H-NAMe: a hidden-node avoidance mechanism for wireless sensor networks

The hidden-node problem has been shown to be a major source of Quality-of-Service (QoS) degradation in Wireless Sensor Networks (WSNs) due to factors such as the limited communication range of sensor nodes, link asymmetry and the characteristics of the physical environment. In wireless contention-based Medium Access Control protocols, if two nodes that are not visible to each other transmit to a third node that is visible to the formers, there will be a collision – usually called hidden-node or blind collision. This problem greatly affects network throughput, energy-efficiency and message transfer delays, which might be particularly dramatic in large-scale WSNs. This paper tackles the hiddennode problem in WSNs and proposes H-NAMe, a simple yet efficient distributed mechanism to overcome it. H-NAMe relies on a grouping strategy that splits each cluster of a WSN into disjoint groups of non-hidden nodes and then scales to multiple clusters via a cluster grouping strategy that guarantees no transmission interference between overlapping clusters. We also show that the H-NAMe mechanism can be easily applied to the IEEE 802.15.4/ZigBee protocols with only minor add-ons and ensuring backward compatibility with the standard specifications. We demonstrate the feasibility of H-NAMe via an experimental test-bed, showing that it increases network throughput and transmission success probability up to twice the values obtained without H-NAMe. We believe that the results in this paper will be quite useful in efficiently enabling IEEE 802.15.4/ZigBee as a WSN protocol

i-GAME: an implicit GTS allocation mechanism in IEEE 802.15.4 for time-sensitive wireless sensor networks

The IEEE 802.15.4 Medium Access Control (MAC) protocol is an enabling technology for time sensitive wireless sensor networks thanks to its Guaranteed-Time Slot (GTS) mechanism in the beacon-enabled mode. However, the protocol only supports explicit GTS allocation, i.e. a node allocates a number of time slots in each superframe for exclusive use. The limitation of this explicit GTS allocation is that GTS resources may quickly disappear, since a maximum of seven GTSs can be allocated in each superframe, preventing other nodes to benefit from guaranteed service. Moreover, the GTSs may be only partially used, resulting in wasted bandwidth. To overcome these limitations, this paper proposes i-GAME, an implicit GTS Allocation Mechanism in beacon-enabled IEEE 802.15.4 networks. The allocation is based on implicit GTS allocation requests, taking into account the traffic specifications and the delay requirements of the flows. The i-GAME approach enables the use of a GTS by multiple nodes, while all their (delay, bandwidth) requirements are still satisfied. For that purpose, we propose an admission control algorithm that enables to decide whether to accept a new GTS allocation request or not, based not only on the remaining time slots, but also on the traffic specifications of the flows, their delay requirements and the available bandwidth resources. We show that our proposal improves the bandwidth utilization compared to the explicit allocation used in the IEEE 802.15.4 protocol standard. We also present some practical considerations for the implementation of i-GAME, ensuring backward compatibility with the IEEE 801.5.4 standard with only minor add-ons.

Energy and delay trade-off of the GTS allocation mechanism in IEEE 802.15.4 for wireless sensor networks

The IEEE 802.15.4 protocol proposes a flexible communication solution for Low-Rate Wireless Personal Area Networks (LR-WPAN) including wireless sensor networks (WSNs). It presents the advantage to fit different requirements of potential applications by adequately setting its parameters. When in beaconenabled mode, the protocol can provide timeliness guarantees by using its Guaranteed Time Slot (GTS) mechanism. However, power-efficiency and timeliness guarantees are often two antagonistic requirements in wireless sensor networks. The purpose of this paper is to analyze and propose a methodology for setting the relevant parameters of IEEE 802.15.4-compliant WSNs that takes into account a proper trade-off between power-efficiency and delay bound guarantees. First, we propose two accurate models of service curves for a GTS allocation as a function of the IEEE 802.15.4 parameters, using Network Calculus formalism. We then evaluate the delay bound guaranteed by a GTS allocation and express it as a function of the duty cycle. Based on the relation between the delay requirement and the duty cycle, we propose a power-efficient superframe selection method that simultaneously reduces power consumption and enables meeting the delay requirements of real-time flows allocating GTSs. The results of this work may pave the way for a powerefficient management of the GTS mechanism in an IEEE 802.15.4 cluster.

