Transitional Probability-Based Model for HPV Clearance in HIV-1-Positive Adolescent Females
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{"title"=>"Transitional probability-based model for HPV clearance in HIV-1-positive adolescent females", "type"=>"journal", "authors"=>[{"first_name"=>"Julia", "last_name"=>"Kravchenko", "scopus_author_id"=>"12778591400"}, {"first_name"=>"Igor", "last_name"=>"Akushevich", "scopus_author_id"=>"7003263443"}, {"first_name"=>"Staci L.", "last_name"=>"Sudenga", "scopus_author_id"=>"36549460600"}, {"first_name"=>"Craig M.", "last_name"=>"Wilson", "scopus_author_id"=>"7404896245"}, {"first_name"=>"Emily B.", "last_name"=>"Levitan", "scopus_author_id"=>"8575183200"}, {"first_name"=>"Sadeep", "last_name"=>"Shrestha", "scopus_author_id"=>"12240535900"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "sgr"=>"84856170157", "doi"=>"10.1371/journal.pone.0030736", "scopus"=>"2-s2.0-84856170157", "pui"=>"364141536", "pmid"=>"22292027"}, "id"=>"8c61e603-f8d6-3261-95ad-0f66b0263dcb", "abstract"=>"HIV-1-positive patients clear the human papillomavirus (HPV) infection less frequently than HIV-1-negative. Datasets for estimating HPV clearance probability often have irregular measurements of HPV status and risk factors. A new transitional probability-based model for estimation of probability of HPV clearance was developed to fully incorporate information on HIV-1-related clinical data, such as CD4 counts, HIV-1 viral load (VL), highly active antiretroviral therapy (HAART), and risk factors (measured quarterly), and HPV infection status (measured at 6-month intervals).", "link"=>"http://www.mendeley.com/research/transitional-probabilitybased-model-hpv-clearance-hiv1positive-adolescent-females", "reader_count"=>20, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Researcher"=>5, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>3, "Student > Master"=>5, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Researcher"=>5, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>3, "Student > Master"=>5, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Mathematics"=>1, "Medicine and Dentistry"=>9, "Agricultural and Biological Sciences"=>2, "Chemical Engineering"=>1, "Chemistry"=>1, "Psychology"=>1, "Social Sciences"=>1, "Computer Science"=>1, "Nursing and Health Professions"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>9}, "Chemistry"=>{"Chemistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Psychology"=>{"Psychology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>2}, "Computer Science"=>{"Computer Science"=>1}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>2}, "Chemical Engineering"=>{"Chemical Engineering"=>1}}, "reader_count_by_country"=>{"Spain"=>2}, "group_count"=>4}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/689058"], "description"=>"<p>Note: <sup>†</sup>p<0.05; <sup>‡</sup>p<0.001; ns - not significant; n/a – not applicable.</p>", "links"=>[], "tags"=>["ratios", "hpv", "clearance", "probability", "hiv-1-infected", "females", "univariable", "multivariable", "cox", "proportional", "regression", "presented"], "article_id"=>359532, "categories"=>["Biotechnology", "Infectious Diseases"], "users"=>["Julia Kravchenko", "Igor Akushevich", "Staci L. Sudenga", "Craig M. Wilson", "Emily B. Levitan", "Sadeep Shrestha"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030736.t003", "stats"=>{"downloads"=>7, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hazard_ratios_for_HPV_infection_clearance_probability_for_HIV_1_infected_adolescent_females_from_the_REACH_cohort_univariable_and_multivariable_Cox_proportional_hazard_regression_results_are_presented_with_95_CIs_/359532", "title"=>"Hazard ratios for HPV infection clearance probability for HIV-1-infected adolescent females from the REACH cohort, univariable and multivariable Cox proportional hazard regression (results are presented with 95% CIs).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-01-24 02:38:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/688881"], "description"=>"<p>Note: *The difference with HPV16/16-like type is significant (p<0.05).