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BioJava 5: A community driven open-source bioinformatics library.

Lafita A, Bliven S, Prlić A, Guzenko D, Rose PW, Bradley A, Pavan P, Myers-Turnbull D, Valasatava Y, Heuer M, Larson M, Burley SK, Duarte JM.

PLoS Comput Biol. 2019 Feb 8;15(2):e1006791. doi: 10.1371/journal.pcbi.1006791. [Epub ahead of print]


A mixed-methods, randomized controlled feasibility trial of Eye Movement Desensitization and Reprocessing (EMDR) plus Standard Care (SC) versus SC alone for DSM-5 Posttraumatic Stress Disorder (PTSD) in adults with intellectual disabilities.

Karatzias T, Brown M, Taggart L, Truesdale M, Sirisena C, Walley R, Mason-Roberts S, Bradley A, Paterson D.

J Appl Res Intellect Disabil. 2019 Feb 4. doi: 10.1111/jar.12570. [Epub ahead of print]


Author Correction: Why rankings of biomedical image analysis competitions should be interpreted with care.

Maier-Hein L, Eisenmann M, Reinke A, Onogur S, Stankovic M, Scholz P, Arbel T, Bogunovic H, Bradley AP, Carass A, Feldmann C, Frangi AF, Full PM, van Ginneken B, Hanbury A, Honauer K, Kozubek M, Landman BA, März K, Maier O, Maier-Hein K, Menze BH, Müller H, Neher PF, Niessen W, Rajpoot N, Sharp GC, Sirinukunwattana K, Speidel S, Stock C, Stoyanov D, Taha AA, van der Sommen F, Wang CW, Weber MA, Zheng G, Jannin P, Kopp-Schneider A.

Nat Commun. 2019 Jan 30;10(1):588. doi: 10.1038/s41467-019-08563-w.


Visualization and the Digital Humanities.

Bradley AJ, El-Assady M, Coles K, Alexander E, Chen M, Collins C, Janicke S, Wrisley DJ.

IEEE Comput Graph Appl. 2018 Nov-Dec;38(6):26-38. doi: 10.1109/MCG.2018.2878900.


Health Care Discrimination, Sex Behavior Disclosure, and Awareness of Pre-Exposure Prophylaxis Among Black Men Who Have Sex With Men.

Maksut JL, Eaton LA, Siembida EJ, Fabius CD, Bradley AM.

Stigma Health. 2018 Nov;3(4):330-337. doi: 10.1037/sah0000102. Epub 2017 Sep 18.


The association between sleep and cognitive abnormalities in bipolar disorder.

Bradley AJ, Anderson KN, Gallagher P, McAllister-Williams RH.

Psychol Med. 2019 Jan 16:1-8. doi: 10.1017/S0033291718004038. [Epub ahead of print]


Toxicologic Pathology Forum*: Opinion on Considerations for the Use of Whole Slide Images in GLP Pathology Peer Review.

Bradley A, Jacobsen M.

Toxicol Pathol. 2019 Jan 13:192623318818790. doi: 10.1177/0192623318818790. [Epub ahead of print]


Histopathological Findings in Cynomolgus Macaques ( Macaca fascicularis) Consistent with Secondary Immunological Reaction to Biotherapeutics with an Emphasis on the CNS and Eye.

Naylor SW, Czajkowski M, Harvey W, Smith M, Bradley AE, Cary M.

Toxicol Pathol. 2019 Jan 13:192623318821332. doi: 10.1177/0192623318821332. [Epub ahead of print]


ATM orchestrates the DNA-damage response to counter toxic non-homologous end-joining at broken replication forks.

Balmus G, Pilger D, Coates J, Demir M, Sczaniecka-Clift M, Barros AC, Woods M, Fu B, Yang F, Chen E, Ostermaier M, Stankovic T, Ponstingl H, Herzog M, Yusa K, Martinez FM, Durant ST, Galanty Y, Beli P, Adams DJ, Bradley A, Metzakopian E, Forment JV, Jackson SP.

Nat Commun. 2019 Jan 8;10(1):87. doi: 10.1038/s41467-018-07729-2.


SRPK1 maintains acute myeloid leukemia through effects on isoform usage of epigenetic regulators including BRD4.

Tzelepis K, De Braekeleer E, Aspris D, Barbieri I, Vijayabaskar MS, Liu WH, Gozdecka M, Metzakopian E, Toop HD, Dudek M, Robson SC, Hermida-Prado F, Yang YH, Babaei-Jadidi R, Garyfallos DA, Ponstingl H, Dias JML, Gallipoli P, Seiler M, Buonamici S, Vick B, Bannister AJ, Rad R, Prinjha RK, Marioni JC, Huntly B, Batson J, Morris JC, Pina C, Bradley A, Jeremias I, Bates DO, Yusa K, Kouzarides T, Vassiliou GS.

