julilili42/papers huggingface dataset:
Xanthomonas axonopodis Virulence Is Promoted by a Transcription Activator-Like Effector–Mediated Induction of a SWEET Sugar Transporter in Cassava
2014-08-01

The gene-for-gene concept has historically been applied to describe a specific resistance interaction wherein single genes from the host and the pathogen dictate the outcome. These interactions have been observed across the plant kingdom and all known plant microbial pathogens. In recent years, this concept has been extended to susceptibility phenotypes in the context of transcription activator-like (TAL) effectors that target SWEET sugar transporters. However, because this interaction has only been observed in rice, it was not clear whether the gene-for-gene susceptibility was unique to that system. Here, we show, through a combined systematic analysis of the TAL effector complement of Xanthomonas axonopodis pv. manihotis and RNA sequencing to identify targets in cassava, that TAL20 Xam668 specifically induces the sugar transporter MeSWEET10a to promote virulence. Designer TAL effectors (dTALE) complement TAL20 Xam668 mutant phenotypes, demonstrating that MeSWEET10a is a susceptibility gene in cassava. Sucrose uptake–deficient X. axonopodis pv. manihotis bacteria do not lose virulence, indicating that sucrose may be cleaved extracellularly and taken up as hexoses into X. axonopodis pv. manihotis. Together, our data suggest that pathogen hijacking of plant nutrients is not unique to rice blight but also plays a role in bacterial blight of the dicot cassava.
Orbital and epicyclic frequencies around rapidly rotating compact stars in scalar-tensor theories of gravity
2014-08-01

We study the orbital and epicyclic frequencies of particles orbiting around\\nrapidly rotating neutron stars and strange stars in a particular scalar-tensor\\ntheory of gravity. We find very large deviations of these frequencies, when\\ncompared to their corresponding values in general relativity, for the\\nmaximum-mass rotating models. In contrast, for models rotating with spin\\nfrequency of 700Hz (approximately the largest known rotation rate of neutron\\nstars), the deviations are generally small. Nevertheless, for a very stiff\\nequation of state and a high mass the deviation of one of the epicyclic\\nfrequencies from its GR value is appreciable even at a spin frequency of 700Hz.\\nIn principle, such a deviation could become important in models of\\nquasi-periodic oscillations in low-mass x-ray binaries and could serve as a\\ntest of strong gravity (if other parameters are well constraint). Even though\\nthe present paper is concentrated mainly on orbital and epicyclic frequencies,\\nwe present here for the first time rapidly rotating, scalarized equilibrium\\ncompact stars with realistic hadronic equations of state and strange matter\\nequation of state. We also provide analytical expressions for the exterior\\nspacetime of scalarized neutron stars and their epicyclic frequencies in the\\nnonrotating limit.\\n
A randomized phase II trial of tacrolimus, mycophenolate mofetil and sirolimus after non-myeloablative unrelated donor transplantation
2014-08-01

The study is a randomized phase II trial investigating graft-versus-host disease prophylaxis after non-myeloablative (90 mg/m(2) fludarabine and 2 Gy total body irradiation) human leukocyte antigen matched unrelated donor transplantation. Patients were randomized as follows: arm 1 - tacrolimus 180 days and mycophenolate mofetil 95 days (n=69); arm 2 - tacrolimus 150 days and mycophenolate mofetil 180 days (n=71); arm 3 - tacrolimus 150 days, mycophenolate mofetil 180 days and sirolimus 80 days (n=68). All patients had sustained engraftment. Grade II-IV acute graft-versus-host disease rates in the 3 arms were 64%, 48% and 47% at Day 150, respectively (arm 3 vs. arm 1 (hazard ratio 0.62; P=0.04). Owing to the decreased incidence of acute graft-versus-host disease, systemic steroid use was lower at Day 150 in arm 3 (32% vs. 55% in arm 1 and 49% in arm 2; overall P=0.009 by hazard ratio analysis). The Day 150 incidence of cytomegalovirus reactivation was lower in arm 3 (arm 1, 54%; arm 2, 47%; arm 3, 22%; overall P=0.002 by hazard ratio analysis). Non-relapse mortality was comparable in the three arms at two years (arm 1, 26%; arm 2, 23%; arm 3, 18%). Toxicity rates and other outcome measures were similar between the three arms. The addition of sirolimus to tacrolimus and mycophenolate mofetil is safe and associated with lower incidence of acute graft-versus-host disease and cytomegalovirus reactivation. (clinicaltrials.gov identifier: 00105001).
What kind of consciousness is minimal?
2014-08-01

