Vaccine and Infectious Disease Division

2012 VIDD Publications

1. Abu-Raddad LJ, Barnabas RV, Janes H, Weiss HA, Kublin JG, Longini IM, et al. Have the explosive HIV epidemics in sub-Saharan Africa been driven by higher community viral load? AIDS (London, England). 2012.

2. Achenbach CJ, Harrington RD, Dhanireddy S, Crane HM, Casper C, Kitahata MM. Paradoxical Immune Reconstitution Inflammatory Syndrome in HIV-Infected Patients Treated With Combination Antiretroviral Therapy After AIDS-Defining Opportunistic Infection. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2012;54(3):424-33.

3. Achenbach CJ, Harrington RD, Dhanireddy S, Crane HM, Casper C, Kitahata MM. Reply to letang et Al. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2012;55(1):158-9.

4. Aizire J, Fowler MG, Wang J, Shetty AK, Stranix-Chibanda L, Kamateeka M, et al. Extended prophylaxis with nevirapine and cotrimoxazole among HIV-exposed uninfected infants is well tolerated. AIDS (London, England). 2012;26(3):325-33.

5. Andersen-Nissen E, Heit A, McElrath MJ. Profiling immunity to HIV vaccines with systems biology. Current opinion in HIV and AIDS. 2012;7(1):32-7.

6. Baden LR, Bensinger WI, Angarone M, Casper C, Dubberke ER, Freifeld AG, et al. Prevention and treatment of cancer-related infections. J Natl Compr Canc Netw. 2012;10(11):1412-45.

7. Baeten JM, Donnell D, Ndase P, Mugo NR, Campbell JD, Wangisi J, et al. Antiretroviral prophylaxis for HIV prevention in heterosexual men and women. N Engl J Med. 2012;367(5):399-410.

8. Baeten JM, Reid SE, Delany-Moretlwe S, Hughes JP, Wang RS, Wilcox E, et al. Clinical and virologic response to episodic acyclovir for genital ulcers among HIV-1 seronegative, herpes simplex virus type 2 seropositive African women: a randomized, placebo-controlled trial. Sexually transmitted diseases. 2012;39(1):21-4.

9. Balkus JE, Jaoko W, Mandaliya K, Richardson BA, Masese L, Gitau R, et al. The posttrial effect of oral periodic presumptive treatment for vaginal infections on the incidence of bacterial vaginosis and Lactobacillus colonization. Sexually transmitted diseases. 2012;39(5):361-5.

10. Balkus JE, Mitchell C, Agnew K, Liu C, Fiedler T, Cohn SE, et al. Detection of hydrogen peroxide-producing Lactobacillus species in the vagina: a comparison of culture and quantitative PCR among HIV-1 seropositive women. BMC Infect Dis. 2012;12:188.

11. Bashashati A, Johnson NA, Khodabakhshi AH, Whiteside MD, Zare H, Scott DW, et al. B cells with high side scatter parameter by flow cytometry correlate with inferior survival in diffuse large B-cell lymphoma. Am J Clin Pathol. 2012;137(5):805-14.

12. Belshe RB, Leone PA, Bernstein DI, Wald A, Levin MJ, Stapleton JT, et al. Efficacy results of a trial of a herpes simplex vaccine. N Engl J Med. 2012;366(1):34-43.

13. Benlahrech A, Meiser A, Herath S, Papagatsias T, Athanasopoulos T, Li F, et al. Fragmentation of SIV-gag Vaccine Induces Broader T Cell Responses. PloS one. 2012;7(10):e48038.

14. Blish CA, Dogan OC, Jaoko W, McClelland RS, Mandaliya K, Odem-Davis KS, et al. Cellular immune responses and susceptibility to HIV-1 superinfection: a case-control study. AIDS (London, England). 2012;26(5):643-6.

15. Blish CA, McClelland RS, Richardson BA, Jaoko W, Mandaliya K, Baeten JM, et al. Genital Inflammation Predicts HIV-1 Shedding Independent of Plasma Viral Load and Systemic Inflammation. Journal of acquired immune deficiency syndromes (1999). 2012;61(4):436-40.

16. Boeckh M. Neutropenic diet - good practice or myth? Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation. 2012;18(9):1318-9.

17. Bonsignori M, Pollara J, Moody MA, Alpert MD, Chen X, Hwang K-K, et al. Antibody-Dependent Cellular Cytotoxicity-Mediating Antibodies from an HIV-1 Vaccine Efficacy Trial Target Multiple Epitopes and Preferentially Use the VH1 Gene Family. Journal of virology. 2012;86(21):11521-32.

18. Bosch M, Dhadda M, Hoegh-Petersen M, Liu Y, Hagel LM, Podgorny P, et al. Immune reconstitution after anti-thymocyte globulin-conditioned hematopoietic cell transplantation. Cytotherapy. 2012;14(10):1258-75.

19. Brockman MA, Chopera DR, Olvera A, Brumme CJ, Sela J, Markle TJ, et al. Uncommon Pathways of Immune Escape Attenuate HIV-1 Integrase Replication Capacity. Journal of virology. 2012;86(12):6913-23.

20. Burns JL, Emerson J, Kuypers J, Campbell AP, Gibson RL, McNamara S, et al. Respiratory viruses in children with cystic fibrosis: viral detection and clinical findings. Influenza Other Respi Viruses. 2012;6(3):218-23.

21. Burton DR, Ahmed R, Barouch DH, Butera ST, Crotty S, Godzik A, et al. A Blueprint for HIV Vaccine Discovery. Cell Host Microbe. 2012;12(4):396-407.

22. Caron F, Doucet A, Gottardo R. On-line changepoint detection and parameter estimation with application to genomic data. Statistics and Computing. 2012;22(2):579 - 95.

23. Chao DL, Bloom JD, Kochin BF, Antia R, Longini IM. The global spread of drug-resistant influenza. Journal of the Royal Society, Interface / the Royal Society. 2012;9(69):648-56.

24. Chao DL, Halstead SB, Halloran ME, Longini IM. Controlling dengue with vaccines in Thailand. PLoS Negl Trop Dis. 2012;6(10):e1876.

