Mapping numbers onto space in preschool children and adults

Tese de Doutoramento em Psicologia - Especialidade em Psicologia Experimental e Ciências Cognitivas

Centrality and rapidity dependence of inclusive jet production in sNN=5.02 TeV proton-lead collisions with the ATLAS detector

Measurements of the centrality and rapidity dependence of inclusive jet production in sNN−−−√=5.02 TeV proton--lead (p+Pb) collisions and the jet cross-section in s√=2.76 TeV proton--proton collisions are presented. These quantities are measured in datasets corresponding to an integrated luminosity of 27.8 nb−1 and 4.0 pb−1, respectively, recorded with the ATLAS detector at the Large Hadron Collider in 2013. The p+Pb collision centrality was characterised using the total transverse energy measured in the pseudorapidity interval −4.9<η<−3.2 in the direction of the lead beam. Results are presented for the double-differential per-collision yields as a function of jet rapidity and transverse momentum (pT) for minimum-bias and centrality-selected p+Pb collisions, and are compared to the jet rate from the geometric expectation. The total jet yield in minimum-bias events is slightly enhanced above the expectation in a pT-dependent manner but is consistent with the expectation within uncertainties. The ratios of jet spectra from different centrality selections show a strong modification of jet production at all pT at forward rapidities and for large pT at mid-rapidity, which manifests as a suppression of the jet yield in central events and an enhancement in peripheral events. These effects imply that the factorisation between hard and soft processes is violated at an unexpected level in proton--nucleus collisions. Furthermore, the modifications at forward rapidities are found to be a function of the total jet energy only, implying that the violations may have a simple dependence on the hard parton--parton kinematics.

Development of a methodology to incorporate risk and uncertainty in electricity power planning

Dissertação de mestrado em Engenharia Industrial

Soil CO2 efflux in central Amazonia: environmental and methodological effects

Soil respiration plays a significant role in the carbon cycle of Amazonian rainforests. Measurements of soil respiration have only been carried out in few places in the Amazon. This study investigated the effects of the method of ring insertion in the soil as well as of rainfall and spatial distribution on CO2 emission in the central Amazon region. The ring insertion effect increased the soil emission about 13-20% for sandy and loamy soils during the firsts 4-7 hours, respectively. After rainfall events below 2 mm, the soil respiration did not change, but for rainfall greater than 3 mm, after 2 hours there was a decrease in soil temperature and respiration of about 10-34% for the loamy and sand soils, with emissions returning to normal after around 15-18 hours. The size of the measurement areas and the spatial distribution of soil respiration were better estimated using the Shuttle Radar Topographic Mission (SRTM) data. The Campina reserve is a mosaic of bare soil, stunted heath forest-SHF and tall heath forest-THF. The estimated total average CO2 emissions from the area was 3.08±0.8 µmol CO2 m-2 s-1. The Cuieiras reserve is another mosaic of plateau, slope, Campinarana and riparian forests and the total average emission from the area was 3.82±0.76 µmol CO2 m-2 s-1. We also found that the main control factor of the soil respiration was soil temperature, with 90% explained by regression analysis. Automated soil respiration datasets are a good tool to improve the technique and increase the reliability of measurements to allow a better understanding of all possible factors driven by soil respiration processes.

Land cover classification of Lago Grande de Curuai floodplain (Amazon, Brazil) using multi-sensor and image fusion techniques

Given the limitations of different types of remote sensing images, automated land-cover classifications of the Amazon várzea may yield poor accuracy indexes. One way to improve accuracy is through the combination of images from different sensors, by either image fusion or multi-sensor classifications. Therefore, the objective of this study was to determine which classification method is more efficient in improving land cover classification accuracies for the Amazon várzea and similar wetland environments - (a) synthetically fused optical and SAR images or (b) multi-sensor classification of paired SAR and optical images. Land cover classifications based on images from a single sensor (Landsat TM or Radarsat-2) are compared with multi-sensor and image fusion classifications. Object-based image analyses (OBIA) and the J.48 data-mining algorithm were used for automated classification, and classification accuracies were assessed using the kappa index of agreement and the recently proposed allocation and quantity disagreement measures. Overall, optical-based classifications had better accuracy than SAR-based classifications. Once both datasets were combined using the multi-sensor approach, there was a 2% decrease in allocation disagreement, as the method was able to overcome part of the limitations present in both images. Accuracy decreased when image fusion methods were used, however. We therefore concluded that the multi-sensor classification method is more appropriate for classifying land cover in the Amazon várzea.

