Granted Patent
B2
US 12,411,144 · App. 17/333,058 · Granted Sep 9, 2025
Compositions and methods for treatment of lung function
Inventors:
Assem Ziady (Newport, KY); Rhonda Szczesniak (Burlington, KY); Emrah Gecili (Cincinnati, OH); Zackary Cleveland (Cincinnati, OH)
Assignee:
Children's Hospital Medical Center
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Abstract
Disclosed herein are methods for detecting protein expression in an individual diagnosed with cystic fibrosis. The methods, in certain aspects, include the steps of obtaining a sample from said individual and detecting expression in said sample of each protein of a protein set. The method may further include the step of determining expression level of one or more proteins of the protein set. The disclosed methods may be used to predict one or more clinical parameters in an individual having cystic fibrosis.
Claims (27)
1. A method for treating an individual at risk for non-linear lung function decline, comprising
a) determining, in said individual, a covariate comprising one or more biomarker selected from Immunoglobulin alpha-1 heavy chain constant region; kappa 1 immunoglobulin constant; Immunoglobulin kappa light chain VLJ region; immunoglobulin lambda; Immunoglobulin lambda constant 2; Immunoglobulin lambda constant 3; Tight junction protein 3; Alpha-1-acid glycoprotein 2 precursor; Signal-induced proliferation-associated 1-like protein 3; Plakophilin 4; Inter-alpha (globulin) inhibitor H2; Absent in melanoma 1 protein; Actin filament-associated protein 1 isoform X2; Serine/threonine-protein phosphatase PP1-beta catalytic subunit; Retinol-binding protein 4; Fermitin family homolog 1; Actin, cytoplasmic 2; Transthyretin; Melanoma inhibitory activity protein 3 isoform X2; Pleckstrin homology domain-containing family G member 1 isoform X3; Pleckstrin homology domain-containing family A member 5 isoforms X1-X9; Pleckstrin; Zinc finger protein 295; Protocadherin Fat 2; Cadherin-related family member 2 isoform X1; Voltage gated calcium channel alpha 1F subunit; Actin filament associated protein; Heat shock 70 kDa protein 1-like; EF-hand calcium binding protein 2; Polyamine modulated factor-1 (PMF1) protein; Keratin 16; Keratin 18; DNA replication ATP-dependent helicase/nuclease DNA2 isoform X4; Non-lens beta gamma-crystallin like protein; Bromodomain and WD repeat-containing protein 1 isoform X1; Collagen type V alpha 3 chain; Collagen type IV alpha; Dynein heavy chain 12, axonemal isoform X5; Serine/arginine repetitive matrix protein 1; Ras-related protein Rap-1A; AT-hook-containing transcription factor isoform 1; Coiled-coil domain-containing protein 18 isoforms X1-X7; Coiled-coil domain-containing protein 180; Patatin-like phospholipase domain-containing protein 2 isoform X1; Alstrom syndrome protein 1 isoform 1; aminopeptidase O isoform X9 (C9orf3); ankyrin-3 isoform 3; ARAP2 protein (ARAP2); Bifunctional glutamate/proline-tRNA ligase (EPRS); C10ORF6; CECR2 protein (CECR2); cingulin-like 1 (CGNL1); coiled-coil domain-containing protein 93 isoform X3 (CCDC93); complement component C2 (C2); complement component C6 isoform X7 (C6); complement factor H (CFH); connector enhancer of kinase suppressor of ras 2 isoform X2 (CNKSR2); CTP:phosphocholine cytidylyltransferase; DNA annealing helicase and endonuclease ZRANB3 (ZRANB3); EPRSN1; fibrinogen alpha chain preproprotein, isoform alpha (FGA); filamin 2 (FLN2); Fras1-related extracellular matrix protein 2 (FREM2); FYVE, RhoGEF and PH domain-containing protein 5 isoform X2 (FGD5); gelsolin isoform X3 (GSN); glutamate receptor-interacting protein 1 isoform X7 (GRIP1); hCG1656772; histidine-rich glycoprotein isoform X1 (HRG); interferon regulatory factor-2 binding protein 2B; junction-mediating and -regulatory protein isoform X2 (JMY); KIAA0328 protein KIAA0328; 1a-related protein 1 isoform X5 LARP1; MAX gene-associated protein isoform X11 (MGA); paraoxanase-3; Platelet glycoprotein Ib alpha chain (GP1BA); PMFBP1 protein (PMFBP1); PRO2841; protein arginine N-methyltransferase 3 isoform X1 (PRMT3); Protein SCAF11 (SCAF11); ral GTPase-activating protein subunit alpha-1 isoform X12 (RALGAPA1); Receptor-type tyrosine-protein phosphatase C (PTPRC); RGS3 isoform C2PA-RGS3 (RGS3); Rho-GTPase activating protein 10 (ARHGAP10); RNA-binding motif protein, Y chromosome, family 1 member B isoform X1 (RBMY1B); protein-methionine sulfoxide oxidase MICAL3 isoform X10 (MICAL3); Protein sidekick-2 (SDK2); sacsin isoform X3 (SACS); SAPS domain family, member 2 (SAPS2); serum aryldialkylphosphatase precursor; spermatogenesis-associated protein 31C1 isoform X1 (SPATA31C1); synaptotagmin-like protein 2 isoform X10 (SYTL2); translation initiation factor (IF2); triadin isoform X17 (TRDN); uridine-cytidine kinase-like 1 isoform X7 (UCKL1); utrophin isoform X4 (UTRN); WD repeat-containing protein 64 isoform X2 (WDR64); zinc finger and AT hook domain containing (ZFAT); Alstrom syndrome protein 1 isoform 1; aminopeptidase O isoform X9 (C9orf3); ankyrin-3 isoform 3; ARAP2 protein (ARAP2); Bifunctional glutamate/proline-tRNA ligase (EPRS); C10ORF6; CECR2 protein (CECR2); cingulin-like 1 (CGNL1); coiled-coil domain-containing protein 93 isoform X3 (CCDC93); complement component C2 (C2); complement component C6 isoform X7 (C6); complement factor H (CFH); connector enhancer of kinase suppressor of ras 2 isoform X2 (CNKSR2); CTP:phosphocholine cytidylyltransferase; DNA annealing helicase and endonuclease ZRANB3 (ZRANB3); EPRSN1; fibrinogen alpha chain preproprotein, isoform alpha (FGA); filamin 2 (FLN2); Fras1-related extracellular matrix protein 2 (FREM2); FYVE, RhoGEF and PH domain-containing protein 5 isoform X2 (FGD5); gelsolin isoform X3 (GSN); glutamate receptor-interacting protein 1 isoform X7 (GRIP1); hCG1656772; histidine-rich glycoprotein isoform X1 (HRG); interferon regulatory factor-2 binding protein 2B; junction-mediating and -regulatory protein isoform X2 (JMY); KIAA0328 protein KIAA0328; 1a-related protein 1 isoform X5 LARP1; MAX gene-associated protein isoform X11 (MGA); paraoxanase-3; Platelet glycoprotein Ib alpha chain (GP1BA); PMFBP1 protein (PMFBP1); PRO2841; protein arginine N-methyltransferase 3 isoform X1 (PRMT3); Protein SCAF11 (SCAF11); ral GTPase-activating protein subunit alpha-1 isoform X12 (RALGAPA1); Receptor-type tyrosine-protein phosphatase C (PTPRC); RGS3 isoform C2PA-RGS3 (RGS3); Rho-GTPase activating protein 10 (ARHGAP10); RNA-binding motif protein, Y chromosome, family 1 member B isoform X1 (RBMYlB); protein-methionine sulfoxide oxidase MICAL3 isoform X10 (MICAL3); Protein sidekick-2 (SDK2); sacsin isoform X3 (SACS); SAPS domain family, member 2 (SAPS2); serum aryldialkylphosphatase precursor; spermatogenesis-associated protein 31C1 isoform X1 (SPATA31C1); synaptotagmin-like protein 2 isoform X10 (SYTL2); translation initiation factor (IF2); triadin isoform X17 (TRDN); uridine-cytidine kinase-like 1 isoform X7 (UCKL1); utrophin isoform X4 (UTRN); WD repeat-containing protein 64 isoform X2 (WDR64); zinc finger and AT hook domain containing (ZFAT);
b) calculating a risk probability score based on said determining of one or more covariate, said risk probability score being used to characterize the individual as having no predicted lung impairment, mild predicted lung impairment, moderate predicted lung impairment, or severe predicted lung impairment wherein said risk probability score comprises a risk probability of said non-linear lung function decline in one or more parameters selected from a decrease in forced expiratory volume in one second (FEV1), pulmonary exacerbation (PE) frequency, FEV1-indicated exacerbation signal (FIES), ventilation defect percent (VDP), abnormal lung heterogeneity in lung as measured via imaging, lung hyperinflation, and combinations thereof; and
c) treating said individual characterized as having mild predicted lung impairment, moderate predicted lung impairment, or severe predicted lung impairment with anti-inflammatory therapy.
2. The method of claim 1 , said determining comprising determining an expression level of a protein of said biomarker.
3. The method of claim 1 , further comprising determining an imaging marker covariate.
4. The method of claim 1 , said imaging marker being a functional lung measurement, a structural lung measurement, or combinations thereof.
5. The method of claim 3 , said imaging marker being obtained by an imaging method.
6. The method of claim 4 , said imaging marker being detected using an image technique selected from hyperpolarized (HP) 129Xe, Ultra-short Echo-time (UTE) Magnetic resonance imaging (MRI), computed tomography (CT), and combinations thereof.
7. The method of claim 3 , said imaging marker being structural remodeling.
8. The method of claim 3 , said imaging marker being bronchiectasis.
9. The method of claim 1 , said predicted lung impairment being a non-linear decline in one or more parameters selected from Ventilation Defect Percentage (VDP), FEV1, partial ventilation, ventilation heterogeneity, ventilation hyper-intensity or a combination thereof.
10. The method of claim 1 , said risk probability score predicting the probability of lung function decline over a period selected from three weeks to four months, or six months, or twelve months.
11. The method of claim 1 , wherein non-linear lung function decline is defined as a rate of change in longitudinal FEV1 that falls below 1.5% predicted/year.
12. The method of claim 1 , wherein non-linear lung function decline is defined by the FEV1-indicated exacerbation signal (FIES) score.
13. The method of claim 1 , further comprising detecting a one-or more covariates comprising a time-varying covariate.
14. The method of claim 13 , said time-varying covariate selected from one or more of an infection with P. aeruginosa, an infection with Methicillin-resistant Staphylococcus aureus (MRSA), and Cystic-Fibrosis-related diabetes.