25. Chemaitelly H, Cremin I, Shelton J, Hallett TB, Abu-Raddad LJ. Distinct HIV discordancy patterns by epidemic size in stable sexual partnerships in sub-Saharan Africa. Sexually transmitted infections. 2012;88(1):51-7.

26. Chen WH, Winokur PL, Edwards KM, Jackson LA, Wald A, Walter EB, et al. Phase 2 assessment of the safety and immunogenicity of two inactivated pandemic monovalent H1N1 vaccines in adults as a component of the U.S. pandemic preparedness plan in 2009. Vaccine. 2012;30(28):4240-8.

27. Chen YQ, Masse B, Wang L, Ou S-S, Li X, Donnell D, et al. Statistical considerations for the HPTN 052 Study to evaluate the effectiveness of early versus delayed antiretroviral strategies to prevent the sexual transmission of HIV-1 in serodiscordant couples. Contemp Clin Trials. 2012;33(6):1280-6.

28. Cheng C, Wang L, Gall JGD, Nason M, Schwartz RM, McElrath MJ, et al. Decreased pre-existing Ad5 capsid and Ad35 neutralizing antibodies increase HIV-1 infection risk in the Step trial independent of vaccination. PloS one. 2012;7(4):e33969.

29. Chirenje ZM, Mâsse BR, Maslankowski LA, Ramjee G, Coletti AS, Tembo TN, et al. Utility of colposcopy in a phase 2 portion of a microbicide clinical trial of BufferGel and 0.5% PRO 2000 Gel. J Int AIDS Soc. 2012;15(2):17376.

30. Choi S-M, Xie H, Campbell AP, Kuypers J, Leisenring W, Boudreault AA, et al. Influenza Viral RNA Detection in Blood as a Marker to Predict Disease Severity in Hematopoietic Cell Transplant Recipients. The Journal of infectious diseases. 2012;206(12):1872-7.

31. Chu H, Lofgren ET, Halloran ME, Kuan PF, Hudgens M, Cole SR. Performance of rapid influenza H1N1 diagnostic tests: a meta-analysis. Influenza Other Respi Viruses. 2012;6(2):80-6.

32. Cohen CR, Lingappa JR, Baeten JM, Ngayo MO, Spiegel CA, Hong T, et al. Bacterial Vaginosis Associated with Increased Risk of Female-to-Male HIV-1 Transmission: A Prospective Cohort Analysis among African Couples. PLoS Med. 2012;9(6):e1001251.

33. Cook L, Diem K, Kim W, Scott JD, Jerome KR. Allele-Specific PCR for Determination of IL28B Genotype. J Clin Microbiol. 2012;50(12):4144-6.

34. Coovadia HM, Brown ER, Fowler MG, Chipato T, Moodley D, Manji K, et al. Efficacy and safety of an extended nevirapine regimen in infant children of breastfeeding mothers with HIV-1 infection for prevention of postnatal HIV-1 transmission (HPTN 046): a randomised, double-blind, placebo-controlled trial. Lancet. 2012;379(9812):221-8.

35. Cousins MM, Ou S-S, Wawer MJ, Munshaw S, Swan D, Magaret CA, et al. Comparison of a High-Resolution Melting Assay to Next-Generation Sequencing for Analysis of HIV Diversity. J Clin Microbiol. 2012;50(9):3054-9.

36. Dai JY, Gilbert PB, Mâsse BR. Partially Hidden Markov Model for Time-Varying Principal Stratification in HIV Prevention Trials. Journal of the American Statistical Association. 2012;107(497):52 - 65.

37. Dai JY, Hughes JP. A unified procedure for meta-analytic evaluation of surrogate end points in randomized clinical trials. Biostatistics (Oxford, England). 2012;13(4):609-24.

38. Dai JY, Logsdon BA, Huang Y, Hsu L, Reiner AP, Prentice RL, et al. Simultaneously testing for marginal genetic association and gene-environment interaction. Am J Epidemiol. 2012;176(2):164-73.

39. de Bruyn G, Magaret A, Baeten JM, Lingappa J, Ndase P, Celum C, et al. Mortality in members of HIV-1 serodiscordant couples in Africa and implications for antiretroviral therapy initiation: Results of analyses from a multicenter randomized trial. BMC Infect Dis. 2012;12(1):277.

40. De Rosa SC, Carter DK, McElrath MJ. OMIP-014: Validated multifunctional characterization of antigen-specific human T cells by intracellular cytokine staining. Cytometry A. 2012;81(12):1019-21.

41. Defawe OD, Fong Y, Vasilyeva E, Pickett M, Carter DK, Gabriel E, et al. Optimization and qualification of a multiplex bead array to assess cytokine and chemokine production by vaccine-specific cells. Journal of immunological methods. 2012;382(1-2):117-28.

42. Delaney S, Gardella C, Daruthayan C, Saracino M, Drolette L, Corey L, et al. A prospective cohort study of partner testing for herpes simplex virus and sexual behavior during pregnancy. The Journal of infectious diseases. 2012;206(4):486-94.

43. Delva W, Wilson DP, Abu-Raddad L, Gorgens M, Wilson D, Hallett TB, et al. HIV treatment as prevention: principles of good HIV epidemiology modelling for public health decision-making in all modes of prevention and evaluation. PLoS Med. 2012;9(7):e1001239.

44. Dezzutti CS, Brown ER, Moncla B, Russo J, Cost M, Wang L, et al. Is wetter better? An evaluation of over-the-counter personal lubricants for safety and anti-HIV-1 activity. PloS one. 2012;7(11):e48328.

45. Dezzutti CS, Richardson BA, Marrazzo JM, Tugetman J, Ramjee G, Taha T, et al. Mucosal Escherichia coli Bactericidal Activity and Immune Mediators Are Associated With HIV-1 Seroconversion in Women Participating in the HPTN 035 Trial. The Journal of infectious diseases. 2012;206(12):1931-5.

46. Doehle BP, Chang K, Fleming L, McNevin J, Hladik F, McElrath MJ, et al. Vpu deficient HIV strains stimulate innate immune signaling responses in target cells. Journal of virology. 2012;86(16):8499-506.

