Providence/Boston Center for Aids Research (CFAR)

Biostatistics Core

The Biostatistics Core ensures that research uses optimal methods for study design and analysis, develops innovative new approaches; expands HIV research; and ensures researchers have a strong base of knowledge about principles related to study design, data analysis, and interpretation.

The Biostatistics Core ensures that all research undertaken by CFAR investigators uses optimal methods for study design and analysis; to develop innovative new approaches that address existing gaps in methodology; to expand the number of quantitative researchers engaging in HIV research; and to ensure, through collaboration, training and mentoring, that CFAR researchers have a strong base of knowledge about principles related to study design, data analysis, and interpretation.

Guidance and collaboration in developing grant applications

Core faculty collaborate on proposal development, addressing hypothesis formulation, study design, power and sample size calculations and data analyses.  Priority is given to junior faculty and those submitting developmental grants.  With the exception of developmental grants and some awards with limited funding, it is expected that Core faculty and staff effort will be budgeted prospectively in the grant application.

Collaboration on study design, conduct, and statistical analyses

Core faculty work closely with investigators on the following activities

  • Create detailed study design and analysis plans that include clearly defined aims and hypotheses, outcome variables, independent variables, covariates, and statistical methods. Identifying appropriate hypotheses, study design, and analysis plan
  • Apply a range of methods, from standard well-established approaches to advanced innovative methods depending on the setting.
  • Collaborate with investigators in the review the results of all statistical analyses as well as the interpretation and presentation of the findings for abstracts, manuscripts, and presentations.

Statistical training and mentoring

Core faculty provide statistical training and mentoring at multiple levels.  This includes

  • Working closely with junior investigators and providing statistical guidance in the development of new grants, abstracts, manuscripts, and conference presentations
  • Conducting didactic workshops on topics such as study design and data analysis
  • Contributing to capacity building at partner institutions in low- and middle-income countries
  • Mentoring junior faculty in biostatistics and data science fields to promote their career development

Facilitate linkages to potential collaborators

The core will make referrals to other members of the biostatistics, epidemiology or informatics faculty where appropriate, or to relevant resources.

Provide guidance and support for accessing EMR data

In collaboration with the BioBehavioral Sciences Core, the Core will provide guidance and support for accessing and analyzing electronic health records (EHR) data from Brown and BU-affiliated hospitals as well as for statistical issues related to analysis of EHR data.

Facilitate access to HIV databases from other centers/programs

The core can facilitate access to data from well-characterized cohorts with substance use and HIV in Russia and Uganda and HIV/TB co-infected cohorts in Brazil, China and South Africa.  Core members are available to assist investigators in preparing formal data requests and analysis plans in order to access these databases.

Develop novel statistical and epidemiologic methods for HIV research

Core members develop, implement, and disseminate novel statistical and epidemiologic methods for HIV research, typically as needed in the context of specific collaborations.

Due to the high demand placed on the Biostatistics Core during preparation of developmental grants (DG), the CFAR has implemented a process for collaboration and consultation.  The process has two objectives:

  • To ensure that core faculty has sufficient time to learn about the goals of the DG proposal, provide meaningful feedback, and schedule meetings as needed.
  • To ensure that applicants have sufficient opportunity to develop a design and analysis plan that is specific to their proposal and is suitable for meeting project goals

Submit an email request for consultation. 

All requests, whether from Brown or Boston University faculty, should be sent to Corinne Wahlberg.

The request should contain a concept page that includes the following:

  • PI name, title and affiliation
  • Working title of DG proposal
  • Current version of specific aims
  • Clear statement of hypotheses to be tested
  • Detailed description of data available or to be collected
  • Anticipated statistical analysis.  

In addition to the CFAR Clinical Research Database (CCRD), the availability of REDCap (Research Electronic Data Capture) portals are open to all CFAR faculty and trainees.  REDCap is a secure web-based application for building and managing online surveys and databases for research. Using REDCap’s streamlined process for rapidly developing projects, users can create and design projects applying:

  • the online method from your web browser via the Online Designer; and/or
  • the offline method by constructing a “data dictionary” template file in Microsoft Excel, which can be later uploaded into REDCap

Both surveys and databases (or a mixture of the two) can be built using these methods. REDCap provides audit trails for tracking data manipulation and user activity, as well as automated export procedures for seamless data downloads to Excel, PDF, and common statistical packages (SPSS, SAS, Stata and R). Also included are a built-in scheduling module and project calendar, ad hoc reporting tools, and advanced features, such as branching logic, file uploading, and calculated fields.

