Going South: Tracing Race and Region in the Post-Emancipation Black Atlantic

The demise of American slavery in 1865 put black Americans in motion to an unprecedented degree. Freed slaves and their descendants migrated from the plantations in the rural South to destinations around the globe. Travelling in a variety of new roles – as missionaries, journalists, agronomists, scientists, athletes, performers, entrepreneurs and political activists – African Americans gained international visibility, inspiring other oppressed populations in the colonial world to struggle for their liberation

A measurement of unpolarized cross sections and polarized cross section differences of deeply virtual compton scattering on the proton at Jefferson Laboratory using Clas

Cette thèse a pour sujet l'étude de la réaction de la Diffusion Compton Profondément Virtuelle (DVCS) sur le proton e + p -> e' + p' + gamma (DVCS). Cette réaction est mesurée en analysant l'expérience e1-dvcs2 qui a eu lieu dans le Hall B du Jefferson Laboratory avec CLAS. La prise de données s'est déroulée du 22 octobre 2008 jusqu'au 23 janvier 2009. Cette analyse a pour but la détermination des sections efficaces non polarisées et les différences de sections efficaces polarisées du DVCS, dans divers bins en xB, Q^2, t et phi. Cette analyse compare les sections efficaces avec plusieurs mesures existantes du DVCS: une analyse parallèle de e1-dvcs2 et une analyse de e1-dvcs1. En factorisant l'élément de matrice qui correspond au DVCS en deux parties, calculables en QCD perturbative et non perturbative, on peut accéder aux Distributions de Partons Généralisées (GPDs) du proton, et ainsi obtenir une vue en 3D des distributions spatiales et en impulsion des quarks et des gluons dans le proton.This thesis focuses on the Deeply Virtual Compton Scattering (DVCS) reaction e + p -> e' + p' + gamma (DVCS). The reaction is measured using the e1-dvcs2 experiment run at Jefferson Laboratory in Hall B using CLAS. The experiment took place from 22 October, 2008 to 23 January, 2009, and experiment run time of 90 days. This analysis focuses on the determination of the DVCS cross section in bins of xB, Q^2, t and phi, and makes a comparison with already existing and parallel analyses of DVCS. By factorizing the cross section of the reaction into perturbative and non-perturbative parts, we may relate the cross section of this reaction to Generalized Parton Distributions (GPDs) for the proton, and in doing so, provide better insight as to the distributions of quarks and gluons within it, including spacial distribution and contributions of angular momentum.PARIS11-SCD-Bib. électronique (914719901) / SudocSudocFranceF

Family reunion via error correction: an efficient analysis of duplex sequencing data

Background Duplex sequencing is the most accurate approach for identification of sequence variants present at very low frequencies. Its power comes from pooling together multiple descendants of both strands of original DNA molecules, which allows distinguishing true nucleotide substitutions from PCR amplification and sequencing artifacts. This strategy comes at a cost—sequencing the same molecule multiple times increases dynamic range but significantly diminishes coverage, making whole genome duplex sequencing prohibitively expensive. Furthermore, every duplex experiment produces a substantial proportion of singleton reads that cannot be used in the analysis and are thrown away. Results In this paper we demonstrate that a significant fraction of these reads contains PCR or sequencing errors within duplex tags. Correction of such errors allows “reuniting” these reads with their respective families increasing the output of the method and making it more cost effective. Conclusions We combine an error correction strategy with a number of algorithmic improvements in a new version of the duplex analysis software, Du Novo 2.0. It is written in Python, C, AWK, and Bash. It is open source and readily available through Galaxy, Bioconda, and Github: https://github.com/galaxyproject/dunovo

Dissemination of scientific software with Galaxy ToolShed

The proliferation of web-based integrative analysis frameworks has enabled users to perform complex analyses directly through the web. Unfortunately, it also revoked the freedom to easily select the most appropriate tools. To address this, we have developed Galaxy ToolShed

