JRIF: Reactive Information Flow Control for Java

A reactive information flow (RIF) automaton for a value v specifies (i) allowed uses for v and (ii) the RIF automaton for any value that might be directly or indirectly derived from v. RIF automata thus specify how transforming a value alters how the result might be used. Such labels are more expressive than existing approaches for controlling downgrading. We devised a type system around RIF automata and incorporated it into Jif, a dialect of Java that supports a classic form of labels for information flow. By implementing a compiler for the resulting JRIF language, we demonstrate how easy it is to replace a classic information-flow type system by a more expressive RIF-based type system. We programmed two example applications in JRIF, and we discuss insights they provide into the benefits of RIF-based security labels.Supported in part by AFOSR grants F9550-06-0019 and FA9550-11-1-0137, National Science Foundation grants 0430161, 0964409, and CCF-0424422 (TRUST), ONR grants N00014-01- 1-0968 and N00014-09-1-0652, and grants from Microsoft

Automatic partitioning of database applications

Database-backed applications are nearly ubiquitous in our daily lives. Applications that make many small accesses to the database create two challenges for developers: increased latency and wasted resources from numerous network round trips. A well-known technique to improve transactional database application performance is to convert part of the application into stored procedures that are executed on the database server. Unfortunately, this conversion is often difficult. In this paper we describe Pyxis, a system that takes database-backed applications and automatically partitions their code into two pieces, one of which is executed on the application server and the other on the database server. Pyxis profiles the application and server loads, statically analyzes the code's dependencies, and produces a partitioning that minimizes the number of control transfers as well as the amount of data sent during each transfer. Our experiments using TPC-C and TPC-W show that Pyxis is able to generate partitions with up to 3x reduction in latency and 1.7x improvement in throughput when compared to a traditional non-partitioned implementation and has comparable performance to that of a custom stored procedure implementation.National Science Foundation (U.S.). Graduate Research Fellowshi

First-Order Logic for Flow-Limited Authorization

We present the Flow-Limited Authorization First-Order Logic (FLAFOL), a logic for reasoning about authorization decisions in the presence of information-flow policies. We formalize the FLAFOL proof system, characterize its proof-theoretic properties, and develop its security guarantees. In particular, FLAFOL is the first logic to provide a non-interference guarantee while supporting all connectives of first-order logic. Furthermore, this guarantee is the first to combine the notions of non-interference from both authorization logic and information-flow systems. All theorems in this paper are proven in Coq.Comment: Coq code can be found at https://github.com/FLAFOL/flafol-co

Cryptographically Secure Information Flow Control on Key-Value Stores

We present Clio, an information flow control (IFC) system that transparently incorporates cryptography to enforce confidentiality and integrity policies on untrusted storage. Clio insulates developers from explicitly manipulating keys and cryptographic primitives by leveraging the policy language of the IFC system to automatically use the appropriate keys and correct cryptographic operations. We prove that Clio is secure with a novel proof technique that is based on a proof style from cryptography together with standard programming languages results. We present a prototype Clio implementation and a case study that demonstrates Clio's practicality.Comment: Full version of conference paper appearing in CCS 201

Crossover recombination and synapsis are linked by adjacent regions within the N terminus of the Zip1 synaptonemal complex protein

Accurate chromosome segregation during meiosis relies on the prior establishment of at least one crossover recombination event between homologous chromosomes. Most meiotic recombination intermediates that give rise to interhomolog crossovers are embedded within a hallmark chromosomal structure called the synaptonemal complex (SC), but the mechanisms that coordinate the processes of SC assembly (synapsis) and crossover recombination remain poorly understood. Among known structural components of the budding yeast SC, the Zip1 protein is unique for its independent role in promoting crossover recombination; Zip1 is specifically required for the large subset of crossovers that also rely on the meiosis-specific MutSgamma complex. Here we report that adjacent regions within Zip1\u27s N terminus encompass its crossover and synapsis functions. We previously showed that deletion of Zip1 residues 21-163 abolishes tripartite SC assembly and prevents robust SUMOylation of the SC central element component, Ecm11, but allows excess MutSgamma crossover recombination. We find the reciprocal phenotype when Zip1 residues 2-9 or 10-14 are deleted; in these mutants SC assembles and Ecm11 is hyperSUMOylated, but MutSgamma crossovers are strongly diminished. Interestingly, Zip1 residues 2-9 or 2-14 are required for the normal localization of Zip3, a putative E3 SUMO ligase and pro-MutSgamma crossover factor, to Zip1 polycomplex structures and to recombination initiation sites. By contrast, deletion of Zip1 residues 15-20 does not detectably prevent Zip3\u27s localization at Zip1 polycomplex and supports some MutSgamma crossing over but prevents normal SC assembly and Ecm11 SUMOylation. Our results highlight distinct N terminal regions that are differentially critical for Zip1\u27s roles in crossing over and SC assembly; we speculate that the adjacency of these regions enables Zip1 to serve as a liaison, facilitating crosstalk between the two processes by bringing crossover recombination and synapsis factors within close proximity of one another

