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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]


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.


Research letter: Changes in melanoma diagnosis after pre-surgical tertiary care center review.

Luo Y, Echols K, Rensch G, Metcalf J, Elston DM.

J Am Acad Dermatol. 2018 May 9. pii: S0190-9622(18)30666-2. doi: 10.1016/j.jaad.2018.04.052. [Epub ahead of print] No abstract available.


Gene expression profiling of primary human type I alveolar epithelial cells exposed to Bacillus anthracis spores reveals induction of neutrophil and monocyte chemokines.

Booth JL, Duggan ES, Patel VI, Wu W, Burian DM, Hutchings DC, White VL, Coggeshall KM, Dozmorov MG, Metcalf JP.

Microb Pathog. 2018 Apr 25;121:9-21. doi: 10.1016/j.micpath.2018.04.039. [Epub ahead of print]


TRAF3-interacting protein 3, a new oncotarget, promotes tumor growth in melanoma.

Nasarre P, Bonilla IV, Metcalf JS, Hilliard EG, Klauber-DeMore N.

Melanoma Res. 2018 Jun;28(3):185-194. doi: 10.1097/CMR.0000000000000440.


Purpuric macule of the right axilla.

Dunn AL, Keeling BH, Bandino JP, Elston DM, Metcalf JS.

Cutis. 2018 Jan;101(1):16;29;30. No abstract available.


Identification of Insulin Receptor Splice Variant B in Neurons by in situ Detection in Human Brain Samples.

Spencer B, Rank L, Metcalf J, Desplats P.

Sci Rep. 2018 Mar 6;8(1):4070. doi: 10.1038/s41598-018-22434-2.


Neither Lys- and DAP-type peptidoglycans stimulate mouse or human innate immune cells via Toll-like receptor 2.

Langer M, Girton AW, Popescu NI, Burgett T, Metcalf JP, Coggeshall KM.

PLoS One. 2018 Feb 23;13(2):e0193207. doi: 10.1371/journal.pone.0193207. eCollection 2018.


Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models.

Belk A, Xu ZZ, Carter DO, Lynne A, Bucheli S, Knight R, Metcalf JL.

Genes (Basel). 2018 Feb 16;9(2). pii: E104. doi: 10.3390/genes9020104.


Coprolites reveal ecological interactions lost with the extinction of New Zealand birds.

Boast AP, Weyrich LS, Wood JR, Metcalf JL, Knight R, Cooper A.

Proc Natl Acad Sci U S A. 2018 Feb 13;115(7):1546-1551. doi: 10.1073/pnas.1712337115.


Correction for Morton et al., "Uncovering the Horseshoe Effect in Microbial Analyses".

Morton JT, Toran L, Edlund A, Metcalf JL, Lauber C, Knight R.

mSystems. 2018 Feb 6;3(1). pii: e00006-18. doi: 10.1128/mSystems.00006-18. eCollection 2018 Jan-Feb.


Comparison of Self-report to Biomarkers of Recent HIV Infection: Findings from the START Trial.

Schlusser KE, Sharma S, de la Torre P, Tambussi G, Draenert R, Pinto AN, Metcalf JA, German D, Neaton JD, Laeyendecker O; INSIGHT START Study Group.

AIDS Behav. 2018 Jul;22(7):2277-2283. doi: 10.1007/s10461-018-2048-y.


Supporting international graduates to success.

Kehoe A, Metcalf J, Carter M, McLachlan JC, Forrest S, Illing J.

Clin Teach. 2018 Jan 31. doi: 10.1111/tct.12760. [Epub ahead of print] No abstract available.


Safety and Efficacy of Catheter Direct Thrombolysis in Management of Acute Iliofemoral Deep Vein Thrombosis: A Systematic Review.

Elbasty A, Metcalf J.

Vasc Specialist Int. 2017 Dec;33(4):121-134. doi: 10.5758/vsi.2017.33.4.121. Epub 2017 Dec 31. Review.


Regulation of influenza virus replication by Wnt/β-catenin signaling.

More S, Yang X, Zhu Z, Bamunuarachchi G, Guo Y, Huang C, Bailey K, Metcalf JP, Liu L.

PLoS One. 2018 Jan 11;13(1):e0191010. doi: 10.1371/journal.pone.0191010. eCollection 2018.


Systemic Inflammation, Coagulation, and Clinical Risk in the START Trial.

Baker JV, Sharma S, Grund B, Rupert A, Metcalf JA, Schechter M, Munderi P, Aho I, Emery S, Babiker A, Phillips A, Lundgren JD, Neaton JD, Lane HC; INSIGHT START (Strategic Timing of AntiRetroviral Treatment) Study Group.

