Systematic uncertainties from halo asphericity in dark matter searches

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Análise da qualidade microbiológica em leite pasteurizado, tipo C, recém pasteurizado e na data de validade

The conservation of raw milk for long periods of time under refrigeration can result in the lost of its quality. This happens because bacterias, capable of developing in low temperatures, as psichrotrophics, in milk, associates with its enzymatic activities, are capable to degradate it. Although the pasteurization of milk sufficiently diminishes the transmission of the illnesses, that generally eliminates such microorganisms, is not a total efficient process because many enzymes produced for such bacterias are termostable, being able to resist the treatment and to remain active, leading to the loss of the quality of milk and its derivatives. The Normative Instruction 51 of 2002 established that milk must be cooled and stored in the production property, what resulted increasing the incidence of such bacteria in population destined milk. In some parts of the world contaminated milk is causing serious risks to the health of the population, assuming great importance in Public Health, mainly in relation to the hygienic-sanitary conditions of the product. ANVISA establishes, thus, maximum bacteriological concentration that must be evidenced before commercializing the product, guaranteeing the quality of milk as proper for consumption. Based on these aspects, the objective of this work is the microbiological analysis of 30 milk samples type C, collected in bakeries of the city Botucatu, in the state of São Paulo. Analysis were made to determinate the most likely number of termotolerants coliforms, as well the number of colony units of psichrotrophics bacterias, the presence of Salmonella and the enumeration of positive Staphylococcus aureus, at the moment of purchase and validity of the products

Cádmio, chumbo, cromo, mercúrio e níquel nos rios do estado de São Paulo e em peixes do Rio Sorocaba (São Paulo, Brasil)

To verify the levels of concentration of some heavy metals in fishes from Sorocaba river (São Paulo, Brazil) and evaluate if this contamination offers health risks to the fishermen, 63 samples of fishes collected from four points along the river were studied for cadmium, lead, chromium, nickel and mercury, with emphasis in this last, since it is the most toxic and most probable as a fish contaminant. Analyzing muscle samples by cold vapor atomic absorption spectrometry it was shown that the fishes are not contaminated. None of the five metals studied were present in prohibitive level and the fishes could be judged secure for human consume. It was also analyzed data from four years of cadmium, lead, chromium, nickel and mercury monitoring made by CETESB, from 1997 to 2000, in water from the main rivers of the State of São Paulo. The study pointed out that the majority of the monitored rivers still present contamination by those metals in a level that requires an improvement of the pollution control actions.

Self-Organizing Maps of Molecular Descriptors for Sesquiterpene Lactones and Their Application to the Chemotaxonomy of the Asteraceae Family

The Asteraceae, one of the largest families among angiosperms, is chemically characterised by the production of sesquiterpene lactones (SLs). A total of 1,111 SLs, which were extracted from 658 species, 161 genera, 63 subtribes and 15 tribes of Asteraceae, were represented and registered in two dimensions in the SISTEMATX, an in-house software system, and were associated with their botanical sources. The respective 11 block of descriptors: Constitutional, Functional groups, BCUT, Atom-centred, 2D autocorrelations, Topological, Geometrical, RDF, 3D-MoRSE, GETAWAY and WHIM were used as input data to separate the botanical occurrences through self-organising maps. Maps that were generated with each descriptor divided the Asteraceae tribes, with total index values between 66.7% and 83.6%. The analysis of the results shows evident similarities among the Heliantheae, Helenieae and Eupatorieae tribes as well as between the Anthemideae and Inuleae tribes. Those observations are in agreement with systematic classifications that were proposed by Bremer, which use mainly morphological and molecular data, therefore chemical markers partially corroborate with these classifications. The results demonstrate that the atom-centred and RDF descriptors can be used as a tool for taxonomic classification in low hierarchical levels, such as tribes. Descriptors obtained through fragments or by the two-dimensional representation of the SL structures were sufficient to obtain significant results, and better results were not achieved by using descriptors derived from three-dimensional representations of SLs. Such models based on physico-chemical properties can project new design SLs, similar structures from literature or even unreported structures in two-dimensional chemical space. Therefore, the generated SOMs can predict the most probable tribe where a biologically active molecule can be found according Bremer classification.

