Re-Annotator: Annotation Pipeline for Microarray Probe Sequences.

Microarray technologies are established approaches for high throughput gene expression, methylation and genotyping analysis. An accurate mapping of the array probes is essential to generate reliable biological findings. However, manufacturers of the microarray platforms typically provide incomplete and outdated annotation tables, which often rely on older genome and transcriptome versions that differ substantially from up-to-date sequence databases. Here, we present the Re-Annotator, a re-annotation pipeline for microarray probe sequences. It is primarily designed for gene expression microarrays but can also be adapted to other types of microarrays. The Re-Annotator uses a custom-built mRNA reference database to identify the positions of gene expression array probe sequences. We applied Re-Annotator to the Illumina Human-HT12 v4 microarray platform and found that about one quarter (25%) of the probes differed from the manufacturer's annotation. In further computational experiments on experimental gene expression data, we compared Re-Annotator to another probe re-annotation tool, ReMOAT, and found that Re-Annotator provided an improved re-annotation of microarray probes. A thorough re-annotation of probe information is crucial to any microarray analysis. The Re-Annotator pipeline is freely available at http://sourceforge.net/projects/reannotator along with re-annotated files for Illumina microarrays HumanHT-12 v3/v4 and MouseRef-8 v2

Re-Annotator: Annotation Pipeline for Microarray Probe Sequences

Microarray technologies are established approaches for high throughput gene expression, methylation and genotyping analysis. An accurate mapping of the array probes is essential to generate reliable biological findings. However, manufacturers of the microarray platforms typically provide incomplete and outdated annotation tables, which often rely on older genome and transcriptome versions that differ substantially from up-to-date sequence databases. Here, we present the Re-Annotator, a re-annotation pipeline for microarray probe sequences. It is primarily designed for gene expression microarrays but can also be adapted to other types of microarrays. The Re-Annotator uses a custom-built mRNA reference database to identify the positions of gene expression array probe sequences. We applied Re-Annotator to the Illumina Human-HT12 v4 microarray platform and found that about one quarter (25%) of the probes differed from the manufacturer's annotation. In further computational experiments on experimental gene expression data, we compared Re-Annotator to another probe re-annotation tool, ReMOAT, and found that Re-Annotator provided an improved re-annotation of microarray probes. A thorough re-annotation of probe information is crucial to any microarray analysis. The Re-Annotator pipeline is freely available at http://sourceforge.net/projects/reannotator along with re-annotated files for Illumina microarrays HumanHT-12 v3/v4 and MouseRef-8 v2

Frauen als Akteurinnen in Friedensprozessen: Begleitstudie zum Werkstattgespräch "Frauen und bewaffnete Konflikte" anlässlich des 10. Jahrestages der UN-Resolution 1325; Veranstaltung des Bundesministeriums für Familie, Senioren, Frauen und Jugend am 20.10.2010 in der Bundesakademie für Sicherheitspolitik Berlin

Die am 31. Oktober 2000 verabschiedete UN - Sicherheitsratsresolution 1325 zu „Frauen, Frieden und Sicherheit“ hat dazu beigetragen, dass das Bewusstsein für die Bedeutung einer Genderperspektive in Friedensprozessen gewachsen ist und anerkannt wird, dass Frauen in anderer Weise als Männer von Konflikten betroffen sind. Gender in bewaffneten Konflikten wurde durch SCR 1325 zu einem der wichtigen Themen der UN und der Europäischen Union (EU), da sie als umfassende Resolution zur Rolle von Frauen in friedensschaffenden Aktivitäten dazu beitragen soll, Genderperspektiven in Friedensoperationen zu integrieren. Der vorliegende Überblick über die Umsetzung von SCR 1325 soll dazu beizutragen, die Wichtigkeit ihrer Umsetzung zu verdeutlichen.(Autorenreferat

Desarrollo del Pensamiento Crítico a través de la estrategia de Comunidad de Indagación del programa de Filosofía para Niños, en estudiantes de grado quinto de básica primaria del Instituto Pedagógico Campestre (La Calera).

Desarrollo del Pensamiento Crítico a través de la estrategia de Comunidad de Indagación del programa de Filosofía para Niños, en estudiantes de grado quinto de básica primaria del Instituto Pedagógico Campestre (La Calera).Este trabajo es un estudio exploratorio correlacional el cual busca mejorar el pensamiento crítico en los estudiantes de grado quinto de primaria del Instituto Pedagógico Campestre. Para ello se emplea un modelo pedagógico basado en la filosofía para niños, y a su vez, acompañado de una estrategia didáctica y concreta como lo es la comunidad de indagación, la cual se basa en las experiencias y vivencias que desarrollan los estudiantes en su diario vivir. Esta propuesta en investigación permite mejorar habilidades de pensamiento en los estudiantes, logrando que los niños piensen antes de actuar y critiquen de manera coherente los actos que realizan en su diario vivir.This work is a correlational exploratory study that seeks to improve critical thinking in the fifth grade students of ‘Instituto Pedagógico Campestre’. To this end, a pedagogical model based on philosophy for children is used, accompanied by a didactic and concrete strategy such as the research community, which is based on the experiences that students develop in their daily lives. This research proposal allows students to improve their thinking skills, making them think before acting and criticize in a coherent way the acts they perform in their daily lives

La división territorial del distrito de santa marta: ¿comunas y corregimientos o localidades?

