2024
Overestimation of Severe Acute Respiratory Syndrome Coronavirus 2 Household Transmission in Settings of High Community Transmission: Insights From an Informal Settlement Community in Salvador, Brazil
Ticona J, Nery N, Hitchings M, Belitardo E, Fofana M, Dorión M, Victoriano R, Cruz J, Santana J, de Moraes L, Cardoso C, Ribeiro G, Reis M, Khouri R, Costa F, Ko A, Cummings D. Overestimation of Severe Acute Respiratory Syndrome Coronavirus 2 Household Transmission in Settings of High Community Transmission: Insights From an Informal Settlement Community in Salvador, Brazil. Open Forum Infectious Diseases 2024, 11: ofae065. PMID: 38516384, PMCID: PMC10957159, DOI: 10.1093/ofid/ofae065.Peer-Reviewed Original ResearchSARS-CoV-2Household transmissionRT-PCR positive casesSecondary attack rateAttack rateSARS-CoV-2 infectionSARS-CoV-2 Omicron variantRisk of infectionCommunity acquisitionTherapeutic optionsCOVID-19-related symptomsCase-finding studyHousehold contactsAcquisition of SARS-CoV-2Increased riskSymptom onsetSecondary infectionBooster vaccinationSevere outcomesBiweekly visitsHighest attack rateRT-PCRInfectionCOVID-19 severe outcomesOmicron BAPrior 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
2023
Molecular Characterization of HER2-Low Invasive Breast Carcinoma by Quantitative RT-PCR Using Oncotype DX Assay
Lin H, Can T, Kahn A, Flannery C, Hoag J, Akkunuri A, Bailey H, Baehner R, Pusztai L, Rozenblit M. Molecular Characterization of HER2-Low Invasive Breast Carcinoma by Quantitative RT-PCR Using Oncotype DX Assay. The Oncologist 2023, 28: e973-e976. PMID: 37656608, PMCID: PMC10546821, DOI: 10.1093/oncolo/oyad249.Peer-Reviewed Original ResearchConceptsHER2 mRNA levelsIHC 0MRNA levelsOncotype DX recurrence score resultsEstrogen receptor-positive breast cancerReceptor-positive breast cancerCurrent adjuvant chemotherapyOncotype DX assayRecurrence Score resultsPositive breast cancerInvasive breast carcinomaIHC score 0Adjuvant chemotherapyQuantitative RT-PCRBreast carcinomaPositive statusScore 0Breast cancerStage IYale cohortHigher mRNA levelsCancerRT-PCRPatientsHER2Identification of risk factors and mosquito vectors associated with dengue virus infection in American Samoa, 2017
Sharp T, Tufa A, Cotter C, Lozier M, Santiago G, Johnson S, Mataia’a M, Waterman S, Muñoz-Jordán J, Paz-Bailey G, Hemme R, Schmaedick M, Anesi S. Identification of risk factors and mosquito vectors associated with dengue virus infection in American Samoa, 2017. PLOS Global Public Health 2023, 3: e0001604. PMID: 37418355, PMCID: PMC10328243, DOI: 10.1371/journal.pgph.0001604.Peer-Reviewed Original ResearchDENV infectionIgM ELISARisk factorsRT-PCRDENV-2Dengue virus infectionPopulation-specific risk factorsFrequency of infectionDENV nucleic acidMosquito vectorsOutbreak of dengueCluster investigationsFebrile illnessMedian ageResidents of householdsRole of AeDengue patientsVirus infectionDENV transmissionSerum specimensZika virusPatient specimensBivariate analysisInfectionAdult female mosquitoesCochlear transcript diversity and its role in auditory functions implied by an otoferlin short isoform
Liu H, Liu H, Wang L, Song L, Jiang G, Lu Q, Yang T, Peng H, Cai R, Zhao X, Zhao T, Wu H. Cochlear transcript diversity and its role in auditory functions implied by an otoferlin short isoform. Nature Communications 2023, 14: 3085. PMID: 37248244, PMCID: PMC10227054, DOI: 10.1038/s41467-023-38621-3.Peer-Reviewed Original ResearchConceptsShort isoformEndocytic membrane retrievalRNA sequencing techniquesDiverse biological functionsInner hair cellsTranscript diversityUnannotated transcriptsRNA-seqAlternative isoformsMembrane retrievalBiological functionsGENCODE databasesKey proteinsIsoform resolutionSequencing techniquesSustained exocytosisIsoformsMechanistic understandingAuditory functionSanger sequencingHair cellsTranscriptsRT-PCRSynaptic transmissionAuditory phenotype
2022
MHC class II-restricted-presentationMHC class II and DM molecules in chickens: different yet again
