Characterization of the Martian magnetic topology response to extreme solar transient events with MGS data

NASA Astrophysics Data System (ADS)

Xu, S.; Curry, S.; Mitchell, D. L.; Luhmann, J. G.; Lillis, R. J.; Dong, C.

2017-12-01

Characterizing how the solar cycle affects the physics of the Mars-solar wind interaction can improve our understanding of Mars' atmospheric evolution and the plasma environment at Mars. In particular, solar transient events such as Interplanetary Coronal Mass Ejections (ICMEs) and Stream Interaction Regions (SIRs) significantly change the solar-wind interaction, including the magnetic topology and ion acceleration. However, both the Mars Express and Mars Atmosphere Volatile EvolutioN (MAVEN) missions have encountered relatively few extreme solar transient events due to the recent low solar activity (2004-2017). In contrast, Mars Global Surveyor (MGS) was operating during a relatively active solar maximum (1999-2003). Based on new results from MAVEN, this study reanalyzes MGS data to better understand how the Martian plasma environment responds to extreme solar events. In particular, we aim to investigate how the magnetic topology during these extreme events differs from the topology during quiet times. We conduct orbit comparisons of the magnetic topology inferred from MGS electron pitch angle distributions during quiet periods and extreme events to determine how the open and closed field patterns respond to extreme events.

The post-genomic era of biological network alignment.

PubMed

Faisal, Fazle E; Meng, Lei; Crawford, Joseph; Milenković, Tijana

2015-12-01

Biological network alignment aims to find regions of topological and functional (dis)similarities between molecular networks of different species. Then, network alignment can guide the transfer of biological knowledge from well-studied model species to less well-studied species between conserved (aligned) network regions, thus complementing valuable insights that have already been provided by genomic sequence alignment. Here, we review computational challenges behind the network alignment problem, existing approaches for solving the problem, ways of evaluating their alignment quality, and the approaches' biomedical applications. We discuss recent innovative efforts of improving the existing view of network alignment. We conclude with open research questions in comparative biological network research that could further our understanding of principles of life, evolution, disease, and therapeutics.

Topological events on the lines of circular polarization in nonparaxial vector optical fields.

PubMed

Freund, Isaac

2017-02-01

In nonparaxial vector optical fields, the following topological events are shown to occur in apparent violation of charge conservation: as one translates the observation plane along a line of circular polarization (a C line), the points on the line (C points) are seen to change not only the signs of their topological charges, but also their handedness, and, at turning points on the line, paired C points with the same topological charge and opposite handedness are seen to nucleate. These counter-intuitive events cannot occur in paraxial fields.

A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities.

PubMed

Bastien, Olivier; Ortet, Philippe; Roy, Sylvaine; Maréchal, Eric

2005-03-10

Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of homologous proteins that would conserve the information of pair-wise sequence alignments, respect probabilistic properties of Z-scores (Monte Carlo methods applied to pair-wise comparisons) and be the basis for a novel method of consistent and stable phylogenetic reconstruction. We have built up a spatial representation of protein sequences using concepts from particle physics (configuration space) and respecting a frame of constraints deduced from pair-wise alignment score properties in information theory. The obtained configuration space of homologous proteins (CSHP) allows the representation of real and shuffled sequences, and thereupon an expression of the TULIP theorem for Z-score probabilities. Based on the CSHP, we propose a phylogeny reconstruction using Z-scores. Deduced trees, called TULIP trees, are consistent with multiple-alignment based trees. Furthermore, the TULIP tree reconstruction method provides a solution for some previously reported incongruent results, such as the apicomplexan enolase phylogeny. The CSHP is a unified model that conserves mutual information between proteins in the way physical models conserve energy. Applications include the reconstruction of evolutionary consistent and robust trees, the topology of which is based on a spatial representation that is not reordered after addition or removal of sequences. The CSHP and its assigned phylogenetic topology, provide a powerful and easily updated representation for massive pair-wise genome comparisons based on Z-score computations.

Current-induced switching of magnetic molecules on topological insulator surfaces

NASA Astrophysics Data System (ADS)

Locane, Elina; Brouwer, Piet W.

2017-03-01

Electrical currents at the surface or edge of a topological insulator are intrinsically spin polarized. We show that such surface or edge currents can be used to switch the orientation of a molecular magnet weakly coupled to the surface or edge of a topological insulator. For the edge of a two-dimensional topological insulator as well as for the surface of a three-dimensional topological insulator the application of a well-chosen surface or edge current can lead to a complete polarization of the molecule if the molecule's magnetic anisotropy axis is appropriately aligned with the current direction. For a generic orientation of the molecule a nonzero but incomplete polarization is obtained. We calculate the probability distribution of the magnetic states and the switching rates as a function of the applied current.

Bi-layer structure of counterstreaming energetic electron fluxes: a diagnostic tool of the acceleration mechanism in the Earth's magnetotail

NASA Astrophysics Data System (ADS)

Sarafopoulos, D. V.

2010-02-01

For the first time we identify a bi-layer structure of energetic electron fluxes in the Earth's magnetotail and establish (using datasets mainly obtained by the Geotail Energetic Particles and Ion Composition (EPIC/ICS) instrument) that it actually provides strong evidence for a purely spatial structure. Each bi-layer event is composed of two distinct layers with counterstreaming energetic electron fluxes, parallel and antiparallel to the local ambient magnetic field lines; in particular, the tailward directed fluxes always occur in a region adjacent to the lobes. Adopting the X-line as a standard reconnection model, we determine the occurrence of bi-layer events relatively to the neutral point, in the substorm frame; four (out of the shown seven) events are observed earthward and three tailward, a result implying that four events probably occurred with the substorm's local recovery phase. We discuss the bi-layer events in terms of the X-line model; they add more constraints for any candidate electron acceleration mechanism. It should be stressed that until this time, none proposed electron acceleration mechanism has discussed or predicted these layered structures with all their properties. Then we discuss the bi-layer events in terms of the much promising "akis model", as introduced by Sarafopoulos (2008). The akis magnetic field topology is embedded in a thinned plasma sheet and is potentially causing charge separation. We assume that as the Rc curvature radius of the magnetic field line tends to become equal to the ion gyroradius rg, then the ions become non-adiabatic. At the limit Rc=rg the demagnetization process is also under way and the frozen-in magnetic field condition is violated by strong wave turbulence; hence, the ion particles in this geometry are stochastically scattered. In addition, ion diffusion probably takes place across the magnetic field, since an intense pressure gradient is directed earthward; hence, ions are ejected tailward of akis. This way, in front of akis an "ion capsule region" is formed with net positive charge. In between them a distinct region with an electric field E⊥ orthogonal to the magnetic field is emerged; E⊥ in front of akis is directed earthward. The field-aligned and highly anisotropic energetic electron populations have probably resulted via spatially separated antiparallel and field-aligned electric fields being the very heart of the acceleration source. We assume that the ultimate cause for the field-aligned electric fields are the net positive capsule charge and the net negative charge trapped at the tip of akis; both charges will be eventually neutralized through field aligned currents, but they remain unshielded for sufficient time to produce the observed events.

L-GRAAL: Lagrangian graphlet-based network aligner.

PubMed

Malod-Dognin, Noël; Pržulj, Nataša

2015-07-01

Discovering and understanding patterns in networks of protein-protein interactions (PPIs) is a central problem in systems biology. Alignments between these networks aid functional understanding as they uncover important information, such as evolutionary conserved pathways, protein complexes and functional orthologs. A few methods have been proposed for global PPI network alignments, but because of NP-completeness of underlying sub-graph isomorphism problem, producing topologically and biologically accurate alignments remains a challenge. We introduce a novel global network alignment tool, Lagrangian GRAphlet-based ALigner (L-GRAAL), which directly optimizes both the protein and the interaction functional conservations, using a novel alignment search heuristic based on integer programming and Lagrangian relaxation. We compare L-GRAAL with the state-of-the-art network aligners on the largest available PPI networks from BioGRID and observe that L-GRAAL uncovers the largest common sub-graphs between the networks, as measured by edge-correctness and symmetric sub-structures scores, which allow transferring more functional information across networks. We assess the biological quality of the protein mappings using the semantic similarity of their Gene Ontology annotations and observe that L-GRAAL best uncovers functionally conserved proteins. Furthermore, we introduce for the first time a measure of the semantic similarity of the mapped interactions and show that L-GRAAL also uncovers best functionally conserved interactions. In addition, we illustrate on the PPI networks of baker's yeast and human the ability of L-GRAAL to predict new PPIs. Finally, L-GRAAL's results are the first to show that topological information is more important than sequence information for uncovering functionally conserved interactions. L-GRAAL is coded in C++. Software is available at: http://bio-nets.doc.ic.ac.uk/L-GRAAL/. n.malod-dognin@imperial.ac.uk Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Multi-resolution Shape Analysis via Non-Euclidean Wavelets: Applications to Mesh Segmentation and Surface Alignment Problems.

PubMed

Kim, Won Hwa; Chung, Moo K; Singh, Vikas

2013-01-01

The analysis of 3-D shape meshes is a fundamental problem in computer vision, graphics, and medical imaging. Frequently, the needs of the application require that our analysis take a multi-resolution view of the shape's local and global topology, and that the solution is consistent across multiple scales. Unfortunately, the preferred mathematical construct which offers this behavior in classical image/signal processing, Wavelets, is no longer applicable in this general setting (data with non-uniform topology). In particular, the traditional definition does not allow writing out an expansion for graphs that do not correspond to the uniformly sampled lattice (e.g., images). In this paper, we adapt recent results in harmonic analysis, to derive Non-Euclidean Wavelets based algorithms for a range of shape analysis problems in vision and medical imaging. We show how descriptors derived from the dual domain representation offer native multi-resolution behavior for characterizing local/global topology around vertices. With only minor modifications, the framework yields a method for extracting interest/key points from shapes, a surprisingly simple algorithm for 3-D shape segmentation (competitive with state of the art), and a method for surface alignment (without landmarks). We give an extensive set of comparison results on a large shape segmentation benchmark and derive a uniqueness theorem for the surface alignment problem.

Topology guided demons registration with local rigidity preservation.

PubMed

Chaojie Zheng; Xiuying Wang; Dagan Feng

2016-08-01

Demons has been well recognized for its deformable registration capability. However, it might lead to misregistration due to the large spatial distance between the expected corresponding contents or erroneous diffusion tendency. In this paper, we propose a new energy function with topology energy, distance function and demons energy for deformable registration. The new energy function incorporates topological relationships to guide the correct diffusion and deformation, and contributes to local rigidity preservation. The distance function contributes to pulling the corresponding regions into accurate alignment despite of a possible large distance gap. The method was validated on synthetic, phantom and real medical image data.

On the topology of flux transfer events

NASA Technical Reports Server (NTRS)

Hesse, Michael; Birn, Joachim; Schindler, Karl

1990-01-01

A topological analysis is made of a simple model magnetic field of a perturbation at the magnetopause that shares magnetic properties with flux transfer events. The aim is to clarify a number of topological aspects that arise in the case of fully three-dimensional magnetic fields. It is shown that a localized perturbation at the magnetopause can in principle open a closed magnetosphere by establishing magnetic connections across the magnetopause by the formation of a ropelike magnetic field structure. For this purpose a global topological model of a closed magnetosphere is considered as the unperturbed state. The topological substructure of the model flux rope is discussed in detail.

Event identification for KM3NeT/ARCA

NASA Astrophysics Data System (ADS)

Heid, Thomas; KM3NeT Collaboration

2017-09-01

KM3NeT is a large research infrastructure consisting of a network of deep-sea neutrino telescopes. KM3NeT/ARCA will be the instrument detecting high-energy neutrinos with energies above 100 TeV. This instrument gives a new opportunity to observe the neutrino sky with very high angular resolution to be able to detect neutrino point sources. Furthermore it will be possible to probe the flavour composition of neutrino fluxes, and hence production mechanisms, with so-far unreached precision. Neutrinos produce different event topologies in the detector according to their flavour, interaction channel and deposited energy. Machine-learning algorithms are able to learn features of topologies to discriminate them. In previous analyses only two event types were regarded, namely the shower and track topology. With good timing resolution and precise reconstruction algorithms it is possible to separate into more event types, for example the double bang topology produced by tau neutrinos. The final goal is to distinguish all three neutrino flavors as much as possible. To resolve this issue the KM3NeT collaboration uses deep neural networks trained with Monte Carlo events of all neutrino types. This contribution shows the ability of KM3NeT/ARCA to classify events in more than two neutrino event topologies. Furthermore, the borders between detectable classes are shown, such as the minimum distance the tau has to travel before decaying into a tau neutrino to be detected as double bang event.

Topology and convection of a northward interplanetary magnetic field reconnection event

NASA Astrophysics Data System (ADS)

Wendel, Deirdre E.

>From observations and global MHD simulations, we deduce the local and global magnetic topology and current structure of a northward IMF reconnection event in the dayside magnetopause. The ESA four-satellite Cluster suite crossed the magnetopause at a location mapping along field lines to an ionospheric H-alpha emission observed by the IMAGE spacecraft. Therefore, we seek reconnection signatures in the Cluster data. From the four-point Cluster observations, we develop a superposed epoch method to find the instantaneous x-line, its associated current sheet, and the nature of the reconnecting particle flows. This method is unique in that it removes the motion of the hyperbolic structure and the magnetopause relative to the spacecraft. We detect singular field line reconnection--planar hyperbolic reconnecting fields superposed on an out-of- plane field. We also detect the non-ideal electric field that is required to certify reconnection at locations where the magnetic field does not vanish, and estimate a reconnection electric field of - 4 mV/m. The current sheet appears bifurcated, embedding a 30 km current sheet of opposite polarity within a broader current sheet about 130 km thick. Using a resistive MHD simulation and ionospheric satellite data, we examine the same event at global length scales. This gives a 3D picture of where reconnection occurs on the magnetopause for northward IMF with B x and B y components and a tilted dipole field. It also demonstrates that northward IMF 3D reconnection couples the reconnection electric field and field-aligned currents to the ionosphere, driving sunward convection in a manner that agrees with satellite measurements of sunward flows. We find singular field line reconnection of the IMF with both open and closed field lines near nulls in both hemispheres. The reconnection in turn produces both open and closed field lines. We discuss for the first time how line-tying in the ionosphere and draping of open and IMF field lines produce a torsion of the reconnecting singular magnetic field lines within the magnetopause. The simulation and data show that magnetopause reconnection topology is three-dimensional in a way that challenges accepted models of neutral lines and x-lines with guide fields.

Sampled-data consensus in switching networks of integrators based on edge events

NASA Astrophysics Data System (ADS)

Xiao, Feng; Meng, Xiangyu; Chen, Tongwen

2015-02-01

This paper investigates the event-driven sampled-data consensus in switching networks of multiple integrators and studies both the bidirectional interaction and leader-following passive reaction topologies in a unified framework. In these topologies, each information link is modelled by an edge of the information graph and assigned a sequence of edge events, which activate the mutual data sampling and controller updates of the two linked agents. Two kinds of edge-event-detecting rules are proposed for the general asynchronous data-sampling case and the synchronous periodic event-detecting case. They are implemented in a distributed fashion, and their effectiveness in reducing communication costs and solving consensus problems under a jointly connected topology condition is shown by both theoretical analysis and simulation examples.

Topology of surfaces for molecular Stark energy, alignment, and orientation generated by combined permanent and induced electric dipole interactions.

PubMed

Schmidt, Burkhard; Friedrich, Bretislav

2014-02-14

We show that combined permanent and induced electric dipole interactions of linear polar and polarizable molecules with collinear electric fields lead to a sui generis topology of the corresponding Stark energy surfaces and of other observables - such as alignment and orientation cosines - in the plane spanned by the permanent and induced dipole interaction parameters. We find that the loci of the intersections of the surfaces can be traced analytically and that the eigenstates as well as the number of their intersections can be characterized by a single integer index. The value of the index, distinctive for a particular ratio of the interaction parameters, brings out a close kinship with the eigenproperties obtained previously for a class of Stark states via the apparatus of supersymmetric quantum mechanics.

Alignment-free protein interaction network comparison

PubMed Central

Ali, Waqar; Rito, Tiago; Reinert, Gesine; Sun, Fengzhu; Deane, Charlotte M.

2014-01-01

Motivation: Biological network comparison software largely relies on the concept of alignment where close matches between the nodes of two or more networks are sought. These node matches are based on sequence similarity and/or interaction patterns. However, because of the incomplete and error-prone datasets currently available, such methods have had limited success. Moreover, the results of network alignment are in general not amenable for distance-based evolutionary analysis of sets of networks. In this article, we describe Netdis, a topology-based distance measure between networks, which offers the possibility of network phylogeny reconstruction. Results: We first demonstrate that Netdis is able to correctly separate different random graph model types independent of network size and density. The biological applicability of the method is then shown by its ability to build the correct phylogenetic tree of species based solely on the topology of current protein interaction networks. Our results provide new evidence that the topology of protein interaction networks contains information about evolutionary processes, despite the lack of conservation of individual interactions. As Netdis is applicable to all networks because of its speed and simplicity, we apply it to a large collection of biological and non-biological networks where it clusters diverse networks by type. Availability and implementation: The source code of the program is freely available at http://www.stats.ox.ac.uk/research/proteins/resources. Contact: w.ali@stats.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25161230

Observability of Same-Charge Lepton Topologies in Fully Leptonic Top Quark Pair Events in CMS

NASA Astrophysics Data System (ADS)

Lowette, S.

2007-02-01

At the Large Hadron Collider dileptonic tbar t({+jets}) events can be selected with a relatively high signal-to-noise ratio and efficiency, with background events produced via Standard Model diagrams. Within the clean sample of these events, both isolated leptons have an opposite electric charge. In several models beyond the Standard Model tt/ bar t bar t(+{jets}) topologies are predicted, kinematically similar to the Standard Model tbar t({+jets}) signature, where both leptons have an equal electric charge. Such a signal of new physics can be diluted by the mis-identification of the leptons or their electric charge in Standard Model tbar t({+jets}) events. The observability of an excess of same-charge dilepton signals above the mis-reconstruction of the Standard Model background is presented, assuming the same topology. With an integrated luminosity of 30 fb-1, a same-charge dilepton signature of pp to tt/ bar t bar t events with a cross section larger than 1.2 pb is visible in the measurement of the ratio between same-charge and opposite-charge lepton pair events [J. D'Hondt, S. Lowette, G. Hammad, J. Heyninck, P. Van Mulders, ``Observability of same-charge lepton topology in dileptonic events t bar t'', CERN-CMS-NOTE-2006-065.

NCLscan: accurate identification of non-co-linear transcripts (fusion, trans-splicing and circular RNA) with a good balance between sensitivity and precision.

PubMed

Chuang, Trees-Juen; Wu, Chan-Shuo; Chen, Chia-Ying; Hung, Li-Yuan; Chiang, Tai-Wei; Yang, Min-Yu

2016-02-18

Analysis of RNA-seq data often detects numerous 'non-co-linear' (NCL) transcripts, which comprised sequence segments that are topologically inconsistent with their corresponding DNA sequences in the reference genome. However, detection of NCL transcripts involves two major challenges: removal of false positives arising from alignment artifacts and discrimination between different types of NCL transcripts (trans-spliced, circular or fusion transcripts). Here, we developed a new NCL-transcript-detecting method ('NCLscan'), which utilized a stepwise alignment strategy to almost completely eliminate false calls (>98% precision) without sacrificing true positives, enabling NCLscan outperform 18 other publicly-available tools (including fusion- and circular-RNA-detecting tools) in terms of sensitivity and precision, regardless of the generation strategy of simulated dataset, type of intragenic or intergenic NCL event, read depth of coverage, read length or expression level of NCL transcript. With the high accuracy, NCLscan was applied to distinguishing between trans-spliced, circular and fusion transcripts on the basis of poly(A)- and nonpoly(A)-selected RNA-seq data. We showed that circular RNAs were expressed more ubiquitously, more abundantly and less cell type-specifically than trans-spliced and fusion transcripts. Our study thus describes a robust pipeline for the discovery of NCL transcripts, and sheds light on the fundamental biology of these non-canonical RNA events in human transcriptome. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

The floral transcriptomes of four bamboo species (Bambusoideae; Poaceae): support for common ancestry among woody bamboos.

PubMed

Wysocki, William P; Ruiz-Sanchez, Eduardo; Yin, Yanbin; Duvall, Melvin R

2016-05-20

Next-generation sequencing now allows for total RNA extracts to be sequenced in non-model organisms such as bamboos, an economically and ecologically important group of grasses. Bamboos are divided into three lineages, two of which are woody perennials with bisexual flowers, which undergo gregarious monocarpy. The third lineage, which are herbaceous perennials, possesses unisexual flowers that undergo annual flowering events. Transcriptomes were assembled using both reference-based and de novo methods. These two methods were tested by characterizing transcriptome content using sequence alignment to previously characterized reference proteomes and by identifying Pfam domains. Because of the striking differences in floral morphology and phenology between the herbaceous and woody bamboo lineages, MADS-box genes, transcription factors that control floral development and timing, were characterized and analyzed in this study. Transcripts were identified using phylogenetic methods and categorized as A, B, C, D or E-class genes, which control floral development, or SOC or SVP-like genes, which control the timing of flowering events. Putative nuclear orthologues were also identified in bamboos to use as phylogenetic markers. Instances of gene copies exhibiting topological patterns that correspond to shared phenotypes were observed in several gene families including floral development and timing genes. Alignments and phylogenetic trees were generated for 3,878 genes and for all genes in a concatenated analysis. Both the concatenated analysis and those of 2,412 separate gene trees supported monophyly among the woody bamboos, which is incongruent with previous phylogenetic studies using plastid markers.

DNA looping by FokI: the impact of synapse geometry on loop topology at varied site orientations

PubMed Central

Rusling, David A.; Laurens, Niels; Pernstich, Christian; Wuite, Gijs J. L.; Halford, Stephen E.

2012-01-01

Most restriction endonucleases, including FokI, interact with two copies of their recognition sequence before cutting DNA. On DNA with two sites they act in cis looping out the intervening DNA. While many restriction enzymes operate symmetrically at palindromic sites, FokI acts asymmetrically at a non-palindromic site. The directionality of its sequence means that two FokI sites can be bridged in either parallel or anti-parallel alignments. Here we show by biochemical and single-molecule biophysical methods that FokI aligns two recognition sites on separate DNA molecules in parallel and that the parallel arrangement holds for sites in the same DNA regardless of whether they are in inverted or repeated orientations. The parallel arrangement dictates the topology of the loop trapped between sites in cis: the loop from inverted sites has a simple 180° bend, while that with repeated sites has a convoluted 360° turn. The ability of FokI to act at asymmetric sites thus enabled us to identify the synapse geometry for sites in trans and in cis, which in turn revealed the relationship between synapse geometry and loop topology. PMID:22362745

Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals

PubMed Central

Yuri, Tamaki; Kimball, Rebecca T.; Harshman, John; Bowie, Rauri C. K.; Braun, Michael J.; Chojnowski, Jena L.; Han, Kin-Lan; Hackett, Shannon J.; Huddleston, Christopher J.; Moore, William S.; Reddy, Sushma; Sheldon, Frederick H.; Steadman, David W.; Witt, Christopher C.; Braun, Edward L.

2013-01-01

Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP) and a simple maximum likelihood (ML) framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven difficult to recover in previous studies. Moreover, independent lines of evidence typically corroborated the nucleotide topology instead of the gap topology when they disagreed, although the number of conflicting nodes with high bootstrap support was limited. Filtering to remove short indels did not substantially reduce homoplasy or reduce conflict. Combined analyses of nucleotides and gaps resulted in the nucleotide topology, but with increased support, suggesting that gap data may prove most useful when analyzed in combination with nucleotide substitutions. PMID:24832669

Unified Alignment of Protein-Protein Interaction Networks.

PubMed

Malod-Dognin, Noël; Ban, Kristina; Pržulj, Nataša

2017-04-19

Paralleling the increasing availability of protein-protein interaction (PPI) network data, several network alignment methods have been proposed. Network alignments have been used to uncover functionally conserved network parts and to transfer annotations. However, due to the computational intractability of the network alignment problem, aligners are heuristics providing divergent solutions and no consensus exists on a gold standard, or which scoring scheme should be used to evaluate them. We comprehensively evaluate the alignment scoring schemes and global network aligners on large scale PPI data and observe that three methods, HUBALIGN, L-GRAAL and NATALIE, regularly produce the most topologically and biologically coherent alignments. We study the collective behaviour of network aligners and observe that PPI networks are almost entirely aligned with a handful of aligners that we unify into a new tool, Ulign. Ulign enables complete alignment of two networks, which traditional global and local aligners fail to do. Also, multiple mappings of Ulign define biologically relevant soft clusterings of proteins in PPI networks, which may be used for refining the transfer of annotations across networks. Hence, PPI networks are already well investigated by current aligners, so to gain additional biological insights, a paradigm shift is needed. We propose such a shift come from aligning all available data types collectively rather than any particular data type in isolation from others.

AlignMe—a membrane protein sequence alignment web server

PubMed Central

Stamm, Marcus; Staritzbichler, René; Khafizov, Kamil; Forrest, Lucy R.

2014-01-01

We present a web server for pair-wise alignment of membrane protein sequences, using the program AlignMe. The server makes available two operational modes of AlignMe: (i) sequence to sequence alignment, taking two sequences in fasta format as input, combining information about each sequence from multiple sources and producing a pair-wise alignment (PW mode); and (ii) alignment of two multiple sequence alignments to create family-averaged hydropathy profile alignments (HP mode). For the PW sequence alignment mode, four different optimized parameter sets are provided, each suited to pairs of sequences with a specific similarity level. These settings utilize different types of inputs: (position-specific) substitution matrices, secondary structure predictions and transmembrane propensities from transmembrane predictions or hydrophobicity scales. In the second (HP) mode, each input multiple sequence alignment is converted into a hydrophobicity profile averaged over the provided set of sequence homologs; the two profiles are then aligned. The HP mode enables qualitative comparison of transmembrane topologies (and therefore potentially of 3D folds) of two membrane proteins, which can be useful if the proteins have low sequence similarity. In summary, the AlignMe web server provides user-friendly access to a set of tools for analysis and comparison of membrane protein sequences. Access is available at http://www.bioinfo.mpg.de/AlignMe PMID:24753425

A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions

PubMed Central

Burke, Sean V.; Wysocki, William P.; Clark, Lynn G.

2018-01-01

The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from high throughput sequencing libraries and the assemblies represent over 28.7 Mbases of sequence data. Phylogenetic signal was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single and multi-gene studies of grasses. Each of the four main partitions was further refined, alternatively including or excluding positively selected codons and also the gaps introduced by the alignment. All 76 protein coding plastome loci were found to be predominantly under purifying selection, but specific codons were found to be under positive selection in 65 loci. The loci that have been widely used in multi-gene phylogenetic studies had among the highest proportions of positively selected codons, suggesting caution in the interpretation of these earlier results. Plastome phylogenomic analyses confirmed the backbone topology for Poaceae with maximum bootstrap support (BP). Among the 14 analyses, 82 clades out of 309 resolved were maximally supported in all trees. Analyses of newly sequenced plastomes were in agreement with current classifications. Five of seven partitions in which alignment gaps were removed retrieved Panicoideae as sister to the remaining PACMAD subfamilies. Alternative topologies were recovered in trees from partitions that included alignment gaps. This suggests that ambiguities in aligning these uncertain regions might introduce a false signal. Resolution of these and other critical branch points in the phylogeny of Poaceae will help to better understand the selective forces that drove the radiation of the BOP and PACMAD clades comprising more than 99.9% of grass diversity. PMID:29416954

Multiple network alignment via multiMAGNA+.

PubMed

Vijayan, Vipin; Milenkovic, Tijana

2017-08-21

Network alignment (NA) aims to find a node mapping that identifies topologically or functionally similar network regions between molecular networks of different species. Analogous to genomic sequence alignment, NA can be used to transfer biological knowledge from well- to poorly-studied species between aligned network regions. Pairwise NA (PNA) finds similar regions between two networks while multiple NA (MNA) can align more than two networks. We focus on MNA. Existing MNA methods aim to maximize total similarity over all aligned nodes (node conservation). Then, they evaluate alignment quality by measuring the amount of conserved edges, but only after the alignment is constructed. Directly optimizing edge conservation during alignment construction in addition to node conservation may result in superior alignments. Thus, we present a novel MNA method called multiMAGNA++ that can achieve this. Indeed, multiMAGNA++ outperforms or is on par with existing MNA methods, while often completing faster than existing methods. That is, multiMAGNA++ scales well to larger network data and can be parallelized effectively. During method evaluation, we also introduce new MNA quality measures to allow for more fair MNA method comparison compared to the existing alignment quality measures. MultiMAGNA++ code is available on the method's web page at http://nd.edu/~cone/multiMAGNA++/.

Topological transformations of Hopf solitons in chiral ferromagnets and liquid crystals.

PubMed

Tai, Jung-Shen B; Ackerman, Paul J; Smalyukh, Ivan I

2018-01-30

Liquid crystals are widely known for their facile responses to external fields, which forms a basis of the modern information display technology. However, switching of molecular alignment field configurations typically involves topologically trivial structures, although singular line and point defects often appear as short-lived transient states. Here, we demonstrate electric and magnetic switching of nonsingular solitonic structures in chiral nematic and ferromagnetic liquid crystals. These topological soliton structures are characterized by Hopf indices, integers corresponding to the numbers of times that closed-loop-like spatial regions (dubbed "preimages") of two different single orientations of rod-like molecules or magnetization are linked with each other. We show that both dielectric and ferromagnetic response of the studied material systems allow for stabilizing a host of topological solitons with different Hopf indices. The field transformations during such switching are continuous when Hopf indices remain unchanged, even when involving transformations of preimages, but discontinuous otherwise.

Topology-function conservation in protein-protein interaction networks.

PubMed

Davis, Darren; Yaveroğlu, Ömer Nebil; Malod-Dognin, Noël; Stojmirovic, Aleksandar; Pržulj, Nataša

2015-05-15

Proteins underlay the functioning of a cell and the wiring of proteins in protein-protein interaction network (PIN) relates to their biological functions. Proteins with similar wiring in the PIN (topology around them) have been shown to have similar functions. This property has been successfully exploited for predicting protein functions. Topological similarity is also used to guide network alignment algorithms that find similarly wired proteins between PINs of different species; these similarities are used to transfer annotation across PINs, e.g. from model organisms to human. To refine these functional predictions and annotation transfers, we need to gain insight into the variability of the topology-function relationships. For example, a function may be significantly associated with specific topologies, while another function may be weakly associated with several different topologies. Also, the topology-function relationships may differ between different species. To improve our understanding of topology-function relationships and of their conservation among species, we develop a statistical framework that is built upon canonical correlation analysis. Using the graphlet degrees to represent the wiring around proteins in PINs and gene ontology (GO) annotations to describe their functions, our framework: (i) characterizes statistically significant topology-function relationships in a given species, and (ii) uncovers the functions that have conserved topology in PINs of different species, which we term topologically orthologous functions. We apply our framework to PINs of yeast and human, identifying seven biological process and two cellular component GO terms to be topologically orthologous for the two organisms. © The Author 2015. Published by Oxford University Press.

Continuous theory of active matter systems with metric-free interactions.

PubMed

Peshkov, Anton; Ngo, Sandrine; Bertin, Eric; Chaté, Hugues; Ginelli, Francesco

2012-08-31

We derive a hydrodynamic description of metric-free active matter: starting from self-propelled particles aligning with neighbors defined by "topological" rules, not metric zones-a situation advocated recently to be relevant for bird flocks, fish schools, and crowds-we use a kinetic approach to obtain well-controlled nonlinear field equations. We show that the density-independent collision rate per particle characteristic of topological interactions suppresses the linear instability of the homogeneous ordered phase and the nonlinear density segregation generically present near threshold in metric models, in agreement with microscopic simulations.

Global Network Alignment in the Context of Aging.

PubMed

Faisal, Fazle Elahi; Zhao, Han; Milenkovic, Tijana

2015-01-01

Analogous to sequence alignment, network alignment (NA) can be used to transfer biological knowledge across species between conserved network regions. NA faces two algorithmic challenges: 1) Which cost function to use to capture "similarities" between nodes in different networks? 2) Which alignment strategy to use to rapidly identify "high-scoring" alignments from all possible alignments? We "break down" existing state-of-the-art methods that use both different cost functions and different alignment strategies to evaluate each combination of their cost functions and alignment strategies. We find that a combination of the cost function of one method and the alignment strategy of another method beats the existing methods. Hence, we propose this combination as a novel superior NA method. Then, since human aging is hard to study experimentally due to long lifespan, we use NA to transfer aging-related knowledge from well annotated model species to poorly annotated human. By doing so, we produce novel human aging-related knowledge, which complements currently available knowledge about aging that has been obtained mainly by sequence alignment. We demonstrate significant similarity between topological and functional properties of our novel predictions and those of known aging-related genes. We are the first to use NA to learn more about aging.