47. Doehle BP, Chang K, Rustagi A, McNevin J, McElrath MJ, Gale M. Vpu mediates IRF3 depletion during HIV infection by a lysosomal-dependent mechanism. Journal of virology. 2012.

48. Donaldson MM, Kao S-F, Eslamizar L, Gee C, Koopman G, Lifton M, et al. Optimization and qualification of an 8-color intracellular cytokine staining assay for quantifying T cell responses in rhesus macaques for pre-clinical vaccine studies. Journal of immunological methods. 2012;386(1-2):10-21.

49. Donnell DJ, Hall HI, Gamble T, Beauchamp G, Griffin AB, Torian LV, et al. Use of HIV Case Surveillance System to Design and Evaluate Site-Randomized Interventions in an HIV Prevention Study: HPTN 065. Open AIDS J. 2012;6:122-30.

50. Drake AL, Roxby AC, Kiarie J, Richardson BA, Wald A, John-Stewart G, et al. Infant safety during and after maternal valacyclovir therapy in conjunction with antiretroviral HIV-1 prophylaxis in a randomized clinical trial. PloS one. 2012;7(4):e34635.

51. Drake AL, Roxby AC, Ongecha-Owuor F, Kiarie J, John-Stewart G, Wald A, et al. Valacyclovir Suppressive Therapy Reduces Plasma and Breast Milk HIV-1 RNA Levels During Pregnancy and Postpartum: A Randomized Trial. The Journal of infectious diseases. 2012;205(3):366-75.

52. Duerr A. HIV treatment as protection:  next steps. Current opinion in HIV and AIDS. 2012;7(2):97-8.

53. Duerr A, Altice FL, Harries AD, Sohn AH. Antiretroviral treatment in resource-limited settings 2012. AIDS Res Treat. 2012;2012:346708.

54. Duerr A, Huang Y, Buchbinder S, Coombs RW, Sanchez J, del Rio C, et al. Extended Follow-up Confirms Early Vaccine-Enhanced Risk of HIV Acquisition and Demonstrates Waning Effect Over Time Among Participants in a Randomized Trial of Recombinant Adenovirus HIV Vaccine (Step Study). The Journal of infectious diseases. 2012;206(2):258-66.

55. Edelstein ZR, Schwartz SM, Hawes S, Hughes JP, Feng Q, Stern ME, et al. Rates and determinants of oral human papillomavirus infection in young men. Sexually transmitted diseases. 2012;39(11):860-7.

56. Etter P, Landovitz R, Sibeko S, Sobieszczyk ME, Riddler SA, Karg C, et al. Recommendations for the follow-up of study participants with breakthrough HIV infections during HIV/AIDS biomedical prevention studies. AIDS (London, England). 2012.

57. Finak G, Jiang W, Pardo J, Asare A, Gottardo R. QUAliFiER: An automated pipeline for quality assessment of gated flow cytometry data. BMC Bioinformatics. 2012;13(1):252.

58. Finton KA, Strong RK. Structural insights into activation of antiviral NK cell responses. Immunol Rev. 2012;250(1):239-57.

59. Fogel JM, Mwatha A, Richardson P, Brown ER, Chipato T, Alexandre M, et al. Impact of Maternal and Infant Antiretroviral Drug Regimens on Drug Resistance in HIV-Infected Breastfeeding Infants. The Pediatric infectious disease journal. 2012.

60. Fong Y, Wakefield J, De Rosa S, Frahm N. A Robust Bayesian Random Effects Model for Nonlinear Calibration Problems. Biometrics. 2012;68(4):1103-12.

61. Frahm N, Decamp AC, Friedrich DP, Carter DK, Defawe OD, Kublin JG, et al. Human adenovirus-specific T cells modulate HIV-specific T cell responses to an Ad5-vectored HIV-1 vaccine. The Journal of clinical investigation. 2012;122(1):359-67.

62. Fukazawa Y, Park H, Cameron MJ, Lefebvre F, Lum R, Coombes N, et al. Lymph node T cell responses predict the efficacy of live attenuated SIV vaccines. Nat Med. 2012;18(11):1673-81.

63. Gilbert PB, Grove D, Gabriel E, Huang Y, Gray G, Hammer SM, et al. A Sequential Phase 2b Trial Design for Evaluating Vaccine Efficacy and Immune Correlates for Multiple HIV Vaccine Regimens. Statistical Communications in Infectious Diseases. 2012;3(1).

64. Gilbert PB, Rossini AJ, Shankarappa R. Response to Reader Reaction to "Two-Sample Tests for Comparing Intra-Individual Genetic Sequence Diversity Between Populations". Biometrics. 2012;68(4):1326.

65. Goo L, Jalalian-Lechak Z, Richardson BA, Overbaugh J. A Combination of Broadly Neutralizing HIV-1 Monoclonal Antibodies Targeting Distinct Epitopes Effectively Neutralizes Variants Found in Early Infection. Journal of virology. 2012;86(19):10857-61.

66. Gopal S, Wood WA, Lee SJ, Shea TC, Naresh KN, Kazembe PN, et al. Meeting the challenge of hematologic malignancies in sub-Saharan Africa. Blood. 2012;119(22):5078-87.

67. Gorse GJ, Newman MJ, DeCamp A, Hay CM, De Rosa SC, Noonan E, et al. DNA and modified vaccinia virus Ankara vaccines encoding multiple cytotoxic and helper T-lymphocyte epitopes of human immunodeficiency virus type 1 (HIV-1) are safe but weakly immunogenic in HIV-1-uninfected, vaccinia virus-naive adults. Clin Vaccine Immunol. 2012;19(5):649-58.

68. Green ML, Leisenring W, Stachel D, Pergam SA, Sandmaier BM, Wald A, et al. Efficacy of a Viral Load-Based, Risk-Adapted, Preemptive Treatment Strategy for Prevention of Cytomegalovirus Disease after Hematopoietic Cell Transplantation. Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation. 2012;18(11):1687-99.