Wise D, Halabi S, Afrache H, Fakiola M, Parker A, Kaufman J. MHC class II-restricted-presentationMHC class II and DM molecules in chickens: different yet again. Molecular Immunology 2022, 150: 32-33. DOI: 10.1016/j.molimm.2022.05.108.Peer-Reviewed Original ResearchIntestinal epithelial cellsClass II moleculesKO cellsClass II A genesII moleculesClass I systemResistance to infectious diseasesRT-PCRBF2 genesWestern blottingDM locusClass II BI systemA geneChicken MHCGenetic associationTapasin geneCRISPR-Cas9DMB1Tissue section stainingGenesBLB2Closely-linkedB2-microglobulinGut tissueTesting for COVID-19 is Much More Effective When Performed Immediately Prior to Social Mixing
Wells CR, Gokcebel S, Pandey A, Galvani AP, Townsend JP. Testing for COVID-19 is Much More Effective When Performed Immediately Prior to Social Mixing. International Journal Of Public Health 2022, 67: 1604659. PMID: 35967267, PMCID: PMC9363582, DOI: 10.3389/ijph.2022.1604659.Peer-Reviewed Original ResearchComparative analyses of eighteen rapid antigen tests and RT-PCR for COVID-19 quarantine and surveillance-based isolation
Wells CR, Pandey A, Moghadas SM, Singer BH, Krieger G, Heron RJL, Turner DE, Abshire JP, Phillips KM, Michael Donoghue A, Galvani AP, Townsend JP. Comparative analyses of eighteen rapid antigen tests and RT-PCR for COVID-19 quarantine and surveillance-based isolation. Communications Medicine 2022, 2: 84. PMID: 35822105, PMCID: PMC9271059, DOI: 10.1038/s43856-022-00147-y.Peer-Reviewed Original ResearchRT-PCR testingRT-PCR testAntigen testRA testRT-PCRSerial testingSingle RT-PCR testSARS-CoV-2 infectionRapid antigen testEmergency use authorizationUnited States FoodExtent of transmissionDrug AdministrationCOVID-19 infectiousnessEffective reproduction numberStates FoodCOVID-19 quarantineQuarantine durationTest specificitySpread of diseaseDiagnostic characteristicsTesting strategiesReproduction numberFalse positive rateQuarantineInhibitory Effect of Biotransformed-Fucoidan on the Differentiation of Osteoclasts Induced by Receptor for Activation of Nuclear Factor-κB Ligand
Park B, Yu S, Kim S, Lee J, Choi S, Chang J, Yang E, Kim K, Ahn S. Inhibitory Effect of Biotransformed-Fucoidan on the Differentiation of Osteoclasts Induced by Receptor for Activation of Nuclear Factor-κB Ligand. Journal Of Microbiology And Biotechnology 2022, 32: 1017-1025. PMID: 35879294, PMCID: PMC9628933, DOI: 10.4014/jmb.2203.03001.Peer-Reviewed Original ResearchConceptsNuclear factor-κB ligandBone marrow macrophagesOsteoclast differentiationBone homeostasisBackground of osteoporosisLow molecular weight fucoidanExpression of NFATc1Effect of fucoidanDifferentiation of osteoclastsResistant acid phosphatase activityHarmful side effectsSide effectsPharmaceutical treatmentWeight fucoidanKey transcriptional factorOsteoporosisMarrow macrophagesDifferentiated osteoclastsInhibitory effectOsteoclastsRT-PCRC-fosSafe natural productVirus isolation data improve host predictions for New World rodent orthohantaviruses
Mull N, Carlson C, Forbes K, Becker D. Virus isolation data improve host predictions for New World rodent orthohantaviruses. Journal Of Animal Ecology 2022, 91: 1290-1302. PMID: 35362148, DOI: 10.1111/1365-2656.13694.Peer-Reviewed Original ResearchConceptsRisk of pathogen spilloverHost associationsMulti-host pathogensRT-PCR dataVirus isolation dataBRT modelsTrait profilesEcological traitsReservoir host speciesPathogen spilloverRT-PCRHost speciesPathogen maintenancePathogen hostsRegression treesBRTHost predictionHost competenceHantavirus cardiopulmonary syndromeZoonotic reservoirsPrioritizing surveillanceRodent phylogenyMultiple data typesIsolation dataMuroid rodentsQuarantine and testing strategies to ameliorate transmission due to travel during the COVID-19 pandemic: a modelling study
