MySQL extension automatic porting to PDO for PHP migration and security improvement

In software management, the upgrade of programming languages may introduce critical issues. This is the case of PHP, the fifth version of which is going towards the end of the support. The new release improves on different aspects, but removes the old deprecated MySQL extensions, and supports only the newer library of functions for the connection to the databases. The software systems already in place need to be renewed to be compliant with respect to the new language version. The conversion of the source code, to be safe against injection attacks, should involve also the transformation of the query code. The purpose of this work is the design of specific tool that automatically applies the required transformation yielding to a precise and efficient conversion procedure. The tool has been applied to different projects to provide evidence of its effectiveness

Tuning adhesion failure strength for tissue-specific applications

Soft tissue adhesives are employed to repair and seal many different organs, which range in both tissue surface chemistry and mechanical challenges during organ function. This complexity motivates the development of tunable adhesive materials with high resistance to uniaxial or multiaxial loads dictated by a specific organ environment. Co-polymeric hydrogels comprising aminated star polyethylene glycol and dextran aldehyde (PEG:dextran) are materials exhibiting physico-chemical properties that can be modified to achieve this organ- and tissue-specific adhesion performance. Here we report that resistance to failure under specific loading conditions, as well as tissue response at the adhesive material–tissue interface, can be modulated through regulation of the number and density of adhesive aldehyde groups. We find that atomic force microscopy (AFM) can characterize the material aldehyde density available for tissue interaction, and in this way enable rapid, informed material choice. Further, the correlation between AFM quantification of nanoscale unbinding forces with macroscale measurements of adhesion strength by uniaxial tension or multiaxial burst pressure allows the design of materials with specific cohesion and adhesion strengths. However, failure strength alone does not predict optimal in vivo reactivity. Thus, we demonstrate that the development of adhesive materials is significantly enabled when experiments are integrated along length scales to consider organ chemistry and mechanical loading states concurrently with adhesive material properties and tissue response.National Science Foundation (U.S.) (Career Award)American Society for Engineering Education. National Defense Science and Engineering Graduate FellowshipNational Institutes of Health (U.S.) (Grant ERE GM 49039

Tuning of Collagen Scaffold Properties Modulates Embedded Endothelial Cell Regulatory Phenotype in Repair of Vascular Injuries In Vivo

Perivascularly implanted matrix embedded endothelial cells (MEECs) are potent regulators of inflammation and intimal hyperplasia following vascular injuries. Endothelial cells (ECs) in collagen scaffolds adopt a reparative phenotype with significant therapeutic potential. Although the biology of MEECs is increasingly understood, tuning of scaffold properties to control cell-substrate interactions is less well-studied. It is hypothesized that modulating scaffold degradation would change EC phenotype. Scaffolds with differential degradation are prepared by cross-linking and predegradation. Vascular injury increases degradation and the presence of MEECs retards injury-mediated degradation. MEECs respond to differential scaffold properties with altered viability in vivo, suppressed smooth muscle cell (SMC) proliferation in vitro, and altered interleukin-6 and matrix metalloproteinase-9 expression. When implanted perivascularly to a murine carotid wire injury, tuned scaffolds change MEEC effects on vascular repair and inflammation. Live animal imaging enables real-time tracking of cell viability, inflammation, and scaffold degradation, affording an unprecedented understanding of interactions between cells, substrate, and tissue. MEEC-treated injuries improve endothelialization and reduce SMC hyperplasia over 14 d. These data demonstrate the potent role material design plays in tuning MEEC efficacy in vivo, with implications for the design of clinical therapies.National Institutes of Health (U.S.) (Grant R01 GM 49039

In vivo and in vitro tracking of erosion in biodegradable materials using non-invasive fluorescence imaging

Author Manuscript 2012 March 1.The design of erodible biomaterials relies on the ability to program the in vivo retention time, which necessitates real-time monitoring of erosion. However, in vivo performance cannot always be predicted by traditional determination of in vitro erosion[superscript 1, 2] , and standard methods sacrifice samples or animals[superscript 3], preventing sequential measures of the same specimen. We harnessed non-invasive fluorescence imaging to sequentially follow in vivo material-mass loss to model the degradation of materials hydrolytically (PEG:dextran hydrogel) and enzymatically (collagen). Hydrogel erosion rates in vivo and in vitro correlated, enabling the prediction of in vivo erosion of new material formulations from in vitro data. Collagen in vivo erosion was used to infer physiologic in vitro conditions that mimic erosive in vivo environments. This approach enables rapid in vitro screening of materials, and can be extended to simultaneously determine drug release and material erosion from a drug-eluting scaffold, or cell viability and material fate in tissue-engineering formulations.National Institutes of Health (U.S.) (GM/HL 49039)National Institutes of Health (U.S.) (UL1 RR 025758