Open Forum Infect Dis. 2017 Nov 28;4(4):ofx262. doi: 10.1093/ofid/ofx262. eCollection 2017 Fall.


Evaluating the impact of domestication and captivity on the horse gut microbiome.

Metcalf JL, Song SJ, Morton JT, Weiss S, Seguin-Orlando A, Joly F, Feh C, Taberlet P, Coissac E, Amir A, Willerslev E, Knight R, McKenzie V, Orlando L.

Sci Rep. 2017 Nov 14;7(1):15497. doi: 10.1038/s41598-017-15375-9.


Rapid Communication: 16S ribosomal ribonucleic acid characterization of liver abscesses in feedlot cattle from three states in the United States.

Weinroth MD, Carlson CR, Martin JN, Metcalf JL, Morley PS, Belk KE.

J Anim Sci. 2017 Oct;95(10):4520-4525. doi: 10.2527/jas2017.1743.


A mechanistic spatio-temporal framework for modelling individual-to-individual transmission-With an application to the 2014-2015 West Africa Ebola outbreak.

Lau MSY, Gibson GJ, Adrakey H, McClelland A, Riley S, Zelner J, Streftaris G, Funk S, Metcalf J, Dalziel BD, Grenfell BT.

PLoS Comput Biol. 2017 Oct 30;13(10):e1005798. doi: 10.1371/journal.pcbi.1005798. eCollection 2017 Oct.


The Effects of Captivity on the Mammalian Gut Microbiome.

McKenzie VJ, Song SJ, Delsuc F, Prest TL, Oliverio AM, Korpita TM, Alexiev A, Amato KR, Metcalf JL, Kowalewski M, Avenant NL, Link A, Di Fiore A, Seguin-Orlando A, Feh C, Orlando L, Mendelson JR, Sanders J, Knight R.

Integr Comp Biol. 2017 Oct 1;57(4):690-704. doi: 10.1093/icb/icx090.


L-Serine-Mediated Neuroprotection Includes the Upregulation of the ER Stress Chaperone Protein Disulfide Isomerase (PDI).

Dunlop RA, Powell JT, Metcalf JS, Guillemin GJ, Cox PA.

Neurotox Res. 2018 Jan;33(1):113-122. doi: 10.1007/s12640-017-9817-7. Epub 2017 Oct 3.


L-Serine: a Naturally-Occurring Amino Acid with Therapeutic Potential.

Metcalf JS, Dunlop RA, Powell JT, Banack SA, Cox PA.

Neurotox Res. 2018 Jan;33(1):213-221. doi: 10.1007/s12640-017-9814-x. Epub 2017 Sep 19. Review.


RIG-I overexpression decreases mortality of cigarette smoke exposed mice during influenza A virus infection.

Wang X, Wu W, Zhang W, Leland Booth J, Duggan ES, Tian L, More S, Zhao YD, Sawh RN, Liu L, Zou MH, Metcalf JP.

Respir Res. 2017 Sep 2;18(1):166. doi: 10.1186/s12931-017-0649-z.


β-N-methylamino-l-alanine analysis in the brains of patients with Kii ALS/PDC.

Kokubo Y, Banack SA, Morimoto S, Murayama S, Togashi T, Metcalf JS, Cox PA, Kuzuhara S.

Neurology. 2017 Sep 5;89(10):1091-1092. doi: 10.1212/WNL.0000000000004310. Epub 2017 Aug 9. No abstract available.


Analysis of Neurotoxic Amino Acids from Marine Waters, Microbial Mats, and Seafood Destined for Human Consumption in the Arabian Gulf.

Chatziefthimiou AD, Deitch EJ, Glover WB, Powell JT, Banack SA, Richer RA, Cox PA, Metcalf JS.

Neurotox Res. 2018 Jan;33(1):143-152. doi: 10.1007/s12640-017-9772-3. Epub 2017 Aug 1.


Analysis of BMAA enantiomers in cycads, cyanobacteria, and mammals: in vivo formation and toxicity of D-BMAA.

Metcalf JS, Lobner D, Banack SA, Cox GA, Nunn PB, Wyatt PB, Cox PA.

Amino Acids. 2017 Aug;49(8):1427-1439. doi: 10.1007/s00726-017-2445-y. Epub 2017 Jun 15.


Abrupt weaning reduces postweaning growth and is associated with alterations in gastrointestinal markers of development in dairy calves fed an elevated plane of nutrition during the preweaning period.