Fine time scaling of purifying selection on human nonsynonymous mtDNA mutations based on the worldwide population tree and mother-child pairs

A high-resolution mtDNA phylogenetic tree allowed us to look backward in time to investigate purifying selection. Purifying selection was very strong in the last 2,500 years, continuously eliminating pathogenic mutations back until the end of the Younger Dryas (∼11,000 years ago), when a large population expansion likely relaxed selection pressure. This was preceded by a phase of stable selection until another relaxation occurred in the out-of-Africa migration. Demography and selection are closely related: expansions led to relaxation of selection and higher pathogenicity mutations significantly decreased the growth of descendants. The only detectible positive selection was the recurrence of highly pathogenic nonsynonymous mutations (m.3394T>C-m.3397A>G-m.3398T>C) at interior branches of the tree, preventing the formation of a dinucleotide STR (TATATA) in the MT-ND1 gene. At the most recent time scale in 124 mother-children transmissions, purifying selection was detectable through the loss of mtDNA variants with high predicted pathogenicity. A few haplogroup-defining sites were also heteroplasmic, agreeing with a significant propensity in 349 positions in the phylogenetic tree to revert back to the ancestral variant. This nonrandom mutation property explains the observation of heteroplasmic mutations at some haplogroup-defining sites in sequencing datasets, which may not indicate poor quality as has been claimed.

Ontological representation of tumor-node-metastasis classification and an ontology-driven classifier: a study on colorectal cancer

Dissertação de mestrado integrado em Engenharia Biomédica (área de especialização em Informática Médica)

An R package for the integrated analysis of metabolomics and spectral data

Recently, there has been a growing interest in the field of metabolomics, materialized by a remarkable growth in experimental techniques, available data and related biological applications. Indeed, techniques as Nuclear Magnetic Resonance, Gas or Liquid Chromatography, Mass Spectrometry, Infrared and UV-visible spectroscopies have provided extensive datasets that can help in tasks as biological and biomedical discovery, biotechnology and drug development. However, as it happens with other omics data, the analysis of metabolomics datasets provides multiple challenges, both in terms of methodologies and in the development of appropriate computational tools. Indeed, from the available software tools, none addresses the multiplicity of existing techniques and data analysis tasks. In this work, we make available a novel R package, named specmine, which provides a set of methods for metabolomics data analysis, including data loading in different formats, pre-processing, metabolite identification, univariate and multivariate data analysis, machine learning, and feature selection. Importantly, the implemented methods provide adequate support for the analysis of data from diverse experimental techniques, integrating a large set of functions from several R packages in a powerful, yet simple to use environment. The package, already available in CRAN, is accompanied by a web site where users can deposit datasets, scripts and analysis reports to be shared with the community, promoting the efficient sharing of metabolomics data analysis pipelines.

Evaluación del efecto del láser y magnetoterapia en miopatía experimental valorando biomarcadores de estrés oxidativo, histomorfometría y actividad enzimática mitocondrial. Evaluation of the effect of laser and magnetic therapy in experimental myopathy assessing oxidative stress biomarkers, histomorphometry and mitochondrial enzyme activity