In addition to access to portals at Lifespan, Boston University and Tufts University, google groups are available and serve as a communication forum for usage questions, troubleshooting and brainstorming.

CFAR researchers within Brown University and Lifespan affiliated hospitals can set-up new accounts and access the Lifespan portal through the Lifespan Biostats Core.  Lifespan REDCap Users Group

CFAR researchers within Boston University and Boston Medical Center can set-up new accounts and access the Boston University portal free-of-charge through the Boston University Clinical & Translational Sciences Institute by completing an on-line request.

CFAR researchers within Tufts University and Tufts Medical Center can set-up new accounts and access the Tufts University portal through the Tufts University Clinical & Translational Sciences Institute.

Drop in sessions are available at the various sites to obtain additional information.

Ayaya S, DeLong A, Embleton L, Ayuku D, Sang E, Hogan JW, Kamanda A, Atwoli L, Makori D, Ott MA, Ombok C, Braitstein P (2021+). Prevalence, incidence and chronicity of child abuse among orphaned, separated and street-connected children and adolescents in western Kenya: What is the impact of care environment? Child Abuse & Neglect, in press. https://doi.org/10.1016/j.chiabu.2020.104920. PMID 33485648

Bhatraju E, Liebschutz JM, Lodi S, Forman LS, Lira MC, Kim TW, Colasanti J, Del Rio C, Samet JH, Tsui JI. Post-traumatic stress disorder and risky opioid use among persons living with HIV and chronic pain. AIDS Care. 2021 Feb 04; 1-8. PMID: 33535800.

Chammartin F, Lodi S, Logan RW, Ryom L, Mocroft A, Kirk O, d’Arminio Monforte A, Reiss P, Phillips A, El-Sadr W, Hatleberg CI, Pradier C, Bonnet F, Law M, De Wit S, Sabin C, Lundgren JL, Bucher HC for the D: A: D Study Group. Risk of non-AIDS defining and AIDS defining malignancies of early versus delayed initiation strategies of antiretroviral therapy: The D: A: D cohort study. 2021. In press. Annals of Internal Medicine. PMID: 33721519

Chavez K, Palfai TP, Cheng DM, Blokhina E, Gnatienko N, Quinn EK, Krupitsky E, Samet JH.Hazardous Alcohol Use, Impulsivity, and HIV-Risk Behavior Among HIV-Positive Russian Patients With a History of Injection Drug Use. Am J Addict. 2020 Dec 30. doi: 10.1111/ajad.13112. Online ahead of print. PMID: 33378082

Chen K, Chrysanthopoulou SA, Galárraga O. Analysis of the impact of cash transfer programs on HIV risk behaviors in Kenya. Journal of Global Health Reports. 2020;4:e2020004. doi:10.29392/001c.12101 PMID: 28403211

Foley JD, Sheinfil A, Woolf-King SE, Fatch R, Emenyonu NI, Muyindike WR, Kekibiina A, Ngabirano C, Samet JH, Cheng DM, Hahn JA. Assessing the interaction between depressive symptoms and alcohol use prior to antiretroviral therapy on viral suppression among people living with HIV in Rural Uganda. AIDS Care. 2020 Oct;32(10):1251-1257. doi: 10.1080/09540121.2020.1770671. Epub 2020 Jun 1. PMID: 32482097

Freiberg MS, Cheng DM, Gnatienko N, Blokhina E, Coleman SM, Doyle MF, Yaroslavtseva T, Bridden C, So-Armah K, Tracy R, Bryant K, Lioznov D, Krupitsky E, Samet JH. Effect of Zinc Supplementation vs Placebo on Mortality Risk and HIV Disease Progression Among HIV-Positive Adults With Heavy Alcohol Use: A Randomized Clinical Trial. JAMA Netw Open. 2020 May 1;3(5):e204330. doi: 10.1001/jamanetworkopen.2020.4330. PMID: 32383748

