64 research outputs found
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When formal institutions impede entrepreneurship: how and why refugees establish new ventures in the Dadaab refugee camps
For this paper we investigated refugee entrepreneurship in the Dadaab
refugee camps, Kenya, a place where humanitarian aid practices and
domestic legislation impede entrepreneurship, yet hundreds of new ventures
have been established by refugees. The analysis finds that refugee
camp entrepreneurs erode formal institutions, recombine conducive
aspects of both formal and informal institutions, and exploit the advantages
of institutional misalignment. We explain how entrepreneurs strategically
maintain rather than overcome institutional misalignment for venture creation.
Second, we show how self-determination, rather than mere subsistence
or necessity, is an important yet often overlooked motivator for
entrepreneurship in low and lower middle-income contexts
Organizing refugee camps: 'respected space' and 'listening posts'
We examine an organizational form that has received little attention despite its social significance – the refugee camp. From an in-depth case study of the Dadaab refugee camp in Kenya we explain how these organizations maintain social stability even though refugees live for decades in them and are deprived of the freedom to move or work outside the camp’s boundaries. Our analysis finds that refugee camps are characterized by a parallel organizational structure in which the institutional worlds of (primarily Western) camp officials and (in our case, primarily Somali) refugees coexist. Mutual dependence between camp officials and refugees enables the use of a respected space of reciprocal tolerance and minimal intrusion, and a listening post that is perceived as a legitimate communication arrangement and that acts as a safety valve. These complementary mechanisms provide the means by which to allay the otherwise high potential of severe discontent
Accurate reconstruction of insertion-deletion histories by statistical phylogenetics
The Multiple Sequence Alignment (MSA) is a computational abstraction that
represents a partial summary either of indel history, or of structural
similarity. Taking the former view (indel history), it is possible to use
formal automata theory to generalize the phylogenetic likelihood framework for
finite substitution models (Dayhoff's probability matrices and Felsenstein's
pruning algorithm) to arbitrary-length sequences. In this paper, we report
results of a simulation-based benchmark of several methods for reconstruction
of indel history. The methods tested include a relatively new algorithm for
statistical marginalization of MSAs that sums over a stochastically-sampled
ensemble of the most probable evolutionary histories. For mammalian
evolutionary parameters on several different trees, the single most likely
history sampled by our algorithm appears less biased than histories
reconstructed by other MSA methods. The algorithm can also be used for
alignment-free inference, where the MSA is explicitly summed out of the
analysis. As an illustration of our method, we discuss reconstruction of the
evolutionary histories of human protein-coding genes.Comment: 28 pages, 15 figures. arXiv admin note: text overlap with
arXiv:1103.434
PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment
<p>Abstract</p> <p>Background</p> <p>The Monte Carlo simulation of sequence evolution is routinely used to assess the performance of phylogenetic inference methods and sequence alignment algorithms. Progress in the field of molecular evolution fuels the need for more realistic and hence more complex simulations, adapted to particular situations, yet current software makes unreasonable assumptions such as homogeneous substitution dynamics or a uniform distribution of indels across the simulated sequences. This calls for an extensible simulation framework written in a high-level functional language, offering new functionality and making it easy to incorporate further complexity.</p> <p>Results</p> <p><monospace>PhyloSim</monospace> is an extensible framework for the Monte Carlo simulation of sequence evolution, written in R, using the Gillespie algorithm to integrate the actions of many concurrent processes such as substitutions, insertions and deletions. Uniquely among sequence simulation tools, <monospace>PhyloSim</monospace> can simulate arbitrarily complex patterns of rate variation and multiple indel processes, and allows for the incorporation of selective constraints on indel events. User-defined complex patterns of mutation and selection can be easily integrated into simulations, allowing <monospace>PhyloSim</monospace> to be adapted to specific needs.</p> <p>Conclusions</p> <p>Close integration with <monospace>R</monospace> and the wide range of features implemented offer unmatched flexibility, making it possible to simulate sequence evolution under a wide range of realistic settings. We believe that <monospace>PhyloSim</monospace> will be useful to future studies involving simulated alignments.</p
Clonal chromosomal mosaicism and loss of chromosome Y in elderly men increase vulnerability for SARS-CoV-2
The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) had an estimated overall case fatality ratio of 1.38% (pre-vaccination), being 53% higher in males and increasing exponentially with age. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, we found 133 cases (1.42%) with detectable clonal mosaicism for chromosome alterations (mCA) and 226 males (5.08%) with acquired loss of chromosome Y (LOY). Individuals with clonal mosaic events (mCA and/or LOY) showed a 54% increase in the risk of COVID-19 lethality. LOY is associated with transcriptomic biomarkers of immune dysfunction, pro-coagulation activity and cardiovascular risk. Interferon-induced genes involved in the initial immune response to SARS-CoV-2 are also down-regulated in LOY. Thus, mCA and LOY underlie at least part of the sex-biased severity and mortality of COVID-19 in aging patients. Given its potential therapeutic and prognostic relevance, evaluation of clonal mosaicism should be implemented as biomarker of COVID-19 severity in elderly people. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, individuals with clonal mosaic events (clonal mosaicism for chromosome alterations and/or loss of chromosome Y) showed an increased risk of COVID-19 lethality
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