Studies of CMS data access patterns with machine learning techniques

This thesis presents a study of the Grid data access patterns in distributed analysis in the CMS experiment at the LHC accelerator. This study ranges from the deep analysis of the historical patterns of access to the most relevant data types in CMS, to the exploitation of a supervised Machine Learning classification system to set-up a machinery able to eventually predict future data access patterns - i.e. the so-called dataset “popularity” of the CMS datasets on the Grid - with focus on specific data types. All the CMS workflows run on the Worldwide LHC Computing Grid (WCG) computing centers (Tiers), and in particular the distributed analysis systems sustains hundreds of users and applications submitted every day. These applications (or “jobs”) access different data types hosted on disk storage systems at a large set of WLCG Tiers. The detailed study of how this data is accessed, in terms of data types, hosting Tiers, and different time periods, allows to gain precious insight on storage occupancy over time and different access patterns, and ultimately to extract suggested actions based on this information (e.g. targetted disk clean-up and/or data replication). In this sense, the application of Machine Learning techniques allows to learn from past data and to gain predictability potential for the future CMS data access patterns. Chapter 1 provides an introduction to High Energy Physics at the LHC. Chapter 2 describes the CMS Computing Model, with special focus on the data management sector, also discussing the concept of dataset popularity. Chapter 3 describes the study of CMS data access patterns with different depth levels. Chapter 4 offers a brief introduction to basic machine learning concepts and gives an introduction to its application in CMS and discuss the results obtained by using this approach in the context of this thesis.

Distribution of Light in the Human Retina under Natural Viewing Conditions

Age-related macular degeneration (AMD) is the leading cause of blindness inAmerica. The fact that AMD wreaks most of the damage in the center of the retina raises the question of whether light, integrated over long periods, is more concentrated in the macula. A method, based on eye-tracking, was developed to measure the distribution of light in the retina under natural viewing conditions. The hypothesis was that integrated over time, retinal illumination peaked in the macula. Additionally a possible relationship between age and retinal illumination was investigated. The eye tracker superimposed the subject’s gaze position on a video recorded by a scene camera. Five informed subjects were employed in feasibility tests, and 58 naïve subjects participated in 5 phases. In phase 1 the subjects viewed a gray-scale image. In phase 2, they observed a sequence of photographic images. In phase 3 they viewed a video. In phase 4, they worked on a computer; in phase 5, the subjects walked around freely. The informed subjects were instructed to gaze at bright objects in the field of view and then at dark objects. Naïve subjects were allowed to gaze freely for all phases. Using the subject’s gaze coordinates, and the video provided by the scene camera, the cumulative light distribution on the retina was calculated for ~15° around the fovea. As expected for control subjects, cumulative retinal light distributions peaked and dipped in the fovea when they gazed at bright or dark objects respectively. The light distribution maps obtained from the naïve subjects presented a tendency to peak in the macula for phases 1, 2, and 3, a consistent tendency in phase 4 and a variable tendency in phase 5. The feasibility of using an eye-tracker system to measure the distribution of light in the retina was demonstrated, thus helping to understand the role played by light exposure in the etiology of AMD. Results showed that a tendency for light to peak in the macula is a characteristic of some individuals and of certain tasks. In these situations, risk of AMD could be increased. No significant difference was observed based on age.

Normative reference values for the 20-meter shuttlerun test in a population-based sample of schoolchildren in Bogota, Colombia: The FUPRECOL Study

Our aim was to determine the normative reference values of cardiorespiratory fitness (CRF) and to establish the proportion of subjects with low CRF suggestive of future cardio-metabolic risk.

Estado de las enfermedades raras que cursan con discapacidad intelectual en Colombia

Las enfermedades raras o huérfano son una problemática que ha tomado mucha importancia en el contexto mundial del presente siglo, estas se han definido como crónicas, de difícil tratamiento de sus síntomas y con baja prevalencia en la población; muchas de estas enfermedades cursan con varios tipos de discapacidad, siendo el objetivo del presente trabajo el enfocarse en aquellas enfermedades raras que cursan con discapacidad intelectual. Para poder profundizar en estas enfermedades se realizó una revisión teórica sobre las enfermedades raras, así como de la discapacidad psíquica y su importancia a nivel mundial y nacional. A partir de estas definiciones, se revisaron en profundidad 3 enfermedades raras que cursan con discapacidad intelectual en el contexto colombiano, como son: el síndrome de Rett, el síndrome de Prader-Willi y el síndrome de X frágil. En cada una de estas enfermedades además se explicaron los tipos de diagnóstico, intervención, prevención, grupos de apoyo y tipos de evaluación que más se usan en el contexto nacional

Adesão ao regime medicamentoso dos adolescentes submetidos a transplante hepático: fatores motivacionais.

