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 ResearchConceptsEntity normalizationChemical mentionsNatural language modelDictionary-based methodsDictionary-based approachCRAFT corpusDownstream tasksLanguage modelChemical Entities of Biological InterestPubMedBERT modelDisambiguationChEBIDownstream applicationsArticle abstractsRelationship typesMentionsPubMedBERTOntologyDementia literatureTaskDementia CohortMethodEntitiesAccuracyDementiaPrior Influenza Infection Mitigates SARS-CoV-2 Disease in Syrian Hamsters
Di Pietro C, Haberman A, Lindenbach B, Smith P, Bruscia E, Allore H, Vander Wyk B, Tyagi A, Zeiss C. Prior Influenza Infection Mitigates SARS-CoV-2 Disease in Syrian Hamsters. Viruses 2024, 16: 246. PMID: 38400021, PMCID: PMC10891789, DOI: 10.3390/v16020246.Peer-Reviewed Original ResearchConceptsTransient gene expressionSARS-CoV-2Viral replication pathwayReplication pathwayAntiviral pathwaysEndemism patternsUpregulation of innateGene expressionQuantitative RT-PCRMitigated weight lossDual-infected animalsSARS-CoV-2 viral loadSARS-CoV-2 infectionSyrian hamstersSeasonal infection ratesSARS-CoV-2 inoculationLungs of animalsIndividual virusesSARS-CoV-2 diseaseUpper respiratory tractH1N1 infectionRT-PCRBronchoalveolar lavageViral loadCytokine levels
2021
Comparative Milestones in Rodent and Human Postnatal Central Nervous System Development
Zeiss CJ. Comparative Milestones in Rodent and Human Postnatal Central Nervous System Development. Toxicologic Pathology 2021, 49: 1368-1373. PMID: 34569375, DOI: 10.1177/01926233211046933.Peer-Reviewed Original ResearchConceptsPostnatal developmentCentral nervous system immaturityPostnatal central nervous system developmentRodent olfactory bulbCentral nervous system developmentRodent brain developmentPostnatal injuryDentate gyrusPostnatal neurogenesisNervous system developmentOlfactory bulbSynaptic maturationSynaptic pruningNeurodevelopmental toxicityGuinea pigsBrain developmentAltricial rodentsCNS developmentPrecocial guinea pigCerebellar developmentRodentsRatsMyelinationNeurogenesisBirthAge‐related calcium dysregulation linked with tau pathology and impaired cognition in non‐human primates
Datta D, Leslie SN, Wang M, Morozov YM, Yang S, Mentone S, Zeiss C, Duque A, Rakic P, Horvath TL, van Dyck C, Nairn AC, Arnsten AFT. Age‐related calcium dysregulation linked with tau pathology and impaired cognition in non‐human primates. Alzheimer's & Dementia 2021, 17: 920-932. PMID: 33829643, PMCID: PMC8195842, DOI: 10.1002/alz.12325.Peer-Reviewed Original ResearchConceptsTau pathologyCalcium leakTau phosphorylationNeuronal firingAlzheimer's diseaseEarly tau phosphorylationPyramidal cell dendritesSporadic Alzheimer's diseasePrimary cortical neuronsPotential therapeutic targetCognitive performanceAge-related reductionMacaque dorsolateral prefrontal cortexDorsolateral prefrontal cortexNon-human primatesCalcium dysregulationCell dendritesCortical neuronsCalcium-binding proteinsAD biomarkersPathology markersTherapeutic targetAnimal modelsAged monkeysPrefrontal cortex
2020
AgRP neurons control compulsive exercise and survival in an activity-based anorexia model
Miletta MC, Iyilikci O, Shanabrough M, Šestan-Peša M, Cammisa A, Zeiss CJ, Dietrich MO, Horvath TL. AgRP neurons control compulsive exercise and survival in an activity-based anorexia model. Nature Metabolism 2020, 2: 1204-1211. PMID: 33106687, DOI: 10.1038/s42255-020-00300-8.Peer-Reviewed Original ResearchConceptsAgRP neuronsActivity-based anorexia modelAgRP neuronal activityVivo fiber photometryFood-restricted miceFood-restricted animalsCompulsive exerciseAnorexia modelHypothalamic agoutiNeuropeptide YExercise volumeFood intakeMouse modelNeuronal activityFiber photometryDaily activationNeuronal circuitsPsychiatric conditionsAnorexia nervosaChemogenetic toolsNeuronsLong-term behavioral impactElevated fat contentVoluntary cessationFat contentUtility of spontaneous animal models of Alzheimer’s disease in preclinical efficacy studies
