Miracle-dz/UniFAR-FTUs huggingface dataset:
Holographic stress tensor for non-relativistic theories

We discuss the calculation of the field theory stress tensor from the dual geometry for two recent proposals for gravity duals of non-relativistic conformal field theories. The first of these has a Schrodinger symmetry including Galilean boosts, while the second has just an anisotropic scale invariance (the Lifshitz case). For the Lifshitz case, we construct an appropriate action principle. We propose a definition of the non-relativistic stress tensor complex for the field theory as an appropriate variation of the action in both cases. In the Schrodinger case, we show that this gives physically reasonable results for a simple black hole solution and agrees with an earlier proposal to determine the stress tensor from the familiar AdS prescription. In the Lifshitz case, we solve the linearised equations of motion for a general perturbation around the background, showing that our stress tensor is finite on-shell.
Conformational polymorphism or structural invariance in DNA photoinduced lesions: implications for repair rates

Abstract DNA photolesions constitute a particularly deleterious class of molecular defects responsible for the insurgence of a vast majority of skin malignant tumors. Dimerization of two adjacent thymines or cytosines mostly gives rise to cyclobutane pyrimidine dimers (CPD) and pyrimidine(6-4)pyrimidone 64-PP as the most common defects. We perform all-atom classical simulations, up to 2 μs, of CPD and 64-PP embedded in a 16-bp duplex, which reveal the constrasted behavior of the two lesions. In particular we evidence a very limited structural deformation induced by CPD while 64-PP is characterized by a complex structural polymorphism. Our simulations also allow to unify the contrasting experimental structural results obtained by nuclear magnetic resonance or Förster Resonant Energy Transfer method, showing that both low and high bent structures are indeed accessible. These contrasting behaviors can also explain repair resistance or the different replication obstruction, and hence the genotoxicity of these two photolesions.
Tools for the analysis and design of communication networks with Markovian dynamics

The stochastic properties of a class of communication networks whose dynamics are Markovian are analysed. The asymptotic behaviour of such a network in terms of the first and second moments of a stochastic process that describes the network dynamics is characterised and tools for their calculation are provided. Specifically, computation techniques for the calculation of these statistics are provided and that these algorithms converge exponentially fast is shown. Finally, how the results may be used for the design of network routers to realise networks with desired statistical properties is suggested.
Imaging condition for nonlinear scattering-based imaging: Estimate of power loss in scattering

Imaging highly complex subsurface structures is a challenging problem because it must ultimately deal with nonlinear multiple-scattering effects (e.g., migration of multiples, wavefield extrapolation with nonlinear model interactions, amplitude-preserving migration) to overcome the limitations of linear imaging. Most of the current migration techniques rely on the linear single-scattering assumption, and therefore, fail to handle these complex scattering effects. Recently, seismic imaging has been related to scattering-based image-domain interferometry to address the fully nonlinear imaging problem. Building on this connection between imaging and interferometry, we define the seismic image as a locally scattered wavefield and introduce a new imaging condition that is suitable and practical for nonlinear imaging. A previous formulation of nonlinear scattering-based imaging requires the evaluation of volume integrals that cannot easily be incorporated in current imaging algorithms. Our method consisted of a.
A DNA binding winged helix domain in CAF-1 functions with PCNA to stabilize CAF-1 at replication forks

Abstract Chromatin assembly factor 1 (CAF-1) is a histone H3–H4 chaperone that deposits newly synthesized histone (H3–H4)2 tetramers during replication-coupled nucleosome assembly. However, how CAF-1 functions in this process is not yet well understood. Here, we report the crystal structure of C terminus of Cac1 (Cac1C), a subunit of yeast CAF-1, and the function of this domain in stabilizing CAF-1 at replication forks. We show that Cac1C forms a winged helix domain (WHD) and binds DNA in a sequence-independent manner. Mutations in Cac1C that abolish DNA binding result in defects in transcriptional silencing and increased sensitivity to DNA damaging agents, and these defects are exacerbated when combined with Cac1 mutations deficient in PCNA binding. Similar phenotypes are observed for corresponding mutations in mouse CAF-1. These results reveal a mechanism conserved in eukaryotic cells whereby the ability of CAF-1 to bind DNA is important for its association with the DNA replication forks and subsequent nucleosome assembly.
Exploring the hyper-grid idea with grand challenge applications: the DEISA-TeraGrid interoperability demonstration

