2024
Lubricating gel influence on vaginal microbiome sampling
Amitai Komem D, Hadar R, Paulson J, Mordechai Y, Eskandarian H, Efroni G, Amir A, Haberman Y, Tsur A. Lubricating gel influence on vaginal microbiome sampling. Scientific Reports 2024, 14: 18223. PMID: 39107405, PMCID: PMC11303677, DOI: 10.1038/s41598-024-68948-w.Peer-Reviewed Original ResearchConceptsMicrobial compositionVaginal samplesVaginal microbiome samplesBeta diversityVaginal microbiome studiesMicrobiome studiesMicrobiome samplesTaxa abundanceGynecological examinationPregnant womenLubricant gelReduce painMicrobial dataGel exposureEmergency roomSterile swabsEffect of gelMicrobial analysisPrediction of Benefit From Adjuvant Pertuzumab by 80-Gene Signature in the APHINITY (BIG 4-11) Trial
Krop I, Mittempergher L, Paulson J, Andre F, Bonnefoi H, Loi S, Loibl S, Gelber R, Caballero C, Bhaskaran R, Dreezen C, Menicucci A, Bernards R, van ’t Veer L, Piccart M. Prediction of Benefit From Adjuvant Pertuzumab by 80-Gene Signature in the APHINITY (BIG 4-11) Trial. JCO Precision Oncology 2024, 8: e2200667. PMID: 38237097, DOI: 10.1200/po.22.00667.Peer-Reviewed Original ResearchConceptsInvasive disease-free survivalHER2 typeLuminal typeInvasive disease-free survival eventsHazard ratioEarly-stage breast cancerLuminal-type tumorsMolecular subtype signaturesAnti-HER2 therapyHER2-positive tumorsDisease-free survivalStandard adjuvant chemotherapyBasal-type tumorsBasal typePredictive of benefitAdjuvant pertuzumabAPHINITY trialHER2-typeHER2-positiveInferior prognosisAdjuvant chemotherapyTumor subtypesNo significant differenceAnti-HER2Breast tumors
2022
Prognostic mutational subtyping in de novo diffuse large B-cell lymphoma
Kim E, Jiang Y, Xu T, Bazeos A, Knapp A, Bolen C, Humphrey K, Nielsen T, Penuel E, Paulson J. Prognostic mutational subtyping in de novo diffuse large B-cell lymphoma. BMC Cancer 2022, 22: 231. PMID: 35236331, PMCID: PMC8892802, DOI: 10.1186/s12885-022-09237-5.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAntineoplastic Combined Chemotherapy ProtocolsBridged Bicyclo Compounds, HeterocyclicClinical Trials, Phase II as TopicClinical Trials, Phase III as TopicEnhancer of Zeste Homolog 2 ProteinExome SequencingFemaleHumansLymphoma, Large B-Cell, DiffuseMaleMiddle AgedMutationPrognosisProto-Oncogene Proteins c-bcl-2RNA-SeqSulfonamidesTreatment OutcomeConceptsSequence dataWhole-exome sequencing dataExome-sequencing dataTargeted sequencing platformsExome sequencing dataTargeted sequencing dataBackgroundDiffuse large B-cell lymphomaLarge B-cell lymphomaSequencing platformsRNA-seqDe novo DLBCLImproved overall survivalTarget sequenceB-cell lymphomaVenetoclax therapyMutation subtypesPrognostic subsetsMutationsOverall survivalMolecular subsetsSubset distributionMutation groupSurvival outcomesMutation profilesClinical associationsCytomegalovirus infections in infants in Uganda: Newborn-mother pairs, neonates with sepsis, and infants with hydrocephalus
Hehnly C, Ssentongo P, Bebell L, Burgoine K, Bazira J, Fronterre C, Kumbakumba E, Mulondo R, Mbabazi-Kabachelor E, Morton S, Ngonzi J, Ochora M, Olupot-Olupot P, Mugamba J, Onen J, Roberts D, Sheldon K, Sinnar S, Smith J, Ssenyonga P, Kiwanuka J, Paulson J, Meier F, Ericson J, Broach J, Schiff S. Cytomegalovirus infections in infants in Uganda: Newborn-mother pairs, neonates with sepsis, and infants with hydrocephalus. International Journal Of Infectious Diseases 2022, 118: 24-33. PMID: 35150915, PMCID: PMC9058984, DOI: 10.1016/j.ijid.2022.02.005.Peer-Reviewed Original ResearchConceptsNewborn-mother pairsCMV prevalenceClinical sepsisCytomegalovirus infectionCerebrospinal fluidPrevalence of CMVQuantitative PCRCMV positivityPostinfectious hydrocephalusVaginal sheddingCMV infectionHIV seropositivityNeonatal ageMaternal ageMaternal vaginalRisk factorsMedical CenterLong-term consequencesMother pairsSepsisNeonatesInfantsPrevalenceHydrocephalusCMV
