Mise au point d'un test ELISA pour détecter les anticorps anti-Chlamydia pneumoniae

Lorsque nous avons entrepris de mettre au point un test ELISA basé sur la protéine MOMP pour détecter les anticorps anti-Chlamydia pneumoniae, nous espérions entre autre montrer qu'il s'agissait de la protéine immunodominante de cette bactérie mais qu'on [n']a pas pu l'identifier puisqu'il fallait la dénaturer pour l'isoler. Nous voulions aussi se doter d'un test de diagnostic efficace pour retracer les anticorps anti-C. pneumoniae et ainsi être capable d'identifier un facteur de risque de l'athérosclérose quand l'implication de C. pneumoniae dans le développement de cette maladie serait reconnue officiellement. L'identité de la protéine immunodominante de C. pneumoniae va demeurer encore mystérieuse car même si on a été capable d'exprimer la protéine MOMP dans E. coli grâce aux vecteurs pMAL, il nous a été impossible de la produire dans sa conformation native. Cet échec en a entrainé un autre c'est-à-dire la production d'un test ELISA sensible et efficace pour détecter les anticorps produits suite à une infection à C. pneumoniae et par conséquent de faire une corrélation entre leur présence dans l'organisme et le développement de l'athérosclérose. Cependant on a montré qu'un test ELISA est envisageable à condition d'avoir la protéine MOMP native ou une toute autre protéine de C. pneumoniae facile à produire ou insensible à la dénaturation, puisqu'on à [i.e. a] mis au point un test efficace pour détecter les anticorps dirigés contre la protéine MOMP de C. trachomatis

Specification and Model-driven Trace Checking of Complex Temporal Properties

Offline trace checking is a procedure used to evaluate requirement properties over a trace of recorded events. System properties verified in the context of trace checking can be specified using different specification languages and formalisms; in this thesis, we consider two classes of complex temporal properties: 1) properties defined using aggregation operators; 2) signal-based temporal properties from the Cyber Physical System (CPS) domain. The overall goal of this dissertation is to develop methods and tools for the specification and trace checking of the aforementioned classes of temporal properties, focusing on the development of scalable trace checking procedures for such properties. The main contributions of this thesis are: i) the TEMPSY-CHECK-AG model-driven approach for trace checking of temporal properties with aggregation operators, defined in the TemPsy-AG language; ii) a taxonomy covering the most common types of Signal-based Temporal Properties (SBTPs) in the CPS domain; iii) SB-TemPsy, a trace-checking approach for SBTPs that strikes a good balance in industrial contexts in terms of efficiency of the trace checking procedure and coverage of the most important types of properties in CPS domains. SB-TemPsy includes: 1) SB-TemPsy-DSL, a DSL that allows the specification of the types of SBTPs identified in the aforementioned taxonomy, and 2) an efficient trace-checking procedure, implemented in a prototype tool called SB-TemPsy-Check; iv) TD-SB-TemPsy-Report, a model-driven trace diagnostics approach for SBTPs expressed in SB-TemPsy-DSL. TD-SB-TemPsy-Report relies on a set of diagnostics patterns, i.e., undesired signal behaviors that might lead to property violations. To provide relevant and detailed information about the cause of a property violation, TD-SB-TemPsy-Report determines the diagnostics information specific to each type of diagnostics pattern. Our technological contributions rely on model-driven approaches for trace checking and trace diagnostics. Such approaches consist in reducing the problem of checking (respectively, determining the diagnostics information of) a property over an execution trace to the problem of evaluating an OCL (Object Constraint Language) constraint (semantically equivalent to ) on an instance (equivalent to ) of a meta-model of the trace. The results — in terms of efficiency of our model-driven tools—presented in this thesis are in line with those presented in previous work, and confirm that model-driven technologies can lead to the development of tools that exhibit good performance from a practical standpoint, also when applied in industrial contexts

