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Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient.

Fang X, Monk JM, Nurk S, Akseshina M, Zhu Q, Gemmell C, Gianetto-Hill C, Leung N, Szubin R, Sanders J, Beck PL, Li W, Sandborn WJ, Gray-Owen SD, Knight R, Allen-Vercoe E, Palsson BO, Smarr L.

Front Microbiol. 2018 Oct 30;9:2559. doi: 10.3389/fmicb.2018.02559. eCollection 2018.


Identifying and Predicting Novelty in Microbiome Studies.

Su X, Jing G, McDonald D, Wang H, Wang Z, Gonzalez A, Sun Z, Huang S, Navas J, Knight R, Xu J.

MBio. 2018 Nov 13;9(6). pii: e02099-18. doi: 10.1128/mBio.02099-18.


Multiple Sclerosis-Associated Changes in the Composition and Immune Functions of Spore-Forming Bacteria.

Cekanaviciute E, Pröbstel AK, Thomann A, Runia TF, Casaccia P, Katz Sand I, Crabtree E, Singh S, Morrissey J, Barba P, Gomez R, Knight R, Mazmanian S, Graves J, Cree BAC, Zamvil SS, Baranzini SE.

mSystems. 2018 Nov 6;3(6). pii: e00083-18. doi: 10.1128/mSystems.00083-18. eCollection 2018 Nov-Dec.


High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity.

Minich JJ, Humphrey G, Benitez RAS, Sanders J, Swafford A, Allen EE, Knight R.

mSystems. 2018 Nov 6;3(6). pii: e00166-18. doi: 10.1128/mSystems.00166-18. eCollection 2018 Nov-Dec.


Differential contributions of subthalamic beta rhythms and 1/f broadband activity to motor symptoms in Parkinson's disease.

Martin S, Iturrate I, Chavarriaga R, Leeb R, Sobolewski A, Li AM, Zaldivar J, Peciu-Florianu I, Pralong E, Castro-Jiménez M, Benninger D, Vingerhoets F, Knight RT, Bloch J, Millán JDR.

NPJ Parkinsons Dis. 2018 Nov 5;4:32. doi: 10.1038/s41531-018-0068-y. eCollection 2018.


Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue.

Kodama WA, Xu Z, Metcalf JL, Song SJ, Harrison N, Knight R, Carter DO, Happy CB.

J Forensic Sci. 2018 Nov 8. doi: 10.1111/1556-4029.13949. [Epub ahead of print]


Implementation of a 1-2 keV point-projection x-ray spectrometer on the National Ignition Facility.

King JA, Opachich YP, Huffman EJ, Knight R, Heeter RF, Ahmed M, Liedahl DA, Schneider MB, Thompson NB, Johns HM, Dodd E, Flippo KA, Kline JL, Lopez FE, Archuleta TN, Perry TS.

Rev Sci Instrum. 2018 Oct;89(10):10F101. doi: 10.1063/1.5038092.


Covariates of the Severity of Aggression in Sexual Crimes: Psychopathy and Borderline Characteristics.

Cardona N, Berman AK, Sims-Knight JE, Knight RA.

Sex Abuse. 2018 Nov 4:1079063218807485. doi: 10.1177/1079063218807485. [Epub ahead of print]


p53 mutants cooperate with HIF-1 in transcriptional regulation of extracellular matrix components to promote tumor progression.

Amelio I, Mancini M, Petrova V, Cairns RA, Vikhreva P, Nicolai S, Marini A, Antonov AA, Le Quesne J, Baena Acevedo JD, Dudek K, Sozzi G, Pastorino U, Knight RA, Mak TW, Melino G.

Proc Natl Acad Sci U S A. 2018 Nov 13;115(46):E10869-E10878. doi: 10.1073/pnas.1808314115. Epub 2018 Oct 31.


Species-level functional profiling of metagenomes and metatranscriptomes.

Franzosa EA, McIver LJ, Rahnavard G, Thompson LR, Schirmer M, Weingart G, Lipson KS, Knight R, Caporaso JG, Segata N, Huttenhower C.

Nat Methods. 2018 Nov;15(11):962-968. doi: 10.1038/s41592-018-0176-y. Epub 2018 Oct 30.


Striped UniFrac: enabling microbiome analysis at unprecedented scale.

McDonald D, Vázquez-Baeza Y, Koslicki D, McClelland J, Reeve N, Xu Z, Gonzalez A, Knight R.

Nat Methods. 2018 Nov;15(11):847-848. doi: 10.1038/s41592-018-0187-8. No abstract available.


Gut Microbiota in the First 2 Years of Life and the Association with Body Mass Index at Age 12 in a Norwegian Birth Cohort.

Stanislawski MA, Dabelea D, Wagner BD, Iszatt N, Dahl C, Sontag MK, Knight R, Lozupone CA, Eggesbø M.

MBio. 2018 Oct 23;9(5). pii: e01751-18. doi: 10.1128/mBio.01751-18.


