julilili42/papers huggingface dataset:
Seismic wave propagation in anisotropic ice – Part 2: Effects of crystal anisotropy in geophysical data
2015-02-20

Abstract. We investigate the propagation of seismic waves in anisotropic ice. Two effects are important: (i) sudden changes in crystal orientation fabric (COF) lead to englacial reflections; (ii) the anisotropic fabric induces an angle dependency on the seismic velocities and, thus, recorded travel times. Velocities calculated from the polycrystal elasticity tensor derived for the anisotropic fabric from measured COF eigenvalues of the EDML ice core, Antarctica, show good agreement with the velocity trend determined from vertical seismic profiling. The agreement of the absolute velocity values, however, depends on the choice of the monocrystal elasticity tensor used for the calculation of the polycrystal properties. We make use of abrupt changes in COF as a common reflection mechanism for seismic and radar data below the firn–ice transition to determine COF-induced reflections in either data set by joint comparison with ice-core data. Our results highlight the possibility to complement regional radar surveys with local, surface-based seismic experiments to separate isochrones in radar data from other mechanisms. This is important for the reconnaissance of future ice-core drill sites, where accurate isochrone (i.e. non-COF) layer integrity allows for synchronization with other cores, as well as studies of ice dynamics considering non-homogeneous ice viscosity from preferred crystal orientations.
An Information-Centric Communication Infrastructure for Real-Time State Estimation of Active Distribution Networks
2015-02-20

The evolution toward emerging active distribution networks (ADNs) can be realized via a real-time state estimation (RTSE) application facilitated by the use of phasor measurement units (PMUs). A critical challenge in deploying PMU-based RTSE applications at large scale is the lack of a scalable and flexible communication infrastructure for the timely (i.e., sub-second) delivery of the high volume of synchronized and continuous synchrophasor measurements. We address this challenge by introducing a communication platform called C-DAX based on the information-centric networking (ICN) concept. With a topic-based publish-subscribe engine that decouples data producers and consumers in time and space, C-DAX enables efficient synchrophasor measurement delivery, as well as flexible and scalable (re) configuration of PMU data communication for seamless full observability of power conditions in complex and dynamic scenarios. Based on the derived set of requirements for supporting PMU-based RTSE in ADNs, we design the ICN-based C-DAX communication platform, together with a joint optimized physical network resource provisioning strategy, in order to enable the agile PMU data communications in near real-time. In this paper, C-DAX is validated via a field trial implementation deployed over a sample feeder in a real-distribution network; it is also evaluated through simulation-based experiments using a large set of real medium voltage grid topologies currently operating live in The Netherlands. This is the first work that applies emerging communication paradigms, such as ICN, to smart grids while maintaining the required hard real-time data delivery as demonstrated through field trials at national scale. As such, it aims to become a blueprint for the application of ICN-based general purpose communication platforms to ADNs.
EpiToolKit—a web-based workbench for vaccine design
2015-02-20

Abstract Summary: EpiToolKit is a virtual workbench for immunological questions with a focus on vaccine design. It offers an array of immunoinformatics tools covering MHC genotyping, epitope and neo-epitope prediction, epitope selection for vaccine design, and epitope assembly. In its recently re-implemented version 2.0, EpiToolKit provides a range of new functionality and for the first time allows combining tools into complex workflows. For inexperienced users it offers simplified interfaces to guide the users through the analysis of complex immunological data sets. Availability and implementation: http://www.epitoolkit.de Contact: schubert@informatik.uni-tuebingen.de Supplementary information: Supplementary data are available at Bioinformatics online.
Interface Dipole and Growth Mode of Partially and Fully Fluorinated Rubrene on Au(111) and Ag(111)
2015-02-20

Thin films of fully and partially fluorinated rubrene deposited on Au(111) and Ag(111) were investigated using ultraviolet and X-ray photoelectron spectroscopy. We demonstrate that fluorination of the molecules is an efficient way for tuning the metal–organic interface dipole and the hole injection barrier. Moreover, the results indicate that the pronounced electrostatic dipole moment of partially fluorinated rubrene (F14-RUB) has a strong impact on the growth mode of these molecules. Most notably, we infer that the first layer of F14-RUB on Au(111) and Ag(111) is formed by molecules with alternating orientation of their dipole moments whereas the second layer shows a nearly uniform orientation.
Unexpected dimerization of 1,3‐dimethyl‐5‐methylenebarbituric acid revealed by a combined experimental and computational study
2015-02-20

