Cobra: a light-weight tool for static and dynamic program analysis

Static source code analysis tools have become indispensable for the development of reliable software applications. The best analyzers can reveal subtle flaws in a code base, but they can also be slow. In part this is due to the collection of detailed information about the possible data and control flow of an application to support the broadest possible range of analyses. For larger code bases it is not unusual that even the best of breed static analyzers can take an hour or more to complete an analysis. In this paper we describe a framework for a much faster, but more light-weight type of static analysis that can support interactive use for standard types of queries. The Cobra tool we designed for this purpose can scale to explore millions of lines of code interactively. The tool is mostly language agnostic, and can therefore easily be configured to resolve even dynamic program analysis queries.     

A mini challenge: build a verifiable filesystem

We propose tackling a “mini challenge” problem: a nontrivial verification effort that can be completed in 2–3 years, and will help establish notational standards, common formats, and libraries of benchmarks that will be essential in order for the verification community to collaborate on meeting Hoare’s 15-year verification grand challenge. We believe that a suitable candidate for such a mini challenge is the development of a filesystem that is verifiably reliable and secure. The paper argues why we believe a filesystem is the right candidate for a mini challenge and describes a project in which we are building a small embedded filesystem for use with flash memory. The work described in this paper was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration.     

Increased susceptibility to postoperative sepsis in patients with impaired monocyte IL-12 production

IL-12 is a potent immunoregulatory cytokine that is essential for the development of protective immunity, as demonstrated by numerous animal models of infection. Here, we provide evidence for a critical role of IL-12 in human sepsis. The results of a prospective study of 184 patients undergoing major elective surgery of the upper and lower gastrointestinal tract revealed that, in contrast to patients showing uneventful recovery, monocyte IL-12 production was severely and selectively impaired in patients developing postoperative sepsis. Moreover, the extent of monocyte IL-12 suppression correlated with the severity of postoperative sepsis. Monocyte IL-12 secretion was suppressed before surgery and remained low until the onset of sepsis. Therefore, the suppression of IL-12 secretion preceded the onset of postoperative sepsis but did not occur as a consequence of major surgery. In contrast, IL-1beta production was only reduced during the late postoperative course in patients developing postoperative sepsis, and TNF-alpha release was even increased at different time intervals before the onset of sepsis. Thus, reduced IL-12 release does not reflect a general defect in monocyte cytokine production. Consequently, these results establish a critical role for IL-12 in early resistance to postoperative infection and may allow for the development of novel therapeutic strategies designed to stimulate host defense mechanisms and to reduce the incidence and severity of septic complications.     

The influence of tempering on cleavage fracture stress and transition behaviour of bainitic 2.25Cr1Mo steel

The effect of tempering on the mechanical properties and on the cleavage fracture stress of bainitic 2.25Cr1Mo steel was studied in a variety of structures with the Hollomon-Jaffe parameter M ranging between 18.23 × 10³ and 21.70 × 10³. The rapid decrease in yield stress and UTS was observed up to value M = 20 × 10³. For values M > 20 × 10³ the reduction of yield stress and UTS slows down. The cleavage fracture stress continuously decreases with increasing value of M. Concurrently, the changes in dislocation density and in carbide size, morphology and distribution were observed. Various theories of cleavage origin of tempered bainitic microstructures are discussed. The transition temperatures, determined from impact Charpy test, reach minimum at M = 20 × 10³. Using Orowan's theory of initiation of the brittle fracture in steels, the minimum of transition temperatures may be explained by the different reduction rates of cleavage fracture stress and yield stress with value of M.     

Improved precision of iTRAQ and TMT quantification by an axial extraction field in an Orbitrap HCD cell

Improving analytical precision is a major goal in quantitative differential proteomics as high precision ensures low numbers of outliers, a source of false positives with regard to quantification. In addition, higher precision increases statistical power, i.e., the probability to detect significant differences. With chemical labeling using isobaric tags for relative and absolute quantitation (iTRAQ) or tandem mass tag (TMT) reagents, quantification is based on the extraction of reporter ions from tandem mass spectrometry (MS/MS) spectra. We compared the performance of two versions of the LTQ Orbitrap higher energy collisional dissociation (HCD) cell with and without an axial electric field with regard to reporter ion quantification. The HCD cell with the axial electric field was designed to push fragment ions into the C-trap and this version is mounted in current Orbitrap XL ETD and Orbitrap Velos instruments. Our goal was to evaluate whether the purported improvement in ion transmission had a measurable impact on the precision of MS/MS based quantification using peptide labeling with isobaric tags. We show that the axial electric field led to an increased percentage of HCD spectra in which the complete set of reporter ions was detected and, even more important, to a reduction in overall variance, i.e., improved analytical precision of the acquired data. Notably, adequate precision of HCD-based quantification was maintained even for low precursor ion intensities of a complex biological sample. These findings may help researchers in their design of quantitative proteomics studies using isobaric tags and establish HCD-based quantification on the LTQ Orbitrap as a highly precise approach in quantitative proteomics.     

State-space caching revisited

State-space caching is a verification technique for finite-state concurrent systems. It performs an exhaustive exploration of the state space of the system being checked while storing only all states of just one execution sequence plus as many other previously visited states as available memory allows. So far, this technique has been of little practical significance: it allows one to reduce memory usage by only twoo to three times, before an unacceptable blow-up of the run-time overhead sets in. The explosion of the run-time requirements is due to redundant multiple explorations of unstored parts of the state space. Indeed, almost all states in the state space of concurrent systems are typically reached several times during the search.In this paper, we present a method to tackle the main cause of this prohibitive state matching: the exploration of all possible interleavings of concurrent executions of the system which all lead to the same state. Then, we show that, in many cases, with this method, most reachable states are visited only once during state-space exploration. This enables one not to store most of the states that have already been visited without incurring too much redundant explorations of parts of the state space, and makes therefore state-space caching a much more attractive verification method. As an example, we were able to competely explore a state space of 250,000 states while storing simultaneously no more than 500 states and with only a three-fold increas of the run-time requirements.