A supercomputing hyper-grid spanning two continents was created to move a step towards interoperability of leading grids. A dedicated network connection was established between DEISA, the leading European supercomputing grid, and TeraGrid, the leading American supercomputing grid. Both grids have adopted the approach of establishing a common, high performance global file system, the wide-area version of IBM's GPFS. Teragrid's approach is based on a single site server solution under Linux, hosted by San Diego Supercomputer Centre, DEISA's approach is a multi-site server solution, with currently servers in France, Germany and Italy. These two grid-internal global file systems were interconnected over a dedicated, trusted network connection. During the Supercomputing Conference 2005, grand challenge applications were carried out both within DEISA and within TeraGrid, and results were written transparently to the combined global file system with physically distributed locations of the involved disk systems. Simulations were carried out in Europe and in America, and results were directly written to the respective remote continent, accessible for all participating scientists in both continents, and were then directly further processed for visualization in a third location, the SC05 exhibition hall in Seattle. Grand challenge applications used for the demo included a protein structure prediction and a cosmological simulation carried out at San Diego Supercomputer Center (SDSC), US (www.sdsc.edu) and a Gyrokinetic turbulence simulation and also a cosmological simulation carried out at Garching Computing Centre of the Max Planck Society (RZG), Germany (www.rzg.mpg.de)
dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications

Protein modification is an extremely important post-translational regulation that adjusts the physical and chemical properties, conformation, stability and activity of a protein; thus altering protein function. Due to the high throughput of mass spectrometry (MS)-based methods in identifying site-specific post-translational modifications (PTMs), dbPTM (http://dbPTM.mbc.nctu.edu.tw/) is updated to integrate experimental PTMs obtained from public resources as well as manually curated MS/MS peptides associated with PTMs from research articles. Version 3.0 of dbPTM aims to be an informative resource for investigating the substrate specificity of PTM sites and functional association of PTMs between substrates and their interacting proteins. In order to investigate the substrate specificity for modification sites, a newly developed statistical method has been applied to identify the significant substrate motifs for each type of PTMs containing sufficient experimental data. According to the data statistics in dbPTM, >60% of PTM sites are located in the functional domains of proteins. It is known that most PTMs can create binding sites for specific protein-interaction domains that work together for cellular function. Thus, this update integrates protein–protein interaction and domain–domain interaction to determine the functional association of PTM sites located in protein-interacting domains. Additionally, the information of structural topologies on transmembrane (TM) proteins is integrated in dbPTM in order to delineate the structural correlation between the reported PTM sites and TM topologies. To facilitate the investigation of PTMs on TM proteins, the PTM substrate sites and the structural topology are graphically represented. Also, literature information related to PTMs, orthologous conservations and substrate motifs of PTMs are also provided in the resource. Finally, this version features an improved web interface to facilitate convenient access to the resource.
ABSOLUTE PHYSICAL CALIBRATION IN THE INFRARED

