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Search Results: 1 - 10 of 461886 matches for " Jed A. Duersch "
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True BLAS-3 Performance QRCP using Random Sampling
Jed A. Duersch,Ming Gu
Mathematics , 2015,
Abstract: The dominant contribution to communication complexity in factorizing a matrix using QR with column pivoting is due to column-norm updates that are required to process pivot decisions. We use randomized sampling to approximate this process which dramatically reduces communication in column selection. We also introduce a sample update formula to reduce the cost of sampling trailing matrices. Using our column selection mechanism we observe results that are comparable to those obtained from the QRCP algorithm, but with performance near unpivoted QR. We also demonstrate strong parallel scalability on shared memory multiple core systems using an implementation in Fortran with OpenMP. This work immediately extends to produce low-rank truncated approximations of large matrices. We propose a truncated QR factorization with column pivoting that avoids trailing matrix updates which are used in current implementations of BLAS-3 QR and QRCP. Provided the truncation rank is small, avoiding trailing matrix updates reduces approximation time by nearly half. By using these techniques and employing a variation on Stewart's QLP algorithm, we develop an approximate truncated SVD that runs nearly as fast as truncated QR.
The Sociology of Knowledge, Citizenship and the Purification of Politics  [PDF]
Jed Donoghue, Bob White
Sociology Mind (SM) , 2013, DOI: 10.4236/sm.2013.31003
Abstract:

We reinterpret citizenship using Mannheim’s classical sociology of knowledge and through a more recent variant on them in Latour’s argument that “we have never been modern” (Latour, 1991). On that basis, we understand citizenship as a recursive effect of disputes over belonging and membership (Isin, 2002), where those disputes entail the three forms of political rationality or “thought styles” which Mannheim and Latour variously suggested: the linearly individual rationality of liberalism; dialectically collective socialism; and culturally collective conservatism. Marshall defines citizenship as a “status bestowed on those who are full members of a community” (Marshall, 1973). He presents an image of evolutionary progress, from civil to political rights and finally to the social form, in Britain. We argue that Marshall was entangled in evolutionary and teleological images of citizenship. We reinterpret citizenship using Mannheim’s classical sociology of knowledge. We suggest that sociologies of knowledge allow a re-reading of “citizenship” that can accommodate conceptual difficulties. Mannheim called into question the “progress” implied or stated in theories of “stages”. He stressed instead the continuing interaction between different ways of knowing social reality, or between what he called “thought styles”. We apply Mannheim to “citizenship” in order to lift two “purifications”, so that humanity is both natural and political.

Recent advances of novel targeted therapy in non-small cell lung cancer
Jed A Katzel, Michael P Fanucchi, Zujun Li
Journal of Hematology & Oncology , 2009, DOI: 10.1186/1756-8722-2-2
Abstract: Lung cancer is the leading cause of cancer deaths for both men and women. It accounts for an estimated 15% of all new cancer cases diagnosed in the United States in 2008, and is responsible for an estimated 29% of all cancer deaths [1]. World-wide, the impact of lung cancer is enormous, with 1.35 million cases and approximately 1.18 million deaths [2]. Non-small cell lung cancer (NSCLC), which accounts for approximately 85% of all cases of lung cancer, will cause an estimated 161,840 deaths in the United States in 2008 [1]. Approximately 70% of patients with NSCLC have inoperable locally advanced tumors or metastatic disease at the time of diagnosis.In the past two decades the median survival has improved disappointingly little. In 1975 the 5-year relative survival rate for all patients with lung cancer was 13%. In the period from 1996 to 2003 the 5-year survival rate increased to only 16% despite the incorporation of modern chemotherapy regimens and great advances in supportive care [1]. Yet, the future for lung cancer is bright. Chemotherapy improves survival when administered postoperatively to patients with stage II and IIIA NSCLC and when administered with radiation in patients with unresectable stage III disease. The median survival for patients with advanced disease in particular has increased with use of improved chemotherapy, targeted therapies and better supportive care. New insights into the pathogenesis of lung cancer are helping to identify more targets for novel therapies. Some of these exciting new agents will be highlighted here.Where normal cells require growth factors in their culture medium in order to grow, cancer cells have a greatly reduced dependence on growth factors for their growth and survival. The reason for this inconsistency was uncovered in 1984 when the sequence of the EGF receptor was identified and found to be similar to the erbB oncogene. This oncogene was originally discovered in the genome of the avian erythroblastosis virus, a t