El láser de baja y media energía y la magnetoterapia son utilizados en desórdenes osteomioarticulares por sus efectos analgésico, antiinflamatorio y trófico, entre los más destacados. Sin embargo, son insuficientes las investigaciones sobre su mecanismo de acción y antecedentes científicos que avalen sus efectos. Es por ello, que la determinación de acontecimientos celulares y moleculares que ocurren durante la interacción de estos tipos de energía con el sistema muscular, sería relevante para el conocimiento y optimización de tales terapias en las ciencias biomédicas. En las miopatías inflamatorias idiopáticas, se encuentra afectada la estructura, morfología y bioquímica del tejido muscular. La energía que éste requiere para el normal funcionamiento es generada en la mitocondria. Esta organela también es la responsable de la generación de especies oxidantes provocando estrés oxidativo y el inicio de los procesos de apoptosis. Por lo antes dicho, consideramos que la determinación de los biomarcadores inflamatorios asociados a estrés oxidativo, realizando el análisis histomorfométrico ultraestructural y valorando la actividad de los complejos enzimáticos mitocondriales, permitiría una evaluación de la acción terapéutica del láser y la magnetoterapia en un modelo experimental de miopatía. Para ello se propone evaluar el efecto de la magnetoterapia y del láser de baja energía (He-Ne y As.Ga) en miopatía experimental determinando indicadores inflamatorios asociados a estrés oxidativo, análisis histomorfométrico y valoración de la actividad enzimática mitocondrial. Específicamente: -Determinar indicadores inflamatorios y de estrés oxidativo: Oxido Nítrico, Grupos carbonilos, L-citrulina, Fibrinógeno, Superóxido dismutasa, Glutation peroxidasa y Catalasa por espectrofotometría. -Identificar los cambios anatomopatológicos del músculo esquelético por microscopía óptica (MO): cuantificación del infiltrado inflamatorio; MO de alta resolución (MOAR) y por microscopía electrónica: histomorfometría de la ultraestructura miofibrilar y mitocondrial. -Valorar las actividades enzimáticas de la citrato sintasa y de los complejos: I (NADH-ubiquinona reductasa), II (succinato-ubiquinona-reductasa) III (ubiquinona-citocromo c-reductasa) y IV (citocromo c-oxidasa); en mitocondrias de tejido muscular por espectrofotometría. -Evaluar la actividad apoptótica en las fibras musculares de los diferentes grupos por ténica de T.U.N.E.L. Las mediciones mitocondriales (por ME) y de infiltrado inflamatorio (por MO) se realizarán en un total de 5 fotos de aumentos similares en forma aleatoria por grupo estudiado (n=10). Los cambios estructurales observados se analizarán en el programa Axiovision 4.8, para cuantificar el área total ocupada, número total y grado de alteración de las mitocondrias y el porcentaje de infiltrado inflamatorio determinando el grado de inflamación. Los resultados de los datos cuantitativos se analizarán aplicando ANAVA (test de Fisher para comparaciones múltiples); y para los datos categóricos se utilizará Chi cuadrado (test de Pearson), estableciéndose un nivel de significación de p < 0.05 para todos los casos. Importancia del Proyecto: La salud y el bienestar del hombre son los logros perseguidos por las ciencias de la salud. La obtención de terapias curativas o paliativas con un mínimo de efectos colaterales para el enfermo se incluye en estos logros. Por esto y todo lo anteriormente expuesto es que consideramos de gran importancia poder esclarecer desde las ciencias básicas los efectos celulares y moleculares en modelos experimentales la acción de la terapia con láser y magnetoterapia para una aplicación clínica con base científica en todas las áreas de las Ciencias Médicas. In the idiopathic inflammatory myopathies, is affected the structure, morphology and biochemistry of muscle tissue. The mitochondria is responsible for the generation of oxidizing species leading to oxidative stress and the beginning of the process of apoptosis. As said before, we consider the determination of inflammatory biomarkers related to oxidative stress, by ultrastructural morphometric analysis and assessing the activity of mitochondrial enzyme complexes, permit an evaluation of the therapeutic action of laser and magnetic therapy in an experimental model myopathy. We propose to evaluate the effect of the treatment identifying indicators in experimental inflammatory myopathy associated with oxidative stress, histomorphometric analysis and assessment of mitochondrial enzyme activity. Specifically -determining: Nitric oxide, carbonyl groups, L-citrulline, fibrinogen, superoxide dismutase, glutathione peroxidase and catalase by spectrophotometry. -Identify the pathological changes in skeletal muscle by optical microscopy (OM): quantification of the inflammatory infiltrate, OM high resolution (MOAR) and electron microscopy, histomorphometry of myofibrillar and mitochondrial ultrastructure. -Evaluate the enzymatic activity of citrate synthase and complexes: I, II, III and IV in mitochondria muscle tissue by spectrophotometry. -Evaluate apoptotic activity in muscle fibers by TUNEL technique of Mitochondrial measurements and inflammatory infiltration (by OM) was performed in a total of 5 photos of similar increases in random by the study group (n = 10). The structural changes observed are discussed in the program Axiovision 4.8, to quantify number, degree of alteration of mitochondria and the percentage of inflammatory infiltrate determining the degree of inflammation. The results of the quantitative data were analyzed using ANOVA (Fisher test), and categorical data with Chi-square (Pearson test), establishing a significance level of p <0.05.