Zeiss CJ. Utility of spontaneous animal models of Alzheimer’s disease in preclinical efficacy studies. Cell And Tissue Research 2020, 380: 273-286. PMID: 32337614, DOI: 10.1007/s00441-020-03198-6.Peer-Reviewed Original ResearchConceptsHuman Alzheimer's diseaseSpontaneous animal modelAlzheimer's diseaseAnimal modelsBiomarker progressionProgression of neuropathologyLate-onset Alzheimer's diseasePreclinical efficacy studiesHuman clinical trialsOnset Alzheimer's diseaseUsable outcome measuresAD-associated mutationsFamilial Alzheimer's diseaseNon-human primatesAmyloid neuropathologyInterventional studyClinical trialsSpontaneous modelHuman trialsOutcome measuresTherapeutic successPotential therapyNew therapiesRodent studiesEfficacy studies
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 ResearchDoxorubicin-Induced Cardiotoxicity in Collaborative Cross (CC) Mice Recapitulates Individual Cardiotoxicity in Humans
Zeiss CJ, Gatti DM, Toro-Salazar O, Davis C, Lutz CM, Spinale F, Stearns T, Furtado MB, Churchill GA. Doxorubicin-Induced Cardiotoxicity in Collaborative Cross (CC) Mice Recapitulates Individual Cardiotoxicity in Humans. G3: Genes, Genomes, Genetics 2019, 9: 2637-2646. PMID: 31263061, PMCID: PMC6686936, DOI: 10.1534/g3.119.400232.Peer-Reviewed Original ResearchConceptsCardiac diseaseCardiac pathologyCardiac troponin I levelsUltimate severityChronic cardiac injuryTroponin I levelsPotential predictive biomarkersDoxorubicin-Induced CardiotoxicityComplete blood countPanel of biomarkersCurrent mouse modelsEffect of treatmentCardiac troponin IProgressive cardiotoxicityLight chain 3Acute periodAcute phaseCardiac injuryRenal toxicityBlood countPredictive biomarkersChronic timepointsCollaborative Cross miceSame doseI levelsAn ABCA4 loss-of-function mutation causes a canine form of Stargardt disease
Mäkeläinen S, Gòdia M, Hellsand M, Viluma A, Hahn D, Makdoumi K, Zeiss CJ, Mellersh C, Ricketts SL, Narfström K, Hallböök F, Ekesten B, Andersson G, Bergström TF. An ABCA4 loss-of-function mutation causes a canine form of Stargardt disease. PLOS Genetics 2019, 15: e1007873. PMID: 30889179, PMCID: PMC6424408, DOI: 10.1371/journal.pgen.1007873.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsATP Binding Cassette Transporter, Subfamily A, Member 4ATP-Binding Cassette TransportersBase SequenceCodon, NonsenseDisease Models, AnimalDog DiseasesDogsFemaleGenes, RecessiveHomozygoteHumansLipofuscinMacular DegenerationMaleMicroscopy, FluorescenceModels, MolecularMutagenesis, InsertionalMutationPedigreeProtein ConformationRetinaStargardt DiseaseWhole Genome SequencingConceptsRetinal pigment epitheliumStargardt diseaseAutosomal recessive retinal degenerative diseaseRetinal degenerationABCA4 geneVisual impairmentCentral visual impairmentFull-length ABCA4 proteinFunction mutationsLabrador Retriever dogsLarge animal modelRetinal degenerative diseasesAutosomal recessive retinal degenerationMember 4 geneRecessive retinal degenerationStandard treatmentClinical trialsClinical signsLipofuscin depositsPigment epitheliumAnimal modelsCanine modelUnaffected dogsAffected dogsCone photoreceptors
2018
Investigating the role of interleukin-1 beta and glutamate in inflammatory bowel disease and epilepsy using discovery browsing
Rindflesch TC, Blake CL, Cairelli MJ, Fiszman M, Zeiss CJ, Kilicoglu H. Investigating the role of interleukin-1 beta and glutamate in inflammatory bowel disease and epilepsy using discovery browsing. Journal Of Biomedical Semantics 2018, 9: 25. PMID: 30587224, PMCID: PMC6307110, DOI: 10.1186/s13326-018-0192-y.Peer-Reviewed Original ResearchConceptsInflammatory bowel diseaseInterleukin-1 betaBowel diseaseAdverse drug reactionsBetter healthcare outcomesElectronic health recordsDrug reactionsGlutamate levelsClinical dataEarlier population studiesStructured clinical dataEpilepsyHealthcare outcomesHealth recordsImproved treatmentDiseasePopulation studiesDrug developmentGlutamateBetaEtiologyMethodsInStudyPathology 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 ResearchConceptsAnimal 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 ResearchSafety and Efficacy of AAV5 Vectors Expressing Human or Canine CNGB3 in CNGB3-Mutant Dogs
