Epidemic Dissemination in Ad Hoc Networks

Peer-to-Peer (P2P) and ad hoc networks have many points in common: both represent a decentralized self-organizing network structure. However few existing P2P algorithms are specifically designed to operate efficiently over ad hoc networks. And few ad hoc networks are designed to benefit from P2P infrastructures. We have worked on an epidemic dissemination protocol to maintain soft-state in a decentralized, peer-to-peer fashion, in ad hoc networks. This protocol is an enhancement of Passive Distributed Indexing (PDI) method proposed by Lindemann and Waldhorst. PDI is a method for distributing information in a P2P structure which is particularly suited to ad hoc networks, and does not involve an overlay topology. It makes use of broadcast messages to spread information via passive epidemic dissemination. We have enhanced PDI in order to reduce the number of broadcast messages when the search for an item may span several hops. Three enhancements are proposed: 1) Lazy query propagation to delay the propagation of query messages such that local responses can inhibit unnecessary search. 2) Quench waves to stop an already initiated query propagation when still possible. A decision algorithm determines whether to start a quench wave or not based solely on local information. 3) The use of Multi-Point Relay (MPR) or similar protocol and algorithm, to reduce redundant broadcast messages. This talk will present the current state of this research, and discuss several open aspects with the purpose of stimulating debate. The talk will also include an overview of related work such as epidemic models from biology, other epidemic protocols for P2P overlays and MANETs, including gossip (active) and promiscuous (passive) dissemination modes. Such protocols could be used for many different purposes, roughly any task requiring distributed soft-state maintenance in the ad hoc network, including DNS and identifier mappings, network monitoring and configuration, and so on. During the talk we will also exploit the possibility of using the protocol to disseminate service information for on-demand service deployment, and further, to assist in self-composing protocol structures

Self-Healing Protocol Implementations

Current studies on self-configuring and adaptive networks aim at developing specific and fixed protocols which are able to optimize their configuration in a variable network environment. In this talk we study the problem where the protocols need to cope with a defective execution, including the lossy execution or the injection of foreign code. One guiding question will be the creation of robust execution circuits which can distribute over a network and which continue their service despite parts of the implementation being knocked out. The ultimate goal is to enable protocol implementations to detect by themselves that they are malfunctioning and to let them correct their own operation mode and code base. As a show case, we present a protocol implementation which is robust against deletion (knock-out) of any single instruction, regardless whether this deletion affects the core protocol functionality or the resilience logic. The technique used in this first of its kind example is the self-modification of the running program, which can be naturally situated in an active networking context. Ultimately, a self-correcting protocol implementation has to constantly rewrite itself according to the (self-)observed performance. In this talk we will also point to related fields like self-correcting software, fault tolerant quantum computing and self-healing properties of biological systems. This is joint work with Lidia Yamamoto, Hitachi Europe

Adaptive Applications over Active Networks: Case Study on Layered Multicast

peer reviewedIn this paper we study the potential and limitations of active networks in the context of adaptive applications. We present a survey of active networking research applied to adaptive applications, and a case study on a layered multicast active application. This active application is a congestion control protocol that selectively discards data in the active routers, and prunes multicast tree branches affected by persistent congestion. Our first results indicate that active networks can indeed help such an application to adapt to heterogeneous receivers, with a minimum amount of state overhead, equivalent to that of a single IP multicast group

Identificação e diferenciação de espécies de Candida de pacientes pediátricos por amplificação aleatória de DNA polimórfico

Thirty-four Candida isolates were analyzed by random amplified polymorphic DNA using the primer OPG-10:24 Candida albicans; 4 Candida tropicalis; 2 Candida parapsilosis; 2 Candida dubliniensis; 1 Candida glabrata and 1 Candida krusei. The UPGMA-Pearson correlation coefficient was used to calculate the genetic distance between the different Candida groupings. Samples were classified as identical (correlation of 100%); highly related samples (90%); moderately related samples (80%) and unrelated samples (< 70%). The results showed that the RAPD proposed was capable of classifying the isolates coherently (such that same species were in the same dendrogram), except for two isolates of Candida parapsilosis and the positive control (Netherlands, 1973), probably because they are now recognized as three different species. Concerning the only fluconazole-resistant Candida tropicalis isolate with a genotype that was different to the others, the data were insufficient to affirm that the only difference was the sensitivity to fluconazole. We concluded that the Random Amplified Polymorphic DNA proposed might be used to confirm Candida species identified by microbiological methods.Trinta e quatro isolados de Candida foram analisados por amplificação aleatória de DNA polimórfico (primer OPG-10): 24 Candida albicans, 4 Candida tropicalis, 2 Candida parapsilosis, 2 Candida dubliniensis, 1 Candida glabrata e 1 Candida krusei. O coeficiente de correlação de Pearson-UPGMA calculou a distância genética entre os diferentes agrupamentos de Candida: amostras idênticas (100% de correlação), amostras muito relacionadas (90%), moderadamente relacionadas (80%), e não relacionadas (< 70%). Os resultados demonstram que a amplificação aleatória de DNA polimórfico proposta é capaz de classificar os isolados de forma coerente, ficando os de mesma espécie em um mesmo dendograma, com exceção dos dois isolados de Candida parapsilosis e o controle positivo (Holanda, 1973), provavelmente por serem atualmente classificadas em três espécies diferentes. Quanto ao único isolado de Candida tropicalis resistente ao fluconazol com genótipo diferente dos outros, os dados não são suficientes para afirmar que a única característica distinta fosse a sensibilidade ao fluconazol. Concluímos que a amplificação aleatória de DNA polimórfico proposta poderia ser usada para a confirmação das espécies de Candida identificadas nos testes microbiológicos

