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Post-mortem magnetic resonance imaging in patients with suspected prion disease: Pathological confirmation, sensitivity, specificity and observer reliability. A national registry.

Gibson LM, Chappell FM, Summers D, Collie DA, Sellar R, Best J, Knight R, Ironside JW, Wardlaw JM.

PLoS One. 2018 Aug 7;13(8):e0201434. doi: 10.1371/journal.pone.0201434. eCollection 2018.


Are microbiome studies ready for hypothesis-driven research?

Tripathi A, Marotz C, Gonzalez A, Vázquez-Baeza Y, Song SJ, Bouslimani A, McDonald D, Zhu Q, Sanders JG, Smarr L, Dorrestein PC, Knight R.

Curr Opin Microbiol. 2018 Jul 27;44:61-69. doi: 10.1016/j.mib.2018.07.002. [Epub ahead of print] Review.


Corruption practices in drug prescribing in Vietnam - an analysis based on qualitative interviews.

Nguyen TA, Knight R, Mant A, Razee H, Brooks G, Dang TH, Roughead EE.

BMC Health Serv Res. 2018 Jul 28;18(1):587. doi: 10.1186/s12913-018-3384-3.


Criminalization of HIV non-disclosure: Narratives from young men living in Vancouver, Canada.

Knight R, Krüsi A, Carson A, Fast D, Shannon K, Shoveller J.

PLoS One. 2018 Jul 24;13(7):e0201110. doi: 10.1371/journal.pone.0201110. eCollection 2018.


Who's challenging who training for staff empathy towards adults with challenging behaviour: cluster randomised controlled trial.

Hastings RP, Gillespie D, Flynn S, McNamara R, Taylor Z, Knight R, Randell E, Richards L, Moody G, Mitchell A, Przybylak P, Williams B, Hunt PH.

J Intellect Disabil Res. 2018 Jul 23. doi: 10.1111/jir.12536. [Epub ahead of print]


Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism.

Zarrinpar A, Chaix A, Xu ZZ, Chang MW, Marotz CA, Saghatelian A, Knight R, Panda S.

Nat Commun. 2018 Jul 20;9(1):2872. doi: 10.1038/s41467-018-05336-9.


Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota.

Hua ZS, Qu YN, Zhu Q, Zhou EM, Qi YL, Yin YR, Rao YZ, Tian Y, Li YX, Liu L, Castelle CJ, Hedlund BP, Shu WS, Knight R, Li WJ.

Nat Commun. 2018 Jul 19;9(1):2832. doi: 10.1038/s41467-018-05284-4.


Unexplained fever after pancreas transplantation.

Klasek R, Kuten SA, Patel SJ, Graviss EA, Nguyen DT, Hobeika MJ, Gaber OA, Podder H, Knight RJ.

Clin Transplant. 2018 Jul 17:e13351. doi: 10.1111/ctr.13351. [Epub ahead of print]


Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes.

Amato KR, G Sanders J, Song SJ, Nute M, Metcalf JL, Thompson LR, Morton JT, Amir A, J McKenzie V, Humphrey G, Gogul G, Gaffney J, L Baden A, A O Britton G, P Cuozzo F, Di Fiore A, J Dominy N, L Goldberg T, Gomez A, Kowalewski MM, J Lewis R, Link A, L Sauther M, Tecot S, A White B, E Nelson K, M Stumpf R, Knight R, R Leigh S.

ISME J. 2018 Jul 11. doi: 10.1038/s41396-018-0175-0. [Epub ahead of print]


Integrated analysis of anatomical and electrophysiological human intracranial data.

Stolk A, Griffin S, van der Meij R, Dewar C, Saez I, Lin JJ, Piantoni G, Schoffelen JM, Knight RT, Oostenveld R.

Nat Protoc. 2018 Jul;13(7):1699-1723. doi: 10.1038/s41596-018-0009-6.


Environmental radiation alters the gut microbiome of the bank vole Myodes glareolus.

Lavrinienko A, Mappes T, Tukalenko E, Mousseau TA, Møller AP, Knight R, Morton JT, Thompson LR, Watts PC.

ISME J. 2018 Jul 9. doi: 10.1038/s41396-018-0214-x. [Epub ahead of print]


Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2018 Jul 6;36(7):660. doi: 10.1038/nbt0718-660a. No abstract available.


Decoding Inner Speech Using Electrocorticography: Progress and Challenges Toward a Speech Prosthesis.

