Calculation and comparison of different permanent sample plot types

Summary

Event-related potentials and changes of brain rhythm oscillations during working memory activation in patients with first-episode psychosis.

Background: Earlier contributions have documented significant changes in sensory, attention-related endogenous event-related potential (ERP) components and θ band oscillatory responses during working memory activation in patients with schizophrenia. In patients with first-episode psychosis, such studies are still scarce and mostly focused on auditory sensory processing. The present study aimed to explore whether subtle deficits of cortical activation are present in these patients before the decline of working memory performance. Methods: We assessed exogenous and endogenous ERPs and frontal θ event-related synchronization (ERS) in patients with first-episode psychosis and healthy controls who successfully performed an adapted 2-back working memory task, including 2 visual n-backworking memory tasks as well as oddball detection and passive fixation tasks. Results: We included 15 patients with first-episode psychosis and 18 controls in this study. Compared with controls, patients with first-episode psychosis displayed increased latencies of early visual ERPs and phasic θ ERS culmination peak in all conditions. However, they also showed a rapid recruitment of working memory-related neural generators, even in pure attention tasks, as indicated by the decreased N200 latency and increased amplitude of sustained θ ERS in detection compared with controls. Limitations: Owing to the limited sample size, no distinction was made between patients with first-episode psychosis with positive and negative symptoms. Although we controlled for the global load of neuroleptics, medication effect cannot be totally ruled out. Conclusion: The present findings support the concept of a blunted electroencephalographic response in patients with first-episode psychosis who recruit the maximum neural generators in simple attention conditions without being able to modulate their brain activation with increased complexity of working memory tasks.

Large scale assessment of regulatory evolution and transcriptome complexity in mammals

AbstractIn addition to genetic changes affecting the function of gene products, changes in gene expression have been suggested to underlie many or even most of the phenotypic differences among mammals. However, detailed gene expression comparisons were, until recently, restricted to closely related species, owing to technological limitations. Thus, we took advantage of the latest technologies (RNA-Seq) to generate extensive qualitative and quantitative transcriptome data for a unique collection of somatic and germline tissues from representatives of all major mammalian lineages (placental mammals, marsupials and monotremes) and birds, the evolutionary outgroup.In the first major project of my thesis, we performed global comparative analyses of gene expression levels based on these data. Our analyses provided fundamental insights into the dynamics of transcriptome change during mammalian evolution (e.g., the rate of expression change across species, tissues and chromosomes) and allowed the exploration of the functional relevance and phenotypic implications of transcription changes at a genome-wide scale (e.g., we identified numerous potentially selectively driven expression switches).In a second project of my thesis, which was also based on the unique transcriptome data generated in the context of the first project we focused on the evolution of alternative splicing in mammals. Alternative splicing contributes to transcriptome complexity by generating several transcript isoforms from a single gene, which can, thus, perform various functions. To complete the global comparative analysis of gene expression changes, we explored patterns of alternative splicing evolution. This work uncovered several general and unexpected patterns of alternative splicing evolution (e.g., we found that alternative splicing evolves extremely rapidly) as well as a large number of conserved alternative isoforms that may be crucial for the functioning of mammalian organs.Finally, the third and final project of my PhD consisted in analyzing in detail the unique functional and evolutionary properties of the testis by exploring the extent of its transcriptome complexity. This organ was previously shown to evolve rapidly both at the phenotypic and molecular level, apparently because of the specific pressures that act on this organ and are associated with its reproductive function. Moreover, my analyses of the amniote tissue transcriptome data described above, revealed strikingly widespread transcriptional activity of both functional and nonfunctional genomic elements in the testis compared to the other organs. To elucidate the cellular source and mechanisms underlying this promiscuous transcription in the testis, we generated deep coverage RNA-Seq data for all major testis cell types as well as epigenetic data (DNA and histone methylation) using the mouse as model system. The integration of these complete dataset revealed that meiotic and especially post-meiotic germ cells are the major contributors to the widespread functional and nonfunctional transcriptome complexity of the testis, and that this "promiscuous" spermatogenic transcription is resulting, at least partially, from an overall transcriptionally permissive chromatin state. We hypothesize that this particular open state of the chromatin results from the extensive chromatin remodeling that occurs during spermatogenesis which ultimately leads to the replacement of histones by protamines in the mature spermatozoa. Our results have important functional and evolutionary implications (e.g., regarding new gene birth and testicular gene expression evolution).Generally, these three large-scale projects of my thesis provide complete and massive datasets that constitute valuables resources for further functional and evolutionary analyses of mammalian genomes.

