An Empirical Study of Real-World SPARQL Queries

Understanding how users tailor their SPARQL queries is crucial when designing query evaluation engines or fine-tuning RDF stores with performance in mind. In this paper we analyze 3 million real-world SPARQL queries extracted from logs of the DBPedia and SWDF public endpoints. We aim at finding which are the most used language elements both from syntactical and structural perspectives, paying special attention to triple patterns and joins, since they are indeed some of the most expensive SPARQL operations at evaluation phase. We have determined that most of the queries are simple and include few triple patterns and joins, being Subject-Subject, Subject-Object and Object-Object the most common join types. The graph patterns are usually star-shaped and despite triple pattern chains exist, they are generally short.Comment: 1st International Workshop on Usage Analysis and the Web of Data (USEWOD2011) in the 20th International World Wide Web Conference (WWW2011), Hyderabad, India, March 28th, 201

State-of-the-art techniques for calculating spectral functions in models for correlated materials

The dynamical mean field theory (DMFT) has become a standard technique for the study of strongly correlated models and materials overcoming some of the limitations of density functional approaches based on local approximations. An important step in this method involves the calculation of response functions of a multiorbital impurity problem which is related to the original model. Recently there has been considerable progress in the development of techniques based on the density matrix renormalization group (DMRG) and related matrix product states (MPS) implying a substantial improvement to previous methods. In this article we review some of the standard algorithms and compare them to the newly developed techniques, showing examples for the particular case of the half-filled two-band Hubbard model.Comment: 8 pages, 4 figures, to be published in EPL Perspective

Complete sequence of the genome of the human isolate of Andes virus CHI-7913: comparative sequence and protein structure analysis

Indexación: ScieloWe report here the complete genomic sequence of the Chilean human isolate of Andes virus CHI-7913. The S, M, and L genome segment sequences of this isolate are 1,802, 3,641 and 6,466 bases in length, with an overall GC content of 38.7%. These genome segments code for a nucleocapsid protein of 428 amino acids, a glycoprotein precursor protein of 1,138 amino acids and a RNA-dependent RNA polymerase of 2,152 amino acids. In addition, the genome also has other ORFs coding for putative proteins of 34 to 103 amino acids. The encoded proteins have greater than 98% overall similarity with the proteins of Andes virus isolates AH-1 and Chile R123. Among other sequenced Hantavirus, CHI-7913 is more closely related to Sin Nombre virus, with an overall protein similarity of 92%. The characteristics of the encoded proteins of this isolate, such as hydrophobic domains, glycosylation sites, and conserved amino acid motifs shared with other Hantavirus and other members of the Bunyaviridae family, are identified and discussed

Single cell mechanics: stress stiffening and kinematic hardening

Cell mechanical properties are fundamental to the organism but remain poorly understood. We report a comprehensive phenomenological framework for the nonlinear rheology of single fibroblast cells: a superposition of elastic stiffening and viscoplastic kinematic hardening. Our results show, that in spite of cell complexity its mechanical properties can be cast into simple, well-defined rules, which provide mechanical cell strength and robustness via control of crosslink slippage.Comment: 4 pages, 6 figure

Improved image quality in pinhole SPECT by accurate modeling of the point spread function in low magnification systems

PURPOSE: Single photon emission computed tomography (SPECT) has become an important noninvasive imaging technique in small-animal research. Due to the high resolution required in small-animal SPECT systems, the spatially variant system response needs to be included in the reconstruction algorithm. Accurate modeling of the system response should result in a major improvement in the quality of reconstructed images. The aim of this study was to quantitatively assess the impact that an accurate modeling of spatially variant collimator/detector response has on image-quality parameters, using a low magnification SPECT system equipped with a pinhole collimator and a small gamma camera. METHODS: Three methods were used to model the point spread function (PSF). For the first, only the geometrical pinhole aperture was included in the PSF. For the second, the septal penetration through the pinhole collimator was added. In the third method, the measured intrinsic detector response was incorporated. Tomographic spatial resolution was evaluated and contrast, recovery coefficients, contrast-to-noise ratio, and noise were quantified using a custom-built NEMA NU 4-2008 image-quality phantom. RESULTS: A high correlation was found between the experimental data corresponding to intrinsic detector response and the fitted values obtained by means of an asymmetric Gaussian distribution. For all PSF models, resolution improved as the distance from the point source to the center of the field of view increased and when the acquisition radius diminished. An improvement of resolution was observed after a minimum of five iterations when the PSF modeling included more corrections. Contrast, recovery coefficients, and contrast-to-noise ratio were better for the same level of noise in the image when more accurate models were included. Ring-type artifacts were observed when the number of iterations exceeded 12. CONCLUSIONS: Accurate modeling of the PSF improves resolution, contrast, and recovery coefficients in the reconstructed images. To avoid the appearance of ring-type artifacts, the number of iterations should be limited. In low magnification systems, the intrinsic detector PSF plays a major role in improvement of the image-quality parameters.Gobierno de EspañaCDTI-CENIT (AMIT project)Instituto de Salud Carlos III (ISCIII