Assignment of Putative Functions to Membrane "Hypothetical Proteins" from the Trypanosoma cruzi Genome

Protozoan parasites cause thousands of deaths each year in developing countries. The genome projects of these parasites opened a new era in the identification of therapeutic targets. However, the putative function could be predicted for fewer than half of the protein-coding genes. In this work, all Trypanosoma cruzi proteins containing predicted transmembrane spans were processed through an automated computational routine and further analyzed in order to assign the most probable function. The analysis consisted of dissecting the whole predicted protein in different regions. More than 5,000 sequences were processed, and the predicted biological functions were grouped into 19 categories according to the hits obtained after analysis. One focus of interest, due to the scarce information available on trypanosomatids, is the proteins involved in signal-transduction processes. In the present work, we identified 54 proteins belonging to this group, which were individually analyzed. The results show that by means of a simple pipeline it was possible to attribute probable functions to sequences annotated as coding for "hypothetical proteins.'' Also, we successfully identified the majority of candidates participating in the signal-transduction pathways in T. cruzi.

Hereditary Autoinflammatory Syndromes: A Brazilian Multicenter Study

To evaluate the prevalence of genetic defects in clinically suspected autoinflammatory syndromes (AIS) in a Brazilian multicenter study. The study included 102 patients with a clinical diagnosis of Cryopyrin Associated Periodic Syndromes (CAPS), TNF Receptor Associated Periodic Syndrome (TRAPS), Familial Mediterranean Fever (FMF), Mevalonate Kinase Deficiency (MKD) and Pediatric Granulomatous Arthritis (PGA). One of the five AIS-related genes (NLRP3, TNFRSF1A, MEFV, MVK and NOD2) was evaluated in each patient by direct DNA sequencing, based on the most probable clinical suspect. Clinical diagnoses of the 102 patients were: CAPS (n = 28), TRAPS (n = 31), FMF (n = 17), MKD (n = 17) and PGA (n = 9). Of them, 27/102 (26 %) had a confirmed genetic diagnosis: 6/28 (21 %) CAPS patients, 7/31 (23 %) TRAPS, 3/17 (18 %) FMF, 3/17 (18 %) MKD and 8/9 (89 %) PGA. We have found that approximately one third of the Brazilian patients with a clinical suspicion of AIS have a confirmed genetic diagnosis.

Use of Leptospira spp. strains isolated in Brazil in the microscopic agglutination test applied to diagnosis of leptospirosis in cattle herds in eight brazilian states

Sarmento A.M.C., Azevedo S.S., Morais Z.M., Souza G.O., Oliveira F.C.S., Goncales A.P., Miraglia F. & Vasconcellos S.A. 2012. [Use of Leptospira spp. strains isolated in Brazil in the microscopic agglutination test applied to diagnosis of leptospirosis in cattle herds in eight brazilian states.] Emprego de estirpes Leptospira spp. isoladas no Brasil na microtecnica de soroaglutinacao microscopica aplicada ao diagnostico da leptospirose em rebanhos bovinos de oito estados brasileiros. Pesquisa Veterinaria Brasileira 32(7);601-606. Universidade de Sao Paulo, Faculdade de Medicina Veterinaria e Zootecnia, Departamento de Medicina Veterinaria Preventiva e Saude Animal, Av. Prof. Dr. Orlando Marques de Paiva 87, Sao Paulo, SP 05508-270, Brazil. E-mail: savasco@usp.br The aim of this study was to investigate the adequacy of the use of autochthonous strains of leptospires isolated in Brazil, added to antigen collection of the microscopic agglutination test (MAT) applied to the diagnosis of bovine leptospirosis. By means of non-probability sampling, 109 farms and 9,820 cattle, females at reproductive age were chosen from 85 municipalities in the states of Goias, Mato Grosso, Mato Grosso do Sul, Minas Gerais, Parana, Rio Grande do Sul, Santa Catarina and Sao Paulo. Among the 9,820 examined animals, 5,806 (59.12%) were reactants at MAT for at least one serovar using the 23 reference serovars. Employing the collection of reference serovars and the ten autochthonous strains, 6,400 (65.24%) reactants and significant difference (p=0.001) was found. The most probable serovars identified by the collection of reference antigens were Hardjo (43.03%), Shermani (20%), Wolfi (9.96%), Grippothyphosa (5.42%) and Pomona (4.28%). With the collection amplified with the ten strains isolated in Brazil, the most probable serovars were Hardjo (31%), Guaricura-M4/84 (22.50%), Shermani (15.43%), Wolffi (4.76%), Grippothyphosa (3.71%) and Autumnalis (3.24%). The serovar Guaricura, strain M4/84, isolated from bovines and buffaloes in the State of Sao Paulo, was ranked as one of the three most probable serovars in the states of Goias, Mato Grosso, Mato Grosso do Sul, Minas Gerais and Sao Paulo. The addition of autochthonous strains to the MAT antigen collection provided the confirmation of the diagnosis of leptospirosis in 594 cattle (6%) which have been classified as non-reactants by the reference collection (p=0.001).

