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First Report of Nemesia ring necrosis virus in North America in Ornamental Plants from California.

Mathews DM, Dodds JA.

Plant Dis. 2006 Sep;90(9):1263. doi: 10.1094/PD-90-1263C.


Conservation of location of several specific inhibitory codon pairs in the Saccharomyces sensu stricto yeasts reveals translational selection.

Ghoneim DH, Zhang X, Brule CE, Mathews DH, Grayhack EJ.

Nucleic Acids Res. 2018 Dec 21. doi: 10.1093/nar/gky1262. [Epub ahead of print]


The iCook 4-H Study: Report on Physical Activity and Sedentary Time in Youth Participating in a Multicomponent Program Promoting Family Cooking, Eating, and Playing Together.

Kattelmann KK, Meendering JR, Hofer EJ, Merfeld CM, Olfert MD, Hagedorn RL, Colby SE, Franzen-Castle L, Moyer J, Mathews DR, White AA.

J Nutr Educ Behav. 2018 Dec 1. pii: S1499-4046(18)30788-7. doi: 10.1016/j.jneb.2018.09.002. [Epub ahead of print]


Development and Testing of Program Evaluation Instruments for the iCook 4-H Curriculum.

Mathews D, Kunicki ZJ, Colby S, Franzen-Castle L, Kattelmann K, Olfert MD, White AA.

J Nutr Educ Behav. 2018 Nov 21. pii: S1499-4046(18)30858-3. doi: 10.1016/j.jneb.2018.10.014. [Epub ahead of print]


Design of highly active double-pseudoknotted ribozymes: a combined computational and experimental study.

Yamagami R, Kayedkhordeh M, Mathews DH, Bevilacqua PC.

Nucleic Acids Res. 2019 Jan 10;47(1):29-42. doi: 10.1093/nar/gky1118.


Ventilation perfusion pulmonary scintigraphy in the evaluation of pre-and post-lung transplant patients.

Pinho DF, Banga A, Torres F, Mathews D.

Transplant Rev (Orlando). 2018 Oct 23. pii: S0955-470X(18)30080-6. doi: 10.1016/j.trre.2018.10.003. [Epub ahead of print] Review.


Risk perception before and after presymptomatic genetic testing for Huntington's disease: Not always what one might expect.

Stuttgen K, Dvoskin R, Bollinger J, McCague A, Shpritz B, Brandt J, Mathews D.

Mol Genet Genomic Med. 2018 Nov;6(6):1140-1147. doi: 10.1002/mgg3.494. Epub 2018 Nov 4.


Chemically Accurate Relative Folding Stability of RNA Hairpins from Molecular Simulations.

Smith LG, Tan Z, Spasic A, Dutta D, Salas-Estrada LA, Grossfield A, Mathews DH.

J Chem Theory Comput. 2018 Nov 27. doi: 10.1021/acs.jctc.8b00633. [Epub ahead of print]


mRNAs and lncRNAs intrinsically form secondary structures with short end-to-end distances.

Lai WC, Kayedkhordeh M, Cornell EV, Farah E, Bellaousov S, Rietmeijer R, Salsi E, Mathews DH, Ermolenko DN.

Nat Commun. 2018 Oct 18;9(1):4328. doi: 10.1038/s41467-018-06792-z.


Identification of new high affinity targets for Roquin based on structural conservation.

Braun J, Fischer S, Xu ZZ, Sun H, Ghoneim DH, Gimbel AT, Plessmann U, Urlaub H, Mathews DH, Weigand JE.

Nucleic Acids Res. 2018 Dec 14;46(22):12109-12125. doi: 10.1093/nar/gky908.


CD122 signaling in CD8+ memory T cells drives costimulation-independent rejection.

Mathews DV, Dong Y, Higginbotham LB, Kim SC, Breeden CP, Stobert EA, Jenkins J, Tso JY, Larsen CP, Adams AB.

J Clin Invest. 2018 Oct 1;128(10):4557-4572. doi: 10.1172/JCI95914. Epub 2018 Sep 17.


Analysis of RNA nearest neighbor parameters reveals interdependencies and quantifies the uncertainty in RNA secondary structure prediction.

Zuber J, Cabral BJ, McFadyen I, Mauger DM, Mathews DH.

RNA. 2018 Nov;24(11):1568-1582. doi: 10.1261/rna.065102.117. Epub 2018 Aug 13.


Accelerated RNA secondary structure design using preselected sequences for helices and loops.

