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Search Results: 1 - 10 of 300010 matches for " Robin J. Ryder "
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Missing data in a stochastic Dollo model for cognate data, and its application to the dating of Proto-Indo-European
Robin J. Ryder,Geoff K. Nicholls
Statistics , 2009,
Abstract: Nicholls and Gray (2008) describe a phylogenetic model for trait data. They use their model to estimate branching times on Indo-European language trees from lexical data. Alekseyenko et al. (2008) extended the model and give applications in genetics. In this paper we extend the inference to handle data missing at random. When trait data are gathered, traits are thinned in a way that depends on both the trait and missing-data content. Nicholls and Gray (2008) treat missing records as absent traits. Hittite has 12% missing trait records. Its age is poorly predicted in their cross-validation. Our prediction is consistent with the historical record. Nicholls and Gray (2008) dropped seven languages with too much missing data. We fit all twenty four languages in the lexical data of Ringe (2002). In order to model spatial-temporal rate heterogeneity we add a catastrophe process to the model. When a language passes through a catastrophe, many traits change at the same time. We fit the full model in a Bayesian setting, via MCMC. We validate our fit using Bayes factors to test known age constraints. We reject three of thirty historically attested constraints. Our main result is a unimodel posterior distribution for the age of Proto-Indo-European centered at 8400 years BP with 95% HPD equal 7100-9800 years BP.
The Wang-Landau algorithm reaches the flat histogram criterion in finite time
Pierre E. Jacob,Robin J. Ryder
Statistics , 2011, DOI: 10.1214/12-AAP913
Abstract: The Wang-Landau algorithm aims at sampling from a probability distribution, while penalizing some regions of the state space and favoring others. It is widely used, but its convergence properties are still unknown. We show that for some variations of the algorithm, the Wang-Landau algorithm reaches the so-called flat histogram criterion in finite time, and that this criterion can be never reached for other variations. The arguments are shown in a simple context - compact spaces, density functions bounded from both sides - for the sake of clarity, and could be extended to more general contexts.
Three discussions of the paper "sequential quasi-Monte Carlo sampling", by M. Gerber and N. Chopin
Julyan Arbel,Igor Prunster,Christian P. Robert,Robin J. Ryder
Statistics , 2015, DOI: 10.1111/rssb.12104
Abstract: This is a collection of three written discussions of the paper "sequential quasi-Monte Carlo sampling" by M. Gerber and N. Chopin, following the presentation given before the Royal Statistical Society in London on December 10th, 2014.
On the geometry of border rank algorithms for n x 2 by 2 x 2 matrix multiplication
J. M. Landsberg,Nicholas Ryder
Computer Science , 2015,
Abstract: We make an in-depth study of the known border rank (i.e. approximate) algorithms for the matrix multiplication tensor encoding the multiplication of an n x 2 matrix by a 2 x 2 matrix.
Calcaneal acrometastasis from urothelial carcinoma of the ureter: a case report and literature review
Ryder JH,McGarry SV,Wang J
Clinical Interventions in Aging , 2013,
Abstract: Jonathan H Ryder,1 Sean V McGarry,2 Jue Wang1 1Division of Oncology/Hematology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA; 2Department of Orthopaedic Surgery and Rehabilitation, University of Nebraska Medical Center, Omaha, Nebraska, USA Purpose: Ureteral cancer is a rare entity. Typical symptoms are painless hematuria as well as flank pain. Bone metastasis of ureteral cancer can occur in nearby bone structures, such as the spine, pelvis, and hip bone. Distal bone metastasis, such as that in the calcaneus bone, however, is rare. Case report: An 82-year-old woman presented to the orthopedic clinic at the university hospital with a 3-month history of left heel pain. A magnetic resonance imaging (MRI) of her foot demonstrated a calcaneal lytic lesion. A biopsy of the lytic lesion showed urothelial carcinoma with squamous differentiation. A computed tomography (CT) scan of the abdomen and pelvis showed left hydronephrosis and an obstructive mass in the left ureter, at the iliac crossing. The patient received combined therapy that included local radiation, bisphosphonate, and chemotherapy, with complete resolution of her cancer-related symptoms. However, she eventually died from the progressive disease, 20 months after the initial diagnosis. Conclusion: This case highlights the rare presentation of ureter cancer with an initial presentation of foot pain, secondary to calcaneal metastasis. Multimodality therapy provides effective palliation of symptoms and improved quality of life. We also reviewed the literature and discuss the clinical benefits of multidisciplinary cancer care in elderly patients. Keywords: urothelial carcinoma, elderly, calcaneal acrometastasis, multimodality therapy, chemotherapy, radiation
Mutants and SU(3)_q invariants
H. R. Morton,H. J. Ryder
Mathematics , 1998,
Abstract: Details of quantum knot invariant calculations using a specific SU(3)_q-module are given which distinguish the Conway and Kinoshita-Teresaka pair of mutant knots. Features of Kuperberg's skein-theoretic techniques for SU(3)_q invariants in the context of mutant knots are also discussed.
Approximate Bayesian Computational methods
Jean-Michel Marin,Pierre Pudlo,Christian P. Robert,Robin Ryder
Statistics , 2011,
Abstract: Also known as likelihood-free methods, approximate Bayesian computational (ABC) methods have appeared in the past ten years as the most satisfactory approach to untractable likelihood problems, first in genetics then in a broader spectrum of applications. However, these methods suffer to some degree from calibration difficulties that make them rather volatile in their implementation and thus render them suspicious to the users of more traditional Monte Carlo methods. In this survey, we study the various improvements and extensions made to the original ABC algorithm over the recent years.