Ganguly AP, Lira MC, Lodi S, Forman LS, Colasanti JA, Williams EC, Liebschutz JM, del Rio C, Samet JH, Tsui JI. Race and Satisfaction with Pain Management among Patients with HIV Receiving Long-Term Opioid Therapy. 2021 In press. Drug and Alcohol Dependence. 2021 Mar 18;108662. doi: 10.1016/j.drugalcdep.2021.108662. PMID: 33775447

Kimaina, A, Dick, J, DeLong, A, Chrysanthopoulou, SA, Kantor, R, & Hogan, JW. 2020, Comparison of machine learning methods for predicting viral failure: a case study using electronic health record data, Statistical Communications in Infectious Diseases, 12(s1), 20190017. doi: https://doi.org/10.1515/scid-2019-0017

Kimmel SD, Walley AY, Lodi S, Forman LS, Liebschutz JM, Lira MC, Kim TW, del Rio C, Samet JH, Tsui JI. Naloxone receipt and overdose prevention care among people with HIV on chronic opioid therapy AIDS. 2021 Mar 15; 35(4):697-700. PMID: 33587441

KM Byrd, CG Beckwith, JM Garland, JE Johnson, S Aung, S Cu-uvin, D Farmakiotis, T Flanigan, F Gillani, R Macias-Gil, M Mileno, B Ramratnam, N Rybak, M Sanchez, K Tashima, E Mylonakis, R Kantor, Rami; SARS-CoV-2 and HIV Coinfection: Clinical Experience from Rhode Island, United States, Journal of the International AIDS Society (JIAS), 23 (7), e25573, 2020 Jul;23(7):e25573. doi: 10.1002/jia2.25573. PMID: 32657527 PMCID: PMC7357287

Lee K, Tilling K, Cornish R, Little RJA, Bell M, Goetghebeur E, Hogan JW, Carpenter J (2021+). Framework for the treatment and reporting of missing data in observational studies: the TARMOS framework. Journal of Clinical Epidemiology, in press. https://doi.org/10.1016/j.jclinepi.2021.01.008 PMID: 33539930

Liu T, Hogan JW. Unifying instrumental variable and inverse probability weighting approaches for inference of causal treatment effect and unmeasured confounding in observational studies. Stat Methods Med Res. 2020 Nov 19:962280220971835. doi: 10.1177/0962280220971835. Online ahead of print. PMID: 33213292

Lodi S, Freiberg M, Gnatienko N, Blokhina E, Yaroslavtseva T, Krupitsky E, Murray E, Samet JH, Cheng DM. Per-protocol analysis of the ZINC trial for HIV Disease Among Alcohol Users. 2021 Mar 23;22(1):226. doi: 10.1186/s13063-021-05178-9. PMID: 33757560 PMCID: PMC7989012

Margarette Lartey, Ernest Kenu, Anyetei Lassey, Michael Ntumy, Vincent Ganu, Miriam Sam, Isaac Boamah, Fizza Gilani, Hongmei Yang, Gena Burch, Jennifer Norman, Charles Peloquin, Awewura Kwara; Pharmacokinetics of Efavirenz 600 mg Once daily during Pregnancy and Postpartum in Ghanaian Women Living with Human Immunodeficiency Virus, Clin Ther. 2020 Sep;42(9):1818-1825. doi: 10.1016/j.clinthera.2020.07.008. Epub 2020 Aug 15.PMID: 32811669 PMCID: PMC7578077

Merchant RC, Marks SJ, Clark MA, Carey MP, Liu T. Comparison of a video to a pictorial brochure in improving HIV/AIDS and HIV testing knowledge and increasing HIV testing motivation and behavioral skills among adult emergency department patients. J Am Coll Emerg Physicians Open. 2020 Mar 20;1(3):202-213. doi: 10.1002/emp2.12024. eCollection 2020 Jun. PMID: 33000035 PMCID: PMC7493585

Merchant RC, Marks SJ, Clark MA, Carey MP, Liu T. Limited Ability of Three Health Literacy Screening Items to Identify Adult English- and Spanish-Speaking Emergency Department Patients With Lower Health Literacy. Ann Emerg Med. 2020 Jun;75(6):691-703. Doi: 10.1016/j.annemergmed.2020.01.019. Epub 2020 Mar 20. PMID: 32200999

Muyindike WR, Fatch R, Cheng DM, Emenyonu NI, Ngabirano C, Adong J, Linas BP, Jacobson KR, Hahn JA. Tuberculin skin test positivity among HIV-infected alcohol drinkers on antiretrovirals in south-western Uganda. PLoS One. 2020 Jul 2;15(7):e0235261. doi: 10.1371/journal.pone.0235261. eCollection 2020. PMID: 32614873

Noska A, Liu T, Kuo I, Bazerman L, Kantor R, Beckwith C. Validity of self-reported HCV status among justice-involved persons living with HIV.Journal of Correctional Health Care. Forthcoming.