Bellaousov S, Kayedkhordeh M, Peterson RJ, Mathews DH.

RNA. 2018 Nov;24(11):1555-1567. doi: 10.1261/rna.066324.118. Epub 2018 Aug 10.


Perspectives on Genetic Testing and Return of Results from the First Cohort of Presymptomatically Tested Individuals At Risk of Huntington Disease.

Stuttgen KM, Bollinger JM, Dvoskin RL, McCague A, Shpritz B, Brandt J, Mathews DJH.

J Genet Couns. 2018 Dec;27(6):1428-1437. doi: 10.1007/s10897-018-0274-0. Epub 2018 Jul 2.


Structure of HIV TAR in complex with a Lab-Evolved RRM provides insight into duplex RNA recognition and synthesis of a constrained peptide that impairs transcription.

Belashov IA, Crawford DW, Cavender CE, Dai P, Beardslee PC, Mathews DH, Pentelute BL, McNaughton BR, Wedekind JE.

Nucleic Acids Res. 2018 Jul 27;46(13):6401-6415. doi: 10.1093/nar/gky529.


Endophthalmitis Following XEN Stent Exposure.

Karri B, Gupta C, Mathews D.

J Glaucoma. 2018 Oct;27(10):931-933. doi: 10.1097/IJG.0000000000001012.


An Atypical Case of Bartonella henselae Osteomyelitis and Hepatic Disease.

Mathews DM, Vance KM, McMahon PM, Boston C, Bolton MT.

Case Rep Pediatr. 2018 Apr 5;2018:2750275. doi: 10.1155/2018/2750275. eCollection 2018.


Improving RNA nearest neighbor parameters for helices by going beyond the two-state model.

Spasic A, Berger KD, Chen JL, Seetin MG, Turner DH, Mathews DH.

Nucleic Acids Res. 2018 Jun 1;46(10):4883-4892. doi: 10.1093/nar/gky270.


Surprising Sequence Effects on GU Closure of Symmetric 2 × 2 Nucleotide RNA Internal Loops.

Berger KD, Kennedy SD, Schroeder SJ, Znosko BM, Sun H, Mathews DH, Turner DH.

Biochemistry. 2018 Apr 10;57(14):2121-2131. doi: 10.1021/acs.biochem.7b01306. Epub 2018 Mar 23.


Enhancing Autonomy in Biobank Decisions: Too Much of a Good Thing?

Mitchell PB, Ziniel SI, Savage SK, Christensen KD, Weitzman ER, Green RC, Huntington NL, Mathews DJ, Holm IA.

J Empir Res Hum Res Ethics. 2018 Apr;13(2):125-138. doi: 10.1177/1556264617753483. Epub 2018 Feb 23.


Molecular dynamics correctly models the unusual major conformation of the GAGU RNA internal loop and with NMR reveals an unusual minor conformation.

Spasic A, Kennedy SD, Needham L, Manoharan M, Kierzek R, Turner DH, Mathews DH.

RNA. 2018 May;24(5):656-672. doi: 10.1261/rna.064527.117. Epub 2018 Feb 6.


Widespread temperature sensitivity and tRNA decay due to mutations in a yeast tRNA.

Payea MJ, Sloma MF, Kon Y, Young DL, Guy MP, Zhang X, De Zoysa T, Fields S, Mathews DH, Phizicky EM.

RNA. 2018 Mar;24(3):410-422. doi: 10.1261/rna.064642.117. Epub 2017 Dec 19.


Improving patient safety during procedural sedation via respiratory volume monitoring: A randomized controlled trial.

Mathews DM, Oberding MJ, Simmons EL, O'Donnell SE, Abnet KR, MacDonald K.

J Clin Anesth. 2018 May;46:118-123. doi: 10.1016/j.jclinane.2017.08.004. Epub 2017 Dec 8.


The Therapeutic "Mis"conception: An Examination of its Normative Assumptions and a Call for its Revision.

Mathews DJH, Fins JJ, Racine E.

Camb Q Healthc Ethics. 2018 Jan;27(1):154-162. doi: 10.1017/S0963180117000482.


Modeling RNA secondary structure folding ensembles using SHAPE mapping data.

Spasic A, Assmann SM, Bevilacqua PC, Mathews DH.

Nucleic Acids Res. 2018 Jan 9;46(1):314-323. doi: 10.1093/nar/gkx1057.