Introduction: In liver transplantation the immunosuppression is essential for the survival of the graft and of the receiver. Although characteristics of adolescent development may influence medication non-adherence, the literature on the subject is scarce. The high prevalence and consequences of non-adherence makes it essential to identify the non-adherent adolescent with the intention of promoting medication adherence. Methods: The aim of this descriptive cross-sectional study is to characterize adolescents undergoing liver transplantation, and to determine the degree of medication non-adherence, using the Measure Treatment Adherence (MAT) scale and immunosuppression blood values. Moreover, the study seeks to explore the relationship between adherence and motivation - using the Treatment Self-Regulation Questionnaire (TSRQ), and adherence and competency - using Perceived Competence Scale (PCS). Results: The sample consisted of 32 adolescents (Age M=14,44 (SD=2,66); 56,3% (n=18) male) who underwent liver transplantation at a Portuguese pediatric hospital. Adolescents self-reported medication adherence scores in the MAT were significantly higher (100%) than what was expected based on the mean value of the three blood values of tacrolimus obtained within one year prior to completing the questionnaire (66,7%). As a subjective self-reported measure, the MAT is prone to bias and inflated self assessed adherence is commonly found in the literature. On the other hand, the mean value of the three blood levels of tacrolimus obtained widely and considered objective adherences measure, they may individually vary in terms of pharmacokinetic response and absorption. Adolescents showed a predominantly autonomous motivation to fulfill the medication prescription, being that motivation high (TSRQ autonomous motivation subscale presents an average value of 6.5, in a range of 1 to 7). They showed themselves confident and believing in their capacity to follow the medication regimen, due to the high perceived competence (PCS presents an average value of 6.65, in a range of 1 to 7). Opposed to what was postulated by the Self-determination Theory and other investigation's results, motivation and perceived competence are not related to adherence to the medication regimen in this study (rs=,119 p=,523; rs=,283 p=,123, respectively). Thus, perceived competence seems to have a positive influence on the autonomous motivation of these adolescents (rs=,482 p=,006). Conclusion: This study shows that medication adherence when evaluated subjectively scores higher compared to the blood values of immunosuppression. Also, Motivation and Perceived Competence do not seem to influence the adherence to the medication regimen. More multi-centre studies are needed, based on solid theory to examine adherence behaviour more.

Régime thermique en période de maturation du raisin dans le géoclimat viticole.