Most evidence speaks for non-unitary models of minimal consciousness. If these models are correct, patients with MCS may have, in addition to temporal fluctuations, a lower level of consciousness compared with fully conscious individuals. A still lower level could characterize patients diagnosed as unresponsive wakefulness syndrome (UWS). From this point of view, therefore, the difference between UWS and MCS is gradual rather than qualitative. However, due to methodological limitations of the available studies, the evidence for non-unitary models cannot be regarded as definite.
Exploring Syntactic Features for Native Language Identification: A Variationist Perspective on Feature Encoding and Ensemble Optimization
2014-08-01

In this paper, we systematically explore lexicalized and non-lexicalized local syntactic features for the task of Native Language Identification (NLI). We investigate different types of feature representations in single- and cross-corpus settings, including two representations inspired by a variationist perspective on the choices made in the linguistic system. To combine the different models, we use a probabilities-based ensemble classifier and propose a technique to optimize and tune it. Combining the best performing syntactic features with four types of n-grams outperforms the best approach of the NLI Shared Task 2013.
Divalent Transition Metal Silylamide Ate Complexes
2014-08-01

Abstract Dimetallic ate complexes were synthesized from the divalent transition metal silylamide complexes {Fe[N(SiMe 3 ) 2 ] 2 } 2 , Cr[N(SiMe 3 ) 2 ] 2 (thf), Co[N(SiMe 3 ) 2 ] 2 (thf) 2 , and {Mn[N(SiHMe 2 ) 2 ] 2 } 2 (thf = tetrahydrofuran) by the addition of the corresponding lithium or sodium silylamide salt. Accordingly, donor‐free LiFe[N(SiMe 3 ) 2 ] 3 and NaMn[N(SiHMe 2 ) 2 ] 3 as well as thf‐coordinated (thf)NaCr[N(SiMe 3 ) 2 ] 3 and (thf)NaCo[N(SiMe 3 ) 2 ] 3 were obtained. The thf‐containing mixed iron(II)/lithium bis(trimethylsilyl)amide complex (thf)LiFe[N(SiMe 3 ) 2 ] 3 was synthesized by the simple addition of thf to the donor‐free complex LiFe[N(SiMe 3 ) 2 ] 3 . All of the complexes were characterized by IR spectroscopy and elemental analysis, and the effective magnetic moments in solution were determined by the Evans method. The solid‐state structures of these bis(trimethylsilyl)amido‐derived complexes were additionally determined by X‐ray crystallography.
Mineralogy and crystallography of some Itokawa particles returned by the Hayabusa asteroidal sample return mission
2014-08-01

We studied seven Itokawa particles provided by the Japan Aerospace Exploration Agency (JAXA) as first International Announcement of Opportunity (AO) study mainly using electron and synchrotron radiation X-ray beam techniques. All the analyzed particles were collected from the first-touchdown site and composed of olivine and plagioclase with traces of Ca phosphate and chromite, and do not contain pyroxenes. Optical microscopy of these particles shows minor undulatory extinction of olivine and plagioclase, suggesting minor shock metamorphism (shock stage: S2). The electron microprobe analysis shows that olivine is Fo(70-73) and plagioclase is An(13-10)Or(5-7). The synchrotron radiation X-ray diffraction (SR-XRD) analysis of olivine crystals gives cell dimensions of a = 4.708 to 4.779 angstrom, b = 10.271 to 10.289 angstrom, c = 6.017 to 6.024 angstrom, corresponding to the Fo content of Fo(similar to 70) by Vegard's law. This composition matches the result obtained by the electron microprobe analysis. The olivine compositions of the analyzed particles are consistent with those of LL chondrites. The cell dimensions of two plagioclase crystals (a = 8.180 to 8.194 angstrom, b = 12.53 to 12.893 angstrom, c = 7.125 to 7.23 angstrom, a = 92.6 degrees to 93.00 degrees, beta = 116.36 degrees to 116.75 degrees, gamma = 90.03 degrees to 90.17 degrees) indicate that their equilibration temperatures are 800 degrees C +/- 10 degrees C. This temperature is near the peak metamorphic temperature recorded by equilibrated ordinary chondrites. The size of plagioclase crystals and the homogeneity of olivine compositions indicate that their petrologic type is &amp;gt;= 5. We also analyzed plagioclase by SR iron X-ray absorption near-edge structure (SR-XANES) and found that its Fe3+/(Fe2+ + Fe3+) ratio is approximately 0.5. Such high Fe3+ abundance indicates the formation under a relatively oxidizing environment. Thus, all these analyses have reconfirmed that the Itokawa particles returned by the Hayabusa spacecraft are very weakly shocked equilibrated LL chondrites, which matches the results of the preliminary examination team.
A New Geometric Approach for Faster Solving the Perspective-Three-Point Problem
2014-08-01

