Do bugs foreshadow vulnerabilities? An in-depth study of the chromium project

As developers face an ever-increasing pressure to engineer secure software, researchers are building an understanding of security-sensitive bugs (i.e. vulnerabilities). Research into mining software repositories has greatly increased our understanding of software quality via empirical study of bugs. Conceptually, however, vulnerabilities differ from bugs: they represent an abuse of functionality as opposed to insufficient functionality commonly associated with traditional, non-security bugs. We performed an in-depth analysis of the Chromium project to empirically examine the relationship between bugs and vulnerabilities. We mined 374,686 bugs and 703 post-release vulnerabilities over five Chromium releases that span six years of development. We used logistic regression analysis, ranking analysis, bug type classifications, developer experience, and vulnerability severity metrics to examine the overarching question: are bugs and vulnerabilities in the same files? While we found statistically significant correlations between pre-release bugs and post-release vulnerabilities, we found the association to be weak. Number of features, source lines of code, and pre-release security bugs are, in general, more closely associated with post-release vulnerabilities than any of our non-security bug categories. In further analysis, we examined sub-types of bugs, such as stability-related bugs, and the associations did not improve. Even the files with the most severe vulnerabilities (by measure of CVSS or bounty payouts) did not show strong correlations with number of bugs. These results indicate that bugs and vulnerabilities are empirically dissimilar groups, motivating the need for security engineering research to target vulnerabilities specifically.     

Dynamic visualization of coexpression in systems genetics data

Biologists hope to address grand scientific challenges by exploring the abundance of data made available through modern microarray technology and other high-throughput techniques. The impact of this data, however, is limited unless researchers can effectively assimilate such complex information and integrate it into their daily research; interactive visualization tools are called for to support the effort. Specifically, typical studies of gene co-expression require novel visualization tools that enable the dynamic formulation and fine-tuning of hypotheses to aid the process of evaluating sensitivity of key parameters. These tools should allow biologists to develop an intuitive understanding of the structure of biological networks and discover genes residing in critical positions in networks and pathways. By using a graph as a universal representation of correlation in gene expression, our system employs several techniques that when used in an integrated manner provide innovative analytical capabilities. Our tool for interacting with gene co-expression data integrates techniques such as: graph layout, qualitative subgraph extraction through a novel 2D user interface, quantitative subgraph extraction using graph-theoretic algorithms or by compound queries, dynamic level-of-detail abstraction, and template-based fuzzy classification. We demonstrate our system using a real-world workflow from a large-scale, systems genetics study of mammalian gene co-expression.     

Top-down proteomic analysis by MALDI-TOF profiling: Concentration-independent biomarkers

Although numerous protein biomarkers have been correlated with advanced disease states, no new clinical assays have been developed. Goals often anticipate disease-specific protein changes that exceed values among healthy individuals, a property common to acute phase reactants. This review considers somewhat different approaches. It focuses on intact protein isoform ratios that present a biomarker without change in the total concentration of the protein. These will seldom be detected by peptide level analysis or by most antibody-based assays. For example, application of an inexpensive method to large sample groups resulted in observation of several polymorphisms, including the first structural polymorphism of apolipoprotein C1. Isoform distribution of this protein was altered and was eventually linked to increased obesity. Numerous other protein isoforms included C- and N-terminal proteolysis, changes of glycoisoform ratios and certain types of sulfhydryl oxidation. While many of these gave excellent statistical correlation with advanced disease, clinical utility was not apparent. More important may be that protein isoform ratios were very stable in each individual. Diagnosis by longitudinal analysis of the same individual might increase sensitivity of protein biomarkers by 20-fold or more. Protein changes that exceed the range of values found among healthy individuals may be uncommon.     

Toward a psychophysiology of performance: Sport psychology principles dealing with anxiety.

In this applied case study during an off-season period, a unique and innovative internal imagery/video/electroencephalogram (EEG) biofeedback protocol was used to train visual attention and increase self-confidence of a collegiate baseball player struggling to recover from a serious eye injury. Results from the ensuing competitive season revealed that self-confidence increased and hitting and fielding performance improved dramatically. In the subsequent competitive season, without psychological skill training, hitting and fielding performance declined to preintervention levels. Although EEG biofeedback has been slow to gain acceptance among applied practitioners, used in conjunction with video and internal imagery, it appears to have potential as a tool for training visual attention in athletes within a variety of externally paced sports, such as baseball, softball, and racquet sports. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Redundant Sensor Calibration Monitoring Using Independent Component Analysis and Principal Component Analysis

This paper presents a comparison of methods for industrial on-line sensor calibration monitoring for redundant sensors. Principal component analysis (PCA) and independent component analysis (ICA) techniques are developed and compared using both simulated data and data sets from an operating nuclear power plant. The performance is dependent on the types of noise sources; however, under most conditions ICA outperforms PCA, based on the bias and variance of their respective parameter estimates. A case study is included to demonstrate the usefulness of both techniques for the early detection of sensor drift.     