69. Gründer C, van Dorp S, Hol S, Drent E, Straetemans T, Heijhuurs S, et al. γ9 and δ2CDR3 domains regulate functional avidity of T cells harboring γ9δ2TCRs. Blood. 2012;120(26):5153-62.

70. Guerrero A, Riddell SR, Storek J, Stevens-Ayers T, Storer BE, Zaia JA, et al. Cytomegalovirus Viral Load and Virus-Specific Immune Reconstitution after Peripheral Blood Stem Cell versus Bone Marrow Transplantation. Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation. 2012;18(1):66-75.

71. Guthrie BL, Lohman-Payne B, Liu AY, Bosire R, Nuvor SV, Choi RY, et al. HIV-1-Specific Enzyme-Linked Immunosorbent Spot Assay Responses in HIV-1-Exposed Uninfected Partners in Discordant Relationships Compared to Those in Low-Risk Controls. Clin Vaccine Immunol. 2012;19(11):1798-805.

72. Halloran ME, Hudgens MG. Comparing bounds for vaccine effects on infectiousness. Epidemiology. 2012;23(6):931-2.

73. Halloran ME, Hudgens MG. Causal Inference for Vaccine Effects on Infectiousness. 2012;8(2):Article 6.

74. Haynes BF, Gilbert PB, McElrath MJ, Zolla-Pazner S, Tomaras GD, Alam SM, et al. Immune-correlates analysis of an HIV-1 vaccine efficacy trial. N Engl J Med. 2012;366(14):1275-86.

75. Heffron R, Donnell D, Rees H, Celum C, Mugo N, Were E, et al. Use of hormonal contraceptives and risk of HIV-1 transmission: a prospective cohort study. The Lancet infectious diseases. 2012;12(1):19-26.

76. Hensley TR, Easter AB, Gerdts SE, De Rosa SC, Heit A, McElrath MJ, et al. Enumeration of major peripheral blood leukocyte populations for multicenter clinical trials using a whole blood phenotyping assay. J Vis Exp. 2012 (67):e4302.

77. Huang Y, Gilbert PB, Janes H. Assessing Treatment-Selection Markers using a Potential Outcomes Framework. Biometrics. 2012;68(3):687-96.

78. Huang Y, Gottardo R. Comparability and reproducibility of biomedical data. Brief Bioinformatics. 2012.

79. Huang Y, Huang Y, Moodie Z, Li S, Self S. Comparing and combining data across multiple sources via integration of paired-sample data to correct for measurement error. Statistics in medicine. 2012;31(28):3748-59.

80. Hughes JP, Baeten JM, Lingappa JR, Magaret AS, Wald A, de Bruyn G, et al. Determinants of Per-Coital-Act HIV-1 Infectivity Among African HIV-1-Serodiscordant Couples. The Journal of infectious diseases. 2012;205(3):358-65.

81. Ishida K, Arnold M, Stupp P, Kizito P, Ichwara J. Exploring the connections between HIV serostatus and individual, household, and community socioeconomic resources: evidence from two population-based surveys in Kenya. Soc Sci Med. 2012;74(2):185-95.

82. Jackson LA, Chen WH, Stapleton JT, Dekker CL, Wald A, Brady RC, et al. Immunogenicity and Safety of Varying Dosages of a Monovalent 2009 H1N1 Influenza Vaccine Given With and Without AS03 Adjuvant System in Healthy Adults and Older Persons. The Journal of infectious diseases. 2012;206(6):811-20.

83. Jacob ST, Banura P, Baeten JM, Moore CC, Meya D, Nakiyingi L, et al. The impact of early monitored management on survival in hospitalized adult Ugandan patients with severe sepsis: A prospective intervention study. Critical care medicine. 2012;40(7):2050-8.

84. James MM, Wang L, Donnell D, Cousins MM, Barlow-Mosha L, Fogel JM, et al. Use of a High Resolution Melting Assay to Analyze HIV Diversity in HIV-infected Ugandan Children. The Pediatric infectious disease journal. 2012;31(11):E222-E8.

85. Janes H, Frahm N, DeCamp A, Rolland M, Gabriel E, Wolfson J, et al. MRKAd5 HIV-1 Gag/Pol/Nef Vaccine-Induced T-Cell Responses Inadequately Predict Distance of Breakthrough HIV-1 Sequences to the Vaccine or Viral Load. PloS one. 2012;7(8):e43396.

86. Jhingran A, Mar KB, Kumasaka DK, Knoblaugh SE, Ngo LY, Segal BH, et al. Tracing conidial fate and measuring host cell antifungal activity using a reporter of microbial viability in the lung. Cell Rep. 2012;2(6):1762-73.

87. Jing L, Haas J, Chong TM, Bruckner JJ, Dann GC, Dong L, et al. Cross-presentation and genome-wide screening reveal candidate T cells antigens for a herpes simplex virus type 1 vaccine. The Journal of clinical investigation. 2012;122(2):654-73.

88. Johnston C, Saracino M, Kuntz S, Magaret AS, Selke S, Huang M-L, et al. Standard-dose and high-dose daily antiviral therapy for short episodes of genital HSV-2 reactivation: three randomised, open-label, cross-over trials. Lancet. 2012;379(9816):641-7.

89. Kagan JM, Rosas SR, Siskind RL, Campbell RD, Gondwe D, Munroe D, et al. Community-researcher partnerships at NIAID HIV/AIDS clinical trials sites: insights for evaluation and enhancement. Prog Community Health Partnersh. 2012;6(3):311-20.

90. Kahle EM, Hughes JP, Lingappa JR, John-Stewart G, Celum C, Nakku-Joloba E, et al. An empiric risk scoring tool for identifying high-risk heterosexual HIV-1 serodiscordant couples for targeted HIV-1 prevention. Journal of acquired immune deficiency syndromes (1999). 2012.

91. Kalams SA, Parker S, Jin X, Elizaga M, Metch B, Wang M, et al. Safety and Immunogenicity of an HIV-1 Gag DNA Vaccine with or without IL-12 and/or IL-15 Plasmid Cytokine Adjuvant in Healthy, HIV-1 Uninfected Adults. PloS one. 2012;7(1):e29231.