Irreversible Markov chains in spin models: Topological excitations

NASA Astrophysics Data System (ADS)

Lei, Ze; Krauth, Werner

2018-01-01

We analyze the convergence of the irreversible event-chain Monte Carlo algorithm for continuous spin models in the presence of topological excitations. In the two-dimensional XY model, we show that the local nature of the Markov-chain dynamics leads to slow decay of vortex-antivortex correlations while spin waves decorrelate very quickly. Using a Fréchet description of the maximum vortex-antivortex distance, we quantify the contributions of topological excitations to the equilibrium correlations, and show that they vary from a dynamical critical exponent z∼ 2 at the critical temperature to z∼ 0 in the limit of zero temperature. We confirm the event-chain algorithm's fast relaxation (corresponding to z = 0) of spin waves in the harmonic approximation to the XY model. Mixing times (describing the approach towards equilibrium from the least favorable initial state) however remain much larger than equilibrium correlation times at low temperatures. We also describe the respective influence of topological monopole-antimonopole excitations and of spin waves on the event-chain dynamics in the three-dimensional Heisenberg model.

Measurement of the top quark-pair production cross section with ATLAS in pp collisions at $$\\sqrt{s}=7$$  TeV

DOE PAGES

Aad, G.; Abbott, B.; Abdallah, J.; ...

2011-03-01

A measurement of the production cross-section for top quark pairs (more » $$t\\bar{t}$$) in pp collisions at √s =7 TeVis presented using data recorded with the ATLAS detector at the Large Hadron Collider. Events are selected in two different topologies: single lepton (electron e or muon μ) with large missing transverse energy and at least four jets, and dilepton (ee, μμ or eμ) with large missing transverse energy and at least two jets. In a data sample of 2.9 pb –1, 37 candidate events are observed in the single-lepton topology and 9 events in the dilepton topology. The corresponding expected backgrounds from non-$$t\\bar{t}$$Standard Model processes are estimated using data-driven methods and determined to be 12.2 ± 3.9 events and 2.5± 0.6 events, respectively.« less

Genome-Wide Networks of Amino Acid Covariances Are Common among Viruses

PubMed Central

Donlin, Maureen J.; Szeto, Brandon; Gohara, David W.; Aurora, Rajeev

2012-01-01

Coordinated variation among positions in amino acid sequence alignments can reveal genetic dependencies at noncontiguous positions, but methods to assess these interactions are incompletely developed. Previously, we found genome-wide networks of covarying residue positions in the hepatitis C virus genome (R. Aurora, M. J. Donlin, N. A. Cannon, and J. E. Tavis, J. Clin. Invest. 119:225–236, 2009). Here, we asked whether such networks are present in a diverse set of viruses and, if so, what they may imply about viral biology. Viral sequences were obtained for 16 viruses in 13 species from 9 families. The entire viral coding potential for each virus was aligned, all possible amino acid covariances were identified using the observed-minus-expected-squared algorithm at a false-discovery rate of ≤1%, and networks of covariances were assessed using standard methods. Covariances that spanned the viral coding potential were common in all viruses. In all cases, the covariances formed a single network that contained essentially all of the covariances. The hepatitis C virus networks had hub-and-spoke topologies, but all other networks had random topologies with an unusually large number of highly connected nodes. These results indicate that genome-wide networks of genetic associations and the coordinated evolution they imply are very common in viral genomes, that the networks rarely have the hub-and-spoke topology that dominates other biological networks, and that network topologies can vary substantially even within a given viral group. Five examples with hepatitis B virus and poliovirus are presented to illustrate how covariance network analysis can lead to inferences about viral biology. PMID:22238298

Twisted trees and inconsistency of tree estimation when gaps are treated as missing data - The impact of model mis-specification in distance corrections.

PubMed

McTavish, Emily Jane; Steel, Mike; Holder, Mark T

2015-12-01

Statistically consistent estimation of phylogenetic trees or gene trees is possible if pairwise sequence dissimilarities can be converted to a set of distances that are proportional to the true evolutionary distances. Susko et al. (2004) reported some strikingly broad results about the forms of inconsistency in tree estimation that can arise if corrected distances are not proportional to the true distances. They showed that if the corrected distance is a concave function of the true distance, then inconsistency due to long branch attraction will occur. If these functions are convex, then two "long branch repulsion" trees will be preferred over the true tree - though these two incorrect trees are expected to be tied as the preferred true. Here we extend their results, and demonstrate the existence of a tree shape (which we refer to as a "twisted Farris-zone" tree) for which a single incorrect tree topology will be guaranteed to be preferred if the corrected distance function is convex. We also report that the standard practice of treating gaps in sequence alignments as missing data is sufficient to produce non-linear corrected distance functions if the substitution process is not independent of the insertion/deletion process. Taken together, these results imply inconsistent tree inference under mild conditions. For example, if some positions in a sequence are constrained to be free of substitutions and insertion/deletion events while the remaining sites evolve with independent substitutions and insertion/deletion events, then the distances obtained by treating gaps as missing data can support an incorrect tree topology even given an unlimited amount of data. Copyright © 2015 Elsevier Inc. All rights reserved.

Odd-frequency superconductivity induced in topological insulators with and without hexagonal warping.

PubMed

Vasenko, A S; Golubov, A A; Silkin, V M; Chulkov, E V

2017-07-26

We study the effect of the Fermi surface anisotropy on the odd-frequency spin-triplet pairing component of the induced pair potential. We consider a superconductor/ ferromagnetic insulator (S/FI) hybrid structure formed on the 3D topological insulator (TI) surface. In this case three ingredients ensure the possibility of the odd-frequency pairing: (1) the topological surface states, (2) the induced pair potential, and (3) the magnetic moment of a nearby ferromagnetic insulator. We take into account the strong anisotropy of the Dirac point in topological insulators when the chemical potential lies well above the Dirac cone and its constant energy contour has a snowflake shape. Within this model, we propose that the S/FI boundary should be properly aligned with respect to the snowflake constant energy contour to have an odd-frequency symmetry of the corresponding pairing component and to insure the Majorana bound state at the S/FI boundary. For arbitrary orientation of the boundary, the Majorana bound state is absent. This provides a selection rule to the realization of Majorana modes in S/FI hybrid structures, formed on the topological insulator surface.

Fuzzy adaptive iterative learning coordination control of second-order multi-agent systems with imprecise communication topology structure

NASA Astrophysics Data System (ADS)

Chen, Jiaxi; Li, Junmin

2018-02-01

In this paper, we investigate the perfect consensus problem for second-order linearly parameterised multi-agent systems (MAS) with imprecise communication topology structure. Takagi-Sugeno (T-S) fuzzy models are presented to describe the imprecise communication topology structure of leader-following MAS, and a distributed adaptive iterative learning control protocol is proposed with the dynamic of leader unknown to any of the agent. The proposed protocol guarantees that the follower agents can track the leader perfectly on [0,T] for the consensus problem. Under alignment condition, a sufficient condition of the consensus for closed-loop MAS is given based on Lyapunov stability theory. Finally, a numerical example and a multiple pendulum system are given to illustrate the effectiveness of the proposed algorithm.

Tracking cells in Life Cell Imaging videos using topological alignments.

PubMed

Mosig, Axel; Jäger, Stefan; Wang, Chaofeng; Nath, Sumit; Ersoy, Ilker; Palaniappan, Kannap-pan; Chen, Su-Shing

2009-07-16

With the increasing availability of live cell imaging technology, tracking cells and other moving objects in live cell videos has become a major challenge for bioimage informatics. An inherent problem for most cell tracking algorithms is over- or under-segmentation of cells - many algorithms tend to recognize one cell as several cells or vice versa. We propose to approach this problem through so-called topological alignments, which we apply to address the problem of linking segmentations of two consecutive frames in the video sequence. Starting from the output of a conventional segmentation procedure, we align pairs of consecutive frames through assigning sets of segments in one frame to sets of segments in the next frame. We achieve this through finding maximum weighted solutions to a generalized "bipartite matching" between two hierarchies of segments, where we derive weights from relative overlap scores of convex hulls of sets of segments. For solving the matching task, we rely on an integer linear program. Practical experiments demonstrate that the matching task can be solved efficiently in practice, and that our method is both effective and useful for tracking cells in data sets derived from a so-called Large Scale Digital Cell Analysis System (LSDCAS). The source code of the implementation is available for download from http://www.picb.ac.cn/patterns/Software/topaln.

Flux transfer events: Reconnection without separators. [magnetopause

NASA Technical Reports Server (NTRS)

Hesse, M.; Birn, J.; Schindler, K.

1989-01-01

A topological analysis of a simple model magnetic field of a perturbation at the magnetopause modeling an apparent flux transfer event is presented. It is shown that a localized perturbation at the magnetopause can in principle open a closed magnetosphere by establishing magnetic connections across the magnetopause. Although the model field exhibits neutral points, these are not involved in the magnetic connection of the flux tubes. The topological substructure of a localized perturbation is analyzed in a simpler configuration. The presence of both signs of the magnetic field component normal to the magnetopause leads to a linkage of topologically different flux tubes, described as a flux knot, and a filamentary substructure of field lines of different topological types which becomes increasingly complicated for decreasing magnetic shear at the magnetopause.

Defense Against Cannibalism: The SdpI Family of Bacterial Immunity/Signal Transduction Proteins

PubMed Central

Povolotsky, Tatyana Leonidovna; Orlova, Ekaterina; Tamang, Dorjee G.

2010-01-01

The SdpI family consists of putative bacterial toxin immunity and signal transduction proteins. One member of the family in Bacillus subtilis, SdpI, provides immunity to cells from cannibalism in times of nutrient limitation. SdpI family members are transmembrane proteins with 3, 4, 5, 6, 7, 8, or 12 putative transmembrane α-helical segments (TMSs). These varied topologies appear to be genuine rather than artifacts due to sequencing or annotation errors. The basic and most frequently occurring element of the SdpI family has 6 TMSs. Homologues of all topological types were aligned to determine the homologous TMSs and loop regions, and the positive-inside rule was used to determine sidedness. The two most conserved motifs were identified between TMSs 1 and 2 and TMSs 4 and 5 of the 6 TMS proteins. These showed significant sequence similarity, leading us to suggest that the primordial precursor of these proteins was a 3 TMS–encoding genetic element that underwent intragenic duplication. Various deletional and fusional events, as well as intragenic duplications and inversions, may have yielded SdpI homologues with topologies of varying numbers and positions of TMSs. We propose a specific evolutionary pathway that could have given rise to these distantly related bacterial immunity proteins. We further show that genes encoding SdpI homologues often appear in operons with genes for homologues of SdpR, SdpI’s autorepressor. Our analyses allow us to propose structure–function relationships that may be applicable to most family members. Electronic supplementary material The online version of this article (doi:10.1007/s00232-010-9260-7) contains supplementary material, which is available to authorized users. PMID:20563570

Charge topology of the coherent dissociation of relativistic 11C and 12N nuclei

NASA Astrophysics Data System (ADS)

Artemenkov, D. A.; Bradnova, V.; Zaitsev, A. A.; Zarubin, P. I.; Zarubina, I. G.; Kattabekov, R. R.; Kornegrutsa, N. K.; Mamatkulov, K. Z.; Rukoyatkin, P. A.; Rusakova, V. V.; Stanoeva, R.

2015-09-01

The charge topology of coherent-dissociation events is presented for 11С and 12N nuclei of energy 1.2 GeV per nucleon bombarding nuclear track emulsions. This topology is compared with respective data for 7Be, 8,10B, 9,10C, and 14N nuclei.

Topological data analyses and machine learning for detection, classification and characterization of atmospheric rivers

NASA Astrophysics Data System (ADS)

Muszynski, G.; Kashinath, K.; Wehner, M. F.; Prabhat, M.; Kurlin, V.

2017-12-01

We investigate novel approaches to detecting, classifying and characterizing extreme weather events, such as atmospheric rivers (ARs), in large high-dimensional climate datasets. ARs are narrow filaments of concentrated water vapour in the atmosphere that bring much of the precipitation in many mid-latitude regions. The precipitation associated with ARs is also responsible for major flooding events in many coastal regions of the world, including the west coast of the United States and western Europe. In this study we combine ideas from Topological Data Analysis (TDA) with Machine Learning (ML) for detecting, classifying and characterizing extreme weather events, like ARs. TDA is a new field that sits at the interface between topology and computer science, that studies "shape" - hidden topological structure - in raw data. It has been applied successfully in many areas of applied sciences, including complex networks, signal processing and image recognition. Using TDA we provide ARs with a shape characteristic as a new feature descriptor for the task of AR classification. In particular, we track the change in topology in precipitable water (integrated water vapour) fields using the Union-Find algorithm. We use the generated feature descriptors with ML classifiers to establish reliability and classification performance of our approach. We utilize the parallel toolkit for extreme climate events analysis (TECA: Petascale Pattern Recognition for Climate Science, Prabhat et al., Computer Analysis of Images and Patterns, 2015) for comparison (it is assumed that events identified by TECA is ground truth). Preliminary results indicate that our approach brings new insight into the study of ARs and provides quantitative information about the relevance of topological feature descriptors in analyses of a large climate datasets. We illustrate this method on climate model output and NCEP reanalysis datasets. Further, our method outperforms existing methods on detection and classification of ARs. This work illustrates that TDA combined with ML may provide a uniquely powerful approach for detection, classification and characterization of extreme weather phenomena.

Scalable designs for quasiparticle-poisoning-protected topological quantum computation with Majorana zero modes

NASA Astrophysics Data System (ADS)

Karzig, Torsten; Knapp, Christina; Lutchyn, Roman M.; Bonderson, Parsa; Hastings, Matthew B.; Nayak, Chetan; Alicea, Jason; Flensberg, Karsten; Plugge, Stephan; Oreg, Yuval; Marcus, Charles M.; Freedman, Michael H.

2017-06-01

We present designs for scalable quantum computers composed of qubits encoded in aggregates of four or more Majorana zero modes, realized at the ends of topological superconducting wire segments that are assembled into superconducting islands with significant charging energy. Quantum information can be manipulated according to a measurement-only protocol, which is facilitated by tunable couplings between Majorana zero modes and nearby semiconductor quantum dots. Our proposed architecture designs have the following principal virtues: (1) the magnetic field can be aligned in the direction of all of the topological superconducting wires since they are all parallel; (2) topological T junctions are not used, obviating possible difficulties in their fabrication and utilization; (3) quasiparticle poisoning is abated by the charging energy; (4) Clifford operations are executed by a relatively standard measurement: detection of corrections to quantum dot energy, charge, or differential capacitance induced by quantum fluctuations; (5) it is compatible with strategies for producing good approximate magic states.

Topological interface states in the natural heterostructure (PbSe)5(Bi2Se3 )6 with BiPb defects

NASA Astrophysics Data System (ADS)

Momida, Hiroyoshi; Bihlmayer, Gustav; Blügel, Stefan; Segawa, Kouji; Ando, Yoichi; Oguchi, Tamio

2018-01-01

We study theoretically the electronic band structure of (PbSe) 5(Bi2Se3 )6, which consists of an ordinary insulator PbSe and a topological insulator Bi2Se3 . The first-principles calculations show that this material has a gapped Dirac-cone energy dispersion inside the bulk, which originates from the topological states of Bi2Se3 layers encapsulated by PbSe layers. Furthermore, we calculate the band structures of (BixPb1 -xSe )5(Bi2Se3 )6 with BiPb antisite defects included in the PbSe layers. The result shows that a high density of BiPb defects can exist in real materials, consistent with the experimentally estimated x of more than 30%. The BiPb defects strongly modify the band alignment between Bi2Se3 and PbSe layers, while the topological interface states of Bi2Se3 are kept as a gapped Dirac-cone-like dispersion.

Determinants of Chromosome Architecture: Insulator Pairing in cis and in trans

PubMed Central

Fujioka, Miki; Mistry, Hemlata; Schedl, Paul; Jaynes, James B.

2016-01-01

The chromosomes of multicellular animals are organized into a series of topologically independent looped domains. This domain organization is critical for the proper utilization and propagation of the genetic information encoded by the chromosome. A special set of architectural elements, called boundaries or insulators, are responsible both for subdividing the chromatin into discrete domains and for determining the topological organization of these domains. Central to the architectural functions of insulators are homologous and heterologous insulator:insulator pairing interactions. The former (pairing between copies of the same insulator) dictates the process of homolog alignment and pairing in trans, while the latter (pairing between different insulators) defines the topology of looped domains in cis. To elucidate the principles governing these architectural functions, we use two insulators, Homie and Nhomie, that flank the Drosophila even skipped locus. We show that homologous insulator interactions in trans, between Homie on one homolog and Homie on the other, or between Nhomie on one homolog and Nhomie on the other, mediate transvection. Critically, these homologous insulator:insulator interactions are orientation-dependent. Consistent with a role in the alignment and pairing of homologs, self-pairing in trans is head-to-head. Head-to-head self-interactions in cis have been reported for other fly insulators, suggesting that this is a general principle of self-pairing. Homie and Nhomie not only pair with themselves, but with each other. Heterologous Homie-Nhomie interactions occur in cis, and we show that they serve to delimit a looped chromosomal domain that contains the even skipped transcription unit and its associated enhancers. The topology of this loop is defined by the heterologous pairing properties of Homie and Nhomie. Instead of being head-to-head, which would generate a circular loop, Homie-Nhomie pairing is head-to-tail. Head-to-tail pairing in cis generates a stem-loop, a configuration much like that observed in classical lampbrush chromosomes. These pairing principles provide a mechanistic underpinning for the observed topologies within and between chromosomes. PMID:26910731

The effect of the magnetic topology of the Magnetic Clouds over the Solar Energetic Particle Events

NASA Astrophysics Data System (ADS)

Medina, J.; Hidalgo, M.; Blanco, J.; Rodriguez-Pacheco, J.

2007-12-01

We have simulated the effect of the magnetic topology of the Magnetic Clouds (MCs) over the solar energetic particle event (SEPe) fluxes (0.5-100 MeV) provided by solar flares. When a SEPe passes through a MC a characteristic behaviour in the data corresponding to the ion and electron fluxes is observed: a depression after a strong maximum of the flux. Using our cross-section circular and elliptical MC models we have tried to explain that effect, understanding the importance of the topology of the MC. In sight of the results of the preliminary analysis we conclude that the magnitude of the magnetic field seems not to play a significant role but the helicoidal topology associated with topology of the MCs. This work has been supported by the Spanish Comisión Internacional de Ciencia y Tecnologia (CICYT), grant ESP2005-07290-C02-01 and ESP2006-08459. This work is performed inside COST Action 724.

Detecting fixation on a target using time-frequency distributions of a retinal birefringence scanning signal

PubMed Central

2013-01-01

Background The fovea, which is the most sensitive part of the retina, is known to have birefringent properties, i.e. it changes the polarization state of light upon reflection. Existing devices use this property to obtain information on the orientation of the fovea and the direction of gaze. Such devices employ specific frequency components that appear during moments of fixation on a target. To detect them, previous methods have used solely the power spectrum of the Fast Fourier Transform (FFT), which, unfortunately, is an integral method, and does not give information as to where exactly the events of interest occur. With very young patients who are not cooperative enough, this presents a problem, because central fixation may be present only during very short-lasting episodes, and can easily be missed by the FFT. Method This paper presents a method for detecting short-lasting moments of central fixation in existing devices for retinal birefringence scanning, with the goal of a reliable detection of eye alignment. Signal analysis is based on the Continuous Wavelet Transform (CWT), which reliably localizes such events in the time-frequency plane. Even though the characteristic frequencies are not always strongly expressed due to possible artifacts, simple topological analysis of the time-frequency distribution can detect fixation reliably. Results In all six subjects tested, the CWT allowed precise identification of both frequency components. Moreover, in four of these subjects, episodes of intermittent but definitely present central fixation were detectable, similar to those in Figure 4. A simple FFT is likely to treat them as borderline cases, or entirely miss them, depending on the thresholds used. Conclusion Joint time-frequency analysis is a powerful tool in the detection of eye alignment, even in a noisy environment. The method is applicable to similar situations, where short-lasting diagnostic events need to be detected in time series acquired by means of scanning some substrate along a specific path. PMID:23668264

Distributions of topological observables in inclusive three- and four-jet events in pp collisions at

NASA Astrophysics Data System (ADS)

Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.; Adam, W.; Bergauer, T.; Dragicevic, M.; Erö, J.; Friedl, M.; Frühwirth, R.; Ghete, V. M.; Hartl, C.; Hörmann, N.; Hrubec, J.; Jeitler, M.; Kiesenhofer, W.; Knünz, V.; Krammer, M.; Krätschmer, I.; Liko, D.; Mikulec, I.; Rabady, D.; Rahbaran, B.; Rohringer, H.; Schöfbeck, R.; Strauss, J.; Treberer-Treberspurg, W.; Waltenberger, W.; Wulz, C.-E.; Mossolov, V.; Shumeiko, N.; Suarez Gonzalez, J.; Alderweireldt, S.; Bansal, S.; Cornelis, T.; De Wolf, E. A.; Janssen, X.; Knutsson, A.; Lauwers, J.; Luyckx, S.; Ochesanu, S.; Rougny, R.; Van De Klundert, M.; Van Haevermaet, H.; Van Mechelen, P.; Van Remortel, N.; Van Spilbeeck, A.; Blekman, F.; Blyweert, S.; D'Hondt, J.; Daci, N.; Heracleous, N.; Keaveney, J.; Lowette, S.; Maes, M.; Olbrechts, A.; Python, Q.; Strom, D.; Tavernier, S.; Van Doninck, W.; Van Mulders, P.; Van Onsem, G. P.; Villella, I.; Caillol, C.; Clerbaux, B.; De Lentdecker, G.; Dobur, D.; Favart, L.; Gay, A. P. R.; Grebenyuk, A.; Léonard, A.; Mohammadi, A.; Perniè, L.; Randle-conde, A.; Reis, T.; Seva, T.; Thomas, L.; Vander Velde, C.; Vanlaer, P.; Wang, J.; Zenoni, F.; Adler, V.; Beernaert, K.; Benucci, L.; Cimmino, A.; Costantini, S.; Crucy, S.; Dildick, S.; Fagot, A.; Garcia, G.; Mccartin, J.; Ocampo Rios, A. A.; Ryckbosch, D.; Salva Diblen, S.; Sigamani, M.; Strobbe, N.; Thyssen, F.; Tytgat, M.; Yazgan, E.; Zaganidis, N.; Basegmez, S.; Beluffi, C.; Bruno, G.; Castello, R.; Caudron, A.; Ceard, L.; Da Silveira, G. G.; Delaere, C.; du Pree, T.; Favart, D.; Forthomme, L.; Giammanco, A.; Hollar, J.; Jafari, A.; Jez, P.; Komm, M.; Lemaitre, V.; Nuttens, C.; Pagano, D.; Perrini, L.; Pin, A.; Piotrzkowski, K.; Popov, A.; Quertenmont, L.; Selvaggi, M.; Vidal Marono, M.; Vizan Garcia, J. M.; Beliy, N.; Caebergs, T.; Daubie, E.; Hammad, G. H.; Júnior, W. L. Aldá; Alves, G. A.; Brito, L.; Correa Martins Junior, M.; Martins, T. Dos Reis; Mora Herrera, C.; Pol, M. E.; Rebello Teles, P.; Carvalho, W.; Chinellato, J.; Custódio, A.; Da Costa, E. M.; De Jesus Damiao, D.; De Oliveira Martins, C.; Fonseca De Souza, S.; Malbouisson, H.; Matos Figueiredo, D.; Mundim, L.; Nogima, H.; Prado Da Silva, W. L.; Santaolalla, J.; Santoro, A.; Sznajder, A.; Tonelli Manganote, E. J.; Vilela Pereira, A.; Bernardes, C. A.; Dogra, S.; Fernandez Perez Tomei, T. R.; Gregores, E. M.; Mercadante, P. G.; Novaes, S. F.; Padula, Sandra S.; Aleksandrov, A.; Genchev, V.; Hadjiiska, R.; Iaydjiev, P.; Marinov, A.; Piperov, S.; Rodozov, M.; Sultanov, G.; Vutova, M.; Dimitrov, A.; Glushkov, I.; Litov, L.; Pavlov, B.; Petkov, P.; Bian, J. G.; Chen, G. M.; Chen, H. S.; Chen, M.; Cheng, T.; Du, R.; Jiang, C. H.; Plestina, R.; Romeo, F.; Tao, J.; Wang, Z.; Asawatangtrakuldee, C.; Ban, Y.; Li, Q.; Liu, S.; Mao, Y.; Qian, S. J.; Wang, D.; Xu, Z.; Zou, W.; Avila, C.; Cabrera, A.; Chaparro Sierra, L. F.; Florez, C.; Gomez, J. P.; Gomez Moreno, B.; Sanabria, J. C.; Godinovic, N.; Lelas, D.; Polic, D.; Puljak, I.; Antunovic, Z.; Kovac, M.; Brigljevic, V.; Kadija, K.; Luetic, J.; Mekterovic, D.; Sudic, L.; Attikis, A.; Mavromanolakis, G.; Mousa, J.; Nicolaou, C.; Ptochos, F.; Razis, P. A.; Bodlak, M.; Finger, M.; Finger, M.; Assran, Y.; Ellithi Kamel, A.; Mahmoud, M. A.; Radi, A.; Kadastik, M.; Murumaa, M.; Raidal, M.; Tiko, A.; Eerola, P.; Fedi, G.; Voutilainen, M.; Härkönen, J.; Karimäki, V.; Kinnunen, R.; Kortelainen, M. J.; Lampén, T.; Lassila-Perini, K.; Lehti, S.; Lindén, T.; Luukka, P.; Mäenpää, T.; Peltola, T.; Tuominen, E.; Tuominiemi, J.; Tuovinen, E.; Wendland, L.; Talvitie, J.; Tuuva, T.; Besancon, M.; Couderc, F.; Dejardin, M.; Denegri, D.; Fabbro, B.; Faure, J. L.; Favaro, C.; Ferri, F.; Ganjour, S.; Givernaud, A.; Gras, P.; Hamel de Monchenault, G.; Jarry, P.; Locci, E.; Malcles, J.; Rander, J.; Rosowsky, A.; Titov, M.; Baffioni, S.; Beaudette, F.; Busson, P.; Charlot, C.; Dahms, T.; Dalchenko, M.; Dobrzynski, L.; Filipovic, N.; Florent, A.; Granier de Cassagnac, R.; Mastrolorenzo, L.; Miné, P.; Mironov, C.; Naranjo, I. N.; Nguyen, M.; Ochando, C.; Ortona, G.; Paganini, P.; Regnard, S.; Salerno, R.; Sauvan, J. B.; Sirois, Y.; Veelken, C.; Yilmaz, Y.; Zabi, A.; Agram, J.-L.; Andrea, J.; Aubin, A.; Bloch, D.; Brom, J.-M.; Chabert, E. C.; Collard, C.; Conte, E.; Fontaine, J.-C.; Gelé, D.; Goerlach, U.; Goetzmann, C.; Le Bihan, A.-C.; Skovpen, K.; Van Hove, P.; Gadrat, S.; Beauceron, S.; Beaupere, N.; Boudoul, G.; Bouvier, E.; Brochet, S.; Carrillo Montoya, C. 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M.; Paramesvaran, S.; Poll, A.; Sakuma, T.; Senkin, S.; Smith, V. J.; Bell, K. W.; Belyaev, A.; Brew, C.; Brown, R. M.; Cockerill, D. J. A.; Coughlan, J. A.; Harder, K.; Harper, S.; Olaiya, E.; Petyt, D.; Shepherd-Themistocleous, C. H.; Thea, A.; Tomalin, I. R.; Williams, T.; Womersley, W. J.; Worm, S. D.; Baber, M.; Bainbridge, R.; Buchmuller, O.; Burton, D.; Colling, D.; Cripps, N.; Dauncey, P.; Davies, G.; Della Negra, M.; Dunne, P.; Ferguson, W.; Fulcher, J.; Futyan, D.; Hall, G.; Iles, G.; Jarvis, M.; Karapostoli, G.; Kenzie, M.; Lane, R.; Lucas, R.; Lyons, L.; Magnan, A.-M.; Malik, S.; Mathias, B.; Nash, J.; Nikitenko, A.; Pela, J.; Pesaresi, M.; Petridis, K.; Raymond, D. M.; Rogerson, S.; Rose, A.; Seez, C.; Sharp, P.; Tapper, A.; Vazquez Acosta, M.; Virdee, T.; Zenz, S. C.; Cole, J. E.; Hobson, P. R.; Khan, A.; Kyberd, P.; Leggat, D.; Leslie, D.; Reid, I. D.; Symonds, P.; Teodorescu, L.; Turner, M.; Dittmann, J.; Hatakeyama, K.; Kasmi, A.; Liu, H.; Scarborough, T.; Charaf, O.; Cooper, S. I.; Henderson, C.; Rumerio, P.; Avetisyan, A.; Bose, T.; Fantasia, C.; Lawson, P.; Richardson, C.; Rohlf, J.; St. John, J.; Sulak, L.; Alimena, J.; Berry, E.; Bhattacharya, S.; Christopher, G.; Cutts, D.; Demiragli, Z.; Dhingra, N.; Ferapontov, A.; Garabedian, A.; Heintz, U.; Kukartsev, G.; Laird, E.; Landsberg, G.; Luk, M.; Narain, M.; Segala, M.; Sinthuprasith, T.; Speer, T.; Swanson, J.; Breedon, R.; Breto, G.; De La Barca Sanchez, M. Calderon; Chauhan, S.; Chertok, M.; Conway, J.; Conway, R.; Cox, P. T.; Erbacher, R.; Gardner, M.; Ko, W.; Lander, R.; Mulhearn, M.; Pellett, D.; Pilot, J.; Ricci-Tam, F.; Shalhout, S.; Smith, J.; Squires, M.; Stolp, D.; Tripathi, M.; Wilbur, S.; Yohay, R.; Cousins, R.; Everaerts, P.; Farrell, C.; Hauser, J.; Ignatenko, M.; Rakness, G.; Takasugi, E.; Valuev, V.; Weber, M.; Burt, K.; Clare, R.; Ellison, J.; Gary, J. W.; Hanson, G.; Heilman, J.; Ivova Rikova, M.; Jandir, P.; Kennedy, E.; Lacroix, F.; Long, O. R.; Luthra, A.; Malberti, M.; Negrete, M. Olmedo; Shrinivas, A.; Sumowidagdo, S.; Wimpenny, S.; Branson, J. G.; Cerati, G. B.; Cittolin, S.; D'Agnolo, R. T.; Holzner, A.; Kelley, R.; Klein, D.; Letts, J.; Macneill, I.; Olivito, D.; Padhi, S.; Palmer, C.; Pieri, M.; Sani, M.; Sharma, V.; Simon, S.; Tadel, M.; Tu, Y.; Vartak, A.; Welke, C.; Würthwein, F.; Yagil, A.; Barge, D.; Bradmiller-Feld, J.; Campagnari, C.; Danielson, T.; Dishaw, A.; Dutta, V.; Flowers, K.; Franco Sevilla, M.; Geffert, P.; George, C.; Golf, F.; Gouskos, L.; Incandela, J.; Justus, C.; Mccoll, N.; Richman, J.; Stuart, D.; To, W.; West, C.; Yoo, J.; Apresyan, A.; Bornheim, A.; Bunn, J.; Chen, Y.; Duarte, J.; Mott, A.; Newman, H. B.; Pena, C.; Pierini, M.; Spiropulu, M.; Vlimant, J. R.; Wilkinson, R.; Xie, S.; Zhu, R. Y.; Azzolini, V.; Calamba, A.; Carlson, B.; Ferguson, T.; Iiyama, Y.; Paulini, M.; Russ, J.; Vogel, H.; Vorobiev, I.; Cumalat, J. P.; Ford, W. T.; Gaz, A.; Krohn, M.; Luiggi Lopez, E.; Nauenberg, U.; Smith, J. G.; Stenson, K.; Wagner, S. R.; Alexander, J.; Chatterjee, A.; Chaves, J.; Chu, J.; Dittmer, S.; Eggert, N.; Mirman, N.; Nicolas Kaufman, G.; Patterson, J. R.; Ryd, A.; Salvati, E.; Skinnari, L.; Sun, W.; Teo, W. D.; Thom, J.; Thompson, J.; Tucker, J.; Weng, Y.; Winstrom, L.; Wittich, P.; Winn, D.; Abdullin, S.; Albrow, M.; Anderson, J.; Apollinari, G.; Bauerdick, L. A. T.; Beretvas, A.; Berryhill, J.; Bhat, P. C.; Bolla, G.; Burkett, K.; Butler, J. N.; Cheung, H. W. K.; Chlebana, F.; Cihangir, S.; Elvira, V. D.; Fisk, I.; Freeman, J.; Gao, Y.; Gottschalk, E.; Gray, L.; Green, D.; Grünendahl, S.; Gutsche, O.; Hanlon, J.; Hare, D.; Harris, R. M.; Hirschauer, J.; Hooberman, B.; Jindariani, S.; Johnson, M.; Joshi, U.; Kaadze, K.; Klima, B.; Kreis, B.; Kwan, S.; Linacre, J.; Lincoln, D.; Lipton, R.; Liu, T.; Lykken, J.; Maeshima, K.; Marraffino, J. M.; Martinez Outschoorn, V. I.; Maruyama, S.; Mason, D.; McBride, P.; Merkel, P.; Mishra, K.; Mrenna, S.; Nahn, S.; Newman-Holmes, C.; O'Dell, V.; Prokofyev, O.; Sexton-Kennedy, E.; Sharma, S.; Soha, A.; Spalding, W. J.; Spiegel, L.; Taylor, L.; Tkaczyk, S.; Tran, N. V.; Uplegger, L.; Vaandering, E. W.; Vidal, R.; Whitbeck, A.; Whitmore, J.; Yang, F.; Acosta, D.; Avery, P.; Bortignon, P.; Bourilkov, D.; Carver, M.; Curry, D.; Das, S.; De Gruttola, M.; Di Giovanni, G. P.; Field, R. D.; Fisher, M.; Furic, I. K.; Hugon, J.; Konigsberg, J.; Korytov, A.; Kypreos, T.; Low, J. F.; Matchev, K.; Mei, H.; Milenovic, P.; Mitselmakher, G.; Muniz, L.; Rinkevicius, A.; Shchutska, L.; Snowball, M.; Sperka, D.; Yelton, J.; Zakaria, M.; Hewamanage, S.; Linn, S.; Markowitz, P.; Martinez, G.; Rodriguez, J. L.; Adams, T.; Askew, A.; Bochenek, J.; Diamond, B.; Haas, J.; Hagopian, S.; Hagopian, V.; Johnson, K. F.; Prosper, H.; Veeraraghavan, V.; Weinberg, M.; Baarmand, M. M.; Hohlmann, M.; Kalakhety, H.; Yumiceva, F.; Adams, M. R.; Apanasevich, L.; Berry, D.; Betts, R. R.; Bucinskaite, I.; Cavanaugh, R.; Evdokimov, O.; Gauthier, L.; Gerber, C. E.; Hofman, D. J.; Kurt, P.; Moon, D. H.; O'Brien, C.; Sandoval Gonzalez, l. D.; Silkworth, C.; Turner, P.; Varelas, N.; Bilki, B.; Clarida, W.; Dilsiz, K.; Haytmyradov, M.; Merlo, J.-P.; Mermerkaya, H.; Mestvirishvili, A.; Moeller, A.; Nachtman, J.; Ogul, H.; Onel, Y.; Ozok, F.; Penzo, A.; Rahmat, R.; Sen, S.; Tan, P.; Tiras, E.; Wetzel, J.; Yi, K.; Barnett, B. A.; Blumenfeld, B.; Bolognesi, S.; Fehling, D.; Gritsan, A. V.; Maksimovic, P.; Martin, C.; Swartz, M.; Baringer, P.; Bean, A.; Benelli, G.; Bruner, C.; Kenny, R. P.; Malek, M.; Murray, M.; Noonan, D.; Sanders, S.; Sekaric, J.; Stringer, R.; Wang, Q.; Wood, J. S.; Chakaberia, I.; Ivanov, A.; Khalil, S.; Makouski, M.; Maravin, Y.; Saini, L. K.; Skhirtladze, N.; Svintradze, I.; Gronberg, J.; Lange, D.; Rebassoo, F.; Wright, D.; Baden, A.; Belloni, A.; Calvert, B.; Eno, S. C.; Gomez, J. A.; Hadley, N. J.; Kellogg, R. G.; Kolberg, T.; Lu, Y.; Mignerey, A. C.; Pedro, K.; Skuja, A.; Tonjes, M. B.; Tonwar, S. C.; Apyan, A.; Barbieri, R.; Busza, W.; Cali, I. A.; Chan, M.; Di Matteo, L.; Gomez Ceballos, G.; Goncharov, M.; Gulhan, D.; Klute, M.; Lai, Y. S.; Lee, Y.-J.; Levin, A.; Luckey, P. D.; Paus, C.; Ralph, D.; Roland, C.; Roland, G.; Stephans, G. S. F.; Sumorok, K.; Velicanu, D.; Veverka, J.; Wyslouch, B.; Yang, M.; Zanetti, M.; Zhukova, V.; Dahmes, B.; Gude, A.; Kao, S. C.; Klapoetke, K.; Kubota, Y.; Mans, J.; Pastika, N.; Rusack, R.; Singovsky, A.; Tambe, N.; Turkewitz, J.; Acosta, J. G.; Oliveros, S.; Avdeeva, E.; Bloom, K.; Bose, S.; Claes, D. R.; Dominguez, A.; Gonzalez Suarez, R.; Keller, J.; Knowlton, D.; Kravchenko, I.; Lazo-Flores, J.; Meier, F.; Ratnikov, F.; Snow, G. R.; Zvada, M.; Dolen, J.; Godshalk, A.; Iashvili, I.; Kharchilava, A.; Kumar, A.; Rappoccio, S.; Alverson, G.; Barberis, E.; Baumgartel, D.; Chasco, M.; Massironi, A.; Morse, D. M.; Nash, D.; Orimoto, T.; Trocino, D.; Wang, R. J.; Wood, D.; Zhang, J.; Hahn, K. A.; Kubik, A.; Mucia, N.; Odell, N.; Pollack, B.; Pozdnyakov, A.; Schmitt, M.; Stoynev, S.; Sung, K.; Velasco, M.; Won, S.; Brinkerhoff, A.; Chan, K. M.; Drozdetskiy, A.; Hildreth, M.; Jessop, C.; Karmgard, D. J.; Kellams, N.; Lannon, K.; Lynch, S.; Marinelli, N.; Musienko, Y.; Pearson, T.; Planer, M.; Ruchti, R.; Smith, G.; Valls, N.; Wayne, M.; Wolf, M.; Woodard, A.; Antonelli, L.; Brinson, J.; Bylsma, B.; Durkin, L. S.; Flowers, S.; Hart, A.; Hill, C.; Hughes, R.; Kotov, K.; Ling, T. Y.; Luo, W.; Puigh, D.; Rodenburg, M.; Winer, B. L.; Wolfe, H.; Wulsin, H. W.; Driga, O.; Elmer, P.; Hardenbrook, J.; Hebda, P.; Hunt, A.; Koay, S. A.; Lujan, P.; Marlow, D.; Medvedeva, T.; Mooney, M.; Olsen, J.; Piroué, P.; Quan, X.; Saka, H.; Stickland, D.; Tully, C.; Werner, J. S.; Zuranski, A.; Brownson, E.; Malik, S.; Mendez, H.; Ramirez Vargas, J. E.; Barnes, V. E.; Benedetti, D.; Bortoletto, D.; De Mattia, M.; Gutay, L.; Hu, Z.; Jha, M. K.; Jones, M.; Jung, K.; Kress, M.; Leonardo, N.; Miller, D. H.; Neumeister, N.; Radburn-Smith, B. C.; Shi, X.; Shipsey, I.; Silvers, D.; Svyatkovskiy, A.; Wang, F.; Xie, W.; Xu, L.; Zablocki, J.; Parashar, N.; Stupak, J.; Adair, A.; Akgun, B.; Ecklund, K. M.; Geurts, F. J. M.; Li, W.; Michlin, B.; Padley, B. P.; Redjimi, R.; Roberts, J.; Zabel, J.; Betchart, B.; Bodek, A.; Covarelli, R.; de Barbaro, P.; Demina, R.; Eshaq, Y.; Ferbel, T.; Garcia-Bellido, A.; Goldenzweig, P.; Han, J.; Harel, A.; Khukhunaishvili, A.; Korjenevski, S.; Petrillo, G.; Vishnevskiy, D.; Ciesielski, R.; Demortier, L.; Goulianos, K.; Mesropian, C.; Arora, S.; Barker, A.; Chou, J. P.; Contreras-Campana, C.; Contreras-Campana, E.; Duggan, D.; Ferencek, D.; Gershtein, Y.; Gray, R.; Halkiadakis, E.; Hidas, D.; Kaplan, S.; Lath, A.; Panwalkar, S.; Park, M.; Patel, R.; Salur, S.; Schnetzer, S.; Somalwar, S.; Stone, R.; Thomas, S.; Thomassen, P.; Walker, M.; Rose, K.; Spanier, S.; York, A.; Bouhali, O.; Castaneda Hernandez, A.; Eusebi, R.; Flanagan, W.; Gilmore, J.; Kamon, T.; Khotilovich, V.; Krutelyov, V.; Montalvo, R.; Osipenkov, I.; Pakhotin, Y.; Perloff, A.; Roe, J.; Rose, A.; Safonov, A.; Suarez, I.; Tatarinov, A.; Ulmer, K. A.; Akchurin, N.; Cowden, C.; Damgov, J.; Dragoiu, C.; Dudero, P. R.; Faulkner, J.; Kovitanggoon, K.; Kunori, S.; Lee, S. W.; Libeiro, T.; Volobouev, I.; Appelt, E.; Delannoy, A. G.; Greene, S.; Gurrola, A.; Johns, W.; Maguire, C.; Mao, Y.; Melo, A.; Sharma, M.; Sheldon, P.; Snook, B.; Tuo, S.; Velkovska, J.; Arenton, M. W.; Boutle, S.; Cox, B.; Francis, B.; Goodell, J.; Hirosky, R.; Ledovskoy, A.; Li, H.; Lin, C.; Neu, C.; Wood, J.; Clarke, C.; Harr, R.; Karchin, P. E.; Kottachchi Kankanamge Don, C.; Lamichhane, P.; Sturdy, J.; Belknap, D. A.; Carlsmith, D.; Cepeda, M.; Dasu, S.; Dodd, L.; Duric, S.; Friis, E.; Hall-Wilton, R.; Herndon, M.; Hervé, A.; Klabbers, P.; Lanaro, A.; Lazaridis, C.; Levine, A.; Loveless, R.; Mohapatra, A.; Ojalvo, I.; Perry, T.; Pierro, G. A.; Polese, G.; Ross, I.; Sarangi, T.; Savin, A.; Smith, W. H.; Taylor, D.; Vuosalo, C.; Woods, N.