Mots clés :indice de fraîcheur des nuits, amplitude thermique, Système CCM Géoviticole, zonage, qualité. Key words: cool night index, thermal amplitude, MCC System for World Viticulture, zoning, quality. RESUME Le régime thermique en période de maturation du raisin est l?une des variables déterminantes de la coloration du raisin et de la richesse en arômes, anthocyanes et polyphénols des vins. L?objectif du travail est de caractériser le régime thermique, notamment la fraîcheur des nuits et l?amplitude thermique au cours de la maturation, au niveau du climat viticole mondial, sur une base des données de 100 régions viticoles dans 30 pays, obtenue par l?intermédiaire de l?Organisation Mondiale de la Météorologie - OMM. Plusieurs indices climatiques viticoles ont été calculés: l?Indice de Fraîcheur des Nuits ?IF (ºC), l?Indice Héliothermique de Huglin ?IH (ºC) et l?Indice de Sécheresse ?IS (mm) du Système de Classification Climatique Multicritères Géoviticole, et l?amplitude thermique moyenne en août et septembre Aa-s (ºC). Egalement, sur la période véraison-récolte ?v-r(moyenne des 30 jours précédant la date de récolte, estimée sur la base d?un Indice Héliothermique de HUGLIN égal à 1.900 - approximatif pour la maturation du Cabernet-Sauvignon): la fraîcheur des nuits (FNv -r), la température moyenne de l?air (Tv-r), la température maximale de l?air (Txv-r) et l?amplitude thermique (Av-r). Les résultats montrent que IH est corrélé avec Tv-r (r=0,79**) et avec Txv-r (r=0,80**). IH représente donc bien les conditions thermiques générales de la période de maturation en ce qui concerne la température moyenne et maximale de l?air. Mais IH n?est pas corrélé ni avec Aa-s ni avec Av-r. Par contre, IF est corrélé avec Aa-s (r=-0,70**) et FNv-r est corrélé avec Av-r (r=-0,69**). Cette corrélation doit justifier, en partie, l?usage assez courant de l?amplitude thermique comme indicateur de bonnes conditions thermiques de maturation pour les régions qui présentent des valeurs élevées. Mais ce raisonnement peut amener à des caractérisations erronées. Le travail met en évidence, également, ?importance de considérer le bilan hydrique des régions (IS) dans l?analyse du régime thermique sur la qualité du raisin. On peut onclure que pour avoir une bonne caractérisation du régime thermique en période de maturation il faut considérer la fraîcheur des nuits (IF étant un bon indicateur de FNv-r moyen des régions, avec un r=0,80**), caractérisation qui peut être améliorée avec l?information des températures maximales et de sur 11l?amplitude thermique en période de maturation du raisin. Les éléments présentés peuvent servir à améliorer les indices climatiques pour estimer le potentiel qualitatif du raisin des différentes régions viticoles, notamment en complément de IF. ABSTRACT The thermal conditions during the grape ripening period are important variables related to colour of the grapes, anthocyanins, polyphenols and flavour of the wine. The main purpose of this work was to characterise the thermal conditions, especially the night coolness and the thermal amplitude during maturation, in the geoclimate of the world vine culture. A database of 100 grape-growing regions of 30 countries obtained from the World Meteorology Organisation (WMO) was used. Some climatic indexes were calculated: Cool Night Index ?IF (°C), Huglin?s Heliothermal Index ?IH (°C) and Dryness Index ?IS (mm), from the Multicriteria Climatic Classification System for World Viticulture, and the thermal amplitude in August and September Aa-s (°C). Over véraison-harvest period ?v-r(mean of the 30 days before harvesting date, estimated on the basis of HUGLIN Heliothermal Index equal to 1,900 ? approximately value to ripen Cabernet-Sauvignon) similar indexes were obtained: the cool night (FNv-r), the mean air temperature (Tv-r), the maximal air temperature (Txv-r) and the thermal amplitude (Av-r). The results showed that IH is positively correlated with Tv-r (r=0.79**), Txv-r (r=0.80)and IF (r=0.67**). Therefore, IH represents well the general thermal conditions during maturation period, specially concerning the mean and the maximal air temperature. owever, IH was correlated neither with Aa-s nor to Av-r. IF was negatively correlated with Aa-s (r= -0.70**) and FNv-r was negatively correlated with Av-r (r=-0.69**). The correlation to some extent explains the current use of the thermal amplitude to predict good ripening thermal conditions for those regions that show high values. As here we have described, this thinking may give incorrect results. This work has also showed the importance to consider the water balance of the regions (IS) in the effect of the thermal conditions in grape quality. We conclude that the characterisation of the thermal conditions during the ripening period do need the cool night index (in this case, IFis a good index to provide the mean FNv-r of the regions, r=0,80**). Factors other than cool night which influence this characterisation are both maximal air temperature and thermal amplitude data. The elements presented in this work, in addition to IF , may improve the climatic indexes to be used to predict the qualitative potential of grapes from different regions.

Zonage climatique viticole et cartographie numérique du Rio Grande do Sul - Brésil, par les indices du Système CCM Géoviticole.