We determine an absolute calibration for the Multiband Imaging Photometer for Spitzer 24 μm band and recommend adjustments to the published calibrations for Two Micron All Sky Survey (2MASS), Infrared Array Camera (IRAC), and IRAS photometry to put them on the same scale. We show that consistent results are obtained by basing the calibration on either an average A0V star spectral energy distribution (SED), or by using the absolutely calibrated SED of the Sun in comparison with solar-type stellar photometry (the solar analog method). After the rejection of a small number of stars with anomalous SEDs (or bad measurements), upper limits of ∼1.5% root mean square (rms) are placed on the intrinsic infrared (IR) SED variations in both A-dwarf and solar-type stars. These types of stars are therefore suitable as general-purpose standard stars in the IR. We provide absolutely calibrated SEDs for a standard zero magnitude A star and for the Sun to allow extending this work to any other IR photometric system. They allow the recommended calibration to be applied from 1 to 25 μm with an accuracy of ∼2%, and with even higher accuracy at specific wavelengths such as 2.2, 10.6, and 24 μm, near which there are direct measurements. However, we confirm earlier indications that Vega does not behave as a typical A0V star between the visible and the IR, making it problematic as the defining star for photometric systems. The integration of measurements of the Sun with those of solar-type stars also provides an accurate estimate of the solar SED from 1 through 30 μm, which we show agrees with theoretical models.
Influence of landscape heterogeneity on spatial patterns of wood productivity, wood specific density and above ground biomass in Amazonia

Abstract. Long-term studies using the RAINFOR network of forest plots have generated significant insights into the spatial and temporal dynamics of forest carbon cycling in Amazonia. In this work, we map and explore the landscape context of several major RAINFOR plot clusters using Landsat ETM+ satellite data. In particular, we explore how representative the plots are of their landscape context, and test whether bias in plot location within landscapes may be influencing the regional mean values obtained for important forest biophysical parameters. Specifically, we evaluate whether the regional variations in wood productivity, wood specific density and above ground biomass derived from the RAINFOR network could be driven by systematic and unintentional biases in plot location. Remote sensing data covering 45 field plots were aggregated to generate landscape maps to identify the specific physiognomy of the plots. In the Landsat ETM+ data, it was possible to spectrally differentiate three types of terra firme forest, three types of forests over Paleovarzea geomorphologycal formation, two types of bamboo-dominated forest, palm forest, Heliconia monodominant vegetation, swamp forest, disturbed forests and land use areas. Overall, the plots were generally representative of the forest physiognomies in the landscape in which they are located. Furthermore, the analysis supports the observed regional trends in those important forest parameters. This study demonstrates the utility of landscape scale analysis of forest physiognomies for validating and supporting the finds of plot based studies. Moreover, the more precise geolocation of many key RAINFOR plot clusters achieved during this research provides important contextual information for studies employing the RAINFOR database.
THE SINS/zC-SINF SURVEY OF z ∼ 2GALAXY KINEMATICS: THE NATURE OF DISPERSION-DOMINATED GALAXIES

We analyze the spectra, spatial distributions, and kinematics of Hα, [N ii], and [S ii] emission in a sample of 38, z ∼ 2.2 UV/optically selected star-forming galaxies (SFGs) from the SINS and zC-SINF surveys, 34 of which were observed in the adaptive optics mode of SINFONI and 30 of those contain data presented for the first time here. This is supplemented by kinematic data from 43 z ∼ 1–2.5 galaxies from the literature. None of these 81 galaxies is an obvious major merger. We find that the kinematic classification of high-z SFGs as “dispersion dominated” or “rotation dominated” correlates most strongly with their intrinsic sizes. Smaller galaxies are more likely “dispersion-dominated” for two main reasons: (1) the rotation velocity scales linearly with galaxy size but intrinsic velocity dispersion does not depend on size or may even increase in smaller galaxies, and as such, their ratio is systematically lower for smaller galaxies, and (2) beam smearing strongly decreases large-scale velocity gradients and increases observed dispersion much more for galaxies with sizes at or below the resolution. Dispersion-dominated SFGs may thus have intrinsic properties similar to “rotation-dominated” SFGs, but are primarily more compact, lower mass, less metal enriched, and may have higher gas fractions, plausibly because they represent an earlier evolutionary state.
Characterization of a c/s-Diamrninedichloroplatinum(II)-resistant Human Ovarian Cancer Cell Line and Its Use in Evaluation of Platinum Analogues1

