The Medicago genome provides insight into the evolution of rhizobial symbioses

Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation1. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Myr ago). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species2. Medicago truncatula is a long-established model for the study of legume biology. Here we describe the draft sequence of the M. truncatula euchromatin based on a recently completed BAC assembly supplemented with Illumina shotgun sequence, together capturing ~94% of all M. truncatula genes. A whole-genome duplication (WGD) approximately 58 Myr ago had a major role in shaping the M. truncatula genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the M. truncatula genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max and Lotus japonicus. M. truncatula is a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa’s genomic toolbo

Leray and LANS-α\alpha modeling of turbulent mixing

Mathematical regularisation of the nonlinear terms in the Navier-Stokes equations provides a systematic approach to deriving subgrid closures for numerical simulations of turbulent flow. By construction, these subgrid closures imply existence and uniqueness of strong solutions to the corresponding modelled system of equations. We will consider the large eddy interpretation of two such mathematical regularisation principles, i.e., Leray and LANS$-\alpha$ regularisation. The Leray principle introduces a {\bfi smoothed transport velocity} as part of the regularised convective nonlinearity. The LANS$-\alpha$ principle extends the Leray formulation in a natural way in which a {\bfi filtered Kelvin circulation theorem}, incorporating the smoothed transport velocity, is explicitly satisfied. These regularisation principles give rise to implied subgrid closures which will be applied in large eddy simulation of turbulent mixing. Comparison with filtered direct numerical simulation data, and with predictions obtained from popular dynamic eddy-viscosity modelling, shows that these mathematical regularisation models are considerably more accurate, at a lower computational cost.Comment: 42 pages, 12 figure

Distributed utterances

I propose an apparatus for handling intrasentential change in context. The standard approach has problems with sentences with multiple occurrences of the same demonstrative or indexical. My proposal involves the idea that contexts can be complex. Complex contexts are built out of (“simple”) Kaplanian contexts by ordered n-tupling. With these we can revise the clauses of Kaplan’s Logic of Demonstratives so that each part of a sentence is taken in a different component of a complex context. I consider other applications of the framework: to agentially distributed utterances (ones made partly by one speaker and partly by another); to an account of scare-quoting; and to an account of a binding-like phenomenon that avoids what Kit Fine calls “the antinomy of the variable.

Huge decreases in the risk of breast cancer relapse over the last three decades

Introduction The aim of this study was to evaluate local and systemic breast cancer control by comparing the risk of relapse in breast cancer patients in 2003–2004 with that in 1972–1979 and in 1980–1986. Methods About 8,570 women diagnosed with invasive breast cancer in 2003–2004 were selected from the population-based Netherlands Cancer Registry and compared with 133 patients treated in 1972–1979 and 174 in 1980–1986. Five-year risk of relapse was calculated by the Kaplan–Meier method. Cox-proportional hazard models were applied to adjust for tumour size, nodal status and age at diagnosis. Results Patients diagnosed in 2003–2004 had smaller tumours and a less advanced nodal stage than patients diagnosed in 1972–1986. In 1972–1979, 1980–1986 and 2003–2004, treatment included mastectomy in 94%, 72% and 47%; postmastectomy radiotherapy in 75%, 70% and 30%; chemotherapy in 9%, 14% and 37% and hormonal therapy in 3%, 3% and 42% of patients, respectively. Five-year risk of locoregional and distant recurrence decreased from 37% and 34% to 15%, respectively. The 5-year risk of second primary breast cancer did not differ and was 1%, 4% and 2%, respectively. The improved relapse-free survival in patients diagnosed in 2003–2004 as compared with 1972–1979 hardly changed after adjustment (HR = 0.38, 95% CI = 0.28–0.52). Conclusion Over the last decades, local breast cancer therapies have become less rigorous, whereas systemic therapy use has increased. Simultaneously, the risk of breast cancer relapse has tremendously decreased. Future novel therapies may lead to such small additional decreases in relapse rates, while the long-term side effects in breast cancer survivors will increas

An immersed boundary method for computing heat and fluid flow in porous media

A volume-penalizing immersed boundary (IB) method is presented that facilitates the computation of fluid flow in complex porous media. The computational domain is composed of a uniform Cartesian grid, and solid bodies are approximated on this grid using a series of grid cells (i.e., a ''staircase'' approximation). Solid bodies are distinguished from fluid regions using a binary phase-indicator function: Taking the value of ''1'' in the solid parts of the domain and ''0'' in the fluid parts. The effect of solid bodies on the flow is modeled using a source term in the momentum equations. The source term is active only within solid parts of the domain, and enforces the no-slip boundary condition. Fluid regions are governed by the incompressible Navier-Stokes equations. An extension of the IB method is proposed to tackle coupled fluid-solid heat transfer. The extended IB method is validated for Poiseuille flow, which allows for a direct comparison of the numerical results against a closed analytical solution. We subsequently apply the extended IB method to flow in a structured porous medium and focus on bulk properties such as the gradient of the average pressure and the Nusselt number. Reliable qualitative results were obtained with 16-32 grid points per singly-connected fluid region

ADHD subtypes: do they differ in their executive functioning profile?

