Validated prediction of clinical outcome in sarcomas and multiple types of cancer on the basis of a gene expression signature related to genome complexity.

Sarcomas are heterogeneous and aggressive mesenchymal tumors. Histological grading has so far been the best predictor for metastasis-free survival, but it has several limitations, such as moderate reproducibility and poor prognostic value for some histological types. To improve patient grading, we performed genomic and expression profiling in a training set of 183 sarcomas and established a prognostic gene expression signature, complexity index in sarcomas (CINSARC), composed of 67 genes related to mitosis and chromosome management. In a multivariate analysis, CINSARC predicts metastasis outcome in the training set and in an independent 127 sarcomas validation set. It is superior to the Fédération Francaise des Centres de Lutte Contre le Cancer grading system in determining metastatic outcome for sarcoma patients. Furthermore, it also predicts outcome for gastrointestinal stromal tumors (GISTs), breast carcinomas and lymphomas. Application of the signature will permit more selective use of adjuvant therapies for people with sarcomas, leading to decreased iatrogenic morbidity and improved outcomes for such individuals.

Correlação linear e espacial entre a produtividade de forragem, a porosidade total e a densidade do solo de Pereira Barreto (SP)

Em relação aos sistemas de manejo adotados pelo homem, a porosidade total e a densidade do solo são atributos ativamente alterados, refletindo decisivamente sobre a produtividade vegetal agrícola. No ano agrícola de 2005, na Fazenda Bonança, no município de Pereira Barreto, Estado de São Paulo, Brasil, foram analisadas a produtividade de forragem do milho outonal (MSF) no sistema plantio direto irrigado, a porosidade total (PT) e a densidade do solo (DS) em profundidade, em um Latossolo Vermelho distrófico. O objetivo foi estudar a variabilidade e as correlações lineares e espaciais entre os atributos da planta e do solo, visando selecionar um indicador da qualidade física do solo de boa representatividade para produtividade da forragem. Foi instalada a malha geoestatística, para coleta de dados do solo e planta, contendo 125 pontos amostrais, numa área de 2.500 m². Os atributos estudados, além de não terem variado aleatoriamente, apresentaram variabilidade dos dados entre média e baixa e seguiram padrões espaciais bem definidos, com alcance entre 6,8 e 23,7 m. Por sua vez, a correlação linear entre o atributo da planta e os do solo, em razão do elevado número de observações, foi baixa. As observações de melhor correlação com a MSF foram a DS1 e a PT1. Entretanto, do ponto de vista espacial, houve excelente correlação inversa entre a MSF e a DS1, assim como entre a DS1 e a PT1. Nos sítios onde a DS1 aumentou (1,45-1,64 kg dm-3) a MSF variou entre 11.653 e 14.552 kg ha-1; já naqueles onde diminuiu (1,35-1,45 kg dm-3) a MSF, ficou entre 14.552 e 17.450 kg ha-1. Portanto, a densidade global, avaliada na camada de 0-0,10 m (DS1), apresentou-se como satisfatório indicador da qualidade física do solo de Pereira Barreto (SP), quando destinado à produtividade de forragem do milho outonal.

Correlação linear e espsacial entre a produtividade de feijão e a porosidade de um Latossolo Vermelho de Selvíria (MS)

A porosidade do solo exerce grande influência sobre o crescimento e desenvolvimento vegetal, uma vez que o crescimento das raízes, tal como a produtividade das culturas, é limitado pela profundidade que atingem. Portanto, o objetivo deste trabalho foi estudar a variabilidade espacial e as correlações lineares entre a produtividade de feijão e a porosidade do solo. No ano de 2004/2005, no município de Selvíria, MS, foram analisadas a produtividade de grãos de feijão (PG), cultivar IAC Carioca, irrigado, a macroporosidade (MA), a microporosidade (MI) e a porosidade total (PT) do solo em quatro profundidades: 1 (0,0-0,10); 2(0,10-0,20); 3(0,20-0,30) e 4(0,30-0,40 m), num Latossolo Vermelho distroférrico. As amostras de solo e planta foram coletadas em uma malha geoestatística com 75 pontos espaçados de 10 x 10 m, mais 60 pontos de quatro malhas de refinamento numa área de 50 x 150 m. Os atributos estudados, além de não terem variado aleatoriamente, apresentaram média e baixa variabilidades. Seguiram padrões espaciais bem definidos, com alcances entre 11,70 e 104,40 m. A correlação linear entre o atributo da planta e os do solo, em função do elevado número de observações, foi baixa. As de melhor correlação linear com a PG foram a MA1, MI1 e a PT3. Entretanto, do ponto de vista espacial, houve excelente correlação inversa entre a PG e a #PT2. Assim, nos sítios onde a #PT2 diminuiu (0,030-0,045 m³ m-3 ), a PG variou entre 2.173 e 3.529 kg ha-1. Já naqueles onde aumentou (0,045-0,076 m³ m-3 ), a PG ficou entre 1.630-2.173 kg ha-1. Assim, a porosidade total do solo, quando avaliada na camada de 0,10-0,20 m (#PT2), indicou a importância do contato raiz/solo e, de modo inverso, apresentou satisfatório indicador da qualidade física do solo estudado, quando destinado à produtividade de grãos de feijão irrigado.