Uncovering the components of the Francisella tularensis virulence stealth strategy
Bradley D. Jones,Jed A. Rasmussen,Joshua R. Fletcher
Frontiers in Cellular and Infection Microbiology , 2014, DOI: 10.3389/fcimb.2014.00032
Abstract: Over the last decade, studies on the virulence of the highly pathogenic intracellular bacterial pathogen Francisella tularensis have increased dramatically. The organism produces an inert LPS, a capsule, escapes the phagosome to grow in the cytosol (FPI genes mediate phagosomal escape) of a variety of host cell types that include epithelial, endothelial, dendritic, macrophage, and neutrophil. This review focuses on the work that has identified and characterized individual virulence factors of this organism and we hope to highlight how these factors collectively function to produce the pathogenic strategy of this pathogen. In addition, several recent studies have been published characterizing F. tularensis mutants that induce host immune responses not observed in wild type F. tularensis strains that can induce protection against challenge with virulent F. tularensis. As more detailed studies with attenuated strains are performed, it will be possible to see how host models develop acquired immunity to Francisella. Collectively, detailed insights into the mechanisms of virulence of this pathogen are emerging that will allow the design of anti-infective strategies.
Computation of a combined spherical-elastic and viscous-half-space earth model for ice sheet simulation
Ed Bueler,Craig S. Lingle,Jed A. Kallen-Brown
Physics , 2006, DOI: 10.3189/172756407782871567
Abstract: This report starts by describing the continuum model used by Lingle & Clark (1985) to approximate the deformation of the earth under changing ice sheet and ocean loads. That source considers a single ice stream, but we apply their underlying model to continent-scale ice sheet simulation. Their model combines Farrell's (1972) elastic spherical earth with a viscous half-space overlain by an elastic plate lithosphere. The latter half-space model is derivable from calculations by Cathles (1975). For the elastic spherical earth we use Farrell's tabulated Green's function, as do Lingle & Clark. For the half-space model, however, we propose and implement a significantly faster numerical strategy, a spectral collocation method (Trefethen 2000) based directly on the Fast Fourier Transform. To verify this method we compare to an integral formula for a disc load. To compare earth models we build an accumulation history from a growing similarity solution from (Bueler, et al.~2005) and and simulate the coupled (ice flow)-(earth deformation) system. In the case of simple isostasy the exact solution to this system is known. We demonstrate that the magnitudes of numerical errors made in approximating the ice-earth system are significantly smaller than pairwise differences between several earth models, namely, simple isostasy, the current standard model used in ice sheet simulation (Greve 2001, Hagdorn 2003, Zweck & Huybrechts 2005), and the Lingle & Clark model. Therefore further efforts to validate different earth models used in ice sheet simulations are, not surprisingly, worthwhile.
Teaching civic engagement: Evaluating an integrative service-learning program
Jed Metzger
Gateways : International Journal of Community Research & Engagement , 2012,
Abstract: The demands on successfully teaching intervention skills in macro (community) environments are numerous and extend beyond the confines of any one academic discipline. In particular, when considering community, the compounding of the multiple factors of social economics, diversity, social policy, history and political agendas requires an integrative approach. This mixed-methods retrospective article analyses the use of service-learning in an advanced Master of Social Work community practice course. Special attention is given to the construction of academic and community experience that facilitates learning integration and understanding of the ways in which factors compound on community wellbeing. Specifically this project involved students in efforts constructed to address violence directed by and against inner-city youth in a mid-sized northeastern city in the United States that is beset with gang violence and has led its state in per capita murders for four of the past five years. Recommendations and lessons learned presented in this article are directed at exploring a construction of service-learning that could address integrative learning in community intervention courses. Keywords: Service-learning, teaching, macro practice, violence
Rectangular tileability and complementary tileability are undecidable
Jed Yang
Computer Science , 2012,
Abstract: Does a given a set of polyominoes tile some rectangle? We show that this problem is undecidable. In a different direction, we also consider tiling a cofinite subset of the plane. The tileability is undecidable for many variants of this problem. However, we present an algorithm for testing whether the complement of a finite region is tileable by a set of rectangles.