Nat Commun. 2018 Dec 19;9(1):5378. doi: 10.1038/s41467-018-07620-0.


Sulfur isotope analysis of microcrystalline iron sulfides using SIMS imaging: Extracting local paleo-environmental information from modern and ancient sediments.

Bryant RN, Jones C, Raven MR, Gomes ML, Berelson WM, Bradley AS, Fike DA.

Rapid Commun Mass Spectrom. 2018 Dec 18. doi: 10.1002/rcm.8375. [Epub ahead of print]


PiggyBac Transposon-Based Insertional Mutagenesis in Mice.

Friedrich MJ, Bronner IF, Liu P, Bradley A, Rad R.

Methods Mol Biol. 2019;1907:171-183. doi: 10.1007/978-1-4939-8967-6_14.


Why rankings of biomedical image analysis competitions should be interpreted with care.

Maier-Hein L, Eisenmann M, Reinke A, Onogur S, Stankovic M, Scholz P, Arbel T, Bogunovic H, Bradley AP, Carass A, Feldmann C, Frangi AF, Full PM, van Ginneken B, Hanbury A, Honauer K, Kozubek M, Landman BA, März K, Maier O, Maier-Hein K, Menze BH, Müller H, Neher PF, Niessen W, Rajpoot N, Sharp GC, Sirinukunwattana K, Speidel S, Stock C, Stoyanov D, Taha AA, van der Sommen F, Wang CW, Weber MA, Zheng G, Jannin P, Kopp-Schneider A.

Nat Commun. 2018 Dec 6;9(1):5217. doi: 10.1038/s41467-018-07619-7. Erratum in: Nat Commun. 2019 Jan 30;10(1):588.


Discrimination of contagious and environmental strains of Streptococcus uberis in dairy herds by means of mass spectrometry and machine-learning.

Esener N, Green MJ, Emes RD, Jowett B, Davies PL, Bradley AJ, Dottorini T.

Sci Rep. 2018 Nov 30;8(1):17517. doi: 10.1038/s41598-018-35867-6.


Adapting the Breast Cancer Surgery Decision Quality Instrument for Lower Socioeconomic Status: Improving Readability, Acceptability, and Relevance.

Durand MA, Song J, Yen RW, Sepucha K, Politi MC, Dhage S, Rosenkranz K, Margenthaler J, Tosteson ANA, Crayton E, Jackson S, Bradley A, O'Malley AJ, Volk RJ, Ozanne E, Percac-Lima S, Acosta J, Mir N, Scalia P, Ward A, Elwyn G.

MDM Policy Pract. 2018 Nov 25;3(2):2381468318811839. doi: 10.1177/2381468318811839. eCollection 2018 Jul-Dec.


Agricultural conservation practices in Iowa watersheds: comparing actual implementation with practice potential.

Rundhaug TJ, Geimer GR, Drake CW, Arenas Amado A, Bradley AA, Wolter CF, Weber LJ.

Environ Monit Assess. 2018 Oct 22;190(11):659. doi: 10.1007/s10661-018-6977-8.


Is Self-Compassion a Worthwhile Therapeutic Target for ICD-11 Complex PTSD (CPTSD)?

Karatzias T, Hyland P, Bradley A, Fyvie C, Logan K, Easton P, Thomas J, Philips S, Bisson JI, Roberts NP, Cloitre M, Shevlin M.

Behav Cogn Psychother. 2018 Oct 2:1-13. doi: 10.1017/S1352465818000577. [Epub ahead of print]


Protein Family-Specific Models Using Deep Neural Networks and Transfer Learning Improve Virtual Screening and Highlight the Need for More Data.

Imrie F, Bradley AR, van der Schaar M, Deane CM.

J Chem Inf Model. 2018 Nov 26;58(11):2319-2330. doi: 10.1021/acs.jcim.8b00350. Epub 2018 Oct 16.


Nationwide Strategy for Addressing the Opioid Health Crisis in the Emergency Department and Beyond.

Bradley A.

J Emerg Nurs. 2018 Sep;44(5):443. doi: 10.1016/j.jen.2018.03.002. No abstract available.


Derealization and self-harm strategies are used to regulate disgust, fear, and sadness in adult survivors of childhood sexual abuse.

Bradley A, Karatzias T, Coyle E.

Clin Psychol Psychother. 2019 Jan;26(1):94-104. doi: 10.1002/cpp.2333. Epub 2018 Oct 16.