92. Karasavvas N, Billings E, Rao M, Williams C, Zolla-Pazner S, Bailer RT, et al. The Thai Phase III HIV Type 1 Vaccine Trial (RV144) Regimen Induces Antibodies That Target Conserved Regions Within the V2 Loop of gp120. AIDS research and human retroviruses. 2012;28(11):1444-57.

93. Kaufman DR, Li F, Cruz AN, Self SG, Barouch DH. Focus and breadth of cellular immune responses elicited by a heterologous insert prime-boost vaccine regimen in rhesus monkeys. Vaccine. 2012;30(3):506-9.

94. Keller MJ, Carpenter CA, Lo Y, Einstein MH, Liu C, Fredricks DN, et al. Phase I randomized safety study of twice daily dosing of acidform vaginal gel: candidate antimicrobial contraceptive. PloS one. 2012;7(10):e46901.

95. Keller MJ, Madan RP, Shust G, Carpenter CA, Torres NM, Cho S, et al. Changes in the Soluble Mucosal Immune Environment during Genital Herpes Outbreaks. Journal of acquired immune deficiency syndromes (1999). 2012;61(2):194-202.

96. Keller MJ, Malone AM, Carpenter CA, Lo Y, Huang M, Corey L, et al. Safety and pharmacokinetics of aciclovir in women following release from a silicone elastomer vaginal ring. The Journal of antimicrobial chemotherapy. 2012;67(8):2005-12.

97. Kharfan-Dabaja MA, Boeckh M, Wilck MB, Langston AA, Chu AH, Wloch MK, et al. A novel therapeutic cytomegalovirus DNA vaccine in allogeneic haemopoietic stem-cell transplantation: a randomised, double-blind, placebo-controlled, phase 2 trial. The Lancet infectious diseases. 2012;12(4):290-9.

98. Kiem H-P, Jerome KR, Deeks SG, McCune JM. Hematopoietic-stem-cell-based gene therapy for HIV disease. Cell Stem Cell. 2012;10(2):137-47.

99. Kim Y-J, Boeckh M, Cook L, Stempel H, Jerome KR, Boucek R, et al. Cytomegalovirus infection and ganciclovir resistance caused by UL97 mutations in pediatric transplant recipients. Transpl Infect Dis. 2012;14(6):611-7.

100. Kinnebrew MA, Buffie CG, Diehl GE, Zenewicz LA, Leiner I, Hohl TM, et al. Interleukin 23 Production by Intestinal CD103(+)CD11b(+) Dendritic Cells in Response to Bacterial Flagellin Enhances Mucosal Innate Immune Defense. Immunity. 2012;36(2):276-87.

101. Kintu K, Andrew P, Musoke P, Richardson P, Asiimwe-Kateera B, Nakyanzi T, et al. Feasibility and Safety of ALVAC-HIV vCP1521 Vaccine in HIV- exposed Infants in Uganda: Results from the First HIV Vaccine Trial in Infants in Africa. Journal of acquired immune deficiency syndromes (1999). 2012.

102. Kublin JG, Morgan CA, Day TA, Gilbert PB, Self SG, McElrath MJ, et al. HIV Vaccine Trials Network: activities and achievements of the first decade and beyond. Clinical investigation. 2012;2(3):245-54.

103. Kurth AE, Mayer K, Beauchamp G, McKinstry L, Farrior J, Buchacz K, et al. Clinician Practices and Attitudes Regarding Early Antiretroviral Therapy in the US. Journal of acquired immune deficiency syndromes (1999). 2012;61(5):e65-9.

104. Kuypers J, Campbell AP, Guthrie KA, Wright NL, Englund JA, Corey L, et al. WU and KI Polyomaviruses in Respiratory Samples from Allogeneic Hematopoietic Cell Transplant Recipients. Emerging Infect Dis. 2012;18(10):1580-8.

105. Laeyendecker O, Brookmeyer R, Mullis CE, Donnell D, Lingappa J, Celum C, et al. Specificity of four laboratory approaches for cross-sectional HIV Incidence determination: analysis of samples from adults with known nonrecent HIV infection from five African countries. AIDS research and human retroviruses. 2012;28(10):1177-83.

106. Laing KJ, Dong L, Sidney J, Sette A, Koelle DM. Immunology in the Clinic Review Series; focus on host responses: T cell responses to herpes simplex viruses. Clin Exp Immunol. 2012;167(1):47-58.

107. Latka MH, Fielding K, Gray GE, Bekker L-G, Nchabeleng M, Mlisana K, et al. Pregnancy incidence and correlates during the HVTN 503 Phambili HIV vaccine trial conducted among South African women. PloS one. 2012;7(4):e31387.

108. Lesokhin A, Hohl TM, Kitano S, Cortez C, Hirschhorn-Cymerman D, Avogadri F, et al. Monocytic CCR2+ Myeloid Derived Suppressor Cells Promote Immune Escape By Limiting Activated CD8 T Cell Infiltration Into The Tumor Microenvironment. Cancer research. 2012;72(4):876-86.

109. Livaudais JC, Hershman DL, Habel L, Kushi L, Gomez SL, Li CI, et al. Racial/ethnic differences in initiation of adjuvant hormonal therapy among women with hormone receptor-positive breast cancer. Breast cancer research and treatment. 2012;131(2):607-17.

110. Lo K, Gottardo R. Flexible mixture modeling via the multivariate t distribution with the Box-Cox transformation: an alternative to the skew-t distribution. Statistics and computing. 2012;22(1):33-52.

111. Logsdon BA, Carty CL, Reiner AP, Dai JY, Kooperberg C. A novel variational Bayes multiple locus Z-statistic for genome-wide association studies with Bayesian model averaging. Bioinformatics (Oxford, England). 2012;28(13):1738-44.

112. Lohman-Payne B, Slyker JA, Moore S, Maleche-Obimbo E, Wamalwa DC, Richardson BA, et al. Breast milk cellular HIV-specific interferon γ responses are associated with protection from peripartum HIV transmission. AIDS (London, England). 2012;26(16):2007-16.