A comparison of experimental and calculated 13 C‐nuclear magnetic resonance chemical shifts reveals the molecular structure of a dimer that was obtained by an unexpected dimerization of 1,3‐dimethyl‐5‐methylenebarbituric acid. Furthermore, the puckering angle of the cyclobutane unit linking the six‐membered rings is discussed in detail. The influence of substituents on 1,3‐position of the cyclobutane ring on the puckering angle is demonstrated based on 1,1,3,3‐tetramethylcyclobutane. Copyright © 2015 John Wiley &amp; Sons, Ltd.
Structural and Enzymatic Analysis of TarM Glycosyltransferase from Staphylococcus aureus Reveals an Oligomeric Protein Specific for the Glycosylation of Wall Teichoic Acid
2015-02-21

Anionic glycopolymers known as wall teichoic acids (WTAs) functionalize the peptidoglycan layers of many Gram-positive bacteria. WTAs play central roles in many fundamental aspects of bacterial physiology, and they are important determinants of pathogenesis and antibiotic resistance. A number of enzymes that glycosylate WTA in Staphylococcus aureus have recently been identified. Among these is the glycosyltransferase TarM, a component of the WTA de novo biosynthesis pathway. TarM performs the synthesis of α-O-N-acetylglycosylated poly-5'-phosphoribitol in the WTA structure. We have solved the crystal structure of TarM at 2.4 Å resolution, and we have also determined a structure of the enzyme in complex with its substrate UDP-GlcNAc at 2.8 Å resolution. The protein assembles into a propeller-like homotrimer in which each blade contains a GT-B-type glycosyltransferase domain with a typical Rossmann fold. The enzymatic reaction retains the stereochemistry of the anomeric center of the transferred GlcNAc-moiety on the polyribitol backbone. TarM assembles into a trimer using a novel trimerization domain, here termed the HUB domain. Structure-guided mutagenesis experiments of TarM identify residues critical for enzyme activity, assign a putative role for the HUB in TarM function, and allow us to propose a likely reaction mechanism.
OH‐Directed Alkynylation of 2‐Vinylphenols with Ethynyl Benziodoxolones: A Fast Access to Terminal 1,3‐Enynes
2015-02-23

Abstract The first direct alkynylation of 2‐vinylphenols was developed. The rationally optimized hypervalent iodine reagent TIPS‐EBX* in combination with [(Cp*RhCl 2 ) 2 ] as a CH‐activating transition metal catalyst enables the construction of a variety of highly substituted 1,3‐enynes in high yields of up to 98 %. This novel CH activation method shows excellent chemoselectivity and exclusive ( Z )‐stereoselectivity, and it is also remarkably mild and tolerates a variety of functional groups. Furthermore, synthetic modifications of the resulting 1,3‐enynes were demonstrated. To our knowledge, this is the first example for an OH‐directed CH alkynylation with hypervalent iodine reagents.
Rapidly progressive hypertrophic cardiomyopathy in an infant with Noonan syndrome with multiple lentigines: Palliative treatment with a rapamycin analog
2015-02-23

Noonan syndrome with multiple lentigines (NSML) frequently manifests with hypertrophic cardiomyopathy (HCM). Recently, it was demonstrated that mTOR inhibition reverses HCM in NSML mice. We report for the first time on the effects of treatment with a rapamycin analog in an infant with LS and malignant HCM. In the boy, progressive HCM was diagnosed during the first week of life and a diagnosis of NSML was established at age 20 weeks by showing a heterozygous Q510E mutation in PTPN11 . Immunoblotting with antibodies against pERK, pAkt, and pS6RP in fibroblasts demonstrated enhanced Akt/mTOR pathway activity. Because of the patient's critical condition, everolimus therapy was started at age 24 weeks and continued until heart transplantation at age 36 weeks. Prior to surgery, heart failure improved from NYHA stage IV to II and brain natriuretic peptide values decreased from 9,600 to &lt;1,000 pg/ml, but no reversal of cardiac hypertrophy was observed. Examination of the explanted heart revealed severe hypertrophy and myofiber disarray with extensive perivascular fibrosis. These findings provide evidence that Akt/mTOR activity is enhanced in NSML with HCM and suggest that rapamycin treatment could principally be feasible for infantile NSML. The preliminary experiences made in this single patient indicate that therapy should start early to prevent irreversible cardiac remodelling. © 2015 Wiley Periodicals, Inc.
Diffusive–Dispersive and Reactive Fronts in Porous Media: Iron(II) Oxidation at the Unsaturated–Saturated Interface
2015-02-23