Formal Specification, Implementation, and Evaluation of the AdoBPRIM Approach

Modeling is one of the fundamental aspects of Risk-aware Business Process Management. The conceptualization of new modeling approaches needs to integrate all abstraction layers of risk and business process concepts and requires a highly specialized knowledge in conceptual modeling foundations and formal specification of meta-models. This paper introduces a risk-aware business process modeling approach based on the BPRIM method. In order to comprehensively and unambiguously specify the proposed approach, we revert to the FDMM formalism. Furthermore, a corresponding software prototype called AdoBPRIM has been implemented using the ADOxx meta-modeling platform to assess the technical feasibility of the approach. The usability of the tool has been empirically evaluated and a healthcare process-based example is presented as a proof-of-concept. We show that the AdoBPRIM approach enables Risk-aware Business Process Management with an excellent usability. In summary, this paper constitutes a best-practice for formally specifying, technically implementing, and empirically evaluating modeling method conceptualizations

A Model-driven Approach to Trace Checking of Temporal Properties with Aggregations

The verification of complex software systems often requires to check quantitative properties that rely on aggregation operators (e.g., the average response time of a service). One way to ease the specification of these properties is to use property specification patterns, such as the ones for “service provisioning”, previously proposed in the literature. In this paper we focus on the problem of performing offline trace checking of temporal properties containing aggregation operators. We first present TemPsy-AG, an extension of TemPsy—an existing pattern-based language for the specification of temporal properties—to support service provisioning patterns that use aggregation operators. We then extend an existing model-driven procedure for trace checking, to verify properties expressed in TemPsy-AG. The trace checking procedure relies on the efficient mapping of temporal properties written in TemPsy-AG into OCL constraints on a meta-model of execution traces. We have implemented this procedure in the TemPsy-Check-AG tool and evaluated its performance: our approach scales linearly with respect to the length of the input trace and can deal with much larger traces than a state-of-the-art tool

Trace Diagnostics for Signal-based Temporal Properties

Trace checking is a verification technique widely used in Cyber-physical system (CPS) development, to verify whether execution traces satisfy or violate properties expressing system requirements. Often these properties characterize complex signal behaviors and are defined using domain-specific languages, such as SB-TemPsy-DSL, a pattern-based specification language for signal-based temporal properties. Most of the trace-checking tools only yield a Boolean verdict. However, when a property is violated by a trace, engineers usually inspect the trace to understand the cause of the violation; such manual diagnostic is time-consuming and error-prone. Existing approaches that complement trace-checking tools with diagnostic capabilities either produce low-level explanations that are hardly comprehensible by engineers or do not support complex signal-based temporal properties. In this paper, we propose TD-SB-TemPsy, a trace-diagnostic approach for properties expressed using SB-TemPsy-DSL. Given a property and a trace that violates the property, TD-SB-TemPsy determines the root cause of the property violation. TD-SB-TemPsy relies on the concepts of violation cause, which characterizes one of the behaviors of the system that may lead to a property violation, and diagnoses, which are associated with violation causes and provide additional information to help engineers understand the violation cause. As part of TD-SB-TemPsy, we propose a language-agnostic methodology to define violation causes and diagnoses. In our context, its application resulted in a catalog of 34 violation causes, each associated with one diagnosis, tailored to properties expressed in SB-TemPsy-DSL. We assessed the applicability of TD-SB-TemPsy on two datasets, including one based on a complex industrial case study. The results show that TD-SB-TemPsy could finish within a timeout of 1 min for ≈ 83.66% of the trace-property combinations in the industrial dataset, yielding a diagnosis in ≈ 99.84% of these cases; moreover, it also yielded a diagnosis for all the trace-property combinations in the other dataset. These results suggest that our tool is applicable and efficient in most cases

TLN-4601 suppresses growth and induces apoptosis of pancreatic carcinoma cells through inhibition of Ras-ERK MAPK signaling

Abstract Background TLN-4601 is a structurally novel farnesylated dibenzodiazepinone discovered using Thallion's proprietary DECIPHER® technology, a genomics and bioinformatics platform that predicts the chemical structures of secondary metabolites based on gene sequences obtained by scanning bacterial genomes. Our recent studies suggest that TLN-4601 inhibits the Ras-ERK MAPK pathway post Ras prenylation and prior to MEK activation. The Ras-ERK MAPK signaling pathway is a well-validated oncogenic cascade based on its central role in regulating the growth and survival of cells from a broad spectrum of human tumors. Furthermore, RAS isoforms are the most frequently mutated oncogenes, occurring in approximately 30% of all human cancers, and KRAS is the most commonly mutated RAS gene, with a greater than 90% incidence of mutation in pancreatic cancer. Results To evaluate whether TLN-4601 interferes with K-Ras signaling, we utilized human pancreatic epithelial cells and demonstrate that TLN-4601 treatment resulted in a dose- and time-dependent inhibition of Ras-ERK MAPK signaling. The compound also reduced Ras-GTP levels and induced apoptosis. Finally, treatment of MIA PaCa-2 tumor-bearing mice with TLN-4601 resulted in antitumor activity and decreased tumor Raf-1 protein levels. Conclusion These data, together with phase I/II clinical data showing tolerability of TLN-4601, support conducting a clinical trial in advanced pancreatic cancer patients

