A comprehensive simulation study of slotted CSMA/CA for IEEE 802.15.4 wireless sensor networks

In this paper, we analyze the performance limits of the slotted CSMA/CA mechanism of IEEE 802.15.4 in the beacon-enabled mode for broadcast transmissions in WSNs. The motivation for evaluating the beacon-enabled mode is due to its flexibility for WSN applications as compared to the non-beacon enabled mode. Our analysis is based on an accurate simulation model of the slotted CSMA/CA mechanism on top of a realistic physical layer, with respect to the IEEE 802.15.4 standard specification. The performance of the slotted CSMA/CA is evaluated and analyzed for different network settings to understand the impact of the protocol attributes (superframe order, beacon order and backoff exponent) on the network performance, namely in terms of throughput (S), average delay (D) and probability of success (Ps). We introduce the concept of utility (U) as a combination of two or more metrics, to determine the best offered load range for an optimal behavior of the network. We show that the optimal network performance using slotted CSMA/CA occurs in the range of 35% to 60% with respect to an utility function proportional to the network throughput (S) divided by the average delay (D).

On the performance limits of slotted CSMA/CA in IEEE 802.15.4 for broadcast transmissions in wireless sensor networks

The IEEE 802.15.4 has been adopted as a communication protocol standard for Low-Rate Wireless Private Area Networks (LRWPANs). While it appears as a promising candidate solution for Wireless Sensor Networks (WSNs), its adequacy must be carefully evaluated. In this paper, we analyze the performance limits of the slotted CSMA/CA medium access control (MAC) mechanism in the beacon-enabled mode for broadcast transmissions in WSNs. The motivation for evaluating the beacon-enabled mode is due to its flexibility and potential for WSN applications as compared to the non-beacon enabled mode. Our analysis is based on an accurate simulation model of the slotted CSMA/CA mechanism on top of a realistic physical layer, with respect to the IEEE 802.15.4 standard specification. The performance of the slotted CSMA/CA is evaluated and analyzed for different network settings to understand the impact of the protocol attributes (superframe order, beacon order and backoff exponent), the number of nodes and the data frame size on the network performance, namely in terms of throughput (S), average delay (D) and probability of success (Ps). We also analytically evaluate the impact of the slotted CSMA/CA overheads on the saturation throughput. We introduce the concept of utility (U) as a combination of two or more metrics, to determine the best offered load range for an optimal behavior of the network. We show that the optimal network performance using slotted CSMA/CA occurs in the range of 35% to 60% with respect to an utility function proportional to the network throughput (S) divided by the average delay (D).

Multi-elemental analysis of ready-to-eat “baby leaf” vegetables using microwave digestion and high-resolution continuum source atomic absorption spectrometry

The mineral content (phosphorous (P), potassium (K), sodium (Na), calcium (Ca), magnesium (Mg), iron (Fe), manganese (Mn), zinc (Zn) and copper (Cu)) of eight ready-to-eat baby leaf vegetables was determined. The samples were subjected to microwave-assisted digestion and the minerals were quantified by High-Resolution Continuum Source Atomic Absorption Spectrometry (HR-CS-AAS) with flame and electrothermal atomisation. The methods were optimised and validated producing low LOQs, good repeatability and linearity, and recoveries, ranging from 91% to 110% for the minerals analysed. Phosphorous was determined by a standard colorimetric method. The accuracy of the method was checked by analysing a certified reference material; results were in agreement with the quantified value. The samples had a high content of potassium and calcium, but the principal mineral was iron. The mineral content was stable during storage and baby leaf vegetables could represent a good source of minerals in a balanced diet. A linear discriminant analysis was performed to compare the mineral profile obtained and showed, as expected, that the mineral content was similar between samples from the same family. The Linear Discriminant Analysis was able to discriminate different samples based on their mineral profile.