Human ovarian cancer cell lines with stable cisplatin resistance have been developed by chronic exposure of the parent cisplatin-sensitive A27X0line to increasing concentrations of cisplatin. 2780eâ„¢(CP8 refers to this cell line's growth in medium containing 8 MMcisplatin) has several clonal cytogenetic abnormalities but lacks homogeneously staining re gions or double-minute chromosomes. It has a significantly greater monolayer growth rate, cloning efficiency in agarose, and total glutathione content compared to the A2780 line, but similar activities of several glutathione-dependent enzymes. The 2780"'* subline is 73-fold resistant to cisplatin compared to the A2780 line, as well as cross-resistant to irradiation and melphalan. It is not cross-resistant to Adriamycin, but this develops with increased cisplatin resistance (14-fold) obtained by further cisplatin exposure of 2780"'*. Of the cisplatin analogues tested which are of current clinical interest, carboplatin, iproplatin, and tetraplatin, only the latter is more cytotoxic than cisplatin in the A2780 and 2780eâ„¢lines. The 2780eâ„¢subline is also cross-resistant to these ana logues in the relative order carboplatin > iproplatin > tetraplatin (most to least cross-resistant). Treatment of a highly cisplatin resistant cell line (2780""") with either melphalan or cisplatin was associated with a significant increase in [3H)thymidine incorporation into DNA in the presence of 10 m\i hydroxyurea compared with the parent sensitive cell line which showed essentially no capacity to repair DNA damage by these drugs. A2780 and its cisplatin-resistant cell lines may thus be useful in studying drug resistance mechanisms, in screening new drugs for activity (especially against drug resistant tumors), and in formulating induction and salvage therapies for ovarian cancer.
The Sentient Visor : Towards a Browser for the Internet of Things

As we advance towards an Internet of Things (IoT), it becomes necessary to conceive new forms of interaction between people and the everyday objects that surround them. A world full of internetworked objects with sensing capabilities requires effective tools in order to interpret contextual data gathered from the environment and services provided by smart objects. We aim to provide a browser for the IoT through what have referred to as a sentient visor. In this paper, we present a working prototype of a sentient visor by exposing its core technology and applications. The sentient visor incorporates mechanisms to identify smart objects, interact with them and infer information from contextual data by using semantic web technologies. We also pose some limitations and future directions of our approach. Keywords—Sentient Visor, Internet of Things, Semantic Information
On-line Signature Biometrics using Support Vector Machine

Handwritten signature has long been established as the most diffuse mean for personal verification in our daily life. It is commonly, in general, in all kind of legal documents and transactions. Therefore, within all biometric modalities, signature is probably the widest accepted. On the other hand, signature is a behavioural characteristic of individuals, and therefore is considered being weaker against fraud. Signature verification is the process in which, for a given signature who belongs to a user, a decision is made whether the signature has been made by that user, a genuine signature, or has been made by another user, a forgery signature. Typically, forged signatures have been classified into three groups: (1) random, (2) simple and (3) skilled [SB00]. The different methods for signature verification can be divided in two main groups: off-line (static) and on-line (dynamic). The off-line techniques are based in processing the digitalized grey-scale image of the signature written on a paper. On the contrary, on-line techniques take into account dynamic characteristics of the signature such as pressure exerted, tilts, position or velocity of the stylus. All this signals provide, not only information of the signature, but also information about the act of signing, which is consider more related to the specific user.
Impact of Link Distance on End-to-End Throughput in Multi-Rate, Multi-Hop Wireless Networks