Abstract: The State Rio Grande do Sul is the main producer of Brazilian fine wines, with four viticultural regions. The objective is the characterization of the viticultural climatic potential of the State (total surface of 281.749 km2). The methodology use the Géoviticulture Multicriteria Climatic Classification System (Géoviticulture MCC System), based on three climatic indices ? Dryness Index (DI), Heliotermal Index (HI) and Cool Night Index (CI). Based on latitude, longitude, altitude and distance from Atlantic Ocean, the 3 viticultural climatic indices were modeled and the algorithms applied to a DTM using GIS. The results show that Rio Grande do Sul has the following classes of viticultural climate: according to DI ? Moderately Dry, Sub-humid, Humid; according to HI ? Cool, Temperate, Temperate warm, Warm and Very Warm; according to CI ? Cool nights, Temperate nights, Warm nights. Based on the total surface, the most representatives viticultural climates are: « Humid x Temperate » (3,1%), « Humid x Temperate warm » (14,4%), « Humid x Warm » (52,6%), « Sub-humid x Warm » (20,0%) and « Sub-humid x Very warm » (5,8%). According to CI, the viticultural climates have a range of variation as a function of the interaction between « earlyness of the varieties x heliothermal availability ». Key words: climate classification, climate models, climatic Groups, zoning

Effet du climat viticole sur la perception sensorielle du vin: éléments méthodologiques pour une modélisation au niveau mondial.

Summary The objective of this study was to develop a methodology capable of modeling the effect of viticultural climate on wine sensory characteristics. The climate was defined by the Géoviticulture Multicriteria Climatic Classification System (Tonietto and Carbonneau, 2004), based on the Heliothermal index (HI), Cool Night index (CI) and Dryness index (DI). The sensory wine description was made according with the methodology established by Zanus and Tonietto (2007). In this study we focused on the 5 principal wine producing regions of Brazil: Serra Gaúcha, Serra do Sudeste, Campanha (Meridional and Central), Planalto Catarinense and Vale do Submédio São Francisco. The results from Principal Component Analysis (PCA) show the HI and CI opposed to the DI. High HI values were associated to a lower perception of acidity, as well as to a lower perception of concentration (palate) and persistence by mouth. For the red wines, high HI values were positively associated with alcohol (palate), conversely to the DI index, which showed high values related to the perception of tanins and acidity. The higher the CI, the lower were the color intensity, tanins, concentration and persistence by mouth. It may be concluded that viticultural climate - expressed by the HI, CI and DI indexes ? adequately explained much of the sensory differences of the wines made in different regions. The methodology proposed and the enlargement of the database it will maybe open the possibility of modeling the part of wine sensory characteristics as dependent variables of the viticultural climate, as defined by the Géoviticulture MCC System. Keywords: viticultural climate, modeling, wine, tipicity.

ALGUNOS FACTORES QUE INCIDEN EN LA VALORACION DEL SUELO URBANO

Este ensayo tuvo como finalidad primordial señalar la importancia que encierra, para fines planificadores, el conocimiento de la distribución de los valores del suelo dentro de un área urbana determinada. Asi tomada como el area de estudio; el distrito 1 o el Carmen, y localizada en la porción noroeste de la ciudad capital de Costa Rica, toda una serie de factores o variables que presentan gran relevancia en la fijación de valores para su suelo, fuero fijados y analizados, una vez caracterizada el area bajo análisis. En búsqueda de un modelo que se adapte a tal situación, se realizo una revisión bibliográfica y los principios modelo sobre el valor del suelo fueron presentados. Con los datos e informaciones recibidos en las diferentes instituciones mencionadas a lo largo del trabajo, y con el material recopilado en el campo, se llevo a cabo una cuantificación de los mismos, principalmente mediante el uso de un sistema de clasificación del dato esencial (valor del suelo) y, posteriormente, una serie de correlaciones –regresiones, simples y múltiples-, fue realizada con el fin de comprobarlas hipótesis planteadas y  con ello llegar a un análisis de los resultados obtenidos que permitiese brindar algunas recomendaciones al respecto. Otra finalidad de este consiste en demostrar la importancia del trabajo del geógrafo en el proceso  de la fijación de los valores para el terreno, sea urbano, sea rural, y cualquiera sea el fin que persiga: valores fiscales, valores reales, comerciales y, por qué no, hasta especulativos. SUMARY The main objetive of this investigation is to demonstrate the importance of the distribution of land values in an urban area in regards to the planning process. The chosen study area is the first district (Carmen) located in the northeast section of  the capital city of San José. Once the study area had been chosen, a series of factors and variables relavant to the fixation of land values, were chosen and analyzed. In the search for a model that could be adapted to the situation, a bibliographic revision was made concerning the topic of land values, and a list of possible land values, and a list of possible land value models was presented. In was possible to quantify the data information obtained from the different institutions mentioned in the investigation as well as from the material collected in the field; principally by means of a classification system of essential data ( land values), and later, series of simple and multiple correlation regressions were applied with the primary purpose being to confirm  the main hypothesis and then, arrive at an analysis of the obtained results that permit respective recommendations. Another purpose of the investigation consisted in demonstrating the importance of the geographer in the process of determining urban and rural land values and even for speculative purposes.