Energy-dispersive x-ray fluorescence analysis of modern coloured glasses from Marinha Grande (Portugal)

X-Ray Spectrom. 2003; 32: 396–401

Performance Analysis of IEEE 802.15.6 Contention-based MAC Protocol

IEEE International Conference on Communications (IEEE ICC 2015). 8 to 12, Jun, 2015, IEEE ICC 2015 - Communications QoS, Reliability and Modeling, London, United Kingdom.

Analysis of outcome and cancer stem cells status in patients with resectable pancreatic adenocarcinoma

RESUMO: Actualmente, a única possibilidade de cura para doentes com adenocarcinoma do pâncreas (PDAC) é a ressecção cirúrgica, no início deste estudo, perguntamo-nos se os predictores clínico-patológicos clássicos de prognostico poderiam ser validados em uma grande cohort de doentes com cancro do pâncreas ressecável e se outros predictores clínicos poderiam ter um papel na decisão de que doentes beneficiariam de ressecção cirúrgica. No capítulo 2, observamos que até 30% dos doentes morrem no primeiro ano após a ressecção cirúrgica, pelo que o nosso objectivo foi determinar factores pré-operatórios que se correlacionam com mortalidade precoce após ressecação cirúrgica com recurso a um instrumento estatisticamente validado, o Charlson-Age Comorbidity Index (CACI), determinamos que um CACI score superior a 4 foi preditivo de internamentos prolongados (p <0,001), complicações pós-operatórias (p = 0,042), e mortalidade em 1 ano pós- ressecção cirúrgica (p <0,001). Um CACI superior a 6 triplicou a mortalidade no primeiro ano pós-cirurgia e estes doentes têm menos de 50% de probabilidade de estarem vivos um ano após a cirurgia. No capítulo 3, o nosso objectivo foi identificar uma proteína de superfície que se correlacionasse estatisticamente com o prognostico de doentes com adenocarcinoma do pâncreas e permitisse a distinção de subgrupos de doentes de acordo com as suas diferenças moleculares, perguntamo-nos ainda se essa proteína poderia ser um marcador de células-estaminais. No nosso trabalho anterior observamos que as células tumorais na circulação sanguínea apresentavam genes com características bifenotípica epitelial e mesenquimal, enriquecimento para genes de células estaminais (ALDH1A1 / ALDH1A2 e KLF4), e uma super-expressão de genes da matriz extracelular (colagénios, SPARC, e DCN) normalmente identificados no estroma de PDAC. Após a avaliação dos tumores primários com RNA-ISH, muitos dos genes identificados, foram encontrados co-localizando em uma sub-população de células na região basal dos ductos pancreáticos malignos. Além disso, observamos que estas células expressam o marcador SV2A neuroendócrino, e o marcador de células estaminais ALDH1A1/2. Em comparação com tumores negativos para SV2, os doentes com tumores SV2 positivos apresentaram níveis mais baixos de CA 19-9 (69% vs. 52%, p = 0,012), tumores maiores (> 4 cm, 23% vs. 10%, p = 0,0430), menor invasão de gânglios linfáticos (69% vs. 86%, p = 0,005) e tumores mais diferenciados (69% vs. 57%, p = 0,047). A presença de SV2A foi associada com uma sobrevida livre de doença mais longa (HR: 0,49 p = 0,009) bem como melhor sobrevida global (HR: 0,54 p = 0,018). Em conjunto, esta informação aponta para dois subtipos diferentes de adenocarcinoma do pâncreas, e estes subtipos co-relacionam estatisticamente com o prognostico de doentes, sendo este subgrupo definido pela presença do clone celular SV2A / ALDH1A1/2 positivo com características neuroendócrinas. No Capítulo 4, a expressão de SV2A no cancro do pâncreas foi validado em linhas celulares primárias. Demonstramos a heterogeneidade do adenocarcinoma do pâncreas de acordo com características clonais neuroendócrinas. Ao comparar as linhas celulares expressando SV2 com linhas celulares negativas, verificamos que as linhas celulares SV2+ eram mais diferenciadas, diferindo de linhas celulares SV2 negativas no que respeita a mutação KRAS, proliferação e a resposta à quimioterapia. No capítulo 5, perguntamo-nos se o clone celular SV2 positivo poderia explicar a resistência a quimioterapia observada em doentes. Observamos um aumento absoluto de clones celulares expressando SV2A, em múltiplas linhas de evidência - doentes, linhas de células primárias e xenotransplantes. Embora, tenhamos sido capazes de demonstrar que o adenocarcinoma do pâncreas é uma doença heterogénea, consideramos que a caracterização genética destes clones celulares expressando SV2A é de elevada importância. Pretendemos colmatar esta limitação com as seguintes estratégias: Após o tratamento com quimioterapia neoadjuvante na nossa coorte, realizamos microdissecação a laser das amostras primarias em parafina, de forma a analisar mutações genéticas observadas no adenocarcinoma pancreático; em segundo lugar, pretendemos determinar consequências de knockdown da expressão de SV2A em nossas linhas celulares seguindo-se o tratamento com gemicitabina para determinação do papel funcional de SV2A; finalmente, uma vez que os nossos esforços anteriores com um promotor - repórter e SmartFlare ™ falharam, o próximo passo será realizar RNA-ISH PrimeFlow™ seguido de FACS e RNA-seq para caracterização deste clone celular. Em conjunto, conseguimos provar com várias linhas de evidência, que o adenocarcinoma pancreático é uma doença heterogénea, definido por um clone de células que expressam SV2A, com características neuroendócrinas. A presença deste clone no tecido de doentes correlaciona-se estatisticamente com o prognostico da doença, incluindo sobrevida livre de doença e sobrevida global. Juntamente com padrões de proliferação e co-expressão de ALDH1A1/2, este clone parece apresentar um comportamento de células estaminais e está associado a resistência a quimioterapia, uma vez que a sua expressão aumenta após agressão química, quer em doentes, quer em linhas de células primárias.