Flow-sensitive, context-sensitive, and object-sensitive information flow control based on program dependence graphs

Information flow control (IFC) checks whether a program can leak secret data to public ports, or whether critical computations can be influenced from outside. But many IFC analyses are imprecise, as they are flow-insensitive, context-insensitive, or object-insensitive; resulting in false alarms. We argue that IFC must better exploit modern program analysis technology, and present an approach based on program dependence graphs (PDG). PDGs have been developed over the last 20 years as a standard device to represent information flow in a program, and today can handle realistic programs. In particular, our dependence graph generator for full Java bytecode is used as the basis for an IFC implementation which is more precise and needs less annotations than traditional approaches. We explain PDGs for sequential and multi-threaded programs, and explain precision gains due to flow-, context-, and object-sensitivity. We then augment PDGs with a lattice of security levels and introduce the flow equations for IFC. We describe algorithms for flow computation in detail and prove their correctness. We then extend flow equations to handle declassification, and prove that our algorithm respects monotonicity of release. Finally, examples demonstrate that our implementation can check realistic sequential programs in full Java bytecode.     

Apoptosis and its role in human disease

In a landmark paper published over two decades ago, Kerr et al. proposed the term apoptosis "for a hitherto little recognized mechanism of controlled cell deletion, which appears to play a complementary but opposite role to mitosis in the regulation of animal cell populations". In the ensuing years, this natural cell death process was studied at the basic science level, primarily with a view to understanding its roles in cancer and in the development and maintenance of the immune system. More recently, however, evidence has suggested a role for the failure of normal apoptosis control in many of the major diseases of the industrialized world. Though complex, apoptosis appears amenable to therapeutic intervention. The range of modern pharmaceutical strategies available to treat such disregulated gene-directed processes offers promise for advances in the control of cancer, immune system and neurodegenerative disorders, heart disease, and perhaps even the aging process itself.     

Natural ligands of the B cell adhesion molecule CD22 beta can be masked by 9-O-acetylation of sialic acids

CD22 beta is a B cell-restricted phosphoprotein expressed on the surface of mature resting B cells. It mediates interactions with other cells partly or exclusively via recognition of alpha 2-6-linked sialic acids on glycoconjugates. The sialylated N-linked oligosaccharides recognized best by CD22 beta are common to many glycoproteins, suggesting that additional regulatory mechanisms may exist. Since the exocyclic side chain of sialic acid is required for recognition, we explored the effects of a naturally occurring modification of the side chain, 9-O-acetylation. Semisynthetic N-linked oligosaccharides terminating with 9-O-acetylated, alpha 2-6-linked sialic acids showed markedly reduced binding to CD22 beta relative to their non-O-acetylated counterparts. Murine lymphoid cells were probed for natural CD22 beta ligands that might be O-acetylated using recombinant soluble forms of CD22 beta (CD22 beta Rg) and influenza C esterase (CHE-Fc, which specifically removes 9-O-acetyl esters from sialic acids). By flow cytometry analysis, CD22 beta Rg binding to splenic B cells and a subset of T cells was increased by pretreatment with CHE-Fc, indicating that some potential CD22 beta ligands are naturally "masked" by 9-O-acetylation. Unmasking of these CD22 beta ligands by removal of 9-O-acetyl esters from intact splenocytes substantially increases their CD22 beta-dependent adhesion in an in vitro adhesion assay. Probing of murine lymphoid tissue sections by CD22 beta Rg and CHE-Fc treatment demonstrates regionally restricted and differentially expressed patterns of distribution between masked and unmasked ligands. For example, lymph node-associated follicular B cells express high levels of CD22 beta ligands, none of which are masked by 9-O-acetylation. In contrast, the ligands on lymph node-associated dendritic cells are almost completely masked by 9-O-acetylation, suggesting that masking may regulate interactions between CD22 beta-positive B cells and dendritic cells. In the thymus, only medullary cells express CD22 beta ligands, and a significant portion of these are masked by 9-O-acetylation, particularly at the cortical-medullary junction. Thus, 9-O-acetylation of sialic acids on immune cells is in a position to negatively regulate CD22 beta adhesion events in a manner depending on both cell type and tissue localization.     

Isolation and characterization of a monoclonal anti-quadruplex DNA antibody from autoimmune "viable motheaten" mice

A cell line that produces an autoantibody specific for DNA quadruplex structures has been isolated and cloned from a hybridoma library derived from 3-month-old nonimmunized autoimmune, immunodeficient "viable motheaten" mice. This antibody has been tested extensively in vitro and found to bind specifically to DNA quadruplex structures formed by two biologically relevant sequence motifs. Scatchard and nonlinear regression analyses using both one- and two-site models were used to derive association constants for the antibody-DNA binding reactions. In both cases, quadruplexes had higher association constants than triplex and duplex molecules. The anti-quadruplex antibody binds to the quadruplex formed by the promoter-region-derived oligonucleotide d(CGCG4GCG) (Ka = 3.3 x 10(6) M-1), and has enhanced affinity for telomere-derived quadruplexes formed by the oligonucleotides d(TG4) and d(T2G4T2G4T2G4T2G4) (Ka = 5.38 x 10(6) and 1.66 x 10(7) M-1, respectively). The antibody binds both types of quadruplexes but has preferential affinity for the parallel four-stranded structure. In vitro radioimmunofilter binding experiments demonstrated that purified anti-DNA quadruplex antibodies from anti-quadruplex antibody-producing tissue culture supernatants have at least 10-fold higher affinity for quadruplexes than for triplex and duplex DNA structures of similar base composition and length. The antibody binds intramolecular DNA triplexes formed by d(G4T3G4T3C4) and d(C4T3G4T3G4), and the duplex d(CGCGCGCGCG)2 with an affinities of 6. 76 x 10(5), 5.59 x 10(5), and 8.26 x 10(5) M-1, respectively. Competition experiments showed that melted quadruplexes are not effective competitors for antibody binding when compared to native structures, confirming that the quadruplex is bound structure-specifically. To our knowledge, this is the first immunological reagent known to specifically recognize quadruplex structures. Subsequent sequence analysis demonstrates homologies between the antibody complementarity determining regions and sequences from Myb family telomere binding proteins, which are hypothesized to control cell aging via telomeric DNA interactions. The presence of this antibody in the autoimmune repertoire suggests a possible linkage between autoimmunity, telomeric DNA binding proteins, and aging.     