15. The method of claim 1 , wherein said biomarker is one or more biomarkers selected from selected from Immunoglobulin alpha-1 heavy chain constant region; kappa 1 immunoglobulin constant; Immunoglobulin kappa light chain VLJ region; immunoglobulin lambda; Immunoglobulin lambda constant 2; Immunoglobulin lambda constant 3; Tight junction protein 3; Alpha-1-acid glycoprotein 2 precursor; Signal-induced proliferation-associated 1-like protein 3; Plakophilin 4; Inter-alpha (globulin) inhibitor H2; Absent in melanoma 1 protein; Actin filament-associated protein 1 isoform X2; Serine/threonine-protein phosphatase PP1-beta catalytic subunit; Retinol-binding protein 4; Fermitin family homolog 1; Actin, cytoplasmic 2; Transthyretin; Melanoma inhibitory activity protein 3 isoform X2; Pleckstrin homology domain-containing family G member 1 isoform X3; Pleckstrin homology domain-containing family A member 5 isoforms X1-X9; Pleckstrin; Zinc finger protein 295; Protocadherin Fat 2; Cadherin-related family member 2 isoform X1; Voltage gated calcium channel alpha 1F subunit; Actin filament associated protein; Heat shock 70 kDa protein 1-like; E F-hand calcium binding protein 2; Polyamine modulated factor-1 (PMF1) protein; Keratin 16 (KKRT16A); Keratin 18 (KRT18); DNA replication ATP-dependent helicase/nuclease DNA2 isoform X4; Non-lens beta gamma-crystallin like protein; Bromodomain and WD repeat-containing protein 1 isoform X1; Collagen type V alpha 3 chain; Collagen type IV alpha; Dynein heavy chain 12, axonemal isoform X5; Serine/arginine repetitive matrix protein 1; Ras-related protein Rap-1A; AT-hook-containing transcription factor isoform 1; Coiled-coil domain-containing protein 18 isoforms X1-X7; Coiled-coil domain-containing protein 180; and Patatin-like phospholipase domain-containing protein 2 isoform X1.
16. The method of claim 1 , wherein said individual is diagnosed with cystic fibrosis (CF).
17. The method of claim 1 wherein said individual has a normal forced expiratory volume in one second (FEV1) as measured by spirometry.
18. The method of claim 1 , wherein said individual is a pediatric patient.
19. The method of claim 1 , wherein said individual is a patient under the age of 13 years of age.
20. The method of claim 1 , wherein said method forecasts lung function trajectory for a period of about three weeks to about six months, or about six months to about twelve months.
21. The method of claim 1 , further comprising applying a statistical algorithm to estimate correlation between said covariate value and predicted lung function.
22. The method of claim 1 , wherein said method is carried out via a computer system, and wherein said method comprises capturing and displaying information related to said characterization of said individual using a graphical user interface (GUI).
23. The method of claim 1 , further comprising assessing a variable selected from one or more of sex, body mass index (BMI), pulmonary exacerbation (PE), number of hospitalizations, antibiotic status, infection status, and combinations thereof, in said individual.
24. The method of claim 1 , wherein said lung function decline is defined by one or more of absolute change in FEV1, rate of decline, risk of non-linear decline, and FIES.
Assignments (2)
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded May 29, 2026
From: ZIADY, ASSEM; SZCZESNIAK, RHONDA; CLANCY, JOHN
To: CHILDREN'S HOSPITAL MEDICAL CENTER
Reel/Frame 074792/0832 →
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded May 29, 2026
From: BROKAMP, COLE
To: CHILDREN'S HOSPITAL MEDICAL CENTER
Reel/Frame 074793/0024 →
Continuity (4)
Provisional Application
62474739
· Mar 22, 2017
References Cited (360)
US 4208479A
· Zuk et al.
· 1980
[cited by applicant]
US 7741038B2
· Sarwal et al.
· 2010
[cited by applicant]
US 8017577B2
· Cooper et al.
· 2011
[cited by applicant]
US 8911786B2
· Desai et al.
· 2014
[cited by applicant]
US 9018179B2
· Kay et al.
· 2015
[cited by applicant]
US 9993494B2
· Appleman et al.
· 2018
[cited by applicant]
US 20060142225A1
· McSwiggen
· 2006
[cited by applicant]
US 20060148828A1
· Gianella-Borradori et al.
· 2006
[cited by applicant]
US 20060153808A1
· Cristofanilli et al.
· 2006
[cited by applicant]
US 20060241028A1
· Bevec
· 2006
[cited by examiner]
US 20060292562A1
· Pollard et al.
· 2006
[cited by applicant]
US 20080133141A1
· Frost
· 2008
[cited by examiner]
US 20130143752A1
· Edmiston et al.
· 2013
[cited by applicant]
US 20170042819A1
· Goomer
· 2017
[cited by applicant]
US 20170314074A1
· Kossen et al.
· 2017
[cited by applicant]
US 20190128901A1
· Cozma
· 2019
[cited by applicant]
US 20200341009A1
· Ziady et al.
· 2020
[cited by applicant]
US 20230330121A1
· Ziady et al.
· 2023
[cited by applicant]
US 20230416782A1
· Ziady et al.
· 2023
[cited by applicant]
US 20240066021A1
· Ziady et al.
· 2024
[cited by applicant]
AU 2013270447A1
· 2014
[cited by applicant]
WO 2009038913A2
· 2009
[cited by applicant]
WO 2009055671A1
· 2009
[cited by applicant]
WO 2011038901A1
· 2011
[cited by applicant]
WO 2015157546A1
· 2015
[cited by applicant]
WO 2018208849A1
· 2018
[cited by applicant]
WO 2021053058A1
· 2021
[cited by applicant]
WO 2022031877A1
· 2022
[cited by applicant]
Long (Zhongguo Shiyong Neike Zashi 2015 vol. 35, p. 938-940; English translation) (Year: 2015).
[cited by examiner]
Ni (Intl. J. COPD 2015 vol. 10: 1465-1475). (Year: 2015).
[cited by examiner]
Martinez-Garcia (Clinical Pulmonary Medicine 2015 vol. 22: 123-127). (Year: 2015).
[cited by examiner]
Tepper (Eur Radiol 2016 26.4563-4599) (Year. 2016).
[cited by examiner]
Schaad (Pediatric Research 1990 27:508-513) (Year 1990).
[cited by examiner]
Hassan (Immunological investigateion 1994 23: 1-13) (Year: 1994).
[cited by examiner]
Accurso FJ, et al., “Effect of VX-770 in Persons with Cystic Fibrosis and the G551D-CFTR Mutation.” N Engl J Med, Nov. 18, 2010, 363(21):1991-2003, 13 pgs.
[cited by applicant]
Ahmed, H., et al., “Emerging Gene Therapies for Genetic Hearing Loss,” J Assoc Res Otolaryngol, Aug. 16, 2017, 22 pgs.
[cited by applicant]
Albert PS, et al., “An Approach For Jointly Modeling Multivariate Longitudinal Measurements And Discrete Time-To-Event Data,” Ann Appl Stat, 2010, 4(3): 1517-1532, 16 pgs.
[cited by applicant]
Asar O, et al., “mmm: An R package for analyzing multivariate longitudinal data with multivariate marginal models,” Comput Methods Programs Biomed, 2013, 112(3):649-654, 6 pgs.
[cited by applicant]
Brebner JA, et al., “Polyclonal free light chains: a biomarker of inflammatory disease or treatment target?” F1000 Med Rep, 2013, 5:4, 6 pgs.
[cited by applicant]
Bundgaard, H., (ed.),
[cited by applicant]
Cai, X., et al., “Gene delivery to mitotic and postmitotic photoreceptors via compacted DNA nanoparticles results in improved phenotype in a mouse model of retinitis pigmentosa,” FASEB J, Apr. 2010, 24(4):1178-91, 25 pg…
[cited by applicant]
Chatterjee N, et al., “Constrained Maximum Likelihood Estimation for Model Calibration Using Summary-level Information from External Big Data Sources” J Am Stat Assoc, 2016, 111(513):107-117, 11 pgs.
[cited by applicant]
Chen J, et al., “Dysfunction of Nrf-2 in CF Epithelia Leads to Excess Intracellular H
[cited by applicant]
Chen X, et al., “Nucleolin-Mediated Cellular Trafficking of DNA Nanoparticle Is Lipid Raft and Microtubule Dependent and Can Be Modulated by Glucocorticoid,” Mol Ther, 2011, 19(1):93-102, 10 pgs.
[cited by applicant]
Chipman HA, et al., “BART: Bayesian Additive Regression Trees,” Ann Appl Stat, 2014, 23(1):42-59, 33 pgs.
[cited by applicant]
Chirkova T, et al., “CX3CR1 is an important surface molecule for respiratory syncytial virus infection in human airway epithelial cells,” J Gen Virol, 2015, 96:2543-2556, 14 pgs.
[cited by applicant]
Chmiel J, et al., “The Effect of Sulforaphane In Broccoli Sprouts On Nrf2 Activation, Glutathione, Markers of Oxidative Stress, and Neutrophil Migration,” Pediatr Pulmonol, 2012, 47(S35):250; 2012 Cystic Fibrosis Confer…
[cited by applicant]
Chromy, B.A., et al., “Proteomic Analysis of Human Serum by Two-Dimensional Differential Gel Electrophoresis after Depletion of High-Abundant Proteins,” Journal of Proteome Research, 2004, 3:1120-1127, 8 pgs.
[cited by applicant]
Chui, CK, et al., “Interpolation by Multivariate Splines,” Math Comput, 1988, 51(183):203-218, 16 pgs.
[cited by applicant]
Clancy JP, et al., “Personalized Medicine in Cystic Fibrosis: Dawning of a New Era,” Am J Respir Crit Care Med, 2012, 186(7):593-597, 5 pgs.
[cited by applicant]
Diggle Pj, et al., “Real-time monitoring of progression towards renal failure in primary care patients,” Biostatistics, 2015, 16(3):522-536, 15 pgs.
[cited by applicant]
Ding, X.Q., et al., “Ocular delivery of compacted DNA-nanoparticles does not elicit toxicity in the mouse retina,” PLoS One, 2009, 4(10):e7410, 11 pgs.
[cited by applicant]
Drumm ML, et al., “Genetic Variation and Clinical Heterogeneity in Cystic Fibrosis,” Annu Rev Pathol, 2012, 7:267-282, 18 pgs.