Site localization of Cd impurities in sapphire

By combining first-principles electronic structure calculations and existing time-differential gamma-gamma perturbed-angular-correlation experiments we studied the site localization, the local environment, and the electronic structure of Cd impurities in sapphire (alpha-Al2O3) single crystals in different charged states. The ab initio calculations were performed with the full-potential augmented plane wave plus local orbitals method and the projector augmented wave method. Comparing the calculated electric-field-gradient tensor at the Cd nuclei in the alpha-Al2O3 host lattice and the corresponding available experimental values, we have seen that it is equally possible for Cd to replace an Al atom (in a negative charge state) or to be placed in an interstitial site (in a neutral charge state). To finally address the issue of the Cd impurity localization, we performed formation energy calculations. These results have shown that Cd placed in the substitutional Al site, in the negatively charged state, is the most probable configuration.

Stochastic competitive learning in complex networks

Competitive learning is an important machine learning approach which is widely employed in artificial neural networks. In this paper, we present a rigorous definition of a new type of competitive learning scheme realized on large-scale networks. The model consists of several particles walking within the network and competing with each other to occupy as many nodes as possible, while attempting to reject intruder particles. The particle's walking rule is composed of a stochastic combination of random and preferential movements. The model has been applied to solve community detection and data clustering problems. Computer simulations reveal that the proposed technique presents high precision of community and cluster detections, as well as low computational complexity. Moreover, we have developed an efficient method for estimating the most likely number of clusters by using an evaluator index that monitors the information generated by the competition process itself. We hope this paper will provide an alternative way to the study of competitive learning.

Behavior of respiratory metabolism and pyridine nucleotide levels in Oxyrrhis marina during starvation

Máster en Oceanografía

3D probability tomography: theoretical developments and applications to high-resolution geophysical prospecting

The theory of the 3D multipole probability tomography method (3D GPT) to image source poles, dipoles, quadrupoles and octopoles, of a geophysical vector or scalar field dataset is developed. A geophysical dataset is assumed to be the response of an aggregation of poles, dipoles, quadrupoles and octopoles. These physical sources are used to reconstruct without a priori assumptions the most probable position and shape of the true geophysical buried sources, by determining the location of their centres and critical points of their boundaries, as corners, wedges and vertices. This theory, then, is adapted to the geoelectrical, gravity and self potential methods. A few synthetic examples using simple geometries and three field examples are discussed in order to demonstrate the notably enhanced resolution power of the new approach. At first, the application to a field example related to a dipole–dipole geoelectrical survey carried out in the archaeological park of Pompei is presented. The survey was finalised to recognize remains of the ancient Roman urban network including roads, squares and buildings, which were buried under the thick pyroclastic cover fallen during the 79 AD Vesuvius eruption. The revealed anomaly structures are ascribed to wellpreserved remnants of some aligned walls of Roman edifices, buried and partially destroyed by the 79 AD Vesuvius pyroclastic fall. Then, a field example related to a gravity survey carried out in the volcanic area of Mount Etna (Sicily, Italy) is presented, aimed at imaging as accurately as possible the differential mass density structure within the first few km of depth inside the volcanic apparatus. An assemblage of vertical prismatic blocks appears to be the most probable gravity model of the Etna apparatus within the first 5 km of depth below sea level. Finally, an experimental SP dataset collected in the Mt. Somma-Vesuvius volcanic district (Naples, Italy) is elaborated in order to define location and shape of the sources of two SP anomalies of opposite sign detected in the northwestern sector of the surveyed area. The modelled sources are interpreted as the polarization state induced by an intense hydrothermal convective flow mechanism within the volcanic apparatus, from the free surface down to about 3 km of depth b.s.l..

