Verifying the Safety of a Flight-Critical System

This paper describes our work on demonstrating verification technologies on a flight-critical system of realistic functionality, size, and complexity. Our work targeted a commercial aircraft control system named Transport Class Model (TCM), and involved several stages: formalizing and disambiguating requirements in collaboration with do- main experts; processing models for their use by formal verification tools; applying compositional techniques at the architectural and component level to scale verification. Performed in the context of a major NASA milestone, this study of formal verification in practice is one of the most challenging that our group has performed, and it took several person months to complete it. This paper describes the methodology that we followed and the lessons that we learned.Comment: 17 pages, 5 figure

The Alteration History of Clovis Class Rocks in Gusev Crater as Determined by Ti-Normalzed Mass Balance Analysis

The West Spur Clovis class rocks in Gusev Crater are some of the most altered rocks in Gusev Crater and likely contain a mixed sulfate and phyllosilicate mineralogy [1,2]. The high S and Cl content of the Clovis rocks suggests that acidic vapors or fluids of H2SO4 and HCl reacted with the Clovis parent rock to form Ca, Mg,- sulfates, iron-oxyhydroxides and secondary aluminosilicates (approx.60 wt.%) of a poorly crystalline nature (e.g., allophane) [1]. Up to 14-17 wt.% phyllosilicates (e.g., kaolinite, chlorite, serpentine) are hypothesized to exist in the Clovis materials suggesting that Clovis parent materials while possibly exposed to acidic pHs were likely neutralized by basalt dissolution which resulted in mildly acidic pHs (4-6) [1, 2]. This work proposes that subsequent to the alteration of the Clovis rocks, alteration fluids became concentrated in ions resulting in the addition of silicate and salts. The objective of this work is to utilize Ti-normalized mass balance analysis to evaluate (1) mineral gains and losses and (2) elemental gains and losses in the Clovis rocks. Results of this work will be used evaluate the nature of geochemical conditions that affect phyllosilicate and sulfate formation at Gusev crater

Characterization of Overlap in Observational Studies

Overlap between treatment groups is required for non-parametric estimation of causal effects. If a subgroup of subjects always receives the same intervention, we cannot estimate the effect of intervention changes on that subgroup without further assumptions. When overlap does not hold globally, characterizing local regions of overlap can inform the relevance of causal conclusions for new subjects, and can help guide additional data collection. To have impact, these descriptions must be interpretable for downstream users who are not machine learning experts, such as policy makers. We formalize overlap estimation as a problem of finding minimum volume sets subject to coverage constraints and reduce this problem to binary classification with Boolean rule classifiers. We then generalize this method to estimate overlap in off-policy policy evaluation. In several real-world applications, we demonstrate that these rules have comparable accuracy to black-box estimators and provide intuitive and informative explanations that can inform policy making.Comment: To appear at AISTATS 202

Effects of Oxygen During Long-term Hypothermic Machine Perfusion in a Porcine Model of Kidney Donation After Circulatory Death

International audienceBackground:Hypothermic machine perfusion (HMP) has become standard care in many center’s to preserve kidneys donated after circulatory death (DCD). Despite a significant reduction in metabolism at low temperatures, remaining cellular activity requires oxygen. Since the role and safety of oxygen during HMP has not been fully clarified, its supply during HMP is not standard yet. This study investigates the effect of administering oxygen during HMP on renal function in a porcine DCD model.Methods: After 30 minutes of warm ischemia, porcine slaughterhouse kidneys were preserved for 24 hours by means of cold storage (CS), or HMP with Belzer Machine Perfusion Solution (UW- MPS) supplemented with no oxygen, 21% or 100% oxygen. Next, kidneys were reperfused for 4 hours in a normothermic machine perfusion (NMP) setup.Results:HMP resulted in significantly better kidney function during NMP. Thiobarbituric acid-reactive substances (TBARS), markers of oxidative stress, were significantly lower in HMP preserved kidneys. HMP preserved kidneys showed significantly lower ASAT and LDH levels compared to kidneys preserved by CS. No differences were found between the HMP groups subjected to different oxygen concentrations. ATP levels significantly improved during HMP when active oxygenation was applied.Conclusion:This study showed that preservation of DCD kidneys with HMP is superior to CS. Although the addition of oxygen to HMP did not result in significantly improved renal function, beneficial effects were found in terms of reduced oxidative stress and energy status. Oxygen addition proofed to be safe and did not show detrimental effects