[cited by applicant]
Duan LL, et at., “Bayesian Ensemble Trees (BET) for Clustering and Prediction in Heterogeneous Data,” J Comput Graph Stat, 2016, 25(3):748-761, 14 pgs.
[cited by applicant]
Duan LL, et al., “Joint Hierarchical Gaussian Process Model with Application to Forecast in Medical Monitoring,” 2014, eprint arXiv:1408.4660, 23 pgs.
[cited by applicant]
Farjo, R., et al., “Efficient non-viral ocular gene transfer with compacted DNA nanoparticles,” PLoS One, 2006, 1:e38, 12 pgs.
[cited by applicant]
Feng, S., et al., “Recombinant adenoviral vector expressing human wild-type p53, GM-CSF, and B7-1 genes suppresses the growth of glioma in vivo,” Tumor Biol, 2014, 35:441-4417, 7 pgs.
[cited by applicant]
Fieuws S, et al., “Predicting renal graft failure using multivariate longitudinal profiles,” Biostatistics, 2008, 9(3):419-431, 13 pgs.
[cited by applicant]
Fieuws S, et al., “Random-effects models for multivariate repeated measures,” Stat Methods Med Res, Oct. 2007, 16(5):387-397, 11 pgs.
[cited by applicant]
Fischer K, et al., “Biomarker Profiling by Nuclear Magnetic Resonance Spectroscopy for the Prediction of All-Cause Mortality: An Observational Study of 17,345 Persons,” PLoS Med, Feb. 2014, 11(2):e1001606, 12 pgs.
[cited by applicant]
Fletcher, A.M., et al., “Transgene expression in the striatum following intracerebral injections of DNA nanoparticles encoding for human glial cell line-derived neurotrophic factor,” Neuroscience, Oct. 27, 2011, 194:220…
[cited by applicant]
Green, PJ, et al., “Nonparametric regression and generalized linear models: a roughness penalty approach,” 1
[cited by applicant]
Groot Kormelink, T., et al., “Immunoglobulin Free Light Chains Are Increased in Hypersensitivity Pneumonitis and Idiopathic Pulmonary Fibrosis,” PLoS one, 2011, 6(9):e25392, 7 pgs.
[cited by applicant]
Harun SN, et al., “A systematic review of studies examining the rate of lung function decline in patients with cystic fibrosis,” Paediatr Respir Rev, 2016, 20:55-66, 12 pgs.
[cited by applicant]
Hastie T, et al.,
[cited by applicant]
Huang, J., et al., “CRISPR Editing in Biological and Biomedical Investigation,” J Cell Physiol, Aug. 8, 2017, 19 pgs.
[cited by applicant]
Huang, L., et al., “Highly Selective Targeting of Hepatic Stellate Cells for Liver Fibrosis Treatment Using a D-Enantiomeric Peptide Ligand of Fn14 Identified by Mirror-Image mRNA Display,” Mol Pharmaceutics, 2017, 14:1…
[cited by applicant]
James GM, et al., “Principal component models for sparse functional data,” Biometrika, 2000, 87(3):587-602, 16 pgs.
[cited by applicant]
Jiang C-R, et al., “Covariate Adjusted Functional Principal Components Analysis For Longitudinal Data,” The Annals of Statistics, 2010, 38(2): 1194-1226, 34 pgs.
[cited by applicant]
Kim PY, et al., “Identification of plasma Complement C3 as a potential biomarker for neuroblastoma using a quantitative proteomic approach,” J Proteomics, 2014, 96:1-12, 12 pgs.
[cited by applicant]
Koirala, A., et al., “S/MAR-containing DNA nanoparticles promote persistent RPE gene expression and improvement in RPE65-associated LCA,” Hum Mol Genet, Apr. 15, 2013, 22(8):1632-42, 11 pgs.
[cited by applicant]
Kolodziej, M., et al., “Roscotirine has anti-proliferative and pro-apoptotic effects on glioblastoma cell lines: A pilot study,” Oncology Reports, 2015, 34:1549-1556, 8 pgs.
[cited by applicant]
Konstan, M.W., et al., “Compacted DNA nanoparticles administered to the nasal mucosa of cystic fibrosis subjects are safe and demonstrate partial to complete cystic fibrosis transmembrane regulator reconstitution,” Hum.…
[cited by applicant]
La Rosa PS, et al., “Hypothesis Testing and Power Calculations for Taxonomic-Based Human Microbiome Data,” PLoS One, 2012, 7(12):e52078, 13 pgs.
[cited by applicant]
Laguna TA, et al., “Sputum Desmosine During Hospital Admission for Pulmonary Exacerbation in Cystic Fibrosis,” Chest, Dec. 2009, 136(6):1561-1568, 8 pgs.
[cited by applicant]
Lancioni CL, et al., “
[cited by applicant]
Li Q, et al., “Rv2468c, a novel
[cited by applicant]
Liou TG, et al., “Year-to-year changes in lung function in individuals with cystic fibrosis,” J Cyst Fibros, 2010, 9(4):250-6, 7 pgs.
[cited by applicant]
Naso, M.F., et al., “Adeno-Associated Virus (AAV) as a Vector for Gene Therapy,” Bio Drugs, Jul. 1, 2017, 31:317-334, 18 pgs.
[cited by applicant]
Nick JA, et al., “Blood mRNA biomarkers for detection of treatment response in acute pulmonary exacerbations of cystic fibrosis,” Thorax, 2013, 68(10):929-937, 9 pgs.
[cited by applicant]
Obuchowski NA, et al., “Sample Size Determination for Diagnostic Accuracy Studies Involving Binormal ROC Curve Indices,” Stat Med, 1997, 16(13):1529-1542, 14 pgs.
[cited by applicant]
Peila, C., et al., “Effects of Holder pasteurization on the protein profile of human milk, ” Italian journal of Pediatrics, 2016, 42:36, 8 pgs.
[cited by applicant]
Peng, J., et al., “A Geometric Approach to Maximum Likelihood Estimation of the Functional Principal Components From Sparse Longitudinal Data,” J Comput Graph Stat, 2009, 18(4):995-1015, Technical Report 2007a, 87 pgs.
[cited by applicant]
Peng, J., Restricted MLE for Functional Principal Components Analysis (R package fpca) 2015. Available from: https://CRAN.R-project.org/package=fpca, 12 pgs.
[cited by applicant]
Ramsay JO, et al., Functional data analysis, Second Ed., Springer Science + Business Media, Inc., New York., NY, 2005, p. 426, (Table of Contents only) 13 pgs.
[cited by applicant]
Ratjen F, et al., “Effect of Azithromycin on Systemic Markers of Inflammation in Patients With Cystic Fibrosis Uninfected With
[cited by applicant]
Rosenfeld M, et al., “Baseline Characteristics and Factors Associated With Nutritional and Pulmonary Status at Enrollment in the Cystic Fibrosis EPIC Observational Cohort,” Pediatr Pulmonol, 2010, 45(9):934-944, 11 pgs.
[cited by applicant]
Rosenfeld M, et al., “Decline in Lung Function Does not Predict Future Decline in Lung Function in Cystic Fibrosis Patients,” Pediatr Pulmonol, 2015, 50(9):856-862, 7 pgs.
[cited by applicant]
Sagel SD, et al., “Effect of Treatment of Cystic Fibrosis Pulmonary Exacerbations on Systemic Inflammation,” Ann Am Thorac Soc, 2015, 12(5):708-717, 10 pgs.
[cited by applicant]
Sagel SD, et al., “Validation of Candidate Serum Protein and Lipid Markers of Disease Severity In CF,” Pediatr Pulmonol, 2014, 49(S38):288, 2014 Cystic Fibrosis Conference, Poster Session Abstract 205*, 1 pg.
[cited by applicant]
Sanders DB, et al., “Failure to Recover to Baseline Pulmonary Function after Cystic Fibrosis Pulmonary Exacerbation,” Am J Respir Crit Care Med, 2010, 182(5):627-632, 6 pgs.
[cited by applicant]
Schluchter MD, et al., “Classifying Severity of Cystic Fibrosis Lung Disease Using Longitudinal Pulmonary Function Data,” Am J Respir Crit Care Med, 2006, 174(7):780-786, 7 pgs.
[cited by applicant]
Sinha C, et al., “PKA and actin play critical roles as downstream effectors in MRP4-mediated regulation of fibroblast migration,” Cell Signal, 2015, 27(7):1345-1355, 11 pgs.
[cited by applicant]
Sinha C, et al., “Capturing the Direct Binding of CFTR Correctors to CFTR by Using Click Chemistry,” Chembiochem, 2015, 16:2017-2022, 6 pgs.
[cited by applicant]
Slobodianik NH, et al., “Inflammatory biomarker profile in children with cystic fibrosis: preliminary study,” Proc Nutr Soc, 3
[cited by applicant]
Sun, W., et al., “Real-Time Imaging of Gene Delivery and Expression with DNA Nanoparticle Technologies,” Chapter 33, In: Foote R., Lee J. (eds) Micro and Nano Technologies in Bioanalysis. Methods in Molecular Biology (M…
[cited by applicant]
Szczesniak RD, et al., “A semiparametric approach to estimate rapid lung function decline in cystic fibrosis,” Annals of Epidemiology, 2013, 23(12):771-777, 7 pgs.
[cited by applicant]
Szczesniak RD, et al., “Phenotypes of Rapid Cystic Fibrosis Lung Disease Progression during Adolescence and Young Adulthood,” American Journal of Respiratory and Critical Care Medicine, 2017, 196(4): 471-478, 8 pgs.
[cited by applicant]
Szczesniak RD, et al., “Predicting Future Lung Function Decline in Cystic Fibrosis Patients: Statistical Methods and Clinical Connections,” Pediatr Pulmonol, Letter to the Editor, 2016, 51(2):217-218, 2 pgs.
[cited by applicant]
Tang Y, et al., “Developing Adaptive Personalized Therapy for Cystic Fibrosis Using Reinforcement Learning,” Submitted to Ann Appl Stat, 2012, 28 pgs.
[cited by applicant]
Taylor-Robinson D, et al., “Understanding the natural progression in %FEV
[cited by applicant]
Tibshirani RJ., “Regression Shrinkage and Selection via the Lasso,” J R Statist Soc B, 1996, 58(1):267-288, 22 pgs.
[cited by applicant]
Tucholska M, et al., “Human Serum Proteins Fractionated by Preparative Partition Chromatography Prior to LC-ESI-MS/MS,” J Proteome Res, 2009, 8(3):1143-1155, 13 pgs.
[cited by applicant]
Verbeke G, et al., “The analysis of multivariate longitudinal data: A review,” Stat Methods Med Res, 2014, 23(1):42-59, 18 pgs.