Systematic reviews on leptospirosis

OBJECTIVES: To find the existing clinical evidence on interventions for leptospirosis. The objective is to evaluate the effectiveness and safety of any intervention on leptospirosis through systematic reviews of randomized controlled trials (RCTs). DATA SOURCE: The sources of studies used (where there were no limitations concerning language, date, or other restrictions) were: EMBASE, LILACS, MEDLINE, the Cochrane Controlled Clinical Trials Database, and the Cochrane Hepato-Biliary Group Randomized Trials register. SELECTION OF STUDIES: Type of Study: All systematic reviews of randomized controlled trials. Participants: patients with clinical and/or laboratorial diagnosis of leptospirosis, and subjects potencially exposed to leptospirosis as defined by the authors Interventions: any intervention for leptospirosis (as antibiotics or vaccines for prevention or treatment). DATA COLLECTION: The assessment will be independently made by the reviewers and cross-checked. The external validity was assessed by analysis of: studies, interventions, and outcomes. DATA SYNTHESIS: Located 163 studies using the search strategy described above, at the electronic databases above. Only 2 hits were selected, which are protocols of systematic reviews of Cochrane Collaboration, and not full reviews. One of the protocols evaluates antibiotics for treatment, and the other evaluates antibiotics for prevention of leptospirosis. CONCLUSIONS: There were not complete systematic reviews on interventions for leptospirosis. Any interventions for leptospirosis, such as prevention and treatment remains unclear for guidelines and practice.

Bilateral giant renal angiomyolipoma associated with hepatic lipoma in a patient with tuberous sclerosis

OBJECTIVE: To report a case of bilateral giant renal angiomyolipoma associated with tuberous sclerosis, with successful treatment, and to review the literature concerning angiomyolipoma treatment. CASE REPORT: Patient with tuberous sclerosis and angiomyolipoma diagnosed by ultrasonography during her pregnancy. At that time, the angiomyolipoma on the right side was 9 cm in diameter. Conservative management was selected during her pregnancy. The patient returned 7 years later, with a 24.7 x 19.2 x 10.7 cm tumor on the right side and another of 13 x 11.5 x 6.5 cm on the left side, in addition to multiple small angiomyolipomas. A nephron-sparing surgery with tumoral enucleation was performed on the right side, and after 3 months, the tumor on the left side was removed. Renal function in the post-operative period was preserved, and contrast medium progression was uniform and adequate in both kidneys. CONCLUSION: We conclude that an angiomyolipoma larger than 4 cm should be removed surgically, since they have a greater growth rate and pose a risk of hemorrhage. Resection of smaller tumors is safe and has decreased morbidity. Tumoral enucleation is an effective treatment method that preserves kidney function.