Aging phenotype(s) in kidneys of diabetic mice are p66ShcA dependent.

Vashistha H, Marrero L, Reiss K, Cohen AJ, Malhotra A, Javed T, Bradley A, Abbruscato F, Giusti S, Jimenez A, Mehra S, Kaushal D, Giorgio M, Pelicci PG, Kakoki M, Singhal PC, Bunnell B, Meggs LG.

Am J Physiol Renal Physiol. 2018 Dec 1;315(6):F1833-F1842. doi: 10.1152/ajprenal.00608.2017. Epub 2018 Sep 12.


Erratum: Repair of double-strand breaks induced by CRISPR-Cas9 leads to large deletions and complex rearrangements.

Kosicki M, Tomberg K, Bradley A.

Nat Biotechnol. 2018 Sep 6;36(9):899. doi: 10.1038/nbt0918-899c. No abstract available.


Organic carbon burial during OAE2 driven by changes in the locus of organic matter sulfurization.

Raven MR, Fike DA, Gomes ML, Webb SM, Bradley AS, McClelland HO.

Nat Commun. 2018 Aug 24;9(1):3409. doi: 10.1038/s41467-018-05943-6.


Inter-homologue repair in fertilized human eggs?

Egli D, Zuccaro MV, Kosicki M, Church GM, Bradley A, Jasin M.

Nature. 2018 Aug;560(7717):E5-E7. doi: 10.1038/s41586-018-0379-5. Epub 2018 Aug 8. No abstract available.


Prospective cohort study of C-reactive protein as a predictor of clinical events in adults with congenital heart disease: results of the Boston adult congenital heart disease biobank.

Opotowsky AR, Valente AM, Alshawabkeh L, Cheng S, Bradley A, Rimm EB, Landzberg MJ.

Eur Heart J. 2018 Sep 7;39(34):3253-3261. doi: 10.1093/eurheartj/ehy362.


Repair of double-strand breaks induced by CRISPR-Cas9 leads to large deletions and complex rearrangements.

Kosicki M, Tomberg K, Bradley A.

Nat Biotechnol. 2018 Sep;36(8):765-771. doi: 10.1038/nbt.4192. Epub 2018 Jul 16.


Evaluation of an incidental cardiac finding in a patient with bronchitis.

Bradley AJ, Lewis JF, Choi AD.

Heart. 2018 Sep;104(17):1469-1470. doi: 10.1136/heartjnl-2018-313412. Epub 2018 Jun 22.


Mesoscopic Dynamical Differences from Quantum State Preparation in a Bose-Hubbard Trimer.

Olsen MK, Neely TW, Bradley AS.

Phys Rev Lett. 2018 Jun 8;120(23):230406. doi: 10.1103/PhysRevLett.120.230406.


Short- and long-term association between individual levels of milk antibody against Ostertagia ostertagi and first-lactation heifer's production performances.

Bellet C, Green MJ, Bradley AJ, Kaler J.

Vet Parasitol. 2018 May 30;256:1-8. doi: 10.1016/j.vetpar.2018.04.008. Epub 2018 Apr 18.


Pan-European agreement on dry cow therapy.

Bradley A, De Vliegher S, Farre M, Jimenez LM, Peters T, de Leemput ES, van Werven T.

Vet Rec. 2018 Jun 2;182(22):637. doi: 10.1136/vr.k2382. No abstract available.


Multiple traumatisation and subsequent psychopathology in people with intellectual disabilities and DSM-5 PTSD: a preliminary study.

Mason-Roberts S, Bradley A, Karatzias T, Brown M, Paterson D, Walley R, Truesdale M, Taggart L, Sirisena C.

J Intellect Disabil Res. 2018 Aug;62(8):730-736. doi: 10.1111/jir.12505. Epub 2018 Jun 1.


NGL viewer: web-based molecular graphics for large complexes.

Rose AS, Bradley AR, Valasatava Y, Duarte JM, Prlic A, Rose PW.

Bioinformatics. 2018 Nov 1;34(21):3755-3758. doi: 10.1093/bioinformatics/bty419.


What is a troland?

Thibos LN, Lopez-Gil N, Bradley A.

J Opt Soc Am A Opt Image Sci Vis. 2018 May 1;35(5):813-816. doi: 10.1364/JOSAA.35.000813.


Search for Neutrinoless Double-β Decay in ^{76}Ge with the Majorana Demonstrator.