Anatomic approximation approach to correction of transverse facial clefts.

Tse RW, Knight RJ, Fisher DM.

J Plast Reconstr Aesthet Surg. 2018 Nov;71(11):1600-1608. doi: 10.1016/j.bjps.2018.05.020. Epub 2018 Jun 12.


Differential Activation of Hepatic Invariant NKT Cell Subsets Plays a Key Role in Progression of Nonalcoholic Steatohepatitis.

Maricic I, Marrero I, Eguchi A, Nakamura R, Johnson CD, Dasgupta S, Hernandez CD, Nguyen PS, Swafford AD, Knight R, Feldstein AE, Loomba R, Kumar V.

J Immunol. 2018 Nov 15;201(10):3017-3035. doi: 10.4049/jimmunol.1800614. Epub 2018 Oct 15.


Preserving microbial diversity.

Bello MGD, Knight R, Gilbert JA, Blaser MJ.

Science. 2018 Oct 5;362(6410):33-34. doi: 10.1126/science.aau8816. No abstract available.


Hair follicle miRNAs: a novel biomarker for primary blast Induced-Mild traumatic brain injury.

Zhang J, Knight R, Wang Y, Sawyer TW, Martyniuk CJ, Langlois VS.

Biomarkers. 2018 Nov 13:1-14. doi: 10.1080/1354750X.2018.1531929. [Epub ahead of print]


Corrigendum: The Role of Personality Traits in Young Adult Fruit and Vegetable Consumption.

Conner TS, Thompson LM, Knight RL, Flett JAM, Richardson AC, Brookie KL.

Front Psychol. 2018 Sep 20;9:1597. doi: 10.3389/fpsyg.2018.01597. eCollection 2018.


Qiita: rapid, web-enabled microbiome meta-analysis.

Gonzalez A, Navas-Molina JA, Kosciolek T, McDonald D, Vázquez-Baeza Y, Ackermann G, DeReus J, Janssen S, Swafford AD, Orchanian SB, Sanders JG, Shorenstein J, Holste H, Petrus S, Robbins-Pianka A, Brislawn CJ, Wang M, Rideout JR, Bolyen E, Dillon M, Caporaso JG, Dorrestein PC, Knight R.

Nat Methods. 2018 Oct;15(10):796-798. doi: 10.1038/s41592-018-0141-9. Epub 2018 Oct 1.


Differences in gut microbiome composition between persons with chronic schizophrenia and healthy comparison subjects.

Nguyen TT, Kosciolek T, Maldonado Y, Daly RE, Martin AS, McDonald D, Knight R, Jeste DV.

Schizophr Res. 2018 Sep 26. pii: S0920-9964(18)30572-3. doi: 10.1016/j.schres.2018.09.014. [Epub ahead of print]


Behavioural activation versus guided self-help for depression in adults with learning disabilities: the BeatIt RCT.

Jahoda A, Hastings R, Hatton C, Cooper SA, McMeekin N, Dagnan D, Appleton K, Scott K, Fulton L, Jones R, McConnachie A, Zhang R, Knight R, Knowles D, Williams C, Briggs A, Melville C.

Health Technol Assess. 2018 Sep;22(53):1-130. doi: 10.3310/hta22530.


Supporting people with intellectual disabilities in psychological therapies for depression: A qualitative analysis of supporters' experiences.

Scott K, Hatton C, Knight R, Singer K, Knowles D, Dagnan D, Hastings RP, Appleton K, Cooper SA, Melville C, Jones R, Williams C, Jahoda A.

J Appl Res Intellect Disabil. 2018 Sep 28. doi: 10.1111/jar.12529. [Epub ahead of print]


Niche partitioning of a pathogenic microbiome driven by chemical gradients.

Quinn RA, Comstock W, Zhang T, Morton JT, da Silva R, Tran A, Aksenov A, Nothias LF, Wangpraseurt D, Melnik AV, Ackermann G, Conrad D, Klapper I, Knight R, Dorrestein PC.

Sci Adv. 2018 Sep 26;4(9):eaau1908. doi: 10.1126/sciadv.aau1908. eCollection 2018 Sep.


Comparison of oral collection methods for studies of microbiota.

Vogtmann E, Chen J, Kibriya MG, Amir A, Shi J, Chen Y, Islam T, Eunes M, Ahmed A, Naher J, Rahman A, Barmon B, Knight R, Chia N, Ahsan H, Abnet CC, Sinha R.

Cancer Epidemiol Biomarkers Prev. 2018 Sep 27. pii: cebp.0312.2018. doi: 10.1158/1055-9965.EPI-18-0312. [Epub ahead of print]


Author Correction: Regional variation limits applications of healthy gut microbiome reference ranges and disease models.

He Y, Wu W, Zheng HM, Li P, McDonald D, Sheng HF, Chen MX, Chen ZH, Ji GY, Zheng ZD, Mujagond P, Chen XJ, Rong ZH, Chen P, Lyu LY, Wang X, Wu CB, Yu N, Xu YJ, Yin J, Raes J, Knight R, Ma WJ, Zhou HW.