Increased Mutability of Staphylococci in Biofilms as a Consequence of Oxidative Stress
Victoria J. Ryder, Ian Chopra, Alex J. O’Neill
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0047695
Abstract: Objectives To investigate the development of mutational resistance to antibiotics in staphylococcal biofilms. Methods Mutation frequencies to resistance against mupirocin and rifampicin were determined for planktonic cultures and for biofilms generated using either a novel static biofilm model or by continuous flow. DNA microarray analysis was performed to detect differences in transcriptional profiles between planktonic and biofilm cultures. Results The mutability of biofilm cultures increased up to 60-fold and 4-fold for S. aureus and S. epidermidis, respectively, compared with planktonic cultures. Incorporation of antioxidants into S. aureus biofilms reduced mutation frequencies, indicating that increased oxidative stress underlies the heightened mutability. Transcriptional profiling of early biofilm cultures revealed up-regulation of the superoxide dismutase gene, sodA, also suggestive of enhanced oxidative stress in these cultures. The addition of catalase to biofilms of S. aureus SH1000 reduced mutation frequencies, a finding which implicated hydrogen peroxide in increased biofilm mutability. However, catalase had no effect on biofilm mutability in S. aureus UAMS-1, suggesting that there is more than one mechanism by which the mutability of staphylococci may increase during the biofilm mode of growth. Conclusion Our findings suggest that biofilms represent an enriched source of mutational resistance to antibiotics in the staphylococci.
Near-infrared line imaging of NGC 7771
J. Reunanen,J. K. Kotilainen,S. Laine,S. D. Ryder
Physics , 1999,
Abstract: We present high spatial resolution near-infrared broad-band JHK images and, for the first time, BrGamma 2.1661 micron and H_2 1-0 S(1) 2.122 micron emission line images of the circumnuclear star forming ring (major axis diameter 7" = 2 kpc) in the starburst galaxy NGC 7771. These data are used to investigate the morphology and extinction of the starburst ring and to study its star forming properties and history by comparing the observed quantities with an evolutionary population synthesis model. The clumpy morphology of NGC 7771 varies strongly with wavelength, due to the combination of extinction (for which we derive an average value of A_V = 2.8), emission from hot dust and red supergiants, and several stellar generations in the ring. Also, the ellipticity and the position angle of the ring depend on the wavelength. The starburst ring in NGC 7771 exhibits small BrGamma equivalent widths. Assuming a constant star formation model with M_u = 100 M_sun results in very long lifetimes of the star forming regions (up to 1 Gyr), in disagreement with the clumpy near-infrared morphology and the observed radio spectral index of NGC 7771. This situation is only slightly remedied by assuming a reduced upper mass cutoff (M_u = 30 M_sun), resulting in ages between 8 and 180 Myr. We prefer an instantaneous star formation model with M_u = 100 M_sun which can explain the derived BrGamma equivalent widths if a single starburst occurred 6-7 Myr ago. The main excitation mechanism of the molecular gas, based on the observed S(1)/BrGamma ratio, appears to be excitation by UV radiation from hot young stars. We derive M = 1900 M_sun for the mass of the excited H_2.
Near-infrared line imaging of the circumnuclear starburst rings in the active galaxies NGC 1097 and NGC 6574
J. K. Kotilainen,J. Reunanen,S. Laine,S. D. Ryder
Physics , 1999, DOI: 10.1023/A:1017054609723
Abstract: We present high spatial resolution near-infrared broad-band JHK and Br_gamma 2.166 micron and H_2 1-0 S(1) 2.121 micron emission line images of the circumnuclear star formation rings in the LINER/Seyfert 1 galaxy NGC 1097 and the Seyfert 2 galaxy NGC 6574. We investigate the morphology, extinction, and the star formation properties and history of the rings, by comparing the observed properties with an evolutionary population synthesis model. The clumpy morphology in both galaxies varies strongly with wavelength, due to a combination of extinction, hot dust and red supergiants, and the age of the stellar populations. The near-infrared and radio morphologies are in general agreement, although there are differences in the detailed morphology. From the comparison of Br_gamma and H_alpha fluxes, we derive average extinctions toward the hot spots A_V = 1.3 for NGC 1097 and A_V = 2.1 for NGC 6574. The observed H_2/Br_gamma ratios indicate that in both rings the main excitation mechanism of the molecular gas is UV radiation from hot young stars, while shocks can contribute only in a few regions. The starburst rings in both galaxies exhibit small Br_gamma equivalent widths. Assuming a constant star formation rate with M_u = 100 M_o results in extremely long ages (up to 1 Gyr), in disagreement with the morphology and the radio spectral index of the galaxies. This situation is only slightly remedied by a reduced upper mass cutoff (M_u = 30 M_o). We prefer a model of an instantaneous burst of star formation with M_u = 100 M_o occurring ~6-7 Myr ago. Gaseous nuclear bars parallel to the stellar nuclear bar were detected in both galaxies, with M ~100 M_o for the mass of the excited nuclear H_2 emission. Finally, we briefly discuss the connection between the rings, bars and the fuelling of nuclear activity.
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