Temporal code-driven stimulation: definition and application to electric fish signaling

This Document is Protected by copyright and was first published by Frontiers. All rights reserved. it is reproduced with permissionClosed-loop activity-dependent stimulation is a powerful methodology to assess information processing in biological systems. In this context, the development of novel protocols, their implementation in bioinformatics toolboxes and their application to different description levels open up a wide range of possibilities in the study of biological systems. We developed a methodology for studying biological signals representing them as temporal sequences of binary events. A specific sequence of these events (code) is chosen to deliver a predefined stimulation in a closed-loop manner. The response to this code-driven stimulation can be used to characterize the system. This methodology was implemented in a real time toolbox and tested in the context of electric fish signaling. We show that while there are codes that evoke a response that cannot be distinguished from a control recording without stimulation, other codes evoke a characteristic distinct response. We also compare the code-driven response to open-loop stimulation. The discussed experiments validate the proposed methodology and the software toolbox.This work was funded by Spanish projects of Ministerio de Economia y Competitividad/FEDER TIN-2010-19607, TIN2014-54580-R, TIN-2012-30883, DPI2015 65833-P (http://www.mineco.gob.es/), ONRG grant N62909-14-1-N279, Brazilian Agency of Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (http://www.cnpq.br/) and Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (www.fapesp.br). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Microscopic and NanoSIMS characterization of black shale-hosted pre-kinematic pyrites: Possible gold source of the orogenic gold deposits in the Truchas Syncline (Variscan Iberian Massif)

[EN] The Truchas Syncline contains orogenic gold deposits (OGDs), hosted mainly by the Armorican Quartzite Fm. In order to look for the source of gold in these deposits, pre-kinematic sulphides from black shales from the overlying Luarca Fm. were studied using both optical and scanning electron (SEM) microscopy, as well as nanoscale secondary ion mass spectrometry (NanoSIMS). NanoSIMS images allowed the observation of relevant structures (pyrite with high As content nodules) hidden to SEM. Microscopy and 36S, 75As32S, 75As, 75As34S, and 197Au mappings, as well as δ34S analysis (‰ Vienna-Canyon Diablo Troilite) allowed 4 types of pyrite to be characterized. According to their sequence of deposition, the pyrite types identified are the following: (1) framboid nuclei (FmPy), with δ34S between +4.1‰ and +57.5‰; (2) overgrowths (OgPy), with presence of Au, As and δ34S of approximately +20.5‰; (3) pyrite with high As content (AsPy), replacing previous pyrites, with δ34S of approximately +23‰, nodular shapes and non-detected Au; (4) subhedral pyrite (ShPy), with δ34S of approximately +19.7‰ and Au and As distribution showing (a) nuclei, (b) rims with Au and As and (c) structures interpreted as replacements of previous pyrite. Luarca Fm. pyrite framboids reach 75 μm in size, larger than framboids described in most previous NanoSIMS work, with microcrystals sufficiently large to be analyzed without contamination from edge effects. The FmPy formed in early diagenetic conditions by dissimilatory reduction of marine sulphate plus Rayleigh distillation or anaerobic oxidation of methane processes. The first FmPy nuclei formed in the periphery of framboids, and then started to form in the central region until completion of the framboidal structure. Growth of OgPy, AsPy and ShPy corresponded to more advanced diagenetic conditions, although the last stage of ShPy growth followed an aggregation model, in which ShPy metamorphic pyrites grew over ShPy diagenetic pyrites. The sulphur isotopic signature of the four types of pyrite is in good agreement with a source from Ordovician marine sulphate. A hypothesis stating that the source of Au in OGDs in the district could be in Luarca Fm. is supported by the results of the present research. Firstly, a source of Au in the district could have been the replacement of previous pyrites by AsPy and the release of Au to the system, instead of the framboidal to euhedral pyrite recrystallization process observed in other gold deposits. Secondly, by the correspondence between δ34S isotopic signature of the pyrites from Luarca Fm. and those from sulphides in OGDs. However, these results do not rule out other possible sources.SIThis project was funded by Project 0284_ESMIMET_3_E (INTERREG V-A Spain-Portugal Cooperation Programme, 2014-20) and by Project LE167G18 (Junta de Castilla y Le´on, Spain)