2021
Polatuzumab vedotin plus obinutuzumab and lenalidomide in patients with relapsed or refractory follicular lymphoma: a cohort of a multicentre, single-arm, phase 1b/2 study
Diefenbach C, Kahl B, McMillan A, Briones J, Banerjee L, Cordoba R, Miall F, Burke J, Hirata J, Jiang Y, Paulson J, Chang Y, Musick L, Abrisqueta P. Polatuzumab vedotin plus obinutuzumab and lenalidomide in patients with relapsed or refractory follicular lymphoma: a cohort of a multicentre, single-arm, phase 1b/2 study. The Lancet Haematology 2021, 8: e891-e901. PMID: 34826412, DOI: 10.1016/s2352-3026(21)00311-2.Peer-Reviewed Original ResearchConceptsRecommended phase 2 doseRefractory follicular lymphomaPhase 2 dosePolatuzumab vedotinFollicular lymphomaAdverse eventsDay 1Dose escalationResponse rateRefractory diffuse large B-cell lymphomaCohort 3Treatment due to disease progressionCohort 2Diffuse large B-cell lymphomaEastern Cooperative Oncology Group performance statusCycles of induction treatmentDose-limiting toxicity eventsLarge B-cell lymphomaTyrosine kinase inhibitor treatmentComponent drugsPhase 1b/2 studyPhase 1b/2 trialComplete response rateDose-escalation phaseDose-limiting toxicityVaginal microbiome topic modeling of laboring Ugandan women with and without fever
Movassagh M, Bebell L, Burgoine K, Hehnly C, Zhang L, Moran K, Sheldon K, Sinnar S, Mbabazi-Kabachelor E, Kumbakumba E, Bazira J, Ochora M, Mulondo R, Nsubuga B, Weeks A, Gladstone M, Olupot-Olupot P, Ngonzi J, Roberts D, Meier F, Irizarry R, Broach J, Schiff S, Paulson J. Vaginal microbiome topic modeling of laboring Ugandan women with and without fever. Npj Biofilms And Microbiomes 2021, 7: 75. PMID: 34508087, PMCID: PMC8433417, DOI: 10.1038/s41522-021-00244-1.Peer-Reviewed Original ResearchConceptsIntrapartum feverClinical variablesHigh prevalenceVaginal microbiomeUgandan womenLonger labour durationMaternal clinical featuresYoung maternal ageDuration of pregnancyOnset of laborMicrobial communitiesVaginal microbial communitiesAfebrile mothersFebrile mothersPeripartum courseMaternal feverNeonatal outcomesLabor durationClinical featuresMaternal ageVaginal microbesFeverOutcome riskVeillonella genusMicrobiome influencesNormal childhood brain growth and a universal sex and anthropomorphic relationship to cerebrospinal fluid
Peterson M, Cherukuri V, Paulson J, Ssentongo P, Kulkarni A, Warf B, Monga V, Schiff S. Normal childhood brain growth and a universal sex and anthropomorphic relationship to cerebrospinal fluid. Journal Of Neurosurgery Pediatrics 2021, 28: 458-468. PMID: 34243147, PMCID: PMC8594737, DOI: 10.3171/2021.2.peds201006.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAlgorithmsAnalysis of VarianceAnthropometryBody WeightBrainCerebrospinal FluidChildChild DevelopmentChild, PreschoolCohort StudiesFemaleFunctional LateralityHumansHydrocephalusInfantInfant, NewbornMagnetic Resonance ImagingMaleOrgan SizePopulationReference StandardsSex CharacteristicsConceptsBrain growthBrain volumeFluid accumulationRatio of brainHealthy pediatric subjectsTotal brain volumeAge 18 yearsYears of ageRegional brain volumesNormal brain growthAge-dependent relationshipCSF accumulationPediatric subjectsChildhood diseasesCerebrospinal fluidCSF volumeCongenital disorderVolume trajectoriesEarly childhoodNormative growth curvesNumerous conditionsSexMagnetic resonanceBrain sizeNasal Microbiota and Infectious Complications After Elective Surgical Procedures