Implementation of the i-GAME mechanism in IEEE 802.15.4 WPANs

This technical report describes the implementation details of the Implicit GTS Allocation Mechanism (i-GAME), for the IEEE 802.15.4 protocol. The i-GAME was implemented in nesC/TinyOS for the CrossBow MICAz mote, over our own implementation of the IEEE 802.15.4 protocol stack. This document provides the implementation details, including a description of the i-GAME software interfaces.

A simple approach to numerical modelling of propane combustion in fluidized beds

A mathematical model is proposed for the evolution of temperature, chemical composition, and energy release in bubbles, clouds, and emulsion phase during combustion of gaseous premixtures of air and propane in a bubbling fluidized bed. The analysis begins as the bubbles are formed at the orifices of the distributor, until they explode inside the bed or emerge at the free surface of the bed. The model also considers the freeboard region of the fluidized bed until the propane is thoroughly burned. It is essentially built upon the quasi-global mechanism of Hautman et al. (1981) and the mass and heat transfer equations from the two-phase model of Davidson and Harrison (1963). The focus is not on a new modeling approach, but on combining the classical models of the kinetics and other diffusional aspects to obtain a better insight into the events occurring inside a fluidized bed reactor. Experimental data are obtained to validate the model by testing the combustion of commercial propane, in a laboratory-scale fluidized bed, using four sand particle sizes: 400–500, 315–400, 250–315, and 200–250 µm. The mole fractions of CO2, CO, and O2 in the flue gases and the temperature of the fluidized bed are measured and compared with the numerical results.

Negotiation mechanism for self-organized scheduling system with collective intelligence

Current Manufacturing Systems challenges due to international economic crisis, market globalization and e-business trends, incites the development of intelligent systems to support decision making, which allows managers to concentrate on high-level tasks management while improving decision response and effectiveness towards manufacturing agility. This paper presents a novel negotiation mechanism for dynamic scheduling based on social and collective intelligence. Under the proposed negotiation mechanism, agents must interact and collaborate in order to improve the global schedule. Swarm Intelligence (SI) is considered a general aggregation term for several computational techniques, which use ideas and inspiration from the social behaviors of insects and other biological systems. This work is primarily concerned with negotiation, where multiple self-interested agents can reach agreement over the exchange of operations on competitive resources. Experimental analysis was performed in order to validate the influence of negotiation mechanism in the system performance and the SI technique. Empirical results and statistical evidence illustrate that the negotiation mechanism influence significantly the overall system performance and the effectiveness of Artificial Bee Colony for makespan minimization and on the machine occupation maximization.

Caracterização da função do monóxido de azoto e glutationo hepáticos na sensabilidade periférica à insulina

