2024
Chemical entity normalization for successful translational development of Alzheimer’s disease and dementia therapeutics
Mullin S, McDougal R, Cheung K, Kilicoglu H, Beck A, Zeiss C. Chemical entity normalization for successful translational development of Alzheimer’s disease and dementia therapeutics. Journal Of Biomedical Semantics 2024, 15: 13. PMID: 39080729, PMCID: PMC11290083, DOI: 10.1186/s13326-024-00314-1.Peer-Reviewed Original ResearchMeSH KeywordsAlzheimer DiseaseBiological OntologiesDementiaHumansNatural Language ProcessingTranslational Research, BiomedicalConceptsEntity normalizationChemical mentionsNatural language modelDictionary-based methodsDictionary-based approachCRAFT corpusDownstream tasksLanguage modelChemical Entities of Biological InterestPubMedBERT modelDisambiguationChEBIDownstream applicationsArticle abstractsRelationship typesMentionsPubMedBERTOntologyDementia literatureTaskDementia CohortMethodEntitiesAccuracyDementia
2019
Menagerie: A text-mining tool to support animal-human translation in neurodegeneration research
Zeiss CJ, Shin D, Wyk B, Beck AP, Zatz N, Sneiderman CA, Kilicoglu H. Menagerie: A text-mining tool to support animal-human translation in neurodegeneration research. PLOS ONE 2019, 14: e0226176. PMID: 31846471, PMCID: PMC6917268, DOI: 10.1371/journal.pone.0226176.Peer-Reviewed Original ResearchAnimalsBiomedical ResearchData MiningHumansNeurodegenerative DiseasesOutcome Assessment, Health CareTranslational Research, Biomedical
2018
Pathology Study Design, Conduct, and Reporting to Achieve Rigor and Reproducibility in Translational Research Using Animal Models.
Everitt JI, Treuting PM, Scudamore C, Sellers R, Turner PV, Ward JM, Zeiss CJ. Pathology Study Design, Conduct, and Reporting to Achieve Rigor and Reproducibility in Translational Research Using Animal Models. ILAR Journal 2018, 59: 4-12. PMID: 30624739, DOI: 10.1093/ilar/ily020.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsHumansPathologyReproducibility of ResultsResearch DesignTranslational Research, BiomedicalConceptsAnimal modelsAnimal model-based researchAnimal study dataPreclinical animal modelsHuman clinical experienceHuman clinical trialsPreclinical animal studiesAnimal-based studiesPreclinical animal experimentsPreclinical investigatorsClinical trialsPotential therapyAnimal studiesClinical experiencePathology analysisPathology practiceStudy designAnimal experimentsPathology methodsTranslational researchTissue collectionLimited concordanceComparative pathologistsReproducibility of dataToxicologic Pathology
2017
Immune responses to the real world
Zeiss CJ, Brayton CF. Immune responses to the real world. Lab Animal 2017, 47: 13-14. PMID: 29297473, DOI: 10.1038/laban.1384.Peer-Reviewed Original ResearchBridging the Gap between Reproducibility and Translation: Data Resources and Approaches.
Zeiss CJ, Johnson LK. Bridging the Gap between Reproducibility and Translation: Data Resources and Approaches. ILAR Journal 2017, 58: 1-3. PMID: 28586416, DOI: 10.1093/ilar/ilx017.Peer-Reviewed Original ResearchAnimalsComputational BiologyGenomicsHumansMicePrimatesRatsReproducibility of ResultsTranslational Research, BiomedicalFrom Reproducibility to Translation in Neurodegenerative Disease.
Zeiss CJ. From Reproducibility to Translation in Neurodegenerative Disease. ILAR Journal 2017, 58: 106-114. PMID: 28444192, DOI: 10.1093/ilar/ilx006.Peer-Reviewed Original ResearchMeSH KeywordsAnimal ExperimentationAnimalsHumansNeurodegenerative DiseasesReproducibility of ResultsResearch DesignTranslational Research, BiomedicalConceptsNeurodegenerative diseasesPreclinical studiesDisease-altering treatmentsComplex human neurodegenerative diseasesBody of evidenceAnimal study designHuman neurodegenerative diseasesOutcome measuresTherapeutic studiesPreclinical successPharmacologic criteriaTherapeutic potentialStudy designDiseaseIndividual diseasesAnimal experimentsBiomarker dataTranslational purposesCell-based systemsConcept studyStudy design methodsPredictive validityPhenotypic variabilityPatientsStudyEstablished patterns of animal study design undermine translation of disease-modifying therapies for Parkinson’s disease
Zeiss CJ, Allore HG, Beck AP. Established patterns of animal study design undermine translation of disease-modifying therapies for Parkinson’s disease. PLOS ONE 2017, 12: e0171790. PMID: 28182759, PMCID: PMC5300282, DOI: 10.1371/journal.pone.0171790.Peer-Reviewed Original ResearchConceptsDisease-modifying therapiesClinical outcome measuresDisease-modifying interventionsNon-human primatesParkinson's diseaseOutcome measuresStudy designHuman studiesToxin-induced modelsHuman interventional studiesLongitudinal clinical outcomesPreclinical study designStudy design dataToxic protocolsClinical outcomesContemporary cohortNeuropathologic dataStudy design factorsInterventional studyMultiple time pointsPD phenotypeAnimal studiesIntervention characteristicsIntervention categoriesProgressive nature
2014
Improving the predictive value of interventional animal models data
Zeiss CJ. Improving the predictive value of interventional animal models data. Drug Discovery Today 2014, 20: 475-482. PMID: 25448761, PMCID: PMC4417064, DOI: 10.1016/j.drudis.2014.10.015.Peer-Reviewed Original ResearchConceptsAnimal studiesSignificant potential confoundersAnimal model dataPercent of interventionsMore animal modelsPotential confoundersChronic diseasesImproved outcomesAmyloid hypothesisAnimal modelsPredictive valueAlzheimer's diseasePositive outcomesDiseaseTranslational successOutcomesPositive-outcome biasInterventionAdditional mechanismAnimalsMemantineConfoundersDonepezil
2013
Translational models of ocular disease
Zeiss CJ. Translational models of ocular disease. Veterinary Ophthalmology 2013, 16: 15-33. PMID: 23750503, DOI: 10.1111/vop.12065.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnimals, DomesticAnimals, LaboratoryEye DiseasesHumansTranslational Research, BiomedicalConceptsLarge animal modelIntraocular neoplasiaStromal diseaseOcular diseasesAnimal modelsRetinal dystrophyTherapeutic potentialTranslational modelClinical veterinary medicineLaboratory animalsDomestic animalsDiseaseHuman medicineAnimalsVeterinary medicineMechanistic discoveriesGenetic contributionHumansMedicineUveitis