Subshifts with Simple Cellular Automata

A subshift is a set of in nite one- or two-way sequences over a xed nite set, de ned by a set of forbidden patterns. In this thesis, we study subshifts in the topological setting, where the natural morphisms between them are ones de ned by a (spatially uniform) local rule. Endomorphisms of subshifts are called cellular automata, and we call the set of cellular automata on a subshift its endomorphism monoid. It is known that the set of all sequences (the full shift) allows cellular automata with complex dynamical and computational properties. We are interested in subshifts that do not support such cellular automata. In particular, we study countable subshifts, minimal subshifts and subshifts with additional universal algebraic structure that cellular automata need to respect, and investigate certain criteria of `simplicity' of the endomorphism monoid, for each of them. In the case of countable subshifts, we concentrate on countable so c shifts, that is, countable subshifts de ned by a nite state automaton. We develop some general tools for studying cellular automata on such subshifts, and show that nilpotency and periodicity of cellular automata are decidable properties, and positive expansivity is impossible. Nevertheless, we also prove various undecidability results, by simulating counter machines with cellular automata. We prove that minimal subshifts generated by primitive Pisot substitutions only support virtually cyclic automorphism groups, and give an example of a Toeplitz subshift whose automorphism group is not nitely generated. In the algebraic setting, we study the centralizers of CA, and group and lattice homomorphic CA. In particular, we obtain results about centralizers of symbol permutations and bipermutive CA, and their connections with group structures.

INTERCROPPING CORN WITH A COMBINATION OF TREE SPECIES TO CONTROL WEEDS

ABSTRACT The combination of crop residues or crop extracts is often more advantageous in controlling weeds, than the application of each residue or extract singly. This suggests that in intercropping with maize, the combination of tree species can be more advantageous than species isolated in weed control. The objective of this study was to evaluate the effects of intercropping with a combination of leguminous on the weed growth and corn yield. A randomized-block design with split plots (cultivars in plots) and five replicates was established. The cultivars BR 205 and AG 1041 were subject to the following treatments: two weedings (A), intercropping with sabiá (B), gliricidia (C), gliricidia + sabiá (D) and no weeding (E). In the B and C, 30 viable seeds m-2 of the leguminous were sown. In the D, 15 seeds of each species were sown m-2. The legumes were sown by random casting during corn planting. The sequence of the best treatments in reducing the growth of weeds is A > B = C = D = E. The sequence of the best treatments when are considered the yields of baby corn, green corn and grain is A > B > C > D > E. The cultivars do not differ in regards to the reduction in weed growth. In terms of corn yield cultivar BR 205 is the best.

Getting Started with Islandora

Workshop at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Glyphosate Herbicide Use in Urochloa brizantha Management in Intercropping With Herbicide-Resistant Maize

The success of the intercropping among cultivated species depends on the adoption of practices that provide, in due course, greater competitive ability of a species over another. The objective of this study was to evaluate the use of glyphosate herbicide in the suppression of Brachiaria (signalgrass) intercropped with maize. The experiment was conducted in a randomized complete block design with four replications. The treatments were arranged in a 5 x 2 + 2 factorial arrangement, the first factor corresponding to the doses of glyphosate (48, 96, 144, 240, 480 g ha-1 of the acid equivalent (a.e)) and the second one to the vegetative stages of the signalgrass at the time of application (2 and 4 tillers). Two controls were added to the treatment list, comprising controls without herbicide application and hand removal of the signalgrass. The number of plants, tillers and dry matter of signalgrass was reduced with glyphosate. The increase of the glyphosate doses enhanced the injure to the forage plants, mainly when the compound was sprayed at the two-tiller vegetative stage. The dry matter of maize plants increased proportionally to the glyphosate dose. However, the height of the maize plants was not affected. The grain mass and productivity of maize grain increased with increasing dose of glyphosate. The maize yield was negatively influenced on the untreated control. Glyphosate at 96 and 144 g ha-1, when applied at 2 and 4 tiller stage, respectively, reduces the growth of signalgrass and does not affect the maize grain yield.

Genetic control of characters associated with bean golden mosaic geminivirus resistance in Phaseolus vulgaris L.