xi RESUMO A acção da insulina no músculo esquelético depende de um reflexo parassimpático hepático que conduz à libertação de uma substância hepática sensibilizadora da insulina, designada por HISS, responsável por cerca de 55% do efeito hipoglicemiante da insulina. A acção da HISS é finamente regulada pelo monóxido de azoto (NO) hepático e pelo estado prandial, aumentando no período pós-prandial imediato e diminuindo progressivamente com as horas de jejum. A secreção da HISS pode ser inibida cirúrgica ou farmacologicamente, quer por desnervação selectiva do plexo anterior hepático, quer por administração de atropina, quer por inibição do sintase do NO (NOS) hepático. O objectivo geral do trabalho apresentado nesta dissertação foi a caracterização da via de transdução de sinal que conduz à libertação da HISS. O modelo utilizado neste estudo foi o rato Wistar. A sensibilidade à insulina foi avaliada através do teste rápido de sensibilidade à insulina (RIST). A primeira hipótese de trabalho testada foi que a sequência de eventos que conduzem à secreção da HISS inicia-se com a activação do sistema parassimpático hepático seguida de activação do NOS hepático com subsequente produção de NO e activação do guanilato ciclase (GC). Observou-se que a administração de um dador de NO reverteu a resistência à insulina induzida, quer por inibição do NOS hepático, quer por antagonismo dos receptores muscarínicos com atropina. Em contraste, a resistência à insulina produzida por inibição do NOS hepático não foi revertida por administração intraportal de acetilcolina (ACh). Constatou-se que a inibição do GC hepático diminuiu a sensibilidade à insulina. Estes resultados sugerem que: a ACh libertada no fígado induz a síntese de NO hepático que conduz à libertação da HISS, que por sua vez é modulada pelo GC hepático. A libertação da HISS em resposta à insulina é regulada pelo estado prandial. Uma vez que os níveis hepáticos de glutationo (GSH) se encontram, tal como a HISS, diminuídos no estado de jejum e aumentados após a ingestão de uma refeição, testou-se a hipótese de que o GSH hepático está envolvido na secreção da HISS. Observou-se que a depleção do GSH hepático induziu resistência à insulina, comparável à obtida após inibição do NOS hepático. Estes resultados suportam a hipótese de que o GSH hepático desempenha um papel crítico na acção periférica da insulina. Considerando que, no estado de jejum, tanto os níveis de GSH hepático como os níveis de NO hepático são baixos, testou-se a hipótese de que a co-administração intraportal de um dador de GSH e de um dador de NO promove um aumento da sensibilidade à insulina no estado de jejum, devido ao restabelecimento do mecanismo da HISS. Observou-se que a administração sequencial de dadores de GSH e de NO no fígado provocou um aumento na sensibilidade à insulina, dependente da dose de dador de GSH administrada. Concluiu-se portanto que ambos, GSH e NO, são essenciais para que o mecanismo da HISS esteja completamente funcional. O GSH e o NO reagem para formar um S-nitrosotiol, o S-nitrosoglutationo (GSNO). Os resultados supra-mencionados conduziram à formulação da hipótese de que a secreção/acção da HISS depende da formação de GSNO. Observou-se que a administração intravenosa de S-nitrosotióis (RSNOs) aumentou a sensibilidade à insulina, em animais submetidos a um período de jejum, ao contrário da administração intraportal destes fármacos, o que RSNOs têm uma acção periférica, mas não hepática, na sensibilidade à insulina. Os resultados obtidos conduziram à reformulação da hipótese da HISS, sugerindo que a ingestão de uma refeição activa os nervos parassimpáticos hepáticos levando à libertação de ACh no fígado que, por sua vez activa o