Evolving trees for the retrieval of mass spectrometry-based bacteria fingerprints

In this paper, we investigate the application of Evolving Trees (ET) for the analysis of mass spectrometric data of bacteria. Evolving Trees are extensions of self-organizing maps (SOMs) developed for hierarchical classification systems. Therefore, they are well suited for taxonomic problems such as the identification of bacteria. Here, we focus on three topics, an appropriate pre-processing and encoding of the spectra, an adequate data model by means of a hierarchical Evolving Tree and an interpretable visualization. First, the high dimensionality of the data is reduced by a compact representation. Here, we employ sparse coding, specifically tailored for the processing of mass spectra. In the second step, the topographic information which is expected in the fingerprints is used for advanced tree evaluation and analysis. We adapted the original topographic product for SOMs for ET to achieve a judgment of topography. Additionally we transferred the concept of U-matrix for evaluation of the separability of SOMs to their analog in ET. We demonstrate these extensions for two mass spectrometric data sets of bacteria fingerprints and show their classification and evaluation capabilities in comparison to state of the art techniques.     

Reduced cross‐talk in shutter‐glass‐based stereoscopic LCD

Abstract— It is expected that 3‐D will be the next step in the enhanced viewing experience. At present, there are two competing 3‐D technologies for glasses‐based consumer TVs: active shutter glasses and passive polarized glasses. With the ongoing reduction in response time of liquid‐crystal displays (LCDs), this article will focus on shutter‐glass‐based stereoscopic LCDs. In this paper, the properties of such a display system is described and it is demonstrated that by adding a line‐scanning backlight, the cross‐talk can be reduced to less than 1.4%, allowing for excellent 3‐D portrayal. For images of extreme contrast, this is perceivable, but not judged annoying by a panel of expert viewers. Which characteristics of the display and shutter glasses that should be optimized to create an inexpensive, cross‐talk‐free, 3‐D LCD are discussed.     

An Internet-based negotiation server for e-commerce

This paper describes the design and implementation of a replicable, Internet-based negotiation server for conducting bargaining-type negotiations between enterprises involved in e-commerce and e-business. Enterprises can be buyers and sellers of products/services or participants of a complex supply chain engaged in purchasing, planning, and scheduling. Multiple copies of our server can be installed to complement the services of Web servers. Each enterprise can install or select a trusted negotiation server to represent his/her interests. Web-based GUI tools are used during the build-time registration process to specify the requirements, constraints, and rules that represent negotiation policies and strategies, preference scoring of different data conditions, and aggregation methods for deriving a global cost-benefit score for the item(s) under negotiation. The registration information is used by the negotiation servers to automatically conduct bargaining type negotiations on behalf of their clients. In this paper, we present the architecture of our implementation as well as a framework for automated negotiations, and describe a number of communication primitives which are used in the underlying negotiation protocol. A constraint satisfaction processor (CSP) is used to evaluate a negotiation proposal or counterproposal against the registered requirements and constraints of a client company. In case of a constraint violation, an event is posted to trigger the execution of negotiation strategic rules, which either automatically relax the violated constraint, ask for human intervention, invoke an application, or perform other remedial operations. An Event-Trigger-Rule (ETR) server is used to manage events, triggers, and rules. Negotiation strategic rules can be added or modified at run-time. A cost-benefit analysis component is used to perform quantitative analysis of alternatives. The use of negotiation servers to conduct automated negotiation has been demonstrated in the context of an integrated supply chain scenario. Received: 30 October 2000 / Accepted: 12 January 2001 Published online: 2 August 2001     

NOX removal in excess oxygen by plasma-enhanced selective catalytic reduction

In the off-gases of internal combustion engines running with oxygen excess, non-thermal plasmas (NTPs) have an oxidative potential, which results in an effective conversion of NO to NO₂. In combination with appropriate catalysts and ammonia (NH₃-SCR) or hydrocarbons (HC-SCR) as a reducing agent, this can be utilized to reduce nitric oxides (NO and NO₂) synergistically to molecular nitrogen.

The combination of SCR and cold plasma enhanced the overall reaction rate and allowed an effective removal of NO_X at low temperatures. Using NH₃ as a reducing agent, NO_X was converted to N₂ on zeolites or NH₃-SCR catalysts like V₂O₅–WO₃/TiO₂ at temperatures as low as 100–200 °C. Significant synergetic effects of plasma and catalyst treatment were observed both for NH₃ stored by ion exchange on the zeolite and for continuous NH₃ supply.

Certain modifications of Al₂O₃ and ZrO₂ have been found to be effective as catalysts in the plasma-assisted HC-SCR in oxygen excess. With an energy supply of about 30 eV/NO-molecule, 500 ppm NO was reduced by more than half at a temperature of 300 °C and a space velocity of 20 000 h⁻¹ at the catalyst. The synergistic combinations of NTP and both NH₃- and HC-SCR have been verified under real diesel engine exhaust conditions.