2015-07-01

This paper presents distributions of topological observables in inclusive three- and four-jet events produced in pp collisions at a centre-of-mass energy of 7 with a data sample collected by the CMS experiment corresponding to a luminosity of 5.1. The distributions are corrected for detector effects, and compared with several event generators based on two- and multi-parton matrix elements at leading order. Among the considered calculations, MadGraph interfaced with pythia6 displays the overall best agreement with data.

Multiple alignment analysis on phylogenetic tree of the spread of SARS epidemic using distance method

NASA Astrophysics Data System (ADS)

Amiroch, S.; Pradana, M. S.; Irawan, M. I.; Mukhlash, I.

2017-09-01

Multiple Alignment (MA) is a particularly important tool for studying the viral genome and determine the evolutionary process of the specific virus. Application of MA in the case of the spread of the Severe acute respiratory syndrome (SARS) epidemic is an interesting thing because this virus epidemic a few years ago spread so quickly that medical attention in many countries. Although there has been a lot of software to process multiple sequences, but the use of pairwise alignment to process MA is very important to consider. In previous research, the alignment between the sequences to process MA algorithm, Super Pairwise Alignment, but in this study used a dynamic programming algorithm Needleman wunchs simulated in Matlab. From the analysis of MA obtained and stable region and unstable which indicates the position where the mutation occurs, the system network topology that produced the phylogenetic tree of the SARS epidemic distance method, and system area networks mutation.

On-shell constrained M 2 variables with applications to mass measurements and topology disambiguation

NASA Astrophysics Data System (ADS)

Cho, Won Sang; Gainer, James S.; Kim, Doojin; Matchev, Konstantin T.; Moortgat, Filip; Pape, Luc; Park, Myeonghun

2014-08-01

We consider a class of on-shell constrained mass variables that are 3+1 dimensional generalizations of the Cambridge M T2 variable and that automatically incorporate various assumptions about the underlying event topology. The presence of additional on-shell constraints causes their kinematic distributions to exhibit sharper endpoints than the usual M T2 distribution. We study the mathematical properties of these new variables, e.g., the uniqueness of the solution selected by the minimization over the invisible particle 4-momenta. We then use this solution to reconstruct the masses of various particles along the decay chain. We propose several tests for validating the assumed event topology in missing energy events from new physics. The tests are able to determine: 1) whether the decays in the event are two-body or three-body, 2) if the decay is two-body, whether the intermediate resonances in the two decay chains are the same, and 3) the exact sequence in which the visible particles are emitted from each decay chain.

Nanofiber Alignment Regulates NIH3T3 Cell Orientation and Cytoskeletal Gene Expression on Electrospun PCL+Gelatin Nanofibers.

PubMed

Fee, Timothy; Surianarayanan, Swetha; Downs, Crawford; Zhou, Yong; Berry, Joel

2016-01-01

To examine the influence of substrate topology on the behavior of fibroblasts, tissue engineering scaffolds were electrospun from polycaprolactone (PCL) and a blend of PCL and gelatin (PCL+Gel) to produce matrices with both random and aligned nanofibrous orientations. The addition of gelatin to the scaffold was shown to increase the hydrophilicity of the PCL matrix and to increase the proliferation of NIH3T3 cells compared to scaffolds of PCL alone. The orientation of nanofibers within the matrix did not have an effect on the proliferation of adherent cells, but cells on aligned substrates were shown to elongate and align parallel to the direction of substrate fiber alignment. A microarray of cyotoskeleton regulators was probed to examine differences in gene expression between cells grown on an aligned and randomly oriented substrates. It was found that transcriptional expression of eight genes was statistically different between the two conditions, with all of them being upregulated in the aligned condition. The proteins encoded by these genes are linked to production and polymerization of actin microfilaments, as well as focal adhesion assembly. Taken together, the data indicates NIH3T3 fibroblasts on aligned substrates align themselves parallel with their substrate and increase production of actin and focal adhesion related genes.

Gold nanocrystals with DNA-directed morphologies.

PubMed

Ma, Xingyi; Huh, June; Park, Wounjhang; Lee, Luke P; Kwon, Young Jik; Sim, Sang Jun

2016-09-16

Precise control over the structure of metal nanomaterials is important for developing advanced nanobiotechnology. Assembly methods of nanoparticles into structured blocks have been widely demonstrated recently. However, synthesis of nanocrystals with controlled, three-dimensional structures remains challenging. Here we show a directed crystallization of gold by a single DNA molecular regulator in a sequence-independent manner and its applications in three-dimensional topological controls of crystalline nanostructures. We anchor DNA onto gold nanoseed with various alignments to form gold nanocrystals with defined topologies. Some topologies are asymmetric including pushpin-, star- and biconcave disk-like structures, as well as more complex jellyfish- and flower-like structures. The approach of employing DNA enables the solution-based synthesis of nanocrystals with controlled, three-dimensional structures in a desired direction, and expands the current tools available for designing and synthesizing feature-rich nanomaterials for future translational biotechnology.

Pair creation, motion, and annihilation of topological defects in two-dimensional nematic liquid crystals

NASA Astrophysics Data System (ADS)

Cortese, Dario; Eggers, Jens; Liverpool, Tanniemola B.

2018-02-01

We present a framework for the study of disclinations in two-dimensional active nematic liquid crystals and topological defects in general. The order tensor formalism is used to calculate exact multiparticle solutions of the linearized static equations inside a planar uniformly aligned state so that the total charge has to vanish. Topological charge conservation then requires that there is always an equal number of q =1 /2 and q =-1 /2 charges. Starting from a set of hydrodynamic equations, we derive a low-dimensional dynamical system for the parameters of the static solutions, which describes the motion of a half-disclination pair or of several pairs. Within this formalism, we model defect production and annihilation, as observed in experiments. Our dynamics also provide an estimate for the critical density at which production and annihilation rates are balanced.

Gold nanocrystals with DNA-directed morphologies

NASA Astrophysics Data System (ADS)

Ma, Xingyi; Huh, June; Park, Wounjhang; Lee, Luke P.; Kwon, Young Jik; Sim, Sang Jun

2016-09-01

Precise control over the structure of metal nanomaterials is important for developing advanced nanobiotechnology. Assembly methods of nanoparticles into structured blocks have been widely demonstrated recently. However, synthesis of nanocrystals with controlled, three-dimensional structures remains challenging. Here we show a directed crystallization of gold by a single DNA molecular regulator in a sequence-independent manner and its applications in three-dimensional topological controls of crystalline nanostructures. We anchor DNA onto gold nanoseed with various alignments to form gold nanocrystals with defined topologies. Some topologies are asymmetric including pushpin-, star- and biconcave disk-like structures, as well as more complex jellyfish- and flower-like structures. The approach of employing DNA enables the solution-based synthesis of nanocrystals with controlled, three-dimensional structures in a desired direction, and expands the current tools available for designing and synthesizing feature-rich nanomaterials for future translational biotechnology.

Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria.

PubMed

Padial, José M; Grant, Taran; Frost, Darrel R

2014-06-26

Brachycephaloidea is a monophyletic group of frogs with more than 1000 species distributed throughout the New World tropics, subtropics, and Andean regions. Recently, the group has been the target of multiple molecular phylogenetic analyses, resulting in extensive changes in its taxonomy. Here, we test previous hypotheses of phylogenetic relationships for the group by combining available molecular evidence (sequences of 22 genes representing 431 ingroup and 25 outgroup terminals) and performing a tree-alignment analysis under the parsimony optimality criterion using the program POY. To elucidate the effects of alignment and optimality criterion on phylogenetic inferences, we also used the program MAFFT to obtain a similarity-alignment for analysis under both parsimony and maximum likelihood using the programs TNT and GARLI, respectively. Although all three analytical approaches agreed on numerous points, there was also extensive disagreement. Tree-alignment under parsimony supported the monophyly of the ingroup and the sister group relationship of the monophyletic marsupial frogs (Hemiphractidae), while maximum likelihood and parsimony analyses of the MAFFT similarity-alignment did not. All three methods differed with respect to the position of Ceuthomantis smaragdinus (Ceuthomantidae), with tree-alignment using parsimony recovering this species as the sister of Pristimantis + Yunganastes. All analyses rejected the monophyly of Strabomantidae and Strabomantinae as originally defined, and the tree-alignment analysis under parsimony further rejected the recently redefined Craugastoridae and Pristimantinae. Despite the greater emphasis in the systematics literature placed on the choice of optimality criterion for evaluating trees than on the choice of method for aligning DNA sequences, we found that the topological differences attributable to the alignment method were as great as those caused by the optimality criterion. Further, the optimal tree-alignment indicates that insertions and deletions occurred in twice as many aligned positions as implied by the optimal similarity-alignment, confirming previous findings that sequence turnover through insertion and deletion events plays a greater role in molecular evolution than indicated by similarity-alignments. Our results also provide a clear empirical demonstration of the different effects of wildcard taxa produced by missing data in parsimony and maximum likelihood analyses. Specifically, maximum likelihood analyses consistently (81% bootstrap frequency) provided spurious resolution despite a lack of evidence, whereas parsimony correctly depicted the ambiguity due to missing data by collapsing unsupported nodes. We provide a new taxonomy for the group that retains previously recognized Linnaean taxa except for Ceuthomantidae, Strabomantidae, and Strabomantinae. A phenotypically diagnosable superfamily is recognized formally as Brachycephaloidea, with the informal, unranked name terrarana retained as the standard common name for these frogs. We recognize three families within Brachycephaloidea that are currently diagnosable solely on molecular grounds (Brachycephalidae, Craugastoridae, and Eleutherodactylidae), as well as five subfamilies (Craugastorinae, Eleutherodactylinae, Holoadeninae, Phyzelaphryninae, and Pristimantinae) corresponding in large part to previous families and subfamilies. Our analyses upheld the monophyly of all tested genera, but we found numerous subgeneric taxa to be non-monophyletic and modified the taxonomy accordingly.

Measuring Orbital Angular Momentum (OAM) States of Vortex Beams with Annular Gratings

PubMed Central

Zheng, Shuang; Wang, Jian

2017-01-01

Measuring orbital angular momentum (OAM) states of vortex beams is of great importance in diverse applications employing OAM-carrying vortex beams. We present a simple and efficient scheme to measure OAM states (i.e. topological charge values) of vortex beams with annular gratings. The magnitude of the topological charge value is determined by the number of dark fringes after diffraction, and the sign of the topological charge value is distinguished by the orientation of the diffraction pattern. We first theoretically study the diffraction patterns using both annular amplitude and phase gratings. The annular phase grating shows almost 10-dB better diffraction efficiency compared to the annular amplitude grating. We then experimentally demonstrate the OAM states measurement of vortex beams using annular phase grating. The scheme works well even for high-order vortex beams with topological charge value as high as ± 25. We also experimentally show the evolution of diffraction patterns when slightly changing the fractional topological charge value of vortex beam from 0.1 to 1.0. In addition, the proposed scheme shows potential large tolerance of beam alignment during the OAM states measurement of vortex beams. PMID:28094325

Measuring Orbital Angular Momentum (OAM) States of Vortex Beams with Annular Gratings.

PubMed

Zheng, Shuang; Wang, Jian

2017-01-17

Measuring orbital angular momentum (OAM) states of vortex beams is of great importance in diverse applications employing OAM-carrying vortex beams. We present a simple and efficient scheme to measure OAM states (i.e. topological charge values) of vortex beams with annular gratings. The magnitude of the topological charge value is determined by the number of dark fringes after diffraction, and the sign of the topological charge value is distinguished by the orientation of the diffraction pattern. We first theoretically study the diffraction patterns using both annular amplitude and phase gratings. The annular phase grating shows almost 10-dB better diffraction efficiency compared to the annular amplitude grating. We then experimentally demonstrate the OAM states measurement of vortex beams using annular phase grating. The scheme works well even for high-order vortex beams with topological charge value as high as ± 25. We also experimentally show the evolution of diffraction patterns when slightly changing the fractional topological charge value of vortex beam from 0.1 to 1.0. In addition, the proposed scheme shows potential large tolerance of beam alignment during the OAM states measurement of vortex beams.

A new graph-based method for pairwise global network alignment

PubMed Central

Klau, Gunnar W

2009-01-01

Background In addition to component-based comparative approaches, network alignments provide the means to study conserved network topology such as common pathways and more complex network motifs. Yet, unlike in classical sequence alignment, the comparison of networks becomes computationally more challenging, as most meaningful assumptions instantly lead to NP-hard problems. Most previous algorithmic work on network alignments is heuristic in nature. Results We introduce the graph-based maximum structural matching formulation for pairwise global network alignment. We relate the formulation to previous work and prove NP-hardness of the problem. Based on the new formulation we build upon recent results in computational structural biology and present a novel Lagrangian relaxation approach that, in combination with a branch-and-bound method, computes provably optimal network alignments. The Lagrangian algorithm alone is a powerful heuristic method, which produces solutions that are often near-optimal and – unlike those computed by pure heuristics – come with a quality guarantee. Conclusion Computational experiments on the alignment of protein-protein interaction networks and on the classification of metabolic subnetworks demonstrate that the new method is reasonably fast and has advantages over pure heuristics. Our software tool is freely available as part of the LISA library. PMID:19208162

MaxAlign: maximizing usable data in an alignment.

PubMed

Gouveia-Oliveira, Rodrigo; Sackett, Peter W; Pedersen, Anders G

2007-08-28

The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. In phylogenetic and other analyses, for instance, gapped columns are often discarded entirely from the alignment. MaxAlign is a program that optimizes the alignment prior to such analyses. Specifically, it maximizes the number of nucleotide (or amino acid) symbols that are present in gap-free columns - the alignment area - by selecting the optimal subset of sequences to exclude from the alignment. MaxAlign can be used prior to phylogenetic and bioinformatical analyses as well as in other situations where this form of alignment improvement is useful. In this work we test MaxAlign's performance in these tasks and compare the accuracy of phylogenetic estimates including and excluding gapped columns from the analysis, with and without processing with MaxAlign. In this paper we also introduce a new simple measure of tree similarity, Normalized Symmetric Similarity (NSS) that we consider useful for comparing tree topologies. We demonstrate how MaxAlign is helpful in detecting misaligned or defective sequences without requiring manual inspection. We also show that it is not advisable to exclude gapped columns from phylogenetic analyses unless MaxAlign is used first. Finally, we find that the sequences removed by MaxAlign from an alignment tend to be those that would otherwise be associated with low phylogenetic accuracy, and that the presence of gaps in any given sequence does not seem to disturb the phylogenetic estimates of other sequences. The MaxAlign web-server is freely available online at http://www.cbs.dtu.dk/services/MaxAlign where supplementary information can also be found. The program is also freely available as a Perl stand-alone package.

Coherent clusters of inertial particles in homogeneous turbulence

NASA Astrophysics Data System (ADS)

Baker, Lucia; Frankel, Ari; Mani, Ali; Coletti, Filippo

2016-11-01

Clustering of heavy particles in turbulent flows manifests itself in a broad spectrum of physical phenomena, including sediment transport, cloud formation, and spray combustion. However, a clear topological definition of particle cluster has been lacking, limiting our ability to describe their features and dynamics. Here we introduce a definition of coherent cluster based on self-similarity, and apply it to the distribution of heavy particles in direct numerical simulations of homogeneous isotropic turbulence. We consider a range of particle Stokes numbers, with and without the effect of gravity. Clusters show self-similarity at length scales larger than twice the Kolmogorov length, with a specific fractal dimension. In the absence of gravity, clusters demonstrate a tendency to sample regions of the flow where strain is dominant over vorticity, and to align themselves with the local vorticity vector; when gravity is present, the clusters tend to align themselves with gravity, and their fall speed is different from the average settling velocity. This approach yields observations which are consistent with findings obtained from previous studies while opening new avenues for analysis of the topology and evolution of particle clusters in a wealth of applications.

On decomposing stimulus and response waveforms in event-related potentials recordings.

PubMed

Yin, Gang; Zhang, Jun

2011-06-01

Event-related potentials (ERPs) reflect the brain activities related to specific behavioral events, and are obtained by averaging across many trial repetitions with individual trials aligned to the onset of a specific event, e.g., the onset of stimulus (s-aligned) or the onset of the behavioral response (r-aligned). However, the s-aligned and r-aligned ERP waveforms do not purely reflect, respectively, underlying stimulus (S-) or response (R-) component waveform, due to their cross-contaminations in the recorded ERP waveforms. Zhang [J. Neurosci. Methods, 80, pp. 49-63, 1998] proposed an algorithm to recover the pure S-component waveform and the pure R-component waveform from the s-aligned and r-aligned ERP average waveforms-however, due to the nature of this inverse problem, a direct solution is sensitive to noise that disproportionally affects low-frequency components, hindering the practical implementation of this algorithm. Here, we apply the Wiener deconvolution technique to deal with noise in input data, and investigate a Tikhonov regularization approach to obtain a stable solution that is robust against variances in the sampling of reaction-time distribution (when number of trials is low). Our method is demonstrated using data from a Go/NoGo experiment about image classification and recognition.

Distributions of topological observables in inclusive three- and four-jet events in pp collisions at [Formula: see text][Formula: see text].

PubMed

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Gaz, A; Krohn, M; Luiggi Lopez, E; Nauenberg, U; Smith, J G; Stenson, K; Wagner, S R; Alexander, J; Chatterjee, A; Chaves, J; Chu, J; Dittmer, S; Eggert, N; Mirman, N; Nicolas Kaufman, G; Patterson, J R; Ryd, A; Salvati, E; Skinnari, L; Sun, W; Teo, W D; Thom, J; Thompson, J; Tucker, J; Weng, Y; Winstrom, L; Wittich, P; Winn, D; Abdullin, S; Albrow, M; Anderson, J; Apollinari, G; Bauerdick, L A T; Beretvas, A; Berryhill, J; Bhat, P C; Bolla, G; Burkett, K; Butler, J N; Cheung, H W K; Chlebana, F; Cihangir, S; Elvira, V D; Fisk, I; Freeman, J; Gao, Y; Gottschalk, E; Gray, L; Green, D; Grünendahl, S; Gutsche, O; Hanlon, J; Hare, D; Harris, R M; Hirschauer, J; Hooberman, B; Jindariani, S; Johnson, M; Joshi, U; Kaadze, K; Klima, B; Kreis, B; Kwan, S; Linacre, J; Lincoln, D; Lipton, R; Liu, T; Lykken, J; Maeshima, K; Marraffino, J M; Martinez Outschoorn, V I; Maruyama, S; Mason, D; McBride, P; Merkel, P; Mishra, K; Mrenna, S; Nahn, S; Newman-Holmes, C; O'Dell, V; Prokofyev, O; Sexton-Kennedy, E; Sharma, S; Soha, A; Spalding, W J; Spiegel, L; Taylor, L; Tkaczyk, S; Tran, N V; Uplegger, L; Vaandering, E W; Vidal, R; Whitbeck, A; Whitmore, J; Yang, F; Acosta, D; Avery, P; Bortignon, P; Bourilkov, D; Carver, M; Curry, D; Das, S; De Gruttola, M; Di Giovanni, G P; Field, R D; Fisher, M; Furic, I K; Hugon, J; Konigsberg, J; Korytov, A; Kypreos, T; Low, J F; Matchev, K; Mei, H; Milenovic, P; Mitselmakher, G; Muniz, L; Rinkevicius, A; Shchutska, L; Snowball, M; Sperka, D; Yelton, J; Zakaria, M; Hewamanage, S; Linn, S; Markowitz, P; Martinez, G; Rodriguez, J L; Adams, T; Askew, A; Bochenek, J; Diamond, B; Haas, J; Hagopian, S; Hagopian, V; Johnson, K F; Prosper, H; Veeraraghavan, V; Weinberg, M; Baarmand, M M; Hohlmann, M; Kalakhety, H; Yumiceva, F; Adams, M R; Apanasevich, L; Berry, D; Betts, R R; Bucinskaite, I; Cavanaugh, R; Evdokimov, O; Gauthier, L; Gerber, C E; Hofman, D J; Kurt, P; Moon, D H; O'Brien, C; Sandoval Gonzalez, L D; Silkworth, C; Turner, P; Varelas, N; Bilki, B; Clarida, W; 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This paper presents distributions of topological observables in inclusive three- and four-jet events produced in pp collisions at a centre-of-mass energy of 7[Formula: see text] with a data sample collected by the CMS experiment corresponding to a luminosity of 5.1[Formula: see text]. The distributions are corrected for detector effects, and compared with several event generators based on two- and multi-parton matrix elements at leading order. Among the considered calculations, MadGraph interfaced with pythia6 displays the overall best agreement with data.

Distributions of topological observables in inclusive three- and four-jet events in pp collisions at √s = 7 TeV

DOE PAGES

Khachatryan, Vardan

2015-07-01

This paper presents distributions of topological observables in inclusive three- and four-jet events produced in pp collisions at a centre-of-mass energy of 7TeV with a data sample collected by the CMS experiment corresponding to a luminosity of 5.1fb -1. We corrected the distributions for detector effects, and compared with several event generators based on two- and multi-parton matrix elements at leading order. Thus, among the considered calculations, MADGRAPH interfaced with PYTHIA6displays the overall best agreement with data.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Renner, J.; Farbin, A.; Vidal, J. Muñoz

Here, we investigate the potential of using deep learning techniques to reject background events in searches for neutrinoless double beta decay with high pressure xenon time projection chambers capable of detailed track reconstruction. The differences in the topological signatures of background and signal events can be learned by deep neural networks via training over many thousands of events. These networks can then be used to classify further events as signal or background, providing an additional background rejection factor at an acceptable loss of efficiency. The networks trained in this study performed better than previous methods developed based on the usemore » of the same topological signatures by a factor of 1.2 to 1.6, and there is potential for further improvement.« less

Establishing homology between mitochondrial calcium uniporters, prokaryotic magnesium channels and chlamydial IncA proteins.