Predictors of developmental dyslexia in European orthographies with varying complexity.

Background:  The relationship between phoneme awareness, rapid automatized naming (RAN), verbal short-term/working memory (ST/WM) and diagnostic category is investigated in control and dyslexic children, and the extent to which this depends on orthographic complexity. Methods:  General cognitive, phonological and literacy skills were tested in 1,138 control and 1,114 dyslexic children speaking six different languages spanning a large range of orthographic complexity (Finnish, Hungarian, German, Dutch, French, English). Results:  Phoneme deletion and RAN were strong concurrent predictors of developmental dyslexia, while verbal ST/WM and general verbal abilities played a comparatively minor role. In logistic regression models, more participants were classified correctly when orthography was more complex. The impact of phoneme deletion and RAN-digits was stronger in complex than in less complex orthographies. Conclusions:  Findings are largely consistent with the literature on predictors of dyslexia and literacy skills, while uniquely demonstrating how orthographic complexity exacerbates some symptoms of dyslexia.

Correlação linear e espacial entre a resistência do solo ao penetrômetro e a produtividade do feijoeiro irrigado

A resistência do solo ao penetrômetro exerce grande influência sobre o crescimento e desenvolvimento vegetal, uma vez que o crescimento das raízes, assim como o rendimento das culturas, varia de forma inversamente proporcional ao seu valor. Dessa forma, a análise da variabilidade espacial da resistência do solo ao penetrômetro e da produtividade, por meio da geoestatística, pode indicar alternativas de manejo para reduzir os efeitos da variabilidade do solo sobre a produtividade e também melhorar a estimativa de respostas das culturas sob determinadas práticas de manejo. Diante do exposto, o objetivo deste trabalho foi relacionar e caracterizar a variabilidade espacial da resistência do solo ao penetrômetro (RP) e a produtividade do feijoeiro irrigado em sistema de semeadura direta, em duas safras consecutivas. O experimento foi realizado em Latossolo Vermelho distroférrico típico, no campo experimental da Faculdade de Engenharia Agrícola da Unicamp, no município de Campinas-SP, cujas coordenadas geográficas são: 22 ° 48 ' 57 " de latitude sul, 47 ° 03 ' 33 " de longitude oeste e altitude média de 640 m. As avaliações foram realizadas em uma malha regular de amostragem de 3 x 3 m, totalizando 60 pontos amostrais por parcela. A análise da dependência espacial foi avaliada pela geoestatística, e os parâmetros dos semivariogramas utilizados para construir mapas de isolinhas, por meio do interpolador de krigagem do programa Surfer 8.0. A regressão linear simples entre mapas (pixel-a-pixel) mostrou correlação negativa entre os valores de RP e a produtividade; no entanto, a produtividade do feijoeiro irrigado apresentou baixa correlação com a resistência do solo ao penetrômetro em sistema semeadura direta nas duas safras.

Care complexity, mood, and quality of life in liver pre-transplant patients.

RATIONALE: This study was intended to document the frequency of care complexity in liver transplant candidates, and its association with mood disturbance and poor health-related quality of life (HRQoL). METHODS: Consecutive patients fulfilling inclusion criteria, recruited in three European hospitals, were assessed with INTERMED, a reliable and valid method for the early assessment of bio-psychosocial health risks and needs. Blind to the results, they were also assessed with the Hospital Anxiety and Depression Scale (HADS). HRQoL was documented with the EuroQol and the SF36. Statistical analysis included multivariate and multilevel techniques. RESULTS: Among patients fulfilling inclusion criteria, 60 patients (75.9%) completed the protocol and 38.3% of them were identified as "complex" by INTERMED, but significant between-center differences were found. In support of the working hypothesis, INTERMED scores were significantly associated with all measures of both the SF36 and the EuroQol, and also with the HADS. A one point increase in the INTERMED score results in a reduction in 0.93 points in EuroQol and a 20% increase in HADS score. CONCLUSIONS: INTERMED-measured case complexity is frequent in liver transplant candidates but varies widely between centers. The use of this method captures in one instrument multiple domains of patient status, including mood disturbances and reduced HRQoL.

