Analytical and numerical study of polarons

The aim of this thesis is to introduce the polaron concept and to perform a DFT numerical calculation of a small polaron in the rutile phase of TiO2. In the first chapters, we present an analytical study of small and large polarons, based on the Holstein and Fröhlich Hamiltonians. The necessary mathematical formalism and physics fundamentals are briefly reviewed in the first chapter. In the second part of the thesis, Density Functional Theory (DFT) is introduced together with the DFT+U correction and its implementation in the Vienna Ab-Initio Simulation Package (VASP). The calculation of a small polaron in rutile is then described and discussed at a qualitative level. The polaronic solution is compared with the one of a delocalized electron. The calculation showed how the polaron creates a new energy level 0.70 eV below the conduction band. The energy level is visible both in the band structure diagram and in the density of states diagram. The electron is localized on a titanium atom, distorting the surrounding lattice. In particular, the four oxygen atoms closer to the titanium atom are displaced by 0.085 Å outwards, whereas the two further oxygen atoms by 0.023 Å. The results are compatible, at a qualitative level, with the literature. Further developments of this work may try to improve the precision of the results and to quantitatively compare them with the literature.

Analysis of the study design and manuscript deficiencies in research articles submitted to Emergency Medicine

Objective: To describe and analyse the study design and manuscript deficiencies in original research articles submitted to Emergency Medicine. Methods: This was a retrospective, analytical study. Articles were enrolled if the reports of the Section Editor and two reviewers were available. Data were extracted from these reports only. Outcome measures were the mean number and nature of the deficiencies and the mean reviewers’ assessment score. Results: Fifty-seven articles were evaluated (28 accepted for publication, 19 rejected, 10 pending revision). The mean (± SD) number of deficiencies was 18.1 ± 6.9, 16.4 ± 6.5 and 18.4 ± 6.7 for all articles, articles accepted for publication and articles rejected, respectively (P = 0.31 between accepted and rejected articles). The mean assessment scores (0–10) were 5.5 ± 1.5, 5.9 ± 1.5 and 4.7 ± 1.4 for all articles, articles accepted for publication and articles rejected, respectively. Accepted articles had a significantly higher assessment score than rejected articles (P = 0.006). For each group, there was a negative correlation between the number of deficiencies and the mean assessment score (P > 0.05). Significantly more rejected articles ‘… did not further our knowledge’ (P = 0.0014) and ‘… did not describe background information adequately’ (P = 0.049). Many rejected articles had ‘… findings that were not clinically or socially significant’ (P = 0.07). Common deficiencies among all articles included ambiguity of the methods (77%) and results (68%), conclusions not warranted by the data (72%), poor referencing (56%), inadequate study design description (51%), unclear tables (49%), an overly long discussion (49%), limitations of the study not described (51%), inadequate definition of terms (49%) and subject selection bias (40%). Conclusions: Researchers should undertake studies that are likely to further our knowledge and be clinically or socially significant. Deficiencies in manuscript preparation are more frequent than mistakes in study design and execution. Specific training or assistance in manuscript preparation is indicated.

An interdisciplinary approach to the study of colour in portuguese manuscript illuminations

Dissertação apresentada para obtenção do Grau de Doutor em Conservação e Restauro, especialidade Teoria, História e Técnicas, pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics.

MOTIVATION: Microarray results accumulated in public repositories are widely reused in meta-analytical studies and secondary databases. The quality of the data obtained with this technology varies from experiment to experiment, and an efficient method for quality assessment is necessary to ensure their reliability. RESULTS: The lack of a good benchmark has hampered evaluation of existing methods for quality control. In this study, we propose a new independent quality metric that is based on evolutionary conservation of expression profiles. We show, using 11 large organ-specific datasets, that IQRray, a new quality metrics developed by us, exhibits the highest correlation with this reference metric, among 14 metrics tested. IQRray outperforms other methods in identification of poor quality arrays in datasets composed of arrays from many independent experiments. In contrast, the performance of methods designed for detecting outliers in a single experiment like Normalized Unscaled Standard Error and Relative Log Expression was low because of the inability of these methods to detect datasets containing only low-quality arrays and because the scores cannot be directly compared between experiments. AVAILABILITY AND IMPLEMENTATION: The R implementation of IQRray is available at: ftp://lausanne.isb-sib.ch/pub/databases/Bgee/general/IQRray.R. CONTACT: Marta.Rosikiewicz@unil.ch SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Association of adiposity genetic variants with menarche timing in 92,105 women of European descent.

