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  • 1
    In: Autophagy, Informa UK Limited, Vol. 12, No. 1 ( 2016-01-02), p. 1-222
    Type of Medium: Online Resource
    ISSN: 1554-8627 , 1554-8635
    Language: English
    Publisher: Informa UK Limited
    Publication Date: 2016
    detail.hit.zdb_id: 2262043-6
    SSG: 12
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  • 2
    In: International Journal of Surgery, Ovid Technologies (Wolters Kluwer Health), Vol. 39 ( 2017-03), p. 234-237
    Type of Medium: Online Resource
    ISSN: 1743-9191
    Language: English
    Publisher: Ovid Technologies (Wolters Kluwer Health)
    Publication Date: 2017
    detail.hit.zdb_id: 2201966-2
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  • 3
    Online Resource
    Online Resource
    Institute of Mathematical Statistics ; 2015
    In:  Electronic Journal of Probability Vol. 20, No. none ( 2015-1-1)
    In: Electronic Journal of Probability, Institute of Mathematical Statistics, Vol. 20, No. none ( 2015-1-1)
    Type of Medium: Online Resource
    ISSN: 1083-6489
    Language: Unknown
    Publisher: Institute of Mathematical Statistics
    Publication Date: 2015
    detail.hit.zdb_id: 2028416-0
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  • 4
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2001
    In:  Genetics Vol. 159, No. 3 ( 2001-11-01), p. 1299-1318
    In: Genetics, Oxford University Press (OUP), Vol. 159, No. 3 ( 2001-11-01), p. 1299-1318
    Abstract: We introduce a new method for estimating recombination rates from population genetic data. The method uses a computationally intensive statistical procedure (importance sampling) to calculate the likelihood under a coalescent-based model. Detailed comparisons of the new algorithm with two existing methods (the importance sampling method of Griffiths and Marjoram and the MCMC method of Kuhner and colleagues) show it to be substantially more efficient. (The improvement over the existing importance sampling scheme is typically by four orders of magnitude.) The existing approaches not infrequently led to misleading results on the problems we investigated. We also performed a simulation study to look at the properties of the maximum-likelihood estimator of the recombination rate and its robustness to misspecification of the demographic model.
    Type of Medium: Online Resource
    ISSN: 1943-2631
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2001
    detail.hit.zdb_id: 1477228-0
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2002
    In:  Genetics Vol. 160, No. 3 ( 2002-03-01), p. 1231-1241
    In: Genetics, Oxford University Press (OUP), Vol. 160, No. 3 ( 2002-03-01), p. 1231-1241
    Abstract: Determining the amount of recombination in the genealogical history of a sample of genes is important to both evolutionary biology and medical population genetics. However, recurrent mutation can produce patterns of genetic diversity similar to those generated by recombination and can bias estimates of the population recombination rate. Hudson (2001) has suggested an approximate-likelihood method based on coalescent theory to estimate the population recombination rate, 4Ner, under an infinite-sites model of sequence evolution. Here we extend the method to the estimation of the recombination rate in genomes, such as those of many viruses and bacteria, where the rate of recurrent mutation is high. In addition, we develop a powerful permutation-based method for detecting recombination that is both more powerful than other permutation-based methods and robust to misspecification of the model of sequence evolution. We apply the method to sequence data from viruses, bacteria, and human mitochondrial DNA. The extremely high level of recombination detected in both HIV1 and HIV2 sequences demonstrates that recombination cannot be ignored in the analysis of viral population genetic data.
    Type of Medium: Online Resource
    ISSN: 1943-2631
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2002
    detail.hit.zdb_id: 1477228-0
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  • 6
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2007
    In:  Genetics Vol. 177, No. 1 ( 2007-09-01), p. 347-358
    In: Genetics, Oxford University Press (OUP), Vol. 177, No. 1 ( 2007-09-01), p. 347-358
    Abstract: We consider inference for demographic models and parameters based upon postprocessing the output of an MCMC method that generates samples of genealogical trees (from the posterior distribution for a specific prior distribution of the genealogy). This approach has the advantage of taking account of the uncertainty in the inference for the tree when making inferences about the demographic model and can be computationally efficient in terms of reanalyzing data under a wide variety of models. We consider a (simulation-consistent) estimate of the likelihood for variable population size models, which uses importance sampling, and propose two new approximate likelihoods, one for migration models and one for continuous spatial models.
