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

Response maxima in time-modulated turbulence: Direct Numerical Simulations

The response of turbulent flow to time-modulated forcing is studied by direct numerical simulations of the Navier-Stokes equations. The large-scale forcing is modulated via periodic energy input variations at frequency $\omega$. The response is maximal for frequencies in the range of the inverse of the large eddy turnover time, confirming the mean-field predictions of von der Heydt, Grossmann and Lohse (Phys. Rev. E 67, 046308 (2003)). In accordance with the theory the response maximum shows only a small dependence on the Reynolds number and is also quite insensitive to the particular flow-quantity that is monitored, e.g., kinetic energy, dissipation-rate, or Taylor-Reynolds number. At sufficiently high frequencies the amplitude of the kinetic energy response decreases as $1/\omega$. For frequencies beyond the range of maximal response, a significant change in phase-shift relative to the time-modulated forcing is observed.Comment: submitted to Europhysics Letters (EPL), 8 pages, 8 Postscript figures, uses epl.cl

Simple Front End Electronics for Multigap Resistive Plate Chambers

A simple circuit for the presentation of the signals from Multi-gap Resistive Plate Chambers (MRPCs) to standard existing digitization electronics is described. The circuit is based on "off-the-shelf" discrete components. An optimization of the values of specific components is required to match the aspects of the MRPCs for the given application. This simple circuit is an attractive option for the initial signal processing for MRPC prototyping and bench- or beam-testing efforts, as well as for final implementations of small-area Time-of-Flight systems with existing data acquisition systems.Comment: submitted to Nucl. Inst. and Methods, Section

Studying patterns of use of transport modes through data mining - Application to U.S. national household travel survey data set

Data collection activities related to travel require large amounts of financial and human resources to be conducted successfully. When available resources are scarce, the information hidden in these data sets needs to be exploited, both to increase their added value and to gain support among decision makers not to discontinue such efforts. This study assessed the use of a data mining technique, association analysis, to understand better the patterns of mode use from the 2009 U.S. National Household Travel Survey. Only variables related to self-reported levels of use of the different transportation means are considered, along with those useful to the socioeconomic characterization of the respondents. Association rules potentially showed a substitution effect between cars and public transportation, in economic terms but such an effect was not observed between public transportation and nonmotorized modes (e.g., bicycling and walking). This effect was a policy-relevant finding, because transit marketing should be targeted to car drivers rather than to bikers or walkers for real improvement in the environmental performance of any transportation system. Given the competitive advantage of private modes extensively discussed in the literature, modal diversion from car to transit is seldom observed in practice. However, after such a factor was controlled, the results suggest that modal diversion should mainly occur from cars to transit rather than from nonmotorized modes to transi

Landmark detection in 2D bioimages for geometric morphometrics: a multi-resolution tree-based approach

The detection of anatomical landmarks in bioimages is a necessary but tedious step for geometric morphometrics studies in many research domains. We propose variants of a multi-resolution tree-based approach to speed-up the detection of landmarks in bioimages. We extensively evaluate our method variants on three different datasets (cephalometric, zebrafish, and drosophila images). We identify the key method parameters (notably the multi-resolution) and report results with respect to human ground truths and existing methods. Our method achieves recognition performances competitive with current existing approaches while being generic and fast. The algorithms are integrated in the open-source Cytomine software and we provide parameter configuration guidelines so that they can be easily exploited by end-users. Finally, datasets are readily available through a Cytomine server to foster future research

Predicting Fluid Intelligence of Children using T1-weighted MR Images and a StackNet

In this work, we utilize T1-weighted MR images and StackNet to predict fluid intelligence in adolescents. Our framework includes feature extraction, feature normalization, feature denoising, feature selection, training a StackNet, and predicting fluid intelligence. The extracted feature is the distribution of different brain tissues in different brain parcellation regions. The proposed StackNet consists of three layers and 11 models. Each layer uses the predictions from all previous layers including the input layer. The proposed StackNet is tested on a public benchmark Adolescent Brain Cognitive Development Neurocognitive Prediction Challenge 2019 and achieves a mean squared error of 82.42 on the combined training and validation set with 10-fold cross-validation. In addition, the proposed StackNet also achieves a mean squared error of 94.25 on the testing data. The source code is available on GitHub.Comment: 8 pages, 2 figures, 3 tables, Accepted by MICCAI ABCD-NP Challenge 2019; Added ND

Travel Time Prediction using Tree-Based Ensembles

In this paper, we consider the task of predicting travel times between two arbitrary points in an urban scenario. We view this problem from two temporal perspectives: long-term forecasting with a horizon of several days and short-term forecasting with a horizon of one hour. Both of these perspectives are relevant for planning tasks in the context of urban mobility and transportation services. We utilize tree-based ensemble methods that we train and evaluate on a dataset of taxi trip records from New York City. Through extensive data analysis, we identify relevant temporal and spatial features. We also engineer additional features based on weather and routing data. The latter is obtained via a routing solver operating on the road network. The computational results show that the addition of this routing data can be beneficial to the model performance. Moreover, employing different models for short and long-term prediction is useful as short-term models are better suited to mirror current traffic conditions. In fact, we show that accurate short-term predictions may be obtained with only little training data

A long-lasting, complete hematologic and cytogenetic remission of chronic myelogenous leukemia after treatment with busulfan alone

A 44-year-old man suffering from cytogenetically and molecularly proven Philadelphia translocation-positive chronic myelogenous leukemia in chronic phase was treated with busulfan for 18 months and studied during a follow-up period of 13 years. Hematologically and cytogenetically, he attained a continuing complete remission, although at one point (9.5 years) at least, after attaining complete remission molecular analysis indicated the presence of minimal residual disease