Likelihood inferences with interval-censored data

En l’anàlisi de la supervivència el problema de les dades censurades en un interval es tracta, usualment,via l’estimació per màxima versemblança. Amb l’objectiu d’utilitzar una expressió simplificada de la funció de versemblança, els mètodes estàndards suposen que les condicions que produeixen la censura no afecten el temps de fallada. En aquest article formalitzem les condicions que asseguren la validesa d’aquesta versemblança simplificada. Així, precisem diferents condicions de censura no informativa i definim una condició de suma constant anàloga a la derivada en el context de censura per la dreta. També demostrem que les inferències obtingudes amb la versemblançaa simplificada són correctes quan aquestes condicions són certes. Finalment, tractem la identificabilitat de la funció distribució del temps de fallada a partir de la informació observada i estudiem la possibilitat de contrastar el compliment de la condició de suma constant.

Likelihood-based approaches to modeling demand for medical care

We review recent likelihood-based approaches to modeling demand for medical care. A semi-nonparametric model along the lines of Cameron and Johansson's Poisson polynomial model, but using a negative binomial baseline model, is introduced. We apply these models, as well a semiparametric Poisson, hurdle semiparametric Poisson, and finite mixtures of negative binomial models to six measures of health care usage taken from the Medical Expenditure Panel survey. We conclude that most of the models lead to statistically similar results, both in terms of information criteria and conditional and unconditional prediction. This suggests that applied researchers may not need to be overly concerned with the choice of which of these models they use to analyze data on health care demand.

High-resolution spatial mapping of changes in the neurochemical profile after focal ischemia in mice.

After ischemic stroke, the ischemic damage to brain tissue evolves over time and with an uneven spatial distribution. Early irreversible changes occur in the ischemic core, whereas, in the penumbra, which receives more collateral blood flow, the damage is more mild and delayed. A better characterization of the penumbra, irreversibly damaged and healthy tissues is needed to understand the mechanisms involved in tissue death. MRSI is a powerful tool for this task if the scan time can be decreased whilst maintaining high sensitivity. Therefore, we made improvements to a (1) H MRSI protocol to study middle cerebral artery occlusion in mice. The spatial distribution of changes in the neurochemical profile was investigated, with an effective spatial resolution of 1.4 μL, applying the protocol on a 14.1-T magnet. The acquired maps included the difficult-to-separate glutamate and glutamine resonances and, to our knowledge, the first mapping of metabolites γ-aminobutyric acid and glutathione in vivo, within a metabolite measurement time of 45 min. The maps were in excellent agreement with findings from single-voxel spectroscopy and offer spatial information at a scan time acceptable for most animal models. The metabolites measured differed with respect to the temporal evolution of their concentrations and the localization of these changes. Specifically, lactate and N-acetylaspartate concentration changes largely overlapped with the T(2) -hyperintense region visualized with MRI, whereas changes in cholines and glutathione affected the entire middle cerebral artery territory. Glutamine maps showed elevated levels in the ischemic striatum until 8 h after reperfusion, and until 24 h in cortical tissue, indicating differences in excitotoxic effects and secondary energy failure in these tissue types. Copyright © 2011 John Wiley & Sons, Ltd.

Use of DNA profiles for investigation using a simulated national DNA database: Part I. Partial SGM Plus profiles.

In traditional criminal investigation, uncertainties are often dealt with using a combination of common sense, practical considerations and experience, but rarely with tailored statistical models. For example, in some countries, in order to search for a given profile in the national DNA database, it must have allelic information for six or more of the ten SGM Plus loci for a simple trace. If the profile does not have this amount of information then it cannot be searched in the national DNA database (NDNAD). This requirement (of a result at six or more loci) is not based on a statistical approach, but rather on the feeling that six or more would be sufficient. A statistical approach, however, could be more rigorous and objective and would take into consideration factors such as the probability of adventitious matches relative to the actual database size and/or investigator's requirements in a sensible way. Therefore, this research was undertaken to establish scientific foundations pertaining to the use of partial SGM Plus loci profiles (or similar) for investigation.

Functional sphere profiling reveals the complexity of neuroblastoma tumor-initiating cell model.