NOS. Simultaneamente, ocorre um aumento dos níveis de GSH hepático que reage com o NO hepático para formar um composto nitrosado, o GSNO. Este composto mimetiza a acção hipoglicemiante da HISS no músculo esquelético. SUMMARY Insulin action at the skeletal muscle depends on a hepatic parasympathetic reflex that promotes the release of a hepatic insulin sensitizing substance (HISS) from the liver, which contributes 55% to total insulin action. HISS action is modulated by hepatic nitric oxide (NO) and also by the prandial status so as to, in the immediate ostprandial state, HISS action is maximal, decreasing with the duration of fasting. HISS secretion may be inhibited by interruption of the hepatic parasympathetic reflex, achieved either by surgical denervation of the liver or by cholinergic blockade with atropine, or by prevention of hepatic NO release, using NO synthase (NOS) antagonists. The main objective of this work was to characterize the signal transduction pathways that lead to HISS secretion by the liver. Wistar rats were used and insulin sensitivity was evaluated using the rapid insulin sensitivity test (RIST). The first hypothesis tested was that the sequence of events that lead to HISS secretion starts with an increase in the hepatic parasympathetic tone, followed by the activation of hepatic NOS and subsequent triggering of guanylate cyclase (GC). We observed that insulin resistance produced either by muscarinic receptor antagonism with atropine or by hepatic NOS inhibition was reversed by the intraportal administration of an NO donor. In contrast, intraportal acetylcholine (ACh) did not restore insulin sensitivity after NOS inhibition. We also observed that GC inhibition lead to a decrease in insulin sensitivity.These results suggest that the release of ACh in the liver activates hepatic NO synthesis in order to allow HISS secretion, through a signaling pathway modulated by GC. HISS release in response to insulin is controlled by the prandial status. The second hypothesis tested was that glutathione (GSH) is involved in HISS secretion since the hepatic levels of GSH are, like HISS action, decreased in the fasted state and increased after ingestion of a meal. We observed that hepatic GSH depletion led to insulin resistance of the same magnitude of that observed after inhibition of hepatic NOS. These results support the hypothesis that hepatic GSH is crucial in peripheral insulin action. Since, in the fasted state, both hepatic GSH and NO levels are low, we tested the hypothesis that intraportal o-administration of a GSH donor and an NO donor enhances insulin sensitivity in fasted Wistar rats, by restoring HISS secretion. We observed that GSH and NO increased insulin sensitivity in a GSH dose-dependent manner. We concluded that HISS secretion requires elevated levels of both GSH and NO in the liver. GSH and NO react to form a S-nitrosothiol, S-nitrosoglutathione (GSNO). The last hypothesis tested in this work was that HISS secretion/ action depends on the formation of GSNO. We observed that intravenous administration of -nitrosothiols (RSNOs) increased insulin sensitivity in animals fasted for 24 h, in contrast with the intraportal administration of the drug. This result suggests that RSNOs enhanced insulin sensitivity through a peripheral, and not hepatic, mechanism. The results obtained led to a restructuring of the HISS hypothesis, suggesting that the ingestion of a meal triggers the hepatic parasympathetic nerves, leading to the release of Ach in the liver, which in turn activates NOS. Simultaneously, hepatic GSH levels increase and react with NO to form a nitrosated compound, GSNO. S-nitrosoglutathione mimics HISS hypoglycaemic action at the skeletal muscle.