Novitzky V, Steingrimsson J, Howison M, Gillani F, Li Y, Manne A, Fulton J, Spence M, Parillo Z, Marak T, Chan P, Bertrand T, Bandy U, Alexander-Scott N, Dunn C, Hogan JW, Kantor R. Empirical comparison of analytical approaches for identifying molecular HIV-1 clusters. Sci Rep. 2020; 10: 18547. Published online 2020 Oct 29. doi: 10.1038/s41598-020-75560-1 PMCID: PMC7596705 PMID: 33122765

Orang'o EO, Emont JP, Ermel AC, Liu T, Omodi V, Tong Y, Itsura PM, Tonui PK, Maina T, Ong'echa JM, Muthoka K, Kiptoo S, Moormann A, Hogan J, Loehrer PJ, Brown D, Cu-Uvin S. Detection of types of HPV among HIV-infected and HIV-uninfected Kenyan women undergoing cryotherapy or loop electrosurgical excision procedure. Int J Gynaecol Obstet. 2020 Nov;151(2):279-286. doi: 10.1002/ijgo.13330. Epub 2020 Aug 18. PMID: 32715467

Papas RK, Gakinya BN, Mwaniki MM, Lee H, Keter AK, Martino S, Klein DA, Liu T, Loxley MP, Sidle JE, Schlaudt K, Nafula T, Omodi VM, Baliddawa JB, Kinyanjui DW, Maisto SA. A randomized clinical trial of a group cognitive-behavioral therapy to reduce alcohol use among human immunodeficiency virus-infected outpatients in western Kenya. Addiction. 2021 Feb;116(2):305-318. doi: 10.1111/add.15112. Epub 2020 Jul 13. PMID: 32422685

Pastakia SD, Braitstein P, Galarraga O, Genberg B, Said J, Vedanthan R, Wachira J, Hogan JW (2020). Preserving two decades of healthcare gains for Africa in the coronavirus disease 2019 era. AIDS 34, 1761-1763. DOI: 10.1097/QAD.0000000000002605 PMID 32889851

R Kantor, J Fulton, J Steingrimsson, V Novitsky, M Howison, F Gillani, Y Li, A Manne, Z Parillo, M Spence, T Marak, P Chan, CW Dunn, T Bertrand, U Bandy, N Alexander-Scott, JW Hogan. Challenges in Evaluating the Use of Viral Sequence Data to Identify HIV Transmission Networks for Public Health (in press, Statistical Communications in Infectious Diseases).

Samet JH, Tsui JI, Cheng DM, Liebschutz JM, Lira MC, Walley AY, Colasanti JA, Forman LS, Root C, Shanahan CW, Sullivan MM, Bridden CL, Abrams C, Harris C, Outlaw K, Armstrong WS, Del Rio C. Improving the Delivery of Chronic Opioid Therapy among People Living with HIV: A Cluster Randomized Clinical Trial. Clin Infect Dis. 2020 Jul 22:ciaa1025. doi: 10.1093/cid/ciaa1025. Online ahead of print. PMID: 32697847

Serota DP, Capozzi C, Lodi S, Colasanti JA, Forman LS, Tsui JI, Walley AY, Lira MC, Samet J, Del Rio C, Merlin JS. Predictors of pain-related functional impairment among people living with HIV on long-term opioid therapy. AIDS Care. 2020 Apr 03; 1-9. PMID: 32242463.