Spectroscopic and Photometric Study of the Contact Binary BO CVn

We present the results of the study of the contact binary system BO CVn. We have obtained physical parameters of the components based on combined analysis of new, multi-color light curves and spectroscopic mass ratio. This is the first time the latter has been determined for this object. We derived the contact configuration for the system with a very high filling factor of about 88 percent. We were able to reproduce the observed light curve, namely the flat bottom of the secondary minimum, only if a third light has been added into the list of free parameters. The resulting third light contribution is significant, about 20-24 percent, while the absolute parameters of components are: M1=1.16, M2=0.39, R1=1.62 and R2=1.00 (in solar units). The O-C diagram shows an upward parabola which, under the conservative mass transfer assumption, would correspond to a mass transfer rate of dM/dt = 6.3 \times 10-8M\odot/yr, matter being transferred from the less massive component to the more massive one. No cyclic, short-period variations have been found in the O-C diagram (but longer-term variations remain a possibility)Comment: 16 pages, 5 figures, 5 tables, accepted for publication by New Astronom

The impact of histopathology and NAB2-STAT6 fusion subtype in classification and grading of meningeal solitary fibrous tumor/hemangiopericytoma.

Meningeal solitary fibrous tumor (SFT)/hemangiopericytoma (HPC) is a rare tumor with propensity for recurrence and metastasis. Although multiple classification schemes have been proposed, optimal risk stratification remains unclear, and the prognostic impact of fusion status is uncertain. We compared the 2016 WHO CNS tumor grading scheme (CNS-G), a three-tier system based on histopathologic phenotype and mitotic count, to the 2013 WHO soft-tissue counterpart (ST-G), a two-tier system based on mitotic count alone, in a cohort of 133 patients [59 female, 74 male; mean age 54 years (range 20-87)] with meningeal SFT/HPC. Tumors were pathologically confirmed through review of the first tumor resection (n = 97), local recurrence (n = 35), or distant metastasis (n = 1). A STAT6 immunostain showed nuclear expression in 132 cases. NAB2-STAT6 fusion was detected in 99 of 111 successfully tested tumors (89%) including the single STAT6 immunonegative tumor. Tumors were classified by CNS-G as grade 1 (n = 43), 2 (n = 41), or 3 (n = 49), and by ST-G as SFT (n = 84) or malignant SFT (n = 49). Necrosis was present in 16 cases (12%). On follow-up, 42 patients had at least one subsequent recurrence or metastasis (7 metastasis only, 33 recurrence only, 2 patients had both). Twenty-nine patients died. On univariate analysis, necrosis (p = 0.002), CNS-G (p = 0.01), and ST-G (p = 0.004) were associated with recurrence-free (RFS) but not overall survival (OS). NAB2-STAT6 fusion type was not significantly associated with RFS or OS, but was associated with phenotype. A modified ST-G incorporating necrosis showed higher correlation with RFS (p = 0.0006) and remained significant (p = 0.02) when considering only the primary tumors. From our data, mitotic rate and necrosis appear to stratify this family of tumors most accurately and could be incorporated in a future grading scheme

The Proneural Molecular Signature Is Enriched in Oligodendrogliomas and Predicts Improved Survival among Diffuse Gliomas

The Cancer Genome Atlas Project (TCGA) has produced an extensive collection of ‘-omic’ data on glioblastoma (GBM), resulting in several key insights on expression signatures. Despite the richness of TCGA GBM data, the absence of lower grade gliomas in this data set prevents analysis genes related to progression and the uncovering of predictive signatures. A complementary dataset exists in the form of the NCI Repository for Molecular Brain Neoplasia Data (Rembrandt), which contains molecular and clinical data for diffuse gliomas across the full spectrum of histologic class and grade. Here we present an investigation of the significance of the TCGA consortium's expression classification when applied to Rembrandt gliomas. We demonstrate that the proneural signature predicts improved clinical outcome among 176 Rembrandt gliomas that includes all histologies and grades, including GBMs (log rank test p = 1.16e-6), but also among 75 grade II and grade III samples (p = 2.65e-4). This gene expression signature was enriched in tumors with oligodendroglioma histology and also predicted improved survival in this tumor type (n = 43, p = 1.25e-4). Thus, expression signatures identified in the TCGA analysis of GBMs also have intrinsic prognostic value for lower grade oligodendrogliomas, and likely represent important differences in tumor biology with implications for treatment and therapy. Integrated DNA and RNA analysis of low-grade and high-grade proneural gliomas identified increased expression and gene amplification of several genes including GLIS3, TGFB2, TNC, AURKA, and VEGFA in proneural GBMs, with corresponding loss of DLL3 and HEY2. Pathway analysis highlights the importance of the Notch and Hedgehog pathways in the proneural subtype. This demonstrates that the expression signatures identified in the TCGA analysis of GBMs also have intrinsic prognostic value for low-grade oligodendrogliomas, and likely represent important differences in tumor biology with implications for treatment and therapy

