Link anchors in images: is there truth?

While automatic linking in text collections is well understood, little is known about links in images. In this work, we investigate two aspects of anchors, the origin of a link, in images: 1) the requirements of users for such anchors, e.g. the things users would like more information on, and 2) possible evaluation methods assessing anchor selection al- gorithms. To investigate these aspects, we perform a study with 102 users. We find that 59% of the required anchors are image segments, as opposed to the whole image, and most users require information on displayed persons. The agreement of users on the required anchors is too low (often below 30%) for a ground truth-based evaluation, which is the standard IR evaluation method. As an alternative, we propose a novel evaluation method based on improved search performance and user experience

Tip cell overtaking occurs as a side effect of sprouting in computational models of angiogenesis

During angiogenesis, endothelial cells compete for the tip position during angiogenesis: a phenomenon named tip cell overtaking. It is still unclear to what extent tip cell overtaking is a side effect of sprouting or to what extent a biological function. To address this question, we studied tip cell overtaking in two existing cellular Potts models of angiogenic sprouting. In these models angiogenic sprouting-like behavior emerges from a small set of plausible cell behaviors and the endothelial cells spontaneously migrate forwards and backwards within sprouts, suggesting that tip cell overtaking might occur as a side effect of sprouting. In accordance with experimental observations, in our simulations the cells' tendency to occupy the tip position can be regulated when two cell lines with different levels of Vegfr2 expression are contributing to sprouting (mosaic sprouting assay), where cell behavior is regulated by a simple VEGF-Dll4-Notch signaling network. Our modeling results suggest that tip cell overtaking occurs spontaneously due to the stochastic motion of cells during sprouting. Thus, tip cell overtaking and sprouting dynamics may be interdependent and should be studied and interpreted in combination. VEGF-Dll4-Notch can regulate the ability of cells to occupy the tip cell position, but only when cells in the simulation strongly differ in their levels of Vegfr2. We propose that VEGF-Dll4-Notch signaling might not regulate which cell ends up at the tip, but assures that the cell that randomly ends up at the tip position acquires the tip cell phenotype.Comment: 20 pages, 6 figures, 4 supplementary figure

Shared temporoparietal dysfunction in dyslexia and typical readers with discrepantly high IQ

It is currently believed that reading disability (RD) should be defined by reading level without regard to broader aptitude (IQ). There is debate, however, about how to classify individuals who read in the typical range but less well than would be expected by their higher IQ. We used functional magnetic resonance imaging (fMRI) in 49 children to examine whether those with typical reading ability, but discrepantly low relative to IQ, show dyslexia-like activation patterns during reading. Children who were typical readers with high-IQ discrepancy showed reduced activation in left temporoparietal neocortex relative to two control groups of typical readers without IQ discrepancy. This pattern was consistent and spatially overlapping with results in children with RD compared to typically reading children. The results suggest a shared neurological atypicality in regions associated with phonological processing between children with dyslexia and children having typical reading ability that is substantially below their IQ

Black spot diseases in carrot

An important problem in organic carrot production in the Netherlands is the occurrence of black spots during storage. Several different fungal pathogens cause similar symptoms, which are collectively known as black spot diseases. We identified Alternaria radicina, A. dauci and Rhexocercosporidium carotae (syn. Acrothecium carotae) as the most prevalent black spot pathogens. We developed laboratory test methods for resistance to A. radicina and R. carotae, and assessed resistance in a collection of cultivated varieties and more exotic material

Constructive plaquette compilation for the parity architecture

Parity compilation is the challenge of laying out the required constraints for the parity mapping in a local way. We present the first constructive compilation algorithm for the parity architecture using plaquettes for arbitrary higher-order optimization problems. This enables adiabatic protocols, where the plaquette layout can natively be implemented, as well as fully parallelized digital circuits. The algorithm builds a rectangular layout of plaquettes, where in each layer of the rectangle at least one constraint is added. The core idea is that each constraint, consisting of any qubits on the boundary of the rectangle and some new qubits, can be decomposed into plaquettes with a deterministic procedure using ancillas. We show how to pick a valid set of constraints and how this decomposition works. We further give ways to optimize the ancilla count and show how to implement optimization problems with additional constraints.Comment: 8 pages, 5 figure

Space Motions of the Dwarf Spheroidal Galaxies Draco and Sculptor based on HST Proper Motions with ~10-year Time Baseline