[cited by applicant]
Wainwright CE, et al., “Lumacaftor-Ivacaftor in Patients with Cystic Fibrosis Homozygous for Phe508del CFTR,” N Engl J Med, 2015, 373(3):220-231, 12 pgs.
[cited by applicant]
Wang J, et al., “Measuring the impact of apnea and obesity on circadian activity patterns using functional linear modeling of actigraphy data,” J Circadian Rhythms, 2011, 9(1):11, 10 pgs.
[cited by applicant]
Wang X, et al., “Hsp90 Cochaperone Aha1 Downregulation Rescues Misfolding of CFTR in Cystic Fibrosis,” Cell, 2006, 127(4):803-815, 13 pgs.
[cited by applicant]
Wolff, M.E., (ed.),
[cited by applicant]
Xu, Z., et al., “Knocking down necleolin expression in gliomas inhibits tumor growth and induces cell cycle arrest,” J Neurooncol, 2012, 108:59-67, 9 pgs.
[cited by applicant]
Yanagisawa K, et al., “Proteomic patterns of tumour subsets in non-small-cell lung cancer,” Lancet, 2003, 362(9382):433-439, 7 pgs.
[cited by applicant]
Yao, F., et al., “Functional Data Analysis for Sparse Longitudinal Data,” Journal of the American Statistical Association, 2005, 100(470):577-590, 14 pgs.
[cited by applicant]
Yurek, D.M., et al., “Compacted DNA nanoparticle gene transfer of GDNF to the rat striatum enhances the survival of grafted fetal dopamine neurons,” Cell Transplant., 2009, 18(10):1183-96, 15 pgs.
[cited by applicant]
Yurek, D.M., et al., “DNA Nanoparticles: Detection of Long-term Transgene Activity in Brain Using Bioluminescence Imaging,” Mol. Imaging, Apr. 26, 2011, 10(5):327-339, 12 pgs.
[cited by applicant]
Yurek, D.M., et al., “Long-term transgene expression in the central nervous system using DNA nanoparticles,” Mol. Ther., Apr. 2009, 17(4):641-50, 14 pgs.
[cited by applicant]
Zeitzer JM, et al., “Phenotyping Apathy in Individuals With Alzheimer Disease Using Functional Principal Component Analysis,” Am J Geriatr Psychiatry, 2013, 21(4):391-397, 12 pgs.
[cited by applicant]
Zemanick ET, et al., “Inflammation and Airway Microbiota During Cystic Fibrosis Pulmonary Exacerbations,” PLoS One, 2013, 8(4):e62917, 13 pgs.
[cited by applicant]
Zhang, X., et al., “CRISPR/Cas9 system: a powerful technology for in vivo and ex vivo gene therapy,” Sci. China Life Sci, May 2017, 60(5):468-75, 8 pgs.
[cited by applicant]
Ziady, A.G., et al., “Current prospects for gene therapy of cystic fibrosis,” Curr Opin Pharmacol, Oct. 2006, 6(5):515-21, 7 pgs.
[cited by applicant]
Ziady, A.G., et al., “Functional evidence of CFTR gene transfer in nasal epithelium of cystic fibrosis mice in Vivo following luminal application of DNA complexes targeted to the serpin-enzyme complex receptor,” Mol. Th…
[cited by applicant]
Ziady AG, et al., “Interaction with CREB binding protein modulates the activities of Nrf2 and NF-κB in cystic fibrosis airway epithelial cells,” Am J Physiol Lung Cell Mol Physiol, 2012, 302(11):L1221-L1231, 11 pgs.
[cited by applicant]
Ziady, A.G., et al., “Non-viral gene transfer therapy for cystic fibrosis,” Expert Opin Biol Ther, Jun. 2003, 3(3):449-58, 10 pgs.
[cited by applicant]
Ziady AG, et al., “Protein Sequencing with Tandem Mass Spectrometry,” Chapter 21, James Weifu Lee, et al., Eds.
[cited by applicant]
Ziady AG, et al., “Proteomic Analyses of BALF Reveal Potential Biomarkers and Suggest Altered Lipid, Cyclic Nucleotide, and Iron Metabolism in Young CF Children Versus Disease Controls,” Pediatr Pulmonol, 2013, 48(S36):…
[cited by applicant]
Ziady AG, et al., “Proteomic Analyses of Serum From CF Patients With Mild or Severe Disease Reveal the Differential Expression of Proteins That Regulate the Differentiation of Cartilage, Myeloid Leukocytes, and Intestin…
[cited by applicant]
International Search Report and Written Opinion dated Aug. 10, 2020 for Application No. PCT/US2020/030401, 10 pgs.
[cited by applicant]
U.S. Appl. No. 17/121,835, filed Dec. 15, 2020, by Ziady et al., entitled: “Compositions and Methods for Nucleic Acid Transfer.”
[cited by applicant]
Brody, A.S., et al., “High-Resolution Computed Tomography in Young patients with Cystic Fibrosis: Distribution of Abnormalities and Correlation with Pulmonary Function Tests,” J Peds, 2004, 145(1):32-38, 7 pgs.
[cited by applicant]
Chassagnon, G., et al., “Long-term computed tomographic changes in cystic fibrosis patients treated with ivacaftor,” Eur Respir J, 2016, 48(1):249-252, 4 pgs.
[cited by applicant]
Deboer, E.M., et al., “Proteomic profiling identifies novel circulating markers associated with bronchiectasis in cystic fibrosis,” Proteomics Clin Appl, 2017, 11(9-10):1600147, 9 pgs.
[cited by applicant]
Deboer, E.M., et al., “Novel Application of Aptamer Proteomic Analysis in Cystic Fibrosis Bronchoalveolar Lavage Fluid,” Proteomics Clin Appl, 2019, 13:1800085, 8 pgs.
[cited by applicant]
Eichinger, M., et al., “Morphologic and functional scoring of cystic fibrosis lung disease using MRI,” European Journal of Radiology, 2012, 81(6): 1321-1329, 9 pgs.
[cited by applicant]
Fagerland, M.W., et al., “The McNemar test for binary matched-pairs data: mid-p and asymptotic are better than exact conditional,” BMC Med Res Methodol, 2013, 13:91, 8 pgs.
[cited by applicant]
Guo, J., et al., “Longitudinal free-breathing MRI measurement of murine lung physiology in a progressive model of lung fibrosis,” J Appl Physio, 2019, 126(4):1138-1149, 12 pgs.
[cited by applicant]
Hanania, N.A., et al., “Acute bronchodilator responsiveness and health outcomes in COPD patients in the UPLIFT trial,” Respiratory Research, 2011, 12(1):6, 11 pgs.
[cited by applicant]
Higano, N.S., et al., “Retrospective respiratory self-gating and removal of bulk motion in pulmonary UTE MRI of neonates and adults,” Magn Reason Med, 2017, 77(3):1284-1295, 25 pgs.
[cited by applicant]
Higuchi, T., and V. Stella (Eds.),
[cited by applicant]
Hoy, S.M., “Elexacaftor/Ivacaftor/Tezacaftor: First Approval,” Drugs, 2019, 79(18):2001-2007, 7 pgs.
[cited by applicant]
King, T.E., et al., “A Phase 3 Trial of Pirfenidone in Patients with Idiopathic Pulmonary Fibrosis,” N Engl J Med, 2014, 370(22):2083-2092, 10 pgs.
[cited by applicant]
Konstan, M.W., et al., “Assessment of safety and efficacy of long-term treatment with combination lumacaftor and ivacaftor therapy in patients with cystic fibrosis homozygous for the F508del-CFTR mutation (PROGRESS): a …
[cited by applicant]
Lederlin, M., et al., “Three-Dimensional Assessment of Lung Tissue Density Using a Clinical Ultrashort Echo Time at 3 Tesla: A Feasibility Study in Healthy Subjects,” J Magn Reson Imag, 2014, 40(4):839-847, 9 pgs.
[cited by applicant]
Loew, W., et al., “A Volume Saddle Coil for Hyperpolarized
[cited by applicant]
Miller, G.W., et al., “Hyperpolarized
[cited by applicant]
Niedbalski, P.J., et al., “Mapping and correcting hyperpolarized magnetization decay with radial keyhole imaging,” Magn Reson Med, 2019, 82:367-376, 10 pgs.
[cited by applicant]
Pearce, M.S., et al., “Radiation exposure from CT scans in childhood and subsequent risk of leukaemia and brain tumours: a retrospective cohort study,” Lancet, 2012, 380(9840):499-505, 7 pgs.
[cited by applicant]
Pipe, J.G., et al., “A New Design and Rationale for 3D Orthogonally Oversampled κ-Space Trajectories,” Magn Reson Med, 2011, 66(5):1303-1311, 9 pgs.
[cited by applicant]
Roach, D.J., et al., “Ultrashort Echo-Time Magnetic Resonance Imaging Is a Sensitive Method for the Evaluation of Early Cystic Fibrosis Lung Disease,” Ann Am Thorac Soc, 2016, 13(11): 1923-1931, 9 pgs.
[cited by applicant]
Robison, R.K., et al., “Three-Dimensional Ultrashort Echo-Time Imaging Using a FLORET Trajectory,” Magn Reson Med, 2017, 78(3):1038-1049, 12 pgs.
[cited by applicant]
Roche, E.B., (Ed.),
[cited by applicant]
Sawicki, G.S., et al., “Sustained Benefit from Ivacaftor Demonstrated by Combining Clinical Trial and Cystic Fibrosis Patient Registry Data,” Am J Respir Crit Care Med, 2015, 192(7):836-842, 7 pgs.
[cited by applicant]
Stanojevic, S., et al., “Physiologic endpoints for clinical studies for cystic fibrosis,” J Cyst Fibros, 2016, 15(4):416-423, 8 pgs.
[cited by applicant]
Szczesniak, R.D., et al., “Dynamic predictive probabilities to monitor rapid cystic fibrosis disease progression,” Statistics in Medicine, 2020, 39(6):740-756, 17 pgs.
[cited by applicant]
Szczesniak, R.D., et al., “Improving Detection of Rapid Cystic Fibrosis Disease Progression—Early Translation of a Predictive Algorithm Into a Point-of-Care Tool” IEEE Journal of Translational Engineering in Health and …
[cited by applicant]
Szczesniak, R., et al., “Use of FEV
[cited by applicant]
Tepper, L.A., et al., “The development of bronchiectasis on chest computed tomography in children with cystic fibrosis: can pre-stages be identified?” Eur Radiol, 2016, 26(12):4563-4569, 7 pgs.