----------------------------- ABSTRACT: Currently, the only chance of cure for patients with pancreatic adenocarcinoma is surgical resection, at the beginning of my thesis studies, we asked if the classical clinicopathologic predictors of outcome could be validated in a large cohort of patients with early stage pancreatic cancer and if other clinical predictors could have a role on deciding which patients would benefit from surgery. In chapter 2, we found that up to 30% of patients die within the first year after curative intent surgery for pancreatic adenocarcinoma. We aimed at determining pre-operative factors that would correlate with early mortality following resection for pancreatic cancer using a statistically validated tool, the Charlson-Age Comorbidity Index (CACI). We found that a CACI score greater than 4 was predictive of increased length of stay (p<0.001), post-operative complications (p=0.042), and mortality within 1-year of pancreatic resection (p<0.001). A CACI score of 6 or greater increased 3-fold the odds of death within the first year. Patients with a high CACI score have less than 50% likelihood of being alive 1 year after surgery. In chapter 3 we aimed at identifying a surface protein that correlates with patient’s outcome and distinguishes sub-groups of patients according to their molecular differences and if this protein could be a cancer stem cell marker. The most abundant class of circulating tumor cells identified in our previous work was found to have biphenotypic features of epithelial to mesenchymal transition, enrichment for stem-cell associated genes (ALDH1A1/ALDH1A2 and KLF4), and an overexpression of extracellular matrix genes (Collagens, SPARC, and DCN) normally found in the stromal microenvironment of PDAC primary tumors. Upon evaluation of matched primary tumors with RNA-ISH, many of the genes identified were found to co-localize in a sub-population of cells at the basal region of malignant pancreatic ducts. In addition, these cells expressed the neuroendocrine marker SV2A, and the stem cell marker ALDH1A1/2. Compared to SV2 negative tumors, patients with SV2 positive tumors were more likely to present with lower CA 19-9 (69% vs. 52%, p = 0.012), bigger tumors (size > 4 cm, 23% vs. 10%, p= 0.0430), less nodal involvement (69% vs. 86%, p = 0.005) and lower histologic grade (69% vs. 57%, p = 0.047). The presence of SV2A expressing cells was associated with an improved disease free survival (HR: 0.49 p=0.009) and overall survival (HR: 0.54 p=0.018) and correlated linearly with ALDH1A2. Together, this information points to two different sub-types of pancreatic adenocarcinoma, and these sub-types correlated with patients’ outcome and were defined by the presence of a SV2A/ ALDH1A1/2 expressing clone with neuroendocrine features. In Chapter 4, SV2A expression in cancer was validated in primary cell lines. We were able to demonstrate pancreatic adenocarcinoma heterogeneity according to neuroendocrine clonal features. When comparing SV2 expressing cell lines with SV2 negative cell lines, we found that SV2+ cell lines were more differentiated and differ from SV2 negative cell lines regarding KRAS mutation, proliferation and response to chemotherapy. In Chapter 5 we aimed at determining if this SV2 positive clone could explain chemoresistance observed in patients. We found an absolute increase in SV2A expressing cells, with multiple lines of evidence, in patients, primary cell lines and xenografts. Although, we have been able to show evidence that pancreatic adenocarcinoma is a heterogeneous disease, our findings warrant further investigation. To further characterize SV2A expressing clones after treatment with neoadjuvant chemotherapy in our cohort, we have performed laser capture microdissection of the paraffin embedded tissue in this study and will analyze the tissue for known genetic mutations in pancreatic adenocarcinoma; secondly, we want to know what will happen after knocking down SV2A expression in our cell lines followed by treatment with gemcitabine to determine if SV2A is functionally important; finally, since our previous efforts with a promoter – reporter and SmartFlare™ have failed, we will utilize a novel PrimeFlow™ RNA-ISH assay followed by FACS and RNA sequencing to further characterize this cellular clone. Overall our data proves, with multiple lines of evidence, that pancreatic adenocarcinoma is a heterogeneous disease, defined by a clone of SV2A expressing cells, with neuroendocrine features. The presence of this clone in patients’ tissue correlates with patient’s disease free survival and overall survival. Together with patterns of proliferation and ALDH1A1/2 co-expression, this clone seems to present a stem-cell-like behavior and is associated with chemoresistance, since it increases after chemotherapy, both in patients and primary cell lines.