Aalseth CE, Abgrall N, Aguayo E, Alvis SI, Amman M, Arnquist IJ, Avignone FT, Back HO, Barabash AS, Barbeau PS, Barton CJ, Barton PJ, Bertrand FE, Bode T, Bos B, Boswell M, Bradley AW, Brodzinski RL, Brudanin V, Busch M, Buuck M, Caldwell AS, Caldwell TS, Chan YD, Christofferson CD, Chu PH, Collar JI, Combs DC, Cooper RJ, Cuesta C, Detwiler JA, Doe PJ, Dunmore JA, Efremenko Y, Ejiri H, Elliott SR, Fast JE, Finnerty P, Fraenkle FM, Fu Z, Fujikawa BK, Fuller E, Galindo-Uribarri A, Gehman VM, Gilliss T, Giovanetti GK, Goett J, Green MP, Gruszko J, Guinn IS, Guiseppe VE, Hallin AL, Haufe CR, Hehn L, Henning R, Hoppe EW, Hossbach TW, Howe MA, Jasinski BR, Johnson RA, Keeter KJ, Kephart JD, Kidd MF, Knecht A, Konovalov SI, Kouzes RT, LaFerriere BD, Leon J, Lesko KT, Leviner LE, Loach JC, Lopez AM, Luke PN, MacMullin J, MacMullin S, Marino MG, Martin RD, Massarczyk R, McDonald AB, Mei DM, Meijer SJ, Merriman JH, Mertens S, Miley HS, Miller ML, Myslik J, Orrell JL, O'Shaughnessy C, Othman G, Overman NR, Perumpilly G, Pettus W, Phillips DG, Poon AWP, Pushkin K, Radford DC, Rager J, Reeves JH, Reine AL, Rielage K, Robertson RGH, Ronquest MC, Ruof NW, Schubert AG, Shanks B, Shirchenko M, Snavely KJ, Snyder N, Steele D, Suriano AM, Tedeschi D, Tornow W, Trimble JE, Varner RL, Vasilyev S, Vetter K, Vorren K, White BR, Wilkerson JF, Wiseman C, Xu W, Yakushev E, Yaver H, Young AR, Yu CH, Yumatov V, Zhitnikov I, Zhu BX, Zimmermann S; Majorana Collaboration.

Phys Rev Lett. 2018 Mar 30;120(13):132502. doi: 10.1103/PhysRevLett.120.132502.


Accommodative Behavior of Young Eyes Wearing Multifocal Contact Lenses.

Altoaimi BH, Almutairi MS, Kollbaum PS, Bradley A.

Optom Vis Sci. 2018 May;95(5):416-427. doi: 10.1097/OPX.0000000000001214. Erratum in: Optom Vis Sci. 2018 Jul;95(7):628.


Author Correction: Revealing hidden complexities of genomic rearrangements generated with Cas9.

Boroviak K, Fu B, Yang F, Doe B, Bradley A.

Sci Rep. 2018 Apr 5;8(1):5765. doi: 10.1038/s41598-018-23232-6.


Does observability affect prosociality?

Bradley A, Lawrence C, Ferguson E.

Proc Biol Sci. 2018 Mar 28;285(1875). pii: 20180116. doi: 10.1098/rspb.2018.0116. Review.


Oxide-mediated recovery of field-effect mobility in plasma-treated MoS2.

Jadwiszczak J, O'Callaghan C, Zhou Y, Fox DS, Weitz E, Keane D, Cullen CP, O'Reilly I, Downing C, Shmeliov A, Maguire P, Gough JJ, McGuinness C, Ferreira MS, Bradley AL, Boland JJ, Duesberg GS, Nicolosi V, Zhang H.

Sci Adv. 2018 Mar 2;4(3):eaao5031. doi: 10.1126/sciadv.aao5031. eCollection 2018 Mar.


What matters most: protocol for a randomized controlled trial of breast cancer surgery encounter decision aids across socioeconomic strata.

Durand MA, Yen RW, O'Malley AJ, Politi MC, Dhage S, Rosenkranz K, Weichman K, Margenthaler J, Tosteson ANA, Crayton E, Jackson S, Bradley A, Volk RJ, Sepucha K, Ozanne E, Percac-Lima S, Song J, Acosta J, Mir N, Elwyn G.

BMC Public Health. 2018 Feb 13;18(1):241. doi: 10.1186/s12889-018-5109-2.


Demonstration of universal parametric entangling gates on a multi-qubit lattice.