</p>", "links"=>[], "tags"=>["hpv", "clearance", "cd4", "phylogenetic", "hiv-1-positive"], "article_id"=>359369, "categories"=>["Biotechnology", "Infectious Diseases"], "users"=>["Julia Kravchenko", "Igor Akushevich", "Staci L. Sudenga", "Craig M. Wilson", "Emily B. Levitan", "Sadeep Shrestha"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030736.t005", "stats"=>{"downloads"=>2, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Probability_of_HPV_clearance_in_177_SE_at_specific_CD4_levels_by_phylogenetic_HPV_group_in_HIV_1_positive_adolescent_females_REACH_cohort_/359369", "title"=>"Probability of HPV clearance (in %, ±SE) at specific CD4 levels, by phylogenetic HPV group, in HIV-1-positive adolescent females, REACH cohort.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-01-24 02:36:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/688809"], "description"=>"<p>The 3-month HPV type-specific probability of clearance depending on CD4 T-lymphocytes in HIV-1-positive adolescent girls from the REACH cohort.</p>", "links"=>[], "tags"=>["3-month", "hpv", "type-specific", "probability", "clearance", "cd4", "t-lymphocytes", "hiv-1-positive", "girls"], "article_id"=>359290, "categories"=>["Biotechnology", "Infectious Diseases"], "users"=>["Julia Kravchenko", "Igor Akushevich", "Staci L. Sudenga", "Craig M. Wilson", "Emily B. Levitan", "Sadeep Shrestha"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030736.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_3_month_HPV_type_specific_probability_of_clearance_depending_on_CD4_T_lymphocytes_in_HIV_1_positive_adolescent_girls_from_the_REACH_cohort_/359290", "title"=>"The 3-month HPV type-specific probability of clearance depending on CD4 T-lymphocytes in HIV-1-positive adolescent girls from the REACH cohort.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-01-24 02:34:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/689001"], "description"=>"<p>Notes: <sup>1</sup> – results are presented as mean (SD); <sup>2</sup> – number of cases (percent);</p>†<p>– p<0.05 for the difference between HIV-1-positive and HIV-1-negative: continuous variables were analyzed by general linear model, and categorical were analyzed by chi-square;</p>‡<p>– p<0.05 for the difference with the referent group; continuous variables were analyzed by general linear model, and categorical were analyzed by PROC LOGISTIC.</p>", "links"=>[], "tags"=>["characteristics"], "article_id"=>359496, "categories"=>["Biotechnology", "Infectious Diseases"], "users"=>["Julia Kravchenko", "Igor Akushevich", "Staci L. Sudenga", "Craig M. Wilson", "Emily B. Levitan", "Sadeep Shrestha"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030736.t001", "stats"=>{"downloads"=>1, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Demographic_behavioral_and_clinical_characteristics_of_adolescent_female_study_participants_from_the_REACH_cohort_/359496", "title"=>"Demographic, behavioral, and clinical characteristics of adolescent female study participants from the REACH cohort.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-01-24 02:38:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/350912"], "description"=>"<div><h3>Background</h3><p>HIV-1-positive patients clear the human papillomavirus (HPV) infection less frequently than HIV-1-negative. Datasets for estimating HPV clearance probability often have irregular measurements of HPV status and risk factors. A new transitional probability-based model for estimation of probability of HPV clearance was developed to fully incorporate information on HIV-1-related clinical data, such as CD4 counts, HIV-1 viral load (VL), highly active antiretroviral therapy (HAART), and risk factors (measured quarterly), and HPV infection status (measured at 6-month intervals).