Importance of immunoglobulin E (IgE) in the protective mechanism against gastrointestinal nematode infection: looking at the intestinal mucosae

This review discusses experimental evidences that indicate the IgE participation on the effector mechanisms that leads to gastrointestinal nematode elimination. Data discussed here showed that, for most experimental models, the immune response involved in nematode elimination is regulated by Th-2 type cytokines (especially IL-4). However, the mechanism(s) that result in worm elimination is not clear and might be distinct in different nematode species. Parasite specific IgE production, especially the IgE produced by the intestinal mucosae or associated lymphoid organs could participate in the intestinal elimination of Trichinella spiralis from infected rats. Intestinal IgE may also be important to the protective mechanism developed against other gastrointestinal nematodes that penetrate the murine duodenum mucosa tissue, such as Strongyloides venezuelensis and Heligmosomoides polygyrus. At least in Trichinella spiralis infected rats, the results indicated that intestinal IgE might work independently from mast cell degranulation for worm elimination.

The role of ribonuclease R in bacterial adaptation to cold shock

RESUMO:Os microrganismos reagem à súbita descida de temperatura através de uma resposta adaptativa específica que assegura a sua sobrevivência em condições desfavoráveis. Esta adaptação inclui alterações na composição da membrana, na maquinaria de tradução e transcrição. A resposta ao choque térmico pelo frio induz uma repressão da transcrição. No entanto, a descida de temperatura induz a produção de um grupo de proteínas específicas que ajudam a ajustar/re-ajustar o metabolismo celular às novas condições ambientais. Em E. coli o processo de adaptação demora apenas quatro horas, no qual um grupo de proteínas específicas são induzidas. Depois desde período recomeça lentamente a produção de proteínas.A ribonuclease R, uma das proteínas induzidas durante o choque térmico pelo frio, é uma das principais ribonucleases em E. coli envolvidas na degradação do RNA. É uma exoribonuclease que degrada RNA de cadeia dupla, possui funções importantes na maturação e “turnover” do RNA, libertação de ribossomas e controlo de qualidade de proteínas e RNAs. O nível celular desta enzima aumenta até dez vezes após exposição ao frio e estabiliza em células na fase estacionária. A capacidade de degradar RNA de dupla cadeia é importante a baixas temperaturas quando as estruturas de RNA estão mais estáveis. No entanto, este mecanismo é desconhecido. Embora a resposta específica ao “cold shock” tenha sido descoberta há mais de duas décadas e o número de proteínas envolvidas sugerirem que esta adaptação é rápida e simples, continuamos longe de compreender este processo. No nosso trabalho pretendemos descobrir proteínas que interactuem com a RNase R em condições ambientais diferentes através do método “TAP-tag” e espectrometria de massa. A informação obtida pode ser utilizada para deduzir algumas das novas funções da RNase R durante a adaptação bacteriana ao frio e durante a fase estacionária. Mais importante ainda, RNase R poderá ser recrutada para um complexo de proteínas de elevado peso molecular durante o “cold-shock”.------------ABSTRACT:Microorganisms react to the rapid temperature downshift with a specific adaptative response that ensures their survival in unfavorable conditions. Adaptation includes changes in membrane composition, in translation and transcription machinery. Cold shock response leads to overall repression of translation. However, temperature downshift induces production of a set of specific proteins that help to tune cell metabolism and readjust it to the new environmental conditions. For Escherichia coli the adaptation process takes only about four hours with a relatively small set of specifically induced proteins involved. After this time, protein production resumes, although at a slower rate. One of the cold inducible proteins is RNase R, one of the main E. coli ribonucleases involved in RNA degradation. RNase R is an exoribonuclease that digest double stranded RNA, serves important functions in RNA maturation and turnover, release of stalled ribosomes by trans-translation, and RNA and protein quality control. The level of this enzyme increases about ten-fold after cold induction, and it is also stabilised in cells growing in stationary phase. The RNase R ability to digest structured RNA is important at low temperatures where RNA structures are stabilized but the exact role of this mechanism remains unclear. Although specific bacterial cold shock response was discovered over two decades ago and the number of proteins involved suggests that this adaptation is fast and simple, we are still far from understanding this process. In our work we aimed to discover the proteins interacting with RNase R in different environmental conditions using TAP tag method and mass spectrometry analysis. The information obtained can be used to deduce some of the new functions of RNase R during adaptation of bacteria to cold and in stationary growth phase. Most importantly RNase R can be recruited into a high molecular mass complex of protein in cold shock.

Role of iron in the nitric oxide-mediated fungicidal mechanism of IFN-gamma-activated murine macrophages against Paracoccidioides brasiliensis conidia

Iron is an essential growth element of virtually all microorganisms and its restriction is one of the mechanisms used by macrophages to control microbial multiplication. Paracoccidioides brasiliensis, the agent of paracoccidioidomycosis, an important systemic mycosis in Latin America, is inhibited in its conidia-to-yeast conversion in the absence of iron. We studied the participation of iron in the nitric oxide (NO)-mediated fungicidal mechanism against conidia. Peritoneal murine macrophages activated with 50U/mL of IFN-gamma or treated with 35 µM Deferoxamine (DEX) and infected with P. brasiliensis conidia, were co-cultured and incubated for 96 h in the presence of different concentrations of holotransferrin (HOLO) and FeS0(4). The supernatants were withdrawn in order to assess NO2 production by the Griess method. The monolayers were fixed, stained and observed microscopically. The percentage of the conidia-to-yeast transition was estimated by counting 200 intracellular propagules. IFN-gamma-activated or DEX-treated Mthetas presented marked inhibition of the conidia-to-yeast conversion (19 and 56%, respectively) in comparison with non-activated or untreated Mthetas (80%). IFN-gamma-activated macrophages produced high NO levels in comparison with the controls. Additionally, when the activated or treated-macrophages were supplemented with iron donors (HOLO or FeSO4), the inhibitory action was reversed, although NO production remained intact. These results suggest that the NO-mediated fungicidal mechanism exerted by IFN-gamma-activated macrophages against P. brasiliensis conidia, is dependent of an iron interaction.

