Exhaustive analysis of dynamical properties of Biological Regulatory Networks with Answer Set Programming

International audienceThe combination of numerous simple influences between the components of a Biological Regulatory Network (BRN) often leads to behaviors that cannot be grasped intuitively. They thus call for the development of proper mathematical methods to delineate their dynamical properties. As a consequence , formal methods and computer tools for the modeling and simulation of BRNs become essential. Our recently introduced discrete formalism called the Process Hitting (PH), a restriction of synchronous automata networks, is notably suitable to such study. In this paper, we propose a new logical approach to perform model-checking of dynamical properties of BRNs modeled in PH. Our work here focuses on state reachability properties on the one hand, and on the identification of fixed points on the other hand. The originality of our model-checking approach relies in the exhaustive enumeration of all possible simulations verifying the dynamical properties thanks to the use of Answer Set Programming

Abducing Biological Regulatory Networks from Process Hitting models

International audienceThe Process Hitting (PH) is a recently introduced framework to model concurrent processes. It is notably suitable to model Biological Regulatory Networks (BRNs) with partial knowledge of cooperations by defining the most permissive dynamics. On the other hand, the qualitative modeling of BRNs has been widely addressed using René Thomas' formalism. Given a PH model of a BRN, we first tackle the inference of the underlying Interaction Graph between components. Then the inference of corresponding Thomas' models is provided by inferring some parameters and abducing the compatible parametrizations

Identification of Biological Regulatory Networks from Process Hitting models

International audienceQualitative formalisms offer a well-established alternative to the more tradi-tionally used differential equation models of Biological Regulatory Networks (BRNs). These formalisms led to numerous theoretical works and practical tools to understand emerging behaviors. The analysis of the dynamics of very large models is however a rather hard problem, which led us to previously in-troduce the Process Hitting framework (PH), which is a particular class of non-deterministic asynchronous automata network (or safe Petri nets). Its major advantage lies in the efficiency of several static analyses recently designed to assess dynamical properties, making it possible to tackle very large models. In this paper, we address the formal identification of qualitative models of BRNs from PH models. First, the inference of the Interaction Graph from a PH model summarizes the signed influences between the components that are effective for the dynamics. Second, we provide the inference of all René-Thomas models of BRNs that are compatible with a given PH. As the PH allows the specification of nondeterministic interactions between components, our inference emphasizes the ability of PH to deal with large BRNs with incomplete knowledge on interactions, where Thomas's approach fails because of the combinatorics of parameters. The inference of corresponding Thomas models is implemented using An-swer Set Programming, which allows in particular an efficient enumeration of (possibly numerous) compatible parametrizations

High-pressure intrapleural chemotherapy: feasibility in the pig model.

International audienceABSTRACT: BACKGROUND: The usual treatments for pleural malignancies are mostly palliative. In contrast, peritoneal malignancies are often treated with a curative intent by cytoreductive surgery and intraperitoneal chemotherapy. As pressure has been shown to increase antitumor efficacy, we applied the concept of high-pressure intracavitary chemotherapy to the pleural space in a swine model. METHODS: Cisplatin and gemcitabine were selected because of their antineoplasic efficacy in vitro in a wide spectrum of cancer cell lines. The pleural cavity of 21 pigs was filled with saline solution; haemodynamic and respiratory parameters were monitored. The pressure was increased to 15-25 cm H2O. This treatment was associated with pneumonectomy in 6 pigs. Five pigs were treated with chemotherapy under pressure. RESULTS: The combination of gemcitabine (100 mg/l) and cisplatin (30 mg/l) was highly cytotoxic in vitro. The maximum tolerated pressure was 20 cm H20, due to haemodynamic failure. Pneumonectomy was not tolerated, either before or after pleural infusion. Five pigs survived intrapleural chemotherapy associating gemcitabine and cisplatin with 20 cm H2O pressure for 60 min. CONCLUSIONS: High-pressure intrapleural chemotherapy is feasible in pigs. Further experiments will establish the pharmacokinetics and determine whether the benefit already shown in the peritoneum is also obtained in the pleura

Chemical Master Equation Empirical Moment Closure

The numerical solution of the Chemical Master Equation (CME) governing gene regulatory networks and cell signaling processes remains a challenging task due to its complexity, exponentially growing with the number of species involved. When considering separated representations of the probability distribution function within the Proper Generalized Decomposition-PGD-frame-work the complexity of the CME grows only linearly with the number of state space dimensions. In order to speed up calculations moment-based descriptions are usually preferred, however these descriptions involve the necessity of using closure relations whose impact on the calculated solution is most of time unpredictable. In this work we propose an empirical closure, fitted from the solution of the chemical master equation, the last solved within the PGD framework

Incorporating Time Delays in Process Hitting Framework for Dynamical Modeling of Large Biological Regulatory Networks

