Using graphical probability analysis (Bayes Nets) to evaluate a conditional DNA inclusion

This paper discusses the analysis of cases in which the inclusion or exclusion of a particular suspect, as a possible contributor to a DNA mixture, depends on the value of a variable (the number of contributors) that cannot be determined with certainty. It offers alternative ways to deal with such cases, including sensitivity analysis and object-oriented Bayesian networks, that separate uncertainty about the inclusion of the suspect from uncertainty about other variables. The paper presents a case study in which the value of DNA evidence varies radically depending on the number of contributors to a DNA mixture: if there are two contributors, the suspect is excluded; if there are three or more, the suspect is included; but the number of contributors cannot be determined with certainty. It shows how an object-oriented Bayesian network can accommodate and integrate varying perspectives on the unknown variable and how it can reduce the potential for bias by directing attention to relevant considerations and distinguishing different sources of uncertainty. It also discusses the challenge of presenting such evidence to lay audiences.

Treatment-Naive Individuals Are the Major Source of Transmitted HIV-1 Drug Resistance in Men Who Have Sex With Men in the Swiss HIV Cohort Study.

Background. Human immunodeficiency virus type 1 (HIV-1) transmitted drug resistance (TDR) can compromise antiretroviral therapy (ART) and thus represents an important public health concern. Typically, sources of TDR remain unknown, but they can be characterized with molecular epidemiologic approaches. We used the highly representative Swiss HIV Cohort Study (SHCS) and linked drug resistance database (SHCS-DRDB) to analyze sources of TDR. Methods. ART-naive men who have sex with men with infection date estimates between 1996 and 2009 were chosen for surveillance of TDR in HIV-1 subtype B (N = 1674), as the SHCS-DRDB contains pre-ART genotypic resistance tests for >69% of this surveillance population. A phylogeny was inferred using pol sequences from surveillance patients and all subtype B sequences from the SHCS-DRDB (6934 additional patients). Potential sources of TDR were identified based on phylogenetic clustering, shared resistance mutations, genetic distance, and estimated infection dates. Results. One hundred forty of 1674 (8.4%) surveillance patients carried virus with TDR; 86 of 140 (61.4%) were assigned to clusters. Potential sources of TDR were found for 50 of 86 (58.1%) of these patients. ART-naive patients constitute 56 of 66 (84.8%) potential sources and were significantly overrepresented among sources (odds ratio, 6.43 [95% confidence interval, 3.22-12.82]; P < .001). Particularly large transmission clusters were observed for the L90M mutation, and the spread of L90M continued even after the near cessation of antiretroviral use selecting for that mutation. Three clusters showed evidence of reversion of K103N or T215Y/F. Conclusions. Many individuals harboring viral TDR belonged to transmission clusters with other Swiss patients, indicating substantial domestic transmission of TDR in Switzerland. Most TDR in clusters could be linked to sources, indicating good surveillance of TDR in the SHCS-DRDB. Most TDR sources were ART naive. This, and the presence of long TDR transmission chains, suggests that resistance mutations are frequently transmitted among untreated individuals, highlighting the importance of early diagnosis and treatment.

High prevalence of severe vitamin D deficiency in combined antiretroviral therapy-naive and successfully treated Swiss HIV patients.

OBJECTIVES: To evaluate the prevalence of 25-hydroxyvitamin D [25(OH)D] deficiency in HIV-positive patients, a population at risk for osteoporosis. DESIGN: Retrospective assessment of vitamin D levels by season and initiation of combined antiretroviral therapy (cART). METHODS: 25(OH)D was measured in 211 HIV-positive patients: samples were taken before initiation of cART from February to April or from August to October as well as 12 (same season) and 18 months (alternate season) after starting cART. 1,25-Dihydroxyvitamin D [1,25(OH)2D] was measured in a subset of 74 patients. Multivariable analyses included season, sex, age, ethnicity, BMI, intravenous drug use (IDU), renal function, time since HIV diagnosis, previous AIDS, CD4 cell count and cART, in particular nonnucleoside reverse transcriptase inhibitor (NNRTI) and tenofovir (TDF) use. RESULTS: At baseline, median 25(OH)D levels were 37 (interquartile range 20-49) nmol/l in spring and 57 (39-74) nmol/l in the fall; 25(OH)D deficiency less than 30 nmol/l was more prevalent in spring (42%) than in fall (14%), but remained unchanged regardless of cART exposure. In multivariable analysis, 25(OH)D levels were higher in white patients and those with a longer time since HIV diagnosis and lower in springtime measurements and in those with active IDU and NNRTI use. 1-Hydroxylation rates were significantly higher in patients with low 25(OH)D. Hepatitis C seropositivity, previous AIDS and higher CD4 cell counts correlated with lower 1,25(OH)2D levels, whereas BMI and TDF use were associated with higher levels. In TDF-treated patients, higher 1,25(OH)2D correlated with increases in serum alkaline phosphatase. CONCLUSION: Based on the high rate of vitamin D deficiency in HIV-positive patients, systematic screening with consideration of seasonality is warranted. The impact of NNRTIs on 25(OH)D and TDF on 1,25(OH)2D needs further attention.

