556 research outputs found
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 are analyzed by population
dynamics simulations. We found that (1) the lowest temperature for the RS
solution to be stable, , is not a monotonic function of , and (2)
at relatively large connectivity and temperature slightly below the
dynamic transition temperature , 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. Lecture Notes in Computer Science. 7046:208-217. https://doi.org/10.1007/978-3-642-25126-9_31S2082177046Helland, P.: Life beyond distributed transactions: an apostate’s opinion. In: 3rd Biennial Conf. on Innov. Data Syst. Research (CIDR), Asilomar, CA, USA, pp. 132–141 (2007)Finkelstein, S., Jacobs, D., Brendle, R.: Principles for inconsistency. In: 4th Biennial Conf. on Innov. Data Syst. Research (CIDR), Asilomar, CA, USA (2009)Chang, F., Dean, J., Ghemawat, S., Hsieh, W.C., Wallach, D.A., Burrows, M., Chandra, T., Fikes, A., Gruber, R.: Bigtable: A distributed storage system for structured data. In: 7th Symp. on Operat. Syst. Design and Implem. (OSDI), pp. 205–218. USENIX Assoc., Seattle (2006)Cooper, B.F., Baldeschwieler, E., Fonseca, R., Kistler, J.J., Narayan, P.P.S., Neerdaels, C., Negrin, T., Ramakrishnan, R., Silberstein, A., Srivastava, U., Stata, R.: Building a cloud for Yahoo! IEEE Data Eng. 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. Bull. 9, 4–9 (1986)Alonso, G., Kossmann, D., Roscoe, T.: SwissBox: An architecture for data processing appliances. In: 5th Biennial Conf. on Innov. Data Syst. Research (CIDR), Asilomar, CA, USA, pp. 32–37 (2011)Baker, J., Bond, C., Corbett, J.C., Furman, J.J., Khorlin, A., Larson, J., Léon, J.M., Li, Y., Lloyd, A., Yushprakh, V.: Megastore: Providing scalable, highly available storage for interactive services. In: 5th Biennial Conf. on Innov. Data Syst. Research (CIDR), Asilomar, CA, USA, pp. 223–234 (2011)Curino, C., Jones, E.P.C., Popa, R.A., Malviya, N., Wu, E., Madden, S., Balakrishnan, H., Zeldovich, N.: Relational cloud: A database-as-a-service for the cloud. In: 5th Biennial Conf. on Innov. Data Syst. Research (CIDR), Asilomar, CA, USA, pp. 235–240 (2011)Das, S., Agrawal, D., El Abbadi, A.: ElasTraS: An elastic transactional data store in the cloud. CoRR abs/1008.3751 (2010)Vogels, W.: Eventually consistent. Commun. ACM 52, 40–44 (2009)Breitbart, Y., Korth, H.F.: Replication and consistency: being lazy helps sometimes. In: 16th ACM Symp. on Princ. of Database Syst., PODS 1997, pp. 173–184. ACM, New York (1997)Brantner, M., Florescu, D., Graf, D.A., Kossmann, D., Kraska, T.: Building a database on S3. In: Intnl. Conf. on Mngmnt. of Data (SIGMOD), pp. 251–264. ACM Press, Vancouver (2008)Lakshman, A., Malik, P.: Cassandra: a decentralized structured storage system. Operating Systems Review 44, 35–40 (2010)Burrows, M.: The Chubby lock service for loosely-coupled distributed systems. In: 7th Symp. on Operat. Syst. Design and Implem. (OSDI), pp. 335–350. USENIX Assoc., Seattle (2006)Junqueira, F.P., Reed, B.: The life and times of a ZooKeeper. In: 28th Annual ACM Symp. on Princ. of Distrib. Comp. (PODC), p. 4. ACM Press, Calgary (2009)MacCormick, J., Murphy, N., Najork, M., Thekkath, C.A., Zhou, L.: Boxwood: Abstractions as the foundation for storage infrastructure. In: 6th Simp. on Operat. Syst. 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. Research (CIDR), Asilomar, CA, USA, pp. 1–8 (2011)Microsoft Corp.: Windows Azure: Microsoft’s cloud services platform (2011), http://www.microsoft.com/windowsazure/VoltDB, Inc.: VoltDB technical overview: Next generation open-source SQL database with ACID for fast-scaling OLTP applications (2010), Downloadable from: http://voltdb.com/_pdf/VoltDBTechnicalOverviewWhitePaper.pd
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
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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
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