    Type of Medium: Online Resource
    ISSN: 1943-2631
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2007
    detail.hit.zdb_id: 1477228-0
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  • 7
    In: Diseases of the Colon & Rectum, Ovid Technologies (Wolters Kluwer Health), Vol. 64, No. 7 ( 2021-07), p. 861-870
    Abstract: Functional outcomes after ileoanal pouch creation have been studied; however, there is great variability in how relevant outcomes are defined and reported. More importantly, the perspective of patients has not been represented in deciding which outcomes should be the focus of research. OBJECTIVE: The primary aim was to create a patient-centered definition of core symptoms that should be included in future studies of pouch function. DESIGN: This was a Delphi consensus study. SETTING: Three rounds of surveys were used to select high-priority items. Survey voting was followed by a series of online patient consultation meetings used to clarify voting trends. A final online consensus meeting with representation from all 3 expert panels was held to finalize a consensus statement. PATIENTS: Expert stakeholders were chosen to correlate with the clinical scenario of the multidisciplinary team that cares for pouch patients, including patients, colorectal surgeons, and gastroenterologists or other clinicians. MAIN OUTCOME MEASURES: A consensus statement was the main outcome. RESULTS: One hundred ninety-five patients, 62 colorectal surgeons, and 48 gastroenterologists or nurse specialists completed all 3 Delphi rounds. Fifty-three patients participated in online focus groups. One hundred sixty-one stakeholders participated in the final consensus meeting. On conclusion of the consensus meeting, 7 bowel symptoms and 7 consequences of undergoing ileoanal pouch surgery were included in the final consensus statement. LIMITATIONS: The study was limited by online recruitment bias. CONCLUSIONS: This study is the first to identify key functional outcomes after pouch surgery with direct input from a large panel of ileoanal pouch patients. The inclusion of patients in all stages of the consensus process allowed for a true patient-centered approach in defining the core domains that should be focused on in future studies of pouch function. See Video Abstract at http://links.lww.com/DCR/B571. LOS PACIENTES SOMETIDOS A CIRUGÍA DE RESERVORIO ILEOANAL EXPERIMENTAN UNA CONSTELACIÓN DE SÍNTOMAS Y CONSECUENCIAS QUE REPRESENTAN UN SÍNDROME UNICO Un Informe de los Resultados Reportados por los Pacientes Posterior a la Cirugía de Reservorio (PROPS) Estudio de Consenso Delphi ANTECEDENTES: Los resultados funcionales después de la creación del reservorio ileoanal han sido estudiados; sin embargo, existe una gran variabilidad en la forma en que se definen y reportan los resultados relevantes. Más importante aún, la perspectiva de los pacientes no se ha representado a la hora de decidir qué resultados deberían ser el foco de investigación. OBJETIVO: El objetivo principal era crear en el paciente una definición centrada de los síntomas principales que debería incluirse en los estudios futuros de la función del reservorio. DISEÑO: Estudio de consenso Delphi. ENTORNO CLINICO: Se emplearon tres rondas de encuestas para seleccionar elementos de alta prioridad. La votación de la encuesta fue seguida por una serie de reuniones de consulta de pacientes en línea que se utilizan para aclarar las tendencias de votación. Se realizo una reunión de consenso final en línea con representación de los tres paneles de expertos para finalizar una declaración de consenso. PACIENTES: Se eligieron partes interesadas expertas para correlacionar con el escenario clínico del equipo multidisciplinario que atiende a los pacientes con reservorio: pacientes, cirujanos colorrectales, gastroenterólogos / otros médicos. PRINCIPALES MEDIDAS DE VALORACION: Declaración de consenso. RESULTADOS: Ciento noventa y cinco pacientes, 62 cirujanos colorrectales y 48 gastroenterólogos / enfermeras especialistas completaron las tres rondas Delphi. 53 pacientes participaron en grupos focales en línea. 161 interesados participaron en la reunión de consenso final. Al concluir la reunión de consenso, siete síntomas intestinales y siete consecuencias de someterse a una cirugía de reservorio ileoanal se incluyeron en la declaración de consenso final. LIMITACIONES: Sesgo de reclutamiento en línea. CONCLUSIONES: Este estudio es el primero en identificar resultados funcionales claves después de la cirugía de reservorio con información directa de un gran panel de pacientes con reservorio ileoanal. La inclusión de pacientes en todas las etapas del proceso de consenso permitió un verdadero enfoque centrado en el paciente para definir los dominios principales en los que debería centrarse los estudios futuros de la función del reservorio. Consulte Video Resumen en http://links.lww.com/DCR/B571.