Martin S, Iturrate I, Millán JDR, Knight RT, Pasley BN.

Front Neurosci. 2018 Jun 21;12:422. doi: 10.3389/fnins.2018.00422. eCollection 2018. Review.


Author Correction: Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity.

Shalapour S, Lin XJ, Bastian IN, Brain J, Burt AD, Aksenov AA, Vrbanac AF, Li W, Perkins A, Matsutani T, Zhong Z, Dhar D, Navas-Molina JA, Xu J, Loomba R, Downes M, Yu RT, Evans RM, Dorrestein PC, Knight R, Benner C, Anstee QM, Karin M.

Nature. 2018 Jul 4. doi: 10.1038/s41586-018-0304-y. [Epub ahead of print]


Persistent neuronal activity in human prefrontal cortex links perception and action.

Haller M, Case J, Crone NE, Chang EF, King-Stephens D, Laxer KD, Weber PB, Parvizi J, Knight RT, Shestyuk AY.

Nat Hum Behav. 2018 Jan;2(1):80-91. doi: 10.1038/s41562-017-0267-2. Epub 2017 Dec 18.


Ancient Thali Diet: Gut Microbiota, Immunity, and Health.

Shondelmyer K, Knight R, Sanivarapu A, Ogino S, Vanamala JKP.

Yale J Biol Med. 2018 Jun 28;91(2):177-184. eCollection 2018 Jun. Review.


"Twisted Tales: Insights into Genome Diversity of Ciliates Using Single-Cell 'omics".

Maurer-Alcalá XX, Yan Y, Pilling O, Knight R, Katz LA.

Genome Biol Evol. 2018 Jun 26. doi: 10.1093/gbe/evy133. [Epub ahead of print]


ZNF281 inhibits neuronal differentiation and is a prognostic marker for neuroblastoma.

Pieraccioli M, Nicolai S, Pitolli C, Agostini M, Antonov A, Malewicz M, Knight RA, Raschellà G, Melino G.

Proc Natl Acad Sci U S A. 2018 Jul 10;115(28):7356-7361. doi: 10.1073/pnas.1801435115. Epub 2018 Jun 25.


Large-scale replicated field study of maize rhizosphere identifies heritable microbes.

Walters WA, Jin Z, Youngblut N, Wallace JG, Sutter J, Zhang W, González-Peña A, Peiffer J, Koren O, Shi Q, Knight R, Glavina Del Rio T, Tringe SG, Buckler ES, Dangl JL, Ley RE.

Proc Natl Acad Sci U S A. 2018 Jul 10;115(28):7368-7373. doi: 10.1073/pnas.1800918115. Epub 2018 Jun 25.


In silico and ex vivo approaches indicate immune pressure on capsid and non-capsid regions of coxsackie B viruses in the human system.

Kundu R, Knight R, Dunga M, Peakman M.

PLoS One. 2018 Jun 20;13(6):e0199323. doi: 10.1371/journal.pone.0199323. eCollection 2018.


Low-frequency cortical activity is a neuromodulatory target that tracks recovery after stroke.

Ramanathan DS, Guo L, Gulati T, Davidson G, Hishinuma AK, Won SJ, Knight RT, Chang EF, Swanson RA, Ganguly K.

Nat Med. 2018 Jun 18. doi: 10.1038/s41591-018-0058-y. [Epub ahead of print]


Diagnosis of Methionine/Valine Variant Creutzfeldt-Jakob Disease by Protein Misfolding Cyclic Amplification.

Bougard D, Bélondrade M, Mayran C, Bruyère-Ostells L, Lehmann S, Fournier-Wirth C, Knight RS, Will RG, Green AJE.

Emerg Infect Dis. 2018 Jul;24(7):1364-1366. doi: 10.3201/eid2407.172105.


Intermittent Hypoxia and Hypercapnia, a Hallmark of Obstructive Sleep Apnea, Alters the Gut Microbiome and Metabolome.

Tripathi A, Melnik AV, Xue J, Poulsen O, Meehan MJ, Humphrey G, Jiang L, Ackermann G, McDonald D, Zhou D, Knight R, Dorrestein PC, Haddad GG.

mSystems. 2018 Jun 5;3(3). pii: e00020-18. doi: 10.1128/mSystems.00020-18. eCollection 2018 May-Jun.


Short- and midterm results for internal jugular vein extension for short right renal vein kidney transplant.