Bean golden mosaic is the most important viral disease of the bean crop (Phaseolus vulgaris L.) in Latin America. The genetics of resistance to a Brazilian strain of bean golden mosaic virus (BGMV), was studied in a 4 x 4 diallel cross without reciprocals, among the parental genotypes DOR 303, EMGOPA 201 Ouro, Carnaval, and Redlands Greenleaf C. Seedlings of the four parents, six F1 hybrids, 12 backcrosses, and F2 generations for each combination were inoculated on the eighth day after sowing by exposure to a viruliferous whitefly (Bemisia tabaci Genn.) population for 24 h, in a glasshouse, prior to transplantation to field conditions. The full set of two parents, F1, F2 and respective backcrosses for each combination was considered to be a family. Data were recorded and analyzed for foliar yellowing, plant dwarfing, and pod malformation, using a randomized block design, with two replications. Weighted generation mean analysis was performed for each of the six families. An additive gene action model was significant for the three characteristics evaluated. On the other hand, non-additive gene action had greater absolute value in most cases. Resistance to foliar yellowing conferred by genes from DRO 303 was highly heritable and was expressed equally well in the different genetic backgrounds evaluated. Such resistance may be oligogenic. Broad- and narrow-sense heritabilities were relatively high for all response traits. The three traits studied were all positively correlated, indicating that they can be simultaneously selected for enhancement. The highest correlation coefficient was obtained for dwarfing x pod malformation.

A 28-fold increase in secretory protein synthesis is associated with DNA puff activity in the salivary gland of Bradysia hygida (Diptera, Sciaridae)

When the first group of DNA puffs is active in the salivary gland regions S1 and S3 of Bradysia hygida larvae, there is a large increase in the production and secretion of new salivary proteins demonstrable by [3H]-Leu incorporation. The present study shows that protein separation by SDS-PAGE and detection by fluorography demonstrated that these polypeptides range in molecular mass from about 23 to 100 kDa. Furthermore, these proteins were synthesized mainly in the S1 and S3 salivary gland regions where the DNA puffs C7, C5, C4 and B10 are conspicuous, while in the S2 region protein synthesis was very low. Others have shown that the extent of amplification for DNA sequences that code for mRNA in the DNA puffs C4 and B10 was about 22 and 10 times, respectively. The present data for this group of DNA puffs are consistent with the proposition that gene amplification is necessary to provide some cells with additional gene copies for the production of massive amounts of proteins within a short period of time (Spradling AC and Mahowald AP (1980) Proceedings of the National Academy of Sciences, USA, 77: 1096-1100).

Reaction of diphenyl diselenide with hydrogen peroxide and inhibition of delta-aminolevulinate dehydratase from rat liver and cucumber leaves

The interaction of the product of H2O2 and (PhSe)2 with delta-aminolevulinate dehydratase (delta-ALA-D) from mammals and plants was investigated. (PhSe)2 inhibited rat hepatic delta-ALA-D with an IC50 of 10 µM but not the enzyme from cucumber leaves. The reaction of (PhSe)2 with H2O2 for 1 h increased the inhibitory potency of the original compound and the IC50 for animal delta-ALA-D inhibition was decreased from 10 to 2 µM. delta-ALA-D from cucumber leaves was also inhibited by the products of reaction of (PhSe)2 with H2O2 with an IC50 of 4 µM. The major product of reaction of (PhSe)2 with H2O2 was identified as seleninic acid and produced an intermediate with a lambdamax at 265 nm after reaction with t-BuSH. These results suggest that the interaction of (PhSe)2 with mammal delta-ALA-D requires the presence of cysteinyl residues in close proximity. Two cysteine residues in spatial proximity have been recently described for the mammalian enzyme. Analysis of the primary structure of plant delta-ALA-D did not reveal an analogous site. In contrast to (PhSe)2, seleninic acid, as a result of the higher electrophilic nature of its selenium atom, may react with additional cysteinyl residue(s) in mammalian delta-ALA-D and also with cysteinyl residues from cucumber leaves located at a site distinct from that found at the B and A sites in mammals. Although the interaction of organochalcogens with H2O2 may have some antioxidant properties, the formation of seleninic acid as a product of this reaction may increase the toxicity of organic chalcogens such as (PhSe)2.