Hsiao C, Paulson J, Singh S, Mongodin E, Carroll K, Fraser C, Rock P, Faraday N. Nasal Microbiota and Infectious Complications After Elective Surgical Procedures. JAMA Network Open 2021, 4: e218386. PMID: 33914049, PMCID: PMC8085724, DOI: 10.1001/jamanetworkopen.2021.8386.Peer-Reviewed Original ResearchMeSH KeywordsAgedBacteremiaCardiac Surgical ProceduresCase-Control StudiesCraniotomyElective Surgical ProceduresFemaleHumansMaleMicrobiotaMiddle AgedNosePneumoniaPostoperative ComplicationsRisk AssessmentRisk FactorsRNA, Ribosomal, 16SSpinal FusionStaphylococcus aureusSurgical Wound InfectionVascular Surgical ProceduresConceptsBaseline clinical characteristicsSurgical proceduresElective surgical proceduresInfectious complicationsInfectious outcomesPostoperative infectionClinical characteristicsComposite of surgical site infectionsNasal carriage of Staphylococcus aureusNasal microbiotaNo history of autoimmune diseaseCarriage of Staphylococcus aureusHistory of autoimmune diseaseProspective cohort of patientsNasal microbiomeTertiary care university hospitalOccurrence of postoperative infectionsImmune-modulating medicationsPostoperative infectious complicationsHigher oddsSurgical site infectionCohort of patientsIntracranial surgical proceduresAssociated with higher oddsNasal carriageIntraventricular haemorrhage in a Ugandan cohort of low birth weight neonates: the IVHU study
MacLeod R, Paulson J, Okalany N, Okello F, Acom L, Ikiror J, Cowan F, Tann C, Dyet L, Hagmann C, Burgoine K. Intraventricular haemorrhage in a Ugandan cohort of low birth weight neonates: the IVHU study. BMC Pediatrics 2021, 21: 12. PMID: 33407279, PMCID: PMC7786968, DOI: 10.1186/s12887-020-02464-4.Peer-Reviewed Original ResearchConceptsRisk of intraventricular haemorrhageLow birth weight neonatesIntraventricular haemorrhageNeonatal unitAntenatal steroidsOdds ratioGestational ageCranial ultrasoundRisk factorsProspective cohort study of neonatesAssociated with intraventricular haemorrhageCohort study of neonatesDoses of antenatal steroidsPrevention of intraventricular haemorrhageRates of SGA neonatesSeverity of intraventricular haemorrhageDay 7Study of neonatesProspective cohort studyLow-income countriesDay of recruitmentModifiable risk factorsRegional Referral HospitalSGA neonatesVaginal delivery
2020
Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues
Lopes-Ramos C, Chen C, Kuijjer M, Paulson J, Sonawane A, Fagny M, Platig J, Glass K, Quackenbush J, DeMeo D. Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues. Cell Reports 2020, 31: 107795. PMID: 32579922, PMCID: PMC7898458, DOI: 10.1016/j.celrep.2020.107795.Peer-Reviewed Original ResearchConceptsGene regulatory networksTranscription factorsGenotype-Tissue ExpressionRegulatory networksArchitecture of gene regulatory networksRepertoire of transcription factorsSets of transcription factorsRegulatory network structureWhole-genome expression profilingTissue-related functionsGenes associated with Parkinson's diseaseHuman healthy tissuesGene regulationGene expressionMolecular basisSystems-based analysisExpression profilesGenesAlzheimer's diseaseRegulatory processesHuman tissuesExpressionTranscriptionTissueSex differences