Phylogenetic prospecting for cryptic species of the genus Merluccius (Actinopterygii: Merlucciidae).

Hakes of the genus Merluccius include 11 valid species as well a number of rare morphotypes suspected to be “cryptic species”. Concatenated nucDNA ITS1-rDNA and mtDNA cyt b sequences plus nested ITS1Nes sequences allowed to ascribe 14 specimens of nine rare morphotypes from the South Pacific and the South Atlantic to the phylogenetic backbone of this genus. Bayesian analyses pointed to M. bilinearis and M. albidus as the oldest species of the genus and the New World cluster, respectively. The phylogenetic status of M. angustimanus from the upper Gulf of California suggests its hybrid origin between M. gayi and M. productus from about 0.25 MYA, although an ever since confinement of a subset of those species cannot be ruled out. The molecular phylodiagnostic test suggests a common origin of all rare morphotypes and the absence of cryptic hake species in the Southern Cone. The molecular background of the morphotypes distributed between the Western Pacific South of New Zealand and the western Atlantic South of Argentina is compatible with their hybrid origin between M. gayi and both, M. australis or M. hubbsi, respectively.This research was partially supported with the project LETSHAKE (AGL2013-4846-R) co-funded by MINECO (Ministerio Español de Economía y Competitividad) and EU-FEDER to M.P. as well as with grant (IN607B 2018/14) to M. P. from Xunta de Galicia-Axencia Galega de Innovación. This work was also partly funded with grants from “Consellería de Educación e Ordenación Universitaria Xunta de Galicia (Galician Regional Government) cofunding from the European Regional Development Fund (ERDF) in the framework of the Operational Program Galicia 2014–2020 (CIM-UVIGO), “A way to build Europe”.Versión del edito

Underlying Resistance Mechanisms in the Cynosurus echinatus Biotype to Acetyl CoA Carboxylase-Inhibiting Herbicides

Hedgehog dogtail (Cynosurus echinatus) is an annual grass, native to Europe, but also widely distributed in North and South America, South Africa and Australia. Two hedgehog dogtail biotypes, one diclofop-methyl (DM)-resistant and one DM-susceptible were studied in detail for experimental dose-response resistance mechanisms. Herbicide rates that inhibited shoot growth by 50% (GR50) were determined for DM, being the resistance factor (GR50R/GR50S) of 43.81. When amitrole (Cyt. P450 inhibitor) was applied before treatment with DM, the R biotype growth was significantly inhibited (GR50 of 1019.9 g ai ha-1) compared with the GR50 (1484.6 g ai ha-1) found for the R biotype without pretreatment with amitrole. However, GR50 values for S biotype do not vary with or without amitrole pretreatment. Dose-response experiments carried out to evaluate cross-resistance, showed resistance to aryloxyphenoxypropionate (APP), cyclohexanodione (CHD) and phenylpyrazoline (PPZ) inhibiting herbicides. Both R and S biotypes had a similar 14C-DM uptake and translocation. The herbicide was poorly distributed among leaves, the rest of the shoot and roots with unappreciable acropetal and/or basipetal DM translocation at 96 HAT. The metabolism of 14C-DM, D-acid and D-conjugate metabolites were identified by thin-layer chromatography. The results showed that DM resistance in C. echinatus is likely due to enhanced herbicide metabolism, involving Cyt. P450 as was demonstrated by indirect assays (amitrole pretreatment). The ACCase in vitro assays showed that the target site was very sensitive to APP, CHD and PPZ herbicides in the C. echinatus S biotype, while the R biotype was insensitive to the previously mentioned herbicides. DNA sequencing studies confirmed that C. echinatus cross-resistance to ACCase inhibitors has been conferred by specific ACCase double point mutations Ile-2041-Asn and Cys-2088-Arg