We present new proper motion (PM) measurements of the dwarf spheroidal galaxies (dSphs) Draco and Sculptor using multi-epoch images obtained with the Hubble Space Telescope ACS/WFC. Our PM results have uncertainties far lower than previous measurements, even made with the same instrument. The PM results for Draco and Sculptor are (mu_W,mu_N)_Dra = (-0.0562+/-0.0099,-0.1765+/-0.0100) mas/yr and (mu_W,mu_N)_Scl = (-0.0296+/-0.0209,-0.1358 +/-0.0214) mas/yr. The implied Galactocentric velocity vectors for Draco and Sculptor have radial and tangential components: (V_rad,V_tan)_Dra = (-88.6,161.4) +/- (4.4,5.6) km/s; and (V_rad,V_tan)_Scl = (72.6,200.2) +/- (1.3,10.8) km/s. We study the detailed orbital history of both Draco and Sculptor via numerical orbit integrations. Orbital periods of Draco and Sculptor are found to be 1-2 and 2-5 Gyrs, respectively, accounting for uncertainties in the MW mass. We also study the influence of the Large Magellanic Cloud (LMC) on the orbits of Draco and Sculptor. Overall, the inclusion of the LMC increases the scatter in the orbital results. Based on our calculations, Draco shows a rather wide range of orbital parameters depending on the MW mass and inclusion/exclusion of the LMC, but Sculptor's orbit is very well constrained with its most recent pericentric approach to the MW being 0.3-0.4 Gyr ago. Our new PMs imply that the orbital trajectories of both Draco and Sculptor are confined within the Disk of Satellites (DoS), better so than implied by earlier PM measurements, and likely rule out the possibility that these two galaxies were accreted together as part of a tightly bound group.Comment: 17 pages, 8 figures, 6 tables. Accepted for publication in Ap

Factors affecting thrips resistance in cabbage

In two field experiments in the Netherlands the development of thrips populations and thrips damage in ten cabbage varieties was monitored. Also a number of morphological, physiological en biochemical plant traits were measured. The most important factors leading to a low level of thrips dam-age were a late development of a compact head, a low dry matter content and a high amount of leaf wax

FitTetra 2.0-improved genotype calling for tetraploids with multiple population and parental data support

BackgroundGenetic studies in tetraploids are lagging behind in comparison with studies of diploids as the complex genetics of tetraploids require much more elaborated computational methodologies. Recent advancements in development of molecular techniques and computational tools facilitate new methods for automated, high-throughput genotype calling in tetraploid species. We report on the upgrade of the widely-used fitTetra software aiming to improve its accuracy, which to date is hampered by technical artefacts in the data.ResultsOur upgrade of the fitTetra package is designed for a more accurate modelling of complex collections of samples. The package fits a mixture model where some parameters of the model are estimated separately for each sub-collection. When a full-sib family is analyzed, we use parental genotypes to predict the expected segregation in terms of allele dosages in the offspring. More accurate modelling and use of parental data increases the accuracy of dosage calling. We tested the package on data obtained with an Affymetrix Axiom 60k array and compared its performance with the original version and the recently published ClusterCall tool, showing that at least 20% more SNPs could be called with our updated.ConclusionOur updated software package shows clearly improved performance in genotype calling accuracy. Estimation of mixing proportions of the underlying dosage distributions is separated for full-sib families (where mixture proportions can be estimated from the parental dosages and inheritance model) and unstructured populations (where they are based on the assumption of Hardy-Weinberg equilibrium). Additionally, as the distributions of signal ratios of the dosage classes can be assumed to be the same for all populations, including parental data for some subpopulations helps to improve fitting other populations as well. The R package fitTetra 2.0 is freely available under the GNU Public License as Additional file with this article.</p

Genomics-based discrimination of 2n gamete formation mechanisms in polyploids: a case study in nonaploid Diospyros kaki ‘Akiou’

Unreduced gametes (2n gametes), possessing double the haploid genome, whatever ploidy that happens to be, are a common source of ploidy variation in plant populations. First and second division restitution (FDR and SDR) are the dominant mechanisms of 2n gamete production; all else being equal, FDR gametes have a higher degree of heterozygosity, thus they are advantageous in breeding. The discrimination of these mechanisms from the consequence of hybridization is challenging, especially in higher polyploids, and usually requires information on centromere location. In this study, we propose a genotyping-based strategy to uncover the mechanisms of 2n gamete formation in progeny that has a higher ploidy than its parents. Simulation of 2n gamete production revealed that FDR and SDR pathways can be discriminated based on allele transmission patterns alone without information on centromere location. We applied this strategy to study the formation mechanism of a nonaploid Diospyros kaki ‘Akiou', which was bred via hybridization between D. kaki hexaploid cultivars. The result demonstrated that ‘Akiou' was derived from the fertilization of a normal female gamete by a 2n male gamete and that this 2n gamete was produced through FDR. Consequently, the distinct duplex transmission pattern in the FDR gamete enabled us to infer the genomic characteristics of polyploid persimmon. The method could be tested only for the plant being polypoid, which allows for the ability to discriminate causes of 2n gamete formation using allele dosage in progeny, and will be useful in future studies of polyploid genomics