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Stress and Burnout Among Graduate Students: Moderation by Sleep Duration and Quality.

Allen HK, Barrall AL, Vincent KB, Arria AM.

Int J Behav Med. 2020 Mar 2. doi: 10.1007/s12529-020-09867-8. [Epub ahead of print]


Substance use and mental health problems among graduate students: Individual and program-level correlates.

Allen HK, Lilly F, Green KM, Zanjani F, Vincent KB, Arria AM.

J Am Coll Health. 2020 Feb 26:1-9. doi: 10.1080/07448481.2020.1725020. [Epub ahead of print]


Outer membrane protein A (OmpA) of extraintestinal pathogenic Escherichia coli.

Nielsen DW, Ricker N, Barbieri NL, Allen HK, Nolan LK, Logue CM.

BMC Res Notes. 2020 Jan 31;13(1):51. doi: 10.1186/s13104-020-4917-5.


Situational context and motives of alcohol use among graduate student drinkers.

Allen HK, Barrall AL, Beck KH, Vincent KB, Arria AM.

Addict Behav. 2020 May;104:106267. doi: 10.1016/j.addbeh.2019.106267. Epub 2019 Dec 24.


Cattle intestinal microbiota shifts following Escherichia coli O157:H7 vaccination and colonization

Mir RA, Schaut RG, Allen HK, Looft T, Loving CL, Kudva IT, Sharma VK.

PLoS One. 2019 Dec 5;14(12):e0226099. doi: 10.1371/journal.pone.0226099. eCollection 2019. Erratum in: PLoS One. 2019 Dec 30;14(12):e0227403.


Investigating the dispersal of antibiotic resistance associated genes from manure application to soil and drainage waters in simulated agricultural farmland systems.

Smith SD, Colgan P, Yang F, Rieke EL, Soupir ML, Moorman TB, Allen HK, Howe A.

PLoS One. 2019 Sep 17;14(9):e0222470. doi: 10.1371/journal.pone.0222470. eCollection 2019.


Shifts in the nasal microbiota of swine in response to different dosing regimens of oxytetracycline administration.

Mou KT, Allen HK, Alt DP, Trachsel J, Hau SJ, Coetzee JF, Holman DB, Kellner S, Loving CL, Brockmeier SL.

Vet Microbiol. 2019 Oct;237:108386. doi: 10.1016/j.vetmic.2019.108386. Epub 2019 Aug 8.


Dietary Resistant Potato Starch Alters Intestinal Microbial Communities and Their Metabolites, and Markers of Immune Regulation and Barrier Function in Swine.

Trachsel J, Briggs C, Gabler NK, Allen HK, Loving CL.

Front Immunol. 2019 Jun 19;10:1381. doi: 10.3389/fimmu.2019.01381. eCollection 2019.


Paenibacillus 79R4, a potential rumen probiotic to enhance nitrite detoxification and methane mitigation in nitrate-treated ruminants.

Latham EA, Pinchak WE, Trachsel J, Allen HK, Callaway TR, Nisbet DJ, Anderson RC.

Sci Total Environ. 2019 Jun 25;671:324-328. doi: 10.1016/j.scitotenv.2019.03.390. Epub 2019 Mar 25.


Excessive drinking and drug use during college: Prospective associations with graduate school plans and attendance.

Arria AM, Allen HK, Caldeira KM, Vincent KB, O'Grady KE.

J Am Coll Health. 2020 Feb-Mar;68(2):132-138. doi: 10.1080/07448481.2018.1535494. Epub 2019 Feb 14.


Driving concerns among older adults: Associations with driving skill, behaviors, and experiences.

Allen HK, Beck KH, Zanjani F.

Traffic Inj Prev. 2019;20(1):45-51. doi: 10.1080/15389588.2018.1528358. Epub 2019 Feb 4.


Fecal microbiota changes associated with dehorning and castration stress primarily affects light-weight dairy calves.

Mir RA, Kleinhenz MD, Coetzee JF, Allen HK, Kudva IT.

PLoS One. 2019 Jan 23;14(1):e0210203. doi: 10.1371/journal.pone.0210203. eCollection 2019.


Graduate degree completion: Associations with alcohol and marijuana use before and after enrollment.