113. Lu Y, Celum C, Wald A, Baeten JM, Cowan F, Delany-Moretlwe S, et al. Acyclovir achieves lower concentration in African HIV-seronegative, HSV-2 seropositive women compared to non-African populations. Antimicrobial agents and chemotherapy. 2012;56(5):2777-9.

114. Mackelprang RD, Baeten JM, Donnell D, Celum C, Farquhar C, de Bruyn G, et al. Quantifying Ongoing HIV-1 Exposure in HIV-1-Serodiscordant Couples to Identify Individuals With Potential Host Resistance to HIV-1. The Journal of infectious diseases. 2012;206(8):1299-308.

115. Madan RP, Carpenter C, Fiedler T, Kalyoussef S, McAndrew TC, Viswanathan S, et al. Altered biomarkers of mucosal immunity and reduced vaginal lactobacillus concentrations in sexually active female adolescents. PloS one. 2012;7(7):e40415.

116. Marrazzo JM, Fiedler TL, Srinivasan S, Thomas KK, Liu C, Ko D, et al. Extravaginal reservoirs of vaginal bacteria as risk factors for incident bacterial vaginosis. The Journal of infectious diseases. 2012;205(10):1580-8.

117. Martin ET, Kuypers J, Wald A, Englund JA. Multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children. Influenza Other Respi Viruses. 2012;6(1):71-7.

118. Martin PJ, Furlong T, Rowley SD, Pergam SA, Lloid M, Schubert MM, et al. Evaluation of Oral Beclomethasone Dipropionate for Prevention of Acute Graft-versus-Host Disease. Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation. 2012;18(6):922-9.

119. Masese L, McClelland RS, Gitau R, Wanje G, Shafi J, Kashonga F, et al. A pilot study of the feasibility of a vaginal washing cessation intervention among Kenyan female sex workers. Sexually transmitted infections. 2012.

120. McClure J, Lovelace ES, Elahi S, Maurice NJ, Wagoner J, Dragavon J, et al. Silibinin inhibits HIV-1 infection by reducing cellular activation and proliferation. PloS one. 2012;7(7):e41832.

121. McElrath MJ, Walker BD. Is an HIV vaccine possible? Journal of acquired immune deficiency syndromes (1999). 2012;60 Suppl 2:S41-3.

122. McGrath CJ, Nduati R, Richardson BA, Kristal AR, Mbori-Ngacha D, Farquhar C, et al. The Prevalence of Stunting Is High in HIV-1-Exposed Uninfected Infants in Kenya. J Nutr. 2012;142(4):757-63.

123. Milano F, Chien JW, Riffkin I, Gutman JA, Newell L, Pergam SA, et al. Stable Long-Term Pulmonary Function After Myeloablative Double Cord Blood Transplant. Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation. 2012;18(2):309-13.

124. Mitchell C, Manhart LE, Thomas K, Fiedler T, Fredricks DN, Marrazzo J. Behavioral Predictors of Colonization with Lactobacillus crispatus or Lactobacillus jensenii after Treatment for Bacterial Vaginosis: A Cohort Study. Infect Dis Obstet Gynecol. 2012;2012:706540.

125. Mitchell CM, Fredricks DN, Winer RL, Koutsky L. Effect of sexual debut on vaginal microbiota in a cohort of young women. Obstet Gynecol. 2012;120(6):1306-13.

126. Montefiori DC, Karnasuta C, Huang Y, Ahmed H, Gilbert P, de Souza MS, et al. Magnitude and Breadth of the Neutralizing Antibody Response in the RV144 and Vax003 HIV-1 Vaccine Efficacy Trials. The Journal of infectious diseases. 2012;206(3):431-41.

127. Moodie Z, Price L, Janetzki S, Britten CM. Response determination criteria for ELISPOT: toward a standard that can be applied across laboratories. Methods Mol Biol. 2012;792:185-96.

128. Moss NJ, Magaret A, Laing KJ, Kask AS, Wang M, Mark KE, et al. Peripheral blood CD4 T-cell and pDC reactivity to HSV-2 and pDC number do not correlate with the clinical or virologic severity of recurrent genital herpes. Journal of virology. 2012;86(18):9952-63.

129. Murnane PM, Hughes JP, Celum C, Lingappa JR, Mugo N, Farquhar C, et al. Using plasma viral load to guide antiretroviral therapy initiation to prevent HIV-1 transmission. PloS one. 2012;7(11):e51192.

130. Ndase P, Celum C, Thomas K, Donnell D, Fife KH, Bukusi E, et al. Outside Sexual Partnerships and Risk of HIV Acquisition for HIV Uninfected Partners in African HIV Serodiscordant Partnerships. Journal of acquired immune deficiency syndromes. 2012;59(1):65-71.

131. O'Connell RJ, Kim JH, Corey L, Michael NL. Human immunodeficiency virus vaccine trials. Cold Spring Harb Perspect Med. 2012;2(12).

132. Pattacini L, Mize GJ, Graham JB, Fluharty TR, Graham TM, Lingnau K, et al. A Novel HIV Vaccine Adjuvanted by IC31 Induces Robust and Persistent Humoral and Cellular Immunity. PloS one. 2012;7(7):e42163.

133. Peng T, Zhu J, Phasouk K, Koelle DM, Wald A, Corey L. An Effector Phenotype of CD8+ T Cells at the Junction Epithelium during Clinical Quiescence of Herpes Simplex Virus 2 Infection. Journal of virology. 2012;86(19):10587-96.

134. Pepin F, Bertos N, Laferriere J, Sadekova S, Souleimanova M, Zhao H, et al. Gene expression profiling of microdissected breast cancer microvasculature identifies distinct tumor vascular subtypes. Breast Cancer Res. 2012;14(4):R120.

135. Pergam SA, Xie H, Sandhu R, Pollack M, Smith J, Stevens-Ayers T, et al. Efficiency and Risk Factors for CMV Transmission in Seronegative Hematopoietic Stem Cell Recipients. Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation. 2012;18(9):1391-400.