Steele MA, Doelman JH, Leal LN, Soberon F, Carson M, Metcalf JA.

J Dairy Sci. 2017 Jul;100(7):5390-5399. doi: 10.3168/jds.2016-12310. Epub 2017 May 17.


Immune plasma for the treatment of severe influenza: an open-label, multicentre, phase 2 randomised study.

Beigel JH, Tebas P, Elie-Turenne MC, Bajwa E, Bell TE, Cairns CB, Shoham S, Deville JG, Feucht E, Feinberg J, Luke T, Raviprakash K, Danko J, O'Neil D, Metcalf JA, King K, Burgess TH, Aga E, Lane HC, Hughes MD, Davey RT; IRC002 Study Team.

Lancet Respir Med. 2017 Jun;5(6):500-511. doi: 10.1016/S2213-2600(17)30174-1. Epub 2017 May 15. Erratum in: Lancet Respir Med. 2017 Jul;5(7):e26.


Exogenous essential amino acids stimulate an adaptive unfolded protein response in the mammary glands of lactating cows.

Nichols K, Doelman J, Kim JJM, Carson M, Metcalf JA, Cant JP.

J Dairy Sci. 2017 Jul;100(7):5909-5921. doi: 10.3168/jds.2016-12387. Epub 2017 May 3.


Microbiome Tools for Forensic Science.

Metcalf JL, Xu ZZ, Bouslimani A, Dorrestein P, Carter DO, Knight R.

Trends Biotechnol. 2017 Sep;35(9):814-823. doi: 10.1016/j.tibtech.2017.03.006. Epub 2017 Mar 30. Review.


Ten simple rules for responsible big data research.

Zook M, Barocas S, Boyd D, Crawford K, Keller E, Gangadharan SP, Goodman A, Hollander R, Koenig BA, Metcalf J, Narayanan A, Nelson A, Pasquale F.

PLoS Comput Biol. 2017 Mar 30;13(3):e1005399. doi: 10.1371/journal.pcbi.1005399. eCollection 2017 Mar. No abstract available.


Traditional Food Items in Ogimi, Okinawa: l-Serine Content and the Potential for Neuroprotection.

Cox PA, Metcalf JS.

Curr Nutr Rep. 2017;6(1):24-31. doi: 10.1007/s13668-017-0191-0. Epub 2017 Feb 7. Review.


Uncovering the Horseshoe Effect in Microbial Analyses.

Morton JT, Toran L, Edlund A, Metcalf JL, Lauber C, Knight R.

mSystems. 2017 Feb 21;2(1). pii: e00166-16. doi: 10.1128/mSystems.00166-16. eCollection 2017 Jan-Feb. Erratum in: mSystems. 2018 Feb 6;3(1):.


Prophage WO genes recapitulate and enhance Wolbachia-induced cytoplasmic incompatibility.

LePage DP, Metcalf JA, Bordenstein SR, On J, Perlmutter JI, Shropshire JD, Layton EM, Funkhouser-Jones LJ, Beckmann JF, Bordenstein SR.

Nature. 2017 Mar 9;543(7644):243-247. doi: 10.1038/nature21391. Epub 2017 Feb 27.


Balance Trees Reveal Microbial Niche Differentiation.

Morton JT, Sanders J, Quinn RA, McDonald D, Gonzalez A, Vázquez-Baeza Y, Navas-Molina JA, Song SJ, Metcalf JL, Hyde ER, Lladser M, Dorrestein PC, Knight R.

mSystems. 2017 Jan 17;2(1). pii: e00162-16. doi: 10.1128/mSystems.00162-16. eCollection 2017 Jan-Feb.


The anticancer drug sunitinib promotes autophagyand protects from neurotoxicity in an HIV-1 Tat model of neurodegeneration.

Fields JA, Metcalf J, Overk C, Adame A, Spencer B, Wrasidlo W, Florio J, Rockenstein E, He JJ, Masliah E.

J Neurovirol. 2017 Apr;23(2):290-303. doi: 10.1007/s13365-016-0502-z. Epub 2017 Jan 19.


Transcriptional Classification and Functional Characterization of Human Airway Macrophage and Dendritic Cell Subsets.

Patel VI, Booth JL, Duggan ES, Cate S, White VL, Hutchings D, Kovats S, Burian DM, Dozmorov M, Metcalf JP.

J Immunol. 2017 Feb 1;198(3):1183-1201. doi: 10.4049/jimmunol.1600777. Epub 2016 Dec 28.


Interleukin-15 (IL-15) Strongly Correlates with Increasing HIV-1 Viremia and Markers of Inflammation.