La importancia del tema que se estudia, radica en que si en Santa Marta se implementara la organización que le corresponde según el tipo de entidad territorial denominado Distrito, ello permitiría no solo la participación directa de la comunidad samaria en la resolución de los problemas que los afectan, habida cuenta que en su respectiva localidad, se contaría con un alcalde local y una junta administradora local constituida por sus respectivos ediles, sino también la descongestión de las complexas labores en cabeza del único alcalde con que cuenta la ciudad actualmente. De este modo, se acerca la administración de la cosa pública a la ciudadanía en general, partiéndose, en consecuencia, la participación de todo el conglomerado social en las decisiones que los afectan. En ese orden de ideas, se enmarca este trabajo en los acontecimientos históricos, jurídicos, sociales, financieros y coyunturales que han mantenido a la capital del Departamento del Magdalena con una denominación como Distrito, pero con su organización político administrativa equivalente a la de un municipio

DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning

Genome-wide association studies (GWAS) identify genetic variants associated with traits or diseases. GWAS never directly link variants to regulatory mechanisms. Instead, the functional annotation of variants is typically inferred by post hoc analyses. A specific class of deep learning-based methods allows for the prediction of regulatory effects per variant on several cell type-specific chromatin features. We here describe \textquotedblDeepWAS\textquotedbl, a new approach that integrates these regulatory effect predictions of single variants into a multivariate GWAS setting. Thereby, single variants associated with a trait or disease are directly coupled to their impact on a chromatin feature in a cell type. Up to 61 regulatory SNPs, called dSNPs, were associated with multiple sclerosis (MS, 4,888 cases and 10,395 controls), major depressive disorder (MDD, 1,475 cases and 2,144 controls), and height (5,974 individuals). These variants were mainly non-coding and reached at least nominal significance in classical GWAS. The prediction accuracy was higher for DeepWAS than for classical GWAS models for 91% of the genome-wide significant, MS-specific dSNPs. DSNPs were enriched in public or cohort-matched expression and methylation quantitative trait loci and we demonstrated the potential of DeepWAS to generate testable functional hypotheses based on genotype data alone. DeepWAS is available at https://github.com/cellmapslab/DeepWAS

Dissecting the Association Between Inflammation, Metabolic Dysregulation, and Specific Depressive Symptoms: A Genetic Correlation and 2-Sample Mendelian Randomization Study.

IMPORTANCE: Observational studies highlight associations of C-reactive protein (CRP), a general marker of inflammation, and interleukin 6 (IL-6), a cytokine-stimulating CRP production, with individual depressive symptoms. However, it is unclear whether inflammatory activity is associated with individual depressive symptoms and to what extent metabolic dysregulation underlies the reported associations. OBJECTIVE: To explore the genetic overlap and associations between inflammatory activity, metabolic dysregulation, and individual depressive symptoms. GWAS DATA SOURCES: Genome-wide association study (GWAS) summary data of European individuals, including the following: CRP levels (204 402 individuals); 9 individual depressive symptoms (3 of which did not differentiate between underlying diametrically opposite symptoms [eg, insomnia and hypersomnia]) as measured with the Patient Health Questionnaire 9 (up to 117 907 individuals); summary statistics for major depression, including and excluding UK Biobank participants, resulting in sample sizes of 500 199 and up to 230 214 individuals, respectively; insomnia (up to 386 533 individuals); body mass index (BMI) (up to 322 154 individuals); and height (up to 253 280 individuals). DESIGN: In this genetic correlation and 2-sample mendelian randomization (MR) study, linkage disequilibrium score (LDSC) regression was applied to infer single-nucleotide variant-based heritability and genetic correlation estimates. Two-sample MR tested potential causal associations of genetic variants associated with CRP levels, IL-6 signaling, and BMI with depressive symptoms. The study dates were November 2019 to April 2020. RESULTS: Based on large GWAS data sources, genetic correlation analyses revealed consistent false discovery rate (FDR)-controlled associations (genetic correlation range, 0.152-0.362; FDR P = .006 to P < .001) between CRP levels and depressive symptoms that were similar in size to genetic correlations of BMI with depressive symptoms. Two-sample MR analyses suggested that genetic upregulation of IL-6 signaling was associated with suicidality (estimate [SE], 0.035 [0.010]; FDR plus Bonferroni correction P = .01), a finding that remained stable across statistical models and sensitivity analyses using alternative instrument selection strategies. Mendelian randomization analyses did not consistently show associations of higher CRP levels or IL-6 signaling with other depressive symptoms, but higher BMI was associated with anhedonia, tiredness, changes in appetite, and feelings of inadequacy. CONCLUSIONS AND RELEVANCE: This study reports coheritability between CRP levels and individual depressive symptoms, which may result from the potentially causal association of metabolic dysregulation with anhedonia, tiredness, changes in appetite, and feelings of inadequacy. The study also found that IL-6 signaling is associated with suicidality. These findings may have clinical implications, highlighting the potential of anti-inflammatory approaches, especially IL-6 blockade, as a putative strategy for suicide prevention.Wellcome Trust (grant code: 201486/Z/16/Z