PubMed

Lee, Andre; Vastermark, Ake; Saier, Milton H

2014-08-01

Mitochondrial calcium uniporters (MCUs) (TC no. 1.A.77) are oligomeric channel proteins found in the mitochondrial inner membrane. MCUs have two well-conserved transmembrane segments (TMSs), connected by a linker, similar to bacterial MCU homologues. These proteins and chlamydial IncA proteins (of unknown function; TC no. 9.B.159) are homologous to prokaryotic Mg(2+) transporters, AtpI and AtpZ, based on comparison scores of up to 14.5 sds. A phylogenetic tree containing all of these proteins showed that the AtpZ proteins cluster coherently as a subset within the large and diverse AtpI cluster, which branches separately from the MCUs and IncAs, both of which cluster coherently. The MCUs and AtpZs share the same two TMS topology, but the AtpIs have four TMSs, and IncAs can have either two (most frequent) or four (less frequent) TMSs. Binary alignments, comparison scores and motif analyses showed that TMSs 1 and 2 align with TMSs 3 and 4 of the AtpIs, suggesting that the four TMS AtpI proteins arose via an intragenic duplication event. These findings establish an evolutionary link interconnecting eukaryotic and prokaryotic Ca(2+) and Mg(2+) transporters with chlamydial IncAs, and lead us to suggest that all members of the MCU superfamily, including IncAs, function as divalent cation channels. © 2014 The Authors.

Establishing homology between mitochondrial calcium uniporters, prokaryotic magnesium channels and chlamydial IncA proteins

PubMed Central

Lee, Andre; Vastermark, Ake

2014-01-01

Mitochondrial calcium uniporters (MCUs) (TC no. 1.A.77) are oligomeric channel proteins found in the mitochondrial inner membrane. MCUs have two well-conserved transmembrane segments (TMSs), connected by a linker, similar to bacterial MCU homologues. These proteins and chlamydial IncA proteins (of unknown function; TC no. 9.B.159) are homologous to prokaryotic Mg2+ transporters, AtpI and AtpZ, based on comparison scores of up to 14.5 sds. A phylogenetic tree containing all of these proteins showed that the AtpZ proteins cluster coherently as a subset within the large and diverse AtpI cluster, which branches separately from the MCUs and IncAs, both of which cluster coherently. The MCUs and AtpZs share the same two TMS topology, but the AtpIs have four TMSs, and IncAs can have either two (most frequent) or four (less frequent) TMSs. Binary alignments, comparison scores and motif analyses showed that TMSs 1 and 2 align with TMSs 3 and 4 of the AtpIs, suggesting that the four TMS AtpI proteins arose via an intragenic duplication event. These findings establish an evolutionary link interconnecting eukaryotic and prokaryotic Ca2+ and Mg2+ transporters with chlamydial IncAs, and lead us to suggest that all members of the MCU superfamily, including IncAs, function as divalent cation channels. PMID:24869855

Nick-free formation of reciprocal heteroduplexes: a simple solution to the topological problem.

PubMed Central

Wilson, J H

1979-01-01

Because the individual strands of DNA are intertwined, formation of heteroduplex structures between duplexes--as in presumed recombination intermediates--presents a topological puzzle, known as the winding problem. Previous approaches to this problem have assumed that single-strand breaks are required to permit formation of fully coiled heteroduplexes. This paper describes a simple, nick-free solution to the winding problem that satisfies all topological constraints. Homologous duplexes associated by their minor-groove surfaces can switch strand pairing to form reciprocal heteroduplexes that coil together into a compact, four-stranded helix throughout the region of pairing. Model building shows that this fused heteroduplex structure is plausible, being composed entirely of right-handed primary helices with Watson-Crick base pairing throughout. Its simplicity of formation, structural symmetry, and high degree of specificity are suggestive of a natural mechanism for alignment by base pairing between intact homologous duplexes. Implications for genetic recombination are discussed. Images PMID:291028

Violation of Ohm's law in a Weyl metal.

PubMed

Shin, Dongwoo; Lee, Yongwoo; Sasaki, M; Jeong, Yoon Hee; Weickert, Franziska; Betts, Jon B; Kim, Heon-Jung; Kim, Ki-Seok; Kim, Jeehoon

2017-11-01

Ohm's law is a fundamental paradigm in the electrical transport of metals. Any transport signatures violating Ohm's law would give an indisputable fingerprint for a novel metallic state. Here, we uncover the breakdown of Ohm's law owing to a topological structure of the chiral anomaly in the Weyl metal phase. We observe nonlinear I-V characteristics in Bi 0.96 Sb 0.04 single crystals in the diffusive limit, which occurs only for a magnetic-field-aligned electric field (E∥B). The Boltzmann transport theory with the charge pumping effect reveals the topological-in-origin nonlinear conductivity, and it leads to a universal scaling function of the longitudinal magnetoconductivity, which completely describes our experimental results. As a hallmark of Weyl metals, the nonlinear conductivity provides a venue for nonlinear electronics, optical applications, and the development of a topological Fermi-liquid theory beyond the Landau Fermi-liquid theory.

New rRNA Gene-Based Phylogenies of the Alphaproteobacteria Provide Perspective on Major Groups, Mitochondrial Ancestry and Phylogenetic Instability

PubMed Central

Ferla, Matteo P.; Thrash, J. Cameron; Giovannoni, Stephen J.; Patrick, Wayne M.

2013-01-01

Bacteria in the class Alphaproteobacteria have a wide variety of lifestyles and physiologies. They include pathogens of humans and livestock, agriculturally valuable strains, and several highly abundant marine groups. The ancestor of mitochondria also originated in this clade. Despite significant effort to investigate the phylogeny of the Alphaproteobacteria with a variety of methods, there remains considerable disparity in the placement of several groups. Recent emphasis on phylogenies derived from multiple protein-coding genes remains contentious due to disagreement over appropriate gene selection and the potential influences of systematic error. We revisited previous investigations in this area using concatenated alignments of the small and large subunit (SSU and LSU) rRNA genes, as we show here that these loci have much lower GC bias than whole genomes. This approach has allowed us to update the canonical 16S rRNA gene tree of the Alphaproteobacteria with additional important taxa that were not previously included, and with added resolution provided by concatenating the SSU and LSU genes. We investigated the topological stability of the Alphaproteobacteria by varying alignment methods, rate models, taxon selection and RY-recoding to circumvent GC content bias. We also introduce RYMK-recoding and show that it avoids some of the information loss in RY-recoding. We demonstrate that the topology of the Alphaproteobacteria is sensitive to inclusion of several groups of taxa, but it is less affected by the choice of alignment and rate methods. The majority of topologies and comparative results from Approximately Unbiased tests provide support for positioning the Rickettsiales and the mitochondrial branch within a clade. This composite clade is a sister group to the abundant marine SAR11 clade (Pelagibacterales). Furthermore, we add support for taxonomic assignment of several recently sequenced taxa. Accordingly, we propose three subclasses within the Alphaproteobacteria: the Caulobacteridae, the Rickettsidae, and the Magnetococcidae. PMID:24349502

Prevalent Exon-Intron Structural Changes in the APETALA1/FRUITFULL, SEPALLATA, AGAMOUS-LIKE6, and FLOWERING LOCUS C MADS-Box Gene Subfamilies Provide New Insights into Their Evolution

PubMed Central

Yu, Xianxian; Duan, Xiaoshan; Zhang, Rui; Fu, Xuehao; Ye, Lingling; Kong, Hongzhi; Xu, Guixia; Shan, Hongyan

2016-01-01

AP1/FUL, SEP, AGL6, and FLC subfamily genes play important roles in flower development. The phylogenetic relationships among them, however, have been controversial, which impedes our understanding of the origin and functional divergence of these genes. One possible reason for the controversy may be the problems caused by changes in the exon-intron structure of genes, which, according to recent studies, may generate non-homologous sites and hamper the homology-based sequence alignment. In this study, we first performed exon-by-exon alignments of these and three outgroup subfamilies (SOC1, AG, and STK). Phylogenetic trees reconstructed based on these matrices show improved resolution and better congruence with species phylogeny. In the context of these phylogenies, we traced evolutionary changes of exon-intron structures in each subfamily. We found that structural changes have occurred frequently following gene duplication and speciation events. Notably, exons 7 and 8 (if present) suffered more structural changes than others. With the knowledge of exon-intron structural changes, we generated more reasonable alignments containing all the focal subfamilies. The resulting trees showed that the SEP subfamily is sister to the monophyletic group formed by AP1/FUL and FLC subfamily genes and that the AGL6 subfamily forms a sister group to the three abovementioned subfamilies. Based on this topology, we inferred the evolutionary history of exon-intron structural changes among different subfamilies. Particularly, we found that the eighth exon originated before the divergence of AP1/FUL, FLC, SEP, and AGL6 subfamilies and degenerated in the ancestral FLC-like gene. These results provide new insights into the origin and evolution of the AP1/FUL, FLC, SEP, and AGL6 subfamilies. PMID:27200066

Topological defects control collective dynamics in neural progenitor cell cultures

NASA Astrophysics Data System (ADS)

Kawaguchi, Kyogo; Kageyama, Ryoichiro; Sano, Masaki

2017-04-01

Cultured stem cells have become a standard platform not only for regenerative medicine and developmental biology but also for biophysical studies. Yet, the characterization of cultured stem cells at the level of morphology and of the macroscopic patterns resulting from cell-to-cell interactions remains largely qualitative. Here we report on the collective dynamics of cultured murine neural progenitor cells (NPCs), which are multipotent stem cells that give rise to cells in the central nervous system. At low densities, NPCs moved randomly in an amoeba-like fashion. However, NPCs at high density elongated and aligned their shapes with one another, gliding at relatively high velocities. Although the direction of motion of individual cells reversed stochastically along the axes of alignment, the cells were capable of forming an aligned pattern up to length scales similar to that of the migratory stream observed in the adult brain. The two-dimensional order of alignment within the culture showed a liquid-crystalline pattern containing interspersed topological defects with winding numbers of +1/2 and -1/2 (half-integer due to the nematic feature that arises from the head-tail symmetry of cell-to-cell interaction). We identified rapid cell accumulation at +1/2 defects and the formation of three-dimensional mounds. Imaging at the single-cell level around the defects allowed us to quantify the velocity field and the evolving cell density; cells not only concentrate at +1/2 defects, but also escape from -1/2 defects. We propose a generic mechanism for the instability in cell density around the defects that arises from the interplay between the anisotropic friction and the active force field.

A goal bias in action: The boundaries adults perceive in events align with sites of actor intent.

PubMed

Levine, Dani; Hirsh-Pasek, Kathy; Pace, Amy; Michnick Golinkoff, Roberta

2017-06-01

We live in a dynamic world comprised of continuous events. Remembering our past and predicting future events, however, requires that we segment these ongoing streams of information in a consistent manner. How is this segmentation achieved? This research examines whether the boundaries adults perceive in events, such as the Olympic figure skating routine used in these studies, align with the beginnings (sources) and endings (goals) of human goal-directed actions. Study 1 showed that a group of experts, given an explicit task with unlimited time to rewatch the event, identified the same subevents as one another, but with greater agreement as to the timing of goals than sources. In Study 2, experts, novices familiarized with the figure skating sequence, and unfamiliarized novices performed an online event segmentation task, marking boundaries as the video progressed in real time. The online boundaries of all groups corresponded with the sources and goals offered by Study 1's experts, with greater alignment of goals than sources. Additionally, expertise, but not mere perceptual familiarity, boosted the alignment of sources and goals. Finally, Study 3, which presented novices with the video played in reverse, indicated, unexpectedly, that even when spatiotemporal cues were disrupted, viewers' perceived event boundaries still aligned with their perception of the actors' intended sources and goals. This research extends the goal bias to event segmentation, and suggests that our spontaneous sensitivity toward goals may allow us to transform even relatively complex and unfamiliar event streams into structured and meaningful representations. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Ligand Binding Site Detection by Local Structure Alignment and Its Performance Complementarity

PubMed Central

Lee, Hui Sun; Im, Wonpil

2013-01-01

Accurate determination of potential ligand binding sites (BS) is a key step for protein function characterization and structure-based drug design. Despite promising results of template-based BS prediction methods using global structure alignment (GSA), there is a room to improve the performance by properly incorporating local structure alignment (LSA) because BS are local structures and often similar for proteins with dissimilar global folds. We present a template-based ligand BS prediction method using G-LoSA, our LSA tool. A large benchmark set validation shows that G-LoSA predicts drug-like ligands’ positions in single-chain protein targets more precisely than TM-align, a GSA-based method, while the overall success rate of TM-align is better. G-LoSA is particularly efficient for accurate detection of local structures conserved across proteins with diverse global topologies. Recognizing the performance complementarity of G-LoSA to TM-align and a non-template geometry-based method, fpocket, a robust consensus scoring method, CMCS-BSP (Complementary Methods and Consensus Scoring for ligand Binding Site Prediction), is developed and shows improvement on prediction accuracy. The G-LoSA source code is freely available at http://im.bioinformatics.ku.edu/GLoSA. PMID:23957286

Background rejection in NEXT using deep neural networks

DOE PAGES

Renner, J.; Farbin, A.; Vidal, J. Muñoz; ...

2017-01-16

Here, we investigate the potential of using deep learning techniques to reject background events in searches for neutrinoless double beta decay with high pressure xenon time projection chambers capable of detailed track reconstruction. The differences in the topological signatures of background and signal events can be learned by deep neural networks via training over many thousands of events. These networks can then be used to classify further events as signal or background, providing an additional background rejection factor at an acceptable loss of efficiency. The networks trained in this study performed better than previous methods developed based on the usemore » of the same topological signatures by a factor of 1.2 to 1.6, and there is potential for further improvement.« less

PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases.

PubMed

Floden, Evan W; Tommaso, Paolo D; Chatzou, Maria; Magis, Cedrik; Notredame, Cedric; Chang, Jia-Ming

2016-07-08

The PSI/TM-Coffee web server performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative (PSI) BLAST searches against a choice of redundant and non-redundant databases. The main novelty of this server is to allow databases of reduced complexity to rapidly perform homology extension. This server also gives the possibility to use transmembrane proteins (TMPs) reference databases to allow even faster homology extension on this important category of proteins. Aside from an MSA, the server also outputs topological prediction of TMPs using the HMMTOP algorithm. Previous benchmarking of the method has shown this approach outperforms the most accurate alignment methods such as MSAProbs, Kalign, PROMALS, MAFFT, ProbCons and PRALINE™. The web server is available at http://tcoffee.crg.cat/tmcoffee. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Supersymmetric black holes with lens-space topology.

PubMed

Kunduri, Hari K; Lucietti, James

2014-11-21

We present a new supersymmetric, asymptotically flat, black hole solution to five-dimensional supergravity. It is regular on and outside an event horizon of lens-space topology L(2,1). It is the first example of an asymptotically flat black hole with lens-space topology. The solution is characterized by a charge, two angular momenta, and a magnetic flux through a noncontractible disk region ending on the horizon, with one constraint relating these.

Energetic Particles Events inside Magnetic Clouds

NASA Astrophysics Data System (ADS)

Medina, Jose; Hidalgo, Miguel Angel; Blanco, Juan Jose; Rodriguez-Pacheco, Javier

The effect of the magnetic topology of the Magnetic Clouds (MCs) over the energetic particle event (EPe) fluxes (0.5-100 MeV) have been simulated. In the data corresponding to the ion and electron fluxes, a depression after a strong maximum is observed when a EPe passes through a MC. Using our cross-section circular and elliptical MC models (Journal of Geophysical Research 107(1), doi:10.1029/2001JA900100 (2002) and Solar Physics 207(1), 187-198 (2002)) we have tried to explain that effect, understanding the importance of the topology of the MC. In sight of the results of the preliminary analysis we conclude that the magnitude of the magnetic field seems not to play a significant role but the helicoidal topology associated with topology of the MCs. This work has been supported by the Spanish Comisín Internacional de o Ciencia y Tecnoloǵ (CICYT), grant ESP2005-07290-C02-01 and ESP2006-08459. This work ıa is performed inside COST Action 724.

Acquired prior knowledge modulates audiovisual integration.

PubMed

Van Wanrooij, Marc M; Bremen, Peter; John Van Opstal, A

2010-05-01

Orienting responses to audiovisual events in the environment can benefit markedly by the integration of visual and auditory spatial information. However, logically, audiovisual integration would only be considered successful for stimuli that are spatially and temporally aligned, as these would be emitted by a single object in space-time. As humans do not have prior knowledge about whether novel auditory and visual events do indeed emanate from the same object, such information needs to be extracted from a variety of sources. For example, expectation about alignment or misalignment could modulate the strength of multisensory integration. If evidence from previous trials would repeatedly favour aligned audiovisual inputs, the internal state might also assume alignment for the next trial, and hence react to a new audiovisual event as if it were aligned. To test for such a strategy, subjects oriented a head-fixed pointer as fast as possible to a visual flash that was consistently paired, though not always spatially aligned, with a co-occurring broadband sound. We varied the probability of audiovisual alignment between experiments. Reaction times were consistently lower in blocks containing only aligned audiovisual stimuli than in blocks also containing pseudorandomly presented spatially disparate stimuli. Results demonstrate dynamic updating of the subject's prior expectation of audiovisual congruency. We discuss a model of prior probability estimation to explain the results.

Revisiting the phylogeny of Zoanthidea (Cnidaria: Anthozoa): Staggered alignment of hypervariable sequences improves species tree inference.

PubMed

Swain, Timothy D

2018-01-01

The recent rapid proliferation of novel taxon identification in the Zoanthidea has been accompanied by a parallel propagation of gene trees as a tool of species discovery, but not a corresponding increase in our understanding of phylogeny. This disparity is caused by the trade-off between the capabilities of automated DNA sequence alignment and data content of genes applied to phylogenetic inference in this group. Conserved genes or segments are easily aligned across the order, but produce poorly resolved trees; hypervariable genes or segments contain the evolutionary signal necessary for resolution and robust support, but sequence alignment is daunting. Staggered alignments are a form of phylogeny-informed sequence alignment composed of a mosaic of local and universal regions that allow phylogenetic inference to be applied to all nucleotides from both hypervariable and conserved gene segments. Comparisons between species tree phylogenies inferred from all data (staggered alignment) and hypervariable-excluded data (standard alignment) demonstrate improved confidence and greater topological agreement with other sources of data for the complete-data tree. This novel phylogeny is the most comprehensive to date (in terms of taxa and data) and can serve as an expandable tool for evolutionary hypothesis testing in the Zoanthidea. Spanish language abstract available in Text S1. Translation by L. O. Swain, DePaul University, Chicago, Illinois, 60604, USA. Copyright © 2017 Elsevier Inc. All rights reserved.

Artificial gravity field, astrophysical analogues, and topological phase transitions in strained topological semimetals

NASA Astrophysics Data System (ADS)

Yu, Zhiming; Guan, Shan; Yao, Yugui; Yang, Shengyuan

Effective gravity and gauge fields are emergent properties intrinsic for low-energy quasiparticles in topological semimetals. Here, taking two Dirac semimetals as examples, we demonstrate that applied lattice strain can generate warped spacetime, with fascinating analogues in astrophysics. Particularly, we study the possibility of simulating black-hole/white-hole event horizons and gravitational lensing effect. Furthermore, we discover strain-induced topological phase transitions, both in the bulk materials and in their thin films. Especially in thin films, the transition between the quantum spin Hall and the trivial insulating phases can be achieved by a small strain, naturally leading to the proposition of a novel piezo-topological transistor device. Our result not only bridges multiple disciplines, revealing topological semimetals as a unique table-top platform for exploring interesting phenomena in astrophysics and general relativity; it also suggests realistic materials and methods to achieve controlled topological phase transitions with great potential for device applications.

The kinetic activation-relaxation technique: an off-lattice, self-learning kinetic Monte Carlo algorithm with on-the-fly event search

NASA Astrophysics Data System (ADS)

Mousseau, Nomand

2012-02-01

While kinetic Monte Carlo algorithm has been proposed almost 40 years ago, its application in materials science has been mostly limited to lattice-based motion due to the difficulties associated with identifying new events and building usable catalogs when atoms moved into off-lattice position. Here, I present the kinetic activation-relaxation technique (kinetic ART) is an off-lattice, self-learning kinetic Monte Carlo algorithm with on-the-fly event search [1]. It combines ART nouveau [2], a very efficient unbiased open-ended activated method for finding transition states, with a topological classification [3] that allows a discrete cataloguing of local environments in complex systems, including disordered materials. In kinetic ART, local topologies are first identified for all atoms in a system. ART nouveau event searches are then launched for new topologies, building an extensive catalog of barriers and events. Next, all low energy events are fully reconstructed and relaxed, allowing to take complete account of elastic effects in the system's kinetics. Using standard kinetic Monte Carlo, the clock is brought forward and an event is then selected and applied before a new search for topologies is launched. In addition to presenting the various elements of the algorithm, I will discuss three recent applications to ion-bombarded silicon, defect diffusion in Fe and structural relaxation in amorphous silicon.[4pt] This work was done in collaboration with Laurent Karim B'eland, Peter Brommer, Fedwa El-Mellouhi, Jean-Francois Joly and Laurent Lewis.[4pt] [1] F. El-Mellouhi, N. Mousseau and L.J. Lewis, Phys. Rev. B. 78, 153202 (2008); L.K. B'eland et al., Phys. Rev. E 84, 046704 (2011).[2] G.T. Barkema and N. Mousseau, Phys. Rev. Lett. 77, 4358 (1996); E. Machado-Charry et al., J. Chem Phys. 135, 034102, (2011).[3] B.D. McKay, Congressus Numerantium 30, 45 (1981).

Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic.

PubMed

Brown, Peter; Pullan, Wayne; Yang, Yuedong; Zhou, Yaoqi

2016-02-01

The three dimensional tertiary structure of a protein at near atomic level resolution provides insight alluding to its function and evolution. As protein structure decides its functionality, similarity in structure usually implies similarity in function. As such, structure alignment techniques are often useful in the classifications of protein function. Given the rapidly growing rate of new, experimentally determined structures being made available from repositories such as the Protein Data Bank, fast and accurate computational structure comparison tools are required. This paper presents SPalignNS, a non-sequential protein structure alignment tool using a novel asymmetrical greedy search technique. The performance of SPalignNS was evaluated against existing sequential and non-sequential structure alignment methods by performing trials with commonly used datasets. These benchmark datasets used to gauge alignment accuracy include (i) 9538 pairwise alignments implied by the HOMSTRAD database of homologous proteins; (ii) a subset of 64 difficult alignments from set (i) that have low structure similarity; (iii) 199 pairwise alignments of proteins with similar structure but different topology; and (iv) a subset of 20 pairwise alignments from the RIPC set. SPalignNS is shown to achieve greater alignment accuracy (lower or comparable root-mean squared distance with increased structure overlap coverage) for all datasets, and the highest agreement with reference alignments from the challenging dataset (iv) above, when compared with both sequentially constrained alignments and other non-sequential alignments. SPalignNS was implemented in C++. The source code, binary executable, and a web server version is freely available at: http://sparks-lab.org yaoqi.zhou@griffith.edu.au. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Characterizing the topology of probabilistic biological networks.

PubMed

Todor, Andrei; Dobra, Alin; Kahveci, Tamer

2013-01-01

Biological interactions are often uncertain events, that may or may not take place with some probability. This uncertainty leads to a massive number of alternative interaction topologies for each such network. The existing studies analyze the degree distribution of biological networks by assuming that all the given interactions take place under all circumstances. This strong and often incorrect assumption can lead to misleading results. In this paper, we address this problem and develop a sound mathematical basis to characterize networks in the presence of uncertain interactions. Using our mathematical representation, we develop a method that can accurately describe the degree distribution of such networks. We also take one more step and extend our method to accurately compute the joint-degree distributions of node pairs connected by edges. The number of possible network topologies grows exponentially with the number of uncertain interactions. However, the mathematical model we develop allows us to compute these degree distributions in polynomial time in the number of interactions. Our method works quickly even for entire protein-protein interaction (PPI) networks. It also helps us find an adequate mathematical model using MLE. We perform a comparative study of node-degree and joint-degree distributions in two types of biological networks: the classical deterministic networks and the more flexible probabilistic networks. Our results confirm that power-law and log-normal models best describe degree distributions for both probabilistic and deterministic networks. Moreover, the inverse correlation of degrees of neighboring nodes shows that, in probabilistic networks, nodes with large number of interactions prefer to interact with those with small number of interactions more frequently than expected. We also show that probabilistic networks are more robust for node-degree distribution computation than the deterministic ones. all the data sets used, the software implemented and the alignments found in this paper are available at http://bioinformatics.cise.ufl.edu/projects/probNet/.

Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples

PubMed Central

2011-01-01

Background Readthrough fusions across adjacent genes in the genome, or transcription-induced chimeras (TICs), have been estimated using expressed sequence tag (EST) libraries to involve 4-6% of all genes. Deep transcriptional sequencing (RNA-Seq) now makes it possible to study the occurrence and expression levels of TICs in individual samples across the genome. Methods We performed single-end RNA-Seq on three human prostate adenocarcinoma samples and their corresponding normal tissues, as well as brain and universal reference samples. We developed two bioinformatics methods to specifically identify TIC events: a targeted alignment method using artificial exon-exon junctions within 200,000 bp from adjacent genes, and genomic alignment allowing splicing within individual reads. We performed further experimental verification and characterization of selected TIC and fusion events using quantitative RT-PCR and comparative genomic hybridization microarrays. Results Targeted alignment against artificial exon-exon junctions yielded 339 distinct TIC events, including 32 gene pairs with multiple isoforms. The false discovery rate was estimated to be 1.5%. Spliced alignment to the genome was less sensitive, finding only 18% of those found by targeted alignment in 33-nt reads and 59% of those in 50-nt reads. However, spliced alignment revealed 30 cases of TICs with intervening exons, in addition to distant inversions, scrambled genes, and translocations. Our findings increase the catalog of observed TIC gene pairs by 66%. We verified 6 of 6 predicted TICs in all prostate samples, and 2 of 5 predicted novel distant gene fusions, both private events among 54 prostate tumor samples tested. Expression of TICs correlates with that of the upstream gene, which can explain the prostate-specific pattern of some TIC events and the restriction of the SLC45A3-ELK4 e4-e2 TIC to ERG-negative prostate samples, as confirmed in 20 matched prostate tumor and normal samples and 9 lung cancer cell lines. Conclusions Deep transcriptional sequencing and analysis with targeted and spliced alignment methods can effectively identify TIC events across the genome in individual tissues. Prostate and reference samples exhibit a wide range of TIC events, involving more genes than estimated previously using ESTs. Tissue specificity of TIC events is correlated with expression patterns of the upstream gene. Some TIC events, such as MSMB-NCOA4, may play functional roles in cancer. PMID:21261984

Double-Cascade Events from New Physics in Icecube [Double Bangs from New Physics in IceCube

DOE PAGES

Coloma, Pilar; Machado, Pedro A. N.; Martinez-Soler, Ivan; ...

2017-11-16

A variety of new physics models allows for neutrinos to up-scatter into heavier states. If the incident neutrino is energetic enough, the heavy neutrino may travel some distance before decaying. In this work, we consider the atmospheric neutrino flux as a source of such events. At IceCube, this would lead to a “double-bang” (DB) event topology, similar to what is predicted to occur for tau neutrinos at ultrahigh energies. The DB event topology has an extremely low background rate from coincident atmospheric cascades, making this a distinctive signature of new physics. Finally, our results indicate that IceCube should already bemore » able to derive new competitive constraints on models with GeV-scale sterile neutrinos using existing data.« less

Double-Cascade Events from New Physics in Icecube [Double Bangs from New Physics in IceCube

DOE Office of Scientific and Technical Information (OSTI.GOV)

Coloma, Pilar; Machado, Pedro A. N.; Martinez-Soler, Ivan

A variety of new physics models allows for neutrinos to up-scatter into heavier states. If the incident neutrino is energetic enough, the heavy neutrino may travel some distance before decaying. In this work, we consider the atmospheric neutrino flux as a source of such events. At IceCube, this would lead to a “double-bang” (DB) event topology, similar to what is predicted to occur for tau neutrinos at ultrahigh energies. The DB event topology has an extremely low background rate from coincident atmospheric cascades, making this a distinctive signature of new physics. Finally, our results indicate that IceCube should already bemore » able to derive new competitive constraints on models with GeV-scale sterile neutrinos using existing data.« less

CASP10-BCL::Fold efficiently samples topologies of large proteins.

PubMed

Heinze, Sten; Putnam, Daniel K; Fischer, Axel W; Kohlmann, Tim; Weiner, Brian E; Meiler, Jens

2015-03-01

During CASP10 in summer 2012, we tested BCL::Fold for prediction of free modeling (FM) and template-based modeling (TBM) targets. BCL::Fold assembles the tertiary structure of a protein from predicted secondary structure elements (SSEs) omitting more flexible loop regions early on. This approach enables the sampling of conformational space for larger proteins with more complex topologies. In preparation of CASP11, we analyzed the quality of CASP10 models throughout the prediction pipeline to understand BCL::Fold's ability to sample the native topology, identify native-like models by scoring and/or clustering approaches, and our ability to add loop regions and side chains to initial SSE-only models. The standout observation is that BCL::Fold sampled topologies with a GDT_TS score > 33% for 12 of 18 and with a topology score > 0.8 for 11 of 18 test cases de novo. Despite the sampling success of BCL::Fold, significant challenges still exist in clustering and loop generation stages of the pipeline. The clustering approach employed for model selection often failed to identify the most native-like assembly of SSEs for further refinement and submission. It was also observed that for some β-strand proteins model refinement failed as β-strands were not properly aligned to form hydrogen bonds removing otherwise accurate models from the pool. Further, BCL::Fold samples frequently non-natural topologies that require loop regions to pass through the center of the protein. © 2015 Wiley Periodicals, Inc.

Generation of an Atlas of the Proximal Femur and Its Application to Trabecular Bone Analysis

PubMed Central

Carballido-Gamio, Julio; Folkesson, Jenny; Karampinos, Dimitrios C.; Baum, Thomas; Link, Thomas M.; Majumdar, Sharmila; Krug, Roland

2013-01-01

Automatic placement of anatomically corresponding volumes of interest and comparison of parameters against a standard of reference are essential components in studies of trabecular bone. Only recently, in vivo MR images of the proximal femur, an important fracture site, could be acquired with high-spatial resolution. The purpose of this MRI trabecular bone study was two-fold: (1) to generate an atlas of the proximal femur to automatically place anatomically corresponding volumes of interest in a population study and (2) to demonstrate how mean models of geodesic topological analysis parameters can be generated to be used as potential standard of reference. Ten females were used to generate the atlas and geodesic topological analysis models, and 10 females were used to demonstrate the atlas-based trabecular bone analysis. All alignments were based on three-dimensional (3D) multiresolution affine transformations followed by 3D multiresolution free-form deformations. Mean distances less than 1 mm between aligned femora, and sharp edges in the atlas and in fused gray-level images of registered femora indicated that the anatomical variability was well accommodated and explained by the free-form deformations. PMID:21432904

Topological Interference Management for K-User Downlink Massive MIMO Relay Network Channel.

PubMed

Selvaprabhu, Poongundran; Chinnadurai, Sunil; Li, Jun; Lee, Moon Ho

2017-08-17

In this paper, we study the emergence of topological interference alignment and the characterizing features of a multi-user broadcast interference relay channel. We propose an alternative transmission strategy named the relay space-time interference alignment (R-STIA) technique, in which a K -user multiple-input-multiple-output (MIMO) interference channel has massive antennas at the transmitter and relay. Severe interference from unknown transmitters affects the downlink relay network channel and degrades the system performance. An additional (unintended) receiver is introduced in the proposed R-STIA technique to overcome the above problem, since it has the ability to decode the desired signals for the intended receiver by considering cooperation between the receivers. The additional receiver also helps in recovering and reconstructing the interference signals with limited channel state information at the relay (CSIR). The Alamouti space-time transmission technique and minimum mean square error (MMSE) linear precoder are also used in the proposed scheme to detect the presence of interference signals. Numerical results show that the proposed R-STIA technique achieves a better performance in terms of the bit error rate (BER) and sum-rate compared to the existing broadcast channel schemes.