Combined fluorescence and reflectance spectroscopy for in vivo quantification of cancer biomarkers in low - and high- grade glioma surgery

Biomarkers are indicators of biological processes and hold promise for the diagnosis and treatment of disease. Gliomas represent a heterogeneous group of brain tumors with marked intra- and inter-tumor variability. The extent of surgical resection is a significant factor influencing post-surgical recurrence and prognosis. Here, we used fluorescence and reflectance spectral signatures for in vivo quantification of multiple biomarkers during glioma surgery, with fluorescence contrast provided by exogenously-induced protoporphyrin IX (PpIX) following administration of 5-aminolevulinic acid. We performed light-transport modeling to quantify multiple biomarkers indicative of tumor biological processes, including the local concentration of PpIX and associated photoproducts, total hemoglobin concentration, oxygen saturation, and optical scattering parameters.We developed a diagnostic algorithm for intra-operative tissue delineation that accounts for the combined tumor-specific predictive capabilities of these quantitative biomarkers. Tumor tissue delineation achieved accuracies of up to 94% (specificity=94%, sensitivity=94%) across a range of glioma histologies beyond current state-of-the-art optical approaches, including state-of-the-art fluorescence image guidance. This multiple biomarker strategy opens the door to optical methods for surgical guidance that use quantification of well-established neoplastic processes. Future work would seek to validate the predictive power of this proof-of-concept study in a separate larger cohort of patients

Potential of Donation After Unexpected Circulatory Death Programs Defined by Their Demographic Characteristics

BACKGROUND. Donation after unexpected circulatory death (uDCD) donors are often suggested to increase the number of donor organs. In 2014, a uDCD protocol was implemented in three transplant centers in the Netherlands which unfortunately did not result in additional transplantations. This study was initiated to identify demographic factors influencing the potential success of uDCD programs. METHODS. Dutch resuscitation databases covering various demographic regions were analyzed for potential donors. The databases were compared with the uDCD implementation project and successful uDCD programs in Spain, France, and Russia. RESULTS. The resuscitation databases showed that 61% of all resuscitated patients were transferred to an emergency department. Age selection reduced this uDCD potential to 46% with only patients aged 18–65 years deemed eligible. Of these patients, 27% died in the emergency department. The urban region of Amsterdam showed the largest potential in absolute numbers (52 patients/y). Comparison with the uDCD implementation project showed large similarities in the percentage of potential donors; however, in absolute numbers, it showed a much smaller potential. Calculation of the potential per million persons and the extrapolation of the potential based on the international experience revealed the largest potential in urban regions. CONCLUSIONS. Implementation of a uDCD program should not only be based on the number of potential donors calculated from resuscitation databases. They show promising potential uDCD percentages for large rural regions and small urban regions; however, actual numbers per hospital are low, leading to insufficient exposure rates. It is, therefore, recommendable to limit uDCD programs to large urban regions

Proteomic analysis of machine perfusion solution from brain dead donor kidneys reveals that elevated complement, cytoskeleton and lipid metabolism proteins are associated with 1-year outcome

Assessment of donor kidney quality is based on clinical scores or requires biopsies for histological assessment. Noninvasive strategies to identify and predict graft outcome at an early stage are, therefore, needed. We evaluated the perfusate of donation after brain death (DBD) kidneys during nonoxygenated hypothermic machine perfusion (HMP). In particular, we compared perfusate protein profiles of good outcome (GO) and suboptimal outcome (SO) 1-year post-transplantation. Samples taken 15 min after the start HMP (T1) and before the termination of HMP (T2) were analysed using quantitative liquid chromatography-tandem mass spectrometry (LC-MS/MS). Hierarchical clustering of the 100 most abundant proteins showed discrimination between grafts with a GO and SO at T1. Elevated levels of proteins involved in classical complement cascades at both T1 and T2 and a reduced abundance of lipid metabolism at T1 and of cytoskeletal proteins at T2 in GO versus SO was observed. ATP-citrate synthase and fatty acid-binding protein 5 (T1) and immunoglobulin heavy variable 2-26 and desmoplakin (T2) showed 91% and 86% predictive values, respectively, for transplant outcome. Taken together, DBD kidney HMP perfusate profiles can distinguish between outcome 1-year post-transplantation. Furthermore, it provides insights into mechanisms that could play a role in post-transplant outcomes.</p