodation, and scaring areas in Friesland, the Netherlands, to study the most cost-effective management under varying population sizes (i.

CTD tetramers: a new online tool that computationally links curated chemicals, genes, phenotypes, and diseases to inform molecular mechanisms for environmental health.

The molecular mechanisms connecting environmental exposures to adverse endpoints are often unknown, reflecting knowledge gaps. At the Comparative Toxicogenomics Database (CTD), we developed a bioinformatics approach that integrates manually curated, literature-based interactions from CTD to generate a "CGPD-tetramer": a 4-unit block of information organized as a step-wise molecular mechanism linking an initiating Chemical, an interacting Gene, a Phenotype, and a Disease outcome. Here, we describe a novel, user-friendly tool called CTD Tetramers that generates these evidence-based CGPD-tetramers for any curated chemical, gene, phenotype, or disease of interest.

Adverse Effects Associated with Patient-Controlled Analgesia with Ketamine Combined with Opioids and Ketamine Infusion with PCA Bolus in Postoperative Spine Patients: A Retrospective Review.

Objective: There has been increasing use of ketamine at subanesthetic doses as an adjunct to opioids in perioperative pain management. There are several known adverse drug effects (ADEs) associated with ketamine. However, the incidence of ADEs with ketamine infusions with patient-controlled analgesia (PCA) boluses compared with combined opioid and ketamine PCAs is not well described.

Comparative Toxicogenomics Database (CTD): update 2023.

The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) harmonizes cross-species heterogeneous data for chemical exposures and their biological repercussions by manually curating and interrelating chemical, gene, phenotype, anatomy, disease, taxa, and exposure content from the published literature. This curated information is integrated to generate inferences, providing potential molecular mediators to develop testable hypotheses and fill in knowledge gaps for environmental health.

Predicting molecular mechanisms, pathways, and health outcomes induced by Juul e-cigarette aerosol chemicals using the Comparative Toxicogenomics Database.

There is a critical need to understand the health risks associated with vaping e-cigarettes, which has reached epidemic levels among teens. Juul is currently the most popular type of e-cigarette on the market. Using the Comparative Toxicogenomics Database (CTD; http://ctdbase.

CTD Anatomy: analyzing chemical-induced phenotypes and exposures from an anatomical perspective, with implications for environmental health studies.

The Comparative Toxicogenomics Database (CTD) is a freely available public resource that curates and interrelates chemical, gene/protein, phenotype, disease, organism, and exposure data. CTD can be used to address toxicological mechanisms for environmental chemicals and facilitate the generation of testable hypotheses about how exposures affect human health. At CTD, manually curated interactions for chemical-induced phenotypes are enhanced with anatomy terms (tissues, fluids, and cell types) to describe the physiological system of the reported event.

Comparative Toxicogenomics Database (CTD): update 2021.

The public Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) is an innovative digital ecosystem that relates toxicological information for chemicals, genes, phenotypes, diseases, and exposures to advance understanding about human health. Literature-based, manually curated interactions are integrated to create a knowledgebase that harmonizes cross-species heterogeneous data for chemical exposures and their biological repercussions.

Leveraging the Comparative Toxicogenomics Database to Fill in Knowledge Gaps for Environmental Health: A Test Case for Air Pollution-induced Cardiovascular Disease.

Environmental health studies relate how exposures (eg, chemicals) affect human health and disease; however, in most cases, the molecular and biological mechanisms connecting an exposure with a disease remain unknown. To help fill in these knowledge gaps, we sought to leverage content from the public Comparative Toxicogenomics Database (CTD) to identify potential intermediary steps. In a proof-of-concept study, we systematically compute the genes, molecular mechanisms, and biological events for the environmental health association linking air pollution toxicants with 2 cardiovascular diseases (myocardial infarction and hypertension) as a test case.

Temporomandibular disorders, pain in the neck and shoulder area, and headache among musicians.

Background: Uncertainties still exist about the role of playing musical instruments on the report of musculoskeletal complaints and headache.

Objectives: To evaluate the prevalence of and risk indicators for symptoms of temporomandibular disorders, pain in the neck or shoulder, and headache among musicians.

Methods: A questionnaire was distributed among 50 Dutch music ensembles.

Public data sources to support systems toxicology applications.

Public databases provide a wealth of freely available information about chemicals, genes, proteins, biological networks, phenotypes, diseases, and exposure science that can be integrated to construct pathways for systems toxicology applications. Relating this disparate information from public repositories, however, can be challenging since databases use a variety of ways to represent, describe, and make available their content. The use of standard vocabularies to annotate key data concepts, however, allows the information to be more easily exchanged and combined for discovery of new findings.

Are vocalists prone to temporomandibular disorders?

Background: As vocalists demand high physical strains of the masticatory system, singing is frequently mentioned as a risk factor for temporomandibular disorders (TMDs).

Objectives: This study investigated whether vocalists report a higher prevalence of two types of TMDs (viz., TMD pain and temporomandibular joint sounds) compared with instrumentalists who do not load their masticatory system while performing.

The biodistribution and clearance of AlbudAb, a novel biopharmaceutical medicine platform, assessed via PET imaging in humans.

Unlabelled: Conjugation or fusion to AlbudAbs™ (albumin-binding domain antibodies) is a novel approach to extend the half-life and alter the tissue distribution of biological and small molecule therapeutics. To understand extravasation kinetics and extravascular organ concentrations of AlbudAbs in humans, we studied tissue distribution and elimination of a non-conjugated Zr-labeled AlbudAb in healthy volunteers using positron emission tomography/computed tomography (PET/CT).

Methods: A non-conjugated AlbudAb (GSK3128349) was radiolabeled with Zr and a single 1 mg (~ 15 MBq) dose intravenously administered to eight healthy males.

