Transposable elements promote the evolution of genome streamlining

Eukaryotes and prokaryotes have distinct genome architectures, withmarked differences in genome size, the ratio of coding/non-coding DNA,and the abundance of transposable elements (TEs). As TEs replicate inde-pendently of their hosts, the proliferation of TEs is thought to have drivengenome expansion in eukaryotes. However, prokaryotes also have TEs inintergenic spaces, so why do prokaryotes have small, streamlined genomes?Using anin silicomodel describing the genomes of single-celled asexualorganisms that coevolve with TEs, we show that TEs acquired from theenvironment by horizontal gene transfer can promote the evolution ofgenome streamlining. The process depends on local interactions and isunderpinned by rock–paper–scissors dynamics in which populations ofcells with streamlined genomes beat TEs, which beat non-streamlinedgenomes, which beat streamlined genomes, in continuous and repeatingcycles. Streamlining is maladaptive to individual cells, but improves lineageviability by hindering the proliferation of TEs. Streamlining does not evolvein sexually reproducing populations because recombination partially freesTEs from the deleterious effects they cause.This article is part of the theme issue‘The secret lives of microbial mobilegenetic elements’

Fourier Method for Approximating Eigenvalues of Indefinite Stekloff Operator

We introduce an efficient method for computing the Stekloff eigenvalues associated with the Helmholtz equation. In general, this eigenvalue problem requires solving the Helmholtz equation with Dirichlet and/or Neumann boundary condition repeatedly. We propose solving the related constant coefficient Helmholtz equation with Fast Fourier Transform (FFT) based on carefully designed extensions and restrictions of the equation. The proposed Fourier method, combined with proper eigensolver, results in an efficient and clear approach for computing the Stekloff eigenvalues.Comment: 12 pages, 4 figure

Quality Control Process for EQ-5D-5L Valuation Studies

Background: The values of the five-level EuroQol five-dimensional questionnaire (EQ-5D-5L) are elicited using composite time trade-off and discrete choice experiments. Unfortunately, data quality issues and interviewer effects were observed in the first few EQ-5D-5L valuation studies. To prevent these issues from occurring in later studies, the EuroQol Group established a cyclic quality control (QC) process. Objectives: To describe this QC process and show its impact on data quality. Methods: A newly developed QC tool provided information about protocol compliance, interviewer effects, and mean values by health state severity. In a cyclic process, this information is initially used to evaluate whether new interviewers meet minimal quality requirements and later to provide feedback about how their performance may be improved. To investigate the impact of this cyclic process, we compared the quality of the data in Dutch and Spanish valuation studies that did not have this QC process with that in the follow-up studies in the same countries that used the QC process. Data quality was measured using protocol violations, variability between interviewers, the proportion of inconsistent responders, and clustering of composite time trade-off values. Results: In Spain, protocol violations were reduced from 87% in the valuation study to 5% in the follow-up study and in the Netherlands from 20% to 8%. In both countries, interviewers performed more homogeneously in the follow-up studies. The number of inconsistent respondents was reduced by 23.2% in Spain and 23.6% in the Netherlands. Values were less clustered in the follow-up studies. Conclusions: The implementation of a strict QC process in EQ-5D-5L valuation studies increases interviewer protocol compliance and promotes data quality

Balancing equity and efficiency in the Dutch basic benefits package using the principle of proportional shortfall

Economic evaluations are increasingly used to inform decisions regarding the allocation of scarce health care resources. To systematically incorporate societal preferences into these evaluations, quality-adjusted life year gains could be weighted according to some equity principle, the most suitable of which is a matter of frequent debate. While many countries still struggle with equity concerns for priority setting in health care, the Netherlands has reached a broad consensus to use the concept of proportional shortfall. Our study evaluates the concept and its support in the Dutch health care context. We discuss arguments in the Netherlands for using proportional shortfall and difficulties in transitioning from principle to practice. In doing so, we address universal issues leading to a systematic consideration of equity concerns for priority setting in health care. The article thus has relevance to all countries struggling with the formalization of equity concerns for priority setting

Seismic tomography is locally ill-posed

We develop a general convergence analysis for a class of inexact Newton-type regularizations for stably solving nonlinear ill-posed problems. Each of the methods under consideration consists of two components: the outer Newton iteration and an inner regularization scheme which, applied to the linearized system, provides the update. In this paper we give a novel and unified convergence analysis which is not confined to a specific inner regularization scheme but applies to a multitude of schemes including Landweber and steepest decent iterations, iterated Tikhonov method, and method of conjugate gradients