Allocative and productive efficiency in REE with asymetric information

We characterize the divergence between informational and economic efficiency in a rational expectations competitive market with asymmetric information about the costs of production. We find that prices may contain too much or too little information with respect to incentive efficient allocations depending on whether the main role of the price is, respectively, the traditional as index of scarcity or informational. Only when REE degenerate to Cournot equilibria the market solution does not show llocative inefficiency. With multidimensional uncertainty we find that the REE price does not have in general the incentive efficient information mix: It pays to sacrifice allocative efficiency at the REE to improve productive efficiency.

Relating severe poverty and chronic poverty

The severely poor are very poor since their consumption is far below the absolute poverty line, and the chronically poor are very poor since their consumption persists for long periods below the absolute poverty line. A combination of chronic poverty and severe poverty (CSP) must represent the very worst instance of poverty. Yet the exercise in this paper of asking simple questions about CSP shows large research gaps. Quantified statements on CSP at the country level can be made for just 14 countries, and at the household level in just six countries. This data suggests a positive correlation between severe poverty and chronic poverty, both at the country level and the household level. Understanding the CSP relationship – whether it is strong, where it arises, what causes it – may improve our explanation of observed cross-country variation in the elasticity between macroeconomic growth and poverty reduction, and why within countries, some households take better advantage of opportunities afforded by macroeconomic growth. Some limited data suggests similarity in socioeconomic characteristics of the severe poor and the chronic poor in terms of location, household size, gender, education and economic sector of work. Of concern is that microlongitudinal datasets drop large proportions of their base year samples, and how this affects our understanding of CSP is not well evaluated. On causal mechanisms, evidence suggests that CSP may be caused by parental CSP (i.e. an intergenerational CSP cycle) and in households not previously poor, CSP may be caused by a morbidity cycle.

Pareto-improving optimal capital and labor taxes

We show a standard model where the optimal tax reform is to cut labor taxes and leave capital taxes very high in the short and medium run. Only in the very long run would capital taxes be zero. Our model is a version of Chamley??s, with heterogeneous agents, without lump sum transfers, an upper bound on capital taxes, and a focus on Pareto improving plans. For our calibration labor taxes should be low for the first ten to twenty years, while capital taxes should be at their maximum. This policy ensures that all agents benefit from the tax reform and that capital grows quickly after when the reform begins. Therefore, the long run optimal tax mix is the opposite from the short and medium run tax mix. The initial labor tax cut is financed by deficits that lead to a positive long run level of government debt, reversing the standard prediction that government accumulates savings in models with optimal capital taxes. If labor supply is somewhat elastic benefits from tax reform are high and they can be shifted entirely to capitalists or workers by varying the length of the transition. With inelastic labor supply there is an increasing part of the equilibrium frontier, this means that the scope for benefitting the workers is limited and the total benefits from reforming taxes are much lower.

Cognition and psychopathology in nonagenarians and centenarians living in geriatric nursing homes in Switzerland: a focus on anosognosia.