Regulation of dendrimer/dextran material performance by altered tissue microenvironment in inflammation and neoplasia

available in PMC 2015 October 30A “one material fits all” mindset ignores profound differences in target tissues that affect their responses and reactivity. Yet little attention has been paid to the role of diseased tissue on material performance, biocompatibility, and healing capacity. We assessed material-tissue interactions with a prototypical adhesive material based on dendrimer/dextran and colon as a model tissue platform. Adhesive materials have high sensitivity to changes in their environment and can be exploited to probe and quantify the influence of even subtle modifications in tissue architecture and biology. We studied inflammatory colitis and colon cancer and found not only a difference in adhesion related to surface chemical interactions but also the existence of a complex interplay that determined the overall dendrimer/dextran biomaterial compatibility. Compatibility was contextual, not simply a constitutive property of the material, and was related to the extent and nature of immune cells in the diseased environment present before material implantation. We then showed how to use information about local alterations of the tissue microenvironment to assess disease severity. This in turn guided us to an optimal dendrimer/dextran formulation choice using a predictive model based on clinically relevant conditions.National Institutes of Health (U.S.) (NIH grant R01 GM-49039)Deshpande Center for Technological Innovatio

IC-Cut: A Compositional Search Strategy for Dynamic Test Generation

Abstract. We present IC-Cut, short for “Interface-Complexity-based Cut”, a new compositional search strategy for systematically testing large programs. IC-Cut dynamically detects function interfaces that are simple enough to be cost-effective for summarization. IC-Cut then hierarchically decomposes the program into units defined by such functions and their sub-functions in the call graph. These units are tested independently, their test results are recorded as low-complexity function summaries, and the summaries are reused when testing higher-level functions in the call graph, thus limiting overall path explosion. When the decomposed units are tested exhaustively, they constitute verified components of the program. IC-Cut is run dynamically and on-the-fly during the search, typically refining cuts as the search advances. We have implemented this algorithm as a new search strategy in the whitebox fuzzer SAGE, and present detailed experimental results ob-tained when fuzzing the ANI Windows image parser. Our results show that IC-Cut alleviates path explosion while preserving or even increasing code coverage and bug finding, compared to the current generational-search strategy used in SAGE.

Proving Memory Safety of the ANI Windows Image Parser Using Compositional Exhaustive Testing

We report in this paper how we proved memory safety of a complex Windows image parser written in low-level C in only three months of work and using only three core tech-niques, namely (1) symbolic execution at the x86 binary level, (2) exhaustive program path enumeration and testing, and (3) user-guided program decomposition and summariza-tion. We also used a new tool, named MicroX, for executing code fragments in isolation using a custom virtual machine designed for testing purposes. As a result of this work, we are able to prove, for the first time, that a Windows image parser is memory safe, i.e., free of any buffer-overflow secu-rity vulnerabilities, modulo the soundness of our tools and several additional assumptions regarding bounding input-dependent loops, fixing a few buffer-overflow bugs, and ex-cluding some code parts that are not memory safe by design. In the process, we also discovered and fixed several limita-tions in our tools, and narrowed the gap between systematic testing and verification. 1

A Moving Boundary Flux Stabilization Method for Cartesian Cut-Cell Grids using Directional Operator Splitting

An explicit moving boundary method for the numerical solution of time-dependent hyperbolic conservation laws on grids produced by the intersection of complex geometries with a regular Cartesian grid is presented. As it employs directional operator splitting, implementation of the scheme is rather straightforward. Extending the method for static walls from Klein et al., Phil. Trans. Roy. Soc., A367, no. 1907, 4559-4575 (2009), the scheme calculates fluxes needed for a conservative update of the near-wall cut-cells as linear combinations of standard fluxes from a one-dimensional extended stencil. Here the standard fluxes are those obtained without regard to the small sub-cell problem, and the linear combination weights involve detailed information regarding the cut-cell geometry. This linear combination of standard fluxes stabilizes the updates such that the time-step yielding marginal stability for arbitrarily small cut-cells is of the same order as that for regular cells. Moreover, it renders the approach compatible with a wide range of existing numerical flux-approximation methods. The scheme is extended here to time dependent rigid boundaries by reformulating the linear combination weights of the stabilizing flux stencil to account for the time dependence of cut-cell volume and interface area fractions. The two-dimensional tests discussed include advection in a channel oriented at an oblique angle to the Cartesian computational mesh, cylinders with circular and triangular cross-section passing through a stationary shock wave, a piston moving through an open-ended shock tube, and the flow around an oscillating NACA 0012 aerofoil profile.Comment: 30 pages, 27 figures, 3 table