Testing systems of identical components

We consider the problem of testing sequentially the components of a multi-component reliability system in order to figure out the state of the system via costly tests. In particular, systems with identical components are considered. The notion of lexicographically large binary decision trees is introduced and a heuristic algorithm based on that notion is proposed. The performance of the heuristic algorithm is demonstrated by computational results, for various classes of functions. In particular, in all 200 random cases where the underlying function is a threshold function, the proposed heuristic produces optimal solutions

On the size of binary decision diagrams representing Boolean functions

AbstractWe consider the size of the representation of Boolean functions by several classes of binary decision diagrams (BDDs) (also called branching programs), namely the classes of arbitrary BDDs of real time BDD (RBDD) (i.e. BDDs where each computation path is limited to the number of variables), of free BDDs (FBDDs) (also called read-once-only branching programs), of ordered BDDs (OBDDS) i.e. FBDDs where variables are tested in the same order along all paths), and binary decision trees (BDTs).Using well-known techniques, we first establish asymptotically sharp bounds as a function of n on the minimum size of arbitrary BDDs representing almost all Boolean functions of n variables and provide asymptotic lower and upper bounds, differing only by a factor of two, on the minimum size OBDDs representing almost all Boolean functions of n variables.We then, using a method to obtain exponential lower bounds on complexity of computation of Boolean functions by RBDD, FBDD and OBDD that originated in (Breitbart, 1968), present the highest such bounds to date and also present improved bounds on the relative economy of description of particular Boolean functions by the above classes of BDDs. For each nontrivial pair of BDD classes considered, we exhibit infinite families of Boolean functions representable much more concisely by BDDs in one class than by BDDs in the other

Determining the Solution Space of Vertex-Cover by Interactions and Backbones

To solve the combinatorial optimization problems especially the minimal Vertex-cover problem with high efficiency, is a significant task in theoretical computer science and many other subjects. Aiming at detecting the solution space of Vertex-cover, a new structure named interaction between nodes is defined and discovered for random graph, which results in the emergence of the frustration and long-range correlation phenomenon. Based on the backbones and interactions with a node adding process, we propose an Interaction and Backbone Evolution Algorithm to achieve the reduced solution graph, which has a direct correspondence to the solution space of Vertex-cover. By this algorithm, the whole solution space can be obtained strictly when there is no leaf-removal core on the graph and the odd cycles of unfrozen nodes bring great obstacles to its efficiency. Besides, this algorithm possesses favorable exactness and has good performance on random instances even with high average degrees. The interaction with the algorithm provides a new viewpoint to solve Vertex-cover, which will have a wide range of applications to different types of graphs, better usage of which can lower the computational complexity for solving Vertex-cover

Stability analysis on the finite-temperature replica-symmetric and first-step replica-symmetry-broken cavity solutions of the random vertex cover problem

The vertex-cover problem is a prototypical hard combinatorial optimization problem. It was studied in recent years by physicists using the cavity method of statistical mechanics. In this paper, the stability of the finite-temperature replica-symmetric (RS) and the first-step replica-symmetry-broken (1RSB) cavity solutions of the vertex cover problem on random regular graphs of finite vertex-degree $K$ are analyzed by population dynamics simulations. We found that (1) the lowest temperature for the RS solution to be stable, $T_{RS}(K)$, is not a monotonic function of $K$, and (2) at relatively large connectivity $K$ and temperature $T$ slightly below the dynamic transition temperature $T_d(K)$, the 1RSB solutions with small but non-negative complexity values are stable. Similar results are obtained on random Poissonian graphs.Comment: 15 pages, 9 figure

