An Embedding of the BSS Model of Computation in Light Affine Lambda-Calculus

This paper brings together two lines of research: implicit characterization of complexity classes by Linear Logic (LL) on the one hand, and computation over an arbitrary ring in the Blum-Shub-Smale (BSS) model on the other. Given a fixed ring structure K we define an extension of Terui's light affine lambda-calculus typed in LAL (Light Affine Logic) with a basic type for K. We show that this calculus captures the polynomial time function class FP(K): every typed term can be evaluated in polynomial time and conversely every polynomial time BSS machine over K can be simulated in this calculus.Comment: 11 pages. A preliminary version appeared as Research Report IAC CNR Roma, N.57 (11/2004), november 200

Quantum entanglement and the Bell Matrix

We present a class of maximally entangled states generated by a high-dimensional generalisation of the \textsc{cnot} gate. The advantage of our approach is the simple algebraic structure of both entangling operator and resulting entangled states. In order to show that the method can be applied to any dimension, we introduce new sufficient conditions for global and maximal entanglement with respect to Meyer and Wallach's measure.Comment: 11 pages, 3 figure

Implementation of a regulatory gene network to simulate the TH1/2 differentiation in an agent-based model of hypersensitivity reactions

Abstract Motivation: An unbalanced differentiation of T helper cells from precursor type TH0 to the TH1 or TH2 phenotype in immune responses often leads to a pathological condition. In general, immune reactions biased toward TH1 responses may result in auto-immune diseases, while enhanced TH2 responses may cause allergic reactions. The aim of this work is to integrate a gene network of the TH differentiation in an agent-based model of the hyper-sensitivity reaction. The implementation of such a system introduces a second level of description beyond the mesoscopic level of the inter-cellular interaction of the agent-based model. The intra-cellular level consists in the cell internal dynamics of gene activation and transcription. The gene regulatory network includes genes-related molecules that have been found to be involved in the differentiation process in TH cells. Results: The simulator reproduces the hallmarks of an IgE-mediated hypersensitive reaction and provides an example of how to combine the mesoscopic level description of immune cells with the microscopic gene-level dynamics. Availability: The basic version of the simulator of the immune response can be downloaded here: http://www.iac.cnr.it/~filippo/C-ImmSim.html Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

Ten years of cube attacks

In 2009, Dinur and Shamir proposed the cube attack, an algebraic cryptanalysis technique that only requires black box access to a target cipher. Since then, this attack has received both many criticisms and endorsements from crypto community; this work aims at revising and collecting the many attacks that have been proposed starting from it. We categorise all of these attacks in five classes; for each class, we provide a brief summary description along with the state-of-the-art references and the most recent cryptanalysis results. Furthermore, we extend and refine the new notation we proposed in 2021 and we use it to provide a consistent definition for each attack family. Finally, in the appendix, we provide an in-depth description of the kite attack framework, a cipher independent tool we firstly proposed in 2018 that implements the kite attack on GPUs. To prove its effectiveness, we use Mickey2.0 as a use case, showing how to embed it in the framework

Combining Network Modeling and Gene Expression Microarray Analysis to Explore the Dynamics of Th1 and Th2 Cell Regulation

Two T helper (Th) cell subsets, namely Th1 and Th2 cells, play an important role in inflammatory diseases. The two subsets are thought to counter-regulate each other, and alterations in their balance result in different diseases. This paradigm has been challenged by recent clinical and experimental data. Because of the large number of genes involved in regulating Th1 and Th2 cells, assessment of this paradigm by modeling or experiments is difficult. Novel algorithms based on formal methods now permit the analysis of large gene regulatory networks. By combining these algorithms with in silico knockouts and gene expression microarray data from human T cells, we examined if the results were compatible with a counter-regulatory role of Th1 and Th2 cells. We constructed a directed network model of genes regulating Th1 and Th2 cells through text mining and manual curation. We identified four attractors in the network, three of which included genes that corresponded to Th0, Th1 and Th2 cells. The fourth attractor contained a mixture of Th1 and Th2 genes. We found that neither in silico knockouts of the Th1 and Th2 attractor genes nor gene expression microarray data from patients with immunological disorders and healthy subjects supported a counter-regulatory role of Th1 and Th2 cells. By combining network modeling with transcriptomic data analysis and in silico knockouts, we have devised a practical way to help unravel complex regulatory network topology and to increase our understanding of how network actions may differ in health and disease

Immunological network signatures of cancer progression and survival

<p>Abstract</p> <p>Background</p> <p>The immune contribution to cancer progression is complex and difficult to characterize. For example in tumors, immune gene expression is detected from the combination of normal, tumor and immune cells in the tumor microenvironment. Profiling the immune component of tumors may facilitate the characterization of the poorly understood roles immunity plays in cancer progression. However, the current approaches to analyze the immune component of a tumor rely on incomplete identification of immune factors.</p> <p>Methods</p> <p>To facilitate a more comprehensive approach, we created a ranked immunological relevance score for all human genes, developed using a novel strategy that combines text mining and information theory. We used this score to assign an immunological grade to gene expression profiles, and thereby quantify the immunological component of tumors. This immunological relevance score was benchmarked against existing manually curated immune resources as well as high-throughput studies. To further characterize immunological relevance for genes, the relevance score was charted against both the human interactome and cancer information, forming an expanded interactome landscape of tumor immunity. We applied this approach to expression profiles in melanomas, thus identifying and grading their immunological components, followed by identification of their associated protein interactions.</p> <p>Results</p> <p>The power of this strategy was demonstrated by the observation of early activation of the adaptive immune response and the diversity of the immune component during melanoma progression. Furthermore, the genome-wide immunological relevance score classified melanoma patient groups, whose immunological grade correlated with clinical features, such as immune phenotypes and survival.</p> <p>Conclusions</p> <p>The assignment of a ranked immunological relevance score to all human genes extends the content of existing immune gene resources and enriches our understanding of immune involvement in complex biological networks. The application of this approach to tumor immunity represents an automated systems strategy that quantifies the immunological component in complex disease. In so doing, it stratifies patients according to their immune profiles, which may lead to effective computational prognostic and clinical guides.</p

Greedy expansions and sets with deleted digits

AbstractWe generalize a result of Daróczy and Kátai, on the characterization of univoque numbers with respect to a non-integer base (Publ. Math. Debrecen 46(3–4) (1995) 385) by relaxing the digit alphabet to a generic set of real numbers. We apply the result to derive the construction of a Büchi automaton accepting all and only the greedy sequences for a given base and digit set. In the appendix, we prove a more general version of the fact that the expansion of an element x∈Q(q) is ultimately periodic, if q is a Pisot number