</p> <h3>Methodology and Findings</h3><p>Data from 266 HIV-1-positive and 134 at-risk HIV-1-negative adolescent females from the Reaching for Excellence in Adolescent Care and Health (REACH) cohort were used in this study. First, the associations were evaluated using the Cox proportional hazard model, and the variables that demonstrated significant effects on HPV clearance were included in transitional probability models. The new model established the efficacy of CD4 cell counts as a main clearance predictor for all type-specific HPV phylogenetic groups. The 3-month probability of HPV clearance in HIV-1-infected patients significantly increased with increasing CD4 counts for HPV16/16-like (p<0.001), HPV18/18-like (p<0.001), HPV56/56-like (p = 0.05), and low-risk HPV (p<0.001) phylogenetic groups, with the lowest probability found for HPV16/16-like infections (21.60±1.81% at CD4 level 200 cells/mm<sup>3</sup>, p<0.05; and 28.03±1.47% at CD4 level 500 cells/mm<sup>3</sup>). HIV-1 VL was a significant predictor for clearance of low-risk HPV infections (p<0.05). HAART (with protease inhibitor) was significant predictor of probability of HPV16 clearance (p<0.05). HPV16/16-like and HPV18/18-like groups showed heterogeneity (p<0.05) in terms of how CD4 counts, HIV VL, and HAART affected probability of clearance of each HPV infection.</p> <h3>Conclusions</h3><p>This new model predicts the 3-month probability of HPV infection clearance based on CD4 cell counts and other HIV-1-related clinical measurements.</p> </div>", "links"=>[], "tags"=>["transitional", "probability-based", "hpv", "clearance", "hiv-1-positive", "females"], "article_id"=>129365, "categories"=>["Cancer", "Biotechnology"], "users"=>["Julia Kravchenko", "Igor Akushevich", "Staci L. Sudenga", "Craig M. Wilson", "Emily B. Levitan", "Sadeep Shrestha"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030736", "stats"=>{"downloads"=>4, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Transitional_Probability_Based_Model_for_HPV_Clearance_in_HIV_1_Positive_Adolescent_Females/129365", "title"=>"Transitional Probability-Based Model for HPV Clearance in HIV-1-Positive Adolescent Females", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-01-24 02:36:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/688933"], "description"=>"<p>Note:</p><p>*0.05≤p<0.1;</p><p>**p<0.05.<i>u<sub>00</sub></i>, <i>β<sub>00,</sub> u<sub>11,</sub> and β<sub>11</sub></i> are related to the parameters in equation (2)</p>a<p>– the units of <i>β<sub>00</sub></i> and <i>β<sub>11</sub></i> are 1000/[C], where [C] are the units of CD4 cell counts, i.e., cells/mm<sup>3</sup>.</p><p>SEs were obtained by re-estimating the model in which probability at specific value of CD4 cell count was chosen as a model parameter instead of .</p>", "links"=>[], "tags"=>["t-lymphocyte", "counts", "hiv", "vl", "haart", "pi", "probability", "hpv", "phylogenetic", "hiv-1-infected"], "article_id"=>359407, "categories"=>["Biotechnology", "Infectious Diseases"], "users"=>["Julia Kravchenko", "Igor Akushevich", "Staci L. Sudenga", "Craig M. Wilson", "Emily B. Levitan", "Sadeep Shrestha"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030736.t004", "stats"=>{"downloads"=>2, "page_views"=>30, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_CD4_T_lymphocyte_counts_basic_model_M1_HIV_VL_M6_model_and_HAART_with_PI_M7_model_effects_on_probability_of_HPV_clearance_by_phylogenetic_HPV_group_in_HIV_1_infected_adolescent_females_REACH_cohort_/359407", "title"=>"CD4 T-lymphocyte counts (basic model M1), HIV VL (M6 model), and HAART with PI (M7 model) effects on probability of HPV clearance, by phylogenetic HPV group, in HIV-1-infected adolescent females, REACH cohort.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-01-24 02:36:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/688718"], "description"=>"<p>Here, denotes the set of predictors of HPV clearance probability, such as CD4 count, HIV-1 VL, HAART, and HPV type. When one HPV measurement is unknown (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030736#pone-0030736-g001\" target=\"_blank\">Figure 1A</a>), <i>i</i> and <i>j</i> describe the HPV status at the first and third visits, respectively, and parameters and denote the sets of predictors for transitions between first-to-second and second-to-third visits, respectively. The probability of changing HPV status from the first (i.e., known) state of HPV infection <i>i</i> to the status of HPV infection at the second visit (i.e., unknown) is <i>P<sub>i</sub></i><sub>0</sub>(<i>x<sub>a</sub></i>) when HPV status at the second visit is negative (i.e., “0”) or <i>P<sub>i</sub></i><sub>1</sub>(<i>x<sub>a</sub></i>) when it is positive (i.e., “1”). Respectively, at the third visit (with measured/known HPV status) HPV status <i>j</i> can be defined as <i>P</i><sub>0<i>j</i></sub>(<i>x<sub>b</sub></i>) when