The present study was designed to investigate the hypothesis that children with Attention Deficit Hyperactivity Disorder combined subtype (ADHD-C) have a generalized executive functioning (EF) [Barkley, R. A. (1997). Behavioural inhibition, sustained attention, and executive functions: Constructing a unifying theory of AD/HD. Psychological Bulletin, 121, 65-94; Barkley, R. A. (1997). ADHD and the nature of self-control. New York: The Guilford Press]. We tested whether ADHD-C and ADHD inattentive subtype (ADHD-I) can be differentiated from each other on EF measures. We compared 16 normally developing boys with 16 boys with ADHD-C and 16 with ADHD-I on five EF domains. The boys were all matched on age, IQ, and the presence of oppositional defiant disorder (ODD)/conduct disorder (CD). Despite carefully diagnosed groups and methodological controls, the results do not support the EF-hypothesis of ADHD-C. Children with ADHD-C differed from normal controls (NC) on tasks related to inhibition; they did not exhibit EF deficits on all EF tasks. Children with ADHD-C also exhibited deficits on non-EF tasks. Furthermore, the ADHD-C and ADHD-I subtypes did not differ from one another. Neuropsychological findings on the domains under study did not yield evidence for the distinctiveness of ADHD-C and ADHD-I subtypes. © 2004 National Academy of Neuropsychology. Published by Elsevier Ltd. All rights reserved

Large eddy simulation of the velocity-intermittency structure for flow over a field of symmetric dunes

Owing to their frequent occurrence in the natural environment, there has been significant interest in refining our understanding of flow over dunes and other bedforms. Recent work in this area has focused, in particular, on their shear-layer characteristics and the manner by which flow structures are generated. However, field-based studies, are reliant on single-, or multi-point measurements, rather than delimiting flow structures from the velocity gradient tensor, as is possible in numerical work. Here, we extract pointwise time series from a well-resolved large eddy simulation as a means to connect these two approaches. The at-a-point analysis technique is termed the velocity-intermittency quadrant method and relates the fluctuating, longitudinal velocity, (Formula presented.), to its fluctuating pointwise Hölder regularity, (Formula presented.). Despite the difference in boundary conditions, our results agree very well with previous experiments that show the importance, in the region above the dunes, of a quadrant 3 ((Formula presented.), (Formula presented.)) flow configuration. Our higher density of sampling beneath the shear layer and close to the bedforms relative to experimental work reveals a negative correlation between (Formula presented.) and (Formula presented.) in this region. This consists of two distinct layers, with quadrant 4 ((Formula presented.), (Formula presented.)) dominant near the wall and quadrant 2 ((Formula presented.), (Formula presented.)) dominant close to the lower part of the separated shear layer. These results are consistent with a near-wall advection of vorticity into a region downstream of a temporarily foreshortened reattachment region, and the entrainment of slow moving and quiescent fluid into a faster, more turbulent shear layer. A comparison of instantaneous vorticity fields to the velocity-intermittency analysis shows how the pointwise results reflect larger-scale organisation of the flow. We illustrate this using results from two instantaneous datasets. In the former, extreme velocity-intermittency events corresponding to a foreshortened recirculation region (and high pressures on the stoss slope of the dune immediately downstream) arise, and the development of intense flow structures occurs as a consequence. In the other case, development of a ‘skimming flow’ with relatively little exchange between the inner and outer regions results in exceedances because of the coherence associated with this high velocity, high turbulence outer region. Thus, our results shed further light on the characteristics of dune flow in the near-wall region and, importantly for field-based research, show that useful information on flow structure can be obtained from single-point single velocity component measurements

Об этике коммуникаций и этике ответственности

В данной статье на основе пяти принципов этики коммуникаций, выявленных американскими учеными, устанавливаются точки пересечения между основными принципами коммуникации и этикой ответственности субъекта. Осуществлен анализ понятия "этика коммуникаций" и выявлены особенности трансформации данного понятия в современных коммуникативных процессах. Подчеркивается, что ключевой фигурой в глобальности коммуникаций становится человек, создающий значения, определяющий многообразие форм знака в современном коммуникативном пространстве. Сделан вывод о том, что именно такой человек является связующим звеном между человеческими ценностями и основными принципами этики коммуникаций, что создает условия для развития ключевых положений этики ответственности