Obesity is of global health concern. There are well-described inverse relationships between female pubertal timing and obesity. Recent genome-wide association studies of age at menarche identified several obesity-related variants. Using data from the ReproGen Consortium, we employed meta-analytical techniques to estimate the associations of 95 a priori and recently identified obesity-related (body mass index (weight (kg)/height (m)(2)), waist circumference, and waist:hip ratio) single-nucleotide polymorphisms (SNPs) with age at menarche in 92,116 women of European descent from 38 studies (1970-2010), in order to estimate associations between genetic variants associated with central or overall adiposity and pubertal timing in girls. Investigators in each study performed a separate analysis of associations between the selected SNPs and age at menarche (ages 9-17 years) using linear regression models and adjusting for birth year, site (as appropriate), and population stratification. Heterogeneity of effect-measure estimates was investigated using meta-regression. Six novel associations of body mass index loci with age at menarche were identified, and 11 adiposity loci previously reported to be associated with age at menarche were confirmed, but none of the central adiposity variants individually showed significant associations. These findings suggest complex genetic relationships between menarche and overall obesity, and to a lesser extent central obesity, in normal processes of growth and development.

Extended treatment of treatment-naive patients with chronic hepatitis c virus (HCV) genotype 1-infection and slow response to pegylated interferon-alfa and ribavirin: a meta-analysis

Aims: Recently, several clinical trials analyzed if extended duration of treatment with pegylated interferon-alfa and ribavirin over 48 weeks can improve sustained virologic response (SVR) rates in HCV genotype 1-infected patients with slow virologic response. Because results of these clinical trials are conflicting, we performed a metaanalysis to determine the overall impact of extended treatment compared to standard treatment on virologic response rates in treatment-naive HCV genotype 1 slow responders. Methods: Literature search was performed independently by two observers using Pub Med, EMBASE, CENTRAL and abstracts presented in English at international liver and gastroenterology meetings. Randomized controlled clinical trials (RCTs; but studies that re-analyzed data retrospectively RCTs were also allowed) were considered if they included monoinfected treatment-naive HCV genotype 1 patients and compared treatment with pegIFN-alfa 2a or 2b in combination with ribavirin for 48 weeks versus extended treatment (up to 72 weeks) in slow responders. Primary and secondary end points were SVR rates and end-of-treatment (EOT) and relapse rates, respectively. In the present meta-analysis, study endpoints were summarized with a DerSimonian-Laird estimate for binary outcome basing on a random effects model. Results: Literature search yielded seven RTCs addressing the benefit of extended treatment with pegylated interferon-alfa and ribavirin in treatment-naive HCV genotype 1 slow responders. In total, 1330 slow responders were included in our meta-analysis. We show that extended treatment duration compared to the standard of care significantly improves SVR rates in HCV genotype 1 slow responders (12.4% improvement of overall SVR rate, 95% CI 0.055- 0.193, P = 0.0005). In addition, we show that rates of viral relapse were significantly reduced by extended treatment (24.1% reduction of relapse, 95% CI −0.3332 to −0.1487, P < 0.0001), whereas no significant impact of extended treatment on EOT response rates was found. Though extended treatment was burdened with an enhanced rate of premature treatment discontinuation due to interferonalfa- and ribavirin-related side effects, the frequency of serious adverse events was not increased. Conclusions: Treatment extension in HCV genotype 1 slow responders can improve SVR rates in difficult to treat patients and should be considered in patients who need to be treated before specific antivirals will be approved.

The "handwriting brain": a meta-analysis of neuroimaging studies of motor versus orthographic processes.

INTRODUCTION: Handwriting is a modality of language production whose cerebral substrates remain poorly known although the existence of specific regions is postulated. The description of brain damaged patients with agraphia and, more recently, several neuroimaging studies suggest the involvement of different brain regions. However, results vary with the methodological choices made and may not always discriminate between "writing-specific" and motor or linguistic processes shared with other abilities. METHODS: We used the "Activation Likelihood Estimate" (ALE) meta-analytical method to identify the cerebral network of areas commonly activated during handwriting in 18 neuroimaging studies published in the literature. Included contrasts were also classified according to the control tasks used, whether non-specific motor/output-control or linguistic/input-control. These data were included in two secondary meta-analyses in order to reveal the functional role of the different areas of this network. RESULTS: An extensive, mainly left-hemisphere network of 12 cortical and sub-cortical areas was obtained; three of which were considered as primarily writing-specific (left superior frontal sulcus/middle frontal gyrus area, left intraparietal sulcus/superior parietal area, right cerebellum) while others related rather to non-specific motor (primary motor and sensorimotor cortex, supplementary motor area, thalamus and putamen) or linguistic processes (ventral premotor cortex, posterior/inferior temporal cortex). CONCLUSIONS: This meta-analysis provides a description of the cerebral network of handwriting as revealed by various types of neuroimaging experiments and confirms the crucial involvement of the left frontal and superior parietal regions. These findings provide new insights into cognitive processes involved in handwriting and their cerebral substrates.