2019
Polatuzumab Vedotin in Relapsed or Refractory Diffuse Large B-Cell Lymphoma
Sehn L, Herrera A, Flowers C, Kamdar M, McMillan A, Hertzberg M, Assouline S, Kim T, Kim W, Ozcan M, Hirata J, Penuel E, Paulson J, Cheng J, Ku G, Matasar M. Polatuzumab Vedotin in Relapsed or Refractory Diffuse Large B-Cell Lymphoma. Journal Of Clinical Oncology 2019, 38: 155-165. PMID: 31693429, PMCID: PMC7032881, DOI: 10.1200/jco.19.00172.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overAntibodies, MonoclonalAntibodies, Monoclonal, HumanizedAntineoplastic Combined Chemotherapy ProtocolsBendamustine HydrochlorideBiomarkers, TumorFemaleHumansImmunoconjugatesImmunohistochemistryLymphoma, Large B-Cell, DiffuseMaleMiddle AgedProgression-Free SurvivalSurvival RateConceptsProgression-free survivalLarge B-cell lymphomaPolatuzumab vedotinB-cell lymphomaCR rateOverall survivalPola-BRR/R DLBCLRefractory diffuse large B-cell lymphomaIRC-assessed progression-free survivalDiffuse large B-cell lymphomaB-cell receptor componentsSingle-arm cohortsDuration of responseCohort of patientsCox regression methodRisk of deathMedian OSSafety profileKaplan-MeierTreatment optionsB cellsPolatuzumabBendamustineDLBCL
2018
Cancer subtype identification using somatic mutation data
Kuijjer M, Paulson J, Salzman P, Ding W, Quackenbush J. Cancer subtype identification using somatic mutation data. British Journal Of Cancer 2018, 118: 1492-1501. PMID: 29765148, PMCID: PMC5988673, DOI: 10.1038/s41416-018-0109-7.Peer-Reviewed Original ResearchConceptsSomatic mutation dataAssociated with mutationsNext-generation sequencing technologiesMutation dataBiological pathwaysSets of mutationsSignal transduction pathwaysCancer typesPan-cancer subtypesSequencing technologiesPhenotypic dataCancer Genome AtlasCancer subtype identificationTransduction pathwaysMutational driversSomatic mutationsSubgroup of patientsTargeted treatment optionsMutationsMutation patternsGenome AtlasClassification of patientsMutation profilesPrimary tumorPrognostic subtypesMeta-analysis of the lung microbiota in pulmonary tuberculosis
Hong B, Paulson J, Stine O, Weinstock G, Cervantes J. Meta-analysis of the lung microbiota in pulmonary tuberculosis. Tuberculosis 2018, 109: 102-108. PMID: 29559113, DOI: 10.1016/j.tube.2018.02.006.Peer-Reviewed Original ResearchConceptsSpecies signatureNext generation sequencing dataLung microbiotaGeneration sequencing dataClustering of microbiotaMycobacterium tuberculosisCaulobacter henriciiLung microbiota compositionSequence dataBody nichesR. mucilaginosaMicrobiota compositionSputum microbiotaActinomyces graevenitziiBioinformatics analysisMicrobiotaRothia mucilaginosaTB patientsHealthy controlsTB casesAssociated with pulmonary TBHaemophilus parahaemolyticusMeta-analysisLower respiratory tractBody sites
2016
Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment
Pop M, Paulson J, Chakraborty S, Astrovskaya I, Lindsay B, Li S, Bravo H, Harro C, Parkhill J, Walker A, Walker R, Sack D, Stine O. Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment. BMC Genomics 2016, 17: 440. PMID: 27277524, PMCID: PMC4898365, DOI: 10.1186/s12864-016-2777-0.Peer-Reviewed Original ResearchConceptsGene sequencesBackgroundEnterotoxigenic Escherichia coliHuman gut microbiotaRRNA gene sequencesEnterotoxigenic Escherichia coliHuman intestinal microbiotaFecal E. coliCiprofloxacin treatmentETEC infectionETEC diarrheaRibosomal RNAGut microbiotaFecal microbiotaIntestinal microbiotaE. coliMicrobiotaMonthly follow-up visitsCompared to variationsETECFollow-up visitQuantitative PCRHuman challenge studiesCiprofloxacinQuantitative culturesSequence