Topological Interference Management for K-User Downlink Massive MIMO Relay Network Channel

PubMed Central

Li, Jun; Lee, Moon Ho

2017-01-01

In this paper, we study the emergence of topological interference alignment and the characterizing features of a multi-user broadcast interference relay channel. We propose an alternative transmission strategy named the relay space-time interference alignment (R-STIA) technique, in which a K-user multiple-input-multiple-output (MIMO) interference channel has massive antennas at the transmitter and relay. Severe interference from unknown transmitters affects the downlink relay network channel and degrades the system performance. An additional (unintended) receiver is introduced in the proposed R-STIA technique to overcome the above problem, since it has the ability to decode the desired signals for the intended receiver by considering cooperation between the receivers. The additional receiver also helps in recovering and reconstructing the interference signals with limited channel state information at the relay (CSIR). The Alamouti space-time transmission technique and minimum mean square error (MMSE) linear precoder are also used in the proposed scheme to detect the presence of interference signals. Numerical results show that the proposed R-STIA technique achieves a better performance in terms of the bit error rate (BER) and sum-rate compared to the existing broadcast channel schemes. PMID:28817071

Phylogenetic inference under varying proportions of indel-induced alignment gaps

PubMed Central

Dwivedi, Bhakti; Gadagkar, Sudhindra R

2009-01-01

Background The effect of alignment gaps on phylogenetic accuracy has been the subject of numerous studies. In this study, we investigated the relationship between the total number of gapped sites and phylogenetic accuracy, when the gaps were introduced (by means of computer simulation) to reflect indel (insertion/deletion) events during the evolution of DNA sequences. The resulting (true) alignments were subjected to commonly used gap treatment and phylogenetic inference methods. Results (1) In general, there was a strong – almost deterministic – relationship between the amount of gap in the data and the level of phylogenetic accuracy when the alignments were very "gappy", (2) gaps resulting from deletions (as opposed to insertions) contributed more to the inaccuracy of phylogenetic inference, (3) the probabilistic methods (Bayesian, PhyML & "MLε, " a method implemented in DNAML in PHYLIP) performed better at most levels of gap percentage when compared to parsimony (MP) and distance (NJ) methods, with Bayesian analysis being clearly the best, (4) methods that treat gapped sites as missing data yielded less accurate trees when compared to those that attribute phylogenetic signal to the gapped sites (by coding them as binary character data – presence/absence, or as in the MLε method), and (5) in general, the accuracy of phylogenetic inference depended upon the amount of available data when the gaps resulted from mainly deletion events, and the amount of missing data when insertion events were equally likely to have caused the alignment gaps. Conclusion When gaps in an alignment are a consequence of indel events in the evolution of the sequences, the accuracy of phylogenetic analysis is likely to improve if: (1) alignment gaps are categorized as arising from insertion events or deletion events and then treated separately in the analysis, (2) the evolutionary signal provided by indels is harnessed in the phylogenetic analysis, and (3) methods that utilize the phylogenetic signal in indels are developed for distance methods too. When the true homology is known and the amount of gaps is 20 percent of the alignment length or less, the methods used in this study are likely to yield trees with 90–100 percent accuracy. PMID:19698168

Violation of Ohm’s law in a Weyl metal [A hallmark of the Weyl metal state: Breakdown of Ohm's law

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shin, Dongwoo; Lee, Yongwoo; Sasaki, M.

Ohm’s law is a fundamental paradigm in the electrical transport of metals. Any transport signatures violating Ohm’s law would give an indisputable fingerprint for a novel metallic state. Here, we uncover the breakdown of Ohm’s law owing to a topological structure of the chiral anomaly in the Weyl metal phase. We observe nonlinear I–V characteristics in Bi 0.96Sb 0.04 single crystals in the diffusive limit, which occurs only for a magnetic-field-aligned electric field (E∥B). The Boltzmann transport theory with the charge pumping effect reveals the topological-in-origin nonlinear conductivity, and it leads to a universal scaling function of the longitudinal magnetoconductivity,more » which completely describes our experimental results. Furthermore, as a hallmark of Weyl metals, the nonlinear conductivity provides a venue for nonlinear electronics, optical applications, and the development of a topological Fermi-liquid theory beyond the Landau Fermi-liquid theory.« less

Zigzag nanoribbons of two-dimensional silicene-like crystals: magnetic, topological and thermoelectric properties.

PubMed

Wierzbicki, Michał; Barnaś, Józef; Swirkowicz, Renata

2015-12-09

The effects of electron-electron and spin-orbit interactions on the ground-state magnetic configuration and on the corresponding thermoelectric and spin thermoelectric properties in zigzag nanoribbons of two-dimensional hexagonal crystals are analysed theoretically. The thermoelectric properties of quasi-stable magnetic states are also considered. Of particular interest is the influence of Coulomb and spin-orbit interactions on the topological edge states and on the transition between the topological insulator and conventional gap insulator states. It is shown that the interplay of both interactions also has a significant impact on the transport and thermoelectric characteristics of the nanoribbons. The spin-orbit interaction also determines the in-plane magnetic easy axis. The thermoelectric properties of nanoribbons with in-plane magnetic moments are compared to those of nanoribbons with edge magnetic moments oriented perpendicularly to their plane. Nanoribbons with ferromagnetic alignment of the edge moments are shown to reveal spin thermoelectricity in addition to the conventional one.

Violation of Ohm’s law in a Weyl metal [A hallmark of the Weyl metal state: Breakdown of Ohm's law

DOE PAGES

Shin, Dongwoo; Lee, Yongwoo; Sasaki, M.; ...

2017-08-14

Ohm’s law is a fundamental paradigm in the electrical transport of metals. Any transport signatures violating Ohm’s law would give an indisputable fingerprint for a novel metallic state. Here, we uncover the breakdown of Ohm’s law owing to a topological structure of the chiral anomaly in the Weyl metal phase. We observe nonlinear I–V characteristics in Bi 0.96Sb 0.04 single crystals in the diffusive limit, which occurs only for a magnetic-field-aligned electric field (E∥B). The Boltzmann transport theory with the charge pumping effect reveals the topological-in-origin nonlinear conductivity, and it leads to a universal scaling function of the longitudinal magnetoconductivity,more » which completely describes our experimental results. Furthermore, as a hallmark of Weyl metals, the nonlinear conductivity provides a venue for nonlinear electronics, optical applications, and the development of a topological Fermi-liquid theory beyond the Landau Fermi-liquid theory.« less

Cluster Observations of Multiple Dipolarization Fronts

NASA Technical Reports Server (NTRS)

Hwang, Kyoung-Joo; Goldstein, Melvyn L.; Lee, Ensang; Pickett, Jolene S.

2011-01-01

We present Cluster observations of a series of dipolarization fronts (DF 1 to 6) at the central current sheet in Earth's magnetotail. The velocities of fast earthward flow following behind each DF 1-3, are comparable to the Alfven velocity, indicating that the flow bursts might have been generated by bursty reconnection that occurred tailward of the spacecraft. Based on multi-spacecraft timing analysis, DF normals are found to propagate mainly earthward at $160-335$ km/s with a thickness of 900-1500 km, which corresponds to the ion inertial length or gyroradius scale. Each DF is followed by significant fluctuations in the $x$ and $y$ components of the magnetic field whose peaks are found 1-2 minutes after the DF passage. These $(B_{x},B_{y} )$-fluctuations propagate dawnward (mainly) and earthward. Strongly enhanced field-aligned beams are observed coincidently with $(B_{x},B_{y})$ fluctuations, while an enhancement of cross-tail currents is associated with the DFs. From the observed pressure imbalance and flux-tube entropy changes between the two regions separated by the DF, we speculate that interchange instability destabilizes the DFs and causes the deformation of the mid-tail magnetic topology. This process generates significant field-aligned currents, and might power the auroral brightening in the ionosphere. However, this event is neither associated with the main substorm auroral breakup nor the poleward expansion, which might indicate that the observed multiple DFs have been dissipated before they reach the inner plasma sheet boundary.

Cluster Observations of Multiple Dipolarization Fronts

NASA Technical Reports Server (NTRS)

Hwang, K.-J.; Goldstein, M. L.; Lee, E.; Pickett, J. S.

2011-01-01

We present Cluster observations of a series of dipolarization fronts (DF 1 to 6) at the central current sheet in Earth's magnetotail. The velocities of fast earthward flow following behind each DF 1.3 are comparable to the Alfven velocity, indicating that the flow bursts might have been generated by bursty reconnection that occurred tailward of the spacecraft. Based on multispacecraft timing analysis, DF normals are found to propagate mainly earthward at 160.335 km/s with a thickness of 900-1500 km, which corresponds to the ion inertial length or gyroradius scale. Each DF is followed by significant fluctuations in the x and y components of the magnetic field whose peaks are found 1.2 min after the DF passage. These (B(sub x), B(sub y)) fluctuations propagate dawnward (mainly) and earthward. Strongly enhanced field-aligned beams are observed coincidently with (B(sub x), B(sub y)) fluctuations, while an enhancement of cross-tail currents is associated with the DFs. From the observed pressure imbalance and flux tube entropy changes between the two regions separated by the DF, we speculate that interchange instability destabilizes the DFs and causes the deformation of the midtail magnetic topology. This process generates significant field-aligned currents and might power the auroral brightening in the ionosphere. However, this event is associated with neither the main substorm auroral breakup nor the poleward expansion, which might indicate that the observed multiple DFs have been dissipated before they reach the inner plasma sheet boundary.

Fuzzy spaces topology change as a possible solution to the black hole information loss paradox

NASA Astrophysics Data System (ADS)

Silva, C. A. S.

2009-06-01

The black hole information loss paradox is one of the most intricate problems in modern theoretical physics. A proposal to solve this is one related with topology change. However it has found some obstacles related to unitarity and cluster decomposition (locality). In this Letter we argue that modelling the black hole's event horizon as a noncommutative manifold - the fuzzy sphere - we can solve the problems with topology change, getting a possible solution to the black hole information loss paradox.

Three-dimensional magnetic reconnection and the magnetic topology of coronal mass ejection events

NASA Technical Reports Server (NTRS)

Gosling, J. T.; Birn, J.; Hesse, M.

1995-01-01

Measurements of superthermal electron fluxes in the solar wind indicate that field lines within coronal mass ejections, CMEs, near and beyond 1 AU are normally connected to the Sun at both ends. However, on occasion some field lines embedded deep within CMEs appear to be connected to the Sun at only one end. Here we propose an explanation for how such field lines arise in terms of 3-dimensional reconnection close to the Sun. Such reconnection also provides a natural explanation for the flux rope topology characteristic of many CMEs as well as the coronal loops formed during long-duration, solar X-ray events. Our consideration of the field topologies resulting from 3-dimensional reconnection indicates that field lines within and near CMEs may on occasion be connected to the outer heliosphere at both ends.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dorier, Matthieu; Mubarak, Misbah; Ross, Rob

Two-tiered direct network topologies such as Dragonflies have been proposed for future post-petascale and exascale machines, since they provide a high-radix, low-diameter, fast interconnection network. Such topologies call for redesigning MPI collective communication algorithms in order to attain the best performance. Yet as increasingly more applications share a machine, it is not clear how these topology-aware algorithms will react to interference with concurrent jobs accessing the same network. In this paper, we study three topology-aware broadcast algorithms, including one designed by ourselves. We evaluate their performance through event-driven simulation for small- and large-sized broadcasts (in terms of both data sizemore » and number of processes). We study the effect of different routing mechanisms on the topology-aware collective algorithms, as well as their sensitivity to network contention with other jobs. Our results show that while topology-aware algorithms dramatically reduce link utilization, their advantage in terms of latency is more limited.« less

The ATLAS Level-1 Topological Trigger performance in Run 2

NASA Astrophysics Data System (ADS)

Riu, Imma; ATLAS Collaboration

2017-10-01

The Level-1 trigger is the first event rate reducing step in the ATLAS detector trigger system, with an output rate of up to 100 kHz and decision latency smaller than 2.5 μs. During the LHC shutdown after Run 1, the Level-1 trigger system was upgraded at hardware, firmware and software levels. In particular, a new electronics sub-system was introduced in the real-time data processing path: the Level-1 Topological trigger system. It consists of a single electronics shelf equipped with two Level-1 Topological processor blades. They receive real-time information from the Level-1 calorimeter and muon triggers, which is processed to measure angles between trigger objects, invariant masses or other kinematic variables. Complementary to other requirements, these measurements are taken into account in the final Level-1 trigger decision. The system was installed and commissioning started in 2015 and continued during 2016. As part of the commissioning, the decisions from individual algorithms were simulated and compared with the hardware response. An overview of the Level-1 Topological trigger system design, commissioning process and impact on several event selections are illustrated.

The spatial alignment of time: Differences in alignment of deictic and sequence time along the sagittal and lateral axes.

PubMed

Walker, Esther J; Bergen, Benjamin K; Núñez, Rafael

2017-04-01

People use space in a variety of ways to structure their thoughts about time. The present report focuses on the different ways that space is employed when reasoning about deictic (past/future relationships) and sequence (earlier/later relationships) time. In the first study, we show that deictic and sequence time are aligned along the lateral axis in a manner consistent with previous work, with past and earlier events associated with left space and future and later events associated with right space. However, the alignment of time with space is different along the sagittal axis. Participants associated future events and earlier events-not later events-with the space in front of their body and past and later events with the space behind, consistent with the sagittal spatial terms (e.g., ahead, in front of) that we use to talk about deictic and sequence time. In the second study, we show that these associations between sequence time and sagittal space are sensitive to person-perspective. This suggests that the particular space-time associations observed in English speakers are influenced by a variety of different spatial properties, including spatial location and perspective. Copyright © 2016. Published by Elsevier B.V.

First proof of topological signature in the high pressure xenon gas TPC with electroluminescence amplification for the NEXT experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ferrario, P.

2016-01-19

The NEXT experiment aims to observe the neutrinoless double beta decay of xenon in a high-pressure 136Xe gas TPC using electroluminescence (EL) to amplify the signal from ionization. One of the main advantages of this technology is the possibility to reconstruct the topology of events with energies close to Q ββ. This paper presents the first demonstration that the topology provides extra handles to reject background events using data obtained with the NEXT-DEMO prototype. Single electrons resulting from the interactions of 22Na 1275 keV gammas and electron-positron pairs produced by conversions of gammas from the 228Th decay chain were usedmore » to represent the background and the signal in a double beta decay. Furthermore, these data were used to develop algorithms for the reconstruction of tracks and the identification of the energy deposited at the end-points, providing an extra background rejection factor of 24.3 ± 1.4 (stat.)%, while maintaining an efficiency of 66.7 ± 1% for signal events.« less

Pavement cells and the topology puzzle.

PubMed

Carter, Ross; Sánchez-Corrales, Yara E; Hartley, Matthew; Grieneisen, Verônica A; Marée, Athanasius F M

2017-12-01

D'Arcy Thompson emphasised the importance of surface tension as a potential driving force in establishing cell shape and topology within tissues. Leaf epidermal pavement cells grow into jigsaw-piece shapes, highly deviating from such classical forms. We investigate the topology of developing Arabidopsis leaves composed solely of pavement cells. Image analysis of around 50,000 cells reveals a clear and unique topological signature, deviating from previously studied epidermal tissues. This topological distribution is established early during leaf development, already before the typical pavement cell shapes emerge, with topological homeostasis maintained throughout growth and unaltered between division and maturation zones. Simulating graph models, we identify a heuristic cellular division rule that reproduces the observed topology. Our parsimonious model predicts how and when cells effectively place their division plane with respect to their neighbours. We verify the predicted dynamics through in vivo tracking of 800 mitotic events, and conclude that the distinct topology is not a direct consequence of the jigsaw piece-like shape of the cells, but rather owes itself to a strongly life history-driven process, with limited impact from cell-surface mechanics. © 2017. Published by The Company of Biologists Ltd.

Pavement cells and the topology puzzle

PubMed Central

2017-01-01

D'Arcy Thompson emphasised the importance of surface tension as a potential driving force in establishing cell shape and topology within tissues. Leaf epidermal pavement cells grow into jigsaw-piece shapes, highly deviating from such classical forms. We investigate the topology of developing Arabidopsis leaves composed solely of pavement cells. Image analysis of around 50,000 cells reveals a clear and unique topological signature, deviating from previously studied epidermal tissues. This topological distribution is established early during leaf development, already before the typical pavement cell shapes emerge, with topological homeostasis maintained throughout growth and unaltered between division and maturation zones. Simulating graph models, we identify a heuristic cellular division rule that reproduces the observed topology. Our parsimonious model predicts how and when cells effectively place their division plane with respect to their neighbours. We verify the predicted dynamics through in vivo tracking of 800 mitotic events, and conclude that the distinct topology is not a direct consequence of the jigsaw piece-like shape of the cells, but rather owes itself to a strongly life history-driven process, with limited impact from cell-surface mechanics. PMID:29084800

Warp-averaging event-related potentials.

PubMed

Wang, K; Begleiter, H; Porjesz, B

2001-10-01

To align the repeated single trials of the event-related potential (ERP) in order to get an improved estimate of the ERP. A new implementation of the dynamic time warping is applied to compute a warp-average of the single trials. The trilinear modeling method is applied to filter the single trials prior to alignment. Alignment is based on normalized signals and their estimated derivatives. These features reduce the misalignment due to aligning the random alpha waves, explaining amplitude differences in latency differences, or the seemingly small amplitudes of some components. Simulations and applications to visually evoked potentials show significant improvement over some commonly used methods. The new implementation of the dynamic time warping can be used to align the major components (P1, N1, P2, N2, P3) of the repeated single trials. The average of the aligned single trials is an improved estimate of the ERP. This could lead to more accurate results in subsequent analysis.

Alternative probability theories for cognitive psychology.

PubMed

Narens, Louis

2014-01-01

Various proposals for generalizing event spaces for probability functions have been put forth in the mathematical, scientific, and philosophic literatures. In cognitive psychology such generalizations are used for explaining puzzling results in decision theory and for modeling the influence of context effects. This commentary discusses proposals for generalizing probability theory to event spaces that are not necessarily boolean algebras. Two prominent examples are quantum probability theory, which is based on the set of closed subspaces of a Hilbert space, and topological probability theory, which is based on the set of open sets of a topology. Both have been applied to a variety of cognitive situations. This commentary focuses on how event space properties can influence probability concepts and impact cognitive modeling. Copyright © 2013 Cognitive Science Society, Inc.

Data transmission and acquisition in NEMO

NASA Astrophysics Data System (ADS)

Bunkheila, G.

2006-11-01

A comprehensive system for data transmission and acquisition has been developed for an "à la NEMO" underwater neutrino telescope based on Čerenkov light detection using photomultipliers (PMTs) as sensors. Signals generated by each sensor are triggered, sampled and tagged by an electronics board, called Front End Module (FEM). Data streams from up to eight FEMs located on one tower floor are collected by a concentration board called Floor Control Module (FCM) and sent to a twin FCM board—located at the onshore station and plugged into an interface machine (FCM Interface, or FCMI) via a PCI bus—through a DWDM-compliant optical fiber and using a self-synchronous serial protocol. All sensor data reach the onshore lab through FCMI where they are made available to subsequent elaboration processes, such as time-wise alignment and muon track event-triggering. To meet requirements of the latter, onshore data unpacking is carried out with respect to their topological origin. The system promised, and keeps on showing, very light charges on power consumption and infrastructure complexity, while having recently proved to behave at high performance levels in its optical part.

Cognitive Invariants of Geographic Event Conceptualization: What Matters and What Refines?

NASA Astrophysics Data System (ADS)

Klippel, Alexander; Li, Rui; Hardisty, Frank; Weaver, Chris

Behavioral experiments addressing the conceptualization of geographic events are few and far between. Our research seeks to address this deficiency by developing an experimental framework on the conceptualization of movement patterns. In this paper, we report on a critical experiment that is designed to shed light on the question of cognitively salient invariants in such conceptualization. Invariants have been identified as being critical to human information processing, particularly for the processing of dynamic information. In our experiment, we systematically address cognitive invariants of one class of geographic events: single entity movement patterns. To this end, we designed 72 animated icons that depict the movement patterns of hurricanes around two invariants: size difference and topological equivalence class movement patterns endpoints. While the endpoint hypothesis, put forth by Regier (2007), claims a particular focus of human cognition to ending relations of events, other research suggests that simplicity principles guide categorization and, additionally, that static information is easier to process than dynamic information. Our experiments show a clear picture: Size matters. Nonetheless, we also find categorization behaviors consistent with experiments in both the spatial and temporal domain, namely that topology refines these behaviors and that topological equivalence classes are categorized consistently. These results are critical steppingstones in validating spatial formalism from a cognitive perspective and cognitively grounding work on ontologies.

Dodging the crisis of folding proteins with knots

NASA Astrophysics Data System (ADS)

Sulkowska, Joanna

2009-03-01

Proteins with nontrivial topology, containing knots and slipknots, have the ability to fold to their native states without any additional external forces invoked. A mechanism is suggested for folding of these proteins, such as YibK and YbeA, which involves an intermediate configuration with a slipknot. It elucidates the role of topological barriers and backtracking during the folding event. It also illustrates that native contacts are sufficient to guarantee folding in around 1-2% of the simulations, and how slipknot intermediates are needed to reduce the topological bottlenecks. As expected, simulations of proteins with similar structure but with knot removed fold much more efficiently, clearly demonstrating the origin of these topological barriers. Although these studies are based on a simple coarse-grained model, they are already able to extract some of the underlying principles governing folding in such complex topologies.

Characteristics of secondary flows in rough-wall turbulent boundary layers

NASA Astrophysics Data System (ADS)

Vanderwel, Christina; Ganapathisubramani, Bharathram

2015-11-01

Large-scale secondary motions consisting of counter-rotating vortices and low- and high-momentum pathways can form in boundary layers that develop over rough surfaces. We experimentally investigated the sensitivity of these secondary motions to spanwise arrangement of the roughness by studying the flow over streamwise-aligned rows of elevated roughness with systematically-varied spacing. The roughness is created with LEGO blocks mounted along the floor of the wind tunnel and Stereo-PIV is used to measure the velocity field in a cross-plane. Results show that the secondary flows are strongest when the spanwise spacing of the surface topology is comparable with the boundary layer thickness. We discuss how these results are relevant to flows over arbitrary topologies and how these secondary motions influence the Reynolds stress distribution in the boundary layer.

Toroidal ferroelectricity in PbTiO3 nanoparticles.

PubMed

Stachiotti, M G; Sepliarsky, M

2011-04-01

We report from first-principles-based atomistic simulations that ferroelectricity can be sustained in PbTiO(3) nanoparticles of only a few lattice constants in size as a result of a toroidal ordering. We find that size-induced topological transformations lead to the stabilization of a ferroelectric bubble by the alignment of vortex cores along a closed path. These transformations, which are driven by the aspect ratio of the nanostructure, change the topology of the polarization field, producing a rich variety of polar configurations. For sufficiently flat nanostructures, a multibubble state bridges the gap between 0D nanodots and 2D ultrathin films. The thermal properties of the ferroelectric bubbles indicate that this state is suitable for the development of nanometric devices. © 2011 American Physical Society

3D flexible alignment using 2D maximum common substructure: dependence of prediction accuracy on target-reference chemical similarity.

PubMed

Kawabata, Takeshi; Nakamura, Haruki

2014-07-28

A protein-bound conformation of a target molecule can be predicted by aligning the target molecule on the reference molecule obtained from the 3D structure of the compound-protein complex. This strategy is called "similarity-based docking". For this purpose, we develop the flexible alignment program fkcombu, which aligns the target molecule based on atomic correspondences with the reference molecule. The correspondences are obtained by the maximum common substructure (MCS) of 2D chemical structures, using our program kcombu. The prediction performance was evaluated using many target-reference pairs of superimposed ligand 3D structures on the same protein in the PDB, with different ranges of chemical similarity. The details of atomic correspondence largely affected the prediction success. We found that topologically constrained disconnected MCS (TD-MCS) with the simple element-based atomic classification provides the best prediction. The crashing potential energy with the receptor protein improved the performance. We also found that the RMSD between the predicted and correct target conformations significantly correlates with the chemical similarities between target-reference molecules. Generally speaking, if the reference and target compounds have more than 70% chemical similarity, then the average RMSD of 3D conformations is <2.0 Å. We compared the performance with a rigid-body molecular alignment program based on volume-overlap scores (ShaEP). Our MCS-based flexible alignment program performed better than the rigid-body alignment program, especially when the target and reference molecules were sufficiently similar.

Flow topology of rare back flow events and critical points in turbulent channels and toroidal pipes

NASA Astrophysics Data System (ADS)

Chin, C.; Vinuesa, R.; Örlü, R.; Cardesa, J. I.; Noorani, A.; Schlatter, P.; Chong, M. S.

2018-04-01

A study of the back flow events and critical points in the flow through a toroidal pipe at friction Reynolds number Re τ ≈ 650 is performed and compared with the results in a turbulent channel flow at Re τ ≈ 934. The statistics and topological properties of the back flow events are analysed and discussed. Conditionally-averaged flow fields in the vicinity of the back flow event are obtained, and the results for the torus show a similar streamwise wall-shear stress topology which varies considerably for the spanwise wall-shear stress when compared to the channel flow. The comparison between the toroidal pipe and channel flows also shows fewer back flow events and critical points in the torus. This cannot be solely attributed to differences in Reynolds number, but is a clear effect of the secondary flow present in the toroidal pipe. A possible mechanism is the effect of the secondary flow present in the torus, which convects momentum from the inner to the outer bend through the core of the pipe, and back from the outer to the inner bend through the pipe walls. In the region around the critical points, the skin-friction streamlines and vorticity lines exhibit similar flow characteristics with a node and saddle pair for both flows. These results indicate that back flow events and critical points are genuine features of wall-bounded turbulence, and are not artifacts of specific boundary or inflow conditions in simulations and/or measurement uncertainties in experiments.

On the orientation of the backbone dipoles in native folds

PubMed Central

Ripoll, Daniel R.; Vila, Jorge A.; Scheraga, Harold A.

2005-01-01

The role of electrostatic interactions in determining the native fold of proteins has been investigated by analyzing the alignment of peptide bond dipole moments with the local electrostatic field generated by the rest of the molecule with and without solvent effects. This alignment was calculated for a set of 112 native proteins by using charges from a gas phase potential. Most of the peptide dipoles in this set of proteins are on average aligned with the electrostatic field. The dipole moments associated with α-helical conformations show the best alignment with the electrostatic field, followed by residues in β-strand conformations. The dipole moments associated with other secondary structure elements are on average better aligned than in randomly generated conformations. The alignment of a dipole with the local electrostatic field depends on both the topology of the native fold and the charge distribution assumed for all of the residues. The influences of (i) solvent effects, (ii) different sets of charges, and (iii) the charge distribution assumed for the whole molecule were examined with a subset of 22 proteins each of which contains <30 ionizable groups. The results show that alternative charge distribution models lead to significant differences among the associated electrostatic fields, whereas the electrostatic field is less sensitive to the particular set of the adopted charges themselves (empirical conformational energy program for peptides or parameters for solvation energy). PMID:15894608

The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides

PubMed Central

Tsirigos, Konstantinos D.; Peters, Christoph; Shu, Nanjiang; Käll, Lukas; Elofsson, Arne

2015-01-01

TOPCONS (http://topcons.net/) is a widely used web server for consensus prediction of membrane protein topology. We hereby present a major update to the server, with some substantial improvements, including the following: (i) TOPCONS can now efficiently separate signal peptides from transmembrane regions. (ii) The server can now differentiate more successfully between globular and membrane proteins. (iii) The server now is even slightly faster, although a much larger database is used to generate the multiple sequence alignments. For most proteins, the final prediction is produced in a matter of seconds. (iv) The user-friendly interface is retained, with the additional feature of submitting batch files and accessing the server programmatically using standard interfaces, making it thus ideal for proteome-wide analyses. Indicatively, the user can now scan the entire human proteome in a few days. (v) For proteins with homology to a known 3D structure, the homology-inferred topology is also displayed. (vi) Finally, the combination of methods currently implemented achieves an overall increase in performance by 4% as compared to the currently available best-scoring methods and TOPCONS is the only method that can identify signal peptides and still maintain a state-of-the-art performance in topology predictions. PMID:25969446

A new algorithm for distorted fingerprints matching based on normalized fuzzy similarity measure.

PubMed

Chen, Xinjian; Tian, Jie; Yang, Xin

2006-03-01

Coping with nonlinear distortions in fingerprint matching is a challenging task. This paper proposes a novel algorithm, normalized fuzzy similarity measure (NFSM), to deal with the nonlinear distortions. The proposed algorithm has two main steps. First, the template and input fingerprints were aligned. In this process, the local topological structure matching was introduced to improve the robustness of global alignment. Second, the method NFSM was introduced to compute the similarity between the template and input fingerprints. The proposed algorithm was evaluated on fingerprints databases of FVC2004. Experimental results confirm that NFSM is a reliable and effective algorithm for fingerprint matching with nonliner distortions. The algorithm gives considerably higher matching scores compared to conventional matching algorithms for the deformed fingerprints.

The Pandora multi-algorithm approach to automated pattern recognition of cosmic-ray muon and neutrino events in the MicroBooNE detector

NASA Astrophysics Data System (ADS)

Acciarri, R.; Adams, C.; An, R.; Anthony, J.; Asaadi, J.; Auger, M.; Bagby, L.; Balasubramanian, S.; Baller, B.; Barnes, C.; Barr, G.; Bass, M.; Bay, F.; Bishai, M.; Blake, A.; Bolton, T.; Camilleri, L.; Caratelli, D.; Carls, B.; Castillo Fernandez, R.; Cavanna, F.; Chen, H.; Church, E.; Cianci, D.; Cohen, E.; Collin, G. H.; Conrad, J. M.; Convery, M.; Crespo-Anadón, J. I.; Del Tutto, M.; Devitt, D.; Dytman, S.; Eberly, B.; Ereditato, A.; Escudero Sanchez, L.; Esquivel, J.; Fadeeva, A. A.; Fleming, B. T.; Foreman, W.; Furmanski, A. P.; Garcia-Gamez, D.; Garvey, G. T.; Genty, V.; Goeldi, D.; Gollapinni, S.; Graf, N.; Gramellini, E.; Greenlee, H.; Grosso, R.; Guenette, R.; Hackenburg, A.; Hamilton, P.; Hen, O.; Hewes, J.; Hill, C.; Ho, J.; Horton-Smith, G.; Hourlier, A.; Huang, E.-C.; James, C.; Jan de Vries, J.; Jen, C.-M.; Jiang, L.; Johnson, R. A.; Joshi, J.; Jostlein, H.; Kaleko, D.; Karagiorgi, G.; Ketchum, W.; Kirby, B.; Kirby, M.; Kobilarcik, T.; Kreslo, I.; Laube, A.; Li, Y.; Lister, A.; Littlejohn, B. R.; Lockwitz, S.; Lorca, D.; Louis, W. C.; Luethi, M.; Lundberg, B.; Luo, X.; Marchionni, A.; Mariani, C.; Marshall, J.; Martinez Caicedo, D. A.; Meddage, V.; Miceli, T.; Mills, G. B.; Moon, J.; Mooney, M.; Moore, C. D.; Mousseau, J.; Murrells, R.; Naples, D.; Nienaber, P.; Nowak, J.; Palamara, O.; Paolone, V.; Papavassiliou, V.; Pate, S. F.; Pavlovic, Z.; Piasetzky, E.; Porzio, D.; Pulliam, G.; Qian, X.; Raaf, J. L.; Rafique, A.; Rochester, L.; Rudolf von Rohr, C.; Russell, B.; Schmitz, D. W.; Schukraft, A.; Seligman, W.; Shaevitz, M. H.; Sinclair, J.; Smith, A.; Snider, E. L.; Soderberg, M.; Söldner-Rembold, S.; Soleti, S. R.; Spentzouris, P.; Spitz, J.; St. John, J.; Strauss, T.; Szelc, A. M.; Tagg, N.; Terao, K.; Thomson, M.; Toups, M.; Tsai, Y.-T.; Tufanli, S.; Usher, T.; Van De Pontseele, W.; Van de Water, R. G.; Viren, B.; Weber, M.; Wickremasinghe, D. A.; Wolbers, S.; Wongjirad, T.; Woodruff, K.; Yang, T.; Yates, L.; Zeller, G. P.; Zennamo, J.; Zhang, C.

2018-01-01

The development and operation of liquid-argon time-projection chambers for neutrino physics has created a need for new approaches to pattern recognition in order to fully exploit the imaging capabilities offered by this technology. Whereas the human brain can excel at identifying features in the recorded events, it is a significant challenge to develop an automated, algorithmic solution. The Pandora Software Development Kit provides functionality to aid the design and implementation of pattern-recognition algorithms. It promotes the use of a multi-algorithm approach to pattern recognition, in which individual algorithms each address a specific task in a particular topology. Many tens of algorithms then carefully build up a picture of the event and, together, provide a robust automated pattern-recognition solution. This paper describes details of the chain of over one hundred Pandora algorithms and tools used to reconstruct cosmic-ray muon and neutrino events in the MicroBooNE detector. Metrics that assess the current pattern-recognition performance are presented for simulated MicroBooNE events, using a selection of final-state event topologies.

