Formal analysis of security properties in trusted computing protocols

This research introduces a general methodology in order to create a Coloured Petri Net (CPN) model of a security protocol. Then standard or user-defined security properties of the created CPN model are identified. After adding an attacker model to the protocol model, the security property is verified using state space method. This approach is applied to analyse a number of trusted computing protocols. The results show the applicability of proposed method to analyse both standard and user-defined properties.

Security properties analysis in a TPM-based protocol

Security protocols are designed in order to provide security properties (goals). They achieve their goals using cryptographic primitives such as key agreement or hash functions. Security analysis tools are used in order to verify whether a security protocol achieves its goals or not. The analysed property by specific purpose tools are predefined properties such as secrecy (confidentiality), authentication or non-repudiation. There are security goals that are defined by the user in systems with security requirements. Analysis of these properties is possible with general purpose analysis tools such as coloured petri nets (CPN). This research analyses two security properties that are defined in a protocol that is based on trusted platform module (TPM). The analysed protocol is proposed by Delaune to use TPM capabilities and secrets in order to open only one secret from two submitted secrets to a recipient

Analysis of two authorization protocols using Colored Petri Nets

To prevent unauthorized access to protected trusted platform module (TPM) objects, authorization protocols, such as the object-specific authorization protocol (OSAP), have been introduced by the trusted computing group (TCG). By using OSAP, processes trying to gain access to the protected TPM objects need to prove their knowledge of relevant authorization data before access to the objects can be granted. Chen and Ryan’s 2009 analysis has demonstrated OSAP’s authentication vulnerability in sessions with shared authorization data. They also proposed the Session Key Authorization Protocol (SKAP) with fewer stages as an alternative to OSAP. Chen and Ryan’s analysis of SKAP using ProVerif proves the authentication property. The purpose of this paper was to examine the usefulness of Colored Petri Nets (CPN) and CPN Tools for security analysis. Using OSAP and SKAP as case studies, we construct intruder and authentication property models in CPN. CPN Tools is used to verify the authentication property using a Dolev–Yao-based model. Verification of the authentication property in both models using the state space tool produces results consistent with those of Chen and Ryan.

Visualization of complex biological systems: An immune response model using OpenGL

In this paper we present an update on our novel visualization technologies based on cellular immune interaction from both large-scale spatial and temporal perspectives. We do so with a primary motive: to present a visually and behaviourally realistic environment to the community of experimental biologists and physicians such that their knowledge and expertise may be more readily integrated into the model creation and calibration process. Visualization aids understanding as we rely on visual perception to make crucial decisions. For example, with our initial model, we can visualize the dynamics of an idealized lymphatic compartment, with antigen presenting cells (APC) and cytotoxic T lymphocyte (CTL) cells. The visualization technology presented here offers the researcher the ability to start, pause, zoom-in, zoom-out and navigate in 3-dimensions through an idealised lymphatic compartment.

'Take away from the dry sixties style marking': Lecturer and student perceptions and experiences of audio feedback

Providing audio feedback to assessment is relatively uncommon in higher education. However, published research suggests that it is preferred over written feedback by students but lecturers were less convinced. The aim of this paper is to examine further these findings in the context of a third year business ethics unit. Data was collected from two sources. The first is a series of in-depth, semi-structured interviews conducted with three lecturers providing audio feeback for the first time in Semester One 2011. The second source of data was drawn from the university student evaluation system. A total of 363 responses were used providing 'before' and 'after' perspectives about the effectiveness of audio feedback versus written feedback. Between 2005 and 2009 the survey data provided information about student attitudes to written assessment feedback (n=261). From 2010 onwards the data relates to audio (mp3) feedback (n=102). The analysis of he interview data indicated that introducing audio feedback should be done with care. The perception of the participating lecturers was mixed, ranging from sceptism to outright enthusiasm, but over time the overall approach became positive. It was found that particular attention needs to be paid to small (but important) technical details, and lecturers need to be convinced of its effectieness, especially that it is not necessarily more time consuming than providing written feedback. For students, the analysis revealed a clear preference for audio feedback. It is concluded that there is cause for concern and reason for optimism. It is a cause for concern because there is a possibility that scepticism on the part of academic staff seems to be based on assumptions about what students prefer and a concern about using the technology. There is reason for optimism because the evidence points towards students preferring audio feedback and as academic staff become more familiar with the technology the scepticism tends to evaporate. While this study is limited in scope, questions are raised about tackling negative staff perceptions of audio feedback that are worthy of further research.