136. Pitzer VE, Basta NE. Linking data and models: the importance of statistical analyses to inform models for the transmission dynamics of infections. Epidemiology. 2012;23(4):520-2.

137. Plotkin SA, Gilbert PB. Nomenclature for immune correlates of protection after vaccination. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2012;54(11):1615-7.

138. Potter GE, Handcock MS, Longini IM, Halloran ME. ESTIMATING WITHIN-SCHOOL CONTACT NETWORKS TO UNDERSTAND INFLUENZA TRANSMISSION. The annals of applied statistics. 2012;6(1):1-26.

139. Prlic M, Sacks JA, Bevan MJ. Dissociating markers of senescence and protective ability in memory T cells. PloS one. 2012;7(3):e32576.

140. Qureshi H, Ma Z-M, Huang Y, Hodge G, Thomas MA, Dipasquale J, et al. Low-Dose Penile SIVmac251 Exposure of Rhesus Macaques Infected with Adenovirus Type 5 (Ad5) and Then Immunized with a Replication-Defective Ad5-Based SIV gag/pol/nef Vaccine Recapitulates the Results of the Phase IIb Step Trial of a Similar HIV-1 Vaccine. Journal of virology. 2012;86(4):2239-50.

141. Renaud C, Crowley J, Jerome KR, Kuypers J. Comparison of FilmArray Respiratory Panel and laboratory-developed real-time reverse transcription-polymerase chain reaction assays for respiratory virus detection. Diagn Microbiol Infect Dis. 2012;74(4):379-83.

142. Renaud C, Englund JA. Antiviral therapy of respiratory viruses in haematopoietic stem cell transplant recipients. Antivir Ther (Lond). 2012;17(1 Pt B):175-91.

143. Rerks-Ngarm S, Paris RM, Chunsutthiwat S, Premsri N, Namwat C, Bowonwatanuwong C, et al. Extended Evaluation of the Virologic, Immunologic, and Clinical Course of Volunteers Who Acquired HIV-1 Infection in a Phase III Vaccine Trial of ALVAC-HIV and AIDSVAX B/E. The Journal of infectious diseases. 2012.

144. Rickerts V, Khot PD, Ko DL, Fredricks DN. Enhanced fungal DNA-extraction from formalin-fixed, paraffin-embedded tissue specimens by application of thermal energy. Medical mycology : official publication of the International Society for Human and Animal Mycology. 2012;50(6):667-72.

145. Ritchie AJ, Kuldanek K, Moodie Z, Wang ZM, Fox J, Nsubuga RN, et al. Comparison of Sexual Behavior and HIV Risk between Two HIV-1 Serodiscordant Couple Cohorts: The CHAVI 002 Study. PloS one. 2012;7(5):e37727.

146. Robb ML, Rerks-Ngarm S, Nitayaphan S, Pitisuttithum P, Kaewkungwal J, Kunasol P, et al. Risk behaviour and time as covariates for efficacy of the HIV vaccine regimen ALVAC-HIV (vCP1521) and AIDSVAX B/E: a post-hoc analysis of the Thai phase 3 efficacy trial RV 144. The Lancet infectious diseases. 2012;12(7):531-7.

147. Rolland M, Edlefsen PT, Larsen BB, Tovanabutra S, Sanders-Buell E, Hertz T, et al. Increased HIV-1 vaccine efficacy against viruses with genetic signatures in Env V2. Nature. 2012;490(7420):417-20.

148. Rolland M, Gilbert P. Evaluating immune correlates in HIV type 1 vaccine efficacy trials: what RV144 may provide. AIDS research and human retroviruses. 2012;28(4):400-4.

149. Roxby AC, Drake AL, Ongecha-Owuor F, Kiarie JN, Richardson B, Matemo DN, et al. Effects of Valacyclovir on Markers of Disease Progression in Postpartum Women Co-Infected with HIV-1 and Herpes Simplex Virus-2. PloS one. 2012;7(6):e38622.

150. Rubino I, Coste A, Le Roy D, Roger T, Jaton K, Boeckh M, et al. Species-Specific Recognition of Aspergillus fumigatus by Toll-like Receptor 1 and Toll-like Receptor 6. The Journal of infectious diseases. 2012;205(6):944-54.

151. Saganic L, Carr J, Solorio R, Courogen M, Jaenicke T, Duerr A. Comparing Measures of Late HIV Diagnosis in Washington State. AIDS Res Treat. 2012;2012:182672.

152. Schiffer JT, Aubert M, Weber N, Mintzer E, Stone D, Jerome KR. Targeted DNA mutagenesis for the cure of chronic viral infections. Journal of virology. 2012;86(17):8920-36.

153. Schouten JT, Schiffer JT. Equal HIV-1 decay kinetics in HSV-2-infected and HSV-2-uninfected clinical trial participants treated with antiretroviral therapy. Journal of acquired immune deficiency syndromes (1999). 2012;60(1):68-71.

154. Scott-Boyer MP, Imholte GC, Tayeb A, Labbe A, Deschepper CF, Gottardo R. An Integrated Hierarchical Bayesian Model for Multivariate eQTL Mapping. Stat Appl Genet Mol Biol. 2012;11(4).

155. Seo S, Englund JA, Nguyen JT, Pukrittayakamee S, Lindegardh N, Tarning J, et al. Combination therapy with amantadine, oseltamivir, and ribavirin for influenza A infection: safety and pharmacokinetics. Antivir Ther (Lond). 2012.

156. Shepardson KM, Ngo LY, Aimanianda V, Latge J-P, Barker BM, Blosser SJ, et al. Hypoxia enhances innate immune activation to Aspergillus fumigatus through cell wall modulation. Microbes Infect. 2012.

157. Shlapobersky M, Marshak JO, Dong L, Huang M-L, Wei Q, Chu A, et al. Vaxfectin-adjuvanted plasmid DNA vaccine improves protection and immunogenicity in a murine model of genital herpes infection. J Gen Virol. 2012;93(Pt 6):1305-15.

158. Slyker JA, Rowland-Jones SL, Dong T, Reilly M, Richardson B, Emery VC, et al. Acute cytomegalovirus infection is associated with increased frequencies of activated and apoptotic-vulnerable T cells in HIV-1 infected infants. Journal of virology. 2012;86(20):11373-9.

