TY - JOUR AB - Background: Characterizing root system architecture (RSA) is essential to understanding the development and function of vascular plants. Identifying RSA-associated genes also represents an underexplored opportunity for crop improvement. Software tools are needed to accelerate the pace at which quantitative traits of RSA are estimated from images of root networks.Results: We have developed GiA Roots (General Image Analysis of Roots), a semi-automated software tool designed specifically for the high-throughput analysis of root system images. GiA Roots includes user-assisted algorithms to distinguish root from background and a fully automated pipeline that extracts dozens of root system phenotypes. Quantitative information on each phenotype, along with intermediate steps for full reproducibility, is returned to the end-user for downstream analysis. GiA Roots has a GUI front end and a command-line interface for interweaving the software into large-scale workflows. GiA Roots can also be extended to estimate novel phenotypes specified by the end-user.Conclusions: We demonstrate the use of GiA Roots on a set of 2393 images of rice roots representing 12 genotypes from the species Oryza sativa. We validate trait measurements against prior analyses of this image set that demonstrated that RSA traits are likely heritable and associated with genotypic differences. Moreover, we demonstrate that GiA Roots is extensible and an end-user can add functionality so that GiA Roots can estimate novel RSA traits. In summary, we show that the software can function as an efficient tool as part of a workflow to move from large numbers of root images to downstream analysis. AU - Galkovskyi, Taras AU - Mileyko, Yuriy AU - Bucksch, Alexander AU - Moore, Brad AU - Symonova, Olga AU - Price, Charles AU - Topp, Chrostopher AU - Iyer Pascuzzi, Anjali AU - Zurek, Paul AU - Fang, Suqin AU - Harer, John AU - Benfey, Philip AU - Weitz, Joshua ID - 492 JF - BMC Plant Biology TI - GiA Roots: Software for the high throughput analysis of plant root system architecture VL - 12 ER - TY - JOUR AB - The BCI competition IV stands in the tradition of prior BCI competitions that aim to provide high quality neuroscientific data for open access to the scientific community. As experienced already in prior competitions not only scientists from the narrow field of BCI compete, but scholars with a broad variety of backgrounds and nationalities. They include high specialists as well as students.The goals of all BCI competitions have always been to challenge with respect to novel paradigms and complex data. We report on the following challenges: (1) asynchronous data, (2) synthetic, (3) multi-class continuous data, (4) sessionto-session transfer, (5) directionally modulated MEG, (6) finger movements recorded by ECoG. As after past competitions, our hope is that winning entries may enhance the analysis methods of future BCIs. AU - Tangermann, Michael AU - Müller, Klaus AU - Aertsen, Ad AU - Birbaumer, Niels AU - Braun, Christoph AU - Brunner, Clemens AU - Leeb, Robert AU - Mehring, Carsten AU - Miller, Kai AU - Müller Putz, Gernot AU - Nolte, Guido AU - Pfurtscheller, Gert AU - Preissl, Hubert AU - Schalk, Gerwin AU - Schlögl, Alois AU - Vidaurre, Carmen AU - Waldert, Stephan AU - Blankertz, Benjamin ID - 493 JF - Frontiers in Neuroscience TI - Review of the BCI competition IV VL - 6 ER - TY - CONF AB - An automaton with advice is a finite state automaton which has access to an additional fixed infinite string called an advice tape. We refine the Myhill-Nerode theorem to characterize the languages of finite strings that are accepted by automata with advice. We do the same for tree automata with advice. AU - Kruckman, Alex AU - Rubin, Sasha AU - Sheridan, John AU - Zax, Ben ID - 495 T2 - Proceedings GandALF 2012 TI - A Myhill Nerode theorem for automata with advice VL - 96 ER - TY - JOUR AB - Understanding patterns and correlates of local adaptation in heterogeneous landscapes can provide important information in the selection of appropriate seed sources for restoration. We assessed the extent of local adaptation of fitness components in 12 population pairs of the perennial herb Rutidosis leptorrhynchoides (Asteraceae) and examined whether spatial scale (0.7-600 km), environmental distance, quantitative (QST) and neutral (FST) genetic differentiation, and size of the local and foreign populations could predict patterns of adaptive differentiation. Local adaptation varied among populations and fitness components. Including all population pairs, local adaptation was observed for seedling survival, but not for biomass, while foreign genotype advantage was observed for reproduction (number of inflorescences). Among population pairs, local adaptation increased with QST and local population size for biomass. QST was associated with environmental distance, suggesting ecological selection for phenotypic divergence. However, low FST and variation in population structure in small populations demonstrates the interaction of gene flow and drift in constraining local adaptation in R. leptorrhynchoides. Our study indicates that for species in heterogeneous landscapes, collecting seed from large populations from similar environments to candidate sites is likely to provide the most appropriate seed sources for restoration. AU - Pickup, Melinda AU - Field, David AU - Rowell, David AU - Young, Andrew ID - 498 IS - 8 JF - Evolutionary Applications TI - Predicting local adaptation in fragmented plant populations: Implications for restoration genetics VL - 5 ER - TY - CONF AB - We study the expressive power of logical interpretations on the class of scattered trees, namely those with countably many infinite branches. Scattered trees can be thought of as the tree analogue of scattered linear orders. Every scattered tree has an ordinal rank that reflects the structure of its infinite branches. We prove, roughly, that trees and orders of large rank cannot be interpreted in scattered trees of small rank. We consider a quite general notion of interpretation: each element of the interpreted structure is represented by a set of tuples of subsets of the interpreting tree. Our trees are countable, not necessarily finitely branching, and may have finitely many unary predicates as labellings. We also show how to replace injective set-interpretations in (not necessarily scattered) trees by 'finitary' set-interpretations. AU - Rabinovich, Alexander AU - Rubin, Sasha ID - 496 TI - Interpretations in trees with countably many branches ER -