Allen HK, Lilly F, Beck KH, Vincent KB, Arria AM.

Addict Behav Rep. 2018 Dec 19;9:100156. doi: 10.1016/j.abrep.2018.100156. eCollection 2019 Jun.


Complete Genome Sequence of Avian Pathogenic Escherichia coli Strain APEC O2-211.

Nielsen DW, Mangiamele P, Ricker N, Barbieri NL, Allen HK, Nolan LK, Logue CM.

Microbiol Resour Announc. 2018 Sep 27;7(12). pii: e01046-18. doi: 10.1128/MRA.01046-18. eCollection 2018 Sep.


Complete Genome Sequence of the Multidrug-Resistant Neonatal Meningitis Escherichia coli Serotype O75:H5:K1 Strain mcjchv-1 (NMEC-O75).

Nielsen DW, Ricker N, Barbieri NL, Wynn JL, Gómez-Duarte OG, Iqbal J, Nolan LK, Allen HK, Logue CM.

Microbiol Resour Announc. 2018 Sep 13;7(10). pii: e01043-18. doi: 10.1128/MRA.01043-18. eCollection 2018 Sep.


Chlortetracycline Enhances Tonsil Colonization and Fecal Shedding of Multidrug-Resistant Salmonella enterica Serovar Typhimurium DT104 without Major Alterations to the Porcine Tonsillar and Intestinal Microbiota.

Holman DB, Bearson BL, Allen HK, Shippy DC, Loving CL, Kerr BJ, Bearson SMD, Brunelle BW.

Appl Environ Microbiol. 2019 Feb 6;85(4). pii: e02354-18. doi: 10.1128/AEM.02354-18. Print 2019 Feb 15.


Immediate effects of a brief intervention to prevent alcohol and medication interactions among older adults.

Zanjani F, Allen HK, Schoenberg N, Martin C, Clayton R.

Health Educ Res. 2018 Aug 1;33(4):261-270. doi: 10.1093/her/cyy021.


Isolation, characterization and strain selection of a Paenibacillus species for use as a probiotic to aid in ruminal methane mitigation, nitrate/nitrite detoxification and food safety.

Latham EA, Pinchak WE, Trachsel J, Allen HK, Callaway TR, Nisbet DJ, Anderson RC.

Bioresour Technol. 2018 Sep;263:358-364. doi: 10.1016/j.biortech.2018.04.116. Epub 2018 Apr 30.


Butyricicoccus porcorum sp. nov., a butyrate-producing bacterium from swine intestinal tract.

Trachsel J, Humphrey S, Allen HK.

Int J Syst Evol Microbiol. 2018 May;68(5):1737-1742. doi: 10.1099/ijsem.0.002738. Epub 2018 Apr 5.


Porcine Response to a Multidrug-Resistant Salmonella enterica serovar I 4,[5],12:i:- Outbreak Isolate.

Shippy DC, Bearson BL, Holman DB, Brunelle BW, Allen HK, Bearson SMD.

Foodborne Pathog Dis. 2018 May;15(5):253-261. doi: 10.1089/fpd.2017.2378. Epub 2018 Feb 7.


Practical implications of erythromycin resistance gene diversity on surveillance and monitoring of resistance.

Choi J, Rieke EL, Moorman TB, Soupir ML, Allen HK, Smith SD, Howe A.

FEMS Microbiol Ecol. 2018 Apr 1;94(4). doi: 10.1093/femsec/fiy006.


Continuity of drunk and drugged driving behaviors four years post-college.

Caldeira KM, Arria AM, Allen HK, Bugbee BA, Vincent KB, O'Grady KE.

Drug Alcohol Depend. 2017 Nov 1;180:332-339. doi: 10.1016/j.drugalcdep.2017.08.032. Epub 2017 Sep 18.


The In-Feed Antibiotic Carbadox Induces Phage Gene Transcription in the Swine Gut Microbiome.

Johnson TA, Looft T, Severin AJ, Bayles DO, Nasko DJ, Wommack KE, Howe A, Allen HK.

mBio. 2017 Aug 8;8(4). pii: e00709-17. doi: 10.1128/mBio.00709-17.