Diffusive–dispersive mass transfer is important for many groundwater quality problems as it drives the interaction between different reactants, thus influencing a wide variety of biogeochemical processes. In this study, we performed laboratory experiments to quantify O 2 transport in porous media, across the unsaturated–saturated interface, under both conservative and reactive transport conditions. As reactive system we considered the abiotic oxidation of Fe 2+ in the presence of O 2 . We studied the reaction kinetics in batch experiments and its coupling with diffusive and dispersive transport processes by means of one‐dimensional columns and two‐dimensional flow‐through experiments, respectively. A noninvasive optode technique was used to track O 2 transport into the initially anoxic porous medium at highly resolved spatial and temporal scales. The results show significant differences in the propagation of the conservative and reactive O 2 fronts. Under reactive conditions, O 2 , continuously provided from the atmosphere, was considerably retarded due to the interaction with dissolved Fe(II), initially present in the anoxic groundwater. The reaction between dissolved O 2 and Fe 2+ led to the formation of an Fe(III) precipitation zone in the experiments. Reactive transport modeling based on a kinetic PHREEQC module tested in controlled batch experiments allowed a quantitative interpretation of the experimental results in both one‐ and two‐dimensional setups.
Composition of junior research groups and PhD completion rate: disciplinary differences and policy implications
2015-02-23

This paper explores the link between the composition and the performance of junior research groups. The authors argue that the heterogeneity-performance link depends on the type of heterogeneity (cultural vs. study field) and on the disciplinary area. The authors test their hypotheses on a data set of 45 junior research groups and find a U-shaped relation between cultural heterogeneity and performance in the humanities and social sciences, but no link between the two in the natural sciences. The link between study field heterogeneity and performance in the natural sciences is negative, and in the humanities and social sciences study field heterogeneity and performance are not related. Interaction within the group helps reap the benefits of heterogeneity. The study results are derived in the context of junior research groups in Germany, but are generalizable to other countries and contexts where PhD education is taking part in groups.
Pluripotency Gene Expression and Growth Control in Cultures of Peripheral Blood Monocytes during Their Conversion into Programmable Cells of Monocytic Origin (PCMO): Evidence for a Regulatory Role of Autocrine Activin and TGF-β
2015-02-23

Previous studies have shown that peripheral blood monocytes can be converted in vitro to a stem cell-like cell termed PCMO as evidenced by the re-expression of pluripotency-associated genes, transient proliferation, and the ability to adopt the phenotype of hepatocytes and insulin-producing cells upon tissue-specific differentiation. However, the regulatory interactions between cultured cells governing pluripotency and mitotic activity have remained elusive. Here we asked whether activin(s) and TGF-β(s), are involved in PCMO generation. De novo proliferation of PCMO was higher under adherent vs. suspended culture conditions as revealed by the appearance of a subset of Ki67-positive monocytes and correlated with down-regulation of p21WAF1 beyond day 2 of culture. Realtime-PCR analysis showed that PCMO express ActRIIA, ALK4, TβRII, ALK5 as well as TGF-β1 and the βA subunit of activin. Interestingly, expression of ActRIIA and ALK4, and activin A levels in the culture supernatants increased until day 4 of culture, while levels of total and active TGF-β1 strongly declined. PCMO responded to both growth factors in an autocrine fashion with intracellular signaling as evidenced by a rise in the levels of phospho-Smad2 and a drop in those of phospho-Smad3. Stimulation of PCMO with recombinant activins (A, B, AB) and TGF-β1 induced phosphorylation of Smad2 but not Smad3. Inhibition of autocrine activin signaling by either SB431542 or follistatin reduced both Smad2 activation and Oct4A/Nanog upregulation. Inhibition of autocrine TGF-β signaling by either SB431542 or anti-TGF-β antibody reduced Smad3 activation and strongly increased the number of Ki67-positive cells. Furthermore, anti-TGF-β antibody moderately enhanced Oct4A/Nanog expression. Our data show that during PCMO generation pluripotency marker expression is controlled positively by activin/Smad2 and negatively by TGF-β/Smad3 signaling, while relief from growth inhibition is primarily the result of reduced TGF-β/Smad3, and to a lesser extent, activin/Smad2 signaling.
Model Atmosphere Spectrum Fit to the Soft X-Ray Outburst Spectrum of SS Cyg
2015-02-23