    Type of Medium: Online Resource
    ISSN: 0012-3706
    Language: English
    Publisher: Ovid Technologies (Wolters Kluwer Health)
    Publication Date: 2021
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  • 8
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2007
    In:  Genetics Vol. 177, No. 1 ( 2007-09-01), p. 427-434
    In: Genetics, Oxford University Press (OUP), Vol. 177, No. 1 ( 2007-09-01), p. 427-434
    Abstract: We look at how to choose genetic distance so as to maximize the power of detecting spatial structure. We answer this question through analyzing two population genetic models that allow for a spatially structured population in a continuous habitat. These models, like most that incorporate spatial structure, can be characterized by a separation of timescales: the history of the sample can be split into a scattering and a collecting phase, and it is only during the scattering phase that the spatial locations of the sample affect the coalescence times. Our results suggest that the optimal choice of genetic distance is based upon splitting a DNA sequence into segments and counting the number of segments at which two sequences differ. The size of these segments depends on the length of the scattering phase for the population genetic model.
    Type of Medium: Online Resource
    ISSN: 1943-2631
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2007
    detail.hit.zdb_id: 1477228-0
    SSG: 12
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  • 9
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2020
    In:  Journal of the Royal Statistical Society Series B: Statistical Methodology Vol. 82, No. 5 ( 2020-12-01), p. 1167-1221
    In: Journal of the Royal Statistical Society Series B: Statistical Methodology, Oxford University Press (OUP), Vol. 82, No. 5 ( 2020-12-01), p. 1167-1221
    Abstract: This paper introduces a class of Monte Carlo algorithms which are based on the simulation of a Markov process whose quasi-stationary distribution coincides with a distribution of interest. This differs fundamentally from, say, current Markov chain Monte Carlo methods which simulate a Markov chain whose stationary distribution is the target. We show how to approximate distributions of interest by carefully combining sequential Monte Carlo methods with methodology for the exact simulation of diffusions. The methodology introduced here is particularly promising in that it is applicable to the same class of problems as gradient-based Markov chain Monte Carlo algorithms but entirely circumvents the need to conduct Metropolis–Hastings type accept–reject steps while retaining exactness: the paper gives theoretical guarantees ensuring that the algorithm has the correct limiting target distribution. Furthermore, this methodology is highly amenable to ‘big data’ problems. By employing a modification to existing naive subsampling and control variate techniques it is possible to obtain an algorithm which is still exact but has sublinear iterative cost as a function of data size.
    Type of Medium: Online Resource
    ISSN: 1369-7412 , 1467-9868
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 204795-0
    detail.hit.zdb_id: 1490719-7
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  • 10
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2006
    In:  Journal of the Royal Statistical Society Series B: Statistical Methodology Vol. 68, No. 3 ( 2006-06-01), p. 333-382
    In: Journal of the Royal Statistical Society Series B: Statistical Methodology, Oxford University Press (OUP), Vol. 68, No. 3 ( 2006-06-01), p. 333-382
    Abstract: The objective of the paper is to present a novel methodology for likelihood-based inference for discretely observed diffusions. We propose Monte Carlo methods, which build on recent advances on the exact simulation of diffusions, for performing maximum likelihood and Bayesian estimation.
    Type of Medium: Online Resource
    ISSN: 1369-7412 , 1467-9868
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2006
    detail.hit.zdb_id: 204795-0
    detail.hit.zdb_id: 1490719-7
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