Reagor M, Osborn CB, Tezak N, Staley A, Prawiroatmodjo G, Scheer M, Alidoust N, Sete EA, Didier N, da Silva MP, Acala E, Angeles J, Bestwick A, Block M, Bloom B, Bradley A, Bui C, Caldwell S, Capelluto L, Chilcott R, Cordova J, Crossman G, Curtis M, Deshpande S, El Bouayadi T, Girshovich D, Hong S, Hudson A, Karalekas P, Kuang K, Lenihan M, Manenti R, Manning T, Marshall J, Mohan Y, O'Brien W, Otterbach J, Papageorge A, Paquette JP, Pelstring M, Polloreno A, Rawat V, Ryan CA, Renzas R, Rubin N, Russel D, Rust M, Scarabelli D, Selvanayagam M, Sinclair R, Smith R, Suska M, To TW, Vahidpour M, Vodrahalli N, Whyland T, Yadav K, Zeng W, Rigetti CT.

Sci Adv. 2018 Feb 2;4(2):eaao3603. doi: 10.1126/sciadv.aao3603. eCollection 2018 Feb.


The impact of dairy cows' bedding material and its microbial content on the quality and safety of milk - A cross sectional study of UK farms.

Bradley AJ, Leach KA, Green MJ, Gibbons J, Ohnstad IC, Black DH, Payne B, Prout VE, Breen JE.

Int J Food Microbiol. 2018 Mar 23;269:36-45. doi: 10.1016/j.ijfoodmicro.2017.12.022. Epub 2017 Dec 19.


Evolutionary routes and KRAS dosage define pancreatic cancer phenotypes.

Mueller S, Engleitner T, Maresch R, Zukowska M, Lange S, Kaltenbacher T, Konukiewitz B, Öllinger R, Zwiebel M, Strong A, Yen HY, Banerjee R, Louzada S, Fu B, Seidler B, Götzfried J, Schuck K, Hassan Z, Arbeiter A, Schönhuber N, Klein S, Veltkamp C, Friedrich M, Rad L, Barenboim M, Ziegenhain C, Hess J, Dovey OM, Eser S, Parekh S, Constantino-Casas F, de la Rosa J, Sierra MI, Fraga M, Mayerle J, Klöppel G, Cadiñanos J, Liu P, Vassiliou G, Weichert W, Steiger K, Enard W, Schmid RM, Yang F, Unger K, Schneider G, Varela I, Bradley A, Saur D, Rad R.

Nature. 2018 Feb 1;554(7690):62-68. doi: 10.1038/nature25459. Epub 2018 Jan 24.


The role of negative cognitions, emotion regulation strategies, and attachment style in complex post-traumatic stress disorder: Implications for new and existing therapies.

Karatzias T, Shevlin M, Hyland P, Brewin CR, Cloitre M, Bradley A, Kitchiner NJ, Jumbe S, Bisson JI, Roberts NP.

Br J Clin Psychol. 2018 Jun;57(2):177-185. doi: 10.1111/bjc.12172. Epub 2018 Jan 22.


Standoff ultracompact micro-Raman sensor for planetary surface explorations.

Abedin MN, Bradley AT, Misra AK, Bai Y, Hines GD, Sharma SK.

Appl Opt. 2018 Jan 1;57(1):62-68. doi: 10.1364/AO.57.000062.


Experimental investigation of accommodation in eyes fit with multifocal contact lenses using a clinical auto-refractor.

Altoaimi BH, Kollbaum P, Meyer D, Bradley A.

Ophthalmic Physiol Opt. 2018 Mar;38(2):152-163. doi: 10.1111/opo.12438. Epub 2018 Jan 8.


The effect of spherical aberration on visual performance and refractive state for stimuli and tasks typical of night viewing.

Marín-Franch I, Xu R, Bradley A, Thibos LN, López-Gil N.

J Optom. 2018 Jul - Sep;11(3):144-152. doi: 10.1016/j.optom.2017.10.003. Epub 2017 Dec 29.


Simulation of a central scotoma using contact lenses with an opaque centre.

Almutleb ES, Bradley A, Jedlicka J, Hassan SE.

Ophthalmic Physiol Opt. 2018 Jan;38(1):76-87. doi: 10.1111/opo.12422.


Reducing starbursts in highly aberrated eyes with pupil miosis.

Xu R, Kollbaum P, Thibos L, Lopez-Gil N, Bradley A.

Ophthalmic Physiol Opt. 2018 Jan;38(1):26-36. doi: 10.1111/opo.12420.


Quantitative analysis of antimicrobial use on British dairy farms.

Hyde RM, Remnant JG, Bradley AJ, Breen JE, Hudson CD, Davies PL, Clarke T, Critchell Y, Hylands M, Linton E, Wood E, Green MJ.

Vet Rec. 2017 Dec 23;181(25):683. doi: 10.1136/vr.104614. Epub 2017 Dec 20.


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