Wells CR, Pandey A, Fitzpatrick MC, Crystal WS, Singer BH, Moghadas SM, Galvani AP, Townsend JP. Quarantine and testing strategies to ameliorate transmission due to travel during the COVID-19 pandemic: a modelling study. The Lancet Regional Health - Europe 2022, 14: 100304. PMID: 35036981, PMCID: PMC8743228, DOI: 10.1016/j.lanepe.2021.100304.Peer-Reviewed Original ResearchShorter quarantineContacts of casesQuarantine durationCOVID-19 infectionLarge socioeconomic burdenCOVID-19 pandemicRisk stratificationSocioeconomic burdenInfection rateRT-PCRThree daysCanadian InstitutePandemic diseaseNational InstituteHealth researchLonger quarantineEpidemic situationTesting strategies
2021
Optimal diagnostic test allocation strategy during the COVID‐19 pandemic and beyond
Du J, Beesley L, Lee S, Zhou X, Dempsey W, Mukherjee B. Optimal diagnostic test allocation strategy during the COVID‐19 pandemic and beyond. Statistics In Medicine 2021, 41: 310-327. PMID: 34697824, PMCID: PMC8661762, DOI: 10.1002/sim.9238.Peer-Reviewed Original ResearchConceptsHigh-risk patient populationRapid antigen testDiagnostic testsPatient populationRisk patient populationSARS-CoV-2 viral infectionViral diagnostic testsCentral public health challengeAntigen testPatient characteristicsTimely diagnostic testingPublic health challengePublic health decision-makingViral infectionHealth decision-makingPreventing severe diseaseSevere diseaseRT-PCRCOVID-19 pandemic
2020
Partially Differentiated Neuroretinal Cells Promote Maturation of the Retinal Pigment Epithelium
Singh D, Chen X, Xia T, Ghiassi-Nejad M, Tainsh L, Adelman RA, Rizzolo LJ. Partially Differentiated Neuroretinal Cells Promote Maturation of the Retinal Pigment Epithelium. Investigative Ophthalmology & Visual Science 2020, 61: 9-9. PMID: 33151282, PMCID: PMC7671856, DOI: 10.1167/iovs.61.13.9.Peer-Reviewed Original ResearchConceptsRetinal pigment epitheliumRetinal progenitor cellsTransepithelial electrical resistanceNeurosensory retinaPigment epitheliumHuman fetal retinal pigment epitheliumRecoverin-positive cellsFetal retinal pigment epitheliumGanglion cell layerAbility of RPERPE signature genesRed/green opsinTranswell filter insertsStem cellsQuantitative RT-PCRGlial markersHuman stem cellsExpression of rhodopsinInterneuron markersBipolar cellsRetinal culturesRetinaRT-PCRProgenitor cellsPresumptive photoreceptorsAccuracy of the Zika IgM Antibody Capture Enzyme-Linked Immunosorbent Assay from the Centers for Disease Control and Prevention (CDC Zika MAC-ELISA) for Diagnosis of Zika Virus Infection
Portilho M, de Moraes L, Kikuti M, Nascimento L, Reis M, Boaventura V, Khouri R, Ribeiro G. Accuracy of the Zika IgM Antibody Capture Enzyme-Linked Immunosorbent Assay from the Centers for Disease Control and Prevention (CDC Zika MAC-ELISA) for Diagnosis of Zika Virus Infection. Diagnostics 2020, 10: 835. PMID: 33080935, PMCID: PMC7603149, DOI: 10.3390/diagnostics10100835.Peer-Reviewed Original ResearchDays post-symptom onsetZika virus infectionConvalescent-phase seraVirus infectionRT-PCRDengue virusSerological diagnosisDengue casesPost-symptom onsetConvalescent-phase samplesBlood donor samplesIgM antibody capture enzymeEnzyme-linked immunosorbent assayZika IgM antibodySymptom onsetDENV infectionIgM antibodiesZIKV infectionBlood donorsDonor samplesCapture enzymeOutbreak investigationDisease controlInfectionImmunosorbent assayEpidemiologic and spatiotemporal trends of Zika Virus disease during the 2016 epidemic in Puerto Rico
Sharp T, Quandelacy T, Adams L, Aponte J, Lozier M, Ryff K, Flores M, Rivera A, Santiago G, Muñoz-Jordán J, Alvarado L, Rivera-Amill V, Garcia-Negrón M, Waterman S, Paz-Bailey G, Johansson M, Rivera-Garcia B. Epidemiologic and spatiotemporal trends of Zika Virus disease during the 2016 epidemic in Puerto Rico. PLOS Neglected Tropical Diseases 2020, 14: e0008532. PMID: 32956416, PMCID: PMC7529257, DOI: 10.1371/journal.pntd.0008532.Peer-Reviewed Original ResearchConceptsZIKV diseaseDisease casesZika virusZIKV infectionArboviral diseasesEvidence of infectionZika virus diseaseLaboratory-based surveillancePuerto Rico DepartmentPublic health authoritiesIgM ELISAZIKV epidemicHigh incidenceChikungunya virusLaboratory evidenceHealth authoritiesDiseaseEarly detectionRT-PCRInfectionSocioeconomic factorsVirus diseaseEpidemicEarlier midpointIncidenceChallenges in use of saliva for detection of SARS CoV-2 RNA in symptomatic outpatients