Recognition of nonstructural protein-peptides by cytotoxic t-lymphocytes raised against japanese encephalitis-virus

We have previously reported that Lyt(2+) cytotoxic T lymphocytes (CTL) can be raised against Japanese encephalitis virus (JEV) in BALB/c mice. In order to confirm the presence of H-2K(d)-restricted CTL and to examine their cross-recognition of West Wile virus (WNV), we tested the capacity of anti-JEV CTL to lyse uninfected syngeneic target cells that were pulsed with synthetic peptides. The sequence of the synthetic peptides was predicted based upon the H-2K(d) binding consensus motif. We show here that preincubation of uninfected syngeneic targets (P388D1) with JEV NS1- and NS3-derived peptides [NS1 (891-899) and NS3 (1804-1812)], but not with JEV NS5-derived peptide [NS5 (3370-3378)], partially sensitized them for lysis by polyclonal anti-JEV CTL. These results indicate the CTL recognition of NS1- and NS3-derived peptides of JEV.

Surface cathepsin B protects cytotoxic lymphocytes from self-destruction after degranulation.

The granule exocytosis cytotoxicity pathway is the major molecular mechanism for cytotoxic T lymphocyte (CTL) and natural killer (NK) cytotoxicity, but the question of how these cytotoxic lymphocytes avoid self-destruction after secreting perforin has remained unresolved. We show that CTL and NK cells die within a few hours if they are triggered to degranulate in the presence of nontoxic thiol cathepsin protease inhibitors. The potent activity of the impermeant, highly cathepsin B-specific membrane inhibitors CA074 and NS-196 strongly implicates extracellular cathepsin B. CTL suicide in the presence of cathepsin inhibitors requires the granule exocytosis cytotoxicity pathway, as it is normal with CTLs from gld mice, but does not occur in CTLs from perforin knockout mice. Flow cytometry shows that CTLs express low to undetectable levels of cathepsin B on their surface before degranulation, with a substantial rapid increase after T cell receptor triggering. Surface cathepsin B eluted from live CTL after degranulation by calcium chelation is the single chain processed form of active cathepsin B. Degranulated CTLs are surface biotinylated by the cathepsin B-specific affinity reagent NS-196, which exclusively labels immunoreactive cathepsin B. These experiments support a model in which granule-derived surface cathepsin B provides self-protection for degranulating cytotoxic lymphocytes.

Human alveolar T lymphocyte responses to Mycobacterium tuberculosis antigens: role for CD4+ and CD8+ cytotoxic T cells and relative resistance of alveolar macrophages to lysis.

T cell-mediated cytotoxicity against Mycobacterium tuberculosis (MTB)-infected macrophages may be a major mechanism of specific host defense, but little is known about such activities in the lung. Thus, the capacity of alveolar lymphocyte MTB-specific cell lines (AL) and alveolar macrophages (AM) from tuberculin skin test-positive healthy subjects to serve as CTL and target cells, respectively, in response to MTB (H37Ra) or purified protein derivative (PPD) was investigated. Mycobacterial Ag-pulsed AM were targets of blood CTL activity at E:T ratios of > or = 30:1 (51Cr release assay), but were significantly more resistant to cytotoxicity than autologous blood monocytes. PPD- plus IL-2-expanded AL and blood lymphocytes were cytotoxic for autologous mycobacterium-stimulated monocytes at E:T ratios of > or = 10:1. The CTL activity of lymphocytes expanded with PPD was predominantly class II MHC restricted, whereas the CTL activity of lymphocytes expanded with PPD plus IL-2 was both class I and class II MHC restricted. Both CD4+ and CD8+ T cells were enriched in BL and AL expanded with PPD and IL-2, and both subsets had mycobacterium-specific CTL activity. Such novel cytotoxic responses by CD4+ and CD8+ T cells may be a major mechanism of defense against MTB at the site of disease activity.