2014
Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition
Pop M, Walker A, Paulson J, Lindsay B, Antonio M, Hossain M, Oundo J, Tamboura B, Mai V, Astrovskaya I, Bravo H, Rance R, Stares M, Levine M, Panchalingam S, Kotloff K, Ikumapayi U, Ebruke C, Adeyemi M, Ahmed D, Ahmed F, Alam M, Amin R, Siddiqui S, Ochieng J, Ouma E, Juma J, Mailu E, Omore R, Morris J, Breiman R, Saha D, Parkhill J, Nataro J, Stine O. Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition. Genome Biology 2014, 15: r76. PMID: 24995464, PMCID: PMC4072981, DOI: 10.1186/gb-2014-15-6-r76.Peer-Reviewed Original ResearchConceptsMicrobiota compositionAnaerobic lineagesRRNA gene sequencesGut microbiota compositionLevels of PrevotellaDiarrhea-causing pathogensSevere diarrheal diseaseIntestinal microbiota compositionFecal microbiota compositionGene sequencesDiarrheal pathogensDiarrhea pathogensMolecular techniquesPathogensDiarrhea-free controlsGranulicatella speciesEscherichia/ShigellaDiarrheal diseaseLineagesMSD casesYears of ageBackgroundDiarrheal diseasesYoung childrenAssociated with MSDLow-income countries
2013
Survey of Culture, GoldenGate Assay, Universal Biosensor Assay, and 16S rRNA Gene Sequencing as Alternative Methods of Bacterial Pathogen Detection
Lindsay B, Pop M, Antonio M, Walker A, Mai V, Ahmed D, Oundo J, Tamboura B, Panchalingam S, Levine M, Kotloff K, Li S, Magder L, Paulson J, Liu B, Ikumapayi U, Ebruke C, Dione M, Adeyemi M, Rance R, Stares M, Ukhanova M, Barnes B, Lewis I, Ahmed F, Alam M, Amin R, Siddiqui S, Ochieng J, Ouma E, Juma J, Mailu E, Omore R, O'Reilly C, Hannis J, Manalili S, DeLeon J, Yasuda I, Blyn L, Ranken R, Li F, Housley R, Ecker D, Hossain M, Breiman R, Morris J, McDaniel T, Parkhill J, Saha D, Sampath R, Stine O, Nataro J. Survey of Culture, GoldenGate Assay, Universal Biosensor Assay, and 16S rRNA Gene Sequencing as Alternative Methods of Bacterial Pathogen Detection. Journal Of Clinical Microbiology 2013, 51: 3263-3269. PMID: 23884998, PMCID: PMC3811648, DOI: 10.1128/jcm.01342-13.Peer-Reviewed Original ResearchConceptsEnteroaggregative Escherichia coliEnteropathogenic E. coliEnterotoxigenic E. coliDNA samplesShigella sppGoldenGate assaySequencing of 16S rRNA genesRRNA gene sequencesBiosensor assayCultivation-based assaysMolecular technologiesStool samplesIdentification of pathogensBacterial pathogen detectionDetect bacterial pathogensEnzyme-linked immunosorbent assay (ELISA)-based methodVirulence genesRRNA geneVirulence factorsGene sequencesBacterial pathogensDiarrheal pathogensEnteric pathogensPathogen detectionDNA
2011
Anterior Vaginal Wall Tenderness (AVWT) as a Physical Symptom in Chronic Pelvic Pain
Paulson J, Paulson J. Anterior Vaginal Wall Tenderness (AVWT) as a Physical Symptom in Chronic Pelvic Pain. JSLS Journal Of The Society Of Laparoscopic & Robotic Surgeons 2011, 15: 6-9. PMID: 21902934, PMCID: PMC3134698, DOI: 10.4293/108680810x12924466008961.Peer-Reviewed Original ResearchConceptsChronic pelvic painInterstitial cystitisPelvic painTreatment of chronic pelvic painChronic pelvic pain patientsAnterior vaginal wallPelvic pain patientsPositive predictive valuePain patientsVaginal wallEmpty bladderCystitisStudy cohortPhysical examinationEndoscopic proceduresEndometriosisPredictive valueUrinary problemsPatientsPainDiagnosisExaminationTendernessPhysiciansPhysical symptoms