Describing Near Surface, Transient Flow Processes in Unconfined Aquifers below Irrigated Lands: Model Application in the Western San Joaquin Valley, California

In order to rigorously examine near surface, field to field interactions between irrigation management regimes and a shallow fluctuating water table, an enhanced deforming finite element (DFE) model was recently developed. The enhanced DFE model, through a process of iteration within each time step, avoids making common assumptions regarding the changing geometry of an aquifer free surface. This paper demonstrates the usefulness and effectiveness of the model by employing it to an irrigated region in the western San Joaquin Valley, Calif., where shallow subsurface tile drains have been installed to control shallow water tables. By virtue of the problems created by the need to dispose off the drainage water, this region has been the focus of several important regional scale modeling exercises, which have evaluated the utility of management strategies, such as source control, groundwater pumping, and land retirement. By refining the focus of the analysis, the enhanced DFE model is found to be able to show that both sources control and managed pumping could be more effective drainage control strategies than predicted based on the results of regional models.     

The Effect of Scan Length on the Structure and Mechanical Properties of Electron Beam-Melted Ti-6Al-4V

Electron beam melting (EBM) is a powder bed fusion-based additive manufacturing process in which selective areas of a layer of powder are melted with an electron beam and a part is built layer by layer. EBM scanning strategies within the Arcam AB^® A2X EBM system rely upon governing relationships between the scan length of the beam path, the beam current, and speed. As a result, a large parameter process window exists for Ti-6Al-4V. Many studies have reviewed various properties of EBM materials without accounting for this effect. The work performed in this study demonstrates the relationship between scan length and the resulting density, microstructure, and mechanical properties of EBM-produced Ti-6Al-4V using the scanning strategies set by the EBM control software. This emphasizes the criticality of process knowledge and careful experimental design, and provides an alternate explanation for reported orientation-influenced strength differences.     

Molecular Mechanisms Underlying TDP-43 Pathology in Cellular and Animal Models of ALS and FTLD

Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are neurodegenerative disorders that exist on a disease spectrum due to pathological, clinical and genetic overlap. In up to 97% of ALS cases and ~50% of FTLD cases, the primary pathological protein observed in affected tissues is TDP-43, which is hyperphosphorylated, ubiquitinated and cleaved. The TDP-43 is observed in aggregates that are abnormally located in the cytoplasm. The pathogenicity of TDP-43 cytoplasmic aggregates may be linked with both a loss of nuclear function and a gain of toxic functions. The cellular processes involved in ALS and FTLD disease pathogenesis include changes to RNA splicing, abnormal stress granules, mitochondrial dysfunction, impairments to axonal transport and autophagy, abnormal neuromuscular junctions, endoplasmic reticulum stress and the subsequent induction of the unfolded protein response. Here, we review and discuss the evidence for alterations to these processes that have been reported in cellular and animal models of TDP-43 proteinopathy.     

Time of Entry of Salmonella and Campylobacter into the Turkey Brooder House

The prevalence of Campylobacter (>90%) and Salmonella (33%) in turkeys at slaughter has been estimated. This report describes studies to estimate the time of entry of Campylobacter and Salmonella into the brooder house, which is the first stage of commercial turkey production. In trial 1, birds (∼100 per time point) were monitored by conventional culture at three intervals (0, 9, and 16 days of age). Campylobacter spp. were not detected in poults at the day of hatch; Salmonella was isolated from the ceca (3.9%) and yolk sac (0.1%). By day 9, Salmonella were frequently isolated from the ceca (55%) and small intestine (45%) while Campylobacter was not cultured. By day 16, the prevalence of Salmonella in the ceca (21%) and small intestine (5.1%) had declined; Campylobacter was infrequently isolated from either the ceca (2%) or small intestine (3%). In trial 2, poults (50 per time point at 5, 20, and 33 days of age) were monitored for Campylobacter and Salmonella by real-time polymerase chain reaction (PCR); Salmonella was also monitored by conventional culture. Whereas Campylobacter was not detected by real-time PCR in the ceca of 5-day-old birds, it was detected on days 20 (92%) and 33 (90%). In contrast, Salmonella was isolated from young birds at days 5 (98%), 20 (98%), and 33 (98%), after which time the turkeys were moved to the finisher house. At slaughter at 138 days, Salmonella prevalence in the ceca had declined (4.5%) in contrast to the prevalence of Campylobacter (92%). Antimicrobial sensitivity profiles of the Salmonella isolates indicated an increase of sulfonamide-resistant isolates throughout the brooder stage. Genotyping by pulsed-field gel electrophoresis analysis of Salmonella (45 isolates per sampling time) indicated fluctuating populations as the birds matured.