A CD8(+) T cell clone specific for antigen also recognizes peptidomimics present in anti-idiotypic antibody: Implications for T cell memory

The relay hypothesis [R. Nayak, S. Mitra-Kaushik, M.S. Shaila, Perpetuation of immunological memory: a relay hypothesis, Immunology 102 (2001) 387-395] was earlier proposed to explain perpetuation of immunological memory without requiring long lived memory cells or persisting antigen. This hypothesis envisaged cycles of interaction and proliferation of complementary idiotypic B cells (Burnet cells) and anti-idiotypic B cells (Jerne cells) as the primary reason for perpetuation of immunological memory. The presence of pepti-domimics of antigen in anti-idiotypic antibody and their presentation to antigen specific T cells was postulated to be primary reason for perpetuation of T cell memory. Using a viral hemagglutinin as a model, in this work, we demonstrate the presence of peptidomimics in the variable region of ail anti-idiotypic antibody capable of functionally mimicking the antigen derived peptides. A CD8(+) CTL clone was generated against the hemagglutinin protein which specifically responds to either peptidomimic synthesizing cells or peptidomimic pulsed antigen presenting cells. Thus, it appears reasonable that a population of activated antigen specific T cells is maintained in the body by presentation of peptidomimic through Jerne cells and other antigen presenting cells long after immunization. (C) 2007 Elsevier Inc. All rights reserved.

Protection of adult but not newborn mice against lethal intracerebral challenge with Japanese encephalitis virus by adoptively transferred virus-specific cytotoxic T lymphocytes: Requirement for L3T4(+) T cells

The protective ability of cytotoxic T cells (CTL) raised in vitro against Japanese encephalitis virus (JEV) was examined by adoptive transfer experiments. Adoptive transfer of anti-JEV effecters by intracerebral (i.c.) but not by intraperitoneal (i.p.) or intravenous (i.v.) routes protected adult BALB/c mice against lethal i.c. JEV challenge. In contrast to adult mice, adoptive transfer of anti-JEV effecters into newborn (4-day-old) and suckling (8-14-day-old) mice did not confer protection. However, virus-induced death was delayed in suckling mice compared to newborn mice upon adoptive transfer. The specific reasons for lack of protection in newborn mice are not clear but virus load was found to be higher in newborn mice brains compared to those of adults and virus clearance was observed only in adult mice brains but not in newborn mice brains upon adoptive transfer. Specific depletion of Lyt 2.2(+), L3T4(+) or Thy-1(+) T cell populations before adoptive transfer abrogated the protective ability of transferred effecters. However, when Lyt 2.2(+) cell-depleted and L3T4(+) cell-depleted effecters were mixed and transferred into adult mice the protective activity was retained, demonstrating that both Lyt 2.2(+) and L3T4(+) T cells are necessary to confer protection. Although the presence of L3T4(+) T cells in adoptively transferred effector populations enhanced virus-specific serum neutralizing antibodies, the presence of neutralizing antibodies alone without Lyt 2.2(+) cells was not sufficient to confer protection.