Topology for efficient information dissemination in ad-hoc networking

NASA Technical Reports Server (NTRS)

Jennings, E.; Okino, C. M.

2002-01-01

In this paper, we explore the information dissemination problem in ad-hoc wirless networks. First, we analyze the probability of successful broadcast, assuming: the nodes are uniformly distributed, the available area has a lower bould relative to the total number of nodes, and there is zero knowledge of the overall topology of the network. By showing that the probability of such events is small, we are motivated to extract good graph topologies to minimize the overall transmissions. Three algorithms are used to generate topologies of the network with guaranteed connectivity. These are the minimum radius graph, the relative neighborhood graph and the minimum spanning tree. Our simulation shows that the relative neighborhood graph has certain good graph properties, which makes it suitable for efficient information dissemination.

Classification of complex networks based on similarity of topological network features

NASA Astrophysics Data System (ADS)

Attar, Niousha; Aliakbary, Sadegh

2017-09-01

Over the past few decades, networks have been widely used to model real-world phenomena. Real-world networks exhibit nontrivial topological characteristics and therefore, many network models are proposed in the literature for generating graphs that are similar to real networks. Network models reproduce nontrivial properties such as long-tail degree distributions or high clustering coefficients. In this context, we encounter the problem of selecting the network model that best fits a given real-world network. The need for a model selection method reveals the network classification problem, in which a target-network is classified into one of the candidate network models. In this paper, we propose a novel network classification method which is independent of the network size and employs an alignment-free metric of network comparison. The proposed method is based on supervised machine learning algorithms and utilizes the topological similarities of networks for the classification task. The experiments show that the proposed method outperforms state-of-the-art methods with respect to classification accuracy, time efficiency, and robustness to noise.

Summary of Work for Joint Research Interchanges with DARWIN Integrated Product Team 1998

NASA Technical Reports Server (NTRS)

Hesselink, Lambertus

1999-01-01

The intent of Stanford University's SciVis group is to develop technologies that enabled comparative analysis and visualization techniques for simulated and experimental flow fields. These techniques would then be made available under the Joint Research Interchange for potential injection into the DARWIN Workspace Environment (DWE). In the past, we have focused on techniques that exploited feature based comparisons such as shock and vortex extractions. Our current research effort focuses on finding a quantitative comparison of general vector fields based on topological features. Since the method relies on topological information, grid matching and vector alignment is not needed in the comparison. This is often a problem with many data comparison techniques. In addition, since only topology based information is stored and compared for each field, there is a significant compression of information that enables large databases to be quickly searched. This report will briefly (1) describe current technologies in the area of comparison techniques, (2) will describe the theory of our new method and finally (3) summarize a few of the results.

Summary of Work for Joint Research Interchanges with DARWIN Integrated Product Team

NASA Technical Reports Server (NTRS)

Hesselink, Lambertus

1999-01-01

The intent of Stanford University's SciVis group is to develop technologies that enabled comparative analysis and visualization techniques for simulated and experimental flow fields. These techniques would then be made available un- der the Joint Research Interchange for potential injection into the DARWIN Workspace Environment (DWE). In the past, we have focused on techniques that exploited feature based comparisons such as shock and vortex extractions. Our current research effort focuses on finding a quantitative comparison of general vector fields based on topological features. Since the method relies on topological information, grid matching an@ vector alignment is not needed in the comparison. This is often a problem with many data comparison techniques. In addition, since only topology based information is stored and compared for each field, there is a significant compression of information that enables large databases to be quickly searched. This report will briefly (1) describe current technologies in the area of comparison techniques, (2) will describe the theory of our new method and finally (3) summarize a few of the results.

Towards a unified understanding of event-related changes in the EEG: the firefly model of synchronization through cross-frequency phase modulation.

PubMed

Burgess, Adrian P

2012-01-01

Although event-related potentials (ERPs) are widely used to study sensory, perceptual and cognitive processes, it remains unknown whether they are phase-locked signals superimposed upon the ongoing electroencephalogram (EEG) or result from phase-alignment of the EEG. Previous attempts to discriminate between these hypotheses have been unsuccessful but here a new test is presented based on the prediction that ERPs generated by phase-alignment will be associated with event-related changes in frequency whereas evoked-ERPs will not. Using empirical mode decomposition (EMD), which allows measurement of narrow-band changes in the EEG without predefining frequency bands, evidence was found for transient frequency slowing in recognition memory ERPs but not in simulated data derived from the evoked model. Furthermore, the timing of phase-alignment was frequency dependent with the earliest alignment occurring at high frequencies. Based on these findings, the Firefly model was developed, which proposes that both evoked and induced power changes derive from frequency-dependent phase-alignment of the ongoing EEG. Simulated data derived from the Firefly model provided a close match with empirical data and the model was able to account for i) the shape and timing of ERPs at different scalp sites, ii) the event-related desynchronization in alpha and synchronization in theta, and iii) changes in the power density spectrum from the pre-stimulus baseline to the post-stimulus period. The Firefly Model, therefore, provides not only a unifying account of event-related changes in the EEG but also a possible mechanism for cross-frequency information processing.

Towards a Unified Understanding of Event-Related Changes in the EEG: The Firefly Model of Synchronization through Cross-Frequency Phase Modulation

PubMed Central

Burgess, Adrian P.

2012-01-01

Although event-related potentials (ERPs) are widely used to study sensory, perceptual and cognitive processes, it remains unknown whether they are phase-locked signals superimposed upon the ongoing electroencephalogram (EEG) or result from phase-alignment of the EEG. Previous attempts to discriminate between these hypotheses have been unsuccessful but here a new test is presented based on the prediction that ERPs generated by phase-alignment will be associated with event-related changes in frequency whereas evoked-ERPs will not. Using empirical mode decomposition (EMD), which allows measurement of narrow-band changes in the EEG without predefining frequency bands, evidence was found for transient frequency slowing in recognition memory ERPs but not in simulated data derived from the evoked model. Furthermore, the timing of phase-alignment was frequency dependent with the earliest alignment occurring at high frequencies. Based on these findings, the Firefly model was developed, which proposes that both evoked and induced power changes derive from frequency-dependent phase-alignment of the ongoing EEG. Simulated data derived from the Firefly model provided a close match with empirical data and the model was able to account for i) the shape and timing of ERPs at different scalp sites, ii) the event-related desynchronization in alpha and synchronization in theta, and iii) changes in the power density spectrum from the pre-stimulus baseline to the post-stimulus period. The Firefly Model, therefore, provides not only a unifying account of event-related changes in the EEG but also a possible mechanism for cross-frequency information processing. PMID:23049827

Push-Pull and Feedback Mechanisms Can Align Signaling System Outputs with Inputs.

PubMed

Andrews, Steven S; Peria, William J; Yu, Richard C; Colman-Lerner, Alejandro; Brent, Roger

2016-11-23

Many cell signaling systems, including the yeast pheromone response system, exhibit "dose-response alignment" (DoRA), in which output of one or more downstream steps closely matches the fraction of occupied receptors. DoRA can improve the fidelity of transmitted dose information. Here, we searched systematically for biochemical network topologies that produced DoRA. Most networks, including many containing feedback and feedforward loops, could not produce DoRA. However, networks including "push-pull" mechanisms, in which the active form of a signaling species stimulates downstream activity and the nominally inactive form reduces downstream activity, enabled perfect DoRA. Networks containing feedbacks enabled DoRA, but only if they also compared feedback to input and adjusted output to match. Our results establish push-pull as a non-feedback mechanism to align output with variable input and maximize information transfer in signaling systems. They also suggest genetic approaches to determine whether particular signaling systems use feedback or push-pull control. Copyright © 2016 Elsevier Inc. All rights reserved.

Fuzzy spaces topology change and BH thermodynamics

NASA Astrophysics Data System (ADS)

Silva, C. A. S.; Landim, R. R.

2014-03-01

What is the ultimate fate of something that falls into a black hole? From this question arises one of the most intricate problems of modern theoretical physics: the black hole information loss paradox. Bekenstein and Hawking have been shown that the entropy in a black hole is proportional to the surface area of its event horizon, which should be quantized in a multiple of the Planck area. This led G.'t Hooft and L. Susskind to propose the holographic principle which states that all the information inside the black hole can be stored on its event horizon. From this results, one may think if the solution to the information paradox could lies in the quantum properties of the black hole horizon. One way to quantize the event horizon is to see it as a fuzzy sphere, which posses a closed relation with Hopf algebras. This relation makes possible a topology change process where a fuzzy sphere splits in two others. In this work it will be shown that, if one quantize the black hole event horizon as a fuzzy sphere taking into account its quantum symmetry properties, a topology change process to black holes can be defined without break unitarity or locality, and we can obtain a possible solution to the information paradox. Moreover, we show that this model can explain the origin of the black hole entropy, and why black holes obey a generalized second law of thermodynamics.

GaAs digital dynamic IC's for applications up to 10 GHz

NASA Astrophysics Data System (ADS)

Rocchi, M.; Gabillard, B.

1983-06-01

To evaluate the potentiality of GaAs MESFET's as transmitting gates, dynamic TT-bar flip-flops have been fabricated using a self-aligned planar process. The maximum operating frequency is 10.2 GHz, which is the best speed performance ever reported for a digital circuit. The performance of the transmitting gates within the circuits are discussed in detail. Speed improvement and topological simplification of fully static LSI subsystems are investigated.

Heparin/collagen encapsulating nerve growth factor multilayers coated aligned PLLA nanofibrous scaffolds for nerve tissue engineering.

PubMed

Zhang, Kuihua; Huang, Dianwu; Yan, Zhiyong; Wang, Chunyang

2017-07-01

Biomimicing topological structure of natural nerve tissue to direct axon growth and controlling sustained release of moderate neurotrophic factors are extremely propitious to the functional recovery of damaged nervous systems. In this study, the heparin/collagen encapsulating nerve growth factor (NGF) multilayers were coated onto the aligned poly-L-lactide (PLLA) nanofibrous scaffolds via a layer-by-layer (LbL) self-assembly technique to combine biomolecular signals, and physical guidance cues for peripheral nerve regeneration. Scanning electronic microscopy (SEM) revealed that the surface of aligned PLLA nanofibrous scaffolds coated with heparin/collagen multilayers became rougher and appeared some net-like filaments and protuberances in comparison with PLLA nanofibrous scaffolds. The heparin/collagen multilayers did not destroy the alignment of nanofibers. X-ray photoelectron spectroscopy and water contact angles displayed that heparin and collagen were successfully coated onto the aligned PLLA nanofibrous scaffolds and improved its hydrophilicity. Three-dimensional (3 D) confocal microscopy images further demonstrated that collagen, heparin, and NGF were not only coated onto the surface of aligned PLLA nanofibrous scaffolds but also permeated into the inner of scaffolds. Moreover, NGF presented a sustained release for 2 weeks from aligned nanofibrous scaffolds coated with 5.5 bilayers or above and remained good bioactivity. The heparin/collagen encapsulating NGF multilayers coated aligned nanofibrous scaffolds, in particular 5.5 bilayers or above, was more beneficial to Schwann cells (SCs) proliferation and PC12 cells differentiation as well as the SC cytoskeleton and neurite growth along the direction of nanofibrous alignment compared to the aligned PLLA nanofibrous scaffolds. This novel scaffolds combining sustained release of bioactive NGF and aligned nanofibrous topography presented an excellent potential in peripheral nerve regeneration. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 1900-1910, 2017. © 2017 Wiley Periodicals, Inc.

Topologically Micropatterned Collagen and Poly(ε-caprolactone) Struts Fabricated Using the Poly(vinyl alcohol) Fibrillation/Leaching Process To Develop Efficiently Engineered Skeletal Muscle Tissue.

PubMed

Kim, Minseong; Kim, WonJin; Kim, GeunHyung

2017-12-20

Optimally designed three-dimensional (3D) biomedical scaffolds for skeletal muscle tissue regeneration pose significant research challenges. Currently, most studies on scaffolds focus on the two-dimensional (2D) surface structures that are patterned in the micro-/nanoscales with various repeating sizes and shapes to induce the alignment of myoblasts and myotube formation. The 2D patterned surface clearly provides effective analytical results of pattern size and shape of the myoblast alignment and differentiation. However, it is inconvenient in terms of the direct application for clinical usage due to the limited thickness and 3D shapeability. Hence, the present study suggests an innovative hydrogel or synthetic structure that consists of uniaxially surface-patterned cylindrical struts for skeleton muscle regeneration. The alignment of the pattern on the hydrogel (collagen) and poly(ε-caprolactone) struts was attained with the fibrillation of poly(vinyl alcohol) and the leaching process. Various cell culture results indicate that the C2C12 cells on the micropatterned collagen structure were fully aligned, and that a significantly high level of myotube formation was achieved when compared to the collagen structures that were not treated with the micropatterning process.

Comparison of cell behavior on pva/pva-gelatin electrospun nanofibers with random and aligned configuration

NASA Astrophysics Data System (ADS)

Huang, Chen-Yu; Hu, Keng-Hsiang; Wei, Zung-Hang

2016-12-01

Electrospinning technique is able to create nanofibers with specific orientation. Poly(vinyl alcohol) (PVA) have good mechanical stability but poor cell adhesion property due to the low affinity of protein. In this paper, extracellular matrix, gelatin is incorporated into PVA solution to form electrospun PVA-gelatin nanofibers membrane. Both randomly oriented and aligned nanofibers are used to investigate the topography-induced behavior of fibroblasts. Surface morphology of the fibers is studied by optical microscopy and scanning electron microscopy (SEM) coupled with image analysis. Functional group composition in PVA or PVA-gelatin is investigated by Fourier Transform Infrared (FTIR). The morphological changes, surface coverage, viability and proliferation of fibroblasts influenced by PVA and PVA-gelatin nanofibers with randomly orientated or aligned configuration are systematically compared. Fibroblasts growing on PVA-gelatin fibers show significantly larger projected areas as compared with those cultivated on PVA fibers which p-value is smaller than 0.005. Cells on PVA-gelatin aligned fibers stretch out extensively and their intracellular stress fiber pull nucleus to deform. Results suggest that instead of the anisotropic topology within the scaffold trigger the preferential orientation of cells, the adhesion of cell membrane to gelatin have substantial influence on cellular behavior.

Plexciton Dirac points and topological modes

DOE PAGES

Yuen-Zhou, Joel; Saikin, Semion K.; Zhu, Tony; ...

2016-06-09

Plexcitons are polaritonic modes that result from the strong coupling between excitons and plasmons. Here, we consider plexcitons emerging from the interaction of excitons in an organic molecular layer with surface plasmons in a metallic film. We predict the emergence of Dirac cones in the two-dimensional band-structure of plexcitons due to the inherent alignment of the excitonic transitions in the organic layer. An external magnetic field opens a gap between the Dirac cones if the plexciton system is interfaced with a magneto-optical layer. The resulting energy gap becomes populated with topologically protected one-way modes, which travel at the interface ofmore » this plexcitonic system. Furthermore, our theoretical proposal suggests that plexcitons are a convenient and simple platform for the exploration of exotic phases of matter and for the control of energy flow at the nanoscale.« less

When the Stars Align: On the Contributions of Gilbert Gottlieb and Peter C. M. Molenaar to Developmental Science Theory and Method

ERIC Educational Resources Information Center

Lerner, Richard M.; Batanova, Milena; Ettekal, Andrea Vest; Hunter, Cristina

2015-01-01

When truly spectacular events occur in the performing arts or in team sports, when the sets of artists or athletes respectively creating these events are discussed, a common phrase used in America to explain the "good fortune" that was involved in such unique occurrences is that "the stars aligned." In this commentary on:…

The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection

PubMed Central

Yu, Yun; Degnan, James H.; Nakhleh, Luay

2012-01-01

Gene tree topologies have proven a powerful data source for various tasks, including species tree inference and species delimitation. Consequently, methods for computing probabilities of gene trees within species trees have been developed and widely used in probabilistic inference frameworks. All these methods assume an underlying multispecies coalescent model. However, when reticulate evolutionary events such as hybridization occur, these methods are inadequate, as they do not account for such events. Methods that account for both hybridization and deep coalescence in computing the probability of a gene tree topology currently exist for very limited cases. However, no such methods exist for general cases, owing primarily to the fact that it is currently unknown how to compute the probability of a gene tree topology within the branches of a phylogenetic network. Here we present a novel method for computing the probability of gene tree topologies on phylogenetic networks and demonstrate its application to the inference of hybridization in the presence of incomplete lineage sorting. We reanalyze a Saccharomyces species data set for which multiple analyses had converged on a species tree candidate. Using our method, though, we show that an evolutionary hypothesis involving hybridization in this group has better support than one of strict divergence. A similar reanalysis on a group of three Drosophila species shows that the data is consistent with hybridization. Further, using extensive simulation studies, we demonstrate the power of gene tree topologies at obtaining accurate estimates of branch lengths and hybridization probabilities of a given phylogenetic network. Finally, we discuss identifiability issues with detecting hybridization, particularly in cases that involve extinction or incomplete sampling of taxa. PMID:22536161

The Optimizer Topology Characteristics in Seismic Hazards

NASA Astrophysics Data System (ADS)

Sengor, T.

2015-12-01

The characteristic data of the natural phenomena are questioned in a topological space approach to illuminate whether there is an algorithm behind them bringing the situation of physics of phenomena to optimized states even if they are hazards. The optimized code designing the hazard on a topological structure mashes the metric of the phenomena. The deviations in the metric of different phenomena push and/or pull the fold of the other suitable phenomena. For example if the metric of a specific phenomenon A fits to the metric of another specific phenomenon B after variation processes generated with the deviation of the metric of previous phenomenon A. Defining manifold processes covering the metric characteristics of each of every phenomenon is possible for all the physical events; i.e., natural hazards. There are suitable folds in those manifold groups so that each subfold fits to the metric characteristics of one of the natural hazard category at least. Some variation algorithms on those metric structures prepare a gauge effect bringing the long time stability of Earth for largely scaled periods. The realization of that stability depends on some specific conditions. These specific conditions are called optimized codes. The analytical basics of processes in topological structures are developed in [1]. The codes are generated according to the structures in [2]. Some optimized codes are derived related to the seismicity of NAF beginning from the quakes of the year 1999. References1. Taner SENGOR, "Topological theory and analytical configuration for a universal community model," Procedia- Social and Behavioral Sciences, Vol. 81, pp. 188-194, 28 June 2013, 2. Taner SENGOR, "Seismic-Climatic-Hazardous Events Estimation Processes via the Coupling Structures in Conserving Energy Topologies of the Earth," The 2014 AGU Fall Meeting, Abstract no.: 31374, ABD.

Validation of Splicing Events in Transcriptome Sequencing Data

PubMed Central

Kaisers, Wolfgang; Ptok, Johannes; Schwender, Holger; Schaal, Heiner

2017-01-01

Genomic alignments of sequenced cellular messenger RNA contain gapped alignments which are interpreted as consequence of intron removal. The resulting gap-sites, genomic locations of alignment gaps, are landmarks representing potential splice-sites. As alignment algorithms report gap-sites with a considerable false discovery rate, validations are required. We describe two quality scores, gap quality score (gqs) and weighted gap information score (wgis), developed for validation of putative splicing events: While gqs solely relies on alignment data wgis additionally considers information from the genomic sequence. FASTQ files obtained from 54 human dermal fibroblast samples were aligned against the human genome (GRCh38) using TopHat and STAR aligner. Statistical properties of gap-sites validated by gqs and wgis were evaluated by their sequence similarity to known exon-intron borders. Within the 54 samples, TopHat identifies 1,000,380 and STAR reports 6,487,577 gap-sites. Due to the lack of strand information, however, the percentage of identified GT-AG gap-sites is rather low. While gap-sites from TopHat contain ≈89% GT-AG, gap-sites from STAR only contain ≈42% GT-AG dinucleotide pairs in merged data from 54 fibroblast samples. Validation with gqs yields 156,251 gap-sites from TopHat alignments and 166,294 from STAR alignments. Validation with wgis yields 770,327 gap-sites from TopHat alignments and 1,065,596 from STAR alignments. Both alignment algorithms, TopHat and STAR, report gap-sites with considerable false discovery rate, which can drastically be reduced by validation with gqs and wgis. PMID:28545234

Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer.

PubMed

Bromberg, Raquel; Grishin, Nick V; Otwinowski, Zbyszek

2016-06-01

Advances in sequencing have generated a large number of complete genomes. Traditionally, phylogenetic analysis relies on alignments of orthologs, but defining orthologs and separating them from paralogs is a complex task that may not always be suited to the large datasets of the future. An alternative to traditional, alignment-based approaches are whole-genome, alignment-free methods. These methods are scalable and require minimal manual intervention. We developed SlopeTree, a new alignment-free method that estimates evolutionary distances by measuring the decay of exact substring matches as a function of match length. SlopeTree corrects for horizontal gene transfer, for composition variation and low complexity sequences, and for branch-length nonlinearity caused by multiple mutations at the same site. We tested SlopeTree on 495 bacteria, 73 archaea, and 72 strains of Escherichia coli and Shigella. We compared our trees to the NCBI taxonomy, to trees based on concatenated alignments, and to trees produced by other alignment-free methods. The results were consistent with current knowledge about prokaryotic evolution. We assessed differences in tree topology over different methods and settings and found that the majority of bacteria and archaea have a core set of proteins that evolves by descent. In trees built from complete genomes rather than sets of core genes, we observed some grouping by phenotype rather than phylogeny, for instance with a cluster of sulfur-reducing thermophilic bacteria coming together irrespective of their phyla. The source-code for SlopeTree is available at: http://prodata.swmed.edu/download/pub/slopetree_v1/slopetree.tar.gz.

Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer

PubMed Central

Grishin, Nick V.; Otwinowski, Zbyszek

2016-01-01

Advances in sequencing have generated a large number of complete genomes. Traditionally, phylogenetic analysis relies on alignments of orthologs, but defining orthologs and separating them from paralogs is a complex task that may not always be suited to the large datasets of the future. An alternative to traditional, alignment-based approaches are whole-genome, alignment-free methods. These methods are scalable and require minimal manual intervention. We developed SlopeTree, a new alignment-free method that estimates evolutionary distances by measuring the decay of exact substring matches as a function of match length. SlopeTree corrects for horizontal gene transfer, for composition variation and low complexity sequences, and for branch-length nonlinearity caused by multiple mutations at the same site. We tested SlopeTree on 495 bacteria, 73 archaea, and 72 strains of Escherichia coli and Shigella. We compared our trees to the NCBI taxonomy, to trees based on concatenated alignments, and to trees produced by other alignment-free methods. The results were consistent with current knowledge about prokaryotic evolution. We assessed differences in tree topology over different methods and settings and found that the majority of bacteria and archaea have a core set of proteins that evolves by descent. In trees built from complete genomes rather than sets of core genes, we observed some grouping by phenotype rather than phylogeny, for instance with a cluster of sulfur-reducing thermophilic bacteria coming together irrespective of their phyla. The source-code for SlopeTree is available at: http://prodata.swmed.edu/download/pub/slopetree_v1/slopetree.tar.gz. PMID:27336403

Two kissing bolts

NASA Astrophysics Data System (ADS)

Bossard, Guillaume; Katmadas, Stefanos; Turton, David

2018-02-01

The study of non-supersymmetric black hole microstates offers the potential to resolve the black hole information paradox. A system of equations was recently obtained that enables the systematic construction of non-supersymmetric smooth horizonless supergravity solutions, that are candidates to describe microstates of non-extremal black holes. Within this system we construct a family of six-dimensional supergravity solutions that feature two topologically-nontrivial three-cycles known as bolts. The two bolts touch at a single point and are supported by fluxes. We find that the fluxes on the two three-cycles can be either aligned or anti-aligned, and exhibit examples of both. We present several examples of smooth solutions, including near-extremal solutions that have an approximate AdS3 region, and far-from extremal solutions that have arbitrarily small charge compared to their mass.

High-resolution comparative modeling with RosettaCM.

PubMed

Song, Yifan; DiMaio, Frank; Wang, Ray Yu-Ruei; Kim, David; Miles, Chris; Brunette, Tj; Thompson, James; Baker, David

2013-10-08

We describe an improved method for comparative modeling, RosettaCM, which optimizes a physically realistic all-atom energy function over the conformational space defined by homologous structures. Given a set of sequence alignments, RosettaCM assembles topologies by recombining aligned segments in Cartesian space and building unaligned regions de novo in torsion space. The junctions between segments are regularized using a loop closure method combining fragment superposition with gradient-based minimization. The energies of the resulting models are optimized by all-atom refinement, and the most representative low-energy model is selected. The CASP10 experiment suggests that RosettaCM yields models with more accurate side-chain and backbone conformations than other methods when the sequence identity to the templates is greater than ∼15%. Copyright © 2013 Elsevier Ltd. All rights reserved.

Study of Topological Distributions of Inclusive Three- and Four-jet Events at the LHC

NASA Astrophysics Data System (ADS)

Gupta, Ruchi; CMS Collaboration

2016-04-01

A study of inclusive topological distributions of three- and four-jet events has been conducted by the CMS Collaboration at the LHC with a data sample corresponding to an integrated luminosity of 5.1 fb-1 at a centre of mass energy of 7 TeV. Kinematic and angular distributions in inclusive multijet final states serve as a natural probe of quantum chromodynamics and can reveal its inner dynamics. Comparisons are carried out with the data and predictions of leading order calculations and parton shower generators. The compared data results are corrected for detector effects and can be directly compared with other models or next-to-leading order theoretical predictions.

Experimental study of 3-D structure and evolution of foam

NASA Astrophysics Data System (ADS)

Thoroddsen, S. T.; Tan, E.; Bauer, J. M.

1998-11-01

Liquid foam coarsens due to diffusion of gas between adjacent foam cells. This evolution process is slow, but leads to rapid topological changes taking place during localized rearrangements of Plateau borders or disappearance of small cells. We are developing a new imaging technique to construct the three-dimensional topology of real soap foam contained in a small glass container. The technique uses 3 video cameras equipped with lenses having narrow depth-of-field. These cameras are moved with respect to the container, in effect obtaining numerous slices through the foam. Preliminary experimental results showing typical rearrangement events will also be presented. These events involve for example disappearance of either triangular or rectangular cell faces.

The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides.

PubMed

Tsirigos, Konstantinos D; Peters, Christoph; Shu, Nanjiang; Käll, Lukas; Elofsson, Arne

2015-07-01

TOPCONS (http://topcons.net/) is a widely used web server for consensus prediction of membrane protein topology. We hereby present a major update to the server, with some substantial improvements, including the following: (i) TOPCONS can now efficiently separate signal peptides from transmembrane regions. (ii) The server can now differentiate more successfully between globular and membrane proteins. (iii) The server now is even slightly faster, although a much larger database is used to generate the multiple sequence alignments. For most proteins, the final prediction is produced in a matter of seconds. (iv) The user-friendly interface is retained, with the additional feature of submitting batch files and accessing the server programmatically using standard interfaces, making it thus ideal for proteome-wide analyses. Indicatively, the user can now scan the entire human proteome in a few days. (v) For proteins with homology to a known 3D structure, the homology-inferred topology is also displayed. (vi) Finally, the combination of methods currently implemented achieves an overall increase in performance by 4% as compared to the currently available best-scoring methods and TOPCONS is the only method that can identify signal peptides and still maintain a state-of-the-art performance in topology predictions. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Extending Topological Approaches to Microseismic-Derived 3D Fracture Networks

NASA Astrophysics Data System (ADS)

Urbancic, T.; Bosman, K.; Baig, A.; Ardakani, E. P.

2017-12-01

Fracture topology is important for determining the fluid-flow characteristics of a fracture network. In most unconventional petroleum applications, flow through subsurface fracture networks is the primary source of production, as matrix permeability is often in the nanodarcy range. Typical models of reservoir discrete fracture networks (DFNs) are constructed using fracture orientation and average spacing, without consideration of how the connectivity of the fracture network aids the percolation of hydrocarbons back to the wellbore. Topological approaches to DFN characterization have been developed and extensively used in analysis of outcrop data and aerial photography. Such study of the surface expression of fracture networks is straight-forward, and the physical form of the observed fractures is directly reflected in the parameters used to describe the topology. However, this analysis largely ignores the three-dimensional nature of natural fracture networks, which is difficult to define accurately in geological studies. SMTI analysis of microseismic event distributions can produce DFNs, where each event is represented by a penny-shaped crack with radius and orientation determined from the frequency content of the waveforms and assessment of the slip instability of the potential fracture planes, respectively. Analysis of the geometric relationships between a set of fractures can provide details of intersections between fractures, and thus the topological characteristics of the fracture network. Extension of existing 2D topology approaches to 3D fracture networks is non-trivial. In the 2D case, a fracture intersection is a single point (node), and branches connect adjacent nodes along fractures. For the 3D case, intersection "nodes" become lines, and connecting nodes to find branches becomes more complicated. There are several parameters defined in 2D topology to quantify the connectivity of the fracture network. Equivalent quantities must be defined and calibrated for the 3D case to provide a meaningful measurement of fracture network connectivity. We have developed an approach to analyze the topology of 3D fracture networks derived from microseismic moment tensors. We illustrate the utility of the approach with applications to example datasets from hydraulic fracturing completions.

The Pandora multi-algorithm approach to automated pattern recognition of cosmic-ray muon and neutrino events in the MicroBooNE detector

DOE Office of Scientific and Technical Information (OSTI.GOV)

Acciarri, R.; Adams, C.; An, R.

The development and operation of Liquid-Argon Time-Projection Chambers for neutrino physics has created a need for new approaches to pattern recognition in order to fully exploit the imaging capabilities offered by this technology. Whereas the human brain can excel at identifying features in the recorded events, it is a significant challenge to develop an automated, algorithmic solution. The Pandora Software Development Kit provides functionality to aid the design and implementation of pattern-recognition algorithms. It promotes the use of a multi-algorithm approach to pattern recognition, in which individual algorithms each address a specific task in a particular topology. Many tens ofmore » algorithms then carefully build up a picture of the event and, together, provide a robust automated pattern-recognition solution. This paper describes details of the chain of over one hundred Pandora algorithms and tools used to reconstruct cosmic-ray muon and neutrino events in the MicroBooNE detector. Metrics that assess the current pattern-recognition performance are presented for simulated MicroBooNE events, using a selection of final-state event topologies.« less

The Pandora multi-algorithm approach to automated pattern recognition of cosmic-ray muon and neutrino events in the MicroBooNE detector

DOE PAGES

Acciarri, R.; Adams, C.; An, R.; ...

2018-01-29

The development and operation of Liquid-Argon Time-Projection Chambers for neutrino physics has created a need for new approaches to pattern recognition in order to fully exploit the imaging capabilities offered by this technology. Whereas the human brain can excel at identifying features in the recorded events, it is a significant challenge to develop an automated, algorithmic solution. The Pandora Software Development Kit provides functionality to aid the design and implementation of pattern-recognition algorithms. It promotes the use of a multi-algorithm approach to pattern recognition, in which individual algorithms each address a specific task in a particular topology. Many tens ofmore » algorithms then carefully build up a picture of the event and, together, provide a robust automated pattern-recognition solution. This paper describes details of the chain of over one hundred Pandora algorithms and tools used to reconstruct cosmic-ray muon and neutrino events in the MicroBooNE detector. Metrics that assess the current pattern-recognition performance are presented for simulated MicroBooNE events, using a selection of final-state event topologies.« less

Phylogeny of Syndermata (syn. Rotifera): Mitochondrial gene order verifies epizoic Seisonidea as sister to endoparasitic Acanthocephala within monophyletic Hemirotifera.

PubMed

Sielaff, Malte; Schmidt, Hanno; Struck, Torsten H; Rosenkranz, David; Mark Welch, David B; Hankeln, Thomas; Herlyn, Holger

2016-03-01

A monophyletic origin of endoparasitic thorny-headed worms (Acanthocephala) and wheel-animals (Rotifera) is widely accepted. However, the phylogeny inside the clade, be it called Syndermata or Rotifera, has lacked validation by mitochondrial (mt) data. Herein, we present the first mt genome of the key taxon Seison and report conflicting results of phylogenetic analyses: while mt sequence-based topologies showed monophyletic Lemniscea (Bdelloidea+Acanthocephala), gene order analyses supported monophyly of Pararotatoria (Seisonidea+Acanthocephala) and Hemirotifera (Bdelloidea+Pararotatoria). Sequence-based analyses obviously suffered from substitution saturation, compositional bias, and branch length heterogeneity; however, we observed no compromising effects in gene order analyses. Moreover, gene order-based topologies were robust to changes in coding (genes vs. gene pairs, two-state vs. multistate, aligned vs. non-aligned), tree reconstruction methods, and the treatment of the two monogonont mt genomes. Thus, mt gene order verifies seisonids as sister to acanthocephalans within monophyletic Hemirotifera, while deviating results of sequence-based analyses reflect artificial signal. This conclusion implies that the complex life cycle of extant acanthocephalans evolved from a free-living state, as retained by most monogononts and bdelloids, via an epizoic state with a simple life cycle, as shown by seisonids. Hence, Acanthocephala represent a rare example where ancestral transitional stages have counterparts amongst the closest relatives. Copyright © 2015 Elsevier Inc. All rights reserved.