Leptin is not associated independently with hypertension in Japanese-Brazilian women

We evaluated the relationship of leptin with hypertension adjusted for body mass index (BMI) and/or waist circumference in a population of Japanese-Brazilian women aged > or = 30 years with centrally distributed adiposity. After excluding diabetic subjects, the study subjects - who participated in a population-based study on the prevalence of metabolic syndrome - showed prevalence rates of obesity (BMI > or = 25 kg/m²) and central adiposity (waist > or = 80 cm) of 32.0 and 37.8%, respectively. The hypertensive group (N = 162) was older, had higher BMI (24.9 ± 4.2 vs 23.3 ± 3.4 kg/m², P < 0.001), waist circumference (81.1 ± 10.1 vs 76.3 ± 8.2 cm, P < 0.001) and insulin levels (8.0 ± 6.2 vs 7.1 ± 4.9 µU/mL, P < 0.05) than the normotensive group (N = 322) and showed an unfavorable metabolic profile (higher 2-h plasma glucose, C-reactive protein and non-HDL cholesterol levels). Leptin did not differ between groups (8.2 ± 6.8 vs 7.2 ± 6.6 ng/mL, P = 0.09, for hypertensive vs normotensive, respectively) and its levels correlated significantly with anthropometric variables but not with blood pressure. Logistic regression analysis indicated that age and waist were independently associated with hypertension but not with homeostasis model assessment of insulin resistance or leptin levels. The lack of an independent association of hypertension with metabolic parameters (2-h glucose, C-reactive protein and non-HDL cholesterol) after adjustment for central adiposity suggested that visceral fat deposition may be the common mediator of the disturbances of the metabolic syndrome. Our data indicate that age and waist are major determinants of hypertension in this population of centrally obese (waist > or = 80 cm) Japanese-Brazilian women, but do not support a role for leptin in the elevation of blood pressure.

Differential evolution based classification with pool of distances and aggregation operators

The objective of this thesis is to develop and generalize further the differential evolution based data classification method. For many years, evolutionary algorithms have been successfully applied to many classification tasks. Evolution algorithms are population based, stochastic search algorithms that mimic natural selection and genetics. Differential evolution is an evolutionary algorithm that has gained popularity because of its simplicity and good observed performance. In this thesis a differential evolution classifier with pool of distances is proposed, demonstrated and initially evaluated. The differential evolution classifier is a nearest prototype vector based classifier that applies a global optimization algorithm, differential evolution, to determine the optimal values for all free parameters of the classifier model during the training phase of the classifier. The differential evolution classifier applies the individually optimized distance measure for each new data set to be classified is generalized to cover a pool of distances. Instead of optimizing a single distance measure for the given data set, the selection of the optimal distance measure from a predefined pool of alternative measures is attempted systematically and automatically. Furthermore, instead of only selecting the optimal distance measure from a set of alternatives, an attempt is made to optimize the values of the possible control parameters related with the selected distance measure. Specifically, a pool of alternative distance measures is first created and then the differential evolution algorithm is applied to select the optimal distance measure that yields the highest classification accuracy with the current data. After determining the optimal distance measures for the given data set together with their optimal parameters, all determined distance measures are aggregated to form a single total distance measure. The total distance measure is applied to the final classification decisions. The actual classification process is still based on the nearest prototype vector principle; a sample belongs to the class represented by the nearest prototype vector when measured with the optimized total distance measure. During the training process the differential evolution algorithm determines the optimal class vectors, selects optimal distance metrics, and determines the optimal values for the free parameters of each selected distance measure. The results obtained with the above method confirm that the choice of distance measure is one of the most crucial factors for obtaining higher classification accuracy. The results also demonstrate that it is possible to build a classifier that is able to select the optimal distance measure for the given data set automatically and systematically. After finding optimal distance measures together with optimal parameters from the particular distance measure results are then aggregated to form a total distance, which will be used to form the deviation between the class vectors and samples and thus classify the samples. This thesis also discusses two types of aggregation operators, namely, ordered weighted averaging (OWA) based multi-distances and generalized ordered weighted averaging (GOWA). These aggregation operators were applied in this work to the aggregation of the normalized distance values. The results demonstrate that a proper combination of aggregation operator and weight generation scheme play an important role in obtaining good classification accuracy. The main outcomes of the work are the six new generalized versions of previous method called differential evolution classifier. All these DE classifier demonstrated good results in the classification tasks.

