***TASK*** the task is to summarize an input biomedical literature in six sentences 
    ***INPUT*** the input is a biomedical literature 
    ***OUTPUT*** the output is the summary of an input biomedical literature in six sentences 
    ***DOCUMENTATION*** 
    ***EXAMPLES*** 
    Input: Objective : A previous cross-sectional study reported that hormonal contraception may be associated with increased infectivity in HIV-1 infected women . We conducted a prospect i ve study to determine if cervical shedding of HIV-1 increased after initiating hormonal contraception . Design : Shedding of HIV-1 DNA ( a marker of HIV-1 infected cells ) and HIV-1 RNA were measured before and after initiating hormonal contraception . Methods : HIV-1 seropositive women were recruited from a Kenyan family planning clinic . At baseline , cervical secretions were collected for HIV-1 DNA and RNA assays in women initiating hormonal contraception ;  follow-up sample s were collected a median of 64 days later . Results : One-hundred and one women chose depot medroxyprogesterone ( Depo ) , 53 chose low-dose oral contraceptives ( OC ) , seven high-dose OC , and 52 progesterone-only OC . At follow-up , there was a significant increase in the prevalence of cervical HIV-1 DNA detection [ from 42 % to 52 % , odds ratio ( OR ) , 1.62 ; 95 % confidence interval ( CI ) , 1.03–2.63 ) for all hormonal contraception combined , and a trend for an increase for each individual type . Although the prevalence of cervical HIV-1 RNA increased slightly ( from 82 % to 86 % ; OR , 1.56 ; 95 % CI , 0.83–3.03 ) , the concentration of cervical HIV-1 RNA did not change significantly overall ( from 2.81 to 2.84 log10 copies/swab ; P = 0.77 ) or for individual contraception types . Conclusions : A modest but significant increase in shedding of HIV-1 DNA but not of HIV-1 RNA was detected after starting hormonal contraception . Our results may have important implication s regarding the infectivity of women using hormonal contraception , and highlight the need for epidemiologic studies of transmission rates from women using and not using hormonal contraception We examined the association between host factors present near the time of human immunodeficiency virus type 1 ( HIV-1 ) acquisition and subsequent virus loads , in a prospect i ve cohort study of women in Mombasa , Kenya . Women were prospect ively followed monthly before HIV-1 infection . One hundred sixty-one commercial sex workers who became infected with HIV-1 were followed for a median of 34 months , and 991 plasma sample s collected > or = 4 months after infection were tested for HIV-1 RNA . The median virus set point at 4 months after infection was 4.46 log10 copies/mL , and the average virus load increase during subsequent follow-up was 0.0094 log10 copies/mL/month . In a multivariate analysis that controlled for sexual behavior , the use of the injectable contraceptive depot medroxyprogesterone acetate ( DMPA ) at the time of HIV-1 infection was associated with a higher virus set point , and the presence of genital ulcer disease ( GUD ) during the early phase of HIV-1 infection was associated with greater change in virus load during follow-up . These findings suggest that , in women , the use of DMPA  and the presence of GUD during the early phase of HIV-1 infection may influence the natural course of infection Background Underst and ing the correlates of HIV shedding is important to inform strategies to reduce HIV infectiousness . We examined correlates of genital HIV-1 RNA in women who were seropositive for both herpes simplex virus (HSV)-2 and HIV-1 and who were enrolled in a r and omised controlled trial of HSV suppressive therapy ( aciclovir 400 mg b.i.d vs. placebo ) in Tanzania . Methodology Sample s , including a cervico-vaginal lavage , were collected and tested for genital HIV-1 and HSV and reproductive tract infections ( RTIs ) at r and omisation and 6 , 12 and 24 months follow-up . Data from all women at r and omisation and women in the placebo arm during follow-up were analysed using generalised estimating equations to determine the correlates of cervico-vaginal HIV-1 RNA detection and load . Principal Findings Cervico-vaginal HIV-1 RNA was detected at 52.0 % of 971 visits among 482 women , and was independently associated with plasma viral load , presence of genital ulcers , pregnancy , bloody cervical or vaginal discharge , abnormal vaginal discharge , cervical ectopy , Neisseria gonorrhoeae , Chlamydia trachomatis , Trichomonas vaginalis , an intermediate