Method and system for controlling a permanent magnet machine

DOEpatents

Walters, James E.

2003-05-20

Method and system for controlling the start of a permanent magnet machine are provided. The method allows to assign a parameter value indicative of an estimated initial rotor position of the machine. The method further allows to energize the machine with a level of current being sufficiently high to start rotor motion in a desired direction in the event the initial rotor position estimate is sufficiently close to the actual rotor position of the machine. A sensing action allows to sense whether any incremental changes in rotor position occur in response to the energizing action. In the event no changes in rotor position are sensed, the method allows to incrementally adjust the estimated rotor position by a first set of angular values until changes in rotor position are sensed. In the event changes in rotor position are sensed, the method allows to provide a rotor alignment signal as rotor motion continues. The alignment signal allows to align the estimated rotor position relative to the actual rotor position. This alignment action allows for operating the machine over a wide speed range.

HOMFLYPT polynomial is the best quantifier for topological cascades of vortex knots

NASA Astrophysics Data System (ADS)

Ricca, Renzo L.; Liu, Xin

2018-02-01

In this paper we derive and compare numerical sequences obtained by adapted polynomials such as HOMFLYPT, Jones and Alexander-Conway for the topological cascade of vortex torus knots and links that progressively untie by a single reconnection event at a time. Two cases are considered: the alternate sequence of knots and co-oriented links (with positive crossings) and the sequence of two-component links with oppositely oriented components (negative crossings). New recurrence equations are derived and sequences of numerical values are computed. In all cases the adapted HOMFLYPT polynomial proves to be the best quantifier for the topological cascade of torus knots and links.

Topology of magnetic flux ropes and formation of fossil flux transfer events and boundary layer plasmas

NASA Technical Reports Server (NTRS)

Lee, L. C.; Ma, Z. W.; Fu, Z. F.; Otto, A.

1993-01-01

A mechanism for the formation of fossil flux transfer events and the low-level boundary layer within the framework of multiple X-line reconnection is proposed. Attention is given to conditions for which the bulk of magnetic flux in a flux rope of finite extent has a simple magnetic topology, where the four possible connections of magnetic field lines are: IMF to MSP, MSP to IMF, IMF to IMF, and MSP to MSP. For a sufficient relative shift of the X lines, magnetic flux may enter a flux rope from the magnetosphere and exit into the magnetosphere. This process leads to the formation of magnetic flux ropes which contain a considerable amount of magnetosheath plasma on closed magnetospheric field lines. This process is discussed as a possible explanation for the formation of fossil flux transfer events in the magnetosphere and the formation of the low-latitude boundary layer.

Evolutionary profiles from the QR factorization of multiple sequence alignments

PubMed Central

Sethi, Anurag; O'Donoghue, Patrick; Luthey-Schulten, Zaida

2005-01-01

We present an algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of the homologous group. The method, based on the multidimensional QR factorization of numerically encoded multiple sequence alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear dependence, resulting in the identification of a minimal basis set of sequences that spans the evolutionary space of the homologous group of proteins. We observe a general trend that these smaller, more evolutionarily balanced profiles have comparable and, in many cases, better performance in database searches than conventional profiles containing hundreds of sequences, constructed in an iterative and computationally intensive procedure. For more diverse families or superfamilies, with sequence identity <30%, structural alignments, based purely on the geometry of the protein structures, provide better alignments than pure sequence-based methods. Merging the structure and sequence information allows the construction of accurate profiles for distantly related groups. These structure-based profiles outperformed other sequence-based methods for finding distant homologs and were used to identify a putative class II cysteinyl-tRNA synthetase (CysRS) in several archaea that eluded previous annotation studies. Phylogenetic analysis showed the putative class II CysRSs to be a monophyletic group and homology modeling revealed a constellation of active site residues similar to that in the known class I CysRS. PMID:15741270

Genomic Data Quality Impacts Automated Detection of Lateral Gene Transfer in Fungi

PubMed Central

Dupont, Pierre-Yves; Cox, Murray P.

2017-01-01

Lateral gene transfer (LGT, also known as horizontal gene transfer), an atypical mechanism of transferring genes between species, has almost become the default explanation for genes that display an unexpected composition or phylogeny. Numerous methods of detecting LGT events all rely on two fundamental strategies: primary structure composition or gene tree/species tree comparisons. Discouragingly, the results of these different approaches rarely coincide. With the wealth of genome data now available, detection of laterally transferred genes is increasingly being attempted in large uncurated eukaryotic datasets. However, detection methods depend greatly on the quality of the underlying genomic data, which are typically complex for eukaryotes. Furthermore, given the automated nature of genomic data collection, it is typically impractical to manually verify all protein or gene models, orthology predictions, and multiple sequence alignments, requiring researchers to accept a substantial margin of error in their datasets. Using a test case comprising plant-associated genomes across the fungal kingdom, this study reveals that composition- and phylogeny-based methods have little statistical power to detect laterally transferred genes. In particular, phylogenetic methods reveal extreme levels of topological variation in fungal gene trees, the vast majority of which show departures from the canonical species tree. Therefore, it is inherently challenging to detect LGT events in typical eukaryotic genomes. This finding is in striking contrast to the large number of claims for laterally transferred genes in eukaryotic species that routinely appear in the literature, and questions how many of these proposed examples are statistically well supported. PMID:28235827

Topology, structures, and energy landscapes of human chromosomes

PubMed Central

Zhang, Bin; Wolynes, Peter G.

2015-01-01

Chromosome conformation capture experiments provide a rich set of data concerning the spatial organization of the genome. We use these data along with a maximum entropy approach to derive a least-biased effective energy landscape for the chromosome. Simulations of the ensemble of chromosome conformations based on the resulting information theoretic landscape not only accurately reproduce experimental contact probabilities, but also provide a picture of chromosome dynamics and topology. The topology of the simulated chromosomes is probed by computing the distribution of their knot invariants. The simulated chromosome structures are largely free of knots. Topologically associating domains are shown to be crucial for establishing these knotless structures. The simulated chromosome conformations exhibit a tendency to form fibril-like structures like those observed via light microscopy. The topologically associating domains of the interphase chromosome exhibit multistability with varying liquid crystalline ordering that may allow discrete unfolding events and the landscape is locally funneled toward “ideal” chromosome structures that represent hierarchical fibrils of fibrils. PMID:25918364

Polarization domain walls in optical fibres as topological bits for data transmission

PubMed Central

Gilles, M.; Bony, P-Y.; Garnier, J.; Picozzi, A.; Guasoni, M.; Fatome, J.

2016-01-01

Domain walls are topological defects which occur at symmetry-breaking phase transitions. While domain walls have been intensively studied in ferromagnetic materials, where they nucleate at the boundary of neighbouring regions of oppositely aligned magnetic dipoles, their equivalent in optics have not been fully explored so far. Here, we experimentally demonstrate the existence of a universal class of polarization domain walls in the form of localized polarization knots in conventional optical fibres. We exploit their binding properties for optical data transmission beyond the Kerr limits of normally dispersive fibres. In particular, we demonstrate how trapping energy in well-defined train of polarization domain walls allows undistorted propagation of polarization knots at a rate of 28 GHz along a 10 km length of normally dispersive optical fibre. These results constitute the first experimental observation of kink-antikink solitary wave propagation in nonlinear fibre optics. PMID:28168000

Manipulation of radial-variant polarization for creating tunable bifocusing spots.

PubMed

Gu, Bing; Pan, Yang; Wu, Jia-Lu; Cui, Yiping

2014-02-01

We propose and generate a new radial-variant vector field (RV-VF) with a distribution of states of polarization described by the square of the radius and exploit its focusing property. Theoretically, we present the analytical expressions for the three-dimensional electric field of the vector field focused by a thin lens under the nonparaxial and paraxial approximations based on the vectorial Rayleigh-Sommerfeld formulas. Numerical simulations indicate that this focused field exhibits bifocusing spots along the optical axis. The underlying mechanism for generating the bifocusing property is analyzed in detail. We give the analytical formula for the interval between two foci. Experimentally, we generate the RV-VFs with alterable topological charge and demonstrate that the interval between two foci is controllable by tuning the radial topological charge. This particular focal field has specific applications for biparticle trapping, manipulating, alignment, transportation, and accelerating along the optical axis.

Lattice-Matched Epitaxial Graphene Grown on Boron Nitride.

PubMed

Davies, Andrew; Albar, Juan D; Summerfield, Alex; Thomas, James C; Cheng, Tin S; Korolkov, Vladimir V; Stapleton, Emily; Wrigley, James; Goodey, Nathan L; Mellor, Christopher J; Khlobystov, Andrei N; Watanabe, Kenji; Taniguchi, Takashi; Foxon, C Thomas; Eaves, Laurence; Novikov, Sergei V; Beton, Peter H

2018-01-10

Lattice-matched graphene on hexagonal boron nitride is expected to lead to the formation of a band gap but requires the formation of highly strained material and has not hitherto been realized. We demonstrate that aligned, lattice-matched graphene can be grown by molecular beam epitaxy using substrate temperatures in the range 1600-1710 °C and coexists with a topologically modified moiré pattern with regions of strained graphene which have giant moiré periods up to ∼80 nm. Raman spectra reveal narrow red-shifted peaks due to isotropic strain, while the giant moiré patterns result in complex splitting of Raman peaks due to strain variations across the moiré unit cell. The lattice-matched graphene has a lower conductance than both the Frenkel-Kontorova-type domain walls and also the topological defects where they terminate. We relate these results to theoretical models of band gap formation in graphene/boron nitride heterostructures.

Magnetic-proximity-induced magnetoresistance on topological insulators

NASA Astrophysics Data System (ADS)

Chiba, Takahiro; Takahashi, Saburo; Bauer, Gerrit E. W.

2017-03-01

We theoretically study the magnetoresistance (MR) of two-dimensional massless Dirac electrons as found on the surface of three-dimensional topological insulators (TIs) that are capped by a ferromagnetic insulator (FI). We calculate charge and spin transport by Kubo and Boltzmann theories, taking into account the ladder-vertex correction and the in-scattering due to normal and magnetic disorder. The induced exchange splitting is found to generate an electric conductivity that depends on the magnetization orientation, but its form is very different from both the anisotropic and the spin Hall MR. The in-plane MR vanishes identically for nonmagnetic disorder, while out-of-plane magnetizations cause a large MR ratio. On the other hand, we do find an in-plane MR and planar Hall effect in the presence of magnetic disorder aligned with the FI magnetization. Our results may help us understand recent transport measurements on TI |FI systems.

Topological signature in the NEXT high pressure xenon TPC

NASA Astrophysics Data System (ADS)

Ferrario, Paola; NEXT Collaboration

2017-09-01

The NEXT experiment aims to observe the neutrinoless double beta decay of 136Xe in a high-pressure xenon gas TPC using electroluminescence to amplify the signal from ionization. One of the main advantages of this technology is the possibility to use the topology of events with energies close to Qββ as an extra tool to reject background. In these proceedings we show with data from prototypes that an extra background rejection factor of 24.3 ± 1.4 (stat.)% can be achieved, while maintaining an efficiency of 66.7 ± 1.% for signal events. The performance expected in NEW, the next stage of the experiment, is to improve to 12.9% ± 0.6% background acceptance for 66.9% ± 0.6% signal efficiency.

Multidimensional phase space methods for mass measurements and decay topology determination

NASA Astrophysics Data System (ADS)

Altunkaynak, Baris; Kilic, Can; Klimek, Matthew D.

2017-02-01

Collider events with multi-stage cascade decays fill out the kinematically allowed region in phase space with a density that is enhanced at the boundary. The boundary encodes all available information as regards the spectrum and is well populated even with moderate signal statistics due to this enhancement. In previous work, the improvement in the precision of mass measurements for cascade decays with three visible and one invisible particles was demonstrated when the full boundary information is used instead of endpoints of one-dimensional projections. We extend these results to cascade decays with four visible and one invisible particles. We also comment on how the topology of the cascade decay can be determined from the differential distribution of events in these scenarios.

Direct comparison of transient radiation belt topology and dynamics in 1991 based on measurements onboard Mir space station and NOAA satellite.

PubMed

Shurshakov, V A; Huston, S L; Dachev TsP; Petrov, V M; Ivanov YuV; Semkova, J V

1998-01-01

In March 1991 the CRRES spacecraft measured a new transient radiation belt resulting from a solar proton event and subsequent geomagnetic disturbance. The presence of this belt was also noted by dosimeter-radiometers aboard the Mir space station (approx. 400 km, 51 degrees orbit) and by particle telescopes on the NOAA-10 spacecraft (850 km, 98 degrees). This event provides a unique opportunity to compare particle flux and dose measurements made by different instruments in different orbits under changing conditions. We present here a comparison of the measurements made by the different detectors. We discuss the topology and dynamics of the transient radiation belt over a period of more than one year.

Weak reversible cross links may decrease the strength of aligned fiber bundles.

PubMed

Nabavi, S Soran; Hartmann, Markus A

2016-02-21

Reversible cross-linking is an effective strategy to specifically tailor the mechanical properties of polymeric materials that can be found in a variety of biological as well as man-made materials. Using a simple model in this paper the influence of weak, reversible cross-links on the mechanical properties of aligned fiber bundles is investigated. Special emphasis in this analysis is put on the strength of the investigated structures. Using Monte Carlo methods two topologies of cross-links exceeding the strength of the covalent backbone are studied. Most surprisingly only two cross-links are sufficient to break the backbone of a multi chain system, resulting in a reduced strength of the material. The found effect crucially depends on the ratio of inter- to intra-chain cross-links and, thus, on the grafting density that determines this ratio.

Modeling and optimization of atomic layer deposition processes on vertically aligned carbon nanotubes.

PubMed

Yazdani, Nuri; Chawla, Vipin; Edwards, Eve; Wood, Vanessa; Park, Hyung Gyu; Utke, Ivo

2014-01-01

Many energy conversion and storage devices exploit structured ceramics with large interfacial surface areas. Vertically aligned carbon nanotube (VACNT) arrays have emerged as possible scaffolds to support large surface area ceramic layers. However, obtaining conformal and uniform coatings of ceramics on structures with high aspect ratio morphologies is non-trivial, even with atomic layer deposition (ALD). Here we implement a diffusion model to investigate the effect of the ALD parameters on coating kinetics and use it to develop a guideline for achieving conformal and uniform thickness coatings throughout the depth of ultra-high aspect ratio structures. We validate the model predictions with experimental data from ALD coatings of VACNT arrays. However, the approach can be applied to predict film conformality as a function of depth for any porous topology, including nanopores and nanowire arrays.

Spacecraft Observations of Oblique Electron Beams Breaking the Frozen-In Law During Asymmetric Reconnection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Egedal, J.; Le, Ari; Daughton, William

Fully kinetic simulations of asymmetric magnetic reconnection reveal the presence of magnetic-field-aligned beams of electrons flowing toward the topological magnetic x line. Within the ~ 6d e electron-diffusion region, the beams become oblique to the local magnetic field, providing a unique signature of the electron-diffusion region where the electron frozen-in law is broken. These numerical predictions are confirmed by in situ Magnetospheric Multiscale spacecraft observations during asymmetric reconnection at Earth’s dayside magnetopause.

Spacecraft Observations of Oblique Electron Beams Breaking the Frozen-In Law During Asymmetric Reconnection

DOE PAGES

Egedal, J.; Le, Ari; Daughton, William; ...

2018-01-29

Fully kinetic simulations of asymmetric magnetic reconnection reveal the presence of magnetic-field-aligned beams of electrons flowing toward the topological magnetic x line. Within the ~ 6d e electron-diffusion region, the beams become oblique to the local magnetic field, providing a unique signature of the electron-diffusion region where the electron frozen-in law is broken. These numerical predictions are confirmed by in situ Magnetospheric Multiscale spacecraft observations during asymmetric reconnection at Earth’s dayside magnetopause.

Nonadiabatic Berry phase in nanocrystalline magnets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Skomski, R.; Sellmyer, D. J.

2016-12-20

In this study, it is investigated how a Berry phase is created in polycrystalline nanomagnets and how the phase translates into an emergent magnetic field and into a topological Hall-effect contribution. The analysis starts directly from the spin of the conduction electrons and does not involve any adiabatic Hamiltonian. Completely random spin alignment in the nanocrystallites does not lead to a nonzero emergent field, but a modulation of the local magnetization does. As an explicit example, we consider a wire with a modulated cone angle.

Gene Coexpression Network Alignment and Conservation of Gene Modules between Two Grass Species: Maize and Rice[C][W][OA

PubMed Central

Ficklin, Stephen P.; Feltus, F. Alex

2011-01-01

One major objective for plant biology is the discovery of molecular subsystems underlying complex traits. The use of genetic and genomic resources combined in a systems genetics approach offers a means for approaching this goal. This study describes a maize (Zea mays) gene coexpression network built from publicly available expression arrays. The maize network consisted of 2,071 loci that were divided into 34 distinct modules that contained 1,928 enriched functional annotation terms and 35 cofunctional gene clusters. Of note, 391 maize genes of unknown function were found to be coexpressed within modules along with genes of known function. A global network alignment was made between this maize network and a previously described rice (Oryza sativa) coexpression network. The IsoRankN tool was used, which incorporates both gene homology and network topology for the alignment. A total of 1,173 aligned loci were detected between the two grass networks, which condensed into 154 conserved subgraphs that preserved 4,758 coexpression edges in rice and 6,105 coexpression edges in maize. This study provides an early view into maize coexpression space and provides an initial network-based framework for the translation of functional genomic and genetic information between these two vital agricultural species. PMID:21606319

Gene coexpression network alignment and conservation of gene modules between two grass species: maize and rice.

PubMed

Ficklin, Stephen P; Feltus, F Alex

2011-07-01

One major objective for plant biology is the discovery of molecular subsystems underlying complex traits. The use of genetic and genomic resources combined in a systems genetics approach offers a means for approaching this goal. This study describes a maize (Zea mays) gene coexpression network built from publicly available expression arrays. The maize network consisted of 2,071 loci that were divided into 34 distinct modules that contained 1,928 enriched functional annotation terms and 35 cofunctional gene clusters. Of note, 391 maize genes of unknown function were found to be coexpressed within modules along with genes of known function. A global network alignment was made between this maize network and a previously described rice (Oryza sativa) coexpression network. The IsoRankN tool was used, which incorporates both gene homology and network topology for the alignment. A total of 1,173 aligned loci were detected between the two grass networks, which condensed into 154 conserved subgraphs that preserved 4,758 coexpression edges in rice and 6,105 coexpression edges in maize. This study provides an early view into maize coexpression space and provides an initial network-based framework for the translation of functional genomic and genetic information between these two vital agricultural species.

Aligning Metabolic Pathways Exploiting Binary Relation of Reactions.

PubMed

Huang, Yiran; Zhong, Cheng; Lin, Hai Xiang; Huang, Jing

2016-01-01

Metabolic pathway alignment has been widely used to find one-to-one and/or one-to-many reaction mappings to identify the alternative pathways that have similar functions through different sets of reactions, which has important applications in reconstructing phylogeny and understanding metabolic functions. The existing alignment methods exhaustively search reaction sets, which may become infeasible for large pathways. To address this problem, we present an effective alignment method for accurately extracting reaction mappings between two metabolic pathways. We show that connected relation between reactions can be formalized as binary relation of reactions in metabolic pathways, and the multiplications of zero-one matrices for binary relations of reactions can be accomplished in finite steps. By utilizing the multiplications of zero-one matrices for binary relation of reactions, we efficiently obtain reaction sets in a small number of steps without exhaustive search, and accurately uncover biologically relevant reaction mappings. Furthermore, we introduce a measure of topological similarity of nodes (reactions) by comparing the structural similarity of the k-neighborhood subgraphs of the nodes in aligning metabolic pathways. We employ this similarity metric to improve the accuracy of the alignments. The experimental results on the KEGG database show that when compared with other state-of-the-art methods, in most cases, our method obtains better performance in the node correctness and edge correctness, and the number of the edges of the largest common connected subgraph for one-to-one reaction mappings, and the number of correct one-to-many reaction mappings. Our method is scalable in finding more reaction mappings with better biological relevance in large metabolic pathways.

A synoptic study of the nature and effects of field aligned low energy electron precipitation in the auroral regions. Ph.D. Thesis - Catholic Univ. of America

NASA Technical Reports Server (NTRS)

Berko, F. W.

1972-01-01

A synoptic study is presented of field-aligned precipitation events observed during a 16-month period, representing a full 4 pi precession of the satellite orbital plane in magnetic local time. The morphology of this type of precipitation, its nature, and relationships between this phenomenon and other geophysical events are discussed in the context of the 16-month data base.

Comparative genomics meets topology: a novel view on genome median and halving problems.

PubMed

Alexeev, Nikita; Avdeyev, Pavel; Alekseyev, Max A

2016-11-11

Genome median and genome halving are combinatorial optimization problems that aim at reconstruction of ancestral genomes by minimizing the number of evolutionary events between them and genomes of the extant species. While these problems have been widely studied in past decades, their solutions are often either not efficient or not biologically adequate. These shortcomings have been recently addressed by restricting the problems solution space. We show that the restricted variants of genome median and halving problems are, in fact, closely related. We demonstrate that these problems have a neat topological interpretation in terms of embedded graphs and polygon gluings. We illustrate how such interpretation can lead to solutions to these problems in particular cases. This study provides an unexpected link between comparative genomics and topology, and demonstrates advantages of solving genome median and halving problems within the topological framework.

Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity.

PubMed

Leuthaeuser, Janelle B; Knutson, Stacy T; Kumar, Kiran; Babbitt, Patricia C; Fetrow, Jacquelyn S

2015-09-01

The development of accurate protein function annotation methods has emerged as a major unsolved biological problem. Protein similarity networks, one approach to function annotation via annotation transfer, group proteins into similarity-based clusters. An underlying assumption is that the edge metric used to identify such clusters correlates with functional information. In this contribution, this assumption is evaluated by observing topologies in similarity networks using three different edge metrics: sequence (BLAST), structure (TM-Align), and active site similarity (active site profiling, implemented in DASP). Network topologies for four well-studied protein superfamilies (enolase, peroxiredoxin (Prx), glutathione transferase (GST), and crotonase) were compared with curated functional hierarchies and structure. As expected, network topology differs, depending on edge metric; comparison of topologies provides valuable information on structure/function relationships. Subnetworks based on active site similarity correlate with known functional hierarchies at a single edge threshold more often than sequence- or structure-based networks. Sequence- and structure-based networks are useful for identifying sequence and domain similarities and differences; therefore, it is important to consider the clustering goal before deciding appropriate edge metric. Further, conserved active site residues identified in enolase and GST active site subnetworks correspond with published functionally important residues. Extension of this analysis yields predictions of functionally determinant residues for GST subgroups. These results support the hypothesis that active site similarity-based networks reveal clusters that share functional details and lay the foundation for capturing functionally relevant hierarchies using an approach that is both automatable and can deliver greater precision in function annotation than current similarity-based methods. © 2015 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity

PubMed Central

Leuthaeuser, Janelle B; Knutson, Stacy T; Kumar, Kiran; Babbitt, Patricia C; Fetrow, Jacquelyn S

2015-01-01

The development of accurate protein function annotation methods has emerged as a major unsolved biological problem. Protein similarity networks, one approach to function annotation via annotation transfer, group proteins into similarity-based clusters. An underlying assumption is that the edge metric used to identify such clusters correlates with functional information. In this contribution, this assumption is evaluated by observing topologies in similarity networks using three different edge metrics: sequence (BLAST), structure (TM-Align), and active site similarity (active site profiling, implemented in DASP). Network topologies for four well-studied protein superfamilies (enolase, peroxiredoxin (Prx), glutathione transferase (GST), and crotonase) were compared with curated functional hierarchies and structure. As expected, network topology differs, depending on edge metric; comparison of topologies provides valuable information on structure/function relationships. Subnetworks based on active site similarity correlate with known functional hierarchies at a single edge threshold more often than sequence- or structure-based networks. Sequence- and structure-based networks are useful for identifying sequence and domain similarities and differences; therefore, it is important to consider the clustering goal before deciding appropriate edge metric. Further, conserved active site residues identified in enolase and GST active site subnetworks correspond with published functionally important residues. Extension of this analysis yields predictions of functionally determinant residues for GST subgroups. These results support the hypothesis that active site similarity-based networks reveal clusters that share functional details and lay the foundation for capturing functionally relevant hierarchies using an approach that is both automatable and can deliver greater precision in function annotation than current similarity-based methods. PMID:26073648

Multiscale analysis of the invariants of the velocity gradient tensor in isotropic turbulence

NASA Astrophysics Data System (ADS)

Danish, Mohammad; Meneveau, Charles

2018-04-01

Knowledge of local flow-topology, the patterns of streamlines around a moving fluid element as described by the velocity-gradient tensor, is useful for developing insights into turbulence processes, such as energy cascade, material element deformation, or scalar mixing. Much has been learned in the recent past about flow topology at the smallest (viscous) scales of turbulence. However, less is known at larger scales, for instance, at the inertial scales of turbulence. In this work, we present a detailed study on the scale dependence of various quantities of interest, such as the population fraction of different types of flow-topologies, the joint probability distribution of the second and third invariants of the velocity gradient tensor, and the geometrical alignment of vorticity with strain-rate eigenvectors. We perform the analysis on a simulation dataset of isotropic turbulence at Reλ=433 . While quantities appear close to scale invariant in the inertial range, we observe a "bump" in several quantities at length scales between the inertial and viscous ranges. For instance, the population fraction of unstable node-saddle-saddle flow topology shows an increase when reducing the scale from the inertial entering the viscous range. A similar bump is observed for the vorticity-strain-rate alignment. In order to document possible dynamical causes for the different trends in the viscous and inertial ranges, we examine the probability fluxes appearing in the Fokker-Plank equation governing the velocity gradient invariants. Specifically, we aim to understand whether the differences observed between the viscous and inertial range statistics are due to effects caused by pressure, subgrid-scale, or viscous stresses or various combinations of these terms. To decompose the flow into small and large scales, we mainly use a spectrally compact non-negative filter with good spatial localization properties (Eyink-Aluie filter). The analysis shows that when going from the inertial range into the viscous range, the subgrid-stress effect decreases more rapidly as a function of scale than the viscous effects increase. To make up for the difference, the pressure Hessian also behaves somewhat differently in the viscous than in the inertial range. The results have implications for models for the velocity gradient tensor showing that the effects of subgrid scales may not be simply modeled via a constant eddy viscosity in the inertial range if one wishes to reproduce the observed trends.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aalseth, Craig E.; Day, Anthony R.; Fuller, Erin S.

Abstract A new ultra-low-background proportional counter (ULBPC) design was recently developed at Pacific Northwest National Laboratory (PNNL). This design, along with an ultra-low-background counting system (ULBCS) which provides passive and active shielding with radon exclusion, has been developed to complement a new shallow underground laboratory (~30 meters water-equivalent) constructed at PNNL. After these steps to mitigate dominant backgrounds (cosmic rays, external gamma-rays, radioactivity in materials), remaining background events do not exclusively arise from ionization of the proportional counter gas. Digital pulse-shape discrimination (PSD) is thus employed to further improve measurement sensitivity. In this work, a template shape is generated formore » each individual sample measurement of interest, a "self-calibrating" template. Differences in event topology can also cause differences in pulse shape. In this work, the temporal region analyzed for each event is refined to maximize background discrimination while avoiding unwanted sensitivity to event topology. This digital PSD method is applied to sample and background data, and initial measurement results from a biofuel methane sample are presented in the context of low-background measurements currently being developed.« less

Open and disconnected magnetic field lines within coronal mass ejections in the solar wind: Evidence for 3-dimensional reconnection

NASA Technical Reports Server (NTRS)

Gosling, J. T.; Birn, J.; McComas, D. J.; Phillips, J. L.; Hesse, M.

1995-01-01

Measurements of suprathermal electron fluxes in the solar wind at energies greater than approximatley 80 eV indicate that magnetic field lines within coronal mass ejections. CMEs, near and beyond 1 AU are normally connected to the Sun at both ends. However, a preliminary reexamination of events previously identified as CMEs in the ISEE 3 data reveals that about 1/4 of all such events contain limited regions where field lines appear to be either connected to the Sun at only one end or connected to the outer heliosphere at both ends. Similar intervals of open and disconnected field lines within CMEs have been identified in the Ulysses observations. We believe that these anomalous field topologies within CMEs are most naturally interpreted in terms of 3-dimensional reconnection behind CMEs close to the Sun. Such reconnection also provides a natural explanation both for the flux rope topology of many CMEs as well as the coronal loops formed during long-duration solar soft X ray events. Although detailed numerical simulations of 3-dimensional reconnection behind CMEs are not yet available, such simulations have been done for the qualitatively similar geometry that prevails within the geomagnetic tail. Those simulations of plasmoid formation in the geomagnetic tail do produce the mixture of field topologies within plasmoids discussed here for CMEs.

Fate of Majorana fermions and Chern numbers after a quantum quench.

PubMed

Sacramento, P D

2014-09-01

In the sequence of quenches to either nontopological phases or other topological phases, we study the stability of Majorana fermions at the edges of a two-dimensional topological superconductor with spin-orbit coupling and in the presence of a Zeeman term. Both instantaneous and slow quenches are considered. In the case of instantaneous quenches, the Majorana modes generally decay, but for a finite system there is a revival time that scales to infinity as the system size grows. Exceptions to this decaying behavior are found in some cases due to the presence of edge states with the same momentum in the final state. Quenches to a topological Z(2) phase reveal some robustness of the Majorana fermions in the sense that even though the survival probability of the Majorana state is small, it does not vanish. If the pairing is not aligned with the spin-orbit Rashba coupling, it is found that the Majorana fermions are fairly robust with a finite survival probability. It is also shown that the Chern number remains invariant after the quench, until the propagation of the mode along the transverse direction reaches the middle point, beyond which the Chern number fluctuates between increasing values. The effect of varying the rate of change in slow quenches is also analyzed. It is found that the defect production is nonuniversal and does not follow the Kibble-Zurek scaling with the quench rate, as obtained before for other systems with topological edge states.

Coupling between strong warm ENSO events and the phase of the stratospheric QBO.

NASA Astrophysics Data System (ADS)

Christiansen, Bo

2017-04-01

Although there in general are no significant long-term correlations between the QBO and the ENSO in observations we find that the QBO and the ENSO were aligned in the 3 to 4 years after the three strong warm ENSO events in 1982, 1997, and 2015. We study this possible connection between the QBO and the ENSO with a new version of the EC-Earth model which includes non-orographic gravity waves and a well modeled QBO. We analyze the modeled QBO in ensembles consisting of 10 AMIP-type experiments with climatological SSTs and 10 experiments with observed daily SSTs. The model experiments cover the period 1982-2013. For the ENSO we use the multivariate index (MEI). As expected the coherence is strong and statistically significant in the equatorial troposphere in the ensemble with observed SSTs. Here the coherence is a measure of the alignment of the ensemble members. In the ensemble with observed SSTs we find a strong and significant alignment of the ensemble members in the equatorial stratospheric winds in the 2 to 4 years after the strong ENSO event in 1997. This alignment also includes the observed QBO. No such alignment is found in the ensemble with climatological SSTs. These results indicate that strong warm ENSO events can directly influence the phase of the QBO. An open and maybe related question is what caused the anomalous QBO in 2016. This behaviour, which is unprecedented in the 50-60 years with data, has been described as a hiccup or a death-spiral. At least it is clear that in the last 18 months the QBO has been stuck in the same corner of the phase-space spanned by its two leading principal components. The possible connection to the ENSO will be investigated.

Mitotic events in cerebellar granule progenitor cells that expand cerebellar surface area are critical for normal cerebellar cortical lamination in mice.