Mathematical modelling of cytokines, MMPs and fibronectin fragments in osteoarthritic cartilage

Osteoarthritis (OA) is a degenerative disease which causes pain and stiffness in joints. OA progresses through excessive degradation of joint cartilage, eventually leading to significant joint degeneration and loss of function. Cytokines, a group of cell signalling proteins, present in raised concentrations in OA joints, can be classified into pro-inflammatory and anti-inflammatory groups. They mediate cartilage degradation through several mechanisms, primarily the up-regulation of matrix metalloproteinases (MMPs), a group of collagen-degrading enzymes. In this paper we show that the interactions of cytokines within cartilage have a crucial role to play in OA progression and treatment. We develop a four-variable ordinary differential equation model for the interactions between pro- and anti-inflammatory cytokines, MMPs and fibronectin fragments (Fn-fs), a by-product of cartilage degradation and upregulator of cytokines. We show that the model has four classes of dynamic behaviour: homoeostasis, bistable inflammation, tristable inflammation and persistent inflammation. We show that positive and negative feedbacks controlling cytokine production rates can determine either a pre-disposition to OA or initiation of OA. Further, we show that manipulation of cytokine, MMP and Fn-fs levels can be used to treat OA, but we suggest that multiple treatment targets may be essential to halt or slow disease progression

Modulation of the rod outer segment aerobic metabolism diminishes the production of radicals due to light absorption

Oxidative stress is a primary risk factor for both inflammatory and degenerative retinopathies. Our previous data on blue light-irradiated retinas demonstrated an oxidative stress higher in the rod outer segment (OS) than in the inner limb, leading to impairment of the rod OS extra-mitochondrial aerobic metabolism. Here the oxidative metabolism and Reactive Oxygen Intermediates (ROI) production was evaluated in purified bovine rod OS in function of exposure to different illumination conditions. A dose response was observed to varying light intensities and duration in terms of both ROI production and ATP synthesis. Pretreatment with resveratrol, inhibitor of F1Fo-ATP synthase, or metformin, inhibitor of the respiratory complex I, significantly diminished the ROI production. Metformin also diminished the rod OS Complex I activity and reduced the maximal OS response to light in ATP production. Data show for the first time the relationship existing in the rod OS between its -aerobic- metabolism, light absorption, and ROI production. A beneficial effect was exerted by metformin and resveratrol, in modulating the ROI production in the illuminated rod OS, suggestive of their beneficial action also in vivo. Data shed new light on preventative interventions for cone loss secondary to rod damage due to oxidative stress

Functional neuroimaging of visual creativity: a systematic review and meta-analysis

Introduction: The generation of creative visual imagery contributes to technological and scientific innovation, and production of visual art. The underlying cognitive and neural processes are however poorly understood. Methods: This review synthesises functional neuroimaging studies of visual creativity. Seven functional magnetic resonance imaging (fMRI) and 19 electroencephalography (EEG) studies were included, comprising 27 experiments and around 800 participants. Results: Activation likelihood estimation meta-analysis of the fMRI studies comparing visual creativity to non-rest control tasks yielded significant clusters in thalamus, left fusiform gyrus, and right middle and inferior frontal gyri. The EEG studies revealed a tendency for decreased alpha power during visual creativity compared to baseline, but comparisons of visual creativity to non-rest control tasks revealed inconsistent findings. Conclusions: The findings are consistent with suggested contributions to visual creativity of prefrontally-mediated inhibition, evaluation and working memory, as well as visual imagery processes. Findings are discussed in relation to prominent theories of the neural basis of creativity