We present a fast and simple method for solving the perspective-three-point (P3P) problem. The problem is specified as finding the position and orientation of a camera from a single image, showing three points, while the position of the corresponding points in the world is known. Our approach is based on a new geometric parametrization, yielding simpler algebraic terms to compute, compared to all state-of-the-art methods. It is therefore faster and more accurate, since calculations are saved and rounding errors appear less. The method also showed to be robust against noise. A special case of this method has been successfully applied to a robotics scenario. However, the method is feasible for all applications that utilize P3P problem solvers.
Mapping the Internal Structure of Hopewell Tumuli in the Lower Illinois River Valley through Archaeological Geophysics
2014-08-01

Abstract Archaeologists from the Center for American Archeology (CAA) in Kampsville, Illinois, are engaged in a program to test the potential for ground-penetrating radar (GPR) and electrical resistance tomography (ERT) to effectively document the internal structure of a variety of Middle (ca.2200–1550 B.P.) and Late Woodland (ca.1550–950 B.P.) mounds in the Lower Illinois River Valley (LIV). This project, embedded within ongoing CAA regional research efforts and the Arizona State University Kampsville Field School, demonstrates that both GPR and ERT permit the identification and measurement of significant internal mound structures. Key structural elements can be confidently identified in the geophysical data from the five test mounds, and excavation results can be conclusively linked with results of excavation in mounds that have been tested. This study opens the way for the development of a set of procedures for a regional research initiative in the LIV to understand structural variation between Middle and Late Woodland mounds using ground-based remote sensing methods as a primary source of data and thus minimizing invasive and destructive investigation techniques.
Productivity Versus Employment: Quantifying the Economic Effects of an EU–Japan Free Trade Agreement
2014-08-01

Abstract The European Union and Japan recently entered into negotiations over a bilateral free trade agreement intended to stimulate growth and create wealth. Since customs duties are already low, the success of the liberalisation process hinges on the elimination of non‐tariff barriers. The purpose of this paper is to shed light on two possible liberalisation scenarios: a less ambitious liberalisation and a comprehensive liberalisation. In contrast to classic studies, our paper builds on the modern trade literature, accounting for the dominance of intra‐industry trade in both economies and the existence of heterogeneous firms. Furthermore, we model a search‐and‐matching labour market, allowing us to quantify employment effects of trade liberalisation. We find that a comprehensive liberalisation increases Japanese GDP by 0.86 per cent, whereas the EU experiences only an additional 0.21 per cent of real GDP growth. Most of the growth in real GDP is due to firms' efficiency gains, whereas unemployment is reduced by only a small amount. Other world regions experience small reductions of GDP due to trade diversion effects.
ANTSAC: A Generic RANSAC Variant Using Principles of Ant Colony Algorithms
2014-08-01

In this paper, we present a new variant of the well-known Random Sample Consensus (RANSAC) algorithm for robust estimation of model parameters. The idea of our method is based on a kind of volatile memory which is similar to the pheromone evaporation in the ant colony optimization algorithm. Therefore, we call our improved RANSAC like algorithm ANTSAC. We describe our new approach and the influence of its relevant parameters to the achieved performance in detail. ANTSAC is computationally efficient and convincingly easy to implement. It turns out that ANTSAC significantly outperforms RANSAC regarding the number of inliers after a given number of iterations. Further, we show that the advantage of ANTSAC increases with the complexity of the problem, i.e., with the number of model parameters, as well as with the relative number of outliers. ANTSAC is entirely generic, such that no further domain knowledge is required, as it is for many other RANSAC extensions. Nevertheless, we show that it is competitive to state-of-the-art methods even in domain specific scenarios.
Local Image Feature Matching Improvements for Omnidirectional Camera Systems
2014-08-01