Modeling and simulation of molecular systems helps in understanding the behavioral mechanism of biological regulation. Time delays in production and degradation of expressions are important parameters in biological regulation. Constraints on time delays provide insight into the dynamical behavior of a Biological Regulatory Network (BRN). A recently introduced Process Hitting (PH) Framework has been found efficient in static analysis of large BRNs, however, it lacks the inference of time delays and thus determination of their constraints associated with the evolution of the expression levels of biological entities of BRN is not possible. In this paper we propose a Hybrid Process Hitting scheme for introducing time delays in Process Hitting Framework for dynamical modeling and analysis of Large Biological Regulatory Networks. It provides valuable insights into the time delays corresponding to the changes in the expression levels of biological entities thus possibly helping in identification of therapeutic targets. The proposed framework is applied to a well-known BRNs of Bacteriophage λ and ERBB Receptor-regulated G1/S transition involved in the breast cancer to demonstrate the viability of our approach. Using the proposed approach, we are able to perform goal-oriented reduction of the BRN and also determine the constraints on time delays characterizing the evolution (dynamics) of the reduced BRN

Maternal Blood Lead Levels and the Risk of Pregnancy-Induced Hypertension: The EDEN Cohort Study

International audienceBACKGROUND: Prior studies revealed associations of environmental lead exposure with risks of hypertension and elevated blood pressure. OBJECTIVE: We examined the effect of blood lead levels on blood pressure and the incidence of pregnancy-induced hypertension (PIH) in the second and third trimesters of pregnancy. METHODS: One thousand seventeen pregnant women were enrolled in two French municipalities between 2003 and 2005 for the EDEN (Etude des Déterminants pré et post natals du développement et de la santé de l' Enfant) cohort study. Blood lead concentrations were measured by atomic absorption spectrometry in mothers between 24 and 28 weeks of gestation. RESULTS: PIH was diagnosed in 106 subjects (10.9%). Age, parity, weight gain, alcohol, smoking habits, and calcium supplementation were comparable between hypertensive and nonhypertensive women. Lead levels were significantly higher in PIH cases (mean +/- SD, 2.2 +/- 1.4 mug/dL) than in normotensive patients (1.9 +/- 1.2 mug/dL; p = 0.02). Adjustment for potential confounder effects slightly attenuated but did not eliminate the significant association between blood lead levels and the risk of PIH (adjusted odds ratio of PIH = 3.3; 95% confidence interval, 1.1-9.7). We also observed geographic differences in lead exposure and in the incidence of PIH and found significant correlations between blood lead levels and unadjusted as well as adjusted systolic and diastolic blood pressures after 24 weeks of gestation. CONCLUSIONS: These findings confirm the relationship between blood lead levels at mid-pregnancy and blood pressure and suggest that environmental lead exposure may play an etiologic role in PIH

Maternal Personal Exposure to Airborne Benzene and Intrauterine Growth

International audienceBACKGROUND: Studies relying on outdoor pollutants measures have reported associations between air pollutants and birth weight. OBJECTIVE: Our aim was to assess the relation between maternal personal exposure to airborne benzene during pregnancy and fetal growth. METHODS: We recruited pregnant women in two French maternity hospitals in 2005-2006 as part of the EDEN mother-child cohort. A subsample of 271 nonsmoking women carried a diffusive air sampler for a week during the 27th gestational week, allowing assessment of benzene exposure. We estimated head circumference of the offspring by ultrasound measurements during the second and third trimesters of pregnancy and at birth. RESULTS: Median benzene exposure was 1.8 microg/m(3) (5th, 95th percentiles, 0.5, 7.5 microg/m(3)). Log-transformed benzene exposure was associated with a gestational age-adjusted decrease of 68 g in mean birth weight [95% confidence interval (CI), -135 to -1 g] and of 1.9 mm in mean head circumference at birth (95% CI, -3.8 to 0.0 mm). It was associated with an adjusted decrease of 1.9 mm in head circumference assessed during the third trimester (95% CI, -4.0 to 0.3 mm) and of 1.5 mm in head circumference assessed at the end of the second trimester of pregnancy (95% CI, -3.1 to 0 mm). CONCLUSIONS: Our prospective study among pregnant women is one of the first to rely on personal monitoring of exposure; a limitation is that exposure was assessed during 1 week only. Maternal benzene exposure was associated with decreases in birth weight and head circumference during pregnancy and at birth. This association could be attributable to benzene and a mixture of associated traffic-related air pollutants

European survey on national harmonization in clinical research

Background: Clinical trials remain key to the development of evidence-based medical practice. However, they are becoming increasingly complex, mainly in a multinational setting. To address these challenges, the European Union (EU) adopted the Clinical Trial Regulation EU No. 536/2014 (CTR). Once in force, the CTR will lead to more consistent rules and simplification of procedures for conducting clinical trials through-out the EU. Existing harmonization initiatives and “research infrastructures” for clinical trials may facilitate this process. This publication offers a snapshot of the current level of harmonization activities in academic clinical research in Europe. Methods: A survey was performed among the member and observer countries of the European Clinical Research Infrastructure Network (ECRIN), using a standardizedpublishersversionpublishe