[cited by applicant]
Thomen, R.P., et al., “Hyperpolarized
[cited by applicant]
Vestbo, J., et al., “Natural history of COPD: Focusing on change in FEV
[cited by applicant]
Walkup, L.L., et al., “Feasibility, tolerability and safety of pediatric hyperpolarized
[cited by applicant]
Walkup, L.L., et al., “Xenon-129 MRI detects ventilation deficits in pediatric stem-cell transplant patients unable to perform spirometry,” Eur Respir J, 2019, 53(5):1-16, 16 pgs.
[cited by applicant]
Wielputz, M.O., et al., “Magnetic Resonance Imaging Detects Changes in Structure and Perfusion, and Response to Therapy in Early Cystic Fibrosis Lung Disease,” Am J Respir Crit Care Med, 2014, 189(8):956-965, 10 pgs.
[cited by applicant]
Wilcoxon, F., “Individual Comparisons of Grouped Data by Ranking Methods,” Journal of Economic Entomology, 1946, 39(2):269-270, 2 pgs.
[cited by applicant]
Willmering, M.M., et al., “Implementation of the FLORET Ultrashort Echo-Time Sequence for Lung Imaging,” Magn Reson Med, 2019, 82(3):1091-1100, 17 pgs.
[cited by applicant]
Willmering, M.M., et al., “Improved pulmonary
[cited by applicant]
Yu, J., et al., “Comparison of Lung T
[cited by applicant]
Zwart, N.R., et al., “Graphical Programming Interface: A Development Environment for MR1 Methods.,” Magn Reson Med, 2015, 74(5):1449-1460, 12 pgs.
[cited by applicant]
Altieri, D.C., “Validating Survivin as a Cancer Therapeutic Target,” Nat Rev Cancer, 2003, 3(1):46-54, 9 pgs.
[cited by applicant]
Arai, H., et al., “Nestin expression in brain tumors: its utility for pathological diagnosis and correlation with the prognosis of high-grade gliomas,” Brain Tumor Pathol, 2012, 29(3): 160-167, 8 pgs.
[cited by applicant]
Assi, H., et al., “Gene Therapy for Brain Tumors: Basic Developments and Clinical Implementation,” Neurosci Lett, 2012, 527(2):71-77, 14 pgs.
[cited by applicant]
Bhang, H.-E.C., et al., “Tumor-Specific Imaging Through Progression Elevated Gene-3 Promoter-Driven Gene Expression,” Nat Med, 2011, 17(1):123-129, 16 pgs.
[cited by applicant]
Bossen, C., et al., “Interactions of Tumor Necrosis Factor (TNF) and TNF Receptor Family Members in the Mouse and Human,” J Biol Chem, 2006, 281(20):13964-13971, 8 pgs.
[cited by applicant]
Chen, X., et al., “Cell Surface Nucleolin Serves as Receptor for DNA Nanoparticles Composed of Pegylated Polylysine and DNA,” Mol Ther, 2008, 16(2):333-342, 10 pgs.
[cited by applicant]
Christensen, C.L., et al., “Targeted cytosine deaminase-uracil phosphoribosyl transferase suicide gene therapy induces small cell lung cancer-specific cytotoxicity and tumor growth delay,” Clin Cancer Res, 2010, 16(8):2…
[cited by applicant]
Dachs, G.U., et al., “From bench to bedside for gene-directed enzyme prodrug therapy of cancer,” Anti-Cancer Drugs, 2005, 16(4):349-359, 11 pgs.
[cited by applicant]
Debinski, W., et al., “Convection-enhanced delivery for the treatment of brain tumors,” Expert Rev Neurother, 2009, 9(10):1519-1527, 15 pgs.
[cited by applicant]
Fan, X., et al., “hTERT Gene Amplification and Increased mRNA Expression in Central Nervous System Embryonal Tumors,” Am J Pathol, 2003, 162(6):1763-1769, 7 pgs.
[cited by applicant]
Fortin, S.P., et al., “Tumor Necrosis Factor-Like Weak Inducer of Apoptosis (TWEAK) Stimulation of Glioma Cell Survival Is Dependent Upon Akt2 Function,” Mol Cancer Res, 2009, 7(11):1871-1881, 24 pgs.
[cited by applicant]
Galzio, R., et al., “Glycosilated Nucleolin as Marker for Human Gliomas,” J Cell Biochem, 2012, 113(2):571-579, 9 pgs.
[cited by applicant]
Gurunathan, S., et al., “Regulation of Fibroblast Growth Factor-inducible 14 (Fn14) Expression Levels via Ligand-independent Lysosomal Degradation,” J Biol Chem, 2014, 289(19):12976-12988, 13 pgs.
[cited by applicant]
Han, Z., et al., “AAV and Compacted DNA Nanoparticles for the Treatment of Retinal Disorders: Challenges and Future Prospects,” Invest Ophthalmol Vis Sci, 2011, 52(6):3051-3059, 9 pgs.
[cited by applicant]
Haung, L., et al., “Highly Selective Targeting of Hepatic Stellate Cells for Liver Fibrosis Treatment Using a D-Enantiomeric Peptide Ligand of Fn14 Identified by Mirror-Image mRNA Display,” Mol Pharmaceutics, 2017, 14:1…
[cited by applicant]
Hersh, D.S., et al., “The TNF receptor family member Fn14 is highly expressed in recurrent glioblastoma and in GBM patient-derived xenografts with acquired temozolomide resistance,” Neuro Oncol, 2018, 20(10):1321-1330, …
[cited by applicant]
Jiang, X., et al., “The Imprinted Gene PEG3 Inhibits Wnt Signaling and Regulates Glioma Growth,” J Biol Chem, 2010, 285(11):8472-8480, 9 pgs.
[cited by applicant]
Joo, K.M., et al., “Patient-Specific Orthotopic Glioblastoma Xenograft Models Recapitulate the Histopathology and Biology of Human Glioblastomas In Situ,” Cell Rep, 2013, 3(1):260-273, 14 pgs.
[cited by applicant]
Kajiwara, Y., et al., “Expression of Survivin in Astrocytic Tumors: Correlation with Malignant Grade and Prognosis,” Cancer, 2003, 97(4):1077-1083, 7 pgs.
[cited by applicant]
Kibbey, M.C., et al., “A 110-kD Nuclear Shuttling Protein, Nucleolin, Binds to the Neurite-Promoting IKVAV Site of Laminin-1,” J Neurosci Res, 1995, 42(3):314-322, 9 pgs.
[cited by applicant]
Li, A., et al., “Unsupervised Analysis of Transcriptomic Profiles Reveals Six Glioma Subtypes,” Cancer Res, 2009, 69(5):2091-2099, 17 pgs.
[cited by applicant]
Liu, G., et al., “Nanoparticles of Compacted DNA Transfect Postmitotic Cells,” J Biol Chem, 2003, 278(35):32578-32586, 9 pgs.
[cited by applicant]
Martens, T., et al., “Inhibition of Glioblastoma Growth in a Highly Invasive Nude Mouse Model Can Be Achieved by Targeting Epidermal Growth Factor Receptor but not Vascular Endothelial Growth Factor Receptor-2,” Clin Ca…
[cited by applicant]
Mastorakos, P., et al., “Highly PEGylated DNA Nanoparticles Provide Uniform and Widespread Gene Transfer in the Brain,” Adv Healthc Mater, 2015, 4(7):1023-1033, 24 pgs.
[cited by applicant]
Mead, B.P., et al., “Novel Focused Ultrasound Gene Therapy Approach Noninvasively Restores Dopaminergic Neuron Function in a Rat Parkinson's Disease Model,” Nano Lett, 2017, 17(6):3533-3542, 21 pgs.
[cited by applicant]
Nance, E.A., et al., “A Dense Poly(ethylene glycol) Coating Improves Penetration of Large Polymeric Nanoparticles within Brain Tissue,” Sci Transl Med, 2012, 4(149):149ra119, 18 pgs.
[cited by applicant]
Ndesendo, V.M., “Convection-Enhanced Delivery of Neurotherapeutics,” In: V. Pillay and Y.E. Choonara, (Eds.),
[cited by applicant]
Neeves, K.B., et al., “Dilation and degradation of the brain extracellular matrix enhances penetration of infused polymer nanoparticles,” Brain Res, 2007, 1180:121-132, 23 pgs.
[cited by applicant]
Negroni, L., et al., “Treatment of colon cancer cells using the cytosine deaminase/5-fluorocytosine suicide system induces apoptosis, modulation of the proteome, and Hsp90ß phosphorylation,” Mol Cancer Ther, 2007, 6(10)…
[cited by applicant]
O'Mahony, A.M., et al., “Non-viral Nanosystems for Gene and Small Interfering RNA Delivery to the Central Nervous System: Formulating the Solution,” J Pharm Sci, 2013, 102(10):3469-3484, 16 pgs.
[cited by applicant]
Ostrom, Q.T., et al., “CBTRUS Statistical Report: Primary Brain and Central Nervous System Tumors Diagnosed in the United States in 2006-2010,” Neuro-Oncol, 2013, 15(Suppl 2):ii1-ii56, 56 pgs.
[cited by applicant]
Patrizii, M., et al., “Utility of Glioblastoma Patient-Derived Orthotopic Xenografts in Drug Discovery and Personalized Therapy,” Front Oncol, 2018, 8:article 23, 9 pgs.
[cited by applicant]
Pelekanou, V., et al., “BAFF, APRIL, TWEAK, BCMA, TACI and Fn14 Proteins Are Related to Human Glioma Tumor Grade: Immunohistochemistry and Public Microarray Data Meta-Analysis,” PLoS One, 2013, 8(12):e83250, 11 pgs.
[cited by applicant]
Perez, J.G., et al., “The TWEAK Receptor Fn14 is a Potential Cell Surface Portal for Targeted Delivery of Glioblastoma Therapeutics,” Oncogene, 2016, 35(17):2145-2155, 27 pgs.
[cited by applicant]
Phillips, H.S., et al., “Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis,” Cancer Cell, 2006, 9(3):157-173, 17 pgs.
[cited by applicant]
Portsmouth, D., et al., “Suicide genes for cancer therapy,” Mol Aspects Med, 2007, 28(1):4-41, 38 pgs.
[cited by applicant]
Redgate, E.S., et al., “Time of Death of CNS Tumor-Bearing Rats Can Be Reliably Predicted by Body Weight-Loss Patterns,” Lab Anim Sci, 1991, 41(3):269-273, 5 pgs.
