Horseshoe-based Bayesian nonparametric estimation of effective population size trajectories.

Phylodynamics is an area of population genetics that uses genetic sequence data to estimate past population dynamics. Modern state-of-the-art Bayesian nonparametric methods for recovering population size trajectories of unknown form use either change-point models or Gaussian process priors. Change-point models suffer from computational issues when the number of change-points is unknown and needs to be estimated.

Locally Adaptive Smoothing with Markov Random Fields and Shrinkage Priors.

We present a locally adaptive nonparametric curve fitting method that operates within a fully Bayesian framework. This method uses shrinkage priors to induce sparsity in order- differences in the latent trend function, providing a combination of local adaptation and global control. Using a scale mixture of normals representation of shrinkage priors, we make explicit connections between our method and th order Gaussian Markov random field smoothing.

Conservation planning for freshwater-marine carryover effects on Chinook salmon survival.

Experiences of migratory species in one habitat may affect their survival in the next habitat, in what is known as carryover effects. These effects are especially relevant for understanding how freshwater experience affects survival in anadromous fishes. Here, we study the carryover effects of juvenile salmon passage through a hydropower system (Snake and Columbia rivers, northwestern United States).

Simple life-history traits explain key effective population size ratios across diverse taxa.

Effective population size (Ne) controls both the rate of random genetic drift and the effectiveness of selection and migration, but it is difficult to estimate in nature. In particular, for species with overlapping generations, it is easier to estimate the effective number of breeders in one reproductive cycle (Nb) than Ne per generation. We empirically evaluated the relationship between life history and ratios of Ne, Nb and adult census size (N) using a recently developed model (agene) and published vital rates for 63 iteroparous animals and plants.

Modelling evolutionary processes in small populations: not as ideal as you think.

Evolutionary processes are routinely modelled using 'ideal' Wright-Fisher populations of constant size N in which each individual has an equal expectation of reproductive success. In a hypothetical ideal population, variance in reproductive success (V(k)) is binomial and effective population size (N(e)) = N. However, in any actual implementation of the Wright-Fisher model (e.

Phase II trial of carboplatin and paclitaxel in cisplatin-pretreated advanced transitional cell carcinoma: a Southwest Oncology Group study.

Background: The purpose of the study was to assess the efficacy and toxicity of carboplatin and paclitaxel administered every 3 weeks in patients with advanced urothelial carcinoma, previously treated with cisplatin-based therapy.

Methods: Eligibility included metastatic or locally advanced unresectable transitional cell carcinoma of the urothelial tract. Prior chemotherapy, except taxanes, was permitted within 12 months.

A phase II study of flavopiridol in patients with advanced renal cell carcinoma: results of Southwest Oncology Group Trial 0109.

Purpose: Flavopiridol is a cyclin-dependent kinase inhibitor that prevents cell cycle progression and tumor growth. In initial phase I studies, encouraging responses were seen in advanced renal cell cancer (RCC). In a phase II study of flavopiridol given as a 72-h continuous infusion every 2 weeks in RCC, a response rate of 6% was seen but with considerable grade 3 or 4 asthenia, diarrhea, and thrombosis.

Surgical factors influence bladder cancer outcomes: a cooperative group report.

Purpose: A randomized, cooperative group trial (Southwest Oncology Group 8710, Intergroup 0080) reported that neoadjuvant chemotherapy improved the survival of patients with locally advanced bladder cancer who were treated with radical cystectomy. We evaluated whether surgical factors from patients enrolled onto the study predicted bladder cancer outcomes.

Patients And Methods: Surgical and tumor factors were recorded from surgical and pathologic reports from 268 patients with muscle-invasive bladder cancer who received radical cystectomy.

Pathologic evaluation of radical cystectomy specimens: a cooperative group report.

Background: The authors evaluated the pathology of radical cystectomy and pelvic lymph node specimens from patients with bladder carcinoma who were enrolled in a cooperative group trial. Their objective was to determine whether current practices conform to suggested pathology practice guidelines for reporting on radical cystectomy and pelvic lymph node specimens.

Methods: Overall, 268 patients underwent radical cystectomy with pelvic lymph node dissection over 11 years in a total of 109 diverse geographic locations and types of institutions.

Ten-year survival in patients with metastatic prostate cancer.

The objective of this analysis is to identify baseline covariates that predict which patients will be long-term survivors with metastatic prostate cancer. We analyzed data from Southwest Oncology Group (SWOG) S8894, a clinical trial in men with newly diagnosed metastatic prostate cancer, to evaluate pretreatment characteristics associated with 10-year survival. There were 1286 eligible patients randomized to this study.