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Search Results: 1 - 10 of 141578 matches for " Amanda K. Lukens "
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Islamization as Part of Globalization: Some Southeast Asian Examples
Ronald Lukens-Bull,Amanda Pandich,John P. Woods
Journal of International and Global Studies , 2012,
Abstract: In both popular and academic imagination, Islamization and globalization are the opposing processes, representing ”the clash of civilizations” (Huntington, 1993,1996). In Southeast Asia, specifically, globalization is imagined as something distinctly Western and, hence, inherently at odds with Islam, while Islam, meanwhile, is seen as the natural enemy of globalization. This paper instead sees Muslims as active participants in globalization. Further, it explores the concept of “Muslim globalization” to suggest that Islam has long been a globalizing force alongside Western-based capitalism and other forces. It explores this general model by using examples primarily from Southeast Asia.
Human cerebral malaria and Plasmodium falciparum genotypes in Malawi
Danny A Milner, Jimmy Vareta, Clarissa Valim, Jacqui Montgomery, Rachel F Daniels, Sarah K Volkman, Daniel E Neafsey, Daniel J Park, Stephen F Schaffner, Nira C Mahesh, Kayla G Barnes, David M Rosen, Amanda K Lukens, Daria Van Tyne, Roger C Wiegand, Pardis C Sabeti, Karl B Seydel, Simon J Glover, Steve Kamiza, Malcolm E Molyneux, Terrie E Taylor, Dyann F Wirth
Malaria Journal , 2012, DOI: 10.1186/1475-2875-11-35
Abstract: The 24 SNP assay was used to determine predominant genotypes in blood and tissues from autopsy and clinical patients with cerebral malaria.Single genotypes were shared between the peripheral blood, the brain, and other tissues of cerebral malaria patients, while malaria-infected patients who died of non-malarial causes had mixed genetic signatures in tissues examined. Children with retinopathy-positive cerebral malaria had significantly less complex infections than those without retinopathy (OR = 3.7, 95% CI [1.51-9.10]).The complexity of infections significantly decreased over the malaria season in retinopathy-positive patients compared to retinopathy-negative patients.Cerebral malaria patients harbour a single or small set of predominant parasites; patients with incidental parasitaemia sustain infections involving diverse genotypes. Limited diversity in the peripheral blood of cerebral malaria patients and correlation with tissues supports peripheral blood samples as appropriate for genome-wide association studies of parasite determinants of pathogenicity.The global Plasmodium falciparum parasite population is highly diverse, especially in antigens transported to the erythrocyte surface where they can interact with the human immune system [1,2]. The major question being addressed, "Are there parasite genetic determinants of cerebral malaria and can we identify them?" requires careful step-wise considerations. Background multiplicity of Plasmodium falciparum infection in both asymptomatic and symptomatic individuals is high in Malawi due to intense transmission. Several sequencing approaches using material directly from tissue or peripheral blood have been useful for SNP discovery at the population level. Understanding sequencing data from mixed infections however has been difficult to interpret and quantify for an individual parasite genotype within a single patient. Previously, attempts to evaluate individual var gene transcripts from patients by sequencing showe
Genetic Surveillance Detects Both Clonal and Epidemic Transmission of Malaria following Enhanced Intervention in Senegal
Rachel Daniels, Hsiao-Han Chang, Papa Diogoye Séne, Danny C. Park, Daniel E. Neafsey, Stephen F. Schaffner, Elizabeth J. Hamilton, Amanda K. Lukens, Daria Van Tyne, Souleymane Mboup, Pardis C. Sabeti, Daouda Ndiaye, Dyann F. Wirth, Daniel L. Hartl, Sarah K. Volkman
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0060780
Abstract: Using parasite genotyping tools, we screened patients with mild uncomplicated malaria seeking treatment at a clinic in Thiès, Senegal, from 2006 to 2011. We identified a growing frequency of infections caused by genetically identical parasite strains, coincident with increased deployment of malaria control interventions and decreased malaria deaths. Parasite genotypes in some cases persisted clonally across dry seasons. The increase in frequency of genetically identical parasite strains corresponded with decrease in the probability of multiple infections. Further, these observations support evidence of both clonal and epidemic population structures. These data provide the first evidence of a temporal correlation between the appearance of identical parasite types and increased malaria control efforts in Africa, which here included distribution of insecticide treated nets (ITNs), use of rapid diagnostic tests (RDTs) for malaria detection, and deployment of artemisinin combination therapy (ACT). Our results imply that genetic surveillance can be used to evaluate the effectiveness of disease control strategies and assist a rational global malaria eradication campaign.
Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence
Daniel E Neafsey, Stephen F Schaffner, Sarah K Volkman, Daniel Park, Philip Montgomery, Danny A Milner, Amanda Lukens, David Rosen, Rachel Daniels, Nathan Houde, Joseph F Cortese, Erin Tyndall, Casey Gates, Nicole Stange-Thomann, Ousmane Sarr, Daouda Ndiaye, Omar Ndir, Soulyemane Mboup, Marcelo U Ferreira, Sandra Moraes, Aditya P Dash, Chetan E Chitnis, Roger C Wiegand, Daniel L Hartl, Bruce W Birren, Eric S Lander, Pardis C Sabeti, Dyann F Wirth
Genome Biology , 2008, DOI: 10.1186/gb-2008-9-12-r171
Abstract: Using an Affymetrix 3,000 SNP assay array, we found roughly half the assays (1,638) yielded high quality, 100% accurate genotyping calls for both major and minor SNP alleles. Genotype data from 76 global isolates confirm significant genetic differentiation among continental populations and varying levels of SNP diversity and linkage disequilibrium according to geographic location and local epidemiological factors. We further discovered that nonsynonymous and silent (synonymous or noncoding) SNPs differ with respect to within-population diversity, inter-population differentiation, and the degree to which allele frequencies are correlated between populations.The distinct population profile of nonsynonymous variants indicates that natural selection has a significant influence on genomic diversity in P. falciparum, and that many of these changes may reflect functional variants deserving of follow-up study. Our analysis demonstrates the potential for new high-throughput genotyping technologies to enhance studies of population structure, natural selection, and ultimately enable genome-wide association studies in P. falciparum to find genes underlying key phenotypic traits.Plasmodium falciparum is the most virulent species of malaria and the primary cause of malaria-related mortality across the globe. The success of P. falciparum as a pathogen derives in part from its high levels of genetic diversity [1-4], diversity that endows the parasite with the evolutionary agility to rapidly develop resistance to a series of drugs developed for its control [5], to thwart the development of effective vaccines [6], and to efficiently evade immune responses [7-9]. Large-scale genotyping of P. falciparum will improve understanding of these capabilities, and will permit wide-ranging investigation of the parasite's biology, including population structure and history, outcrossing and recombination frequency and instances of natural selection, and inform effective intervention strategies. A
Identification and Functional Validation of the Novel Antimalarial Resistance Locus PF10_0355 in Plasmodium falciparum
Daria Van Tyne equal contributor,Daniel J. Park equal contributor,Stephen F. Schaffner equal contributor,Daniel E. Neafsey equal contributor,Elaine Angelino equal contributor,Joseph F. Cortese,Kayla G. Barnes,David M. Rosen,Amanda K. Lukens,Rachel F. Daniels,Danny A. Milner Jr.,Charles A. Johnson,Ilya Shlyakhter,Sharon R. Grossman,Justin S. Becker,Daniel Yamins,Elinor K. Karlsson,Daouda Ndiaye,Ousmane Sarr,Souleymane Mboup,Christian Happi,Nicholas A. Furlotte,Eleazar Eskin,Hyun Min Kang,Daniel L. Hartl,Bruce W. Birren,Roger C. Wiegand,Eric S. Lander,Dyann F. Wirth ？,Sarah K. Volkman ？,Pardis C. Sabeti ？
PLOS Genetics , 2011, DOI: 10.1371/journal.pgen.1001383
Abstract: The Plasmodium falciparum parasite's ability to adapt to environmental pressures, such as the human immune system and antimalarial drugs, makes malaria an enduring burden to public health. Understanding the genetic basis of these adaptations is critical to intervening successfully against malaria. To that end, we created a high-density genotyping array that assays over 17,000 single nucleotide polymorphisms (~1 SNP/kb), and applied it to 57 culture-adapted parasites from three continents. We characterized genome-wide genetic diversity within and between populations and identified numerous loci with signals of natural selection, suggesting their role in recent adaptation. In addition, we performed a genome-wide association study (GWAS), searching for loci correlated with resistance to thirteen antimalarials; we detected both known and novel resistance loci, including a new halofantrine resistance locus, PF10_0355. Through functional testing we demonstrated that PF10_0355 overexpression decreases sensitivity to halofantrine, mefloquine, and lumefantrine, but not to structurally unrelated antimalarials, and that increased gene copy number mediates resistance. Our GWAS and follow-on functional validation demonstrate the potential of genome-wide studies to elucidate functionally important loci in the malaria parasite genome.