Effect of primary Phacoviscocanalostomy/ Viscocanalostomy on intraocular pressure of normal tension glaucoma patients: 3-year results.

Ho DK, Garrick A, Aazem S, Mathews D.

BMC Ophthalmol. 2017 Nov 6;17(1):201. doi: 10.1186/s12886-017-0596-y.


Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs.

Sloma MF, Mathews DH.

PLoS Comput Biol. 2017 Nov 6;13(11):e1005827. doi: 10.1371/journal.pcbi.1005827. eCollection 2017 Nov.


TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs.

Tan Z, Fu Y, Sharma G, Mathews DH.

Nucleic Acids Res. 2017 Nov 16;45(20):11570-11581. doi: 10.1093/nar/gkx815.


Unusual Cause of Prolonged Fever of Unknown Origin.

Mathews D, McMahon P, Bolton M.

Clin Pediatr (Phila). 2018 Feb;57(2):245-247. doi: 10.1177/0009922817693303. Epub 2017 Feb 1. No abstract available.


Physics-based all-atom modeling of RNA energetics and structure.

Smith LG, Zhao J, Mathews DH, Turner DH.

Wiley Interdiscip Rev RNA. 2017 Sep;8(5). doi: 10.1002/wrna.1422. Review.


Brain Monitoring and the Depth of Anesthesia: Another Goldilocks Dilemma.

Shander A, Lobel GP, Mathews DM.

Anesth Analg. 2018 Feb;126(2):705-709. doi: 10.1213/ANE.0000000000002383. Review. No abstract available.


Modeling RNA Secondary Structure with Sequence Comparison and Experimental Mapping Data.

Tan Z, Sharma G, Mathews DH.

Biophys J. 2017 Jul 25;113(2):330-338. doi: 10.1016/j.bpj.2017.06.039. Epub 2017 Jul 20.


Alloimmunity But Not Viral Immunity Promotes Allograft Loss in a Mouse Model of Polyomavirus-Associated Allograft Injury.

Kim SC, Wang J, Dong Y, Mathews DV, Albrecht JA, Breeden CP, Farris AB, Lukacher AE, Ford ML, Newell KA, Adams AB.

Transplant Direct. 2017 May 12;3(6):e161. doi: 10.1097/TXD.0000000000000677. eCollection 2017 Jun.


Advanced multi-loop algorithms for RNA secondary structure prediction reveal that the simplest model is best.

Ward M, Datta A, Wise M, Mathews DH.

Nucleic Acids Res. 2017 Aug 21;45(14):8541-8550. doi: 10.1093/nar/gkx512.


Belatacept-Resistant Rejection Is Associated With CD28+ Memory CD8 T Cells.

Mathews DV, Wakwe WC, Kim SC, Lowe MC, Breeden C, Roberts ME, Farris AB, Strobert EA, Jenkins JB, Larsen CP, Ford ML, Townsend R, Adams AB.

Am J Transplant. 2017 Sep;17(9):2285-2299. doi: 10.1111/ajt.14349. Epub 2017 Jul 11.


Increased Pretransplant Frequency of CD28+ CD4+ TEM Predicts Belatacept-Resistant Rejection in Human Renal Transplant Recipients.

Cortes-Cerisuelo M, Laurie SJ, Mathews DV, Winterberg PD, Larsen CP, Adams AB, Ford ML.

Am J Transplant. 2017 Sep;17(9):2350-2362. doi: 10.1111/ajt.14350. Epub 2017 Jun 30.


Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA.

Gamache ER, Doh JH, Ritz J, Laederach A, Bellaousov S, Mathews DH, Curcio MJ.

Viruses. 2017 Apr 26;9(5). pii: E93. doi: 10.3390/v9050093.


Interruption of OX40L signaling prevents costimulation blockade-resistant allograft rejection.

Kitchens WH, Dong Y, Mathews DV, Breeden CP, Strobert E, Fuentes ME, Larsen CP, Ford ML, Adams AB.

JCI Insight. 2017 Mar 9;2(5):e90317. doi: 10.1172/jci.insight.90317.


Choices for return of primary and secondary genomic research results of 790 members of families with Mendelian disease.

Fiallos K, Applegate C, Mathews DJ, Bollinger J, Bergner AL, James CA.

Eur J Hum Genet. 2017 May;25(5):530-537. doi: 10.1038/ejhg.2017.21. Epub 2017 Mar 8.


Ectopic Thyroid Tissue in the Mediastinum Characterized by Histology and Functional Imaging with I-123 SPECT/CT.