Extended treatment of treatment-naive patients with chronic hepatitis c virus (HCV) genotype 1-infection and slow response to pegylated interferon-alfa and ribavirin: a meta-analysis

Aims: Recently, several clinical trials analyzed if extended duration of treatment with pegylated interferon-alfa and ribavirin over 48 weeks can improve sustained virologic response (SVR) rates in HCV genotype 1-infected patients with slow virologic response. Because results of these clinical trials are conflicting, we performed a metaanalysis to determine the overall impact of extended treatment compared to standard treatment on virologic response rates in treatment-naive HCV genotype 1 slow responders. Methods: Literature search was performed independently by two observers using Pub Med, EMBASE, CENTRAL and abstracts presented in English at international liver and gastroenterology meetings. Randomized controlled clinical trials (RCTs; but studies that re-analyzed data retrospectively RCTs were also allowed) were considered if they included monoinfected treatment-naive HCV genotype 1 patients and compared treatment with pegIFN-alfa 2a or 2b in combination with ribavirin for 48 weeks versus extended treatment (up to 72 weeks) in slow responders. Primary and secondary end points were SVR rates and end-of-treatment (EOT) and relapse rates, respectively. In the present meta-analysis, study endpoints were summarized with a DerSimonian-Laird estimate for binary outcome basing on a random effects model. Results: Literature search yielded seven RTCs addressing the benefit of extended treatment with pegylated interferon-alfa and ribavirin in treatment-naive HCV genotype 1 slow responders. In total, 1330 slow responders were included in our meta-analysis. We show that extended treatment duration compared to the standard of care significantly improves SVR rates in HCV genotype 1 slow responders (12.4% improvement of overall SVR rate, 95% CI 0.055- 0.193, P = 0.0005). In addition, we show that rates of viral relapse were significantly reduced by extended treatment (24.1% reduction of relapse, 95% CI −0.3332 to −0.1487, P < 0.0001), whereas no significant impact of extended treatment on EOT response rates was found. Though extended treatment was burdened with an enhanced rate of premature treatment discontinuation due to interferonalfa- and ribavirin-related side effects, the frequency of serious adverse events was not increased. Conclusions: Treatment extension in HCV genotype 1 slow responders can improve SVR rates in difficult to treat patients and should be considered in patients who need to be treated before specific antivirals will be approved.

Bayes factor for investigative assessment of selected handwriting features

This paper extends previous research [1] on the use of multivariate continuous data in comparative handwriting examinations, notably for gender classification. A database has been constructed by analyzing the contour shape of loop characters of type a and d by means of Fourier analysis, which allows characters to be described in a global way by a set of variables (e.g., Fourier descriptors). Sample handwritings were collected from right- and left-handed female and male writers. The results reported in this paper provide further arguments in support of the view that investigative settings in forensic science represent an area of application for which the Bayesian approach offers a logical framework. In particular, the Bayes factor is computed for settings that focus on inference of gender and handedness of the author of an incriminated handwritten text. An emphasis is placed on comparing the efficiency for investigative purposes of characters a and d.

From Empirical Bayes to Full Bayes: Methods for Analysing Traffice Safety Data, October 25, 2004

Traffic safety engineers are among the early adopters of Bayesian statistical tools for analyzing crash data. As in many other areas of application, empirical Bayes methods were their first choice, perhaps because they represent an intuitively appealing, yet relatively easy to implement alternative to purely classical approaches. With the enormous progress in numerical methods made in recent years and with the availability of free, easy to use software that permits implementing a fully Bayesian approach, however, there is now ample justification to progress towards fully Bayesian analyses of crash data. The fully Bayesian approach, in particular as implemented via multi-level hierarchical models, has many advantages over the empirical Bayes approach. In a full Bayesian analysis, prior information and all available data are seamlessly integrated into posterior distributions on which practitioners can base their inferences. All uncertainties are thus accounted for in the analyses and there is no need to pre-process data to obtain Safety Performance Functions and other such prior estimates of the effect of covariates on the outcome of interest. In this slight, fully Bayesian methods may well be less costly to implement and may result in safety estimates with more realistic standard errors. In this manuscript, we present the full Bayesian approach to analyzing traffic safety data and focus on highlighting the differences between the empirical Bayes and the full Bayes approaches. We use an illustrative example to discuss a step-by-step Bayesian analysis of the data and to show some of the types of inferences that are possible within the full Bayesian framework.