The performance of four molecular methods for the laboratory diagnosis of congenital toxoplasmosis in amniotic fluid samples

Introduction\ud Toxoplasmosis may be life-threatening in fetuses and in immune-deficient patients. Conventional laboratory diagnosis of toxoplasmosis is based on the presence of IgM and IgG anti-Toxoplasma gondii antibodies; however, molecular techniques have emerged as alternative tools due to their increased sensitivity. The aim of this study was to compare the performance of 4 PCR-based methods for the laboratory diagnosis of toxoplasmosis. One hundred pregnant women who seroconverted during pregnancy were included in the study. The definition of cases was based on a 12-month follow-up of the infants.\ud \ud Methods\ud Amniotic fluid samples were submitted to DNA extraction and amplification by the following 4 Toxoplasma techniques performed with parasite B1 gene primers: conventional PCR, nested-PCR, multiplex-nested-PCR, and real-time PCR. Seven parameters were analyzed, sensitivity (Se), specificity (Sp), positive predictive value (PPV), negative predictive value (NPV), positive likelihood ratio (PLR), negative likelihood ratio (NLR) and efficiency (Ef).\ud \ud Results\ud Fifty-nine of the 100 infants had toxoplasmosis; 42 (71.2%) had IgM antibodies at birth but were asymptomatic, and the remaining 17 cases had non-detectable IgM antibodies but high IgG antibody titers that were associated with retinochoroiditis in 8 (13.5%) cases, abnormal cranial ultrasound in 5 (8.5%) cases, and signs/symptoms suggestive of infection in 4 (6.8%) cases. The conventional PCR assay detected 50 cases (9 false-negatives), nested-PCR detected 58 cases (1 false-negative and 4 false-positives), multiplex-nested-PCR detected 57 cases (2 false-negatives), and real-time-PCR detected 58 cases (1 false-negative).\ud \ud Conclusions\ud The real-time PCR assay was the best-performing technique based on the parameters of Se (98.3%), Sp (100%), PPV (100%), NPV (97.6%), PLR (â^ž), NLR (0.017), and Ef (99%).This work was supported by FAPESP (Fundação de Amparo à Pesquisa do Estado de São Paulo; grant number 2010/15022-1), as well as by CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico; grant number 2011-0/471479)

Gardening Cyber-Physical Systems

cote interne IRCAM: Stepney12aNational audienceToday’s artefacts, from small devices to buildings and cities, are, or are becoming, cyber-physical socio-technical systems, with tightly interwoven material and computational parts. Currently, we have to la- boriously build such systems, component by component, and the results are often difficult to maintain, adapt, and reconfigure. Even “soft”ware is brittle and non-trivial to adapt and change. If we look to nature, how- ever, large complex organisms grow, adapt to their environment, and repair themselves when damaged. In this position paper, we present Gro-CyPhy, an unconventional computational framework for growing cyber-physical systems from com- putational seeds, and gardening the growing systems, in order to adapt them to specific needs. The Gro-CyPhy architecture comprises: a Seed Factory, a process for designing specific computational seeds to meet cyber-physical system requirements; a Growth Engine, providing the computational processes that grow seeds in simulation; and a Computational Garden, where mul- tiple seeds can be planted and grown in concert, and where a high-level gardener can shape them into complex cyber-physical systems. We outline how the Gro-CyPhy architecture might be applied to a significant exemplar application: a (simulated) skyscraper, comprising several mutually interdependent physical and virtual subsystems, such as the shell of exterior and interior walls, electrical power and data net- works, plumbing and rain-water harvesting, heating and air-conditioning systems, and building management control systems