Meta-analysis To Define a Core Microbiota in the Swine Gut.

Holman DB, Brunelle BW, Trachsel J, Allen HK.

mSystems. 2017 May 23;2(3). pii: e00004-17. doi: 10.1128/mSystems.00004-17. eCollection 2017 May-Jun.


Prevalence and incidence of drug use among college students: an 8-year longitudinal analysis.

Arria AM, Caldeira KM, Allen HK, Bugbee BA, Vincent KB, O'Grady KE.

Am J Drug Alcohol Abuse. 2017 Nov;43(6):711-718. doi: 10.1080/00952990.2017.1310219. Epub 2017 Apr 12.


Drug involvement during and after college: Estimates of opportunity and use given opportunity.

Allen HK, Caldeira KM, Bugbee BA, Vincent KB, O'Grady KE, Arria AM.

Drug Alcohol Depend. 2017 May 1;174:150-157. doi: 10.1016/j.drugalcdep.2017.01.025. Epub 2017 Mar 7.


Fermentation products as feed additives mitigate some ill-effects of heat stress in pigs.

Kumar S, Bass BE, Bandrick M, Loving CL, Brockmeier SL, Looft T, Trachsel J, Madson DM, Thomas M, Casey TA, Frank JW, Stanton TB, Allen HK.

J Anim Sci. 2017 Jan;95(1):279-290. doi: 10.2527/jas.2016.0662.


Effect of sole or combined administration of nitrate and 3-nitro-1-propionic acid on fermentation and Salmonella survivability in alfalfa-fed rumen cultures in vitro.

Correa AC, Trachsel J, Allen HK, Corral-Luna A, Gutierrez-Bañuelos H, Ochoa-Garcia PA, Ruiz-Barrera O, Hume ME, Callaway TR, Harvey RB, Beier RC, Anderson RC, Nisbet DJ.

Bioresour Technol. 2017 Apr;229:69-77. doi: 10.1016/j.biortech.2017.01.012. Epub 2017 Jan 12.


Function and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate Transferases and Their Diversity in the Proximal Colon of Swine.

Trachsel J, Bayles DO, Looft T, Levine UY, Allen HK.

Appl Environ Microbiol. 2016 Oct 27;82(22):6788-6798. Print 2016 Nov 15.


Pipeline for amplifying and analyzing amplicons of the V1-V3 region of the 16S rRNA gene.

Allen HK, Bayles DO, Looft T, Trachsel J, Bass BE, Alt DP, Bearson SM, Nicholson T, Casey TA.

BMC Res Notes. 2016 Aug 2;9:380. doi: 10.1186/s13104-016-2172-6.


Drinking Like an Adult? Trajectories of Alcohol Use Patterns Before and After College Graduation.

Arria AM, Caldeira KM, Allen HK, Vincent KB, Bugbee BA, O'Grady KE.

Alcohol Clin Exp Res. 2016 Mar;40(3):583-90. doi: 10.1111/acer.12973. Epub 2016 Feb 19.


A response regulator from a soil metagenome enhances resistance to the β-lactam antibiotic carbenicillin in Escherichia coli.

Allen HK, An R, Handelsman J, Moe LA.

PLoS One. 2015 Mar 17;10(3):e0120094. doi: 10.1371/journal.pone.0120094. eCollection 2015.


Virus ecology and disturbances: impact of environmental disruption on the viruses of microorganisms.

Allen HK, Abedon ST.

Front Microbiol. 2014 Dec 12;5:700. doi: 10.3389/fmicb.2014.00700. eCollection 2014. No abstract available.


Altered egos: antibiotic effects on food animal microbiomes.

Allen HK, Stanton TB.

Annu Rev Microbiol. 2014;68:297-315. doi: 10.1146/annurev-micro-091213-113052. Epub 2014 Jun 16. Review.


Antibiotic resistance gene discovery in food-producing animals.

Allen HK.

Curr Opin Microbiol. 2014 Jun;19:25-29. doi: 10.1016/j.mib.2014.06.001. Epub 2014 Jul 1.


Carbadox has both temporary and lasting effects on the swine gut microbiota.

Looft T, Allen HK, Casey TA, Alt DP, Stanton TB.