Análisis de una iniciativa estudiantil de investigación surgida en Criptogamia, una asignatura optativa de segundo ciclo de Biología = Analysis of a students’ research initiative originating in Cryptogamy, an elective course in the last two years of the Biology degree

Presentamos una experiencia exitosa de aprendizaje que partió de Criptogamia (asignatura optativa de segundo ciclo de Biología), que dio lugar a un proyecto de investigación gestionado por los propios alumnos. La iniciativa se consolidó estableciendo una Asociación de Estudiantes centrada en investigación y divulgación. En poco tiempo, los participantes han presentado comunicaciones científicas, y organizado actividades dirigidas a diversos públicos, dentro y fuera de la comunidad universitaria. Actualmente se plantea una colaboración multidisciplinar con otros organismos de investigación y la extensión de su ámbito de estudio. Abordamos su incidencia en el aprendizaje en varios aspectos: científico (técnicas específicas, rigor, búsqueda de información e interpretación de resultados), comunicativo (estructuración y presentación de la información obtenida, para diversos públicos), y organizativo, incluyendo el trabajo en equipo. Aunque de carácter espontáneo, esta experiencia muestra rasgos evaluables en cuanto a sus posibilidades para otras asignaturas. Analizamos las características y planteamiento de esta optativa, el perfil de sus alumnos, y el contexto universitario que la acoge. Detectamos como factores principales los aspectos participativos de la asignatura, la cohesión del grupo, el carácter voluntario de la implicación, los beneficios percibidos por los estudiantes, y la disponibilidad de recursos humanos (supervisión) y materiales (equipamiento y subvenciones).