Hummel J, Wachsmann J, Carrick K, Oz OK, Mathews D, Peng F.

Case Rep Radiol. 2017;2017:9084207. doi: 10.1155/2017/9084207. Epub 2017 Jan 30.


Fc-Silent Anti-CD154 Domain Antibody Effectively Prevents Nonhuman Primate Renal Allograft Rejection.

Kim SC, Wakwe W, Higginbotham LB, Mathews DV, Breeden CP, Stephenson AC, Jenkins J, Strobert E, Price K, Price L, Kuhn R, Wang H, Yamniuk A, Suchard S, Farris AB 3rd, Pearson TC, Larsen CP, Ford ML, Suri A, Nadler S, Adams AB.

Am J Transplant. 2017 May;17(5):1182-1192. doi: 10.1111/ajt.14197. Epub 2017 Feb 25.


Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics.

Aytenfisu AH, Spasic A, Grossfield A, Stern HA, Mathews DH.

J Chem Theory Comput. 2017 Feb 14;13(2):900-915. doi: 10.1021/acs.jctc.6b00870. Epub 2017 Jan 24.


Erratum to: The need of standardization and of large clinical studies in an emerging indication of [18 F]FDG PET: the autoimmune encephalitis.

Morbelli S, Arbizu J, Booij J, Chen MK, Chetelat G, Cross DJ, Djekidel M, Drzezga A, Ekmekcioglu O, Garibotto V, Hesse S, Ishii K, Jafari L, Lammertsma AA, Law I, Mathews D, Minoshima S, Mosci K, Pagani M, Pappata S, Silverman DH, Signore A, Van De Giessen E, Villemagne V, Barthel H; European Association of Nuclear Medicine (EANM) and of the Society of Nuclear Medicine and Molecular Imaging (SNMMI).

Eur J Nucl Med Mol Imaging. 2017 Mar;44(3):559-560. doi: 10.1007/s00259-016-3598-8. No abstract available.


Absorption and safety of serum-derived bovine immunoglobulin/protein isolate in healthy adults.

Shaw AL, Mathews DW, Hinkle JE, Petschow BW, Weaver EM, Detzel CJ, Klein GL, Bradshaw TP.

Clin Exp Gastroenterol. 2016 Dec 5;9:365-375. eCollection 2016.


The need of standardization and of large clinical studies in an emerging indication of [18F]FDG PET: the autoimmune encephalitis.

Morbelli S, Arbizu J, Booij J, Chen MK, Chetelat G, Cross DJ, Djekidel M, Drzezga A, Ekmekcioglu O, Garibotto V, Hesse S, Ishii K, Jafari L, Lammertsma AA, Law I, Mathews D, Minoshima S, Mosci K, Pagani M, Pappata S, Silverman DH, Signore A, Van De Giessen E, Villemagne V, Barthel H; European Association of Nuclear Medicine (EANM) and of the Society of Nuclear Medicine and Molecular Imaging (SNMMI).

Eur J Nucl Med Mol Imaging. 2017 Mar;44(3):353-357. doi: 10.1007/s00259-016-3589-9. Epub 2016 Dec 6. No abstract available. Erratum in: Eur J Nucl Med Mol Imaging. 2017 Mar;44(3):559-560. Saraf LJ [corrected to Jafari L].


RNA Secondary Structure Prediction.

Mathews DH, Turner DH, Watson RM.

Curr Protoc Nucleic Acid Chem. 2016 Dec 1;67:11.2.1-11.2.19. doi: 10.1002/cpnc.19.


Effects of cytochrome P450 (CYP3A4 and CYP2C19) inhibition and induction on the exposure of selumetinib, a MEK1/2 inhibitor, in healthy subjects: results from two clinical trials.

Dymond AW, So K, Martin P, Huang Y, Severin P, Mathews D, Lisbon E, Mariani G.

Eur J Clin Pharmacol. 2017 Feb;73(2):175-184. doi: 10.1007/s00228-016-2153-7. Epub 2016 Nov 26.


Effects of ranitidine (antacid), food, and formulation on the pharmacokinetics of fostamatinib: results from five phase I clinical studies.

Flanagan T, Martin P, Gillen M, Mathews D, Lisbon E, Kruusmägi M.

Eur J Clin Pharmacol. 2017 Feb;73(2):185-195. doi: 10.1007/s00228-016-2156-4. Epub 2016 Nov 17.


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