Neuroblastoma (NB) is a neural crest-derived childhood tumor characterized by a remarkable phenotypic diversity, ranging from spontaneous regression to fatal metastatic disease. Although the cancer stem cell (CSC) model provides a trail to characterize the cells responsible for tumor onset, the NB tumor-initiating cell (TIC) has not been identified. In this study, the relevance of the CSC model in NB was investigated by taking advantage of typical functional stem cell characteristics. A predictive association was established between self-renewal, as assessed by serial sphere formation, and clinical aggressiveness in primary tumors. Moreover, cell subsets gradually selected during serial sphere culture harbored increased in vivo tumorigenicity, only highlighted in an orthotopic microenvironment. A microarray time course analysis of serial spheres passages from metastatic cells allowed us to specifically "profile" the NB stem cell-like phenotype and to identify CD133, ABC transporter, and WNT and NOTCH genes as spheres markers. On the basis of combined sphere markers expression, at least two distinct tumorigenic cell subpopulations were identified, also shown to preexist in primary NB. However, sphere markers-mediated cell sorting of parental tumor failed to recapitulate the TIC phenotype in the orthotopic model, highlighting the complexity of the CSC model. Our data support the NB stem-like cells as a dynamic and heterogeneous cell population strongly dependent on microenvironmental signals and add novel candidate genes as potential therapeutic targets in the control of high-risk NB.

Cohort profile: Antiretroviral Therapy Cohort Collaboration (ART-CC).

The advent of effective combination antiretroviral therapy (ART) in 1996 resulted in fewer patients experiencing clinical events, so that some prognostic analyses of individual cohort studies of human immunodeficiency virus-infected individuals had low statistical power. Because of this, the Antiretroviral Therapy Cohort Collaboration (ART-CC) of HIV cohort studies in Europe and North America was established in 2000, with the aim of studying the prognosis for clinical events in acquired immune deficiency syndrome (AIDS) and the mortality of adult patients treated for HIV-1 infection. In 2002, the ART-CC collected data on more than 12,000 patients in 13 cohorts who had begun combination ART between 1995 and 2001. Subsequent updates took place in 2004, 2006, 2008, and 2010. The ART-CC data base now includes data on more than 70,000 patients participating in 19 cohorts who began treatment before the end of 2009. Data are collected on patient demographics (e.g. sex, age, assumed transmission group, race/ethnicity, geographical origin), HIV biomarkers (e.g. CD4 cell count, plasma viral load of HIV-1), ART regimen, dates and types of AIDS events, and dates and causes of death. In recent years, additional data on co-infections such as hepatitis C; risk factors such as smoking, alcohol and drug use; non-HIV biomarkers such as haemoglobin and liver enzymes; and adherence to ART have been collected whenever available. The data remain the property of the contributing cohorts, whose representatives manage the ART-CC via the steering committee of the Collaboration. External collaboration is welcomed. Details of contacts are given on the ART-CC website (www.art-cohort-collaboration.org).

Methylation profile of TP53 regulatory pathway and mtDNA alterations in breast cancer patients lacking TP53 mutations.

The present study investigated promoter hypermethylation of TP53 regulatory pathways providing a potential link between epigenetic changes and mitochondrial DNA (mtDNA) alterations in breast cancer patients lacking a TP53 mutation. The possibility of using the cancer-specific alterations in serum samples as a blood-based test was also explored. Triple-matched samples (cancerous tissues, matched adjacent normal tissues and serum samples) from breast cancer patients were screened for TP53 mutations, and the promoter methylation profile of P14(ARF), MDM2, TP53 and PTEN genes was analyzed as well as mtDNA alterations, including D-loop mutations and mtDNA content. In the studied cohort, no mutation was found in TP53 (DNA-binding domain). Comparison of P14(ARF) and PTEN methylation patterns showed significant hypermethylation levels in tumor tissues (P < 0.05 and <0.01, respectively) whereas the TP53 tumor suppressor gene was not hypermethylated (P < 0.511). The proportion of PTEN methylation was significantly higher in serum than in the normal tissues and it has a significant correlation to tumor tissues (P < 0.05). mtDNA analysis revealed 36.36% somatic and 90.91% germline mutations in the D-loop region and also significant mtDNA depletion in tumor tissues (P < 0.01). In addition, the mtDNA content in matched serum was significantly lower than in the normal tissues (P < 0.05). These data can provide an insight into the management of a therapeutic approach based on the reversal of epigenetic silencing of the crucial genes involved in regulatory pathways of the tumor suppressor TP53. Additionally, release of significant aberrant methylated PTEN in matched serum samples might represent a promising biomarker for breast cancer.

