2023
Nearest Neighbors of Multivariate Runs
Kong Y. Nearest Neighbors of Multivariate Runs. 2023, 1-25. DOI: 10.1007/978-1-4614-8414-1_63-1.Peer-Reviewed Original ResearchQuantitative DNA Repair Biomarkers and Immune Profiling for Temozolomide and Olaparib in Metastatic Colorectal Cancer
Cecchini M, Zhang J, Wei W, Sklar J, Lacy J, Zhong M, Kong Y, Zhao H, DiPalermo J, Devine L, Stein S, Kortmansky J, Johung K, Bindra R, LoRusso P, Schalper K. Quantitative DNA Repair Biomarkers and Immune Profiling for Temozolomide and Olaparib in Metastatic Colorectal Cancer. Cancer Research Communications 2023, 3: 1132-1139. PMID: 37387791, PMCID: PMC10305782, DOI: 10.1158/2767-9764.crc-23-0045.Peer-Reviewed Original ResearchConceptsWhole-exome sequencingMGMT protein expressionColorectal cancerStable diseaseQuantitative immunofluorescenceT cellsProtein expressionPromoter hypermethylationLow MGMT protein expressionPARP inhibitorsRadiographic tumor regressionMetastatic colorectal cancerAdvanced colorectal cancerPretreatment tumor biopsiesEffector T cellsTumor-infiltrating lymphocytesMGMT proteinDNA repair biomarkersBaseline CD8Eligible patientsIncreased CD8Methylguanine-DNA methyltransferaseObjective responseProgressive diseaseImmune markersResponse to: Elevated L1 expression in ataxia telangiectasia likely explained by an RNA-seq batch effect
Takahashi T, Stoiljkovic M, Song E, Gao X, Yasumoto Y, Kudo E, Carvalho F, Kong Y, Park A, Shanabrough M, Szigeti-Buck K, Liu Z, Kristant A, Zhang Y, Sulkowski P, Glazer P, Kaczmarek L, Horvath T, Iwasaki A. Response to: Elevated L1 expression in ataxia telangiectasia likely explained by an RNA-seq batch effect. Neuron 2023, 111: 612-613. PMID: 36863323, DOI: 10.1016/j.neuron.2023.02.006.Peer-Reviewed Original ResearchInflammation of the retinal pigment epithelium drives early-onset photoreceptor degeneration in Mertk-associated retinitis pigmentosa
Mercau M, Akalu Y, Mazzoni F, Gyimesi G, Alberto E, Kong Y, Hafler B, Finnemann S, Rothlin C, Ghosh S. Inflammation of the retinal pigment epithelium drives early-onset photoreceptor degeneration in Mertk-associated retinitis pigmentosa. Science Advances 2023, 9: eade9459. PMID: 36662852, PMCID: PMC9858494, DOI: 10.1126/sciadv.ade9459.Peer-Reviewed Original ResearchConceptsRetinal pigment epitheliumEarly-onset photoreceptor degenerationPR degenerationPigment epitheliumPhotoreceptor degenerationMERTK-associated retinitis pigmentosaJAK1/2 inhibitor ruxolitinibMicroglia activationMonocyte infiltrationInhibitor ruxolitinibMouse modelInflammationLoss of functionDefective phagocytosisInflammation drivesRetinitis pigmentosaDegenerationHypomorphic expressionMiceEpitheliumPhagocytosisRuxolitinibPigmentosaSeverity
2022
Gastrointestinal Microbiome Disruption and Antibiotic-Associated Diarrhea in Children Receiving Antibiotic Therapy for Community-Acquired Pneumonia
Kwon J, Kong Y, Wade M, Williams DJ, Creech CB, Evans S, Walter EB, Martin JM, Gerber JS, Newland JG, Hofto ME, Staat MA, Chambers HF, Fowler VG, Huskins WC, Pettigrew M. Gastrointestinal Microbiome Disruption and Antibiotic-Associated Diarrhea in Children Receiving Antibiotic Therapy for Community-Acquired Pneumonia. The Journal Of Infectious Diseases 2022, 226: 1109-1119. PMID: 35249113, PMCID: PMC9492313, DOI: 10.1093/infdis/jiac082.Peer-Reviewed Original ResearchConceptsAAD groupAntibiotic-Associated DiarrheaCommunity-Acquired PneumoniaCommon side effectsStudy days 1Days of diarrheaPatient characteristicsAntibiotic therapyNineteen childrenStool samplesSide effectsDay 1Microbiome disruptionMicrobiota profilesGastrointestinal microbiotaMicrobiota characteristicsDiarrheaBacteroides speciesPneumoniaChildrenAntibioticsΒ-lactamsAADBaseline abundanceDysbiosis
2021
A phase II evaluation of pembrolizumab in recurrent microsatellite instability-high (MSI-H) endometrial cancer patients with Lynch-like versus MLH-1 methylated characteristics (NCT02899793).