The X-ray spectrum of SS Cyg in outburst has a very soft component that can be interpreted as the fast-rotating optically thick boundary layer on the white dwarf surface. This component was carefully investigated by Mauche (2004) using the Chandra LETG spectrum of this object in outburst. The spectrum shows broad ( ≈5 °A) spectral features that have been interpreted as a large number of absorption lines on a blackbody continuum with a temperature of ≈250 kK. Because the spectrum resembles the photospheric spectra of super-soft X-ray sources, we tried to fit it with high gravity hot LTE stellar model atmospheres with solar chemical composition, specially computed for this purpose. We obtained a reasonably good fit to the 60–125 °A spectrum with the following parameters: T&lt;sub&gt;eff&lt;/sub&gt; = 190 kK, log g = 6.2, and NH = 8 · 10&lt;sup&gt;19&lt;/sup&gt; cm&lt;sup&gt;−2&lt;/sup&gt;, although at shorter wavelengths the observed spectrum has a much higher flux. The reasons for this are discussed. The hypothesis of a fast rotating boundary layer is supported by the derived low surface gravity.
Nucleon structure in light-front quark model constrained by AdS/QCD
2015-02-23

Using global fits of valence u and d quark parton distributions and data on quark and nucleon form factors in the Euclidean region, we derive a light-front quark model for the nucleon structure consistent with quark counting rules.
Constraints on an Annihilation Signal from a Core of Constant Dark Matter Density around the Milky Way Center with H.E.S.S.
2015-02-24

An annihilation signal of dark matter is searched for from the central region of the Milky Way. Data acquired in dedicated on-off observations of the Galactic center region with H.E.S.S. are analyzed for this purpose. No significant signal is found in a total of ∼9 h of on-off observations. Upper limits on the velocity averaged cross section, ⟨σv⟩, for the annihilation of dark matter particles with masses in the range of ∼300 GeV to ∼10 TeV are derived. In contrast to previous constraints derived from observations of the Galactic center region, the constraints that are derived here apply also under the assumption of a central core of constant dark matter density around the center of the Galaxy. Values of ⟨σv⟩ that are larger than 3×10^{-24} cm^{3}/s are excluded for dark matter particles with masses between ∼1 and ∼4 TeV at 95% C.L. if the radius of the central dark matter density core does not exceed 500 pc. This is the strongest constraint that is derived on ⟨σv⟩ for annihilating TeV mass dark matter without the assumption of a centrally cusped dark matter density distribution in the search region.
Cytokine and chemokine profile of the innate and adaptive immune response of schistosoma haematobium and plasmodium falciparum single and co-infected school-aged children from an endemic area of Lambaréné, Gabon
2015-02-24

This study provides original information on the cellular immune response of S. haematobium and/or P. falciparum in infected subjects. It rules out an effect of S. haematobium on the cytokine profile of subjects co-infected with P. falciparum.
Dual-Energy CT: Virtual Calcium Subtraction for Assessment of Bone Marrow Involvement of the Spine in Multiple Myeloma
2015-02-25