In vivo clearance of Japanese encephalitis virus by adoptively transferred virus specific cytotoxic T lymphocytes

Japanese encephalitis virus (JEV) is a positive stranded RNA virus that belongs to the flavivirus group, JEV infection damages the central nervous system (CNS) and is one of the main causative agents of acute encephalitis, H-2 restricted virus-specific cytotoxic T lymphocytes (CTL) have been generated specifically against JEV in our laboratory and these CTL have been shown to protect mice against lethal challenge with JEV, Virus replication was found to be inhibited in the brains of animals that mere adoptively transferred with JEV specific CTL as revealed by immunohistological staining as,veil as viral plaque assays. We further show that virus specific CTL could be recovered from such protected mice as long as 45 days after adoptive transfer.

Checking Liveness Properties of Presburger Counter Systems Using Reachability Analysis

Counter systems are a well-known and powerful modeling notation for specifying infinite-state systems. In this paper we target the problem of checking liveness properties in counter systems. We propose two semi decision techniques towards this, both of which return a formula that encodes the set of reachable states of the system that satisfy a given liveness property. A novel aspect of our techniques is that they use reachability analysis techniques, which are well studied in the literature, as black boxes, and are hence able to compute precise answers on a much wider class of systems than previous approaches for the same problem. Secondly, they compute their results by iterative expansion or contraction, and hence permit an approximate solution to be obtained at any point. We state the formal properties of our techniques, and also provide experimental results using standard benchmarks to show the usefulness of our approaches. Finally, we sketch an extension of our liveness checking approach to check general CTL properties.

AIDS 免疫治疗相关腺病毒载体的构建

艾滋病（AIDS）是人类免疫缺陷病毒（HIV）感染后引起的一种严重危害人类健 康的致死性传染病。抗HIV 药物挽救和延长了很多HIV 感染者的生命，提高了其生活 质量，但是仍然不能治愈AIDS 和预防传播。最终有效控制HIV 传播和感染的方法可能 仍将依赖于HIV 疫苗的应用。HIV 感染对感染者以及社会造成的灾难性后果使得发展 一个有效的艾滋病疫苗变得尤为紧迫和重要。 负载HIV-1 抗原的DC 回输到HIV-1 感染者体内可以诱导产生较强的抗HIV-1 细 胞免疫反应，这种免疫反应理论上和临床试验都表明治疗AIDS 有效，而且对HARRT 治疗能够产生很好的协同作用。我们拟用感染了重组腺病毒的DC，回输到HIV-1 感染 者体内，期望可以较好地控制病毒复制和阻止感染。为此，本研究我们制备了重组腺病 毒vAd-gp140、vAd-tat 和vAd-gp140-tat，为后续研究奠定基础。 结构蛋白Env 是激发抗体反应的抗原，由于Env 全长有较大细胞毒性，本文采用 了截短的gp140 分子，删除了gp41 的胞内段，降低了gp140 蛋白的细胞毒性。同时保 留了gp41 的跨膜区，表达的蛋白可被正确地锚定在细胞表面，提高蛋白的免疫原性。 将gp140 分子克隆到复制缺陷型的腺病毒载体中，用Wester Blotting 方法检测到gp140 在293 细胞中的表达。 有效的抗 HIV-1 的疫苗应该能够同时激发针对多种亚型病毒株的细胞和体液免疫 反应。早期病毒蛋白激发的CTL 应答在控制病毒载量上更为有效，而且Tat 蛋白的重 要免疫抗原表位和功能区域在不同HIV-1 病毒株之间是高度保守的。Tat 蛋白的多种生 物学功能使得它成为较强的免疫原、共抗原和佐剂，激发T 细胞抗原表位的Th1 型反 应和CTL 反应，扩大体内T 细胞识别的抗原表位谱，提高T 细胞特异性免疫反应。本 文扩增了HIV-1ⅢB 的tat 基因，克隆到复制缺陷性的腺病毒中，构建了重组腺病毒 vAd-tat，并在293 细胞中表达了分子量大小为15kDa 的蛋白。早期蛋白和结构蛋白的联合免疫能够全面地控制病毒复制，在动物实验中一定程度 上保护了猴子。我们将已得到表达的gp140 和tat 基因进行融合表达。利用融合PCR 技 术，扩增gp140 和tat 的融合基因，构建携有HIV-1 gp140-tat 融合基因的重组腺病毒 vAd-gp140-tat。gp140-tat 在293 细胞中的融合表达还需要进一步验证。 下一步的工作是将构建好的重组腺病毒感染DC，检测外源基因在DC 中的表达水 平，对DC 表面分子表型的影响以及对DC 功能的影响。

