Estimating error models for whole genome sequencing using mixtures of Dirichlet-multinomial distributions

Motivation: Accurate identification of genotypes is an essential part of the analysis of genomic data, including in identification of sequence polymorphisms, linking mutations with disease and determining mutation rates. Biological and technical processes that adversely affect genotyping include copy-number-variation, paralogous sequences, library preparation, sequencing error and reference-mapping biases, among others. Results: We modeled the read depth for all data as a mixture of Dirichlet-multinomial distributions, resulting in significant improvements over previously used models. In most cases the best model was comprised of two distributions. The major-component distribution is similar to a binomial distribution with low error and low reference bias. The minor-component distribution is overdispersed with higher error and reference bias. We also found that sites fitting the minor component are enriched for copy number variants and low complexity regions, which can produce erroneous genotype calls. By removing sites that do not fit the major component, we can improve the accuracy of genotype calls. Availability and Implementation: Methods and data files are available at https://github.com/ CartwrightLab/WuEtAl2017/ (doi:10.5281/zenodo.256858). Contact: [email protected] Supplementary information: Supplementary data is available at Bioinformatics online

Diversity and dissonance: a narrative exploration of adolescent transcultural identity construction within the International School

This qualitative research study explores how the analysis of identity narratives written by transcultural individuals who attended international high schools can strengthen researchers\u27 and international school teachers\u27 understanding of how to better assist this population in negotiating their multicultural identities. This study examines a sample of eight narratives written by adult transculturals now in their twenties who attended high school at the International Christian School of Vienna (ICSV). The analysis of the identity narratives also aims to shed light on how the power structures present in the international school affect transculturals ongoing identity construction and perception of their agency and place on the global stage. The resulting research paper considers the effects that experience had on shaping their current understanding of their cultural identity. It also explores how the interplay of identity, power dynamics and rhetorical/discursive practices within the international school can aid adolescent transculturals in better understanding the construction, negotiation, and ongoing transformation of their multi-faceted identities. This project draws upon the intersecting arenas of intercultural communication identity theories, critical rhetorical/discourse analysis, and the rhetorical impact of narrative

Symposium: Gender, Health and the Constitution: More than Merely Two-legged Wombs : Lessons on Metaphor and Body Politics from Atwood\u27s \u3ci\u3eThe Handmaiden\u27s Tale\u3c/i\u3e (1985)

This essay explores the dehumanizing potential of metaphors used to describe women’s reproductive biology through literary analysis of Margaret Atwood’s canonical feminist novel The Handmaid’s Tale (1985). Attending to the rhetoric that both justifies and contests ritualized rape and forced surrogacy in Atwood’s novel, this essay begins by interrogating the ubiquitous cultural and biomedical metaphors that reduce women and pregnant people to their bodies’ reproductive potential. The first section draws from scholarship in medical anthropology, medical rhetoric, and literary studies to illuminate how gendered stereotypes pervade biomedical, cultural, and legal representations of reproduction, reifying the conflation of women and people who can become pregnant with their reproductive biology. The essay’s second section applies an ecofeminist lens to The Handmaid’s Tale to consider the consequences of this metaphorization amid a simultaneously environmental and public health crisis. The novel renders biomedical metaphors of women’s bodies as reproductive machines literal by legally classifying fertile women as “national resources” within a patriarchal capitalist economy, a dehumanizing abstraction that permits the State first to commodify, then to commandeer and equitably distribute fertile women in the name of public health and ecological crisis management. When considered from this angle, The Handmaid’s Tale inspires closer attention to figurative language’s real-world impact on health law and policy, particularly in moments of environmental catastrophe and political unrest

EDUCATION Policies Prohibiting Bullying: Amend Policies prohibiting Bullying Behavior; Make Changes Relating to Local School Board Policies Regarding Bullying in Student Codes of Conduct; Change the Definition of Bullying Behavior; Provide that Policies Relating to Bullying Behavior Apply to Students in Kindergarten Through Grade 12; Require Training on Bullying Behavior for Certain School System Personnel; Provide that Local School Systems Provide Information to the Department of Education on the Number and Disposition of Bullying Incidents Reported; Repeal Conflicting Laws, and for Other Purposes

Policies Prohibiting Bullying: Amend Policies prohibiting Bullying Behavior; Make Changes Relating to Local School Board Policies Regarding Bullying in Student Codes of Conduct; Change the Definition of Bullying Behavior; Provide that Policies Relating to Bullying Behavior Apply to Students in Kindergarten Through Grade 12; Require Training on Bullying Behavior for Certain School System Personnel; Provide that Local School Systems Provide Information to the Department of Education on the Number and Disposition of Bullying Incidents Reported; Repeal Conflicting Laws, and for Other Purpose

\u27Clean Energy\u27 At What Cost?