BACKGROUND: The number of nonagenarians and centenarians is rising dramatically, and many of them live in nursing homes. Very little is known about psychiatric symptoms and cognitive abilities other than memory in this population. This exploratory study focuses on anosognosia and its relationship with common psychiatric and cognitive symptoms. METHODS: Fifty-eight subjects aged 90 years or older were recruited from geriatric nursing homes and divided into five groups according to Mini-Mental State Examination scores. Assessment included the five-word test, executive clock-drawing task, lexical and categorical fluencies, Anosognosia Questionnaire-Dementia, Neuropsychiatric Inventory, and Charlson Comorbidity Index. RESULTS: Subjects had moderate cognitive impairment, with mean ± SD Mini-Mental State Examination being 15.41 ± 7.04. Anosognosia increased with cognitive impairment and was associated with all cognitive domains, as well as with apathy and agitation. Subjects with mild global cognitive decline seemed less anosognosic than subjects with the least or no impairment. Neither anosognosia nor psychopathological features were related to physical conditions. CONCLUSIONS: Anosognosia in oldest-old nursing home residents was mostly mild. It was associated with both cognitive and psychopathological changes, but whether anosognosia is causal to the observed psychopathological features requires further investigation.

The 16p11.2 locus modulates brain structures common to autism, schizophrenia and obesity

Anatomical structures and mechanisms linking genes to neuropsychiatric disorders are not deciphered. Reciprocal copy number variants at the 16p11.2 BP4-BP5 locus offer a unique opportunity to study the intermediate phenotypes in carriers at high risk for autism spectrum disorder (ASD) or schizophrenia (SZ). We investigated the variation in brain anatomy in 16p11.2 deletion and duplication carriers. Beyond gene dosage effects on global brain metrics, we show that the number of genomic copies negatively correlated to the gray matter volume and white matter tissue properties in cortico-subcortical regions implicated in reward, language and social cognition. Despite the near absence of ASD or SZ diagnoses in our 16p11.2 cohort, the pattern of brain anatomy changes in carriers spatially overlaps with the well-established structural abnormalities in ASD and SZ. Using measures of peripheral mRNA levels, we confirm our genomic copy number findings. This combined molecular, neuroimaging and clinical approach, applied to larger datasets, will help interpret the relative contributions of genes to neuropsychiatric conditions by measuring their effect on local brain anatomy.Molecular Psychiatry advance online publication, 25 November 2014; doi:10.1038/mp.2014.145.

Epidemiology and prevention of cardiovascular disease in the Seychelles Islands (Indian Ocean)

This article presents selected findings and lessons from a cardiovascular research and prevention program initiated in 1989 in the Republic of Seychelles, a country in demographic and epidemiological transition. Rapid and sustained aging of the population (e.g., two-fold increase of people aged 30-39 from 1979 to 1995) implies, over the next few decades, further dramatic increase of the burden of chronic diseases, particularly cardiovascular disease (CVD). Epidemiological surveillance shows high age-specific rates of CVD (particularly stroke), high prevalence of peripheral atherosclerosis (plaques in carotid and femoral arteries), high prevalence of classical modifiable risk factors in the adult population (particularly hypertension), and substantial proportions of children with overweight. Stagnant life expectancy in men and an increase in women have been observed over the last two decades; this occurred despite largely improved health services and reduced infant mortality rates, and may reflect the large CVD burden found in middle-aged men (less so in middle-aged women). A national program of prevention of CVD has been initiated since 1991, which includes a mix of interventions to reduce risk factors in the general population and in high-risk individuals. Substantial research to back the prevention program indeed shows, at the moment, epidemiological patterns in Seychelles similar to those observed in Western countries (e.g., an association between peripheral atherosclerosis [as a proxy of CVD] and low density lipoprotein-cholesterol, smoking, diabetes, and [inversely] walking). This clearly supports the view that promotion of healthy lifestyles and control of conventional risk factors should be the main targets for CVD prevention and control.