bacterial vaginosis score and HSV DNA detection . Similar factors were associated with genital HIV-1 RNA load . Conclusions RTIs were associated with increased presence and quantity of genital HIV-1 RNA in this population . These results highlight the importance of integrating effective RTI treatment into HIV care services BACKGROUND Hormonal contraceptives are used widely but their effects on HIV-1 risk are unclear . We aim ed to assess the association between hormonal contraceptive use and risk of HIV-1 acquisition  by women and HIV-1 transmission from HIV-1-infected women to their male partners . METHODS In this prospect i ve study , we followed up 3790 heterosexual HIV-1-serodiscordant couples participating in two longitudinal studies of HIV-1 incidence in seven African countries . Among  injectable and oral hormonal contraceptive users and non-users , we compared rates of HIV-1 acquisition by women and HIV-1 transmission from women to men . The primary outcome measure was HIV-1 seroconversion . We used Cox proportional hazards regression and marginal structural modelling to assess the effect of contraceptive use on HIV-1 risk . FINDINGS Among 1314 couples in which the HIV-1-seronegative partner was female ( median follow-up 18·0 [ IQR 12·6 - 24·2 ] months ) , rates of HIV-1 acquisition were 6·61 per 100 person-years in women who used hormonal contraception and 3·78 per 100 person-years in those who did not ( adjusted hazard ratio 1·98 , 95 % CI 1·06 - 3·68 , p=0·03 ) . Among 2476 couples in which the HIV-1-seronegative partner was male ( median follow-up 18·7 [ IQR 12·8 - 24·2 ] months ) , rates of HIV-1 transmission from women to men were 2·61 per 100 person-years in couples in which women used hormonal contraception and 1·51 per 100 person-years in couples in which women did not use hormonal contraception ( adjusted hazard ratio 1·97 , 95 % CI 1·12 - 3·45 , p=0·02 ) . Marginal structural model analyses generated much the same results to the Cox proportional hazards regression . INTERPRETATION Women should be counselled about potentially increased risk of HIV-1 acquisition and transmission  with hormonal contraception , especially injectable methods , and about the importance of dual protection with condoms to decrease HIV-1 risk  . Non-hormonal or low-dose hormonal contraceptive methods should be considered for women with or at-risk for HIV-1 . FUNDING US National Institutes of Health and the Bill & Melinda Gates Foundation Genital HIV-1 RNA quantity predicts risk of heterosexual HIV-1 transmission independently of plasma HIV-1 concentration . Elucidating the Insidious Transmission of a Deadly Pathogen The deadly HIV-1 retrovirus that causes AIDS has been a scourge of humanity for nearly 30 years . Although combination therapy with antiretroviral drugs has proved successful , the complex drug regimen and great cost have prevented their widespread use in the developing world where they are most needed . The goal of developing a vaccine that would protect individuals from becoming infected with HIV-1 has remained elusive . Given that 90 % of all HIV infections worldwide are due to sexual transmission , there has been much interest in developing new strategies that could block HIV infection through the genital mucosa . However , the mechanisms underlying mucosal transmission of HIV are still poorly understood . Higher amounts of HIV-1 in genital secretions are thought to reflect a greater chance of sexual transmission , but testing this correlation is a difficult undertaking . Baeten and colleagues have taken on this challenge with their prospect i ve study in Africa of 2521 heterosexual serodiscordant couples ( one partner is HIV-infected and the other partner is not ) . These investigators evaluated the relationship between the quantity of HIV-1 RNA in the genital secretions of the infected partner and the risk of HIV-1 transmission to the uninfected partner in each couple . They tested the amount of HIV-1 RNA in endocervical swabs from 1805 HIV-1–infected women including 46 women known to have transmitted the virus to their male partners . They also tested the amount of HIV-1 RNA  in semen from 716 men , including 32 who had transmitted HIV-1 to their female partners . The authors demonstrate that higher concentrations of HIV-1 RNA in genital secretions are associated with a greater risk of heterosexual transmission of HIV-1 , and that these concentrations provide a new biomarker for predicting the infectiousness of HIV-1–infected individuals . The authors propose that HIV-1 