Ecuador was ‘refounded’ at the turn of the 21st century, with the articulation of progressive and inclusive ideals in a new Constitution. Social movements and leftist intellectuals in Ecuador have expressed that president Rafael Correa has failed to uphold the 2008 Constitution’s goals and values. President Correa and his Alianza PAIS government have utilized the rhetoric of the revolutionary ideals articulated in the Constitution, but in practice, they have continued to implement the status quo Western development model, and a large part of their development strategy involves ‘neo-extractive’ activities. Hydroelectric energy production is contributing to the ‘neo-extractive’ development model in Ecuador, and its implementation has often violated Constitutional rights. This thesis is an analysis of natural resource extraction in Ecuador and its social repercussions, with a focus on hydroelectric energy production. It is shown that the hydroelectric industry in Ecuador is not as “clean,” sustainable, or non-extractive as it is purported to be, through a case study of the San José del Tambo hydroelectric project and the exploration of an international support for hydroelectric extractivism, the United Nations Clean Development Mechanism, and its misleading framing of extractive projects as “sustainable development.” Social movements in Ecuador are acting to reverse the perversion of their originally revolutionary ideals, and to implement a post-extractive model informed by those revolutionary ideals

Sediment properties, biota and local habitat structure explain variation in the erodibility of coastal sediments

Sediment resuspension is a frequent phenomenon in coastal areas and a key driver for many ecosystem functions. Sediment resuspension is often linked to biological and anthropogenic activities, which in combination with hydrodynamic forcing initiate sediment erosion and resuspension, if the erosion threshold (tau(c)) is exceeded. Despite its importance to ecosystem functions very few studies have provided measurements on natural assemblages for subtidal sediments. The aim of this study was to determinate key environmental variables regulating sediment resuspension potential across a sedimentary gradient in a subtidal coastal environment. In order to explore this, we sampled 16 sites encompassing a wide variety in environmental variables (e.g., grain size distribution, macrofaunal communities, vegetation) in the Gulf of Finland, Baltic Sea. A core-based erosion device (EROMES) was used to determine sediment resuspension potential measures of erosion threshold, erosion rate (ER), and erosion constant (m(e)). Based on abiotic and biotic properties sampled, sediments diverged into two distinct groups; cohesive (muddy) and noncohesive (sandy) sediments. Results showed that abiotic sediment properties explained 38-53% and 15-36% of the total variation in resuspension potential measures in muddy and sandy sediments, respectively. In cumulative models, biota accounted for 12-26% and 6-24% to the total variation in muddy and sandy sediments, respectively. Sediment erodibility and resuspension potential of natural sediments is highly variable from local habitats to a larger seascape scale. Our results underline the importance of biota to resuspension potential measures in spatially variable environments.Peer reviewe

THEY “EYEBALLED” THE RIVER AND BUILT THE DAM: LESSONS FROM THE HIDROTAMBO DAM FLOOD DISASTER TO GUIDE IMPROVEMENTS IN ENVIRONMENTAL IMPACT ASSESSMENT LAW IN ECUADOR

Ecuador is a trailblazer in human and environmental rights. The country enshrined in its 2008 Constitution the human right to water and the right to live in a healthy and ecologically balanced environment. It was also the first country in the world to recognize nature as a subject of rights in and of itself. However, the Ecuadorian legislature has failed to fully recognize these rights in the country’s civil law codes. This article explores the shortcomings of Ecuadorian law on Environmental Impact Assessments (EIAs) and proposes modifications to better ensure the protection of international and constitutional human and nature’s rights through the EIA process. Part I describes the environmental review process for the San José del Tambo hydroelectric project and the dam’s socio-environmental impacts in the Dulcepamba watershed over the past two decades. Part II examines international and domestic law governing environmental review and identifies gaps in the Ecuadorian EIA law that hinder the protection of human and nature’s rights. Part III recommends several legal reforms to the Ecuadorian EIA law, “CODA,” which will allow for protection of human and nature’s rights, thereby reducing socio-environmental harm from hydroelectric and other projects in marginalized rural communities. In a period of Ecuadorian history marked by feverish attempts to develop and extract the country’s natural resources, the need for enhanced EIA standards is urgent and essential to realize the rights of marginalized rural communities and of nature

EDUCATION Policies Prohibiting Bullying: Amend Policies prohibiting Bullying Behavior; Make Changes Relating to Local School Board Policies Regarding Bullying in Student Codes of Conduct; Change the Definition of Bullying Behavior; Provide that Policies Relating to Bullying Behavior Apply to Students in Kindergarten Through Grade 12; Require Training on Bullying Behavior for Certain School System Personnel; Provide that Local School Systems Provide Information to the Department of Education on the Number and Disposition of Bullying Incidents Reported; Repeal Conflicting Laws, and for Other Purposes

Policies Prohibiting Bullying: Amend Policies prohibiting Bullying Behavior; Make Changes Relating to Local School Board Policies Regarding Bullying in Student Codes of Conduct; Change the Definition of Bullying Behavior; Provide that Policies Relating to Bullying Behavior Apply to Students in Kindergarten Through Grade 12; Require Training on Bullying Behavior for Certain School System Personnel; Provide that Local School Systems Provide Information to the Department of Education on the Number and Disposition of Bullying Incidents Reported; Repeal Conflicting Laws, and for Other Purpose