A method for using random parameters in analyzing permanent sample plots

Summary

Socioeconomics status and quality of care in a population-based sample of swiss diabetic patients

Introduction: Low socioeconomic status (SES) is associated with higher prevalence of diabetes and worse outcomes; it has also been shown to be associated with worse quality of care. We aimed to explore the relationship between SES and quality of care in the Swiss context. Methods: We used data from a population-based survey including 519 adult diabetic patients living in the canton of Vaud. Self-reported data on patients' and diabetes characteristics, indicators of process and outcomes of care and quality of life were collected. Dependent variables included 6 processes of care (PoC) received during the last 12 months (HbA1C, lipid, microalbuminuria, fundoscopy, feet examination and influenza vaccination) and selected clinical outcomes (blood pressure, LDL, HbA1C, diabetes-specific (ADDQoL) and generic quality of life (SF-12)). Regression analyses were performed to assess the relationship between education and income, respectively, and quality of care as measured by PoC and clinical outcomes. Adjustment was made for age, gender and comorbidities. Results: Mean age was 64.5 years, 40% were women; 19%, 56% and 25% of the patients reported primary (I), secondary (II) and tertiary (III) education. Fundoscopy was the only PoC significantly associated with education, with III education patients more likely to get the exam than those with primary education (adjOR 1.8, 95% CI 1.0-3.3). Use of composite indicators of PoC showed that compared to patients with primary education, patients with III education were more likely to receive ≥5/6 PoC (adjOR 1.9, 95% CI 1.1-3.4), and that those with II or III education were more likely to receive 4/4 PoC (adjOR 1.9, 95% CI 1.0-3.3; adjOR 2.1, 95% CI 1.1-4.1, respectively). Quality of life was the only clinical outcome significantly associated with education, with II and III education patients reporting better quality of life compared to primary education patients, as measured by the ADDQoL (β 0.6, 95% CI 0.3-1.0, β 0.6, 95% CI 0.2-1.0, respectively) and the physical component score of the SF-12 (β 2.5, 95% CI 0.2-4.8, β 3.6, 95% CI 0.9-6.4, respectively). No associations were found between income and quality of care. Conclusion: Social inequalities have been demonstrated in Switzerland for global health indicators. Our results suggest that similar associations are found when considering quality of care measures in individuals with diabetes, but only for a few indicators.

An appropriate data set size for digital soil mapping in Erechim, Rio Grande do Sul, Brazil

Digital information generates the possibility of a high degree of redundancy in the data available for fitting predictive models used for Digital Soil Mapping (DSM). Among these models, the Decision Tree (DT) technique has been increasingly applied due to its capacity of dealing with large datasets. The purpose of this study was to evaluate the impact of the data volume used to generate the DT models on the quality of soil maps. An area of 889.33 km² was chosen in the Northern region of the State of Rio Grande do Sul. The soil-landscape relationship was obtained from reambulation of the studied area and the alignment of the units in the 1:50,000 scale topographic mapping. Six predictive covariates linked to the factors soil formation, relief and organisms, together with data sets of 1, 3, 5, 10, 15, 20 and 25 % of the total data volume, were used to generate the predictive DT models in the data mining program Waikato Environment for Knowledge Analysis (WEKA). In this study, sample densities below 5 % resulted in models with lower power of capturing the complexity of the spatial distribution of the soil in the study area. The relation between the data volume to be handled and the predictive capacity of the models was best for samples between 5 and 15 %. For the models based on these sample densities, the collected field data indicated an accuracy of predictive mapping close to 70 %.

Animal Toxins: How is Complexity Represented in Databases?

Peptide toxins synthesized by venomous animals have been extensively studied in the last decades. To be useful to the scientific community, this knowledge has been stored, annotated and made easy to retrieve by several databases. The aim of this article is to present what type of information users can access from each database. ArachnoServer and ConoServer focus on spider toxins and cone snail toxins, respectively. UniProtKB, a generalist protein knowledgebase, has an animal toxin-dedicated annotation program that includes toxins from all venomous animals. Finally, the ATDB metadatabase compiles data and annotations from other databases and provides toxin ontology.