159. Spellberg B, Ibrahim AS, Chin-Hong PV, Kontoyiannis DP, Morris MI, Perfect JR, et al. The Deferasirox-AmBisome Therapy for Mucormycosis (DEFEAT Mucor) study: a randomized, double-blinded, placebo-controlled trial. The Journal of antimicrobial chemotherapy. 2012;67(3):715-22.

160. Spellberg B, Kontoyiannis DP, Fredricks D, Morris MI, Perfect JR, Chin-Hong PV, et al. Risk factors for mortality in patients with mucormycosis. Medical mycology : official publication of the International Society for Human and Animal Mycology. 2012;50(6):611-8.

161. Stanaway JD, Wald A, Martin ET, Gottlieb SL, Magaret AS. Case-crossover analysis of condom use and herpes simplex virus type 2 acquisition. Sexually transmitted diseases. 2012;39(5):388-93.

162. Stekler JD, Wellman R, Holte S, Maenza J, Stevens CE, Corey L, et al. Are there benefits to starting antiretroviral therapy during primary HIV infection? Conclusions from the Seattle Primary Infection Cohort vary by control group. Int J STD AIDS. 2012;23(3):201-6.

163. Stephenson KE, Hural J, Buchbinder SP, Sinangil F, Barouch DH. Preexisting Adenovirus Seropositivity Is Not Associated With Increased HIV-1 Acquisition in Three HIV-1 Vaccine Efficacy Trials. The Journal of infectious diseases. 2012;205(12):1806-10.

164. Sun Y, Wang HJ, Gilbert PB. Quantile regression for competing risks data with missing cause of failure. Statistica Sinica. 2012;22(2).

165. Thomas PG, Hertz T. Constrained evolution drives limited influenza diversity. BMC Biol. 2012;10:43.

166. Ting LSL, Praestgaard J, Grunenberg N, Yang JC, Leeds JA, Pertel P. A First-in-Human, Randomized, Double-Blind, Placebo-Controlled, Single- and Multiple-Ascending Oral Dose Study To Assess the Safety and Tolerability of LFF571 in Healthy Volunteers. Antimicrobial agents and chemotherapy. 2012;56(11):5946-51.

167. Todd CA, Greene KM, Yu X, Ozaki DA, Gao H, Huang Y, et al. Development and implementation of an international proficiency testing program for a neutralizing antibody assay for HIV-1 in TZM-bl cells. Journal of immunological methods. 2012;375(1-2):57-67.

168. Vallabhaneni S, Li X, Vittinghoff E, Donnell D, Pilcher CD, Buchbinder SP. Seroadaptive Practices: Association with HIV Acquisition among HIV-Negative Men Who Have Sex with Men. PloS one. 2012;7(10):e45718.

169. Van Wagoner NJ, Morrow RA, Lee J, Dixon P, Hook EW. Serologic Screening for Herpes Simplex Virus Type 2 in Persons With Human Immunodeficiency Virus. Am J Med Sci. 2012.

170. Walson J, Singa B, Sangaré L, Naulikha J, Piper B, Richardson B, et al. Empiric deworming to delay HIV disease progression in adults with HIV who are ineligible for initiation of antiretroviral treatment (the HEAT study): a multi-site, randomised trial. The Lancet infectious diseases. 2012;12(12):925-32.

171. Wamalwa D, Benki-Nugent S, Langat A, Tapia K, Ngugi E, Slyker JA, et al. Survival Benefit of Early Infant Antiretroviral Therapy is Compromised when Diagnosis is Delayed. The Pediatric infectious disease journal. 2012;31(7):729-31.

172. Warren EH, Zhang XC, Li S, Fan W, Storer BE, Chien JW, et al. Effect of MHC and non-MHC donor/recipient genetic disparity on the outcome of allogeneic HCT. Blood. 2012;120(14):2796-806.

173. Wecker M, Gilbert P, Russell N, Hural J, Allen M, Pensiero M, et al. Phase I Safety and Immunogenicity Evaluations of an Alphavirus Replicon HIV-1 Subtype C gag Vaccine in Healthy HIV-1-Uninfected Adults. Clin Vaccine Immunol. 2012;19(10):1651-60.

174. Wick WD, Yang OO. Biologically-Directed Modeling Reflects Cytolytic Clearance of SIV-Infected Cells In Vivo in Macaques. PloS one. 2012;7(9):e44778.

175. Wiernik PH, Sun Z, Gundacker H, Dewald G, Slovak ML, Paietta E, et al. Prognostic implications of additional chromosome abnormalities among patients with de novo acute promyelocytic leukemia with t(15;17). Medical oncology (Northwood, London, England). 2012;29(3):2095-101.

176. Winer RL, Hughes JP, Feng Q, Xi L, Lee S-K, O'Reilly SF, et al. Prevalence and risk factors for oncogenic human papillomavirus infections in high-risk mid-adult women. Sexually transmitted diseases. 2012;39(11):848-56.

177. Yang Y, Longini Jr IM, Halloran ME, Obenchain V. A Hybrid EM and Monte Carlo EM Algorithm and Its Application to Analysis of Transmission of Infectious Diseases. Biometrics. 2012;68(4):1238-49.

178. Zak DE, Andersen-Nissen E, Peterson ER, Sato A, Hamilton MK, Borgerding J, et al. Merck Ad5/HIV induces broad innate immune activation that predicts CD8+ T-cell responses but is attenuated by preexisting Ad5 immunity. Proc Natl Acad Sci USA. 2012;109(50):E3503-12.

179. Zerr DM, Boeckh M, Delaney C, Martin PJ, Xie H, Adler AL, et al. HHV-6 Reactivation and Associated Sequelae after Hematopoietic Cell Transplant. Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation. 2012;18(11):1700-8.

180. Zhang X, Robertson G, Woo S, Hoffman BG, Gottardo R. Probabilistic inference for nucleosome positioning with MNase-based or sonicated short-read data. PloS one. 2012;7(2):e32095.

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