Les traces de pneumatiques en sciences forensiques : de l'analyse chimique à l'évaluation de la force probante

This work is focused on the development of a methodology for the use of chemical characteristic of tire traces to help answer the following question: "Is the offending tire at the origin of the trace found on the crime scene?". This methodology goes from the trace sampling on the road to statistical analysis of its chemical characteristics. Knowledge about the composition and manufacture of tread tires as well as a review of instrumental techniques used for the analysis of polymeric materials were studied to select, as an ansi vi cal technique for this research, pyrolysis coupled to a gas Chromatograph with a mass spectrometry detector (Py-GC/MS). An analytical method was developed and optimized to obtain the lowest variability between replicates of the same sample. Within-variability of the tread was evaluated regarding width and circumference with several samples taken from twelve tires of different brands and/or models. The variability within each of the treads (within-variability) and between the treads (between-variability) could be quantified. Different statistical methods have shown that within-variability is lower than between-variability, which helped differentiate these tires. Ten tire traces were produced with tires of different brands and/or models by braking tests. These traces have been adequately sampled using sheets of gelatine. Particles of each trace were analysed using the same methodology as for the tires at their origin. The general chemical profile of a trace or of a tire has been characterized by eighty-six compounds. Based on a statistical comparison of the chemical profiles obtained, it has been shown that a tire trace is not differentiable from the tire at its origin but is generally differentiable from tires that are not at its origin. Thereafter, a sample containing sixty tires was analysed to assess the discrimination potential of the developed methodology. The statistical results showed that most of the tires of different brands and models are differentiable. However, tires of the same brand and model with identical characteristics, such as country of manufacture, size and DOT number, are not differentiable. A model, based on a likelihood ratio approach, was chosen to evaluate the results of the comparisons between the chemical profiles of the traces and tires. The methodology developed was finally blindly tested using three simulated scenarios. Each scenario involved a trace of an unknown tire as well as two tires possibly at its origin. The correct results for the three scenarios were used to validate the developed methodology. The different steps of this work were useful to collect the required information to test and validate the underlying assumption that it is possible to help determine if an offending tire » or is not at the origin of a trace, by means of a statistical comparison of their chemical profile. This aid was formalized by a measure of the probative value of the evidence, which is represented by the chemical profile of the trace of the tire. - Ce travail s'est proposé de développer une méthodologie pour l'exploitation des caractéristiques chimiques des traces de pneumatiques dans le but d'aider à répondre à la question suivante : «Est-ce que le pneumatique incriminé est ou n'est pas à l'origine de la trace relevée sur les lieux ? ». Cette méthodologie s'est intéressée du prélèvement de la trace de pneumatique sur la chaussée à l'exploitation statistique de ses caractéristiques chimiques. L'acquisition de connaissances sur la composition et la fabrication de la bande de roulement des pneumatiques ainsi que la revue de techniques instrumentales utilisées pour l'analyse de matériaux polymériques ont permis de choisir, comme technique analytique pour la présente recherche, la pyrolyse couplée à un chromatographe en phase gazeuse avec un détecteur de spectrométrie de masse (Py-GC/MS). Une méthode analytique a été développée et optimisée afin d'obtenir la plus faible variabilité entre les réplicas d'un même échantillon. L'évaluation de l'intravariabilité de la bande de roulement a été entreprise dans sa largeur et sa circonférence à l'aide de plusieurs prélèvements effectués sur douze pneumatiques de marques et/ou modèles différents. La variabilité au sein de chacune des bandes de roulement (intravariabilité) ainsi qu'entre les bandes de roulement considérées (intervariabilité) a pu être quantifiée. Les différentes méthodes statistiques appliquées ont montré que l'intravariabilité est plus faible que l'intervariabilité, ce qui a permis de différencier ces pneumatiques. Dix traces de pneumatiques ont été produites à l'aide de pneumatiques de marques et/ou modèles différents en effectuant des tests de freinage. Ces traces ont pu être adéquatement prélevées à l'aide de feuilles de gélatine. Des particules de chaque trace ont été analysées selon la même méthodologie que pour les pneumatiques à leur origine. Le profil chimique général d'une trace de pneumatique ou d'un pneumatique a été caractérisé à l'aide de huitante-six composés. Sur la base de la comparaison statistique des profils chimiques obtenus, il a pu être montré qu'une trace de pneumatique n'est pas différenciable du pneumatique à son origine mais est, généralement, différenciable des pneumatiques qui ne sont pas à son origine. Par la suite, un échantillonnage comprenant soixante pneumatiques a été analysé afin d'évaluer le potentiel de discrimination de la méthodologie développée. Les méthodes statistiques appliquées ont mis en évidence que des pneumatiques de marques et modèles différents sont, majoritairement, différenciables entre eux. La méthodologie développée présente ainsi un bon potentiel de discrimination. Toutefois, des pneumatiques de la même marque et du même modèle qui présentent des caractéristiques PTD (i.e. pays de fabrication, taille et numéro DOT) identiques ne sont pas différenciables. Un modèle d'évaluation, basé sur une approche dite du likelihood ratio, a été adopté pour apporter une signification au résultat des comparaisons entre les profils chimiques des traces et des pneumatiques. La méthodologie mise en place a finalement été testée à l'aveugle à l'aide de la simulation de trois scénarios. Chaque scénario impliquait une trace de pneumatique inconnue et deux pneumatiques suspectés d'être à l'origine de cette trace. Les résultats corrects obtenus pour les trois scénarios ont permis de valider la méthodologie développée. Les différentes étapes de ce travail ont permis d'acquérir les informations nécessaires au test et à la validation de l'hypothèse fondamentale selon laquelle il est possible d'aider à déterminer si un pneumatique incriminé est ou n'est pas à l'origine d'une trace, par le biais d'une comparaison statistique de leur profil chimique. Cette aide a été formalisée par une mesure de la force probante de l'indice, qui est représenté par le profil chimique de la trace de pneumatique.