From Empirical Bayes to Full Bayes: Methods for Analyzubg Traffic Safey Data, October 25, 2004

Traffic safety engineers are among the early adopters of Bayesian statistical tools for analyzing crash data. As in many other areas of application, empirical Bayes methods were their first choice, perhaps because they represent an intuitively appealing, yet relatively easy to implement alternative to purely classical approaches. With the enormous progress in numerical methods made in recent years and with the availability of free, easy to use software that permits implementing a fully Bayesian approach, however, there is now ample justification to progress towards fully Bayesian analyses of crash data. The fully Bayesian approach, in particular as implemented via multi-level hierarchical models, has many advantages over the empirical Bayes approach. In a full Bayesian analysis, prior information and all available data are seamlessly integrated into posterior distributions on which practitioners can base their inferences. All uncertainties are thus accounted for in the analyses and there is no need to pre-process data to obtain Safety Performance Functions and other such prior estimates of the effect of covariates on the outcome of interest. In this light, fully Bayesian methods may well be less costly to implement and may result in safety estimates with more realistic standard errors. In this manuscript, we present the full Bayesian approach to analyzing traffic safety data and focus on highlighting the differences between the empirical Bayes and the full Bayes approaches. We use an illustrative example to discuss a step-by-step Bayesian analysis of the data and to show some of the types of inferences that are possible within the full Bayesian framework.

Dynamic modulation of CCR7 expression and function on naive T lymphocytes in vivo.

The chemokine receptor CCR7 is critical for the recirculation of naive T cells. It is required for T cell entry into secondary lymphoid organs (SLO) and for T cell motility and retention within these organs. How CCR7 activity is regulated during these processes in vivo is poorly understood. Here we show strong modulation of CCR7 surface expression and occupancy by the two CCR7 ligands, both in vitro and in vivo. In contrast to blood, T cells in SLO had most surface CCR7 occupied with CCL19, presumably leading to continuous signaling and cell motility. Both ligands triggered CCR7 internalization in vivo as shown in Ccl19(-/-) and plt/plt mice. Importantly, CCR7 occupancy and down-regulation led to strongly impaired chemotactic responses, an effect reversible by CCR7 resensitization. Therefore, during their recirculation, T cells cycle between states of free CCR7 with high ligand sensitivity in blood and occupied CCR7 associated with continual signaling and reduced ligand sensitivity within SLO. We propose that these two states of CCR7 are important to allow the various functions CCR7 plays in T cell recirculation.

Antibody-mediated and cellular immune responses induced in naive volunteers by vaccination with long synthetic peptides derived from the Plasmodium vivax circumsporozoite protein.

Plasmodium vivax circumsporozoite (CS) protein is a leading malaria vaccine candidate. We describe the characterization of specific immune responses induced in 21 malaria-naive volunteers vaccinated with long synthetic peptides derived from the CS protein formulated in Montanide ISA 720. Both antibody- and cell-mediated immune responses were analyzed. Antibodies were predominantly of IgG1 and IgG3 isotypes, recognized parasite proteins on the immunofluorescent antibody test, and partially blocked sporozoite invasion of hepatoma cell lines in vitro. Peripheral blood mononuclear cells from most volunteers (94%) showed IFN-γ production in vitro upon stimulation with both long signal peptide and short peptides containing CD8+ T-cell epitopes. The relatively limited sample size did not allow conclusions about HLA associations with the immune responses observed. In summary, the inherent safety and tolerability together with strong antibody responses, invasion blocking activity, and the IFN-γ production induced by these vaccine candidates warrants further testing in a phase II clinical trial.

One naive T cell, multiple fates in CD8+ T cell differentiation.

The mechanism by which the immune system produces effector and memory T cells is largely unclear. To allow a large-scale assessment of the development of single naive T cells into different subsets, we have developed a technology that introduces unique genetic tags (barcodes) into naive T cells. By comparing the barcodes present in antigen-specific effector and memory T cell populations in systemic and local infection models, at different anatomical sites, and for TCR-pMHC interactions of different avidities, we demonstrate that under all conditions tested, individual naive T cells yield both effector and memory CD8+ T cell progeny. This indicates that effector and memory fate decisions are not determined by the nature of the priming antigen-presenting cell or the time of T cell priming. Instead, for both low and high avidity T cells, individual naive T cells have multiple fates and can differentiate into effector and memory T cell subsets.