Spouse similarity in recollections of parenting received : a study in a nonclinical sample

Rapport de synthèse : L'article constituant le présent travail de thèse décrit une recherche portant sur des couples adultes recrutés dans la population générale, décrivant rétrospectivement les attitudes de leurs parents respectifs envers eux au cours de leur enfance. Le rôle joué par les attitudes d'attachement dans les relations adultes, et notamment les relations de couples, est bien démontré. De même, il est établi que les relations établies avec les parents dans l'enfance influencent le type d'attitude d'attachement qui prédominera à l'âge adulte. Dès lors, nous avons investigué l'existence, au sein de ces couples adultes, de souvenirs similaires quant aux attitudes prodiguées par les parents. Pour réaliser cette recherche, nous avons contacté tous les parents des enfants scolarisés en 2e/3e années et en 6e/7e années au sein des écoles de plusieurs communes de la région lausannoise, permettant de constituer un échantillon de 563 couples de parents. Au moyen d'autoquestionnaires, nous avons évalué pour chaque membre du couple : 1) sa description rétrospective des attitudes de ses deux parents envers lui pendant son enfance ; 2) le degré de sa symptomatologie psychiatrique actuelle ; et 3) son évaluation du degré d'ajustement dyadique actuel au sein du couple. La comparaison des scores des époux respectifs sur « l'échelle de lien parental » (PBI : Parental Bonding Instrument) a montré une ressemblance, au sein des couples, concernant la c chaleur et affection » (« Care ») témoignée au cours de l'enfance parle parent de même sexe que le sujet. Les analyses complémentaires effectuées semblent exclure que cette similarité soit due à des facteurs confondant comme l'âge, l'origine culturelle, le niveau socio-économique, ou le degré de symptomatologie psychiatrique. De même, cette similarité ne semble pas être attribuable à une convergence de vue grandissante des conjoints au cours de leur union. Par ailleurs, le degré d'ajustement dyadique s'est révélé être dépendant du degré cumulé de chaleur et d'affection tel que remémoré par chaque conjoint, et non du degré de similarité dans le couple pour ce qui concerne le souvenir de la chaleur et de l'affection reçues. Bien que basée sur des évaluations rétrospectives des attitudes parentales, et ne disposant pas d'une investigation psychiatrique standardisée incluant les critères diagnostiques, cette étude repose néanmoins sur un grand échantillon, recruté dans la population générale. Nos résultats ont notamment des implications concernant la santé des enfants. En effet, en raison de la similarité mise en évidence dans nos résultats, un enfant dont un des parents a reçu peu de chaleur et d'affection dans son enfance a plus de chances que son autre parent aie lui-même également reçu moins de chaleur et d'affection. De ce fait, d'une part l'ajustement dyadique du couple parental sera particulièrement bas, ce qui peut se répercuter sur les enfants du couple. D'autre part, comme les attitudes parentales se transmettent en partie de génération en génération, le même enfant risque d'être exposé, de la part de ses deux parents, à une attitude comportant peu de chaleur et d'affection, ce qui représente un risque de développement ultérieur des pathologies psychiatriques chez cet enfant.

Prevalence of measured and reported multimorbidity in a representative sample of the Swiss population.

BACKGROUND: Little is known on the prevalence of multimorbidity (MM) in the general population. We aimed to assess the prevalence of MM using measured or self-reported data in the Swiss population. METHODS: Cross-sectional, population-based study conducted between 2003 and 2006 in the city of Lausanne, Switzerland, and including 3714 participants (1967 women) aged 35 to 75 years. Clinical evaluation was conducted by thoroughly trained nurses or medical assistants and the psychiatric evaluation by psychologists or psychiatrists. For psychiatric conditions, two definitions were used: either based on the participant's statements, or on psychiatric evaluation. MM was defined as presenting ≥2 morbidities out of a list of 27 (self-reported - definition A, or measured - definition B) or as the Functional Comorbidity Index (FCI) using measured data - definition C. RESULTS: The overall prevalence and (95% confidence interval) of MM was 34.8% (33.3%-36.4%), 56.3% (54.6%-57.9%) and 22.7% (21.4%-24.1%) for definitions A, B and C, respectively. Prevalence of MM was higher in women (40.2%, 61.7% and 27.1% for definitions A, B and C, respectively, vs. 28.7%, 50.1% and 17.9% in men, p < 0.001); Swiss nationals (37.1%, 58.8% and 24.8% for definitions A, B and C, respectively, vs. 31.4%, 52.3% and 19.7% in foreigners, all p < 0.001); elderly (>65 years: 67.0%, 70.0% and 36.7% for definitions A, B and C, respectively, vs. 23.6%, 50.2% and 13.8% for participants <45 years, p < 0.001); participants with lower educational level; former smokers and obese participants. Multivariate analysis confirmed most of these associations: odds ratio (95% Confidence interval) 0.55 (0.47-0.64), 0.61 (0.53-0.71) and 0.51 (0.42-0.61) for men relative to women for definitions A, B and C, respectively; 1.27 (1.09-1.49), 1.29 (1.11-1.49) and 1.41 (1.17-1.71) for Swiss nationals relative to foreigners, for definitions A, B and C, respectively. Conversely, no difference was found for educational level for definitions A and B and abdominally obese participants for all definitions. CONCLUSIONS: Prevalence of MM is high in the Lausanne population, and varies according to the definition or the data collection method.

