On the application of estimation of distribution algorithms to multi-marker tagging SNP selection

This paper presents an algorithm for the automatic selection of a minimal subset of tagging single nucleotide polymorphisms (SNPs) using an estimation of distribution algorithm (EDA). The EDA stochastically searches the constrained space of possible feasible solutions and takes advantage of the underlying topological structure defined by the SNP correlations to model the problem interactions. The algorithm is evaluated across the HapMap reference panel data sets. The introduced algorithm is effective for the identification of minimal multi-marker SNP sets, which considerably reduce the dimension of the tagging SNP set in comparison with single-marker sets. New reduced tagging sets are obtained for all the HapMap SNP regions considered. We also show that the information extracted from the interaction graph representing the correlations between the SNPs can help to improve the efficiency of the optimization algorithm. keywords: SNPs, tagging SNP selection, multi-marker selection, estimation of distribution algorithms, HapMap

Respuesta de la soya (Glycine max) a la deficiencia de fosfato

El fósforo es uno de los principales nutrimentos requeridos por las plantas, pero también es uno de los elementos menos disponible en los suelos. La forma de fósforo asimilada por las plantas es como iones ortofosfato H2PO4 - y HPO4 2- (Pi), pero su concentración rara vez excede 10 µM; por tanto, las plantas están expuestas a una deficiencia continua de Pi. No se encontraron reportes que describan los cambios que ocurren en plantas de soya (Glycine max) ante la deficiencia de Pi. Por ello, este trabajo tuvo como objetivo evaluar la respuesta de la soya ante la deficiencia de Pi. En la variedad de soya Tapachula 86 en un medio con Pi o diferentes deficiencias de Pi, no cambió el crecimiento de la raíz, pero se detuvo el crecimiento del vástago. La actividad de las fosfatasas ácidas secretadas en plantas desarrolladas en ausencia de fosfato (-Pi) se incrementó casi diez veces, mientras que en los otros tratamientos de deficiencia sólo aumentó entre cuatro y cinco veces. La cantidad de Pi fue mayor en los tratamientos de ácido fítico y fosfato de aluminio, lo que sugiere que las plantas de soya también producen fitasas y ácidos orgánicos que ayudan a movilizar el Pi. Sin embargo, estas adaptaciones no fueron suficientes para promover el crecimiento normal de las plantas

On the application of estimation of distribution algorithms to multi-marker tagging SNP selection

This paper presents an algorithm for the automatic selection of a minimal subset of tagging single nucleotide polymorphisms (SNPs) using an estimation of distribution algorithm (EDA). The EDA stochastically searches the constrained space of possible feasible solutions and takes advantage of the underlying topological structure defined by the SNP correlations to model the problem interactions. The algorithm is evaluated across the HapMap reference panel data sets. The introduced algorithm is effective for the identification of minimal multi-marker SNP sets, which considerably reduce the dimension of the tagging SNP set in comparison with single-marker sets. New reduced tagging sets are obtained for all the HapMap SNP regions considered. We also show that the information extracted from the interaction graph representing the correlations between the SNPs can help to improve the efficiency of the optimization algorithm. keywords: SNPs, tagging SNP selection, multi-marker selection, estimation of distribution algorithms, HapMap

ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues.

High-throughput RNA-sequencing (RNA-seq) technologies provide an unprecedented opportunity to explore the individual transcriptome. Unmapped reads are a large and often overlooked output of standard RNA-seq analyses. Here, we present Read Origin Protocol (ROP), a tool for discovering the source of all reads originating from complex RNA molecules. We apply ROP to samples across 2630 individuals from 54 diverse human tissues. Our approach can account for 99.9% of 1 trillion reads of various read length. Additionally, we use ROP to investigate the functional mechanisms underlying connections between the immune system, microbiome, and disease. ROP is freely available at https://github.com/smangul1/rop/wiki

Additional file 1: of ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues

Supplementary methods. (PDF 789 kb

Additional file 3: of ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues

Table S3. The list of the 2000 SRA RNA-seq samples used in the analysis. SRA samples were randomly selected from the Sequence Read Archive (SRA). (CSV 22 kb

Additional file 2: of ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues

Table S1. The effect of altering order of ROP step on the classification accuracy. Table S2. Concordance of targeted TCRB-Seq and ROP based on three TCGA samples from kidney renal clear cell carcinoma (KIRC). Table S4. RNA-seq datasets overview. Table S5. Genomic profile of unmapped reads reported for each dataset (S1, S2, S3). Table S6. Relative genomic abundance of microbial taxa at different levels of taxonomic classification after removal of reads with human origin (average over all samples of three tissues, performed for in-house RNA-Seqdata). Table S7. Genomic profile of unmapped reads across two SRA RNA-seq samples using ROP v1.0.8. Percentage for each category is calculated as a fraction from the total number of reads. (PDF 100 kb

100 Cartas para Paulo Freire de quienes pretendemos Enseñar

Realizar un texto colectivo como “100 Cartas para Paule Freire de quienes pretendemos Enseñar”, es un desafío al reunir el aprehender desde el sentido profesional de la educación y con el espíritu de transformación, desde la educación como un espacio endógeno de revolución y exógeno a las comunidades y sociedades, en busca de un sentido de identidad. Hoy desde una crítica decolonial, antirracista, feminista y ecologica en la construcción de un sentido real que busque enfrentar el sistema hegemónico y destructivo que se ha impuesto con explotación, sangre y libertades de nuestro pueblo

SARS-CoV-2 vaccination modelling for safe surgery to save lives: data from an international prospective cohort study

Background Preoperative SARS-CoV-2 vaccination could support safer elective surgery. Vaccine numbers are limited so this study aimed to inform their prioritization by modelling. Methods The primary outcome was the number needed to vaccinate (NNV) to prevent one COVID-19-related death in 1 year. NNVs were based on postoperative SARS-CoV-2 rates and mortality in an international cohort study (surgical patients), and community SARS-CoV-2 incidence and case fatality data (general population). NNV estimates were stratified by age (18-49, 50-69, 70 or more years) and type of surgery. Best- and worst-case scenarios were used to describe uncertainty. Results NNVs were more favourable in surgical patients than the general population. The most favourable NNVs were in patients aged 70 years or more needing cancer surgery (351; best case 196, worst case 816) or non-cancer surgery (733; best case 407, worst case 1664). Both exceeded the NNV in the general population (1840; best case 1196, worst case 3066). NNVs for surgical patients remained favourable at a range of SARS-CoV-2 incidence rates in sensitivity analysis modelling. Globally, prioritizing preoperative vaccination of patients needing elective surgery ahead of the general population could prevent an additional 58 687 (best case 115 007, worst case 20 177) COVID-19-related deaths in 1 year. Conclusion As global roll out of SARS-CoV-2 vaccination proceeds, patients needing elective surgery should be prioritized ahead of the general population.The aim of this study was to inform vaccination prioritization by modelling the impact of vaccination on elective inpatient surgery. The study found that patients aged at least 70 years needing elective surgery should be prioritized alongside other high-risk groups during early vaccination programmes. Once vaccines are rolled out to younger populations, prioritizing surgical patients is advantageous