Atualização da diretriz brasileira de insuficiência cardíaca crônica - 2012

Esta atualização da Diretriz de Insuficiência Cardíaca Crônica (IC) - 2012 surge para reavaliar as recomendações através de uma avaliação criteriosa das pesquisas (considerando-se a qualidade dos estudos), fundamental para que se atinja esse propósito. Para tanto, foi dada ênfase ao efeito em desfechos de morte, à qualidade "CONSORT" (Consolidated Standards of Reporting Trials), à descrição qualitativa e quantitativa da otimização da medicação, à população realmente incluída, às metanálises somente de estudos qualidade "CONSORT", à custo-efetividade, à existência de efeito de classe, ao número de pacientes incluídos e à análise de subgrupos apenas para gerar hipóteses. Na área da epidemiologia, as recentes abordagens das características da IC com fração de ejeção preservada (ICFEP) e da importância da IC como causa de morte no Brasil foram revisadas. Além disso, este documento contempla a reavaliação do valor dos biomarcadores no diagnóstico e no seguimento da IC, o papel diagnóstico da angiotomografia coronariana nos casos de risco intermediário ou baixo risco de doença coronariana, a não recomendação de rotina do telemonitoramento; o surgimento da avaliação familiar como recomendação importante, e a reavaliação da restrição da adição de sal na dieta. As clínicas de IC e reabilitação física, apesar de alguns resultados negativos ou controversos quanto à mortalidade, continuam com recomendação importante. No campo do tratamento farmacológico, abrange-se a reavaliação da indicação do nebivolol, introduz-se a ivabradina como um novo paradigma no tratamento, os antagonistas da aldosterona não têm efeito de classe reconhecido, o ômega 3 passa a ser recomendado, o ferro administrado por via endovenosa e o sildenafil recebem indicação em casos selecionados. Todas as recomendações para outras etiologias são expandidas para a Doença de Chagas. Na área da anticoagulação, recomenda-se a utilização dos escores CHA2DS2VASC e o HAS-BLED na fibrilação atrial, com introdução de inibidores da trombina e do fator Xa como alternativas na anticoagulação. No tratamento cirúrgico da IC, considerou-se que resultados neutros do estudo STICH influenciaram as recomendações, o transplante cardíaco continua a ser o tratamento indicado nas fases evolutivas tardias de IC, os dispositivos de assistência circulatória mecânica para terapia de destino passam a ter recomendação, a duração do QRS foi fundamental na indicação de TRV-AV, e o CDI continua com recomendação I para miocardiopatia isquêmica. Entretanto, baseada em análise crítica dos estudos considerando-se o custo-efetividade, o CDI não atingiu recomendação I para classes menos graves devido as limitações dos estudos. Também a importância da cardiotoxicidade por drogas para tratamento de neoplasias foi ressaltada, o tratamento da IC na gravidez e da miocardite foi revisado. Novos potenciais métodos de tratamento em fase de pesquisa são apresentados e novos fluxogramas de diagnóstico e tratamento da IC, reformulados, foram incluídos

A review of the South American catfish tribe Hoplomyzontini (Pisces, Aspredinidae), with descriptions of new species from Ecuador / Donald J. Stewart.

n.s. no.25(1985)

Evolutionary ecology of learning: insights from fruit flies

Ecologically and evolutionarily oriented research on learning has traditionally been carried out on vertebrates and bees. While less sophisticated than those animals, fruit flies (Drosophila) are capable of several forms of learning, and have an advantage of a short generation time, which makes them an ideal system for experimental evolution studies. This review summarizes the insights into evolutionary questions about learning gained in the last decade from evolutionary experiments on Drosophila. These experiments demonstrate that Drosophila have the genetic potential to evolve substantially improved learning performance in ecologically relevant learning tasks. In at least one set of selected populations the improved learning generalized to another task than that used to impose selection, involving a different behavior, different stimuli, and a different sensory channel for the aversive reinforcement. This improvement in learning ability was associated with reduction in other fitness-related traits, such as larval competitive ability and lifespan, pointing out to evolutionary trade-offs of improved learning. These trade-offs were confirmed by other evolutionary experiments where reduction in learning performance was observed as a correlated response to selection for tolerance to larval nutritional stress or for delayed aging. Such trade-offs could be one reason why fruit flies have not fully used up their evolutionary potential for learning ability. Finally, another evolutionary experiment with Drosophila provided the first direct evidence for the long-standing ideas that learning can under some circumstances accelerate and in other slow down genetically-based evolutionary change. These results demonstrate the usefulness of fruit flies as a model system to address evolutionary questions about learning.

A Critical Review on Chagas Disease Chemotherapy

In this "Critical Review" we made a historical introduction of drugs assayed against Chagas disease beginning in 1912 with the works of Mayer and Rocha Lima up to the experimental use of nitrofurazone. In the beginning of the 70s, nifurtimox and benznidazole were introduced for clinical treatment, but results showed a great variability and there is still a controversy about their use for chronic cases. After the introduction of these nitroheterocycles only a few compounds were assayed in chagasic patients. The great advances in vector control in the South Cone countries, and the demonstration of parasite in chronic patients indicated the urgency to discuss the etiologic treatment during this phase, reinforcing the need to find drugs with more efficacy and less toxicity. We also review potential targets in the parasite and present a survey about new classes of synthetic and natural compounds studied after 1992/1993, with which we intend to give to the reader a general view about experimental studies in the area of the chemotherapy of Chagas disease, complementing the previous papers of Brener (1979) and De Castro (1993).