Roque D, Bellone S, Siegel E, Buza N, Bonazzoli E, Guglielmi A, Zammataro L, Nagarkatti N, Zaidi S, Lee J, Schwartz P, Ratner E, Alexandrov L, Iwasaki A, Kong Y, Song E, Dong W, Elvin J, Choi J, Santin A. A phase II evaluation of pembrolizumab in recurrent microsatellite instability-high (MSI-H) endometrial cancer patients with Lynch-like versus MLH-1 methylated characteristics (NCT02899793). Journal Of Clinical Oncology 2021, 39: 5523-5523. DOI: 10.1200/jco.2021.39.15_suppl.5523.Peer-Reviewed Original ResearchObjective response rateImmune checkpoint inhibitorsEndometrial cancer patientsTumor mutational burdenCancer patientsGrade 3/4 treatment-related adverse eventsSolid Tumors version 1.1Treatment-related adverse eventsSporadic tumorsPhase II pilot studyOverall survival proportionPrimary end pointResponse Evaluation CriteriaPhase II evaluationAntigen processing/presentationProcessing/presentationAdverse eventsICI resistancePrognostic significanceMechanisms of resistancePolymerase chain reactionII evaluationClinical studiesMutational burdenPatientsEndogenous retroviruses mediate IFN-independent protection against vaginal HSV-2 infection
Tokuyama M, Jayewickreme R, Mao T, Philbrick W, Kong Y, Dong H, Treger R, Rakib T, Iwasaki A. Endogenous retroviruses mediate IFN-independent protection against vaginal HSV-2 infection. The Journal Of Immunology 2021, 206: 20.39-20.39. DOI: 10.4049/jimmunol.206.supp.20.39.Peer-Reviewed Original ResearchHSV-2 infectionVaginal HSV-2 infectionTight junction proteinsB6 miceVaginal epitheliumHerpes simplex virus type 2 infectionSimplex virus type 2 infectionEnhanced type I interferonIntravaginal HSV-2 infectionVirus type 2 infectionToll-like receptor 7Epithelial tight junction proteinsEndogenous retrovirusesReceptor-deficient miceJunction proteinsType 2 infectionHigh systemic levelsWildtype C57BL/6 miceType I interferonDisease courseC57BL/6 miceInfectious endogenous retrovirusReceptor 7Disease burdenHSV-2
2020
Distributions of successions of arbitrary multisets
Kong Y. Distributions of successions of arbitrary multisets. Communication In Statistics- Theory And Methods 2020, 51: 1693-1705. DOI: 10.1080/03610926.2020.1767137.Peer-Reviewed Original Research
2019
Ketogenic diet activates protective γδ T cell responses against influenza virus infection
Goldberg EL, Molony RD, Kudo E, Sidorov S, Kong Y, Dixit VD, Iwasaki A. Ketogenic diet activates protective γδ T cell responses against influenza virus infection. Science Immunology 2019, 4 PMID: 31732517, PMCID: PMC7189564, DOI: 10.1126/sciimmunol.aav2026.Peer-Reviewed Original ResearchConceptsΓδ T cellsKetogenic dietIAV infectionT cellsGlobal health care concernHigh-fat ketogenic dietΓδ T cell responsesInfection-associated morbidityLethal IAV infectionT cell responsesInfluenza virus infectionHealth care concernHigh-carbohydrate dietInfluenza diseaseKD feedingVirus infectionNew therapiesAntiviral resistanceHepatic ketogenesisCare concernsCell responsesInfectionBarrier functionDietMetabolic adaptationDiscovery and Contribution of Nontypeable Haemophilus influenzae NTHI1441 to Human Respiratory Epithelial Cell Invasion.