树突状细胞在抗HIV-1感染免疫预防与治疗中的应用

树突状细胞(DC)不仅是已知惟一能够激活初始T淋巴细胞的抗原提呈细胞,而且也是已知最强的抗原提呈细胞(APC),其对抗原的提呈能力远大于巨噬细胞.经抗原刺激的DC回输到体内后,能够迁移到淋巴结,释放多种细胞因子,同时激活T淋巴细胞的分化和分裂,产生抗原特异性的细胞毒性T淋巴细胞(CTL),这些细胞因子和特异性CTL能够有效地促进或直接杀伤表达该抗原的细胞.

关于可满足性问题的一些研究及其在模型检测中的应用

命题逻辑证明复杂性的研究自从70年代初期由Cook等人提出开始，就一直迅速发展。 Cook等人提出这一领域的初衷是通过证明NP<>CoNP来证明P<>NP。 这一领域近年来的研究内容包括如下几个方向：第一个方向就是“指数下界”问题:也就是证明对于某一个特定的命题逻辑证明系统，存在一个自然的不可满足的公式实例，该系统对这个实例最短的证明规模都是关于实例长度指数级别的； 第二个方向就是比较不同命题逻辑证明系统之间的能力强弱。另一方面，模型检验技术自从80年代由Clarke等人提出用以自动化的检验软硬件系统性质正确性以来，同样的发展迅速。贯穿模型检验技术发展的一个主线就是试图解决系统状态数目过多无法完全在计算机中存储表示的问题，这个问题我们一般称为“状态爆炸”。为了缓解状态爆炸问题，1999年Biere等人提出把命题逻辑可满足性求解工具应用在模型检测领域的限界模型检测方法，相比传统的模型检验算法，对于部分性质，可以极大的减少需要表示的系统状态空间数目，缓解状态爆炸问题。 本文主要包含两部分的内容：第一部分的内容是关于OBDD证明系统的一个理论结果和实际求解的一个解法器的描述。概括的讲，我们解决了Atserias等人在CP2004会议上提出的关于OBDD证明系统的一个问题：我们给出了针对鸽笼问题的多项式规模的OBDD证明系统的一个直接构造，并严格证明了该构造的多项式规模；并且在这个理论结果的基础之上，我们设计了基于OBDD证明系统的实际的求解器，这个求解器可以在多项式时间内解决鸽笼和其他与鸽笼问题结构上相似的实例，这是其他的已知的基于OBDD的求解器无法做到的。这部分内容可以看做是命题逻辑证明复杂性里面第二个方向下的内容，在这里，我们把鸽笼问题 作为一个标尺问题，可以把OBDD证明系统的能力同其他对鸽笼问题的证明为指数的命题逻辑证明系统区分开来。 第二部分的内容是关于限界模型检测的。限界模型检测，是利用命题逻辑可满足性问题求解器来解决一般模型检测问题的方法。对于原本用来描述系统时序性质的时序逻辑的算子，该方法用命题逻辑公式表达出来（在系统迁移关系步数受限的情况下），这个过程就是编码。编码之后，再使用命题逻辑可满足性求解工具来求解。在这部分工作中，我们关注的逻辑是CTL逻辑的fragments，即ECTL或者ACTL，我们详细研究了并改进了ECTL和ACTL到命题逻辑的编码，并且把这个编码过程实现到了开源的模型检测工具平台NuSMV 2上，通过实验来对比限界模型检测方法的效率。实验结果表明，对于某些性质来说，我们的方法相比于传统的基于OBDD的模型检测算法具有优势。