Role of the naive and memory CD4+T-cell repertoire in transplantation

Purpose: The exact role of individual T cell-subsets in the development of rejection is not clearly defined. Given their distinct phenotypes, effector functions and trafficking patterns, naïve (CD45RBhiCD44lo) and memory (CD45RBloCD44hi) T cells may play distinct roles in anti-donor immunity after transplantation. Furthermore, only the CD4+CD45RBlo population contains CD4+CD25+ T cells, a subset with suppressive functions playing a major role in the maintenance of peripheral tolerance. The aim of this work was to study the contribution of these individual subsets in alloresponses via the direct and indirect pathways using a murine experimental model. Methods and materials: Purified naïve or memory CD4+ T cells were adoptively transferred into lymphopenic mice undergoing a skin allograft. Donor to recipient MHC combinations were chosen in order to study the direct and the indirect pathways of allorecognition separately. Graft survival and in vivo expansion, effector function and trafficking of the transferred T cells was assessed at different time points after transplantation. Results: We found that the cross-reactive CD4+CD45RBlo memory T-cell pool was heterogeneous and contained cells with regulatory potentials, both in the CD4+CD25+ and CD4+CD25-populations. CD4+ T cells capable of inducing strong primary alloreactive responses in vitro and rejection of a first allograft in vivo were mainly contained within the CD45RBhi naïve CD4+ T-cell compartment. CD4+CD45RBlo T cells proliferated less abundantly to allogeneic stimulation than their naïve counterparts both in vitro and in vivo, and allowed prolonged allograft survival even after the depletion of the CD4+CD25+ subset. Interestingly, CD4+CD25-CD45RBlo T cells were capable of prolonging allograft survival, mainly when the indirect pathway was the only mechanism of allorecognition. The indirect pathway response, which was shown to drive true chronic rejection and contribute to chronic allograft dysfunction, was predominantly mediated by naïve CD4+ T cells. Conclusion: This work provides new insights into the mechanisms that drive allograft rejection and should help develop new clinical immunosuppressive protocols. In particular, our results highlight the importance of selectively targeting individual T-cell subsets to prevent graft rejection but at the same time maintain immune protective responses to common pathogens.

Degeneracy of antigen recognition as the molecular basis for the high frequency of naive A2/Melan-a peptide multimer(+) CD8(+) T cells in humans.

In contrast with the low frequency of most single epitope reactive T cells in the preimmune repertoire, up to 1 of 1,000 naive CD8(+) T cells from A2(+) individuals specifically bind fluorescent A2/peptide multimers incorporating the A27L analogue of the immunodominant 26-35 peptide from the melanocyte differentiation and melanoma associated antigen Melan-A. This represents the only naive antigen-specific T cell repertoire accessible to direct analysis in humans up to date. To get insight into the molecular basis for the selection and maintenance of such an abundant repertoire, we analyzed the functional diversity of T cells composing this repertoire ex vivo at the clonal level. Surprisingly, we found a significant proportion of multimer(+) clonotypes that failed to recognize both Melan-A analogue and parental peptides in a functional assay but efficiently recognized peptides from proteins of self- or pathogen origin selected for their potential functional cross-reactivity with Melan-A. Consistent with these data, multimers incorporating some of the most frequently recognized peptides specifically stained a proportion of naive CD8(+) T cells similar to that observed with Melan-A multimers. Altogether these results indicate that the high frequency of Melan-A multimer(+) T cells can be explained by the existence of largely cross-reactive subsets of naive CD8(+) T cells displaying multiple specificities.

Bayes linear spaces

Linear spaces consisting of σ-finite probability measures and infinite measures (improper priors and likelihood functions) are defined. The commutative group operation, called perturbation, is the updating given by Bayes theorem; the inverse operation is the Radon-Nikodym derivative. Bayes spaces of measures are sets of classes of proportional measures. In this framework, basic notions of mathematical statistics get a simple algebraic interpretation. For example, exponential families appear as affine subspaces with their sufficient statistics as a basis. Bayesian statistics, in particular some well-known properties of conjugated priors and likelihood functions, are revisited and slightly extended

IFN-gamma-producing CD45RA+CD8+ and IL-10-producing CD45RA-CD4+ T cells generated in response to LACK in naive subjects never exposed to Leishmania.

Leishmania guyanensis (L.g.)-specific CD8+ T cells can be isolated from PBMC of subjects who have never been previously exposed to Leishmania. Cells that produce IFN-gamma in response to live L.g. are generated from naive CD45RA+CD8+ T cells. The generation of L.g.-specific CD8+ T cells requires the presence of whole L.g. or UV-irradiated parasite but not the soluble antigens from L.g. promastigotes. The IFN-gamma-producing T cells recognize a specific antigen, the Leishmania homologue of receptors of activated C kinases (LACK) and this antigen but not live L.g. can produce a strong IL-10 response in CD45RA-CD4+ memory T cells from naive subjects. A single epitope (amino acid 156-173) is found to induce the IL-10 synthesis. While the IFN-gamma-producing cells are present among CD45RA+CD8+ T cells that are CD62L-CDR7- and CLA-, the LACK-reactive IL-10-producing cells are CD4+ T cells that are CD62L+CCR7- and CLA-.