Front Microbiol. 2014 Jun 10;5:276. doi: 10.3389/fmicb.2014.00276. eCollection 2014.


Finding alternatives to antibiotics.

Allen HK, Trachsel J, Looft T, Casey TA.

Ann N Y Acad Sci. 2014 Sep;1323:91-100. doi: 10.1111/nyas.12468. Epub 2014 Jun 20. Review.


The agricultural antibiotic carbadox induces phage-mediated gene transfer in Salmonella.

Bearson BL, Allen HK, Brunelle BW, Lee IS, Casjens SR, Stanton TB.

Front Microbiol. 2014 Feb 11;5:52. doi: 10.3389/fmicb.2014.00052. eCollection 2014.


Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations.

Looft T, Allen HK, Cantarel BL, Levine UY, Bayles DO, Alt DP, Henrissat B, Stanton TB.

ISME J. 2014 Aug;8(8):1566-76. doi: 10.1038/ismej.2014.12. Epub 2014 Feb 13.


Estimation of viral richness from shotgun metagenomes using a frequency count approach.

Allen HK, Bunge J, Foster JA, Bayles DO, Stanton TB.

Microbiome. 2013 Feb 4;1(1):5. doi: 10.1186/2049-2618-1-5.


That's disturbing! An exploration of the bacteriophage biology of change.

Allen HK, Abedon ST.

Front Microbiol. 2013 Nov 14;4:295. doi: 10.3389/fmicb.2013.00295. eCollection 2013. No abstract available.


Butyrate-producing bacteria, including mucin degraders, from the swine intestinal tract.

Levine UY, Looft T, Allen HK, Stanton TB.

Appl Environ Microbiol. 2013 Jun;79(12):3879-81. doi: 10.1128/AEM.00589-13. Epub 2013 Apr 12.


Profiling the gastrointestinal microbiota in response to Salmonella: low versus high Salmonella shedding in the natural porcine host.

Bearson SM, Allen HK, Bearson BL, Looft T, Brunelle BW, Kich JD, Tuggle CK, Bayles DO, Alt D, Levine UY, Stanton TB.

Infect Genet Evol. 2013 Jun;16:330-40. doi: 10.1016/j.meegid.2013.03.022. Epub 2013 Mar 25.


Treatment, promotion, commotion: antibiotic alternatives in food-producing animals.

Allen HK, Levine UY, Looft T, Bandrick M, Casey TA.

Trends Microbiol. 2013 Mar;21(3):114-9. doi: 10.1016/j.tim.2012.11.001. Review.


Collateral effects of antibiotics on mammalian gut microbiomes.

Looft T, Allen HK.

Gut Microbes. 2012 Sep-Oct;3(5):463-7. Epub 2012 Jul 24. Review.


Estimating population diversity with CatchAll.

Bunge J, Woodard L, Böhning D, Foster JA, Connolly S, Allen HK.

Bioinformatics. 2012 Apr 1;28(7):1045-7. doi: 10.1093/bioinformatics/bts075. Epub 2012 Feb 13.


In-feed antibiotic effects on the swine intestinal microbiome.

Looft T, Johnson TA, Allen HK, Bayles DO, Alt DP, Stedtfeld RD, Sul WJ, Stedtfeld TM, Chai B, Cole JR, Hashsham SA, Tiedje JM, Stanton TB.

Proc Natl Acad Sci U S A. 2012 Jan 31;109(5):1691-6. doi: 10.1073/pnas.1120238109. Epub 2012 Jan 17.


Antibiotics in feed induce prophages in swine fecal microbiomes.

Allen HK, Looft T, Bayles DO, Humphrey S, Levine UY, Alt D, Stanton TB.

mBio. 2011 Nov 29;2(6). pii: e00260-11. doi: 10.1128/mBio.00260-11. Print 2011.


Summer workshop in metagenomics: one week plus eight students equals gigabases of cloned DNA.

Rios-Velazquez C, Williamson LL, Cloud-Hansen KA, Allen HK, McMahon MD, Sabree ZL, Donato JJ, Handelsman J.

J Microbiol Biol Educ. 2011 Dec 1;12(2):120-6. doi: 10.1128/jmbe.v12i2.177. Print 2011.

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