Object and Source Coverage for Critical Applications with the C OUVERTURE Open Analysis Framework

International audienceThis paper presents C OUVERTURE , an open coverage analysis framework for safety-critical software development.C OUVERTURE offers non-intrusive source and object coverage analysis on unmodified user code, using instrumentation of a virtual execution platform based on QEMU , a flexible and efficient open-source CPU emulator

Acute respiratory failure in kidney transplant recipients: a multicenter study

International audienceINTRODUCTION: Data on pulmonary complications in renal transplant recipients are scarce. The aim of this study was to evaluate acute respiratory failure (ARF) in renal transplant recipients. METHODS: We conducted a retrospective observational study in nine transplant centers of consecutive kidney transplant recipients admitted to the intensive care unit (ICU) for ARF from 2000 to 2008. RESULTS: Of 6,819 kidney transplant recipients, 452 (6.6%) required ICU admission, including 200 admitted for ARF. Fifteen (7.5%) of these patients had combined kidney-pancreas transplantations. The most common causes of ARF were bacterial pneumonia (35.5%), cardiogenic pulmonary edema (24.5%) and extrapulmonary acute respiratory distress syndrome (ARDS) (15.5%). Pneumocystis pneumonia occurred in 11.5% of patients. Mechanical ventilation was used in 93 patients (46.5%), vasopressors were used in 82 patients (41%) and dialysis was administered in 104 patients (52%). Both the in-hospital and 90-day mortality rates were 22.5%. Among the 155 day 90 survivors, 115 patients (74.2%) were dialysis-free, including 75 patients (65.2%) who recovered prior renal function. Factors independently associated with in-hospital mortality were shock at admission (odds ratio (OR) 8.70, 95% confidence interval (95% CI) 3.25 to 23.29), opportunistic fungal infection (OR 7.08, 95% CI 2.32 to 21.60) and bacterial infection (OR 2.53, 95% CI 1.07 to 5.96). Five factors were independently associated with day 90 dialysis-free survival: renal Sequential Organ Failure Assessment (SOFA) score on day 1 (OR 0.68/SOFA point, 95% CI 0.52 to 0.88), bacterial infection (OR 0.43, 95% CI 0.21 to 0.90), three or four quadrants involved on chest X-ray (OR 0.44, 95% CI 0.21 to 0.91), time from hospital to ICU admission (OR 0.98/day, 95% CI 0.95 to 0.99) and oxygen flow at admission (OR 0.93/liter, 95% CI 0.86 to 0.99). CONCLUSIONS: In kidney transplant recipients, ARF is associated with high mortality and graft loss rates. Increased Pneumocystis and bacterial prophylaxis might improve these outcomes. Early ICU admission might prevent graft loss

Extracorporeal Membrane Oxygenation for Severe Acute Respiratory Distress Syndrome associated with COVID-19: An Emulated Target Trial Analysis.

RATIONALE: Whether COVID patients may benefit from extracorporeal membrane oxygenation (ECMO) compared with conventional invasive mechanical ventilation (IMV) remains unknown. OBJECTIVES: To estimate the effect of ECMO on 90-Day mortality vs IMV only Methods: Among 4,244 critically ill adult patients with COVID-19 included in a multicenter cohort study, we emulated a target trial comparing the treatment strategies of initiating ECMO vs. no ECMO within 7 days of IMV in patients with severe acute respiratory distress syndrome (PaO2/FiO2 <80 or PaCO2 ≥60 mmHg). We controlled for confounding using a multivariable Cox model based on predefined variables. MAIN RESULTS: 1,235 patients met the full eligibility criteria for the emulated trial, among whom 164 patients initiated ECMO. The ECMO strategy had a higher survival probability at Day-7 from the onset of eligibility criteria (87% vs 83%, risk difference: 4%, 95% CI 0;9%) which decreased during follow-up (survival at Day-90: 63% vs 65%, risk difference: -2%, 95% CI -10;5%). However, ECMO was associated with higher survival when performed in high-volume ECMO centers or in regions where a specific ECMO network organization was set up to handle high demand, and when initiated within the first 4 days of MV and in profoundly hypoxemic patients. CONCLUSIONS: In an emulated trial based on a nationwide COVID-19 cohort, we found differential survival over time of an ECMO compared with a no-ECMO strategy. However, ECMO was consistently associated with better outcomes when performed in high-volume centers and in regions with ECMO capacities specifically organized to handle high demand. This article is open access and distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivatives License 4.0 (http://creativecommons.org/licenses/by-nc-nd/4.0/)

Structural Coverage Criteria for Executable Assertions

International audienceProgramming. In this paper, we describe some of the issues raised by the use of assertions in software programs that need to undergo coverage analysis for certification purposes, typically in the avionics or railway domains. " Assertions " , in this context, designates Boolean expressions expected to always yield True, verifying internal properties of a program at various points of its execution. We can observe an increased use of such constructs in safety critical domains, from more frequent uses of contract based programming techniques. We explain why we believe that the traditional structural coverage criteria defined for Boolean expressions in certification standards aren't quite adequate for assertions. We propose tracks for possible alternative criteria and examine some of their properties. We also discuss possible viewpoints on the role of assertions within a program and consider some options through which structural coverage on assertions can contribute to the assessment of functional coverage. This is still exploratory at this stage. Our goal here is to raise attention on the issues and propose initial lines of possible resolutions, as well as various tracks of further work to refine and strengthen the approach