Factors associated with hyperglycemia and low insulin levels in children undergoing cardiac surgery with cardiopulmonary bypass who received a single high dose of methylprednisolone

OBJECTIVES: Administering steroids before cardiopulmonary bypass in pediatric heart surgery modulates systemic inflammatory response syndrome and improves postoperative recovery. However, the use of steroids aggravates hyperglycemia, which is associated with a poor prognosis. Adult patients with systemic inflammatory response syndrome usually evolve with hyperglycemia and high insulin levels, whereas >;90% of pediatric patients exhibit hyperglycemia and low insulin levels. This study aims to determine: A) the metabolic and inflammatory factors that are associated with hyperglycemia and low insulin levels in children who underwent cardiac surgery with cardiopulmonary bypass and who received a single high dose of methylprednisolone and B) the best predictors of insulin variation using a mathematical model. METHODS: This preliminary study recruited 20 children who underwent heart surgery with cardiopulmonary bypass and received methylprednisolone (30 mg/kg) immediately after anesthesia. Among the 20 patients initially recruited, one was excluded because of the absence of hyperglycemia and lower insulin levels after surgery. However, these abnormalities were confirmed in the remaining 19 children. The C-peptide, CRP, IL-6, and adrenomedullin levels were measured before surgery, immediately after cardiopulmonary bypass, and on the first, second, and third days after cardiac surgery. RESULTS: IL-6, CRP, and adrenomedullin increments were observed, whereas the C-peptide levels remained within reference intervals. CONCLUSION: The multiple regression model demonstrated that in addition to age and glycemia (two well-known factors that are directly involved in glucose metabolism), adrenomedullin and IL-6 levels were independent factors associated with lower insulin concentrations. These four parameters were responsible for 64.7% of the observed insulin variances. In addition, the fact that C-peptide levels did not fall together with insulin could have grounded the medical decision not to administer insulin to patients

Elongation Control in an Algorithmic Chemistry

Abstract. Algorithmic chemistries intended as computation models seldom model energy. This could partly explain some undesirable phenomena such as unlimited elongation of strings in these chemistries, in contrast to nature where polymerization tends to be unfavored. In this paper, we show that a simple yet sufficiently accurate energy model can efficiently steer resource usage, in particular for the case of elongation control. A string chemistry is constructed on purpose to make strings grow arbitrarily large. Simulation results show that the addition of energy control alone is able to keep the molecules within reasonable length bounds, even without mass conservation, and without explicit length thresholds. A narrow energy range is detected where the system neither stays inert nor grows unbounded. At this operating point, interesting phenomena often emerge, such as clusters of autocatalytic molecules, which seem to cooperate.

Significant Performance Variation Among PCR Systems in Diagnosing Congenital Toxoplasmosis in São Paulo, Brazil: Analysis of 467 Amniotic Fluid Samples

INTRODUCTION: Performance variation among PCR systems in detecting Toxoplasma gondii has been extensively reported and associated with target genes, primer composition, amplification parameters, treatment during pregnancy, host genetic susceptibility and genotypes of different parasites according to geographical characteristics. PATIENTS: A total of 467 amniotic fluid samples from T. gondii IgM- and IgG-positive Brazilian pregnant women being treated for 1 to 6 weeks at the time of amniocentesis (gestational ages of 14 to 25 weeks). METHODS: One nested-B1-PCR and three one-round amplification systems targeted to rDNA, AF146527 and the B1 gene were employed. RESULTS: Of the 467 samples, 189 (40.47%) were positive for one-round amplifications: 120 (63.49%) for the B1 gene, 24 (12.69%) for AF146527, 45 (23.80%) for both AF146527 and the B1 gene, and none for rDNA. Fifty previously negative one-round PCR samples were chosen by computer-assisted randomization analysis and re-tested (nested-B1-PCR), during which nine additional cases were detected (9/50 or 18%). DISCUSSION: The B1 gene PCR was far more sensitive than the AF146527 PCR, and the rDNA PCR was the least effective even though the rDNA had the most repetitive sequence. Considering that the four amplification systems were equally affected by treatment, that the amplification conditions were optimized for the target genes and that most of the primers have already been reported, it is plausible that the striking differences found among PCR performances could be associated with genetic diversity in patients and/or with different Toxoplasma gondii genotypes occurring in Brazil. CONCLUSION: The use of PCR for the diagnosis of fetal Toxoplasma infections in Brazil should be targeted to the B1 gene when only one gene can be amplified, preferably by nested amplification with primers B22/B23