Heparinized nanohydroxyapatite/collagen granules for controlled release of vancomycin

The purpose of this study was to develop a bone substitute material capable of preventing or treating osteomyelitis through a sustainable release of vancomycin and simultaneously inducing bone regeneration. Porous heparinized nanohydroxyapatite (nanoHA)/collagen granules were characterized using scanning electron microscopy, micro-computed tomography and attenuated total reflectance Fourier transform infrared spectroscopy. After vancomycin adsorption onto the granules, its releasing profile was studied by UV molecular absorption spectroscopy. The heparinized granules presented a more sustainable release over time, in comparison with nonheparinized nanoHA and nanoHA/collagen granules. Vancomycin was released for 360 h and proved to be bioactive until 216 h. Staphylococcus aureus adhesion was higher on granules containing collagen, guiding the bacteria to the material with antibiotic, improving their eradication. Moreover, cytotoxicity of the released vancomycin was assessed using osteoblast cultures, and after 14 days of culture in the presence of vancomycin, cells were able to remain viable, increasing their metabolic activity and colonizing the granules, as observed by scanning electron microscopy and confocal laser scanning microscopy. These findings suggest that heparinized nanoHA/collagen granules are a promising material to improve the treatment of osteomyelitis, as they are capable of releasing vancomycin, eliminating the bacteria, and presented morphological and chemical characteristics to induce bone regeneration.

Mechanism of interleukin-8 induction by human cytomegalovirus UL76 protein

Dissertation presented to obtain the Ph.D degree in Biology

Evidence for Nevirapine Bioactivation in Man: Searching for the First Step in the Mechanism of Nevirapine Toxicity

Despite its efficacy, including in the prevention of vertical transmission, the antiretroviral nevirapine is associated with severe idiosyncratic hepatotoxicity and skin rash. The mechanisms underlying nevirapine toxicity are not fully understood, but drug bioactivation to reactive metabolites capable of forming stable protein adducts is thought to be involved. This hypothesis is based on the paradigm that drug reactive metabolites have the potential to bind to self-proteins, which results in drug-modified proteins being perceived as foreign by the immune system. The aim of the present work was to identify hemoglobin adducts in HIV patients as biomarkers of nevirapine haptenation upon bioactivation. The ultimate goal is to develop diagnostic methods for predicting the onset of nevirapine-induced toxic reactions. All included subjects were adults on nevirapine-containing antiretroviral therapy for at least 1month. The protocol received prior approval from the Hospital Ethics Committees and patients gave their written informed consent. Nevirapine-derived adducts with the N-terminal valine of hemoglobin were analyzed by an established liquid chromatography-electrospray ionization-tandem mass spectrometry method and characterized on the basis of retention time and mass spectrometric fragmentation pattern by comparison with adduct standards prepared synthetically. The nevirapine adducts were detected in 12/13 patient samples, and quantified in 11/12 samples (2.58±0.8 fmol/g of hemoglobin). This work represents the first evidence of nevirapine-protein adduct formation in man and confirms the ability of nevirapine to modify self-proteins, thus providing clues to the molecular mechanisms underlying nevirapine toxicity. Moreover, the possibility of assessing nevirapine-protein adduct levels has the potential to become useful for predicting the onset of nevirapine-induced adverse reactions.

The mechanism of formate oxidation by metal-dependent formate dehydrogenases

J Biol Inorg Chem (2011) 16:1255–1268 DOI 10.1007/s00775-011-0813-8