Ye GJ, Komáromy AM, Zeiss C, Calcedo R, Harman CD, Koehl KL, Stewart GA, Iwabe S, Chiodo VA, Hauswirth WW, Aguirre GD, Chulay JD. Safety and Efficacy of AAV5 Vectors Expressing Human or Canine CNGB3 in CNGB3-Mutant Dogs. Human Gene Therapy 2017, 28: 197-207. PMID: 29020838, PMCID: PMC5733651, DOI: 10.1089/humc.2017.125.Peer-Reviewed Original ResearchConceptsHuman CNGB3Immune responseHigh dosesT cell immune responsesHigh-dose groupLow-dose groupInherited retinal disorderImmune-mediated toxicitiesHigher vector doseCone photoreceptor functionDifferent dose levelsFocal chorioretinitisRetinal toxicityVisual acuityInflammatory responseAAV vectorsRetinal disordersSubretinal injectionCone functionDose levelsCone photoreceptorsPhotoreceptor functionCNGB3AAV5 vectorVector doseInformatics Support for Basic Research in Biomedicine.
Rindflesch TC, Blake CL, Fiszman M, Kilicoglu H, Rosemblat G, Schneider J, Zeiss CJ. Informatics Support for Basic Research in Biomedicine. ILAR Journal 2017, 58: 80-89. PMID: 28838071, PMCID: PMC5886329, DOI: 10.1093/ilar/ilx004.Peer-Reviewed Original ResearchConceptsSemantic MEDLINEText mining techniquesDocument retrievalHigh-level connectionsMining techniquesBiomedical research literatureUse casesBiomedical entitiesRelation identificationComputer-assisted techniquesInformatics supportPubMed queryUsersInformatics methodologiesBiomedical researchersInformatics methodsResearch areaHypothesis formationBiomedical research areasIterative processLarge amountQueriesLarge numberRetrievalCurrent developmentsBridging 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 ResearchFrom 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 ResearchConceptsNeurodegenerative 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
2015
Clostridium perfringens enterotoxin C‐terminal domain labeled to fluorescent dyes for in vivo visualization of micrometastatic chemotherapy‐resistant ovarian cancer
Cocco E, Shapiro EM, Gasparrini S, Lopez S, Schwab CL, Bellone S, Bortolomai I, Sumi NJ, Bonazzoli E, Nicoletti R, Deng Y, Saltzman WM, Zeiss CJ, Centritto F, Black JD, Silasi DA, Ratner E, Azodi M, Rutherford TJ, Schwartz PE, Pecorelli S, Santin AD. Clostridium perfringens enterotoxin C‐terminal domain labeled to fluorescent dyes for in vivo visualization of micrometastatic chemotherapy‐resistant ovarian cancer. International Journal Of Cancer 2015, 137: 2618-2629. PMID: 26060989, PMCID: PMC4573336, DOI: 10.1002/ijc.29632.Peer-Reviewed Original ResearchConceptsPatient-derived xenograftsTumor fluorescenceChemotherapy-resistant ovarian cancerClaudin-3Human ovarian cancer xenograftsTime of surgeryOvarian cancer patientsNeoadjuvant chemotherapy treatmentOvarian cancer xenograftsHealthy organsVivo visualizationTime of intervalBackground fluorescence ratioClostridium perfringens enterotoxinChemotherapy-naïveMicrometastatic diseaseMalignant ascitesOvarian diseaseResidual diseaseOvarian tumorsCancer patientsCancer xenograftsChemotherapy treatmentIP injectionOvarian cancer
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 ResearchConceptsLarge animal modelIntraocular neoplasiaStromal diseaseOcular diseasesAnimal modelsRetinal dystrophyTherapeutic potentialTranslational modelClinical veterinary medicineLaboratory animalsDomestic animalsDiseaseHuman medicineAnimalsVeterinary medicineMechanistic discoveriesGenetic contributionHumansMedicineUveitis