[cited by applicant]
Saucier-Sawyer, J.K., et al., “Distribution of Polymer Nanoparticles by Convection-Enhanced Delivery to Brain Tumors,” J Control Release, 2016, 232:103-112, 26 pgs.
[cited by applicant]
Sausville, E.A. et al., “Contributions of Human Tumor Xenografts to Anticancer Drug Development,” Cancer Res, 2006, 66(7):3351-3354, discussion 3354, 4 pgs.
[cited by applicant]
Schwartzbaum, J.A., et al., “Epidemiology and molecular pathology of glioma,” Nat Clin Pract Neurol, 2006, 2(9):494-503, 10 pgs.
[cited by applicant]
Shirahata, M., et al., “Gene Expression-Based Molecular Diagnostic System for Malignant Gliomas Is Superior to Histological Diagnosis,” Clin Cancer Res, 2007, 13(24):7341-7356, 16 pgs.
[cited by applicant]
Shirahata, M., et al., “Using gene expression profiling to identify a prognostic molecular spectrum in gliomas,” Cancer Sci, 2009, 100(1):165-172, 8 pgs.
[cited by applicant]
Shirakawa, T., et al., “Cytotoxicity of Adenoviral-Mediated Cytosine Deaminase Plus 5-Fluorocytosine Gene Therapy is Superior to Thymidine Kinase Plus Acyclovir in a Human Renal Cell Carcinoma Model,” J Urol, 1999, 162(…
[cited by applicant]
Soundararajan, S., et al., “Plasma Membrane Nucleolin Is a Receptor for the Anticancer Aptamer AS1411 in MV4-11 Leukemia Cells,” Mol Pharmacol, 2009, 76(5):984-991, 8 pgs.
[cited by applicant]
Taillandier, L., et al., “Models for neuro-oncological preclinical studies: solid orthotopic and heterotopic grafts of human gliomas into nude mice,” J Neurosci Methods, 2003, 125(1-2):147-157, 11 pgs.
[cited by applicant]
Tobias, A., et al., “The art of gene therapy for glioma: a review of the challenging road to the bedside,” J Neurol Neurosurg Psychiatry, 2013, 84(2):213-222, 20 pgs.
[cited by applicant]
Tran, N.L., et al., “Increased Fibroblast Growth Factor-Inducible 14 Expression Levels Promote Glioma Cell Invasion via Racl and Nuclear Factor-KB and Correlate with Poor Patient Outcome,” Cancer Res, 2006, 66(19):9535-…
[cited by applicant]
Tran, N.L., et al., “The Human Fn14 Receptor Gene Is Up-Regulated in Migrating Glioma Cells in Vitro and Overexpressed in Advanced Glial Tumors,” Am J Pathol, 2003, 162(4):1313-1321, 9 pgs.
[cited by applicant]
Trinh, Q.T., et al., “Enzyme/Prodrug Gene Therapy: Comparison of Cytosine Deaminase/5-Fluorocytosine Versus Thymidine Kinase/Ganciclovir Enzyme/Prodrug Systems in a Human Colorectal Carcinoma Cell Line,” Cancer Res, 199…
[cited by applicant]
Vogelbaum, M.A et al., “Convection-enhanced delivery for the treatment of glioblastoma,” Neuro-Oncol, 2015, 17(Suppl 2):ii3-ii8, 6 pgs.
[cited by applicant]
Winkles, J.A., “The TWEAK-Fn14 cytokine-receptor axis: discovery, biology and therapeutic targeting,” Nat Rev Drug Discov, 2008, 7(5):411-425, 32 pgs.
[cited by applicant]
Workman, P., et al., “Guidelines for the welfare and use of animals in cancer research,” Br J Cancer, 2010, 102(11):1555-1577, 23 pgs.
[cited by applicant]
Xu, Z., et al., “Orthotopic Patient-Derived Glioblastoma Xenografts in Mice,” Methods Mol Biol, Ch. 14 in Dimitris G. Placantonakis (ed.),
[cited by applicant]
Yabroff, K.R., et al., “Patterns of care and survival for patients with glioblastoma multiforme diagnosed during 2006,” Neuro-Oncol, 2012, 14(3):351-359, 9 pgs.
[cited by applicant]
Yurek, D., et al., “Intracerebral injections of DNA nanoparticles encoding for a therapeutic gene provide partial neuroprotection in an animal model of neurodegeneration,” Nanomedicine: Nanotechnology, Biology, and Medi…
[cited by applicant]
Yurek, D.M., et al., “Age and lesion-induced increases of GDNF transgene expression in brain following intracerebral injections of DNA nanoparticles,” Neuroscience, 2015, 284:500-512, 28 pgs.
[cited by applicant]
Zarogoulidis, P., et al., “Suicide Gene Therapy for Cancer—Current Strategies,” J Genet Syndr Gene Ther, 2013, 4, 29 pgs.
[cited by applicant]
Zhang, J., et al., “Gene-Directed Enzyme Prodrug Therapy,” AAPS J, 2015, 17(1):102-110, 9 pgs.
[cited by applicant]
Zhou, H., et al., “Development of Human Serine Protease-Based Therapeutics Targeting Fn14 and Identification of Fn14 as a New Target Overexpressed in TNBC,” Mol Cancer Ther, 2014, 13(11):2688-2705, 34 pgs.
[cited by applicant]
Ziady, A.-G., et al., “Minimal Toxicity of Stabilized Compacted DNA Nanoparticles in the Murine Lung,” Mol Ther, 2003, 8(6):948-956, 9 pgs.
[cited by applicant]
Ziady, A.-G., et al., “Transfection of Airway Epithelium by Stable PEGylated Poly-
[cited by applicant]
European Search Report, Extended, and Written Opinion dated Dec. 14, 2021 for Application No. EP 21180569.2, 11 pgs.
[cited by applicant]
Abedin, S., et al., “Predictive Value of Bronchiolitis Obliterans Syndrome Stage 0p in Chronic Graft-versus-Host Disease of the Lung,” Biol Blood Marrow Transplant, 2015, 21(6):1127--1131, 15 pgs.
[cited by applicant]
Amanat, F., et al., “A serological assay to detect SARS-CoV-2 seroconversion in humans,” Nat. Med, 2020, 26(7):1033-1036, 16 pgs.
[cited by applicant]
Aurora, P., et al.,“ Quality Control for Spirometry in Preschool Children with and without Lung Disease,” Am J Respir Crit Care Med, 2004, 169:1152-1159, 8 pgs.
[cited by applicant]
Aziz, M.D., et al., “Disease Risk and GVHD Biomarkers Can Stratify Patients For Risk of Relapse and Non-Relapse Mortality Post Hematopoietic Cell Transplant,” Leukemia, 2020, 34(7):1898-1906, 17 pgs.
[cited by applicant]
Benden, C., et al., “Therapy options for chronic lung allograft dysfunction-bronchiliolitis obliterans syndrome following first-line immunosuppressive strategies: A systematic review,” Jounral of Heart and Lung Transpla…
[cited by applicant]
Bergeron, A., et al., “Noninfectious lung complications after allogeneic haematopoietic stem cell transplantation,” Eur Respir J, 2018, 51:1702617, 13 pgs.
[cited by applicant]
Brewington, J.J., et al., “Detection of CFTR function and modulation in primary human nasal cell spheroids,” J Cyst Fibros, 2018, 17(1):26-33, 17 pgs.
[cited by applicant]
Callow, K.A., et al., “The time course of the immune response to experimental coronavirus infection of man,” Epidemiol Infect, 1990, 105:435-446, 12 pgs.
[cited by applicant]
Casadevall, A., et al., “The convalescent sera option for containing COVID-19,” J Clin Invest, 2020, 130(4):1545-1548.
[cited by applicant]
Centers for Disease Control and Prevention (CDC) Revised U.S. surveillance case definition for severe acute respiratory syndrome (SARS) and update on SARS cases-United States and worldwide, Dec. 2003. MMWR Morb. Mortal.…
[cited by applicant]
Chang, C.-K., et al., “Multiple Nucleic Acid Binding Sites and Intrinsic Disorder of Severe Acute Respiratory Syndrome Coronavirus Nucleocapsid Protein: Implications for Ribonucleocapsid Protein Packaging,” J Virol, 200…
[cited by applicant]
Cheng, G.-S., et al., “Lung Function Trajectory in Bronchiolitis Obliterans Syndrome after Allogeneic Hematopoietic Cell Transplant,” Ann Am Thorac Soc, 2016; 13(11):1932-1939, 8 pgs.
[cited by applicant]
Chi, X., et al., “A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2,” Science, 2020, 369:650-655, 6 pgs.
[cited by applicant]
Chien, J.W., et al., “Bronchiolitis Obliterans Syndrome After Allogeneic Hematopoietic Stem Cell Transplantation: An Increasingly Recognized Manifestation of Chronic Graft-versus-Host Disease,” Biol Blood Marrow Transpl…
[cited by applicant]
Cohen, H.Y., et al., “Calorie Restriction Promotes Mammalian Cell Survival by Inducing the SIRT1 Deacetylase,” Science, 2004, 305(5682):390-392.
[cited by applicant]
Cox, D.R., et al., “Large numbers of explanatory variables, a semi-descriptive analysis,” PNAS, 2017, 114(32):8592-8595, 4 pgs.
[cited by applicant]
De Silva, T., et al., “Markers of rejection of a lung allograft: state of the art,” Biomark Med, 2022, 16(6):483-498, 16 pgs.
[cited by applicant]
Deeks, J.J., et al. “Antibody tests for identification of current and past infection with SARS-CoV-2 (Review),” Cochrane Database Syst Rev, 2020, 6:CD013652, 306 pgs.
[cited by applicant]
Dijkman, R., et al., “Human Coronavirus NL63 and 229E Seroconversion in Children,” J Clin Microbiol, 2008, 46(7):2368-2373, 6 pgs.
[cited by applicant]
Du, L., et al., “The spike protein of SARS-CoV—a target for vaccine and therapeutic development,” Nat Rev Microbiol, 2009, 7:226--236, 11 pgs.
[cited by applicant]
Dunn, M., et al., “Pediatric Bone Marrow Transplant Recipients That Develop Bronchiolitis Obliterans Syndrome Exhibit Significant Changes in Complement Activation, Angiotensin Maturation, and Cholesterol Processing Prio…
[cited by applicant]
Eroshenko, N., et al., “Implications of antibody-dependent enhancement of infection for SARS-CoV-2 countermeasures,” Nat Biotechnol, 2020, 38:789-791, 3 pgs.