Lu T, Yi SG, Bismuth J, Knight RJ, Gaber AO, Bechara CF.

Clin Transplant. 2018 Jun 11:e13312. doi: 10.1111/ctr.13312. [Epub ahead of print]


Variant Creutzfeldt-Jakob disease.

Brandel JP, Knight R.

Handb Clin Neurol. 2018;153:191-205. doi: 10.1016/B978-0-444-63945-5.00011-8.


HIV Incidence Among Men Who Have Sex with Men and Inject Drugs in a Canadian Setting.

Scheim AI, Nosova E, Knight R, Hayashi K, Kerr T.

AIDS Behav. 2018 Jun 6. doi: 10.1007/s10461-018-2185-3. [Epub ahead of print]


Overpumping leads to California groundwater arsenic threat.

Smith R, Knight R, Fendorf S.

Nat Commun. 2018 Jun 5;9(1):2089. doi: 10.1038/s41467-018-04475-3.


Gut microbiome and magnetic resonance spectroscopy study of subjects at ultra-high risk for psychosis may support the membrane hypothesis.

He Y, Kosciolek T, Tang J, Zhou Y, Li Z, Ma X, Zhu Q, Yuan N, Yuan L, Li C, Jin K, Knight R, Tsuang MT, Chen X.

Eur Psychiatry. 2018 Jun 2;53:37-45. doi: 10.1016/j.eurpsy.2018.05.011. [Epub ahead of print]


The gut microbiome of nonhuman primates: Lessons in ecology and evolution.

Clayton JB, Gomez A, Amato K, Knights D, Travis DA, Blekhman R, Knight R, Leigh S, Stumpf R, Wolf T, Glander KE, Cabana F, Johnson TJ.

Am J Primatol. 2018 Jun;80(6):e22867. doi: 10.1002/ajp.22867. Epub 2018 Jun 4. Review.


A lexical semantic hub for heteromodal naming in middle fusiform gyrus.

Forseth KJ, Kadipasaoglu CM, Conner CR, Hickok G, Knight RT, Tandon N.

Brain. 2018 Jul 1;141(7):2112-2126. doi: 10.1093/brain/awy120.


TAp73 contributes to the oxidative stress response by regulating protein synthesis.

Marini A, Rotblat B, Sbarrato T, Niklison-Chirou MV, Knight JRP, Dudek K, Jones C, Bushell M, Knight RA, Amelio I, Willis AE, Melino G.

Proc Natl Acad Sci U S A. 2018 Jun 12;115(24):6219-6224. doi: 10.1073/pnas.1718531115. Epub 2018 May 29.


American Gut: an Open Platform for Citizen Science Microbiome Research.

McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q; American Gut Consortium , Knight R.

mSystems. 2018 May 15;3(3). pii: e00031-18. doi: 10.1128/mSystems.00031-18. eCollection 2018 May-Jun.


Methods for phylogenetic analysis of microbiome data.

Washburne AD, Morton JT, Sanders J, McDonald D, Zhu Q, Oliverio AM, Knight R.

Nat Microbiol. 2018 Jun;3(6):652-661. doi: 10.1038/s41564-018-0156-0. Epub 2018 May 24. Review.


Best practices for analysing microbiomes.

Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, Gonzalez A, Kosciolek T, McCall LI, McDonald D, Melnik AV, Morton JT, Navas J, Quinn RA, Sanders JG, Swafford AD, Thompson LR, Tripathi A, Xu ZZ, Zaneveld JR, Zhu Q, Caporaso JG, Dorrestein PC.

Nat Rev Microbiol. 2018 Jul;16(7):410-422. doi: 10.1038/s41579-018-0029-9. Review.


Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm.

Michaud JM, Thompson LR, Kaul D, Espinoza JL, Richter RA, Xu ZZ, Lee C, Pham KM, Beall CM, Malfatti F, Azam F, Knight R, Burkart MD, Dupont CL, Prather KA.

Nat Commun. 2018 May 22;9(1):2017. doi: 10.1038/s41467-018-04409-z.


Bacterial community changes in an industrial algae production system.

Fulbright SP, Robbins-Pianka A, Berg-Lyons D, Knight R, Reardon KF, Chisholm ST.

Algal Res. 2018 Apr;31:147-156. doi: 10.1016/j.algal.2017.09.010. Epub 2018 Feb 21.


Publisher Correction: The gut-liver axis and the intersection with the microbiome.