Scalable data management in distributed information systems

[EN] In the era of cloud computing and huge information systems, distributed applications should manage dynamic workloads; i.e., the amount of client requests per time unit may vary frequently and servers should rapidly adapt their computing efforts to those workloads. Cloud systems provide a solid basis for this kind of applications but most of the traditional relational database systems are unprepared to scale up with this kind of distributed systems. This paper surveys different techniques being used in modern SQL, NoSQL and NewSQL systems in order to increase the scalability and adaptability in the management of persistent data. © 2011 Springer-Verlag.This work has been supported by EU FEDER and Spanish MICINN under research grants TIN2009-14460-C03-01 and TIN2010-17193Pallardó Lozoya, MR.; Esparza Peidro, J.; García Escriva, JR.; Decker, H.; Muñoz Escoí, FD. (2011). Scalable data management in distributed information systems. 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Bull. 32, 36–43 (2009)DeCandia, G., Hastorun, D., Jampani, M., Kakulapati, G., Lakshman, A., Pilchin, A., Sivasubramanian, S., Vosshall, P., Vogels, W.: Dynamo: Amazon’s highly available key-value store. In: 21st ACM Symp. on Operat. Syst. Princ. (SOSP), Stevenson, Washington, USA, pp. 205–220 (2007)Stonebraker, M., Madden, S., Abadi, D.J., Harizopoulos, S., Hachem, N., Helland, P.: The end of an architectural era (it’s time for a complete rewrite). In: 33rd Intnl. Conf. on Very Large Data Bases (VLDB), pp. 1150–1160. ACM Press, Vienna (2007)Lomet, D.B., Fekete, A., Weikum, G., Zwilling, M.J.: Unbundling transaction services in the cloud. In: 4th Biennial Conf. on Innov. Data Syst. Research (CIDR), Asilomar, CA, USA (2009)Campbell, D.G., Kakivaya, G., Ellis, N.: Extreme scale with full SQL language support in Microsoft SQL Azure. In: Intnl. Conf. on Mngmnt. of Data (SIGMOD), pp. 1021–1024. ACM, New York (2010)Levandoski, J.J., Lomet, D., Mokbel, M.F., Zhao, K.K.: Deuteronomy: Transaction support for cloud data. In: 5th Biennial Conf. on Innov. Data Syst. Research (CIDR), Asilomar, CA, USA, pp. 123–133 (2011)Helland, P., Campbell, D.: Building on quicksand. In: 4th Biennial Conf. on Innov. Data Syst. Research (CIDR), Asilomar, CA, USA (2009)Muñoz-Escoí, F.D., García-Escrivá, J.R., Pallardó-Lozoya, M.R., Esparza-Peidro, J.: Managing scalable persistent data. Technical Report ITI-SIDI-2011/003, Instituto Tecnológico de Informática, Universitat Politècnica de València, Spain (2011)Agrawal, D., El Abbadi, A., Antony, S., Das, S.: Data management challenges in cloud computing infrastructures. In: 6th Intnl. Wshop. on Databases in Networked Information Systems (DNIS), Aizu-Wakamatsu, Japan, pp. 1–10 (2010)Stonebraker, M.: The case for shared nothing. IEEE Database Eng. 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Design and Impl. (OSDI), pp. 105–120. USENIX Assoc., San Francisco (2004)Stonebraker, M., Cattell, R.: Ten rules for scalable performance in ”simple operation” datastores. Commun. ACM 54, 72–80 (2011)Amazon Web Services LLC: Amazon SimpleDB (2011), http://aws.amazon.com/simpledb/Lamport, L.: The part-time parliament. ACM Trans. Comput. Syst. 16, 133–169 (1998)Bernstein, P.A., Reid, C.W., Das, S.: Hyder - a transactional record manager for shared flash. In: 5th Biennial Conf. on Innov. Data Syst. Research (CIDR), Asilomar, CA, USA, pp. 9–20 (2011)Bonnet, P., Bouganim, L.: Flash device support for database management. In: 5th Biennial Conf. on Innov. Data Syst. 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The attitudes of brain cancer patients and their caregivers towards death and dying: a qualitative study

<p>Abstract</p> <p>Background</p> <p>Much money and energy has been spent on the study of the molecular biology of malignant brain tumours. However, little attention has been paid to the wishes of patients afflicted with these incurable tumours, and how this might influence treatment considerations.</p> <p>Methods</p> <p>We interviewed 29 individuals – 7 patients dying of a malignant brain tumor and 22 loved ones. One-on-one interviews were conducted according to a pre-designed interview guide. A combination of open-ended questions, as well as clinical scenarios was presented to participants in order to understand what is meaningful and valuable to them when determining treatment options and management approaches. The results were analyzed, coded, and interpreted using qualitative analytic techniques in order to arrive at several common overarching themes.</p> <p>Results</p> <p>Seven major themes were identified. In general, respondents were united in viewing brain cancer as unique amongst malignancies, due in large part to the premium placed on mental competence and cognitive functioning. Importantly, participants found their experiences, however difficult, led to the discovery of inner strength and resilience. Responses were usually framed within an interpersonal context, and participants were generally grateful for the opportunity to speak about their experiences. Attitudes towards religion, spirituality, and euthanasia were also probed.</p> <p>Conclusion</p> <p>Several important themes underlie the experiences of brain cancer patients and their caregivers. It is important to consider these when managing these patients and to respect not only their autonomy but also the complex interpersonal toll that a malignant diagnosis can have.</p

Viral population estimation using pyrosequencing

The diversity of virus populations within single infected hosts presents a major difficulty for the natural immune response as well as for vaccine design and antiviral drug therapy. Recently developed pyrophosphate based sequencing technologies (pyrosequencing) can be used for quantifying this diversity by ultra-deep sequencing of virus samples. We present computational methods for the analysis of such sequence data and apply these techniques to pyrosequencing data obtained from HIV populations within patients harboring drug resistant virus strains. Our main result is the estimation of the population structure of the sample from the pyrosequencing reads. This inference is based on a statistical approach to error correction, followed by a combinatorial algorithm for constructing a minimal set of haplotypes that explain the data. Using this set of explaining haplotypes, we apply a statistical model to infer the frequencies of the haplotypes in the population via an EM algorithm. We demonstrate that pyrosequencing reads allow for effective population reconstruction by extensive simulations and by comparison to 165 sequences obtained directly from clonal sequencing of four independent, diverse HIV populations. Thus, pyrosequencing can be used for cost-effective estimation of the structure of virus populations, promising new insights into viral evolutionary dynamics and disease control strategies.Comment: 23 pages, 13 figure

