Penalized likelihood for sparse contingency tables with an application to full-length cDNA libraries

<p>Abstract</p> <p>Background</p> <p>The joint analysis of several categorical variables is a common task in many areas of biology, and is becoming central to systems biology investigations whose goal is to identify potentially complex interaction among variables belonging to a network. Interactions of arbitrary complexity are traditionally modeled in statistics by log-linear models. It is challenging to extend these to the high dimensional and potentially sparse data arising in computational biology. An important example, which provides the motivation for this article, is the analysis of so-called full-length cDNA libraries of alternatively spliced genes, where we investigate relationships among the presence of various exons in transcript species.</p> <p>Results</p> <p>We develop methods to perform model selection and parameter estimation in log-linear models for the analysis of sparse contingency tables, to study the interaction of two or more factors. Maximum Likelihood estimation of log-linear model coefficients might not be appropriate because of the presence of zeros in the table's cells, and new methods are required. We propose a computationally efficient ℓ₁-penalization approach extending the Lasso algorithm to this context, and compare it to other procedures in a simulation study. We then illustrate these algorithms on contingency tables arising from full-length cDNA libraries.</p> <p>Conclusion</p> <p>We propose regularization methods that can be used successfully to detect complex interaction patterns among categorical variables in a broad range of biological problems involving categorical variables.</p

Evaluation of European-based polygenic risk score for breast cancer in Ashkenazi Jewish women in Israel

To date, most BC GWASs have been performed Background Polygenic risk score (PRS), calculated in individuals of European (EUR) ancestry, and based on genome-wide association studies (GWASs), the generalisation of EUR-based PRS to other can improve breast cancer (BC) risk assessment. populations is a major challenge. In this study, we examined the performance of EUR-based BC PRS models in Ashkenazi Jewish (AJ) women. Methods We generated PRSs based on data on EUR women from the Breast Cancer Association Consortium (BCAC). We tested the performance of the PRSs in a cohort of 2161 AJ women from Israel (1437 cases and 724 controls) from BCAC (BCAC cohort from Israel (BCAC-IL)). In addition, we tested the performance of these EUR-based BC PRSs, as well as the established 313-SNP EUR BC PRS, in an independent cohort of 181 AJ women from Hadassah Medical Center (HMC) in Israel. Results In the BCAC-IL cohort, the highest OR per 1 SD was 1.56 (±0.09). The OR for AJ women at the top 10% of the PRS distribution compared with the middle quintile was 2.10 (±0.24). In the HMC cohort, the OR per 1 SD of the EUR-based PRS that performed best in the BCAC-IL cohort was 1.58±0.27. The OR per 1 SD of the commonly used 313-SNP BC PRS was 1.64 (±0.28). Conclusions Extant EUR GWAS data can be used for generating PRSs that identify AJ women with markedly elevated risk of BC and therefore hold promise for improving BC risk assessment in AJ women.</p

A Latin American Perspective to Agricultural Ethics

The mixture of political, social, cultural and economic environments in Latin America, together with the enormous diversity in climates, natural habitats and biological resources the continent offers, make the ethical assessment of agricultural policies extremely difficult. Yet the experience gained while addressing the contemporary challenges the region faces, such as rapid urbanization, loss of culinary and crop diversity, extreme inequality, disappearing farming styles, water and land grabs, malnutrition and the restoration of the rule of law and social peace, can be of great value to other regions in similar latitudes, development processes and social problems. This chapter will provide a brief overview of these challenges from the perspective of a continent that is exposed to the consequences of extreme inequality in multiple dimensions and conclude by arguing for the need to have a continuous South-South dialogue on the challenges of establishing socially and environmentally sustainable food systems

Planck 2013 results. VI. High Frequency Instrument data processing

We describe the processing of the 531 billion raw data samples from the High Frequency Instrument (HFI), which we performed to produce six temperature maps from the first 473 days of Planck-HFI survey data. These maps provide an accurate rendition of the sky emission at 100, 143, 217, 353, 545, and 857GHz with an angular resolution ranging from 9.́7 to 4.́6. The detector noise per (effective) beam solid angle is respectively, 10, 6 , 12, and 39 μK in the four lowest HFI frequency channels (100−353GHz) and 13 and 14 kJy sr-1 in the 545 and 857 GHz channels. Relative to the 143 GHz channel, these two high frequency channels are calibrated to within 5% and the 353 GHz channel to the percent level. The 100 and 217 GHz channels, which together with the 143 GHz channel determine the high-multipole part of the CMB power spectrum (50 <ℓ < 2500), are calibrated relative to 143 GHz to better than 0.2%

Euclid Near Infrared Spectrometer and Photometer instrument concept and first test results obtained for different breadboards models at the end of phase C

The Euclid mission objective is to understand why the expansion of the Universe is accelerating through by mapping the geometry of the dark Universe by investigating the distance-redshift relationship and tracing the evolution of cosmic structures. The Euclid project is part of ESA's Cosmic Vision program with its launch planned for 2020 (ref [1]). The NISP (Near Infrared Spectrometer and Photometer) is one of the two Euclid instruments and is operating in the near-IR spectral region (900- 2000nm) as a photometer and spectrometer. The instrument is composed of: - a cold (135K) optomechanical subsystem consisting of a Silicon carbide structure, an optical assembly (corrector and camera lens), a filter wheel mechanism, a grism wheel mechanism, a calibration unit and a thermal control system - a detection subsystem based on a mosaic of 16 HAWAII2RG cooled to 95K with their front-end readout electronic cooled to 140K, integrated on a mechanical focal plane structure made with molybdenum and aluminum. The detection subsystem is mounted on the optomechanical subsystem structure - a warm electronic subsystem (280K) composed of a data processing / detector control unit and of an instrument control unit that interfaces with the spacecraft via a 1553 bus for command and control and via Spacewire links for science data This presentation describes the architecture of the instrument at the end of the phase C (Detailed Design Review), the expected performance, the technological key challenges and preliminary test results obtained for different NISP subsystem breadboards and for the NISP Structural and Thermal model (STM)

¿Es factible el manejo integrado de plagas en el contexto de la producción campesina de los cultivos no tradicionales de agroexportación?

16 p.La producción de cultivos no tradicionales de exportación ha sido promovida en Centroamérica tanto para captar más divisas como para ofrecer al campesinado una alternativa de mayores ingresos. Sin embargo, hoy día el campesino de la región enfrenta serias dificultades para la supervivencia de su modo de producción. Mientras el ajuste estructural ha hecho difícil la producción de alimentos para el consumo doméstico, el ámbito de los no tradicionales es un ambiente extremadamente competitivo, donde muchas veces el que triunfa es el más grande y mejor conectado. Factores como el acceso a la tierra, el crédito, el mercado y la tecnología trabajan en contra del pequeño productor. En tales circunstancias, el MIP fácilmente se convierte en una economía de escala más, que favorece a los productores grandes y las empresas extranjeras. Nuestro reto es evitar que el MIP funcione así

Rural Social Movements and Agroecology: Context, Theory, and Process

Rural social movements have in recent years adopted agroecology and diversified farming systems as part of their discourse and practice. Here, we situate this phenomenon in the evolving context of rural spaces that are increasingly disputed between agribusiness, together with other corporate land-grabbers, and peasants and their organizations and movements. We use the theoretical frameworks of disputed material and immaterial territories and of re-peasantization to explain the increased emphasis on agroecology by movements in this context. We provide examples from the farmer-to-farmer movement to show the advantages that social movements bring to the table in taking agroecology to scale and discuss the growing agroecology networking process in the transnational peasant and family farmer movement La Vía Campesina