Prolactin and cortisol levels in women with endometriosis

Endometriosis is a progressive estrogen-dependent disease affecting women during their reproductive years. The objective of the present study was to investigate whether endometriosis is associated with stress parameters. We determined cortisol and prolactin levels in serum, peritoneal and follicular fluid from infertile women with endometriosis and fertile women without the disease. The extent of the disease was staged according to the revised American Fertility Society classification (1997). Serum and peritoneal fluid were collected from 49 women aged 19 to 39 years undergoing laparoscopy. Eighteen women had stage I-II endometriosis and 10 had stage III-IV. Controls were 21 women undergoing laparoscopy for tubal sterilization. Follicular fluid was obtained from 39 women aged 25-39 years undergoing in vitro fertilization (21 infertile women with endometriosis and 18 infertile women without endometriosis). Serum prolactin levels were significantly higher in infertile women with stage III-IV endometriosis (28.9 ± 2.1 ng/mL) than in healthy controls (13.2 ± 2.1 ng/mL). Serum cortisol levels were significantly higher in infertile women with stage III-IV endometriosis (20.1 ± 1.3 ng/mL) than in controls (10.5 ± 1.4 ng/mL). Cortisol and prolactin levels in follicular fluid and peritoneal fluid did not differ significantly between groups. The high levels of cortisol and prolactin in the serum from women with endometriosis might contribute to the subfertility frequently associated with the disease. Moreover, since higher levels of cortisol and prolactin are often associated with stress, it is probable that stress might contribute to the development of endometriosis and its progression to advanced stages of the disease.

Immunoexpression of cyclooxygenase-1 and -2 in ulcerative colitis

Ulcerative colitis (UC) is a disease of the colon and rectum characterized by a nonspecific chronic inflammation mediated by the concerted response of cellular and humoral events. Prostaglandins are synthesized by cyclooxygenase (COX)-1 and -2 and exhibit both pro- and anti-inflammatory activity. To evaluate COX-1 and COX-2 immunoexpression in 42 cases of UC and to correlate it with clinicopathological parameters, COX-1 and COX-2 expression was investigated by the immunohistochemistry method. Only patients with all pertinent clinical and evolutive data as well as with adequate biopsy material were included in the study. Fifteen samples of colorectal adenocarcinoma and 14 of large bowel with no histological changes were used for positive and negative controls, respectively. UC patients showed COX-1 immunoreactivity in epithelial cells in 29% of the cases and in inflammatory cells in 43%. COX-2 positivity in epithelial and inflammatory cells was found in 69% of the samples. The comparison between UC and the control groups revealed that the UC group had significantly more positive cases for COX-1 and COX-2 in inflammatory cells. Immunohistochemistry allowed the identification of COX-1 and COX-2 expression in epithelial and inflammatory cells in UC biopsies. No significant difference between COX-1 and COX-2 immunoreactivity in epithelial and inflammatory cells was observed regarding the clinicopathological parameters. COX-2 presented low expression in normal colon and high expression in colorectal adenocarcinoma. COX-2 might play a role in the pathophysiologic processes of inflammatory bowel disease and the development of neoplasia. Treatment with selective COX-2 inhibitors might be an additional option for therapy.

Circulating levels of inflammation-associated miR-155 and endothelial-enriched miR-126 in patients with end-stage renal disease

Circulating microRNAs (miRNAs) may represent a potential noninvasive molecular biomarker for various pathological conditions. Moreover, the detection of circulating miRNAs can provide important novel disease-related information. In particular, inflammation-associated miR-155 and endothelial-enriched miR-126 are reported to be associated with vascular homeostasis. Vascular damage is a common event described in end-stage renal disease (ESRD). We hypothesized that miR-155 and miR-126 may be detectable in the circulation and serve as potential biomarkers for risk stratification. In this study, we assessed miR-155 and miR-126 in the plasma of 30 ESRD patients and 20 healthy controls using real-time quantification RT-PCR. The circulating levels of miR-155 and miR-126 were significantly reduced in patients with ESRD compared to healthy controls. However, there was no significant difference of circulating miR-155 and miR-126 levels between prehemodialysis and posthemodialysis patients. Furthermore, both circulating miR-126 and miR-155 correlated positively with estimated glomerular filtration rate (miR-126: r = 0.383, P = 0.037; miR-155: r = 0.494, P = 0.006) and hemoglobin (miR-126: r = 0.515, P = 0.004; miR-155: r = 0.598, P < 0.001) and correlated inversely with phosphate level (miR-126: r = -0.675, P < 0.001; miR-155: r = -0.399, P = 0.029). Pearson’s correlation was used to compare circulating levels of miRNAs with clinical parameters. These results suggested that circulating miR-155 and miR-126 might be involved in the development of ESRD. Further studies are needed to demonstrate the role of circulating miR-155 and miR-126 as candidate biomarkers for risk estimation.