Sugi Min, Fizza S. Gillani, Su Aung, Joseph M Garland, Curt G Beckwith; Evaluating HIV viral rebound among persons on suppressive antiretroviral treatment in the era of “Undetectable equals Untransmittable (U=U)”; Open Forum Infect Dis. 2020 Dec; 7(12): ofaa529. Published online 2020 Nov 16. doi: 10.1093/ofid/ofaa529 PMCID: PMC7731526 PMID: 33335935

Van Santen DK, Boyd A, Matser A, Maher L, Hickman M, Lodi S, Prins M. The effect of needle and syringe program and opioid agonist therapy on the risk of HIV, hepatitis B and C virus infection for people who inject drugs in Amsterdam, the Netherlands: findings from an emulated target trial. Addiction. 2021 Mar 31. doi: 10.1111/add.15503. Online ahead of print. PMID: 33788326

Vedanthan R, Kamano JH, Chrystanhopoulou SA, *Mugo R, Andama B, Bloomfield GS, Chesoli CW, DeLong AK, Edelman D, Finkelstein EA, Horowitz C, Manyara S, Menya D, Naanyu V, Orango V, Pastakia SD, Valente TW, Hogan JW,Fuster V (2021+). Group medical visits and microfinance for patients with diabetes or hypertension in Kenya: BIGPIC Trial. Journal of the American Association of Cardiology, in press.

Velasco, MC, Chrysanthopoulou, SA and Galárraga, O. Cash Transfers and Contraceptive Use: A Regression Discontinuity Analysis. Stud Fam Plann. 2020 Dec;51(4):309-321. doi: 10.1111/sifp.12142. Epub 2020 Dec 6. https://doi.org/10.1111/sifp.12142 PMID: 33283276 PMCID: PMC8011311

Vetrova MV, Cheng DM, Bendiks S, Gnatienko N, Lloyd-Travaglini C, Jiang W, Luoma J, Blokhina E, Krupitsky E, Lioznov D, Ekstrand ML, Raj A, Samet JH, Lunze K. HIV and Substance Use Stigma, Intersectional Stigma and Healthcare Among HIV-Positive PWID in Russia. AIDS Behav. 2021 Jan 28. doi: 10.1007/s10461-021-03172-5. Online ahead of print. PMID: 33506305

Vlad Novitsky, Jon A. Steingrimsson, Mark Howison, Fizza S. Gillani, Yuanning Li, Akarsh Manne, John Fulton, Matthew Spence, Zoanne Parillo, Theodore Marak, Philip A Chan, Thomas Bertrand, Utpala Bandy, Nicole Alexander-Scott, Casey W. Dunn, Joseph Hogan, Rami Kantor; Empirical Comparison of Analytical Approaches for Identifying Molecular HIV-1 Clusters, Sci Rep. 2020; 10: 18547.

Wentz AE, Wang RRC, Marshall BDL, Shireman TI, Liu T, Merchant RC. Variation in opioid analgesia administration and discharge prescribing for emergency department patients with suspected urolithiasis. Am J Emerg Med. 2020 Oct;38(10):2119-2124. doi: 10.1016/j.ajem.2020.07.016. Epub 2020 Jul 10. PMID: 33071098

Were LPO, Were E, Wamai R, Hogan JW, Galarraga O (2020). Effects of social health insurance on access and utilization of obstetric health services: Results from HIV+ pregnant women in Kenya. BMC Public Health. Int J Environ Res Public Health. 2020 Apr; 17(8): 2892. Published online 2020 Apr 22. doi: 10.3390/ijerph17082892 PMID: 32331351 PMCID: PMC7216063

White LF, Jiang W, Ma Y, So-Armah K, Samet JH, Cheng DM. Tutorial in Biostatistics: The use of generalized additive models to evaluate alcohol consumption as an exposure variable.Drug Alcohol Depend. 2020 Apr 1;209:107944. doi: 10.1016/j.drugalcdep.2020.107944. Epub 2020 Feb 27. PMID: 32145664

Y Sereda, T Kiriazova, O Makarenko, JJ Carroll, N Rybak, A Chybisov, S Bendiks, B Idrisov, A Dutta, F Gillani, J Samet, T Flanigan, K Lunze; Stigma and quality of co-located care for HIV-positive people in addiction treatment in Ukraine: a cross-sectional study; J Int AIDS Soc. 2020 May; 23(5): e25492. Published online 2020 May 6. doi: 10.1002/jia2.25492 PMID: 32372534 PMCID: PMC7201176