Traditional routing protocols designed for multi-hop wireless networks select a route with the smallest hop count. The end-to-end throughput in the route may not be the maximum when network has multiple link data rates, as a small hop number implies a large geographic distance (link distance) for each hop. Due to the radio signal attenuation, this results in a low SNR at the receiving node and consequently a low available link data rate. Reducing the link distance by using routes with more hop counts can increase the link data rate. Yet this may not necessarily improve the end-to-end throughput because more nodes have to be included in the routes. In this work we investigate and analyze the impact of link distance on end-to-end throughput in multi-rate, multi-hop wireless networks. Analysis results show that changing link distance affects network throughput. To achieve a high network throughput, a proper link distance requirement has to be set for each hop, depending on different parameters such as load density.
An iterative algebraic approach to TCF matrix estimation

One of the greatest challenges in developing eye- in-hand visual servoing systems is accurate calibration. The central problem of eye-in-hand calibration is to solve the unknown extrinsic parameter X in the homogeneous equation AX = XB. A new formulation using algebraic rearrangement in combination with singular value decomposition is introduced to solve this classical problem. In addition, an iterative algorithm that reduces the error in the initial estimate is used to further improve the results. Experimental results both in simulation and with real data show the method to be easy to use, efficient and accurate. One of the greatest challenges in developing eye-in-hand visual servoing systems is accurate calibration. The central problem of eye-in-hand calibration is to solve the unknown extrinsic parameter X in the homogeneous equation AX = XB. A new formulation using algebraic rearrangement in combination with singular value decomposition is introduced to solve this classical problem. In addition, an iterative algorithm that reduces the error in the initial estimate is used to further improve the results. Experimental results both in simulation and with real data show the method to be easy to use, efficient and accurate.
Physical modeling with B-spline surfaces for interactive design and animation

Physically based modeling has recently become a subject of widespread interest. This paper defines a model of elastic and plastic B-spline surfaces which supports both animation and design operations, including the interference detection, within the "Eplastics"/Alpha_1 modeling environment. We develop "refinement" operations for spring and hinge B-spline models which are compatible with the physics and the mathematics of B-spline models, including refinement. It is also a step towards a more continuous physical representation of a physical model than the more standard discretized geometry point mass models. We present some interactive operations currently in real-time and some which could be real-time with further optimization and use of multiple processors on machines such as the SGI Iris 4D/240GTX. A movie is used to illustrate the results.
Chain-Chain Based Routing Protocol

Wireless sensor network (WSN) is an emerging technology for monitoring physical world. WSNs consist of large numbers of sensor nodes operated by battery mostly in harsh environment. Thus energy conservation is a primary issue for organization of these sensor nodes. Another crucial issue is the data delivery time by sensor nodes to the sink node, especially in Military, medical fields, and security monitoring systems where minimum delay is desirable. Number of protocols has been proposed in the literature for routing. One of such protocols is the cluster based routing protocol LEACH (low energy adaptive clustering hierarchy). LEACH protocol organizes WSN into a set of clusters and a periodic voting for cluster head is performed in order to be evenly distributed among all the sensors of the WSN. This periodical cluster head voting in LEACH, however, consumes an amount of non-negligible energy and other resources. For energy conservation, PEGASIS (power efficient gathering in sensor information systems) a near optimal chain-based protocol has been proposed, however, it is faced with the challenge of long delay for the transmitted data. Another routing protocol called CCM (Chain-Cluster based Mixed routing), which is mainly a hybrid of LEACH and PEGASIS is proposed, the consumed energy increases as network size increases. In this paper, we propose an efficient routing protocol called CCBRP (Chain-Chain based routing protocol), it achieves both minimum energy consumption and minimum delay. The CCBRP protocol mainly divides a WSN into a number of chains (Greedy algorithm is used to form each chain as in PEGSIS protocol) and runs in two phases. In the first phase, sensor nodes in each chain transmit data to their chain leader nodes in parallel. In the second phase, all chain leader nodes form a chain (also, using Greedy algorithm) and choose randomly a leader node then all chain leader nodes send their data to this chosen leader node. This chosen leader node fuses the data and forwards it to the Base Station, BS. Experimental results demonstrate that the proposed CCBRP outperforms LEACH, PEGASIS and CCM with respect to the product of the energy consumed and the experienced delay.