Landry ML, Criscuolo J, Peaper DR. Challenges in use of saliva for detection of SARS CoV-2 RNA in symptomatic outpatients. Journal Of Clinical Virology 2020, 130: 104567. PMID: 32750665, PMCID: PMC7392849, DOI: 10.1016/j.jcv.2020.104567.Peer-Reviewed Original ResearchMeSH KeywordsBetacoronavirusClinical Laboratory TechniquesCoronavirus InfectionsCOVID-19COVID-19 TestingCOVID-19 VaccinesHumansMolecular Diagnostic TechniquesNasopharynxOutpatientsPandemicsPneumonia, ViralProspective StudiesReal-Time Polymerase Chain ReactionRNA, ViralSalivaSARS-CoV-2Specimen HandlingConceptsNasopharyngeal swabsReal-time RT-PCRSymptomatic outpatientsRT-PCRSARS-CoV-2 positivitySaliva samplesSARS-CoV-2 testingMedian cycle threshold valuePure salivaSARS-CoV-2 RNA detectionSARS-CoV-2 RNACoV-2 testingUse of salivaCycle threshold valuesSymptomatic patientsOverall sensitivityRNA detectionSalivaCOVID-19OutpatientsHigh-volume testingPatientsSwabsReply to Suri et al.: COVID-19 Real-Time RT-PCR: Does Positivity on Follow-up RT-PCR Always Imply Infectivity?
Chang D, Mo G, Yuan X, Tao Y, Peng X, Wang F, Xie L, Sharma L, Dela Cruz CS, Qin E. Reply to Suri et al.: COVID-19 Real-Time RT-PCR: Does Positivity on Follow-up RT-PCR Always Imply Infectivity? American Journal Of Respiratory And Critical Care Medicine 2020, 202: 148-148. PMID: 32401535, PMCID: PMC7328309, DOI: 10.1164/rccm.202004-1458le.Commentaries, Editorials and LettersPCR and RT-PCR in the Diagnosis of Laboratory Animal Infections and in Health Monitoring.
Compton SR. PCR and RT-PCR in the Diagnosis of Laboratory Animal Infections and in Health Monitoring. Journal Of The American Association For Laboratory Animal Science 2020, 59: 458-468. PMID: 32580820, PMCID: PMC7479767, DOI: 10.30802/aalas-jaalas-20-000008.Peer-Reviewed Original ResearchAnalysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics
Maddirevula S, Kuwahara H, Ewida N, Shamseldin H, Patel N, Alzahrani F, AlSheddi T, AlObeid E, Alenazi M, Alsaif H, Alqahtani M, AlAli M, Al Ali H, Helaby R, Ibrahim N, Abdulwahab F, Hashem M, Hanna N, Monies D, Derar N, Alsagheir A, Alhashem A, Alsaleem B, Alhebbi H, Wali S, Umarov R, Gao X, Alkuraya F. Analysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics. Genome Biology 2020, 21: 145. PMID: 32552793, PMCID: PMC7298854, DOI: 10.1186/s13059-020-02053-9.Peer-Reviewed Original ResearchConceptsWhole-exome sequencingMendelian disordersMendelian diseasesRNA-seqDiagnosis of Mendelian diseasesRNA analysisNon-coding variantsSuspected Mendelian diseasesSuspected Mendelian disordersBlood-derived RNARNA-based diagnosticsWhole-transcriptome sequencingIn silico predictionGenome sequenceRT-PCRMendelian phenotypesTranscriptome sequencingRNA sourceResults of RT-PCRModulate penetranceRNASequenceConclusionsOur resultsVariantsGenomeAssessment of viral RNA in idiopathic pulmonary fibrosis using RNA-seq
Yin Q, Strong MJ, Zhuang Y, Flemington EK, Kaminski N, de Andrade JA, Lasky JA. Assessment of viral RNA in idiopathic pulmonary fibrosis using RNA-seq. BMC Pulmonary Medicine 2020, 20: 81. PMID: 32245461, PMCID: PMC7119082, DOI: 10.1186/s12890-020-1114-1.Peer-Reviewed Original ResearchConceptsIdiopathic pulmonary fibrosisViral RNA expressionViral infectionPulmonary fibrosisPathogenesis of IPFLung biopsy samplesRNA expressionHerpes virus infectionLow-level evidenceReal-time RT-PCRAcute exacerbationControl lungsLung tissueVirus infectionBiopsy samplesSelect virusesPossible associationInfectionRT-PCRStatistical differenceNext-generation sequencingViral RNAFibrosisVirusRNA-seq results
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