[cited by applicant]
Estenne, M., et al., “Bronchiolitis Obliterans Syndrome 2001: An Update of the Diagnostic Criteria,” J Heart Lung Transplant, 2002; 21:297-310, 14 pgs.
[cited by applicant]
Fink, Z.W., et al., “PepSIRF: a flexible and comprehensive tool for the analysis of data from highly-multiplexed DNA-barcoded peptide assays,” arXiv, 2020, 5 pgs.
[cited by applicant]
Fleri, W., et al., “The Immune Epitope Database and Analysis Resource in Epitope Discovery and Synthetic Vaccine Design,” Front Immunol, 2017, 8:278, 16 pgs.
[cited by applicant]
Friesen, R.H.E., et al., “A common solution to group 2 influenza virus neutralization,” PNAS, 2014, 111(1):445-450, 6 pgs.
[cited by applicant]
Geyer, P.E., et al., “Plasma Proteome Profiling to Assess Human Health and Disease,” Cell Syst, 2016, 2:185-195, 12 pgs.
[cited by applicant]
Geyer, P.E., et al., “Proteomics reveals the effects of sustained weight loss on the human plasma proteome,” Mol Syst Biol, 2016; 12:901, 16 pgs.
[cited by applicant]
Gorse, G.J., et al., “Prevalence of Antibodies to Four Human Coronaviruses is Lower in Nasal Secretions than in Serum,” Clin Vaccine Immunol, 2010, 17(12):1875-1880, 6 pgs.
[cited by applicant]
Gostic, K.M., et al., “Potent Protection against H5N1 and H7N9 Influenza via Childhood Hemagglutinin Imprinting,” Science, 2016, 354(6313):722-726, 16 pgs.
[cited by applicant]
Grassi, N., et al., “Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome,” Genome Med, 2016, 8:44, 13 pgs.
[cited by applicant]
Grifoni, A., et al., “Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals,” Cell, 2020, 181:1489-1501, 29 pgs.
[cited by applicant]
Halstead, S.B., et al., “Antibody-enhanced dengue virus infection in primate leukocytes,” Nature, 1977, 265:739-741, 3 pgs.
[cited by applicant]
Hansen, J., et al., “Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail,” Science, 2020, 369:1010-1014, 5 pgs.
[cited by applicant]
Hartwell, M.J., et al., “An early-biomarker algorithm predicts lethal graft-versus-host disease and survival,” JCI Insight, 2017, 2(3):e89798, 9 pgs.
[cited by applicant]
Heijerman, H.G.M., et al., “Efficacy and safety of the elexacaftor/tezacaftor/ivacaftor combination regimen in people with cystic fibrosis homozygous for the F508del mutation: a double-blind, randomised, phase 3 trial,”…
[cited by applicant]
Heltshe, S.L., et al., “Ivacaftor-treated Patients with Cystic Fibrosis Derive Long-Term Benefit Despite No Short-Term Clinical Improvement,” Am J Respir Crit Care Med, 2018, 197(11): 1483-1486, 4 pgs.
[cited by applicant]
Hildebrandt, G.C., et al., “Diagnosis and treatment of pulmonary chronic GVHD: report from the consensus confrence on clinical practice in chronic GVHD,” Bone Marrow Transplant, 2011, 46(10):1283-1295, 13 pgs.
[cited by applicant]
Hoofnagle, J.H., et al., “Antibody to Hepatitis B Core Antigen. A Sensitive Indicator of Hepatitis B Virus Replication,” N Engl J Med, 1974, 290:1336-1340, 5 pgs.
[cited by applicant]
Huttenhain, R., et al., “A Targeted Mass Spectrometry Strategy for Developing Proteomic Biomarkers: A Case Study of Epithelial Ovarian Cancer,” Mol Cell Proteomics, 2019, 18:1836-1850, 16 pgs.
[cited by applicant]
Jagasia, M.H., et al., “National Institutes of Health Consensus Development Project on Criteria for Clinical Trials in Chronic Graft-versus-Host Disease: I. The 2014 Diagnosis and Staging Working Group Report,” Biol Blo…
[cited by applicant]
Jia, N., et al., “Emergence of human infection with Jingmen tick virus in China: A retrospective study,” EBioMedicine, 2019, 43:317-324, 8 pgs.
[cited by applicant]
Jodele, S., et al., “Complement blockade for TA-TMA: lessons learned from a large pediatric cohort treated with eculizumab,” Blood, 2020, 135(13):1049-1057, 9 pgs.
[cited by applicant]
Jodele, S., et al., “Interferon-complement loop in transplant-associated thrombotic microangiopathy,” Blood Adv, 2020, 4(6):1166-1177, 12 pgs.
[cited by applicant]
Kall, L., et al., “Semi-supervised learning for peptide identification from shotgun proteomics datasets,” Nat Methods, 2007, 4(11):923-925, 3 pgs.
[cited by applicant]
Katzelnick, L.C., et al., “Antibody-dependent enhancement of severe dengue disease in humans,” Science, 2017, 358:929-932, 4 pgs.
[cited by applicant]
Keng, C.-T., et al., “Amino Acids 1055 to 1192 in the S2 Region of Severe Acute Respiratory Syndrome Coronavirus S Protein Induce Neutralizing Antibodies: Implications for the Development of Vaccines and Antiviral Agent…
[cited by applicant]
Keogh, R.H., et al., “Dynamic Predication of Survival in Cystic Fibrosis: A Landmarking Analysis Using UK Patient Registry Data,” Epidemiology, 2019, 30(1):29-37, 9 pgs.
[cited by applicant]
Khan, S., et al., “Analysis of Serologic Cross-Reactivity Between Common Human Coronaviruses and SARS-CoV-2 Using Coronavirus Antigen Microarray,” bioRxiv, 2020, 10 pgs.
[cited by applicant]
Khurana, S., et al., “Vaccine-Induced Anti-HA2 Antibodies Promote Virus Fusion and Enhance Influenza Virus Respiratory Disease,” Sci Transl Med, 2013, 5(200):200ra114, 10 pgs.
[cited by applicant]
Konstan, M.W., et al., “Risk Factors For Rate of Decline in Forced Expiratory Volume in One Second in Children and Adolescents with Cystic Fibrosis,” J Pediatr, 2007, 151(2): 134-139e1, 7 pgs.
[cited by applicant]
Konstan, M.W., et al., “Risk Factors For Rate of Decline in FEV
[cited by applicant]
Kozlov, I.A., et al., “A Highly Scalable Peptide-Based Assay System for Proteomics,” PLoS One, 2012, 7(6):e37441, 10 pgs.
[cited by applicant]
Krammer, F., et al., “Serology assays to manage COVID-19: Measurement of antibodies to SAR-CoV-2 will improve disease management if used correctly,” Science, 2020, 368(6495):1060-1061, 2 pgs.
[cited by applicant]
Krisp, C., et al., “Proteomic phenotyping of metastatic melanoma reveals putative signatures of MEK inhibitor response and prognosis,” Br J Cancer, 2018; 119:713-723, 11 pgs.
[cited by applicant]
Ku, N-O., et al., “Mutation of Human Keratin 18 in Association with Cryptogenic Cirrhosis,” J Clin Invest, 1997, 99(1):19-23, 5 pgs.
[cited by applicant]
Lai, S.-C., et al., “Characterization of neutralizing monoclonal antibodies recognizing a 15-residues epitope on the spike protein HR2 region of severe acute respiratory syndrome coronavirus (SARS-CoV),” J Biomed Sci, 2…
[cited by applicant]
Larman, H.B., et al. “Application of a synthetic human proteome to autoantigen discovery through PhIP-Seq,” Nat Biotechnol, 2011, 29(6):535-541, 19 pgs.
[cited by applicant]
Le, T.T., et al., “The COVID-19 vaccine development landscape,” Nat Rev Drug Discov, 2020, 19:305-306, 2 pgs.
[cited by applicant]
Lederer, D.J., et al., “Control of Confounding and Reporting of Results in Casual Inference Studies: Guidance for Authors form Editors of Respiratory, Sleep, and Critical Care Journals,” Ann Am Thorac Soc, 2019, 16(1):2…
[cited by applicant]
Li, D., et al., “Flexible semiparametric joint modeling: an application to estimate individual long function decline and risk of pulmonary exacerbations in cystic fibrosis,” Emerg Themes Epidemiol, 2017, 14:13, 13 pgs.
[cited by applicant]
Liu, A., et al., “Antibody responses against SARS-CoV-2 in COVID-19 patients,” J Med Virol, 2021, 93:144-148, 5 pgs.
[cited by applicant]
Liu, S., et al., “Interaction between heptad repeat 1 and 2 regions in spike protein of SARS-associated coronavirus: implications for virus fusogenic mechanism and identification of fusion inhibitors,” Lancet, 2004, 363…
[cited by applicant]
Liu, X., et al., “Proteomic Characterization Revels That MMP-3 Correlates With Bronchiolitits Obliterans Syndrome Following Allogeneic Hematopoietic Cell and Lung Transplantation,” Am J Transplant, 2016, 16(8):2342-2351…
[cited by applicant]
Lounder, D.T., et al., “Lower levels of vitamin A are associated with increased gastrointestinal graft-versus-host disease in children,” Blood, 2017, 129(20):2801-2807, 7 pgs.
[cited by applicant]
Lu, R., et al., “Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding,” Lancet, 2020, 395:565-574, 10 pgs.
[cited by applicant]
Lubroth, J., et al., “Absence of protein 2C from clarified foot-and-mouth disease virus vaccines provides the basis for distinguishing convalescent from vaccinated animals,” Vaccine, 1996, 14(5):419-427, 9 pgs.
[cited by applicant]
Lucchese, G., et al., “Peptidology: short amino acid modules in cell biology and immunology,” Amino Acids, 2007, 33:703-707, 5 pgs.
[cited by applicant]
Luebbering, N., et al., “Endothelial injury, F-actin and vitamin D binding protein after hematopoietic stem cell transplant and association with clinical outcomes,” Haematologica, 2021, 106(5):1321-1329, 9 pgs.
[cited by applicant]
Lv, H., et al., “Cross-reactive Antibody Response between SARS-CoV-2 and SARS-CoV Infections,” Cell Rep, 2020, 31:107725, 10 pgs.
[cited by applicant]
Magi, B et al., “Bronchoalveolar lavage fluid protein composition in patients with sarcoidosis and idiopathic pulmonary fibrosis: A two-dimensional electrophoretic study,” Electrophoresis, 2002, 23:3434-3444, 11 pgs.
[cited by applicant]
Major-Monfried, H., et al., “MAGIC biomarkers predict long-term outcomes for steroid-resistant acute GVHD,” Blood, 2018, 131(25):2846-2855, 10 pgs.