The practical application of a meta-analysis of deinstitutionalization : adaptive behaviour outcomes and the piloting of a transitional questionnaire for adults with intellectual disabilities

This investigation examined the effects of de institutionalization on the adaptive behaviour and adjustment of adults with intellectual disabilities (ID). In study 1, a meta-analysis was conducted with 23 studies on deinstitutionalization adaptive behaviour outcomes. Deinstitutionalization was associated with modest improvements in adaptive behaviour however outcomes varied across adaptive behaviour domains and other substantive variables. Clinical and service implications of these results were explicated. Noting the trends from the meta-analysis, study 2 used this information in refining and piloting an Agency Transition Survey used to evaluate community transitions for persons with ID. Information derived from the survey was found to be valuable and adequate for the effective evaluation of transitional success. Potential applications of the survey and meta-analysis results were illustrated.

Farm Poverty in Kerala: A case study of Alappuzha, Trissur, Palakkad and Wayanad

The present study was an attempt to analytically approach the problem of farm poverty in Kerala from an entirely different angle by incorporating an independently developed and reformulated definition of poverty line in terms of physical units of operational holdings (say, acre). The entire discussion on farm poverty emerged out of proper co-ordination of two important factors popularly considered as the distinct features of Istudy on farm poverty, conducted in the light of inter regional variations in farm productivity tried to highlight various grave issues deserving thorough introspection.

Study on the Socio-Psychological Background of Entrepreneur - Managers of Small Scale Industrial Units in Ernakulam District, Kerala

The understanding of the theory of entrepreneurship depends upon one set of definitions which provide the base for analytical study. The main objective of the study was to understand the distribution of entrepreneurship in the manufacturing sector among different categories of people in kerala and to differentiate the socio - psychological background of successful entrepreneur- managers from unsuccessful entrepreneur-managers. The purpose of the study, a sample of 150 entrepreneur-managers of SS1 units spread over Ernakulam district was surveyed through a specially designed questionnaire.

A study of the marketing of fertilisers in India

This is a descriptive and analytical study. It investigates how Fertilisers are marketed in India. It describes and evaluates the system of fertiliser marketing prevalent in the country at the time of this study (1979-82). The study, as the title will indicate, has been conceived on a large canvass and in very broad and generalised terms. Such a large framework has been chosen with the intention of investigating the task of Fertiliser marketing in its totality

Impacto de la cesarea en la morbimortalidad materna y perinatal

Introducción: La cesárea es un procedimiento quirúrgico considerado como inocuo por algunas personas, sin tener en cuenta las posibles consecuencias en los embarazos siguientes. Existe literatura que evidencia un aumento en el riesgo para abrupcio de placenta, acretismo placentario, placenta previa, mortalidad materna, sepsis materna, ingreso a UCI, al igual que apgar bajo, bajo peso neonatal, distress respiratorio,entre otros.El objetivo de este estudio fue evaluar el impacto del antecedente de cesárea en la morbilidad materna y neonatal mediante una revisión sistemática de literatura. Metodología Se realizó una búsqueda en diferentes bases de datos desde 1996 hasta 2011 sobre el antecedente de cesárea y sus posibles riesgos en el desenlace maternos y perinatales. Se utilizaron variaciones de términos MeSH. Resultados La búsqueda arrojó un total de 2.483 artículos, entre los cuales fueron escogidos 247 por criterios de elegibilidad.Estos fueron evaluados en su totalidad. Posteriormente se realizó el análisis metanalítico de cada uno de los desenlaces. Los resultados deben interpretarse con precaución pues la calidad metodológica de algunos estudios fue variable. En el riesgo conjunto se encontraron resultados estadísticamente significativos en placenta previa, apgar bajo, histerectomía periparto. Discusión El antecedente de cesárea presenta un riesgo aumentado para los siguientes embarazos en la morbilidad tanto materna como neonatal. Faltan más estudios analíticos para definir el verdadero papel de la cesarea.