Simultaneous Identification of DNA and RNA Viruses Present in Pig Faeces Using Process-Controlled Deep Sequencing

Background: Animal faeces comprise a community of many different microorganisms including bacteria and viruses. Only scarce information is available about the diversity of viruses present in the faeces of pigs. Here we describe a protocol, which was optimized for the purification of the total fraction of viral particles from pig faeces. The genomes of the purified DNA and RNA viruses were simultaneously amplified by PCR and subjected to deep sequencing followed by bioinformatic analyses. The efficiency of the method was monitored using a process control consisting of three bacteriophages (T4, M13 and MS2) with different morphology and genome types. Defined amounts of the bacteriophages were added to the sample and their abundance was assessed by quantitative PCR during the preparation procedure. Results: The procedure was applied to a pooled faecal sample of five pigs. From this sample, 69,613 sequence reads were generated. All of the added bacteriophages were identified by sequence analysis of the reads. In total, 7.7 % of the reads showed significant sequence identities with published viral sequences. They mainly originated from bacteriophages (73.9%) and mammalian viruses (23.9%); 0.8 % of the sequences showed identities to plant viruses. The most abundant detected porcine viruses were kobuvirus, rotavirus C, astrovirus, enterovirus B, sapovirus and picobirnavirus. In addition, sequences with identities to the chimpanzee stool-associated circular ssDNA virus were identified. Whole genome analysis indicates that this virus, tentatively designated as pig stool-associated circular ssDNA virus (PigSCV), represents a novel pi

Safety and efficacy of VB-111, an anticancer gene therapy, in patients with recurrent glioblastoma: results of a phase I/II study.

BackgroundVB-111 is a non-replicating adenovirus carrying a Fas-chimera transgene, leading to targeted apoptosis of tumor vascular endothelium and induction of a tumor-specific immune response. This phase I/II study evaluated the safety, tolerability, and efficacy of VB-111 with and without bevacizumab in recurrent glioblastoma (rGBM).MethodsPatients with rGBM (n = 72) received VB-111 in 4 treatment groups: subtherapeutic (VB-111 dose escalation), limited exposure (LE; VB-111 monotherapy until progression), primed combination (VB-111 monotherapy continued upon progression with combination of bevacizumab), and unprimed combination (upfront combination of VB-111 and bevacizumab). The primary endpoint was median overall survival (OS). Secondary endpoints were safety, overall response rate, and progression-free survival (PFS).ResultsVB-111 was well tolerated. The most common adverse event was transient mild-moderate fever. Median OS time was significantly longer in the primed combination group compared with both LE (414 vs 223 days; hazard ratio [HR], 0.48; P = 0.043) and unprimed combination (414 vs 141.5 days; HR, 0.24; P = 0.0056). Patients in the combination phase of the primed combination group had a median PFS time of 90 days compared with 60 in the LE group (HR, 0.36; P = 0.032), and 63 in the unprimed combination group (P = 0.72). Radiographic responders to VB-111 exhibited characteristic, expansive areas of necrosis in the areas of initial enhancing disease.ConclusionsPatients with rGBM who were primed with VB-111 monotherapy that continued after progression with the addition of bevacizumab showed significant survival and PFS advantage, as well as specific imaging characteristics related to VB-111 mechanism of action. These results warrant further assessment in a randomized controlled study

PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity

<p>Abstract</p> <p>Background</p> <p>Phages (viruses that infect bacteria) have gained significant attention because of their abundance, diversity and important ecological roles. However, the lack of a universal gene shared by all phages presents a challenge for phage identification and characterization, especially in environmental samples where it is difficult to culture phage-host systems. Homologous conserved genes (or "signature genes") present in groups of closely-related phages can be used to explore phage diversity and define evolutionary relationships amongst these phages. Bioinformatic approaches are needed to identify candidate signature genes and design PCR primers to amplify those genes from environmental samples; however, there is currently no existing computational tool that biologists can use for this purpose.</p> <p>Results</p> <p>Here we present PhiSiGns, a web-based and standalone application that performs a pairwise comparison of each gene present in user-selected phage genomes, identifies signature genes, generates alignments of these genes, and designs potential PCR primer pairs. PhiSiGns is available at (<url>http://www.phantome.org/phisigns/</url>; <url>http://phisigns.sourceforge.net/</url>) with a link to the source code. Here we describe the specifications of PhiSiGns and demonstrate its application with a case study.</p> <p>Conclusions</p> <p>PhiSiGns provides phage biologists with a user-friendly tool to identify signature genes and design PCR primers to amplify related genes from uncultured phages in environmental samples. This bioinformatics tool will facilitate the development of novel signature genes for use as molecular markers in studies of phage diversity, phylogeny, and evolution.</p