The use of the likelihood ratio for evaluative and investigative purposes in comparative forensic handwriting examination

This paper extends previous research and discussion on the use of multivariate continuous data, which are about to become more prevalent in forensic science. As an illustrative example, attention is drawn here on the area of comparative handwriting examinations. Multivariate continuous data can be obtained in this field by analysing the contour shape of loop characters through Fourier analysis. This methodology, based on existing research in this area, allows one describe in detail the morphology of character contours throughout a set of variables. This paper uses data collected from female and male writers to conduct a comparative analysis of likelihood ratio based evidence assessment procedures in both, evaluative and investigative proceedings. While the use of likelihood ratios in the former situation is now rather well established (typically, in order to discriminate between propositions of authorship of a given individual versus another, unknown individual), focus on the investigative setting still remains rather beyond considerations in practice. This paper seeks to highlight that investigative settings, too, can represent an area of application for which the likelihood ratio can offer a logical support. As an example, the inference of gender of the writer of an incriminated handwritten text is forwarded, analysed and discussed in this paper. The more general viewpoint according to which likelihood ratio analyses can be helpful for investigative proceedings is supported here through various simulations. These offer a characterisation of the robustness of the proposed likelihood ratio methodology.

Pharmacokinetic profile of tert-butylaminoethanethiol

A preliminary study of the pharmacokinetic parameters of t-Butylaminoethanethiol (TBAESH) was performed after administration of a single dose (35 mg/kg) either orally or intravenously. Plasma or blood samples were treated with dithiothreitol, perchloric acid and, after filtration, submitted to further purification with anionic resin. In the final step the drug was retained on a cationic resin column, eluted with NaCl lM and detected according to the method of Ellman (1958). The results suggested a pharmacokinetic behavior related to a one open compartment model with the following values for the total drug: area under the intravenous curve (AUC i.v.): 443(+ ou -) 24.0; AUC oral: 85.5(+ ou -) 14.5 ug min.ml(elevado a -1); elimination rate constant: 0.069(+ ou -) 0.0055 min(elevado a -1), biological half-life: 10.0(+ ou -) 0.80 min; distribution volume 1.15(+ ou -) 0.15 ml/g; biodisponibility: 0.19(+ ou -) 0.02. From a pharmacokinetic standpoint, TBAESH seems to have no advantage over the analogous disulfide compound.

Profile of a serial killer: cellular and molecular approaches to study individual cytotoxic T-cells following therapeutic vaccination.

T-cell vaccination may prevent or treat cancer and infectious diseases, but further progress is required to increase clinical efficacy. Step-by-step improvements of T-cell vaccination in phase I/II clinical studies combined with very detailed analysis of T-cell responses at the single cell level are the strategy of choice for the identification of the most promising vaccine candidates for testing in subsequent large-scale phase III clinical trials. Major aims are to fully identify the most efficient T-cells in anticancer therapy, to characterize their TCRs, and to pinpoint the mechanisms of T-cell recruitment and function in well-defined clinical situations. Here we discuss novel strategies for the assessment of human T-cell responses, revealing in part unprecedented insight into T-cell biology and novel structural principles that govern TCR-pMHC recognition. Together, the described approaches advance our knowledge of T-cell mediated-protection from human diseases.