OBJECTIVE. Dual-energy CT (DECT) enables subtraction of calcium, facilitating the visualization of bone marrow (BM) in the axial skeleton. The purpose of this study was to assess whether DECT BM images have the potential to improve the detection of multifocal and diffuse BM infiltration in multiple myeloma (MM) in comparison with regular CT with MRI as the reference standard. SUBJECTS AND METHODS. This study included 32 consecutive patients who had known MM or presented with monoclonal gammopathy of unknown significance and underwent DECT and MRI of the axial skeleton. The degrees (none, n = 14; moderate, n = 10; and high, n = 8) and patterns (diffuse, n = 10 or multifocal, n = 8) of infiltration were assessed on MR images. Attenuation in BM and CT images in known uninvolved and involved areas was measured. Cutoff values of attenuation in BM images for infiltration in lytic and nonlytic lesions were established by ROC analysis. At least 120 days later, sensitivity and specificity for reading CT images alone and when using additional BM images were evaluated. RESULTS. ROC analysis revealed larger AUC in BM images than in CT images; cutoff values for marrow invasion in BM images were 4 and -3 HU in lytic and nonlytic lesions, respectively. In the blinded reading session, BM images improved the sensitivity for the detection of diffuse infiltration from 0 to as much as 75% for cases with high-grade infiltration. In multifocal patterns, BM images did not significantly change the detection rate. CONCLUSION. BM images have the potential to improve the sensitivity for detection of diffuse BM involvement in comparison with regular CT.
Tensor Representation of Spin States
2015-02-25

We propose a generalization of the Bloch sphere representation for arbitrary spin states. It provides a compact and elegant representation of spin density matrices in terms of tensors that share the most important properties of Bloch vectors. Our representation, based on covariant matrices introduced by Weinberg in the context of quantum field theory, allows for a simple parametrization of coherent spin states, and a straightforward transformation of density matrices under local unitary and partial tracing operations. It enables us to provide a criterion for anticoherence, relevant in a broader context such as quantum polarization of light.
A Photorhabdus Natural Product Inhibits Insect Juvenile Hormone Epoxide Hydrolase
2015-02-25

Abstract Simple urea compounds (“phurealipids”) have been identified from the entomopathogenic bacterium Photorhabdus luminescens , and their biosynthesis was elucidated. Very similar analogues of these compounds have been previously developed as inhibitors of juvenile hormone epoxide hydrolase (JHEH), a key enzyme in insect development and growth. Phurealipids also inhibit JHEH, and therefore phurealipids might contribute to bacterial virulence.
Microsaccade Control Signals in the Cerebellum
2015-02-25

Microsaccades, the small saccades made when we try to keep the eyes still, were once believed to be inconsequential for vision, but recent studies suggest that they can precisely relocate gaze to tiny visual targets. Because the cerebellum is necessary for motor precision, we investigated whether microsaccades may exploit this neural machinery in monkeys. Almost all vermal Purkinje cells, which provide the eye-related output of the cerebellar cortex, were found to increase or decrease their simple spike firing rate during microsaccades. At both the single-cell and population level, microsaccade-related activity was highly similar to macrosaccade-related activity and we observed a continuous representation of saccade amplitude that spanned both the macrosaccade and microsaccade domains. Our results suggest that the cerebellum's role in fine-tuning eye movements extends even to the oculomotor system's smallest saccades and add to a growing list of observations that call into question the classical categorical distinction between microsaccades and macrosaccades.
A small-scale hyperacute compound eye featuring active eye tremor: application to visual stabilization, target tracking, and short-range odometry
2015-02-25

In this study, a miniature artificial compound eye (15 mm in diameter) called the curved artificial compound eye (CurvACE) was endowed for the first time with hyperacuity, using similar micro-movements to those occurring in the fly's compound eye. A periodic micro-scanning movement of only a few degrees enables the vibrating compound eye to locate contrasting objects with a 40-fold greater resolution than that imposed by the interommatidial angle. In this study, we developed a new algorithm merging the output of 35 local processing units consisting of adjacent pairs of artificial ommatidia. The local measurements performed by each pair are processed in parallel with very few computational resources, which makes it possible to reach a high refresh rate of 500 Hz. An aerial robotic platform with two degrees of freedom equipped with the active CurvACE placed over naturally textured panels was able to assess its linear position accurately with respect to the environment thanks to its efficient gaze stabilization system. The algorithm was found to perform robustly at different light conditions as well as distance variations relative to the ground and featured small closed-loop positioning errors of the robot in the range of 45 mm. In addition, three tasks of interest were performed without having to change the algorithm: short-range odometry, visual stabilization, and tracking contrasting objects (hands) moving over a textured background.