Linear and nonlinear optical properties of Si nanocrystals in SiO2 deposited by plasma-enhanced chemical-vapor deposition

Linear and nonlinear optical properties of silicon suboxide SiOx films deposited by plasma-enhanced chemical-vapor deposition have been studied for different Si excesses up to 24¿at.¿%. The layers have been fully characterized with respect to their atomic composition and the structure of the Si precipitates. Linear refractive index and extinction coefficient have been determined in the whole visible range, enabling to estimate the optical bandgap as a function of the Si nanocrystal size. Nonlinear optical properties have been evaluated by the z-scan technique for two different excitations: at 0.80¿eV in the nanosecond regime and at 1.50¿eV in the femtosecond regime. Under nanosecond excitation conditions, the nonlinear process is ruled by thermal effects, showing large values of both nonlinear refractive index (n2 ~ ¿10¿8¿cm2/W) and nonlinear absorption coefficient (ß ~ 10¿6¿cm/W). Under femtosecond excitation conditions, a smaller nonlinear refractive index is found (n2 ~ 10¿12¿cm2/W), typical of nonlinearities arising from electronic response. The contribution per nanocrystal to the electronic third-order nonlinear susceptibility increases as the size of the Si nanoparticles is reduced, due to the appearance of electronic transitions between discrete levels induced by quantum confinement.

Shot noise in linear macroscopic resistors

We report on direct experimental evidence of shot noise in a linear macroscopic resistor. The origin of the shot noise comes from the fluctuation of the total number of charge carriers inside the resistor associated with their diffusive motion under the condition that the dielectric relaxation time becomes longer than the dynamic transit time. The present results show that neither potential barriers nor the absence of inelastic scattering are necessary to observe shot noise in electronic devices.

A theoretical and practical study on linear reforms of dual taxes

[cat] En aquest treball extenem les reformes lineals introduïdes per Pfähler (1984) al cas d’impostos duals. Estudiem l’efecte relatiu que els retalls lineals duals d’un impost dual tenen sobre la distribució de la desigualtat -es pot fer un estudi simètric per al cas d’augments d’impostos-. Tambe introduïm mesures del grau de progressivitat d’impostos duals i mostrem que estan connectades amb el criteri de dominació de Lorenz. Addicionalment, estudiem l’elasticitat de la càrrega fiscal de cadascuna de les reformes proposades. Finalment, gràcies a un model de microsimulació i una gran base de dades que conté informació sobre l’IRPF espanyol de l’any 2004, 1) comparem l’efecte que diferents reformes tindrien sobre l’impost dual espanyol i 2) estudiem quina redistribució de la riquesa va suposar la reforma dual de l’IRPF (Llei ’35/2006’) respecte l’anterior impost.

Linear least squares estimation of the first order moving average parameter

We propose an iterative procedure to minimize the sum of squares function which avoids the nonlinear nature of estimating the first order moving average parameter and provides a closed form of the estimator. The asymptotic properties of the method are discussed and the consistency of the linear least squares estimator is proved for the invertible case. We perform various Monte Carlo experiments in order to compare the sample properties of the linear least squares estimator with its nonlinear counterpart for the conditional and unconditional cases. Some examples are also discussed

Systematic trends in self-consistent calculations of linear quantum wires

Systematic trends in the properties of a linear split-gate heterojunction are studied by solving iteratively the Poisson and Schrödinger equations for different gate potentials and temperatures. A two-dimensional approximation is presented that is much simpler in the numerical implementation and that accurately reproduces all significant trends. In deriving this approximation, we provide a rigorous and quantitative basis for the formulation of models that assumes a two-dimensional character for the electron gas at the junction.

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.

Linear relation between deuteron matter radius and the scattering length

We explain the empirical linear relations between the triplet scattering length, or the asymptotic normalization constant, and the deuteron matter radius using the effective range expansion in a manner similar to a recent paper by Bhaduri et al. We emphasize the corrections due to the finite force range and to shape dependence. The discrepancy between the experimental values and the empirical line shows the need for a larger value of the wound extension, a parameter which we introduce here. Short-distance nonlocality of the n-p interaction is a plausible explanation for the discrepancy.