Formalization and Comparison of MCDC and Object Branch Coverage Criteria

International audienceThis paper presents formal results derived from the COUVERTURE project, whose goal was to develop tools to support structural coverage analysis of uninstrumented safety-critical software. After briefly introducing the project context and explaining the need for formal foundations, we focus on the relationships between machine branch coverage and the DO-178B Modified Condition/Decision Coverage (MCDC) criterion. A thorough understanding of those relationships is important, since it provides the foundation for knowing where efficient execution trace techniques can be used to demonstrate compliance with the MCDC criterion. We first present several conjectures that were tested using Alloy models, then provide a formally verified characterization of the situations when coverage of object control-flow edges implies MCDC compliance

Ecotoxicological risk assessment linked to the discharge by hospitals of bio-accumulative pharmaceuticals into aquatic media: The case of mitotane

International audienceThe release of hospital wastewater into the urban sewer networks contributes to the general contamina- tion of aquatic media by pharmaceutical residues. These residues include bio-accumulative pharmaceu- ticals that lead to increased risk for ecosystems because they can concentrate in organisms and food chains, and therefore reach toxic levels. In order to assess the ecotoxicological risks linked to this partic- ular category of residues, we have developed a specific method, by combining a theoretical calculation of pollutant concentrations in organisms to estimate Body Residue (BR), and ecotoxicity biomarkers in fish cell lines, enabling the calculation of a Critical Body Residue (CBR). This method finally results in the cal- culation of a specific risk quotient (Qb = BR/CBR), characterizing the risk linked to this type of pollutant. This method was applied to mitotane, a bio-accumulative pharmaceutical typically found in hospital wastewater, in the framework of an exposure scenario corresponding to the discharge of all the hospital wastewaters into the Rhone River which flows through the city of Lyon, France. This approach leads to risk quotients (Qb and Qbg) much higher than those found with the classical approach, i.e. Q = PEC/PNEC (Predictive Environmental Concentration/Predictive Non Effect Concentration) = 0.0006. This difference in the appreciation of risk is important when using cytotoxicity as the criterion for measuring the toxicity of mitotane (Qb = 0.056) and it is even greater when the criterion used is genotoxicity (Qbg = 6.8). This study must be now consolidated by taking the biomagnification of the pharmaceuticals into consideration

Fully validated assay for the quantification of endogenous nucleoside mono- and triphosphates using online extraction coupled with liquid chromatography-tandem mass spectrometry.

International audienceAn analytical method coupling online solid-phase extraction (SPE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) was developed to quantify 16 endogenous nucleoside mono- and triphosphates in cellular samples. Separation was achieved on a porous graphitic carbon (PGC) column without ion-pairing agent in the mobile phase. Low levels of the ion-pairing agent diethylamine (DEA) added to the reconstitution solution were necessary to prevent peak tailing of nucleoside triphosphates. The mass spectrometer, a triple quadrupole with an electrospray ionisation source, was operated in positive mode. Two multiple reaction monitoring (MRM) segments were programmed, each an internal standard. Extraction and separation of nucleoside mono- and triphosphates were obtained within 20 min. The total duration of a single run was 37 min. Calibration curves, performed with labelled nucleotides added to the sample matrix, ranged from 0.29 to 18.8 pmol injected for deoxyribonucleotides and from 3.9 to 3,156 pmol for ribonucleotides. Accuracy did not deviate more than −14.6 and 10.2 % from nominal values for all compounds at all levels. CV results were all lower than 17.0 % for the LLOQ level and 14.6 % for the other levels. Quality control (QC) samples were also in agreement with acceptance criteria, except for the lower QC of GMP. Ion suppression, matrix effect, extraction recoveries and stability were assessed. After validation, the method was applied to the evaluation of the effects of gemcitabine and hydroxyurea on nucleotide pools in Messa cells

Synthesis and Evaluation of a Molecularly Imprinted Polymer for Selective Solid-Phase Extraction of Irinotecan from Human Serum Samples

A molecularly imprinted polymer (MIP) was synthesized by non-covalent imprinting polymerization using irinotecan as template. Methacrylic acid and 4-vinylpyridine were selected as functional monomers. An optimized procedure coupled to LC-PDA analysis was developed for the selective solid-phase extraction of irinotecan from various organic media. A specific capacity of 0.65 µmol•g−1 for the MIP was determined. The high specificity of this MIP was demonstrated by studying the retention behaviour of two related compounds, camptothecin and SN-38. This support was applied for the extraction of irinotecan from human serum samples

Development of a sensitive and selective LC/MS/MS method for the simultaneous determination of intracellular 1-beta-d-arabinofuranosylcytosine triphosphate (araCTP), cytidine triphosphate (CTP) and deoxycytidine triphosphate (dCTP) in a human follicular lymphoma cell line

International audienceDevelopment of a sensitive and selective LC/MS/MS method for the simultaneous determination of intracellular 1-beta-d-arabinofuranosylcytosine triphosphate (araCTP), cytidine triphosphate (CTP) and deoxycytidine triphosphate (dCTP) in a human follicular lymphoma cell line a b s t r a c t A method was developed for the quantification of araCTP, CTP and dCTP in a human follicular lymphoma cell line. This method involves solid phase extraction (SPE) using a weak anion-exchanger (WAX) cartridge , a porous graphitic carbon high-performance liquid chromatography (HPLC) column separation, and tandem mass spectrometry (MS/MS) detection. By using a triple quadrupole mass spectrometer operating in negative ion multiple reaction monitoring (MRM) mode, the method was able to achieve a lower limit of quantification (LLOQ) of 0.1 g mL −1 for araCTP and of 0.01 g mL −1 for both CTP and dCTP. The method was validated and used to determine the amount of araCTP, CTP and dCTP formed after incubation of araC and an araCMP prodrug in the human follicular lymphoma cell line RL