Asporin is a stromally expressed marker associated with prostate cancer progression.

BACKGROUND: Prostate cancer shows considerable heterogeneity in disease progression and we propose that markers expressed in tumour stroma may be reliable predictors of aggressive tumour subtypes. METHODS: We have used Kaplan-Meier, univariate and multivariate analysis to correlate the expression of Asporin (ASPN) mRNA and protein with prostate cancer progression in independent cohorts. We used immunohistochemistry and H scoring to document stromal localisation of ASPN in a tissue microarray and mouse prostate cancer model, and correlated expression with reactive stroma, defined using Masson Trichrome staining. We used cell cultures of primary prostate cancer fibroblasts treated with serum-free conditioned media from prostate cancer cell lines to examine regulation of ASPN mRNA in tumour stromal cells. RESULTS: We observed increased expression of ASPN mRNA in a data set derived from benign vs tumour microdissected tissue, and a correlation with biochemical recurrence using Kaplan-Meier and Cox proportional hazard analysis. ASPN protein localised to tumour stroma and elevated expression of ASPN was correlated with decreased time to biochemical recurrence, in a cohort of 326 patients with a median follow up of 9.6 years. Univariate and multivariate analysis demonstrated that ASPN was correlated with progression, as were Gleason score, and clinical stage. Additionally, ASPN expression correlated with the presence of reactive stroma, suggesting that it may be a stromal marker expressed in response to the presence of tumour cells and particularly with aggressive tumour subtypes. We observed expression of ASPN in the stroma of tumours induced by p53 inhibition in a mouse model of prostate cancer, and correlation with neuroendocrine marker expression. Finally, we demonstrated that ASPN transcript expression in normal and cancer fibroblasts was regulated by conditioned media derived from the PC3, but not LNCaP, prostate cancer cell lines. CONCLUSIONS: Our results suggest that ASPN is a stromally expressed biomarker that correlates with disease progression, and is observed in reactive stroma. ASPN expression in stroma may be part of a stromal response to aggressive tumour subtypes.British Journal of Cancer advance online publication, 2 February 2017; doi:10.1038/bjc.2017.15 www.bjcancer.com

Identification of genes expressed in a mesenchymal subset regulating prostate organogenesis using tissue and single cell transcriptomics

Abstract Prostate organogenesis involves epithelial growth controlled by inductive signalling from specialised mesenchymal subsets. To identify pathways active in mesenchyme we used tissue and single cell transcriptomics to define mesenchymal subsets and subset-specific transcript expression. We documented transcript expression using Tag-seq and RNA-seq in female rat Ventral Mesenchymal Pad (VMP) as well as adjacent urethra comprised of smooth muscle and peri-urethral mesenchyme. Transcripts enriched in female VMP were identified with Tag-seq of microdissected tissue, RNA-seq of cell populations, and single cells. We identified 400 transcripts as enriched in the VMP using bio-informatic comparisons of Tag-seq and RNA-seq data, and 44 were confirmed by single cell RNA-seq. Cell subset analysis showed that VMP and adjacent mesenchyme were composed of distinct cell types and that each tissue contained two subgroups. Markers for these subgroups were highly subset specific. Thirteen transcripts were validated by qPCR to confirm cell specific expression in microdissected tissues, as well as expression in neonatal prostate. Immunohistochemical staining demonstrated that Ebf3 and Meis2 showed a restricted expression pattern in female VMP and prostate mesenchyme. We conclude that prostate inductive mesenchyme shows limited cellular heterogeneity and that transcriptomic analysis identified new mesenchymal subset transcripts associated with prostate organogenesis