Entwicklung einer Fokalebenen-Driftkammer für niederenergetische Pionen und experimentelle Bestimmung einer inversen Transfermatrix für das Short-Orbit-Spektrometer

Die Drei-Spektrometer-Anlage am Mainzer Institut für Kernphysik wurde um ein zusätzliches Spektrometer ergänzt, welches sich durch seine kurze Baulänge auszeichnet und deshalb Short-Orbit-Spektrometer (SOS) genannt wird. Beim nominellen Abstand des SOS vom Target (66 cm) legen die nachzuweisenden Teilchen zwischen Reaktionsort und Detektor eine mittlere Bahnlänge von 165 cm zurück. Für die schwellennahe Pionproduktion erhöht sich dadurch im Vergleich zu den großen Spektrometern die Überlebenswahrscheinlichkeit geladener Pionen mit Impuls 100 MeV/c von 15% auf 73%. Demzufolge verringert sich der systematische Fehler ("Myon-Kontamination"), etwa bei der geplanten Messung der schwachen Formfaktoren G_A(Q²) und G_P(Q²), signifikant. Den Schwerpunkt der vorliegenden Arbeit bildet die Driftkammer des SOS. Ihre niedrige Massenbelegung (0,03% X_0) zur Reduzierung der Kleinwinkelstreuung ist auf den Nachweis niederenergetischer Pionen hin optimiert. Aufgrund der neuartigen Geometrie des Detektors musste eine eigene Software zur Spurrekonstruktion, Effizienzbestimmung etc. entwickelt werden. Eine komfortable Möglichkeit zur Eichung der Driftweg-Driftzeit-Relation, die durch kubische Splines dargestellt wird, wurde implementiert. Das Auflösungsvermögen des Spurdetektors liegt in der dispersiven Ebene bei 76 µm für die Orts- und 0,23° für die Winkelkoordinate (wahrscheinlichster Fehler) sowie entsprechend in der nicht-dispersiven Ebene bei 110 µm bzw. 0,29°. Zur Rückrechnung der Detektorkoordinaten auf den Reaktionsort wurde die inverse Transfermatrix des Spektrometers bestimmt. Hierzu wurden an Protonen im ¹²C-Kern quasielastisch gestreute Elektronen verwendet, deren Startwinkel durch einen Lochkollimator definiert wurden. Daraus ergeben sich experimentelle Werte für die mittlere Winkelauflösung am Target von sigma_phi = 1,3 mrad bzw. sigma_theta = 10,6 mrad. Da die Impulseichung des SOS nur mittels quasielastischer Streuung (Zweiarmexperiment) durchgeführt werden kann, muss man den Beitrag des Protonarms zur Breite des Piks der fehlenden Masse in einer Monte-Carlo-Simulation abschätzen und herausfalten. Zunächst lässt sich nur abschätzen, dass die Impulsauflösung sicher besser als 1% ist.

The genetic signature of Neolithic in Greece

The Neolithic is characterized by the transition from a subsistence economy, based on hunting and gathering, to one based on food producing. This important change was paralleled by one of the most significant demographic increase in the recent history of European populations. The earliest Neolithic sites in Europe are located in Greece. However, the debate regarding the colonization route followed by the Middle-eastern farmers is still open. Based on archaeological, archaeobotanical, craniometric and genetic data, two main hypotheses have been proposed. The first implies the maritime colonization of North-eastern Peloponnesus from Crete, whereas the second points to an island hopping route that finally brought migrants to Central Greece. To test these hypotheses using a genetic approach, 206 samples were collected from the two Greek regions proposed as the arrival point of the two routes (Korinthian district and Euboea). Expectations for each hypothesis were compared with empirical observations based on the analysis of 60 SNPs and 26 microsatellite loci of Y-chromosome and mitochondrial DNA hypervariable region I. The analysis of Y-chromosome haplogroups revealed a strong genetic affinity of Euboea with Anatolian and Middle-eastern populations. The inferences of the time since population expansion suggests an earlier usage of agriculture in Euboea. Moreover, the haplogroup J2a-M410, supposed to be associated with the Neolithic transition, was observed at higher frequency and variance in Euboea showing, for both these parameters, a decreasing gradient moving from this area. The time since expansion estimates for J2a-M410 was found to be compatible with the Neolithic and slightly older in Euboea. The analysis of mtDNA resulted less informative. However, a higher genetic affinity of Euboea with Anatolian and Middle-eastern populations was confirmed. These results taken as a whole suggests that the most probable route followed by Neolithic farmers during the colonization of Greece was the island hopping route.