Plasma levels and placental expression of vaspin in pregnant women with diabetes mellitus

The present study aimed to investigate visceral adipose tissue-specific serpin (vaspin) concentrations in serum and term placentas and relate these values to insulin resistance and lipid parameters in women with gestational diabetes mellitus (GDM). A total of 30 GDM subjects and 27 age-matched pregnant women with normal glucose tolerance (NGT, control) were included. Serum glucose, glycated hemoglobin (HbA1c), lipid profile, insulin, and vaspin were measured at the end of pregnancy, and homeostasis model of assessment-insulin resistance (HOMA-IR) values were calculated. Vaspin mRNA and protein levels in placentas were measured by real-time fluorescence quantitative reverse transcription polymerase chain reaction (RT-qPCR) and Western blotting, respectively. Serum vaspin levels were significantly lower in the GDM group than in controls (0.49±0.24 vs 0.83±0.27 ng/mL, respectively; P<0.01). Three days after delivery, serum vaspin levels were significantly decreased in subjects with GDM (0.36±0.13 vs0.49±0.24 ng/mL, P<0.01). However, in the GDM group, serum vaspin levels were not correlated with the parameters evaluated. In contrast, in the control group, serum vaspin levels were positively correlated with triglycerides (TG; r=0.45, P=0.02) and very low-density lipoprotein cholesterol (VLDL-C; r=0.42, P=0.03). Placental mRNA vaspin (0.60±0.32 vs0.68±0.32, P=0.46) and protein (0.30±0.08 vs0.39±0.26; P=0.33) levels in the GDM group did not differ significantly from those in the control group, but were negatively correlated with neonatal birth weight in the GDM group (r=-0.48, P=0.03; r=-0.88; P<0.01). Our findings indicated that vaspin may be an important adipokine involved in carbohydrate and lipid metabolism and may also play a role in fetal development.

Teaching sexual abuse prevention skills to two children with intellectual disabilities through game play

The current study examined the effectiveness of a sexual abuse prevention program developed locally for children with intellectual disabilities. The program package included a board game with informational storybooks that were designed to be used in a family setting. Additionally, this research sought to determine if parents could be effective at presenting the sexual abuse pr~vention materials to their children. A multiple baseline across behaviours design was used with two participants with a diagnosis of autism. Through role play scenarios as well as verbal knowledge tests, it was determined that the program was effective at teaching the participants the skills presented for self protection. It was also determined that the skills learned were generalized to scenarios that were untrained during the game play. Finally, with additional supports, it was determined that parents were able to effectively teach their children the required skills.

Les cartes fonctionnelles dans le cortex visuel du chat : nouvelles stratégies d’évaluation en imagerie optique et mise en évidence de l’organisation anatomo-fonctionnelle

Le regroupement des neurones de propriétés similaires est à l’origine de modules permettant d’optimiser l’analyse de l’information. La conséquence est la présence de cartes fonctionnelles dans le cortex visuel primaire de certains mammifères pour de nombreux paramètres tels que l’orientation, la direction du mouvement ou la position des stimuli (visuotopie). Le premier volet de cette thèse est consacré à caractériser l’organisation modulaire dans le cortex visuel primaire pour un paramètre fondamental, la suppression centre / pourtour et au delà du cortex visuel primaire (dans l’aire 21a), pour l’orientation et la direction. Toutes les études ont été effectuées à l’aide de l’imagerie optique des signaux intrinsèques sur le cortex visuel du chat anesthésié. La quantification de la modulation par la taille des stimuli à permis de révéler la présence de modules de forte et de faible suppression par le pourtour dans le cortex visuel primaire (aires 17 et 18). Ce type d’organisation n’avait été observé jusqu’ici que dans une aire de plus haut niveau hiérarchique chez le primate. Une organisation modulaire pour l’orientation, similaire à celle observée dans le cortex visuel primaire a été révélée dans l’aire 21a. Par contre, contrairement à l’aire 18, l’aire 21a ne semblait pas être organisée en domaine de direction. L’ensemble de ces résultats pourront permettre d’alimenter les connaissances sur l’organisation anatomo-fonctionnelle du cortex visuel du chat mais également de mieux comprendre les facteurs qui déterminent la présence d’une organisation modulaire. Le deuxième volet abordé dans cette thèse s’est intéressé à l’amélioration de l’aspect quantitatif apporté par l’analyse temporelle en imagerie optique des signaux intrinsèques. Cette nouvelle approche, basée sur l’analyse de Fourier a permis d’augmenter considérablement le rapport signal / bruit des enregistrements. Toutefois, cette analyse ne s’est basée jusqu’ici que sur la quantification d’une seule harmonique ce qui a limité son emploi à la cartographie de l’orientation et de rétinotopie uniquement. En exploitant les plus hautes harmoniques, un modèle a été proposé afin d’estimer la taille des champs récepteurs et la sélectivité à la direction. Ce modèle a par la suite été validé par des approches conventionnelles dans le cortex visuel primaire.