Colonial Archives and the Arts of Governance

Anthropologists engaged inpost-colonial studies are increasingly adoptingan historical perspective and using archives. Yet their archival activity tends to remain morean extractive than an ethnographic one.Documents are thus still invokedpiecemeal to confirm the colonial invention ofcertain practices or to underscore culturalclaims, silent. Yet such mining of the content of government commissions,reports, and other archival sources rarely paysattention to their peculiar placement and form .Scholars need to move fromarchive-as-source to archive-as-subject. Thisarticle, using document production in the DutchEast Indies as an illustration, argues thatscholars should view archives not as sites ofknowledge retrieval, but of knowledgeproduction, as monuments of states as well assites of state ethnography. This requires asustained engagement with archives as culturalagents of ``fact'' production, of taxonomies inthe making, and of state authority. What constitutes thearchive, what form it takes, and what systemsof classification and epistemology signal atspecific times are (and reflect) critical featuresof colonial politics and state power. The archive was the supreme technology of thelate nineteenth-century imperial state, arepository of codified beliefs that clustered(and bore witness to) connections betweensecrecy, the law, and power.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/41825/1/10502_2004_Article_5096461.pd

From West Indies to East Indies: Archipelagic Interchanges

In this paper, I work to rethink notions of comparison and area studies by viewing my ethnographic work in Indonesia through the lens of theories developed by anthropologists working in the Caribbean region. In bringing 'East Indies' and 'West Indies' together in this way, I explore the possibility of reconfigured networks of citation, collaboration and interchange that might help anthropology respond in new ways to contemporary dynamics of globalisation. © 2006 Copyright Discipline of Anthropology and Sociology, The University of Western Australia

Du Novo pipeline for processing duplex sequencing data

A tool for processing data produced by the duplex sequencing method developed by Schmitt et al. 2012 (doi:10.1073/pnas.1208715109). The main repository of this tool can be found at https://github.com/galaxyproject/dunovo This is release v0.4, which was used in the 2016 publication in Genome Biology

Animal contact and paediatric acute febrile illness in Greater Accra Region, Ghana

To examine the association between animal contact (primarily dogs and cats) and non-malarial fever, as well as with secondary symptoms of headache, nausea, vomiting, and cough, in 687 children in Greater Accra Region, Ghana. Cross-sectional study of acute febrile illness among children aged 1-15 years old between October 2016 and August 2017. Ledzokuku-Krowor Municipal Assembly (LEKMA) Hospital, Teshie, Greater Accra Region. The study included children with acute fever, defined as a measured temperature of greater than 37.5°C, occurring less than seven days before the hospital visit, and afebrile children as controls. Measured fever, self-reported fever, and secondary symptoms, each adjusting for patient household characteristics. Animal contact was neither associated with measured fever (OR = 1.04, 95% CI 0.73-1.49) nor with self-reported fever (OR = 0.97, 95% CI 0.68-1.39). Animal contact was associated with headache (OR = 3.26, 95% CI 2.23-4.77, < .01) and nausea (OR = 3.05, 95% CI 1.99-4.68, < .01), but not with vomiting or cough. Additional models that used alternate inclusion criteria to define non-malarial fever yielded similar results. Several bacterial zoonoses that could plausibly have been transmitted by dogs and cats were diagnosed in the study population. These findings suggest the need for future studies to evaluate animal contact as a risk factor for bacterial zoonoses that may serve as an etiological driver of acute febrile illness. no external funding

Additional file 3: Figure S3. of Streamlined analysis of duplex sequencing data with Du Novo

Here there are two distinct types of mitochondrial genomes: carrying A and G. Because the population of genomes is enriched via PCR, heteroduplex formation takes place, skewing frequency estimates performed using DCSs. If this PCR-derived DNA is now used as the starting material for a duplex sequencing experiment, the heteroduplex molecules will manifest themselves as having an N base at this site (because Du Novo interprets disagreements as Ns during consensus generation). So, DCSs produced from this dataset will have A, G, and N at the polymorphic site. Yet, SSCSs will only have A and G. Thus, SSCS will give a more accurate estimate of the allele frequency at this site in this particular case. (JPEG 196 kb

Additional file 1: Figure S1. of Streamlined analysis of duplex sequencing data with Du Novo

Receiver operating characteristic (ROC) for Du Novo detecting 21 artificial heteroplasmies in a simulated duplex sequencing experiment. Shown are true positives versus false positives detected using different minor allele frequency thresholds, in steps of 0.00001 (the depth of coverage threshold was held constant at 10,000×). At the bottom left, no heteroplasmies at all are detected at a threshold MAF of 0.00016. The first variant is detected at a MAF of 0.00015, with no false positives. Continuing upward, no false positives are detected while increasing true positives are found until the upper left corner at a MAF of 0.00008, with 20 true positives and no false positives. Then, increasing false positives are found with no gain in true positives until the last true single-nucleotide variant (SNV) is found at a MAF of 0.00004, with 46 false positives also observed at that threshold. (PNG 23 kb