Introduction: Self-Tracking, Embodied Differences, and Intersectionality

This is the final version. Available on open access from Catalyst Project via the link in this recordThis introduction to the Special Section “Self-Tracking, Embodied Differences, and the Politics and Ethics of Health” situates self-tracking technologies and practices within the contexts of neoliberalism, gendered and racialized health inequalities, and questions of social justice. It argues that intersectional STS analyses are needed to address the complex ways in which self-tracking technologies draw on, and may reinforce, colonial and racialized hierarchies, gendered histories of surveillance, and normative assumptions of ability and embodiment. The introduction outlines the four key areas of concern that the Special Section articles address: tracking mental health, tracking moving bodies, tracking reproductive health, and art interventions.Wellcome TrustArts and Humanities Research Council (AHRC

Vacancies in CuInSe(2): new insights from hybrid-functional calculations

We calculate the energetics of vacancies in CuInSe(2) using a hybrid functional (HSE06, HSE standing for Heyd, Scuseria and Ernzerhof), which gives a better description of the band gap compared to (semi)local exchange-correlation functionals. We show that, contrary to present beliefs, copper and indium vacancies induce no defect levels within the band gap and therefore cannot account for any experimentally observed levels. The selenium vacancy is responsible for only one level, namely, a deep acceptor level is an element of(0/2-). We find strong preference for V(Cu) and V(Se) over V(In) under practically all chemical conditions

Hydrogen interaction with fullerenes: From C[sub 20] to graphene

The paper presents a systematic study of the trends in the interaction of hydrogen with carbon fullerenes versus their curvature, where graphene is taken as the limit of zero curvature. The efficiency of hydrogen incapsulation in fullerenes, penetration into them, and adsorption on their surface are analyzed and discussed. The effects on magnetism are also considered; in particular, it is shown that hydrogen adsorption to some fullerenes induces magnetism to initially nonmagnetic systems. In addition, highly hydrogen-saturated fullerenes are examined and the suitability of fullerenes for hydrogen storage is discussed.Peer reviewe

Introduction: Queering Health and Biomedicine

This is the final version. Available on open access from Föreningen Lambda Nordica via the DOI in this recordJoint Committee for Nordic Research Councils in the Humanities and Social Sciences (NOS-HS

Prospective Longitudinal ctDNA Workflow Reveals Clinically Actionable Alterations in Ovarian Cancer

PURPOSE Circulating tumor DNA (ctDNA) detection is a minimally invasive technique that offers dynamic molecular snapshots of genomic alterations in cancer. Although ctDNA markers can be used for early detection of cancers or for monitoring treatment efficacy, the value of ctDNA in guiding treatment decisions in solid cancers is controversial. Here, we monitored ctDNA to detect clinically actionable alterations during treatment of high-grade serous ovarian cancer, the most common and aggressive form of epithelial ovarian cancer with a 5-year survival rate of 43%.PATIENTS AND METHODS We implemented a clinical ctDNA workflow to detect clinically actionable alterations in more than 500 cancer-related genes. We applied the workflow to a prospective cohort consisting of 78 ctDNA samples from 12 patients with high-grade serous ovarian cancer before, during, and after treatment. These longitudinal data sets were analyzed using our open-access ctDNA-tailored bioinformatics analysis pipeline and in-house Translational Oncology Knowledgebase to detect clinically actionable genomic alterations. The alterations were ranked according to the European Society for Medical Oncology scale for clinical actionability of molecular targets.RESULTS Our results show good concordance of mutations and copy number alterations in ctDNA and tumor samples, and alterations associated with clinically available drugs were detected in seven patients (58%). Treatment of one chemoresistant patient was changed on the basis of detection of ERBB2amplification, and this ctDNA-guided decision was followed by significant tumor shrinkage and complete normalization of the cancer antigen 125 tumor marker.CONCLUSION Our results demonstrate a proof of concept for using ctDNA to guide clinical decisions. Furthermore, our results show that longitudinal ctDNA samples can be used to identify poor-responding patients after first cycles of chemotherapy. We provide what we believe to be the first comprehensive, open-source ctDNA workflow for detecting clinically actionable alterations in solid cancers. (C) 2019 by American Society of Clinical Oncolog

Making the most of RNA-seq: Pre-processing sequencing data with Opossum for reliable SNP variant detection

RNA-seq (transcriptome sequencing) is primarily considered a method of gene expression analysis but it can also be used to detect DNA variants in expressed regions of the genome. However, current variant callers do not generally behave well with RNA-seq data due to reads encompassing intronic regions. We have developed a software programme called Opossum to address this problem. Opossum pre-processes RNA-seq reads prior to variant calling, and although it has been designed to work specifically with Platypus, it can be used equally well with other variant callers such as GATK HaplotypeCaller. In this work, we show that using Opossum in conjunction with either Platypus or GATK HaplotypeCaller maintains precision and improves the sensitivity for SNP detection compared to the GATK Best Practices pipeline. In addition, using it in combination with Platypus offers a substantial reduction in run times compared to the GATK pipeline so it is ideal when there are only limited time or computational resources available

Making the most of RNA-seq: Pre-processing sequencing data with Opossum for reliable SNP variant detection

RNA-seq (transcriptome sequencing) is primarily considered a method of gene expression analysis but it can also be used to detect DNA variants in expressed regions of the genome. However, current variant callers do not generally behave well with RNA-seq data due to reads encompassing intronic regions. We have developed a software programme called Opossum to address this problem. Opossum pre-processes RNA-seq reads prior to variant calling, and although it has been designed to work specifically with Platypus, it can be used equally well with other variant callers such as GATK HaplotypeCaller. In this work, we show that using Opossum in conjunction with either Platypus or GATK HaplotypeCaller maintains precision and improves the sensitivity for SNP detection compared to the GATK Best Practices pipeline. In addition, using it in combination with Platypus offers a substantial reduction in run times compared to the GATK pipeline so it is ideal when there are only limited time or computational resources available

Effect of sodium incorporation into CuInSe2 from first principles

The presence of small amounts of sodium has been shown to improve the electronic performance of Cu(In,Ga)Se-2 (CIGS) solar cells, but the origins of this effect have not yet been fully resolved. In this work, we have addressed the questions involving the role of sodium in CuInSe2 (CIS) using density-functional-theory-based calculations. We find no direct way how the creation of Na-related point defects in bulk CIS would enhance p-type conductivity. Instead, we demonstrate that Na reduces copper mass transport due to the capture of copper vacancies by Na-Cu defects. This finding provides an explanation for experimental measurements where the presence of Na has been observed to decrease copper diffusion. The suggested mechanism can also impede V-Cu-related cluster formation and lead to measurable effects on defect distribution within the material. (C) 2013 AIP Publishing LLC