Nuevos factores de riesgo para enfermedad cardiovascular en artritis reumatoide

Introducción: Dado que la enfermedad cardiovascular (ECV) es la causa más común de mortalidad en pacientes con artritis reumatoide (AR), el objetivo fue determinar los factores asociados a esta complicación en una serie amplia de pacientes colombianos. Adicionalmente, se efectuó una revisión sistemática de la literatura para abordar el estado del arte sobre los factores de riesgo no tradicionales para la ECV en AR. Métodos: Estudio analítico, de tipo corte transversal en el que 800 pacientes colombianos con AR se evaluaron teniendo en cuenta variables asociadas a ECV. Se siguieron las pautas de los elementos de Información Preferidos para Revisiones Sistemáticas y Meta-análisis (PRISMA). Resultados: Colesterol ≥200 mg/dL (OR 3.44; IC 95% 2.21-5.38; p<0.0001), índice de masa corporal anormal (OR 1.70; IC 95% 1.12-2.58; p=0.011), fueron factores de riesgo tradicionales significativamente asociados con ECV en estos pacientes. Como factores no tradicionales de riesgo, autoinmunidad familiar (OR 2.03; IC 95% 1.13-3.65; p=0.017), más de 10 años de enfermedad (OR 2.12; IC 95% 1.36-3.29; p=0.001), trabajadores en las tareas del hogar (OR 2.29; IC 95% 1.45-3.61; p<0.0001), uso de esteroides sistémicos (OR 2.51; IC 95% 1.18-5.37; p=0.017) se asociaron con ECV en nuestra población. A través de la revisión sistemática varios factores y resultados relacionados con las ECV fueron confirmados e identificados. Conclusiones: Los factores de riesgo tradicionales no explican completamente las altas tasas de ECV en los pacientes con AR. Así, factores de riesgo no tradicionales, relacionados con autoinmunidad se reconocen ahora y actúan sinérgicamente, como predictores de esta comorbilidad.

Presión arterial en preescolares de la localidad de Usaquén en Bogotá

Introducción: La hipertensión arterial es un problema de salud pública tanto en países industrializados como en vía de desarrollo. Su prevalencia en la infancia viene en aumento por lo que es relevante determinarla en niños preescolares a nivel local. Objetivo: Determinar la prevalencia de hipertensión arterial en niños de tres a cinco años de una cohorte de 14 hogares infantiles del ICBF de la localidad de Usaquén en Bogotá. Materiales y métodos: Se realizó un estudio de corte transversal analítico, utilizando la base de datos de un ensayo aleatorizado y controlado del año 200913, y se evaluaron las cifras de tensión arterial de acuerdo a sexo, edad, talla y su correlación con el IMC con un nivel de confianza del 95% y precisión del 1%. Se calcularon las medias, desviaciones estándar, percentiles y prevalencia. Resultados: Se obtuvo una muestra de 1035 casos, encontrándose una prevalencia de 4,5% de HTA sistólica, 10,4% de diastólica, ambas en estadio I; teniendo en cuenta tanto sistólica como diastólica, fue de 11,6% en estadio I. Se determinaron los valores de presión arterial sistólica y diastólica en cuartiles de acuerdo a edad, sexo y talla. El coeficiente de correlación entre el IMC y los niveles de presión arterial sistólica y diastólica fueron de 0.0992 y 0.0362 respectivamente. Conclusión: La prevalencia de HTA general fue de 11,6%, predominando la diastólica en estadio I en niños preescolares. No se encontró correlación entre el IMC y las cifras de tensión arterial sistólica y diastólica.

Cardiovascular disease in latin american patients with systemic lupus erythematosus: a cross-sectional study and a systematic review

Objective. This study was performed to determine the prevalence of and associated risk factors for cardiovascular disease (CVD) in Latin American (LA) patients with systemic lupus erythematosus (SLE). Methods. First, a cross-sectional analytical study was conducted in 310 Colombian patients with SLE in whom CVD was assessed. Associated factors were examined by multivariate regression analyses. Second, a systematic review of the literature on CVD in SLE in LA was performed. Results. There were 133 (36.5%) Colombian SLE patients with CVD. Dyslipidemia, smoking, coffee consumption, and pleural effusion were positively associated with CVD. An independent effect of coffee consumption and cigarette on CVD was found regardless of gender and duration of disease. In the systematic review, 60 articles fulfilling the eligibility criteria were included. A wide range of CVD prevalence was found (4%–79.5%). Several studies reported ancestry, genetic factors, and polyautoimmunity as novel risk factors for such a condition.Conclusions. A high rate of CVD is observed in LA patients with SLE. Awareness of the observed risk factors should encourage preventive population strategies for CVD in patients with SLE aimed at facilitating the suppression of cigarette smoking and coffee consumption as well as at the tight control of dyslipidemia and other modifiable risk factors.