[Singing is not associated with temporomandibular disorders].

This research investigated whether vocalists report pain-related forms of temporomandibular disorders (TMDs) and temporomandibular joint (TMJ) sounds more often than musicians who do not load their masticatory system while playing. In addition, we investigated which risk indicators were associated with TMDs among musicians. A total of 1,470 musicians from 50 different music ensembles completed a questionnaire, including 306 vocalists (the group investigated) and 209 musicians who do not load their jaw while playing (the control group).

Oro-facial pain experience among symphony orchestra musicians in Finland is associated with reported stress, sleep bruxism and disrupted sleep-Independent of the instrument group.

Background: To evaluate whether oro-facial pain experience was related to the type of musical instrument and to learn more about the roles of sleep and sleep-related issues in the pain among professional musicians.

Objectives: A standard questionnaire was sent to all Finnish symphony orchestras (n = 19), with altogether 1005 professional musicians and other personnel.

Methods: The questionnaire covered descriptive data, instrument group, items on perceived quality of sleep, possible sleep bruxism, stress experience and oro-facial pain experience during the past 30 days.

The Comparative Toxicogenomics Database: update 2019.

The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) is a premier public resource for literature-based, manually curated associations between chemicals, gene products, phenotypes, diseases, and environmental exposures. In this biennial update, we present our new chemical-phenotype module that codes chemical-induced effects on phenotypes, curated using controlled vocabularies for chemicals, phenotypes, taxa, and anatomical descriptors; this module provides unique opportunities to explore cellular and system-level phenotypes of the pre-disease state and allows users to construct predictive adverse outcome pathways (linking chemical-gene molecular initiating events with phenotypic key events, diseases, and population-level health outcomes).

Chemical-Induced Phenotypes at CTD Help Inform the Predisease State and Construct Adverse Outcome Pathways.

The Comparative Toxicogenomics Database (CTD; http://ctdbase.org) is a public resource that manually curates the scientific literature to provide content that illuminates the molecular mechanisms by which environmental exposures affect human health. We introduce our new chemical-phenotype module that describes how chemicals can affect molecular, cellular, and physiological phenotypes.

Accessing an Expanded Exposure Science Module at the Comparative Toxicogenomics Database.

The Comparative Toxicogenomics Database (CTD; http://ctdbase.org) is a free resource that provides manually curated information on chemical, gene, phenotype, and disease relationships to advance understanding of the effect of environmental exposures on human health. Four core content areas are independently curated: chemical-gene interactions, chemical-disease and gene-disease associations, chemical-phenotype interactions, and environmental exposure data (e.

The Comparative Toxicogenomics Database: update 2017.

The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) provides information about interactions between chemicals and gene products, and their relationships to diseases. Core CTD content (chemical-gene, chemical-disease and gene-disease interactions manually curated from the literature) are integrated with each other as well as with select external datasets to generate expanded networks and predict novel associations.

Generating Gene Ontology-Disease Inferences to Explore Mechanisms of Human Disease at the Comparative Toxicogenomics Database.

Strategies for discovering common molecular events among disparate diseases hold promise for improving understanding of disease etiology and expanding treatment options. One technique is to leverage curated datasets found in the public domain. The Comparative Toxicogenomics Database (CTD; http://ctdbase.

Advancing Exposure Science through Chemical Data Curation and Integration in the Comparative Toxicogenomics Database.

Background: Exposure science studies the interactions and outcomes between environmental stressors and human or ecological receptors. To augment its role in understanding human health and the exposome, we aimed to centralize and integrate exposure science data into the broader biological framework of the Comparative Toxicogenomics Database (CTD), a public resource that promotes understanding of environmental chemicals and their effects on human health.

Objectives: We integrated exposure data within the CTD to provide a centralized, freely available resource that facilitates identification of connections between real-world exposures, chemicals, genes/proteins, diseases, biological processes, and molecular pathways.

Utility of the Vivosonic Integrity™ auditory brainstem response system as a hearing screening device for difficult-to-test children.

Objective: Inability to complete a behavioral hearing screening is a challenge for children with developmental disorders or who are otherwise difficult to test, defined here as unable or unwilling to complete a behavioral screening. The study compared referral rates from screenings that used behavioral methods alone, with screenings that added a screen with the Vivosonic Integrity™ auditory brainstem response (ABR) device.

Design: Behavioral screening was performed first.

First clinical results of (D)-18F-Fluoromethyltyrosine (BAY 86-9596) PET/CT in patients with non-small cell lung cancer and head and neck squamous cell carcinoma.

Unlabelled: (D)-(18)F-fluoromethyltyrosine (d-(18)F-FMT), or BAY 86-9596, is a novel (18)F-labeled tyrosine derivative rapidly transported by the l-amino acid transporter (LAT-1), with a faster blood pool clearance than the corresponding l-isomer. The aim of this study was to demonstrate the feasibility of tumor detection in patients with non-small cell lung cancer (NSCLC) or head and neck squamous cell cancer (HNSCC) compared with inflammatory and physiologic tissues in direct comparison to (18)F-FDG.

Methods: 18 patients with biopsy-proven NSCLC (n = 10) or HNSCC (n = 8) were included in this Institutional Review Board-approved, prospective multicenter study.

A computerised communication aid in severe aphasia: an exploratory study.

Purpose: To investigate the efficacy of TouchSpeak (TS), a handheld computerised communication aid for aphasia.

Method: A pre-post one-group design was used with a referred sample of 34 patients with a severe aphasia and a need for alternative and augmentative communication (AAC). The participants were trained to use TS in two self-chosen communicative situations.