USE OF SCALED SEMIVARIOGRAMS IN THE PLANNING SAMPLE OF SOIL PHYSICAL PROPERTIES IN SOUTHERN AMAZONAS, BRAZIL

There is a great lack of information from soil surveys in the southern part of the State of Amazonas, Brazil. The use of tools such as geostatistics may improve environmental planning, use and management. In this study, we aimed to use scaled semivariograms in sample design of soil physical properties of some environments in Amazonas. We selected five areas located in the south of the state of Amazonas, Brazil, with varied soil uses, such as forest, archaeological dark earth (ADE), pasture, sugarcane cropping, and agroforestry. Regular mesh grids were set up in these areas with 64 sample points spaced at 10 m from each other. At these points, we determined the particle size composition, soil resistance to penetration, moisture, soil bulk density and particle density, macroporosity, microporosity, total porosity, and aggregate stability in water at a depth of 0.00-0.20 m. Descriptive and geostatistical analyses were performed. The sample density requirements were lower in the pasture area but higher in the forest. We concluded that managed-environments had differences in their soil physical properties compared to the natural forest; notably, the soil in the ADE environment is physically improved in relation to the others. The physical properties evaluated showed a structure of spatial dependence with a slight variability of the forest compared to the others. The use of the range parameter of the semivariogram analysis proved to be effective in determining an ideal sample density.

USE OF SCALED SEMIVARIOGRAMS IN THE PLANNING SAMPLE OF SOIL CHEMICAL PROPERTIES IN SOUTHERN AMAZONAS, BRAZIL

The lack of information concerning the variability of soil properties has been a major concern of researchers in the Amazon region. Thus, the aim of this study was to evaluate the spatial variability of soil chemical properties and determine minimal sampling density to characterize the variability of these properties in five environments located in the south of the State of Amazonas, Brazil. The five environments were archaeological dark earth (ADE), forest, pasture land, agroforestry operation, and sugarcane crop. Regular 70 × 70 m mesh grids were set up in these areas, with 64 sample points spaced at 10 m distance. Soil samples were collected at the 0.0-0.1 m depth. The chemical properties of pH in water, OM, P, K, Ca, Mg, H+Al, SB, CEC, and V were determined at these points. Data were analyzed by descriptive and geostatistical analyses. A large part of the data analyzed showed spatial dependence. Chemical properties were best fitted to the spherical model in almost all the environments evaluated, except for the sugarcane field with a better fit to the exponential model. ADE and sugarcane areas had greater heterogeneity of soil chemical properties, showing a greater range and higher sampling density; however, forest and agroforestry areas had less variability of chemical properties.

Can Soil Penetration Resistance and Bulk Density Be Determined in a Single Undisturbed Sample?

Soil quality indicators such as penetration resistance (PR) and bulk density (BD) are traditionally determined in a single undisturbed soil sample. The aim of this study was to assess the effect of PR measurements of undisturbed samples on the determination of BD in the same sample of two soils differing in clay contents. To this end, samples were collected from the 0.00-0.10 and 0.10-0.20 m layers of two soils of clayey and very clayey texture. Volumetric rings were used to collect a total of 120 undisturbed soil samples from each soil layer that were divided into two subsets containing 60 units each. One sample set, designated “perforated samples”, was used to determine PR and BD in the same undisturbed sample; the other, named “intact samples”, was used to determine BD only. Bulk density values for perforated and intact samples were compared by analysis of variance, using a completely randomized experimental design. Means were compared by the t-test at 5 %. The BD values for the clayey soil were similar in perforated and intact samples from the two layers. However, BD of the very clayey soil was lower in the perforated than in the intact samples at both depths. Therefore, PR and BD in clayey soils can be accurately determined in the same undisturbed sample whereas in very clayey soils, different samples are required for this purpose.