Multilocus sequence analysis reveals the genetic diversity of European fruit tree phytoplasmas and supports the existence of inter-species recombination

The genetic diversity of three temperate fruit tree phytoplasmas ‘Candidatus Phytoplasma prunorum’, ‘Ca. P. mali’ and ‘Ca. P. pyri’ has been established by multilocus sequence analysis. Among the four genetic loci used, the genes imp and aceF distinguished 30 and 24 genotypes, respectively, and showed the highest variability. Percentage of substitution for imp ranged from 50 to 68% according to species. Percentage of substitution varied between 9 and 12% for aceF, whereas it was between 5 and 6% for pnp and secY. In the case of ‘Ca P. prunorum’ the three most prevalent aceF genotypes were detected in both plants and insect vectors, confirming that the prevalent isolates are propagated by insects. The four isolates known to be hypo-virulent had the same aceF sequence, indicating a possible monophyletic origin. Haplotype network reconstructed by eBURST revealed that among the 34 haplotypes of ‘Ca. P. prunorum’, the four hypo-virulent isolates also grouped together in the same clade. Genotyping of some Spanish and Azerbaijanese ‘Ca. P. pyri’ isolates showed that they shared some alleles with ‘Ca. P. prunorum’, supporting for the first time to our knowledge, the existence of inter-species recombination between these two species.

Anàlisi de l'etapa d'introducció del programa CA/AC a centres del Berritzegune de Guipúscoa

Aquest estudi presenta els diferents àmbits d’actuació que composen el Programa CA/AC així com l’explicació de les etapes d’implementació d’aquest programa en la seva modalitat B. Aquesta modalitat ha estat aplicada en diversos centres escolars pertanyents als Berritzegunes (Serveis Educatius) de la província de Guipúscoa durant el curs 2010/11. A partir d’aquesta pràctica, s’ha realitzat l’anàlisi quantitativa de les diferents actuacions dels àmbits A i B de manera que se’n poden analitzar a partir de gràfics, quines han estat les freqüències i el grau d’aplicació de les dinàmiques i de les estructures cooperatives que conformen el programa aplicat.

Expression, purification and biochemical characterization of recombinant Ca-dependent protein kinase 2 of the malaria parasite Plasmodium falciparum.

Calcium-dependent protein kinases (CDPKs) are serine/threonine kinases that react in response to calcium which functions as a trigger for several mechanisms in plants and invertebrates, but not in mammals. Recent structural studies have defined the role of calcium in the activation of CDPKs and have elucidated the important structural changes caused by calcium in order to allow the kinase domain of CDPK to bind and phosphorylate the substrate. However, the role of autophosphorylation in CDPKs is still not fully understood. In Plasmodium falciparum, seven CDPKs have been identified by sequence comparison, and four of them have been characterized and assigned to play a role in parasite motility, gametogenesis and egress from red blood cells. Although PfCDPK2 was already discovered in 1997, little is known about this enzyme and its metabolic role. In this work, we have expressed and purified PfCDPK2 at high purity in its unphosphorylated form and characterized its biochemical properties. Moreover, propositions about putative substrates in P. falciparum are made based on the analysis of the phosphorylation sites on the artificial substrate myelin basic protein (MBP).

Analysis of Irish tourism policy’s contribution to urban tourism: Dublin case study

L’objectiu principal del treball és analitzar les polítiques i plans turístics irlandesos nacionals, regionals i locals, i determinar com aquestos influeixen en el turisme urbà a Dublín. L’objectiu secundari és investigar el concepte de turisme urbà i examinar les tendències turístiques actuals i la seva repercussió en la formulació de polítiques