Tripathi A, Debelius J, Brenner DA, Karin M, Loomba R, Schnabl B, Knight R.

Nat Rev Gastroenterol Hepatol. 2018 May 21. doi: 10.1038/s41575-018-0031-8. [Epub ahead of print]


Defining Host Responses during Systemic Bacterial Infection through Construction of a Murine Organ Proteome Atlas.

Lapek JD Jr, Mills RH, Wozniak JM, Campeau A, Fang RH, Wei X, van de Groep K, Perez-Lopez A, van Sorge NM, Raffatellu M, Knight R, Zhang L, Gonzalez DJ.

Cell Syst. 2018 May 23;6(5):579-592.e4. doi: 10.1016/j.cels.2018.04.010. Epub 2018 May 16.


Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin.

Bokulich NA, Kaehler BD, Rideout JR, Dillon M, Bolyen E, Knight R, Huttley GA, Gregory Caporaso J.

Microbiome. 2018 May 17;6(1):90. doi: 10.1186/s40168-018-0470-z.


The gut-liver axis and the intersection with the microbiome.

Tripathi A, Debelius J, Brenner DA, Karin M, Loomba R, Schnabl B, Knight R.

Nat Rev Gastroenterol Hepatol. 2018 Jul;15(7):397-411. doi: 10.1038/s41575-018-0011-z. Review. Erratum in: Nat Rev Gastroenterol Hepatol. 2018 May 21;:.


A Systematic Review and Meta-Analysis of the Effectiveness of Acetylcholinesterase Inhibitors and Memantine in Treating the Cognitive Symptoms of Dementia.

Knight R, Khondoker M, Magill N, Stewart R, Landau S.

Dement Geriatr Cogn Disord. 2018;45(3-4):131-151. doi: 10.1159/000486546. Epub 2018 May 7.


Gut microbiota utilize immunoglobulin A for mucosal colonization.

Donaldson GP, Ladinsky MS, Yu KB, Sanders JG, Yoo BB, Chou WC, Conner ME, Earl AM, Knight R, Bjorkman PJ, Mazmanian SK.

Science. 2018 May 18;360(6390):795-800. doi: 10.1126/science.aaq0926. Epub 2018 May 3.


Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information.

Janssen S, McDonald D, Gonzalez A, Navas-Molina JA, Jiang L, Xu ZZ, Winker K, Kado DM, Orwoll E, Manary M, Mirarab S, Knight R.

mSystems. 2018 Apr 17;3(3). pii: e00021-18. doi: 10.1128/mSystems.00021-18. eCollection 2018 May-Jun.


Exposure to toxic metals triggers unique responses from the rat gut microbiota.

Richardson JB, Dancy BCR, Horton CL, Lee YS, Madejczyk MS, Xu ZZ, Ackermann G, Humphrey G, Palacios G, Knight R, Lewis JA.

Sci Rep. 2018 Apr 26;8(1):6578. doi: 10.1038/s41598-018-24931-w.


Conversion from tacrolimus-mycophenolate mofetil to tacrolimus-mTOR immunosuppression after kidney-pancreas transplantation reduces the incidence of both BK and CMV viremia.

Knight RJ, Graviss EA, Nguyen DT, Kuten SA, Patel SJ, Gaber L, Gaber AO.

Clin Transplant. 2018 Jun;32(6):e13265. doi: 10.1111/ctr.13265. Epub 2018 May 12.


Hopanoid-producing bacteria in the Red Sea include the major marine nitrite oxidizers.

Kharbush JJ, Thompson LR, Haroon MF, Knight R, Aluwihare LI.

FEMS Microbiol Ecol. 2018 Jun 1;94(6). doi: 10.1093/femsec/fiy063.


Rapid amplification of prions from variant Creutzfeldt-Jakob disease cerebrospinal fluid.

Barria MA, Lee A, Green AJ, Knight R, Head MW.

J Pathol Clin Res. 2018 Apr;4(2):86-92. doi: 10.1002/cjp2.90. Epub 2018 Feb 5.


Earth Microbiome Project and Global Systems Biology.

Gilbert JA, Jansson JK, Knight R.

mSystems. 2018 Apr 10;3(3). pii: e00217-17. doi: 10.1128/mSystems.00217-17. eCollection 2018 May-Jun. No abstract available.


Current understanding of the human microbiome.

Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV, Knight R.

Nat Med. 2018 Apr 10;24(4):392-400. doi: 10.1038/nm.4517. Review.


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