The matching of oriented local image feature descriptors like SIFT, SURF or ORB often includes the refinement and filtering of matches based on the relative orientation of the features. This is important since the computational cost for subsequent tasks like camera pose estimation or object detection increases dramatically with the number of outliers. Simple 2D orientation descriptions are unsuitable for Omni directional images because of image distortions and non-monotonic mapping from camera rotations to image rotations. In this work we introduce 3D orientation descriptors which, unlike 2D descriptors, are suitable for match refinement on Omni directional images and improve matching results on images from cameras and camera rigs with a wide field of view. We evaluate different match refinement strategies based on 2D and 3D orientations and show the fundamental advantages of our approach.
Special Issue on Digital Domains
2014-08-01

More and more archaeologists who once relied on shovels and surveys now regularly collect data with digital sensors and use computer-based management systems to carry out complex analyses. Geographic information systems (GIS) and geographic information science (GISc), satellite remote sensing, aerial and close-range photography, terrestrial and aerial Light Detection and Ranging (LiDAR), near-surface geophysics, and a wide array of visualization schemes designed to integrate and display data from multiple platforms are now integral to every stage of archaeological investigation, interpretation, and reporting. Even though these methods are an increasing part of archaeological research worldwide, there have been few conferences, meetings, or workshops dedicated to sharing methods and applications in digital archaeology in North America or even in the Western Hemisphere, with the exception of a few special sessions in regional or general archaeological conferences. This deficit is particularly striking in comparison with the situation in Europe, where several societies dedicated to archaeological geomatics regularly hold both continental and regional meetings.
Here, there, everywhere
2014-08-03

mRNA localization and localized translation is a common mechanism that contributes to cell polarity and cellular asymmetry. In metazoan, mRNA transport participates in embryonic axis determination and neuronal plasticity. Since the mRNA localization process and its molecular machinery are rather complex in higher eukaryotes, the unicellular yeast Saccharomyces cerevisiae has become an attractive model to study mRNA localization. Although the focus has so far been on the mechanism of ASH1 mRNA transport, it has become evident that mRNA localization also assists in protein sorting to organelles, as well as in polarity establishment and maintenance. A diversity of different pathways has been identified that targets mRNA to their destination site, ranging from motor protein-dependent trafficking of translationally silenced mRNAs to co-translational targeting, in which mRNAs hitch-hike to organelles on ribosomes during nascent polypeptide chain elongation. The presence of these diverse pathways in yeast allows a systemic analysis of the contribution of mRNA localization to the physiology of a cell.
Advances in Dialectometry
2014-08-04

Dialectometry applies computational and statistical analyses within dialectology, making work more easily replicable and understandable. This survey article first reviews the field briefly in order to focus on developments in the past five years. Dialectometry no longer focuses exclusively on aggregate analyses, but rather deploys various techniques to identify representative and distinctive features with respect to areal classifications. Analyses proceeding explicitly from geostatistical techniques have just begun. The exclusive focus on geography as explanation for variation has given way to analyses combining geographical, linguistic, and social factors underlying language variation. Dialectometry has likewise ventured into diachronic studies and has also contributed theoretically to comparative dialectology and the study of dialect diffusion. Although the bulk of research involves lexis and phonology, morphosyntax is receiving increasing attention. Finally, new data sources and new (online) analytical software are expanding dialectometry’s remit and its accessibility.
Correlative assessment of tumor microcirculation using contrast‐enhanced perfusion MRI and intravoxel incoherent motion diffusion‐weighted MRI: is there a link between them?
2014-08-04