[cited by applicant]
Middleton, P.G., et al., “Elexacaftor-Tezacaftor-Ivacaftor for Cystic Fibrosis with a Single Phe508del Allele,” N Engl J Med, 2019, 381(19):1809-1819, 16 pgs.
[cited by applicant]
Mina, M.J., et al., “Measles virus infection diminishes preexisting antibodies that offer protection from other pathogens,” Science, 2019, 366(6465):599-606, 18 pgs.
[cited by applicant]
Monto, A.S., et al., “The Doctrine of Original Antigenic Sin: Separating Good From Evil,” J Infect Dis, 2017, 215:1782-1788, 7 pgs.
[cited by applicant]
Muhlebach, M.S, et al., “Biomarkers for Cystic Fibrosis Drug Development,” J Cyst Fibros, 2016, 15(6):714-723, 20 pgs.
[cited by applicant]
Ni, L., et al., “Detection of SARS-CoV-2-Specific Humoral and Cellular Immunity in COVID-19 Convalescent Individuals,” Immunity, 2020, 52:971-977, 11 pgs.
[cited by applicant]
Nichols, D.P., et al., “The triterpenoid CDDO limits inflammation in preclinical models of cystic fibrosis lung disease,” Am J Physiol Lung Cell Mol Physiol, 2009, 297(5):L828-L836, 9 pgs.
[cited by applicant]
Nie, J., et al., “Establishment and validation of a pseudovirus neutralization assay for SARS-CoV-2,” Emerg Microbes Infect, 2020, 9:680-686, 7 pgs.
[cited by applicant]
Pillay, T.S., “Gene of the month: the 2019-nCoV/SARS-CoV-2 novel coronavirus spike protein,” J Clin Pathol, 2020, 73:366-369, 4 pgs.
[cited by applicant]
Pinto, D., et al., “Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody,” Nature, 2020, 583:290-295, 22 pgs.
[cited by applicant]
Poh, C.M., et al., “Two linear epitopes on the SARS-CoV-2 spike protein that elicit neutralising antibodies in COVID-19 patients,” Nat Commun, 2020, 11:2806, 7 pgs.
[cited by applicant]
Price, J.V., et al., “‘
[cited by applicant]
The R Core Team, “R: A Language and Environment for Statistical Computing, R Version 3.5.2” Vienna, Austria, R Foundation for Statistical Computing, 2018, https://www/R-project.org/, 3636 pgs.
[cited by applicant]
Robbiani, D.F., et al., “Convergent Antibody Responses to SARS-CoV-2 in Convalescent Individuals,” Nature, 2020, 584(7821):437-442, 35 pgs.
[cited by applicant]
Routledge, E., et al., “Analysis of Murine Coronavirus Surface Glycoprotein Functions by Using Monoclonal Antibodies,” J Virol, 1991, 65(1):254-262, 9 pgs.
[cited by applicant]
Rowe, S.M., et al., “Clinical Mechanism of the Cystic Fibrosis Transmembrane Conductance Regulator Potentiator Ivacaftor in G551D-mediated Cystic Fibrosis,” Am J Respir Crit Care Med, 2014, 190(2):175-184, 10 pgs.
[cited by applicant]
Rubin, D.B., “Inference and Missing Data,” Biometrika, 1976, 63(3):581-592, 12 pgs.
[cited by applicant]
Schluchter, M.D., et al., “Jointly modelling the relationship between survival and pulmonary function in cystic fibrosis patients,” Stat Med, 2002, 21:1271-1287, 17 pgs.
[cited by applicant]
Shiryaev, S.A., et al., “New Details of HCV NS3/4A Proteinase Functionality Revealed by a High-Throughput Cleavage Assay,” PLoS One, 2012, 7(4):e35759, 12 pgs.
[cited by applicant]
Soares, H.D., et al., “Biomarkers Associated With the Apolipoprotein E Genotype and Alzheimer Disease,” Arch Neurol, 2012, 69(10):1310-1317, 16 pgs.
[cited by applicant]
Spivak, M., et al., “Improvements to the Percolator algorithm for peptide identification from shotgun proteomics data sets,” J Proteome Res, 2009, 8(7):3737-3745, 22 pgs.
[cited by applicant]
Srinagesh, H.K., et al., “The MAGIC algorithm probability is a validated response biomarker of treatment of acute graft-versus-host disease,” Blood Advances, 2019, 3(23):4034-4042, 9 pgs.
[cited by applicant]
Su, W., et al., “An empirical comparison of segmented and stochastic linear mixed effects models to estimate rapid disease progression in longitudinal biomarker studies,” Stat Biopharm Res, 2021, 13(3):270-279, 22 pgs.
[cited by applicant]
Tamburro, R.F., et al., “Pulmonary Complications of Pediatric Hematopoietic Cell Transplantation: A National Institutes of Health Workshop Summary,” Ann Am Thorac Soc, 2021, 18(3):381-394, 14 pgs.
[cited by applicant]
Tan, C.W., et al., “A SARS-CoV-2 surrogate virus neutralization test based on antibody-mediated blockage of ACE2-spike protein-protein interaction,” Nat Biotech, 2020, 38:1073-1078, 17 pgs.
[cited by applicant]
Tissot, A., et al., “Early Identification of Chronic Lung Allograft Dysfunction: The Need of Biomarkers,” Frontiers in Immunology, 2019, 10:Article 1681, 13 pgs.
[cited by applicant]
Uhl Ving, H.H., et al., “Bronchiolitis obliterans after allo-SCT: clinical criteria and treatment options,” Bone Marrow Transplantation, 2012, 47:1020-1029, 10 pgs.
[cited by applicant]
Van Der Ploeg, E.A., et al., “The potenial of biomarkers of fibrosis in chronic lung allograft dysfunction,” Transplantation Reviews, 2021, 35(3):100626, 11 pgs.
[cited by applicant]
Veraar, C., et al., “Potential novel biomarkers for chronic lung allograft dysfunction and azithromycin responsive allograft dysfunction,” Scientific Reports, 2021, 11(1):6799, 13 pgs.
[cited by applicant]
Verhaeghe, C., et al., “Intrinsic pro-angiogenic status of cystic fibrosis airway epithelial cells,” BioChemical and Biophysical Research Communications, 2007, 356:745-749, 5 pgs.
[cited by applicant]
Verleden, G.M., et al., “Azithromycin Reduces Airway Neutrophilia and Interleukin-8 in Patients with Brochiolitis Obliterans Syndrome,” Am J Respir Crit Care Med, 2006, 174:556-570, 5 pgs.
[cited by applicant]
Verleden, S.E., et al., “Chronic lung allograft dysfunction phenotypes and treatment,” Journal of Thoracic Disease, 2017, 9(8):2650-2659, 11 pgs.
[cited by applicant]
Volkova, N., et al., “Disease progression in patients with cystic fibrosis treated with ivacaftor: Data from national US and UK registries,” J Cystic Fibros, 2020, 19:68-79, 12 pgs.
[cited by applicant]
Walls, A.C., et al., “Tectonic conformational changes of a coronavirus spike glycoprotein promote membrane fusion,” PNAS, 2017, 114(42):11157-11162, 6 pgs.
[cited by applicant]
Waterhouse, A., et al., “SWISS-MODEL: homology modelling of protein structures and complexes,” Nucleic Acids Res, 2018, 46:W296-W303, 8 pgs.
[cited by applicant]
Wewer Albrechtsen, N.J., et al., “Plasma Proteome Profiling Reveals Dynamics of Inflammatory and Lipid Homeostasis Markers after Roux-En-Y Gastric Bypass Surgery,” Cell Syst, 2018, 7:601-612.e1-e3, 16 pgs.
[cited by applicant]
Whitman, J.D., et al., “Test performance evaluation of SARS-CoV-2 serological assays,” Nat Biotechnol, 2020, 38(10):1174-1183, 26 pgs.
[cited by applicant]
Wolff, D., et al., “Biomarkers in chronic graft-versus-host disease—quo vadis?” Bone Marrow Transplant, 2018, 53(7):832-837, 10 pgs.
[cited by applicant]
Woolhouse, M.E.J., et al., “Epidemiological characteristics of human-infective RNA viruses,” Sci Data, 2018, 5:180017, 6 pgs.
[cited by applicant]
Xia, S., et al., “A pan-coronavirus fusion inhibitor targeting the HR1 domain of human coronavirus spike,” Sci Adv, 2019, 5:eaav4580, 15 pgs.
[cited by applicant]
Xu, G.J., et al., “Comprehensive serological profiling of human populations using a synthetic human virome,” Science, 2015, 348(6239):aaa0698, 23 pgs.
[cited by applicant]
Yu, J., et al., “Biomarker Panel for Chronic Graft-Versus-Host Disease,” J Clin Oncol, 2016, 34(22): 2583-2590, 10 pgs.
[cited by applicant]
Yuan, M., et al., “A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV,” Science, 2020, 368:630-633, 4 pgs.
[cited by applicant]
Zhu, N., et al., “A Novel Coronavirus from Patients with Pneumonia in China, 2019,” N Engl J Med, 2020, 382(8):727-733, 7 pgs.
[cited by applicant]
Ziady, A.G., et al., “Redox balance in cystic fibrosis,” Int J Biochem Cell Biol, 2014, 0:113-123, 27 pgs.
[cited by applicant]
Zost, S.J., et al., “Potently neutralizing and protective human antibodies against SARS- CoV-2,” Nature, 2020, 584(7821):443-449, 34 pgs.
[cited by applicant]
European Search Report, Supplementary, and Written Opinion dated May 15, 2023, for Application No. EP 20798040.0, 9 pgs.
[cited by applicant]
International Search Report and Written Opinion dated Dec. 30, 2021 for Application No. PCT/US2021/044587, 14 pgs.
[cited by applicant]
International Search Report and Written Opinion dated Feb. 9, 2021 for Application No. PCT/US2020/054664, 12 pgs.
[cited by applicant]
International Search Report and Written Opinion dated Mar. 28, 2022 for Application No. PCT/US2021/062624, 16 pgs.
[cited by applicant]
International Search Report and Written Opinion dated Jun. 7, 2022 for Application No. PCT/US2022/012561, 21 pgs.
[cited by applicant]
International Search Report and Written Opinion dated Sep. 25, 2023 for Application No. PCT/US2023/020341, 21 pgs.
[cited by applicant]
International Search Report and Written Opinion dated Sep. 25, 2023 for Application No. PCT/US2023/020337, 22 pgs.
[cited by applicant]