Statistical Analysis of Eco-Toxicologic Data of Mammals from a Polluted Area

Several eco-toxicological studies have shown that insectivorous mammals, due to theirfeeding habits, easily accumulate high amounts of pollutants in relation to other mammal species. To assess the bio-accumulation levels of toxic metals and their in°uenceon essential metals, we quantified the concentration of 19 elements (Ca, K, Fe, B, P,S, Na, Al, Zn, Ba, Rb, Sr, Cu, Mn, Hg, Cd, Mo, Cr and Pb) in bones of 105 greaterwhite-toothed shrews (Crocidura russula) from a polluted (Ebro Delta) and a control(Medas Islands) area. Since chemical contents of a bio-indicator are mainly compositional data, conventional statistical analyses currently used in eco-toxicology can givemisleading results. Therefore, to improve the interpretation of the data obtained, weused statistical techniques for compositional data analysis to define groups of metalsand to evaluate the relationships between them, from an inter-population viewpoint.Hypothesis testing on the adequate balance-coordinates allow us to confirm intuitionbased hypothesis and some previous results. The main statistical goal was to test equalmeans of balance-coordinates for the two defined populations. After checking normality,one-way ANOVA or Mann-Whitney tests were carried out for the inter-group balances

The Candida albicans plasma membrane protein Rch1p, a member of the vertebrate SLC10 carrier family, is a novel regulator of cytosolic Ca(2+) homoeostasis.

Candida albicans RCH1 (regulator of Ca(2+) homoeostasis 1) encodes a protein of ten TM (transmembrane) domains, homologous with human SLC10A7 (solute carrier family 10 member 7), and Rch1p localizes in the plasma membrane. Deletion of RCH1 confers hypersensitivity to high concentrations of extracellular Ca(2+) and tolerance to azoles and Li(+), which phenocopies the deletion of CaPMC1 (C. albicans PMC1) encoding the vacuolar Ca(2+) pump. Additive to CaPMC1 mutation, lack of RCH1 alone shows an increase in Ca(2+) sensitivity, Ca(2+) uptake and cytosolic Ca(2+) level. The Ca(2+) hypersensitivity is abolished by cyclosporin A and magnesium. In addition, deletion of RCH1 elevates the expression of CaUTR2 (C. albicans UTR2), a downstream target of the Ca(2+)/calcineurin signalling. Mutational and functional analysis indicates that the Rch1p TM8 domain, but not the TM9 and TM10 domains, are required for its protein stability, cellular functions and subcellular localization. Therefore Rch1p is a novel regulator of cytosolic Ca(2+) homoeostasis, which expands the functional spectrum of the vertebrate SLC10 family.

Tying up the loose ends in simple correspondence analysis

Although correspondence analysis is now widely available in statistical software packages and applied in a variety of contexts, notably the social and environmental sciences, there are still some misconceptions about this method as well as unresolved issues which remain controversial to this day. In this paper we hope to settle these matters, namely (i) the way CA measures variance in a two-way table and how to compare variances between tables of different sizes, (ii) the influence, or rather lack of influence, of outliers in the usual CA maps, (iii) the scaling issue and the biplot interpretation of maps,(iv) whether or not to rotate a solution, and (v) statistical significance of results.

Assessment of microbial community structure changes by amplified ribosomal DNA restriction analysis (ARDRA)

Amplified ribosomal DNA restriction analysis (ARDRA) is a simple method based on restriction endonuclease digestion of the amplified bacterial 16S rDNA. In this study we have evaluated the suitability of this method to detect differences in activated sludge bacterial communities fed on domestic or industrial wastewater, and subject to different operational conditions. The ability of ARDRA to detect these differences has been tested in modified Ludzack-Ettinger (MLE) configurations. Samples from three activated sludge wastewater treatment plants (WWTPs) with the MLE configuration were collected for both oxic and anoxic reactors, and ARDRA patterns using double enzyme digestions AluI+MspI were obtained. A matrix of Dice similarity coefficients was calculated and used to compare these restriction patterns. Differences in the community structure due to influent characteristics and temperature could be observed, but not between the oxic and anoxic reactors of each of the three MLE configurations. Other possible applications of ARDRA for detecting and monitoring changes in activated sludge systems are also discussed