Identification of the N-Linked Glycosylation Sites of the Transcription Factor Rest and Effect of Glycosylation on DNA Binding and Transcriptional Activity

REST is a zinc-finger transcription factor implicated in several processes such as maintenance of embryonic stem cell pluripotency and regulation of mitotic fidelity in non-neuronal cells [Chong et al., 1995]. The gene encodes for a 116-kDa protein that acts as a molecular platform for co-repressors recruitment and promotes modifications of DNA and histones [Ballas, 2005]. REST showed different apparent molecular weights, consistent with the possible presence of post-translational modifications [Lee et al., 2000]. Among these the most common is glycosylation, the covalent attachment of carbohydrates during or after protein synthesis [Apweiler et al., 1999] My thesis has ascertained, for the first time, the presence of glycan chians in the transcription factor REST. Through enzymatic deglycosylation and MS, oligosaccharide composition of glycan chains was evaluated: a complex mixture of glycans, composed of N-acetylgalactosamine, galactose and mannose, was observed thus confirming the presence of O- and N-linked glycan chains. Glycosylation site mapping was done using a 18O-labeling method and MS/MS and twelve potential N-glycosylation sites were identified. The most probable glycosylation target residues were mutated through site-directed mutagenesis and REST mutants were expressed in different cell lines. Variations in the protein molecular weight and mutant REST ability to bind the RE-1 sequence were analyzed. Gene reporter assays showed that, altogether, removal of N-linked glycan chains causes loss of transcriptional repressor function, except for mutant N59 which showed a slight residual repressor activity in presence of IGF-I. Taken togheter these results demonstrate the presence of complex glycan chians in the transcription factor REST: I have depicted their composition, started defining their position on the protein backbone and identified their possible role in the transcription factor functioning. Considering the crucial role of glycosylation and transcription factors activity in the aetiology of many diseases, any further knowledge could find important and interesting pharmacological application.

Fiber-reinforced ceramics for thermostructural applications, produced by polymer impregnation pyrolysis

Several CFCC (Continuous Fiber Composite Ceramics) production processes were tested, concluding that PIP (Polymer Impregnation, or Infiltration, Pyrolysis) and CBC (Chemically Bonded Ceramics) based procedures have interesting potential applications in the construction and transportation fields, thanks to low costs to get potentially useful thermomechanical performances. Among the different processes considered during the Doctorate (from the synthesis of new preceramic polymers, to the PIP production of SiC / SiC composites) the more promising results came from the PIP process with poly-siloxanes on basalt fabrics preforms. Low processing time and costs, together with fairly good thermomechanical properties were demonstrated, even after only one or two PIP steps in nitrogen flow. In alternative, pyrolysis in vacuum was also tested, a procedure still not discussed in literature, but which could originate an interesting reduction of production costs, with only a moderate detrimental effect on the mechanical properties. The resulting CFCC is a basalt / SiCO composite that can be applied for continuous operation up to 600°C, also in oxidant environment, as TG and XRD demonstrated. The failure upon loading is generally pseudo-plastic, being interlaminar delamination the most probable rupture mechanism. . The strength depends on several different factors (microstructure, polymer curing and subsequent ceramic phase evolution, fiber pull-out, fiber strength, fiber percentage) and can only be optimized empirically. In order to be open minded in selecting the best technology, also CBC (Chemically Bonded Ceramics) matrixes were considered during this Doctorate, making some preliminary investigations on fire-resistant phosphate cements. Our results on a commercial product evidenced some interesting thermomechanical capabilities, even after thermal treatments. However the experiments showed also phase change and possible cracking and deformations even on slow drying (at 130°C) and easy rehydration upon exposure to environmental humidity.