at the second visit it supposed to be HPV-negative, and <i>P</i><sub>1<i>j</i></sub>(<i>x<sub>b</sub></i>) when at the second visit it supposed to be HPV-positive. The sum over two possible intermediate states contributes to the total transition probability: so, the transition probability between two subsequent visits with measured HPV status could be presented as . When three subsequent HPV status are unknown (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030736#pone-0030736-g001\" target=\"_blank\">Figure 1B</a>), there are eight different combinations of HPV statuses in these states, each denoted by , , and as unmeasured HPV statuses which can be 0 or 1). Therefore, the transition probability between states with known HPV statuses is calculated as three-fold sum over all combinations of HPV statuses in these three unmeasured states.</p>", "links"=>[], "tags"=>["missed", "hpv", "statuses"], "article_id"=>359210, "categories"=>["Biotechnology", "Infectious Diseases"], "users"=>["Julia Kravchenko", "Igor Akushevich", "Staci L. Sudenga", "Craig M. Wilson", "Emily B. Levitan", "Sadeep Shrestha"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030736.g001", "stats"=>{"downloads"=>3, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reconstruction_of_information_about_the_missed_measurements_when_one_HPV_status_is_unknown_Figure_1A_or_several_e_g_three_HPV_statuses_in_a_raw_are_missed_Figure_1B_/359210", "title"=>"Reconstruction of information about the missed measurements when one HPV status is unknown (<b>Figure 1A</b>) or several (e.g., three) HPV statuses in a raw are missed (<b>Figure 1B</b>).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-01-24 02:33:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/688968"], "description"=>"<p>Note: * 0.05≤p<0.1; ** p<0.05. <i>u<sub>00</sub></i>, <i>β<sub>00,</sub> u<sub>11,</sub> and β<sub>11</sub></i> are related to the parameters in equation (2).</p>a<p>– the units of <i>β<sub>00</sub></i> and <i>β<sub>11</sub></i> are 1000/[C], where [C] are the units of CD4 cell counts, i.e., cells/mm<sup>3</sup>.; b – non-significant.</p><p>SEs were obtained by re-estimating the model in which probability at specific value of CD4 cell count was chosen as a model parameter instead of .</p>", "links"=>[], "tags"=>["t-lymphocyte", "counts", "hiv", "vl", "haart", "hpv", "clearance", "hiv-1-positive"], "article_id"=>359447, "categories"=>["Biotechnology", "Infectious Diseases"], "users"=>["Julia Kravchenko", "Igor Akushevich", "Staci L. Sudenga", "Craig M. Wilson", "Emily B. Levitan", "Sadeep Shrestha"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030736.t006", "stats"=>{"downloads"=>5, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_CD4_T_lymphocyte_counts_basic_model_M1_HIV_VL_M6_model_and_HAART_M7_model_effects_on_HPV_clearance_probability_HPV_type_specific_in_HIV_1_positive_adolescent_females_REACH_cohort_/359447", "title"=>"CD4 T-lymphocyte counts (basic model M1), HIV VL (M6 model), and HAART (M7 model) effects on HPV clearance probability, HPV type-specific, in HIV-1-positive adolescent females, REACH cohort.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-01-24 02:37:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/689083"], "description"=>"<p>Notes: results are presented as number of cases (percent);</p>†<p>– p<0.05 for the difference between HIV-1-positive and HIV-1-negative; categorical variables were analyzed by chi-square.</p>", "links"=>[], "tags"=>["prevalent", "hpv"], "article_id"=>359574, "categories"=>["Biotechnology", "Infectious Diseases"], "users"=>["Julia Kravchenko", "Igor Akushevich", "Staci L. Sudenga", "Craig M. Wilson", "Emily B. Levitan", "Sadeep Shrestha"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0030736.t002", "stats"=>{"downloads"=>6, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Incident_and_prevalent_HPV_infection_by_subtype_in_the_REACH_cohort_/359574", "title"=>"Incident and prevalent HPV infection, by subtype, in the REACH cohort.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-01-24 02:39:34"}

PMC Usage Stats | Further Information

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Relative Metric

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