Nat Med. 2018 Sep 24. doi: 10.1038/s41591-018-0219-z. [Epub ahead of print]


Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians.

Allaband C, McDonald D, Vázquez-Baeza Y, Minich JJ, Tripathi A, Brenner DA, Loomba R, Smarr L, Sandborn WJ, Schnabl B, Dorrestein P, Zarrinpar A, Knight R.

Clin Gastroenterol Hepatol. 2018 Sep 18. pii: S1542-3565(18)31008-5. doi: 10.1016/j.cgh.2018.09.017. [Epub ahead of print] Review.


Human posterior parietal cortex responds to visual stimuli as early as peristriate occipital cortex.

Regev TI, Winawer J, Gerber EM, Knight RT, Deouell LY.

Eur J Neurosci. 2018 Sep 21. doi: 10.1111/ejn.14164. [Epub ahead of print]


Developing and sustaining a Community of Practice through Twitter for work-based learning.

Attenborough J, Knight RA, Brook J.

Evid Based Nurs. 2018 Oct;21(4):89-90. doi: 10.1136/eb-2018-102981. Epub 2018 Sep 18. No abstract available.


Hippocampal CA1 gamma power predicts the precision of spatial memory judgments.

Stevenson RF, Zheng J, Mnatsakanyan L, Vadera S, Knight RT, Lin JJ, Yassa MA.

Proc Natl Acad Sci U S A. 2018 Oct 2;115(40):10148-10153. doi: 10.1073/pnas.1805724115. Epub 2018 Sep 17.


Encoding of Multiple Reward-Related Computations in Transient and Sustained High-Frequency Activity in Human OFC.

Saez I, Lin J, Stolk A, Chang E, Parvizi J, Schalk G, Knight RT, Hsu M.

Curr Biol. 2018 Sep 24;28(18):2889-2899.e3. doi: 10.1016/j.cub.2018.07.045. Epub 2018 Sep 13.


Systematic comparison between a wireless EEG system with dry electrodes and a wired EEG system with wet electrodes.

Kam JWY, Griffin S, Shen A, Patel S, Hinrichs H, Heinze HJ, Deouell LY, Knight RT.

Neuroimage. 2019 Jan 1;184:119-129. doi: 10.1016/j.neuroimage.2018.09.012. Epub 2018 Sep 12.


Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus).

Minich JJ, Zhu Q, Xu ZZ, Amir A, Ngochera M, Simwaka M, Allen EE, Zidana H, Knight R.

Microbiologyopen. 2018 Aug 31:e00716. doi: 10.1002/mbo3.716. [Epub ahead of print]


Regional variation limits applications of healthy gut microbiome reference ranges and disease models.

He Y, Wu W, Zheng HM, Li P, McDonald D, Sheng HF, Chen MX, Chen ZH, Ji GY, Zheng ZD, Mujagond P, Chen XJ, Rong ZH, Chen P, Lyu LY, Wang X, Wu CB, Yu N, Xu YJ, Yin J, Raes J, Knight R, Ma WJ, Zhou HW.

Nat Med. 2018 Oct;24(10):1532-1535. doi: 10.1038/s41591-018-0164-x. Epub 2018 Aug 27. Erratum in: Nat Med. 2018 Sep 24;:.


Neural Mechanisms of Sustained Attention Are Rhythmic.

Helfrich RF, Fiebelkorn IC, Szczepanski SM, Lin JJ, Parvizi J, Knight RT, Kastner S.

Neuron. 2018 Aug 22;99(4):854-865.e5. doi: 10.1016/j.neuron.2018.07.032.


Comparing primary care pediatricians' perceptions of clinics with and without integrated behavioral health.

Lancaster B, Cook A, Bruni T, Sturza J, Sevecke J, Ham H, Knight R, Hoffses K, Wickham CA, Orringer KA.

Prim Health Care Res Dev. 2018 Aug 22:1-5. doi: 10.1017/S1463423618000579. [Epub ahead of print]


Links between environment, diet, and the hunter-gatherer microbiome.

Fragiadakis GK, Smits SA, Sonnenburg ED, Van Treuren W, Reid G, Knight R, Manjurano A, Changalucha J, Dominguez-Bello MG, Leach J, Sonnenburg JL.

Gut Microbes. 2018 Aug 17:1-12. doi: 10.1080/19490976.2018.1494103. [Epub ahead of print]


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 Aug;44:61-69. doi: 10.1016/j.mib.2018.07.002. Epub 2018 Jul 27. 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 Sep;62(9):798-813. doi: 10.1111/jir.12536. Epub 2018 Jul 23.


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 Sep;32(9):e13351. doi: 10.1111/ctr.13351. Epub 2018 Aug 11.


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 Nov;12(11):2801-2806. doi: 10.1038/s41396-018-0214-x. Epub 2018 Jul 9.


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 Sep;561(7721):E1. doi: 10.1038/s41586-018-0304-y.


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.

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