RNA concentrations in genital secretions could also be used as a biomarker to monitor the efficacy of new microbicides and other interventions design ed to block mucosal transmission of the virus . High plasma HIV-1 RNA concentrations are associated with an increased risk of HIV-1 transmission . Although plasma and genital HIV-1 RNA concentrations are correlated , no study has evaluated the relationship between genital HIV-1 RNA and the risk of heterosexual HIV-1 transmission . In a prospect i ve study of 2521 African HIV-1 serodiscordant couples , we assessed genital HIV-1 RNA quantity and HIV-1 transmission risk . HIV-1 transmission linkage was established within the partnership by viral sequence analysis . We tested endocervical sample s from 1805 women , including 46 who transmitted HIV-1 to their partner , and semen sample s from 716 men , including 32 who transmitted HIV-1 to their partner . There was a correlation between genital and plasma HIV-1 RNA concentrations : For endocervical swabs , Spearman ’s rank correlation coefficient ρ was 0.56 , and for semen , ρ was 0.55 . Each 1.0 log10 increase in genital HIV-1 RNA was associated with a 2.20-fold ( for endocervical swabs : 95 % confidence interval , 1.60 to 3.04 ) and a 1.79-fold ( for semen : 95 % confidence interval , 1.30 to 2.47 ) increased risk of HIV-1 transmission . Genital HIV-1 RNA independently predicted HIV-1 transmission risk after adjusting for plasma HIV-1 quantity ( hazard ratio , 1.67 for endocervical swabs and 1.68 for semen ) . Seven female-to-male and four male-to-female HIV-1 transmissions ( incidence < 1 % per year ) occurred from persons with undetectable genital HIV-1 RNA , but in all 11 cases , plasma HIV-1 RNA was detected . Thus , higher genital HIV-1 RNA concentrations are associated with greater risk of heterosexual HIV-1 transmission , and this effect was independent of plasma HIV-1 concentrations . These data suggest that HIV-1 RNA in genital secretions could be used as a marker of HIV-1 sexual transmission risk The past decade has seen the rise of evidence -based medicine , a movement that has focused attention on the importance of using clinical studies for empirical demonstration of the efficacy of medical interventions . Increasingly , physicians are being called on to assess such studies to help them make clinical decisions and underst and the rationale behind recommended practice s. This type of assessment requires an underst and ing of research methods that until recently was not expected of physicians . These research methods include statistical techniques used to assist in drawing conclusions . However , the methods of statistical inference in current use are not evidence -based and thus have contributed to a widespread misperception . The misperception is that absent any consideration of biological plausibility and prior evidence , statistical methods can provide a number that by itself reflects a probability of reaching erroneous conclusions . This belief has damaged the quality of scientific reasoning and discourse , primarily by making it difficult to underst and how the strength of the evidence in a particular study can be related to and combined with the strength of other evidence ( from other laboratory or clinical studies , scientific reasoning , or clinical experience ) . This results in many knowledge cl aims that do not st and the test of time ( 1 , 2 ) . A pair of articles in this issue examines this problem in some depth and proposes a partial solution . In this article , I explore the historical and logical foundations of the dominant school of medical statistics , sometimes referred to as frequentist statistics , which might be described as error-based . I explicate the logical fallacy at the heart of this system and the reason that it maintains such a tenacious hold on the minds of investigators , policymakers , and journal editors . In the second article ( 3 ) , I present an  evidence -based approach  derived from Bayesian statistical methods , an alternative perspective that has been one of the most active areas of biostatistical development during the past 20 years . Bayesian methods have started to make inroads into medical journals ; Annals , for example , has included a section on Bayesian data interpretation in its Information for Authors section since 1 July 1997 . The perspective on Bay 
    Output:
    
CONCLUSION The only direct study on OCPs or injectable contraception and female-to-male HIV transmission suggests increased risk with the use of injectables .