Ahearn C, Kirkham C, Chaves L, Kong Y, Pettigrew M, Murphy T. Discovery and Contribution of Nontypeable Haemophilus influenzae NTHI1441 to Human Respiratory Epithelial Cell Invasion. Infection And Immunity 2019, 87 PMID: 31427451, PMCID: PMC6803334, DOI: 10.1128/iai.00462-19.Peer-Reviewed Original ResearchConceptsChronic obstructive pulmonary diseaseRespiratory epithelial cellsEnzyme-linked immunosorbent assayEpithelial cellsAirways of adultsObstructive pulmonary diseaseCell invasionHuman respiratory epithelial cellsNontypeable Haemophilus influenzaeCell enzyme-linked immunosorbent assayAlveolar epithelial cellsAcute exacerbationLower airwaysPulmonary diseaseSerum IgGNTHi strainsTherapeutic interventionsHaemophilus influenzaeHuman bronchialSurface-exposed epitopesEpithelial cell invasionIsogenic knockout mutantsNTHiImmunosorbent assayIntracellular survival
2018
Decoupling Combinatorial Complexity: a Two-Step Approach to Distributions of Runs
Kong Y. Decoupling Combinatorial Complexity: a Two-Step Approach to Distributions of Runs. Methodology And Computing In Applied Probability 2018, 21: 789-803. DOI: 10.1007/s11009-018-9689-1.Peer-Reviewed Original ResearchRun-related distributionsDistribution of runsMultivariate random sequencesCombinatorial complexityFinite Markov chainsMulti-object systemNearest-neighbor interactionsStatistical physicsCombinatorial difficultiesMarkov chainExplicit formRun statisticsNeighbor interactionsMultinomial coefficientsDifferent systematic approachesGeneral frameworkRun distributionRandom sequenceKinds of objectsTwo-step approachCombinatoricsGeneral formulaIndependent stepsComplexityPhysicsGenerating Function Methods for Run and Scan Statistics
Kong Y. Generating Function Methods for Run and Scan Statistics. 2018, 1-19. DOI: 10.1007/978-1-4614-8414-1_56-1.Peer-Reviewed Original ResearchFinite Markov chainsMulti-object systemNearest-neighbor interactionsStatistical physicsCombinatorial difficultiesGenerating functionMarkov chainExplicit formClassical resultsPattern statisticsNeighbor interactionsCombinatorial complexityFunction methodCombinatorial methodsKinds of objectsDifferent complexityMultiple objectsScan statisticIndividual objectsStatisticsIndependent stepsFirst stepWhole systemComplexityObjectsJoint distribution of rises, falls, and number of runs in random sequences
Kong Y. Joint distribution of rises, falls, and number of runs in random sequences. Communication In Statistics- Theory And Methods 2018, 48: 493-499. DOI: 10.1080/03610926.2017.1414261.Peer-Reviewed Original Research
2017
IFT56 regulates vertebrate developmental patterning by maintaining IFTB complex integrity and ciliary microtubule architecture
Xin D, Christopher K, Zeng L, Kong Y, Weatherbee S. IFT56 regulates vertebrate developmental patterning by maintaining IFTB complex integrity and ciliary microtubule architecture. Journal Of Cell Science 2017, 130: e1.2-e1.2. DOI: 10.1242/jcs.205013.Peer-Reviewed Original Research
2016
The Adventitious Angles Problem: The Lonely Fractional Derived Angle
Kong Y, Zhang S. The Adventitious Angles Problem: The Lonely Fractional Derived Angle. American Mathematical Monthly 2016, 123: 814-816. DOI: 10.4169/amer.math.monthly.123.08.814.Peer-Reviewed Original ResearchThe mth longest runs of multivariate random sequences
Kong Y. The mth longest runs of multivariate random sequences. Annals Of The Institute Of Statistical Mathematics 2016, 69: 497-512. DOI: 10.1007/s10463-015-0551-8.Peer-Reviewed Original ResearchNumber of appearances of events in random sequences: A new approach to non-overlapping runs
Kong Y. Number of appearances of events in random sequences: A new approach to non-overlapping runs. Communication In Statistics- Theory And Methods 2016, 45: 6765-6772. DOI: 10.1080/03610926.2014.968728.Peer-Reviewed Original Research
2015
Number of appearances of events in random sequences: a new generating function approach to Type II and Type III runs
Kong Y. Number of appearances of events in random sequences: a new generating function approach to Type II and Type III runs. Annals Of The Institute Of Statistical Mathematics 2015, 69: 489-495. DOI: 10.1007/s10463-015-0549-2.Peer-Reviewed Original ResearchDistributions of Runs Revisited
Kong Y. Distributions of Runs Revisited. Communication In Statistics- Theory And Methods 2015, 44: 4663-4678. DOI: 10.1080/03610926.2013.793350.Peer-Reviewed Original ResearchExpression of IgA Proteases by Haemophilus influenzae in the Respiratory Tract of Adults With Chronic Obstructive Pulmonary Disease
Murphy TF, Kirkham C, Jones MM, Sethi S, Kong Y, Pettigrew MM. Expression of IgA Proteases by Haemophilus influenzae in the Respiratory Tract of Adults With Chronic Obstructive Pulmonary Disease. The Journal Of Infectious Diseases 2015, 212: 1798-1805. PMID: 25995193, PMCID: PMC4633762, DOI: 10.1093/infdis/jiv299.Peer-Reviewed Original ResearchConceptsChronic obstructive pulmonary diseaseObstructive pulmonary diseaseH. influenzaeIgA protease genePulmonary diseaseHuman airwaysHaemophilus influenzaeIgA proteaseH. influenzae infectionsHuman respiratory epithelial cellsHuman IgA1Respiratory epithelial cellsInfluenzae infectionRespiratory tractIgA protease activitySputum samplesClinical settingInfluenzaeEpithelial cellsInfectionAirwayIgA1 fragmentsDiseaseIgA1Protease gene