Swaminathan S, Qiu J, Rupert AW, Hu Z, Higgins J, Dewar RL, Stevens R, Rehm CA, Metcalf JA, Sherman BT, Baseler MW, Lane HC, Imamichi T.

PLoS One. 2016 Nov 23;11(11):e0167091. doi: 10.1371/journal.pone.0167091. eCollection 2016.


Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies.

Song SJ, Amir A, Metcalf JL, Amato KR, Xu ZZ, Humphrey G, Knight R.

mSystems. 2016 May 3;1(3). pii: e00021-16. eCollection 2016 May-Jun.


Supporting international medical graduates' transition to their host-country: realist synthesis.

Kehoe A, McLachlan J, Metcalf J, Forrest S, Carter M, Illing J.

Med Educ. 2016 Oct;50(10):1015-32. doi: 10.1111/medu.13071. Review.


Human primary airway epithelial cells isolated from active smokers have epigenetically impaired antiviral responses.

Wu W, Zhang W, Booth JL, Hutchings DC, Wang X, White VL, Youness H, Cross CD, Zou MH, Burian D, Metcalf JP.

Respir Res. 2016 Sep 7;17(1):111. doi: 10.1186/s12931-016-0428-2.


Phase I clinical trial of safety of L-serine for ALS patients.

Levine TD, Miller RG, Bradley WG, Moore DH, Saperstein DS, Flynn LE, Katz JS, Forshew DA, Metcalf JS, Banack SA, Cox PA.

Amyotroph Lateral Scler Frontotemporal Degener. 2017 Feb;18(1-2):107-111. doi: 10.1080/21678421.2016.1221971. Epub 2016 Sep 2.


Microbiology of death.

Metcalf JL, Carter DO, Knight R.

Curr Biol. 2016 Jul 11;26(13):R561-R563. doi: 10.1016/j.cub.2016.03.042.


Synergistic roles of climate warming and human occupation in Patagonian megafaunal extinctions during the Last Deglaciation.

Metcalf JL, Turney C, Barnett R, Martin F, Bray SC, Vilstrup JT, Orlando L, Salas-Gismondi R, Loponte D, Medina M, De Nigris M, Civalero T, Fernández PM, Gasco A, Duran V, Seymour KL, Otaola C, Gil A, Paunero R, Prevosti FJ, Bradshaw CJ, Wheeler JC, Borrero L, Austin JJ, Cooper A.

Sci Adv. 2016 Jun 17;2(6):e1501682. doi: 10.1126/sciadv.1501682. eCollection 2016 Jun.


Bacillus anthracis spore movement does not require a carrier cell and is not affected by lethal toxin in human lung models.

Booth JL, Duggan ES, Patel VI, Langer M, Wu W, Braun A, Coggeshall KM, Metcalf JP.

Microbes Infect. 2016 Oct;18(10):615-626. doi: 10.1016/j.micinf.2016.06.004. Epub 2016 Jun 16.


Blue nevus and "malignant blue nevus:" A concise review.

Sugianto JZ, Ralston JS, Metcalf JS, McFaddin CL, Smith MT.

Semin Diagn Pathol. 2016 Jul;33(4):219-24. doi: 10.1053/j.semdp.2016.04.006. Epub 2016 Apr 19. Review.


Do vervets and macaques respond differently to BMAA?

Cox PA, Davis DA, Mash DC, Metcalf JS, Banack SA.

Neurotoxicology. 2016 Dec;57:310-311. doi: 10.1016/j.neuro.2016.04.017. Epub 2016 Apr 28.


Occurrence of microcystins in water, bloom, sediment and fish from a public water supply.

Gurbuz F, Uzunmehmetoğlu OY, Diler Ö, Metcalf JS, Codd GA.

Sci Total Environ. 2016 Aug 15;562:860-868. doi: 10.1016/j.scitotenv.2016.04.027. Epub 2016 Apr 23.


The effects of storage temperature on PBMC gene expression.

Yang J, Diaz N, Adelsberger J, Zhou X, Stevens R, Rupert A, Metcalf JA, Baseler M, Barbon C, Imamichi T, Lempicki R, Cosentino LM.

BMC Immunol. 2016 Mar 15;17:6. doi: 10.1186/s12865-016-0144-1.


Identification and characterization of human dendritic cell subsets in the steady state: a review of our current knowledge.

Patel VI, Metcalf JP.

J Investig Med. 2016 Apr;64(4):833-47. doi: 10.1136/jim-2016-000072. Epub 2016 Mar 8. Review.


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