Some NP-complete edge packing and partitioning problems in planar graphs
Jed Yang
Computer Science , 2014,
Abstract: Graph packing and partitioning problems have been studied in many contexts, including from the algorithmic complexity perspective. Consider the packing problem of determining whether a graph contains a spanning tree and a cycle that do not share edges. Bern\'ath and Kir\'aly proved that this decision problem is NP-complete and asked if the same result holds when restricting to planar graphs. Similarly, they showed that the packing problem with a spanning tree and a path between two distinguished vertices is NP-complete. They also established the NP-completeness of the partitioning problem of determining whether the edge set of a graph can be partitioned into a spanning tree and a (not-necessarily spanning) tree. We prove that all three problems remain NP-complete even when restricted to planar graphs.
Accurate Genome Relative Abundance Estimation Based on Shotgun Metagenomic Reads
Li C. Xia, Jacob A. Cram, Ting Chen, Jed A. Fuhrman, Fengzhu Sun
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0027992
Abstract: Accurate estimation of microbial community composition based on metagenomic sequencing data is fundamental for subsequent metagenomics analysis. Prevalent estimation methods are mainly based on directly summarizing alignment results or its variants; often result in biased and/or unstable estimates. We have developed a unified probabilistic framework (named GRAMMy) by explicitly modeling read assignment ambiguities, genome size biases and read distributions along the genomes. Maximum likelihood method is employed to compute Genome Relative Abundance of microbial communities using the Mixture Model theory (GRAMMy). GRAMMy has been demonstrated to give estimates that are accurate and robust across both simulated and real read benchmark datasets. We applied GRAMMy to a collection of 34 metagenomic read sets from four metagenomics projects and identified 99 frequent species (minimally 0.5% abundant in at least 50% of the data- sets) in the human gut samples. Our results show substantial improvements over previous studies, such as adjusting the over-estimated abundance for Bacteroides species for human gut samples, by providing a new reference-based strategy for metagenomic sample comparisons. GRAMMy can be used flexibly with many read assignment tools (mapping, alignment or composition-based) even with low-sensitivity mapping results from huge short-read datasets. It will be increasingly useful as an accurate and robust tool for abundance estimation with the growing size of read sets and the expanding database of reference genomes.
Recent advances of novel targeted therapy for squamous cell carcinoma of the head and neck
Jed A. Katzel,Michael P. Fanucchi,William A. Cook,Zujun Li
Oncology Reviews , 2011, DOI: 10.4081/89
Abstract: Targeted therapies have proven beneficial for patients suffering from a number of different malignancies, including cancers of the head and neck. Cetuximab, a monoclonal antibody targeting the epidermal growth factor receptor has shown benefit in combination with radiation for untreated patients or as a single agent for patients with platinum resistant disease. Cetuximab is the only targeted agent currently approved by the Federal Drug Administration for the treatment of head and neck cancer. A number of other agents have shown promising initial results including intracellular tyrosine kinase inhibitors, agents targeting vascular endothelial growth factor receptor, as well as other classes of novel therapies. Some of the data supporting the use of targeted therapy, including agents not yet approved in head and neck cancer, will be presented in this review. As our understanding of the cancer cell signaling pathways and novel targeted agents increases, the potential for treatment with reduced toxicity and improved clinical outcomes will become a reality.
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