The purpose of this study was to correlate intravoxel incoherent motion (IVIM) imaging with classical perfusion‐weighted MRI metrics in human gliomas. Parametric images for slow diffusion coefficient ( D ), fast diffusion coefficient ( D *), and fractional perfusion‐related volume ( f ) in patients with high‐grade gliomas were generated. Maps of F p (plasma flow), v p (vascular plasma volume), PS (permeability surface–area product), v e (extravascular, extracellular volume), E (extraction ratio), k e (influx ratio into the interstitium), and t c (vascular transit time) from dynamic contrast‐enhanced (DCE) and dynamic susceptibility contrast‐enhanced (DSC) MRI were also generated. A region‐of‐interest analysis on the contralateral healthy white matter and on the tumor areas was performed and the extracted parameter values were tested for any significant differences among tumor grades or any correlations. Only f could be significantly correlated to DSC‐derived v p and t c in healthy brain tissue. Concerning the tumor regions, F p was significantly positively correlated with D * and inversely correlated with f in DSC measurements. The D *, f , and f × D * values in the WHO grade III gliomas were non‐significantly different from those in the grade IV gliomas. There was a trend to significant negative correlations between f and PS as well as between f × D * and k e in DCE experiments. Presumably due to different theoretical background, tracer properties and modeling of the tumor vasculature in the IVIM theory, there is no clearly evident link between D *, f and DSC‐ and DCE‐derived metrics. Copyright © 2014 John Wiley &amp; Sons, Ltd.
Multi-digit Number Processing
2014-08-04

Abstract Only recently the focus in numerical cognition research has considered multi-digit number processing as a relatively new and yet understudied domain in mathematical cognition. In this chapter: (i) we argue that single-digit number processing is not sufficient to understand multi-digit number processing; (ii) provide an overview on which representations and effects have been investigated for multi-digit numbers; (iii) suggest a conceptual distinction between place-identification, place-value activation, and place-value computation; (iv) identify language influences on multi-digit number processing along that conceptual distinction; and (v) argue that for numerical development indices of multi-digit number processing may be more suitable predictors of later arithmetical performance than classical single-digit measure such as the distance effect or non-numerical variables (e.g., working memory). In the final section, we summarize the important issues in multi-digit number processing, outline future directions and try to encourage readers to contribute to a new, exciting, yet understudied domain of numerical cognition.
Experimental Micromorphology on Burnt Shells of Anomalocardia brasiliana (Gmelin 1791) (Bivalvia, Veneridae) and Its Potential for Identification of Combustion Features on Shell‐Matrix Sites
2014-08-04

The identification of in situ or reworked hearths in archaeological sediments is currently one of the main topics in archaeological micromorphology. In the case of shell‐matrix sites (shell mounds and middens), the clast‐supported matrix and high porosity can hamper the clear identification of combustion features. Previous experimental approaches were useful to identify in thin section the transformations induced by heating in mollusk shells, which are related to its mineralogy. Since different species of mollusks contain diverse mineralogy (aragonite, calcite, or both), it is expected that each species follows a specific thermal behavior, although similar general trends exist. In this short contribution, a set of valves of the mollusk Anomalocardia brasiliana (Gmelin 1791) (Bivalvia, Veneridae), the most important component of Brazilian shell mounds, was heated in a muffle furnace at temperatures from 200°C to 800°C. Thin sections were made and their description is presented for the identification of burnt shell of A. brasiliana . This information can help to infer the temperature of prehistoric fires and can assist in the identification of in situ versus reworked hearths in shell‐matrix sites.
Subliminal cues bias perception of facial affect in patients with social phobia: evidence for enhanced unconscious threat processing
2014-08-04

Socially anxious individuals have been shown to exhibit altered processing of facial affect, especially expressions signaling threat. Enhanced unaware processing has been suggested an important mechanism which may give rise to anxious conscious cognition and behavior. This study investigated whether individuals with social anxiety disorder (SAD) are perceptually more vulnerable to the biasing effects of subliminal threat cues compared to healthy controls. In a perceptual judgment task, 23 SAD and 23 matched control participants were asked to rate the affective valence of parametrically manipulated affective expressions ranging from neutral to angry. Each trial was preceded by subliminal presentation of an angry/neutral cue. The SAD group tended to rate target faces as "angry" when the preceding subliminal stimulus was angry vs. neutral, while healthy participants were not biased by the subliminal stimulus presentation. The perceptual bias in SAD was also associated with higher reaction time latencies in the subliminal angry cue condition. The results provide further support for enhanced unconscious threat processing in SAD individuals. The implications for etiology, maintenance, and treatment of SAD are discussed.