Single-Electron Traps: A Quantitative Comparison of Theory and Experiment
K. A. Matsuoka,K. K. Likharev,P. Dresselhaus,L. Ji,S. Han,J. Lukens
Physics , 1996, DOI: 10.1063/1.364278
Abstract: We have carried out a coordinated experimental and theoretical study of single-electron traps based on submicron aluminum islands and aluminum oxide tunnel junctions. The results of geometrical modeling using a modified version of MIT's FastCap were used as input data for the general-purpose single-electron circuit simulator MOSES. The analysis indicates reasonable quantitative agreement between theory and experiment for those trap characteristics which are not affected by random offset charges. The observed differences between theory and experiment (ranging from a few to fifty percent) can be readily explained by the uncertainty in the exact geometry of the experimental nanostructures.
Universal distribution of transparencies in highly conductive Nb/AlO$_x$/Nb junctions
Y. Naveh,Vijay Patel,D. V. Averin,K. K. Likharev,J. E. Lukens
Physics , 2000, DOI: 10.1103/PhysRevLett.85.5404
Abstract: We report the observation of the universal distribution of transparencies, predicted by Schep and Bauer [Phys. Rev. Lett. {\bf 78}, 3015 (1997)] for dirty sharp interfaces, in uniform Nb/AlO$_x$/Nb junctions with high specific conductance ($10^8$ Ohm$^{-1}$cm$^{-2}$). Experiments used the BCS density of states in superconducting niobium for transparency distribution probing. Experimental results for both the dc $I-V$ curves at magnetic-field-suppressed supercurrent and the Josephson critical current in zero magnetic field coincide remarkably well with calculations based on the multimode theory of multiple Andreev reflections and the Schep-Bauer distribution.
Detection of a Schroedinger's Cat State in an rf-SQUID
Jonathan R. Friedman,Vijay Patel,W. Chen,S. K. Tolpygo,J. E. Lukens
Physics , 2000,
Abstract: We present experimental evidence for a coherent superposition of macroscopically distinct flux states in an rf-SQUID. When the external flux Phi_x applied to the SQUID is near 1/2 of a flux quantum Phi_0, the SQUID has two nearly degenerate configurations: the zero- and one-fluxoid states, corresponding to a few microamperes of current flowing clockwise or counterclockwise, respectively. The system is modeled as a particle in a double-well potential where each well represents a distinct fluxoid state (0 or 1) and the barrier between the wells can be controlled in situ. For low damping and a sufficiently high barrier, the system has a set of quantized energy levels localized in each well. The relative energies of these levels can be varied with Phi_x. External microwaves are used to pump the system from the well-localized ground state of one well into one of a pair of excited states nearer the top of the barrier. We spectroscopically map out the energy of these levels in the neighborhood of their degeneracy point by varying Phi_x as well as the barrier height. We find a splitting between the two states at this point, when both states are below the classical energy barrier, indicating that the system attains a coherent superposition of flux basis states that are macroscopically distinct in that their mean fluxes differ by more than 1/4 Phi_0 and their currents differ by several microamperes.
Generalizations Of The Cartan And Iwasawa Decompositions For SL$_2(k)$
Amanda K. Sutherland
Mathematics , 2014,
Abstract: The Cartan and Iwasawa decompositions of real reductive Lie groups play a fundamental role in the representation theory of the groups and their corresponding symmetric spaces. These decompositions are defined by an involution with a compact fixed-point group, called a Cartan involution. For an arbitrary involution, one can consider similar decompositions. We offer a generalization of the Cartan and Iwasawa decompositions for algebraic groups defined over an arbitrary field $k$ and a general involution.
Aluminum Oxide Layers as Possible Components for Layered Tunnel Barriers
E. Cimpoiasu,S. K. Tolpygo,X. Liu,N. Simonian,J. E. Lukens,R. F. Klie,Y. Zhu,K. K. Likharev
Physics , 2004, DOI: 10.1063/1.1763229
Abstract: We have studied transport properties of Nb/Al/AlOx/Nb tunnel junctions with ultrathin aluminum oxide layers formed by (i) thermal oxidation and (ii) plasma oxidation, before and after rapid thermal post-annealing of the completed structures at temperatures up to 550 deg C. Post-annealing at temperatures above 300 deg C results in a significant decrease of the tunneling conductance of thermally-grown barriers, while plasma-grown barriers start to change only at annealing temperatures above 450 deg C. Fitting the experimental I-V curves of the junctions using the results of the microscopic theory of direct tunneling shows that the annealing of thermally-grown oxides at temperatures above 300 deg C results in a substantial increase of their average tunnel barriers height, from ~1.8 eV to ~2.45 eV, versus the practically unchanged height of ~2.0 eV for plasma-grown layers. This difference, together with high endurance of annealed barriers under electric stress (breakdown field above 10 MV/cm) may enable all-AlOx and SiO2/AlOx layered "crested" barriers for advanced floating-gate memory applications.
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