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

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

Assessment and comparison of bacterial load levels determined by quantitative amplifications in blood culture-positive and negative neonatal sepsis

Bacterial sepsis remains a major cause of mortality and blood cultures are the gold standard of laboratory diagnosis even though they lack sensitivity in neonates. Culturenegative sepsis, also known as clinical sepsis, has long been considered a diagnosis in neonatal intensive care units because, as well as culture-positive infants, culture-negative neonates have worse prognosis in comparison with non-infected ones. Quantitative amplifications are used to detect bacterial infections in neonates but results are considered only in a qualitative way (positive or negative). The aim of the present study was to determine and compare bacterial load levels in blood culture-positive and culture-negative neonatal sepsis. Seventy neonates with clinical and laboratory evidence of infection admitted at three neonatal intensive care units were classified as blood culture-positive or culture-negative. Blood samples obtained at the same time of blood cultures had bacterial load levels assessed through a 16S rDNA qPCR. Blood cultures were positive in 29 cases (41.4%) and qPCR in 64 (91.4%). In the 29 culture-positive cases, 100% were also positive by qPCR, while in the 41 culture-negative cases, 35 (85.4%) were positive by qPCR. Bacterial load levels were in general < 50 CFU/mL, but were significantly higher in culture-positive cases (Mann-Whitney, p = 0.013), although clinical and laboratory findings were similar, excepting for deaths. In conclusion, the present study has shown that blood culture-negative neonates have lower bacteria load levels in their bloodstream when compared to blood culture-positive infants

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)

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

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

Detection of Bartonella henselae DNA in clinical samples including peripheral blood of immune competent and immune compromised patients by three nested amplifications

Bacteria of the genus Bartonella are emerging pathogens detected in lymph node biopsies and aspirates probably caused by increased concentration of bacteria. Twenty-three samples of 18 patients with clinical, laboratory and/or epidemiological data suggesting bartonellosis were subjected to three nested amplifications targeting a fragment of the 60-kDa heat shock protein (HSP), the internal transcribed spacer 16S-23S rRNA (ITS) and the cell division (FtsZ) of Bartonella henselae, in order to improve detection in clinical samples. In the first amplification 01, 04 and 05 samples, were positive by HSP (4.3%), FtsZ (17.4%) and ITS (21.7%), respectively. After the second round six positive samples were identified by nested-HSP (26%), eight by nested-ITS (34.8%) and 18 by nested-FtsZ (78.2%), corresponding to 10 peripheral blood samples, five lymph node biopsies, two skin biopsies and one lymph node aspirate. The nested-FtsZ was more sensitive than nested-HSP and nested-ITS (p < 0.0001), enabling the detection of Bartonella henselae DNA in 15 of 18 patients (83.3%). In this study, three nested-PCR that should be specific for Bartonella henselae amplification were developed, but only the nested-FtsZ did not amplify DNA from Bartonella quintana. We conclude that nested amplifications increased detection of B. henselae DNA, and that the nested-FtsZ was the most sensitive and the only specific to B. henselae in different biological samples. As all samples detected by nested-HSP and nested-ITS, were also by nested-FtsZ, we infer that in our series infections were caused by Bartonella henselae. The high number of positive blood samples draws attention to the use of this biological material in the investigation of bartonellosis, regardless of the immune status of patients. This fact is important in the case of critically ill patients and young children to avoid more invasive procedures such as lymph nodes biopsies and aspirates.Bactérias do gênero Bartonella constituem patógenos emergentes detectados em biópsias de linfonodos e secreções de gânglios provavelmente devido a maior concentração de bactérias. Vinte e três amostras de 18 pacientes com dados clínicos, laboratoriais e/ou epidemiológicos sugestivos de bartonelose foram submetidas a três amplificações duplas para a detecção de fragmento da proteína de choque térmico de 60-kDa (HSP), do espaçador interno 16S-23S rRNA (ITS) e da proteína de divisão celular (FtsZ) de Bartonella henselae, para melhorar a detecção em amostras clínicas. Na primeira amplificação, uma, quatro e cinco amostras, respectivamente, foram positivas pelo HSP (4,3%), FtsZ (17,4%) e pelo ITS (21,7%). Com a segunda amplificação foram identificadas seis amostras positivas pelo nested-HSP (26%), oito pelo nested-ITS (34,8%) e 18 pelo nested- FtsZ (78,2%), correspondentes a 10 amostras de sangue periférico, cinco biópsias de linfonodos, duas biópsias de pele e um aspirado de gânglio. A nested-FtsZ foi mais sensível que a nested-HSP e a nested-ITS (p < 0,0001), possibilitando a detecção de DNA de Bartonella henselae em 15 de 18 pacientes (83,3%). No presente estudo, três nested-PCR, consideradas específicas para a amplificação da Bartonella henselae, foram desenvolvidas, porém somente a nested-FtsZ não amplificou o DNA de Bartonella quintana. Concluímos que amplificações duplas aumentaram a detecção de DNA de B. henselae, e que a nested-FtsZ foi a mais sensível e a única específica para B. henselae em diferentes amostras biológicas. Como todas as amostras detectadas pelo HSP-nested e nested-ITS foram também pela nested-FtsZ, inferimos que, em nossa casuística, as infecções foram causadas por Bartonella henselae. A elevada positividade de amostras de sangue chamou a atenção para a utilização deste material biológico na investigação de bartoneloses, independentemente do estado imune dos pacientes. Este fato é importante no caso de pacientes criticamente enfermos e crianças pequenas para evitar procedimentos mais invasivos, como biópsias e punções de gânglios