PubMed

Chang, Joshua C; Leung, Mark; Gokozan, Hamza Numan; Gygli, Patrick Edwin; Catacutan, Fay Patsy; Czeisler, Catherine; Otero, José Javier

2015-03-01

Late embryonic and postnatal cerebellar folial surface area expansion promotes cerebellar cortical cytoarchitectural lamination. We developed a streamlined sampling scheme to generate unbiased estimates of murine cerebellar surface area and volume using stereologic principles. We demonstrate that, during the proliferative phase of the external granular layer (EGL) and folial surface area expansion, EGL thickness does not change and thus is a topological proxy for progenitor self-renewal. The topological constraints indicate that, during proliferative phases, migration out of the EGL is balanced by self-renewal. Progenitor self-renewal must, therefore, include mitotic events yielding 2 cells in the same layer to increase surface area (β events) and mitotic events yielding 2 cells, with 1 cell in a superficial layer and 1 cell in a deeper layer (α events). As the cerebellum grows, therefore, β events lie upstream of α events. Using a mathematical model constrained by the measurements of volume and surface area, we could quantify intermitotic times for β events on a per-cell basis in postnatal mouse cerebellum. Furthermore, we found that loss of CCNA2, which decreases EGL proliferation and secondarily induces cerebellar cortical dyslamination, shows preserved α-type events. Thus, CCNA2-null cerebellar granule progenitor cells are capable of self-renewal of the EGL stem cell niche; this is concordant with prior findings of extensive apoptosis in CCNA2-null mice. Similar methodologies may provide another layer of depth to the interpretation of results from stereologic studies.

Blowout jets and impulsive eruptive flares in a bald-patch topology

NASA Astrophysics Data System (ADS)

Chandra, R.; Mandrini, C. H.; Schmieder, B.; Joshi, B.; Cristiani, G. D.; Cremades, H.; Pariat, E.; Nuevo, F. A.; Srivastava, A. K.; Uddin, W.

2017-02-01

Context. A subclass of broad extreme ultraviolet (EUV) and X-ray jets, called blowout jets, have become a topic of research since they could be the link between standard collimated jets and coronal mass ejections (CMEs). Aims: Our aim is to understand the origin of a series of broad jets, some of which are accompanied by flares and associated with narrow and jet-like CMEs. Methods: We analyze observations of a series of recurrent broad jets observed in AR 10484 on 21-24 October 2003. In particular, one of them occurred simultaneously with an M2.4 flare on 23 October at 02:41 UT (SOLA2003-10-23). Both events were observed by the ARIES Hα Solar Tower-Telescope, TRACE, SOHO, and RHESSI instruments. The flare was very impulsive and followed by a narrow CME. A local force-free model of AR 10484 is the basis to compute its topology. We find bald patches (BPs) at the flare site. This BP topology is present for at least two days before to events. Large-scale field lines, associated with the BPs, represent open loops. This is confirmed by a global potential free source surface (PFSS) model. Following the brightest leading edge of the Hα and EUV jet emission, we can temporarily associate these emissions with a narrow CME. Results: Considering their characteristics, the observed broad jets appear to be of the blowout class. As the most plausible scenario, we propose that magnetic reconnection could occur at the BP separatrices forced by the destabilization of a continuously reformed flux rope underlying them. The reconnection process could bring the cool flux-rope material into the reconnected open field lines driving the series of recurrent blowout jets and accompanying CMEs. Conclusions: Based on a model of the coronal field, we compute the AR 10484 topology at the location where flaring and blowout jets occurred from 21 to 24 October 2003. This topology can consistently explain the origin of these events. The movie associated to Fig. 1 is available at http://www.aanda.org

Lifshitz Transitions, Type-II Dirac and Weyl Fermions, Event Horizon and All That

NASA Astrophysics Data System (ADS)

Volovik, G. E.; Zhang, K.

2017-12-01

The type-II Weyl and type-II Dirac points emerge in semimetals and also in relativistic systems. In particular, the type-II Weyl fermions may emerge behind the event horizon of black holes. In this case the horizon with Painlevé-Gullstrand metric serves as the surface of the Lifshitz transition. This relativistic analogy allows us to simulate the black hole horizon and Hawking radiation using the fermionic superfluid with supercritical velocity, and the Dirac and Weyl semimetals with the interface separating the type-I and type-II states. The difference between such type of the artificial event horizon and that which arises in acoustic metric is discussed. At the Lifshitz transition between type-I and type-II fermions the Dirac lines may also emerge, which are supported by the combined action of topology and symmetry. The type-II Weyl and Dirac points also emerge as the intermediate states of the topological Lifshitz transitions. Different configurations of the Fermi surfaces, involved in such Lifshitz transition, are discussed. In one case the type-II Weyl point connects the Fermi pockets and the Lifshitz transition corresponds to the transfer of the Berry flux between the Fermi pockets. In the other case the type-II Weyl point connects the outer and inner Fermi surfaces. At the Lifshitz transition the Weyl point is released from both Fermi surfaces. They loose their Berry flux, which guarantees the global stability, and without the topological support the inner surface disappears after shrinking to a point at the second Lifshitz transition. These examples reveal the complexity and universality of topological Lifshitz transitions, which originate from the ubiquitous interplay of a variety of topological characters of the momentum-space manifolds. For the interacting electrons, the Lifshitz transitions may lead to the formation of the dispersionless (flat) band with zero energy and singular density of states, which opens the route to room-temperature superconductivity. Originally, the idea of the enhancement of T_c due to flat band has been put forward by the nuclear physics community, and this also demonstrates the close connections between different areas of physics.

Dynamic Mechanical and Nanofibrous Topological Combinatory Cues Designed for Periodontal Ligament Engineering.

PubMed

Kim, Joong-Hyun; Kang, Min Sil; Eltohamy, Mohamed; Kim, Tae-Hyun; Kim, Hae-Won

2016-01-01

Complete reconstruction of damaged periodontal pockets, particularly regeneration of periodontal ligament (PDL) has been a significant challenge in dentistry. Tissue engineering approach utilizing PDL stem cells and scaffolding matrices offers great opportunity to this, and applying physical and mechanical cues mimicking native tissue conditions are of special importance. Here we approach to regenerate periodontal tissues by engineering PDL cells supported on a nanofibrous scaffold under a mechanical-stressed condition. PDL stem cells isolated from rats were seeded on an electrospun polycaprolactone/gelatin directionally-oriented nanofiber membrane and dynamic mechanical stress was applied to the cell/nanofiber construct, providing nanotopological and mechanical combined cues. Cells recognized the nanofiber orientation, aligning in parallel, and the mechanical stress increased the cell alignment. Importantly, the cells cultured on the oriented nanofiber combined with the mechanical stress produced significantly stimulated PDL specific markers, including periostin and tenascin with simultaneous down-regulation of osteogenesis, demonstrating the roles of topological and mechanical cues in altering phenotypic change in PDL cells. Tissue compatibility of the tissue-engineered constructs was confirmed in rat subcutaneous sites. Furthermore, in vivo regeneration of PDL and alveolar bone tissues was examined under the rat premaxillary periodontal defect models. The cell/nanofiber constructs engineered under mechanical stress showed sound integration into tissue defects and the regenerated bone volume and area were significantly improved. This study provides an effective tissue engineering approach for periodontal regeneration-culturing PDL stem cells with combinatory cues of oriented nanotopology and dynamic mechanical stretch.

Dynamic Mechanical and Nanofibrous Topological Combinatory Cues Designed for Periodontal Ligament Engineering

PubMed Central

Kim, Joong-Hyun; Kang, Min Sil; Eltohamy, Mohamed; Kim, Tae-Hyun; Kim, Hae-Won

2016-01-01

Complete reconstruction of damaged periodontal pockets, particularly regeneration of periodontal ligament (PDL) has been a significant challenge in dentistry. Tissue engineering approach utilizing PDL stem cells and scaffolding matrices offers great opportunity to this, and applying physical and mechanical cues mimicking native tissue conditions are of special importance. Here we approach to regenerate periodontal tissues by engineering PDL cells supported on a nanofibrous scaffold under a mechanical-stressed condition. PDL stem cells isolated from rats were seeded on an electrospun polycaprolactone/gelatin directionally-oriented nanofiber membrane and dynamic mechanical stress was applied to the cell/nanofiber construct, providing nanotopological and mechanical combined cues. Cells recognized the nanofiber orientation, aligning in parallel, and the mechanical stress increased the cell alignment. Importantly, the cells cultured on the oriented nanofiber combined with the mechanical stress produced significantly stimulated PDL specific markers, including periostin and tenascin with simultaneous down-regulation of osteogenesis, demonstrating the roles of topological and mechanical cues in altering phenotypic change in PDL cells. Tissue compatibility of the tissue-engineered constructs was confirmed in rat subcutaneous sites. Furthermore, in vivo regeneration of PDL and alveolar bone tissues was examined under the rat premaxillary periodontal defect models. The cell/nanofiber constructs engineered under mechanical stress showed sound integration into tissue defects and the regenerated bone volume and area were significantly improved. This study provides an effective tissue engineering approach for periodontal regeneration—culturing PDL stem cells with combinatory cues of oriented nanotopology and dynamic mechanical stretch. PMID:26989897

A Magnetohydrodynamic Modeling of the Interchange Cycle for Oblique Northward Interplanetary Magnetic Field

NASA Astrophysics Data System (ADS)

Watanabe, Masakazu; Fujita, Shigeru; Tanaka, Takashi; Kubota, Yasubumi; Shinagawa, Hiroyuki; Murata, Ken T.

2018-01-01

We perform numerical modeling of the interchange cycle in the magnetosphere-ionosphere convection system for oblique northward interplanetary magnetic field (IMF). The interchange cycle results from the coupling of IMF-to-lobe reconnection and lobe-to-closed reconnection. Using a global magnetohydrodynamic simulation code, for an IMF clock angle of 20° (measured from due north), we successfully reproduced the following features of the interchange cycle. (1) In the ionosphere, for each hemisphere, there appears a reverse cell circulating exclusively in the closed field line region (the reciprocal cell). (2) The topology transition of the magnetic field along a streamline near the equatorial plane precisely represents the magnetic flux reciprocation during the interchange cycle. (3) Field-aligned electric fields on the interplanetary-open separatrix and on the open-closed separatrix are those that are consistent with IMF-to-lobe reconnection and lobe-to-closed reconnection, respectively. These three features prove the existence of the interchange cycle in the simulated magnetosphere-ionosphere system. We conclude that the interchange cycle does exist in the real solar wind-magnetosphere-ionosphere system. In addition, the simulation revealed that the reciprocal cell described above is not a direct projection of the diffusion region as predicted by the "vacuum" model in which diffusion is added a priori to the vacuum magnetic topology. Instead, the reciprocal cell is a consequence of the plasma convection system coupled to the so-called NBZ ("northward Bz") field-aligned current system.

Comparative study of topological indices of macro/supramolecular RNA complex networks.

PubMed

Agüero-Chapín, Guillermín; Antunes, Agostinho; Ubeira, Florencio M; Chou, Kuo-Chen; González-Díaz, Humberto

2008-11-01

RNA function annotation is often based on alignment to a previously studied template. In contrast to the study of proteins, there are not many alignment-free methods to predict RNA functions if alignment fails. The use of topological indices (TIs) of RNA complex networks (CNs) to find quantitative structure-activity relationships (QSAR) may be an alternative to incorporate secondary structure or sequence-to-sequence similarity. Here, we introduce new QSAR-like techniques using RNA macromolecular CNs (mmCNs), where nodes are nucleotides, or RNA supramolecular CNs (smCNs), where nodes are RNA sequences. We studied a data set of 198 sequences including 18S-rRNAs (important phylogenetic molecular biomarkers). We constructed three types of RNA mmCNs: sequence-linear (SL), Cartesian-lattice (CL), and sequence-folding CNs (SF-CNs) and two smCNs: sequence-sequence disagreement CN (SSD) and sequence-sequence similarity (SSS-smCN). We reported the first comparative QSAR study with all these CIs and CNs, which includes: (i) spectral moments ( ( i )micro d ( w)) of SL-mmCNs (accuracy = 75.3%), (ii) electrostatic CIs (xi d ) of CL-mmCNs (>90%), (iii) thermodynamic parameters (Delta G, Delta H, Delta S, and T m) of SF-mmCNs (64.7%), (iv) disagreement-distribution moments ( M k ) of the SSD-smCN (79.3%), and (v) node centralities of the SSD-smCN (78.0%). Furthermore, we reported the experimental isolation of a new RNA sequence from Psidum guajava leaf tissue and its QSAR and BLAST prediction to illustrate the practical use of these methods. We also investigated the use of these CNs to explore rRNA diversity on bacteria, plants, and parasites from the Dactylogyrus genus. The HPL-mmCNs model was the best of all found. All the CNs and TIs, except SF-mmCNs, were introduced here by the first time for the QSAR study of RNA, which allowed a comparative study for RNA classification.

Polymer stabilized liquid crystals: Topology-mediated electro-optical behavior and applications

NASA Astrophysics Data System (ADS)

Weng, Libo

There has been a wide range of liquid crystal polymer composites that vary in polymer concentration from as little as 3 wt.% (polymer stabilized liquid crystal) to as high as 60 wt.% (polymer dispersed liquid crystals). In this dissertation, an approach of surface polymerization based on a low reactive monomer concentration about 1 wt.% is studied in various liquid crystal operation modes. The first part of dissertation describes the development of a vertical alignment (VA) mode with surface polymer stabilization, and the effects of structure-performance relationship of reactive monomers (RMs) and polymerization conditions on the electro-optical behaviors of the liquid crystal device has been explored. The polymer topography plays an important role in modifying and enhancing the electro-optical performance of stabilized liquid crystal alignment. The enabling surface-pinned polymer stabilized vertical alignment (PSVA) approach has led to the development of high-performance and fast-switching displays with controllable pretilt angle, increase in surface anchoring energy, high optical contrast and fast response time. The second part of the dissertation explores a PSVA mode with in-plane switching (IPS) and its application for high-efficiency and fast-switching phase gratings. The diffraction patterns and the electro-optical behaviors including diffraction efficiency and response time are characterized. The diffraction grating mechanism and performance have been validated by computer simulation. Finally, the advantages of surface polymerization approach such as good optical contrast and fast response time have been applied to the fringe-field switching (FFS) system. The concentration of reactive monomer on the electro-optical behavior of the FFS cells is optimized. The outstanding electro-optical results and mechanism of increase in surface anchoring strength are corroborated by the director field simulation. The density and topology of nanoscale polymer protrusions are analyzed and confirmed by morphological study. The developed high-performance polymer-stabilized fringe-field-switching (PS-FFS) could open new types of device applications.

Opening the cusp. [using magnetic field topology

NASA Technical Reports Server (NTRS)

Crooker, N. U.; Toffoletto, F. R.; Gussenhoven, M. S.

1991-01-01

This paper discusses the magnetic field topology (determined by the superposition of dipole, image, and uniform fields) for mapping the cusp to the ionosphere. The model results are compared to both new and published observations and are then used to map the footprint of a flux transfer event caused by a time variation in the merging rate. It is shown that the cusp geometry distorts the field lines mapped from the magnetopause to yield footprints with dawn and dusk protrusions into the region of closed magnetic flux.

Exclusive muon neutrino charged current pion-less topologies. ArgoNeuT results and future prospects in LAr TPC detectors

DOE PAGES

Palamara, Ornella

2016-12-29

Results from the analysis of charged current pion-less (CC 0-pion) muon neutrino events in argon collected by the ArgoNeuT experiment on the NuMI beam at Fermilab are presented and compared with predictions from Monte Carlo simulations. A novel analysis method, based on the reconstruction of exclusive topologies, fully exploiting the Liquid argon Time Projection Chamber (LAr TPC) technique capabilities, is used to analyze the events, characterized by the presence at the vertex of a leading muon track eventually accompanied by one or more highly ionizing tracks, and study nuclear effects in neutrino interactions on argon nuclei. Multiple protons accompanying themore » leading muon are visible in the ArgoNeuT events, and measured with a proton reconstruction threshold of 21 MeV kinetic energy. As a result, measurements of (anti-)neutrino CC 0-pion inclusive and exclusive cross sections on argon nuclei are reported. Prospects for future, larger mass LAr TPC detectors are discussed.« less

Chemical disorder in topological insulators: A route to magnetism tolerant topological surface states

DOE PAGES

Martínez-Velarte, M. Carmen; Kretz, Bernhard; Moro-Lagares, Maria; ...

2017-06-13

Here, we show that the chemical inhomogeneity in ternary three-dimensional topological insulators preserves the topological spin texture of their surface states against a net surface magnetization. The spin texture is that of a Dirac cone with helical spin structure in the reciprocal space, which gives rise to spin-polarized and dissipation-less charge currents. Thanks to the nontrivial topology of the bulk electronic structure, this spin texture is robust against most types of surface defects. However, magnetic perturbations break the time-reversal symmetry, enabling magnetic scattering and loss of spin coherence of the charge carriers. This intrinsic incompatibility precludes the design of magnetoelectronicmore » devices based on the coupling between magnetic materials and topological surface states. We demonstrate that the magnetization coming from individual Co atoms deposited on the surface can disrupt the spin coherence of the carriers in the archetypal topological insulator Bi 2Te 3, while in Bi 2Se 2Te the spin texture remains unperturbed. This is concluded from the observation of elastic backscattering events in quasiparticle interference patterns obtained by scanning tunneling spectroscopy. The mechanism responsible for the protection is investigated by energy resolved spectroscopy and ab initio calculations, and it is ascribed to the distorted adsorption geometry of localized magnetic moments due to Se–Te disorder, which suppresses the Co hybridization with the surface states.« less

Chemical disorder in topological insulators: A route to magnetism tolerant topological surface states

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martínez-Velarte, M. Carmen; Kretz, Bernhard; Moro-Lagares, Maria

Here, we show that the chemical inhomogeneity in ternary three-dimensional topological insulators preserves the topological spin texture of their surface states against a net surface magnetization. The spin texture is that of a Dirac cone with helical spin structure in the reciprocal space, which gives rise to spin-polarized and dissipation-less charge currents. Thanks to the nontrivial topology of the bulk electronic structure, this spin texture is robust against most types of surface defects. However, magnetic perturbations break the time-reversal symmetry, enabling magnetic scattering and loss of spin coherence of the charge carriers. This intrinsic incompatibility precludes the design of magnetoelectronicmore » devices based on the coupling between magnetic materials and topological surface states. We demonstrate that the magnetization coming from individual Co atoms deposited on the surface can disrupt the spin coherence of the carriers in the archetypal topological insulator Bi 2Te 3, while in Bi 2Se 2Te the spin texture remains unperturbed. This is concluded from the observation of elastic backscattering events in quasiparticle interference patterns obtained by scanning tunneling spectroscopy. The mechanism responsible for the protection is investigated by energy resolved spectroscopy and ab initio calculations, and it is ascribed to the distorted adsorption geometry of localized magnetic moments due to Se–Te disorder, which suppresses the Co hybridization with the surface states.« less

Interdisciplinary challenges in the study of power grid resilience and stability and their relation to extreme weather events

NASA Astrophysics Data System (ADS)

Heitzig, J.; Fujiwara, N.; Aihara, K.; Kurths, J.

2014-10-01

This topical issue collects contributions to the interdisciplinary study of power grid stability in face of increasing volatility of energy production and consumption due to increasing renewable energy infeed and changing climatic conditions. The individual papers focus on different aspects of this field and bring together modern achievements from various disciplines, in particular complex systems science, nonlinear data analysis, control theory, electrical engineering, and climatology. Main topics considered here are prediction and volatility of renewable infeed, modelling and theoretical analysis of power grid topology, dynamics and stability, relationships between stability and complex network topology, and improvements via topological changes or control. Impacts for the design of smart power grids are discussed in detail.

Dynamical patterns in nematic active matter on a sphere

NASA Astrophysics Data System (ADS)

Henkes, Silke; Marchetti, M. Cristina; Sknepnek, Rastko

2018-04-01

Using simulations of self-propelled agents with short-range repulsion and nematic alignment, we explore the dynamical phases of a dense active nematic confined to the surface of a sphere. We map the nonequilibrium phase diagram as a function of curvature, alignment strength, and activity. Our model reproduces several phases seen in recent experiments on active microtubule bundles confined the surfaces of vesicles. At low driving, we recover the equilibrium nematic ground state with four +1 /2 defects. As the driving is increased, geodesic forces drive the transition to a polar band wrapping around an equator, with large empty spherical caps corresponding to two +1 defects at the poles. Upon further increasing activity, the bands fold onto themselves, and the system eventually transitions to a turbulent state marked by the proliferation of pairs of topological defects. We highlight the key role of the nematic persistence length in controlling pattern formation in these confined systems with positive Gaussian curvature.

A Novel Framework for the Comparative Analysis of Biological Networks

PubMed Central

Pache, Roland A.; Aloy, Patrick

2012-01-01

Genome sequencing projects provide nearly complete lists of the individual components present in an organism, but reveal little about how they work together. Follow-up initiatives have deciphered thousands of dynamic and context-dependent interrelationships between gene products that need to be analyzed with novel bioinformatics approaches able to capture their complex emerging properties. Here, we present a novel framework for the alignment and comparative analysis of biological networks of arbitrary topology. Our strategy includes the prediction of likely conserved interactions, based on evolutionary distances, to counter the high number of missing interactions in the current interactome networks, and a fast assessment of the statistical significance of individual alignment solutions, which vastly increases its performance with respect to existing tools. Finally, we illustrate the biological significance of the results through the identification of novel complex components and potential cases of cross-talk between pathways and alternative signaling routes. PMID:22363585

Ion velocity distributions in dipolarization events: Distributions in the central plasma sheet

NASA Astrophysics Data System (ADS)

Birn, J.; Runov, A.; Zhou, X.-Z.

2017-08-01

Using combined MHD/test particle simulations, we further explore characteristic ion velocity distributions in the central plasma sheet (CPS) in relation to dipolarization events. Distributions in the CPS within the dipolarized flux bundle (DFB) that follows the passage of a dipolarization front typically show two opposing low subthermal-energy beams with a ring-like component perpendicular to the magnetic field at about twice the thermal energy. The dominance of the perpendicular anisotropy and a field-aligned peak at lower energy agree qualitatively with ion distribution functions derived from "Time History of Events and Macroscale Interactions during Substorms" observations. At locations somewhat off the equatorial plane the field-aligned peaks are shifted by a field-aligned component of the bulk flow, such that one peak becomes centered near zero net velocity, which makes it less likely to be observed. The origins of the field-aligned peaks are low-energy lobe (or near plasma sheet boundary layer) regions, while the ring distribution originates mostly from thermal plasma sheet particles on extended field lines. The acceleration mechanisms are also quite different: the beam ions are accelerated first by the E × B drift motion of the DFB and then by a slingshot effect of the earthward convecting DFB (akin to first-order Fermi, type B, acceleration), which causes an increase in field-aligned speed. In contrast, the ring particles are accelerated by successive, betatron-like acceleration after entering the high electric field region of an earthward propagating DFB.

An extensive assessment of network alignment algorithms for comparison of brain connectomes.

PubMed

Milano, Marianna; Guzzi, Pietro Hiram; Tymofieva, Olga; Xu, Duan; Hess, Christofer; Veltri, Pierangelo; Cannataro, Mario

2017-06-06

Recently the study of the complex system of connections in neural systems, i.e. the connectome, has gained a central role in neurosciences. The modeling and analysis of connectomes are therefore a growing area. Here we focus on the representation of connectomes by using graph theory formalisms. Macroscopic human brain connectomes are usually derived from neuroimages; the analyzed brains are co-registered in the image domain and brought to a common anatomical space. An atlas is then applied in order to define anatomically meaningful regions that will serve as the nodes of the network - this process is referred to as parcellation. The atlas-based parcellations present some known limitations in cases of early brain development and abnormal anatomy. Consequently, it has been recently proposed to perform atlas-free random brain parcellation into nodes and align brains in the network space instead of the anatomical image space, as a way to deal with the unknown correspondences of the parcels. Such process requires modeling of the brain using graph theory and the subsequent comparison of the structure of graphs. The latter step may be modeled as a network alignment (NA) problem. In this work, we first define the problem formally, then we test six existing state of the art of network aligners on diffusion MRI-derived brain networks. We compare the performances of algorithms by assessing six topological measures. We also evaluated the robustness of algorithms to alterations of the dataset. The results confirm that NA algorithms may be applied in cases of atlas-free parcellation for a fully network-driven comparison of connectomes. The analysis shows MAGNA++ is the best global alignment algorithm. The paper presented a new analysis methodology that uses network alignment for validating atlas-free parcellation brain connectomes. The methodology has been experimented on several brain datasets.

Evidence of a 2D Fermi surface due to surface states in a p-type metallic Bi2Te3

NASA Astrophysics Data System (ADS)

Shrestha, K.; Marinova, V.; Lorenz, B.; Chu, C. W.

2018-05-01

We present a systematic quantum oscillations study on a metallic, p-type Bi2Te3 topological single crystal in magnetic fields up to B  =  7 T. The maxima/minima positions of oscillations measured at different tilt angles align to one another when plotted as a function of the normal component of magnetic field, confirming the presence of the 2D Fermi surface. Additionally, the Berry phase, β  =  0.4  ±  0.05 obtained from the Landau level fan plot, is very close to the theoretical value of 0.5 for the Dirac particles, confirming the presence of topological surface states in the Bi2Te3 single crystal. Using the Lifshitz–Kosevich analyses, the Fermi energy is estimated to be meV, which is lower than that of other bismuth-based topological systems. The detection of surface states in the Bi2Te3 crystal can be explained by our previous hypothesis of the lower position of the Fermi surface that cuts the ‘M’-shaped valence band maxima. As a result, the bulk state frequency is shifted to higher magnetic fields, which allows measurement of the surface states signal at low magnetic fields.

Inverted Resistance Measurements as a Method for Characterizing the Bulk and Surface Conductivities of Three-Dimensional Topological Insulators

NASA Astrophysics Data System (ADS)

Eo, Y. S.; Sun, K.; Kurdak, ć.; Kim, D.-J.; Fisk, Z.

2018-04-01

We introduce a resistance measurement method that is useful in characterizing materials with both surface and bulk conduction, such as three-dimensional topological insulators. The transport geometry for this resistance measurement configuration consists of one current lead as a closed loop that fully encloses the other current lead on the surface, and two voltage leads that are both placed outside the loop. We show that, in the limit where the transport is dominated by the surface conductivity of the material, the four-terminal resistance measured from such a transport geometry is proportional to σb/σs2, where σb and σs are the bulk and surface conductivities of the material, respectively. We call this type of measurement inverted resistance measurement, as the resistance scales inversely with the bulk resistivity. We discuss possible implementations of this method by performing numerical calculations on different geometries and introduce strategies to extract the bulk and surface conductivities. We also demonstrate inverted resistance measurements on SmB6 , a topological Kondo insulator, using both single-sided and coaxially aligned double-sided Corbino disk transport geometries. Using this method, we are able to measure the bulk conductivity, even at low temperatures, where the bulk conduction is much smaller than the surface conduction in this material.

Discrete-event simulation of a wide-area health care network.

PubMed Central

McDaniel, J G

1995-01-01

OBJECTIVE: Predict the behavior and estimate the telecommunication cost of a wide-area message store-and-forward network for health care providers that uses the telephone system. DESIGN: A tool with which to perform large-scale discrete-event simulations was developed. Network models for star and mesh topologies were constructed to analyze the differences in performances and telecommunication costs. The distribution of nodes in the network models approximates the distribution of physicians, hospitals, medical labs, and insurers in the Province of Saskatchewan, Canada. Modeling parameters were based on measurements taken from a prototype telephone network and a survey conducted at two medical clinics. Simulation studies were conducted for both topologies. RESULTS: For either topology, the telecommunication cost of a network in Saskatchewan is projected to be less than $100 (Canadian) per month per node. The estimated telecommunication cost of the star topology is approximately half that of the mesh. Simulations predict that a mean end-to-end message delivery time of two hours or less is achievable at this cost. A doubling of the data volume results in an increase of less than 50% in the mean end-to-end message transfer time. CONCLUSION: The simulation models provided an estimate of network performance and telecommunication cost in a specific Canadian province. At the expected operating point, network performance appeared to be relatively insensitive to increases in data volume. Similar results might be anticipated in other rural states and provinces in North America where a telephone-based network is desired. PMID:7583646

High Coherence Qubit packaging

NASA Astrophysics Data System (ADS)

Pappas, David P.; Wu, Xian; Olivadese, Salvatore B.; Adiga, V. P.; Hertzberg, Jared B.; Bronn, Nicholas T.; Chow, Jerry M.; NIST Team; IBM Team

Development of sockets and associated interconnects for multi-qubit chips is presented. Considerations include thermalization, RF hygiene, non-magnetic environment, and self-alignment of the chips to allow for rapid testing, scalable integration, and high coherence operation. The sockets include wirebond free, vertical take-off launches with pogopins. This allows for high interconnectivity to non-trivial topology of qubits. Furthermore, vertical grounding is accomplished to reduce chip modes and suppress box modes. Low energy loss and high phase coherence is observed using this paradigm. We acknowledge support from IARPA, LPS, and the NIST Quantum Based Metrology Initiative.

On the interaction mechanisms of a p53 peptide and nutlin with the MDM2 and MDMX proteins: a Brownian dynamics study.

PubMed

ElSawy, Karim M; Verma, Chandra S; Joseph, Thomas L; Lane, David P; Twarock, Reidun; Caves, Leo S D

2013-02-01

The interaction of p53 with its regulators MDM2 and MDMX plays a major role in regulating the cell cycle. Inhibition of this interaction has become an important therapeutic strategy in oncology. Although MDM2 and MDMX share a very high degree of sequence/structural similarity, the small-molecule inhibitor nutlin appears to be an efficient inhibitor only of the p53-MDM2 interaction. Here, we investigate the mechanism of interaction of nutlin with these two proteins and contrast it with that of p53 using Brownian dynamics simulations. In contrast to earlier attempts to examine the bound states of the partners, here we locate initial reaction events in these interactions by identifying the regions of space around MDM2/MDMX, where p53/nutlin experience associative encounters with prolonged residence times relative to that in bulk solution. We find that the initial interaction of p53 with MDM2 is long-lived relative to nutlin, but, unlike nutlin, it takes place at the N- and C termini of the MDM2 protein, away from the binding site, suggestive of an allosteric mechanism of action. In contrast, nutlin initially interacts with MDM2 directly at the clefts of the binding site. The interaction of nutlin with MDMX, however, is very short-lived compared with MDM2 and does not show such direct initial interactions with the binding site. Comparison of the topology of the electrostatic potentials of MDM2 and MDMX and the locations of the initial encounters with p53/nutlin in tandem with structure-based sequence alignment revealed that the origin of the diminished activity of nutlin toward MDMX relative to MDM2 may stem partly from the differing topologies of the electrostatic potentials of the two proteins. Glu25 and Lys51 residues underpin these topological differences and appear to collectively play a key role in channelling nutlin directly toward the binding site on the MDM2 surface and are absent in MDMX. The results, therefore, provide new insight into the mechanism of p53/nutlin interactions with MDM2 and MDMX and could potentially have a broader impact on anticancer drug optimization strategies.

Single-Event Effects in High-Frequency Linear Amplifiers: Experiment and Analysis

NASA Astrophysics Data System (ADS)

Zeinolabedinzadeh, Saeed; Ying, Hanbin; Fleetwood, Zachary E.; Roche, Nicolas J.-H.; Khachatrian, Ani; McMorrow, Dale; Buchner, Stephen P.; Warner, Jeffrey H.; Paki-Amouzou, Pauline; Cressler, John D.

2017-01-01

The single-event transient (SET) response of two different silicon-germanium (SiGe) X-band (8-12 GHz) low noise amplifier (LNA) topologies is fully investigated in this paper. The two LNAs were designed and implemented in 130nm SiGe HBT BiCMOS process technology. Two-photon absorption (TPA) laser pulses were utilized to induce transients within various devices in these LNAs. Impulse response theory is identified as a useful tool for predicting the settling behavior of the LNAs subjected to heavy ion strikes. Comprehensive device and circuit level modeling and simulations were performed to accurately simulate the behavior of the circuits under ion strikes. The simulations agree well with TPA measurements. The simulation, modeling and analysis presented in this paper can be applied for any other circuit topologies for SET modeling and prediction.

Topological congruence between phylogenies of Anacanthorus spp. (Monogenea: Dactylogyridae) and their Characiformes (Actinopterygii) hosts: A case of host-parasite cospeciation

PubMed Central

Fabrin, Thomaz M. C.; Gasques, Luciano S.; Prioli, Sônia M. A. P.; Balbuena, Juan A.; Prioli, Alberto J.; Takemoto, Ricardo M.

2018-01-01

Cophylogenetic studies aim at testing specific hypotheses to understand the nature of coevolving associations between sets of organisms, such as host and parasites. Monogeneans and their hosts provide and interesting platform for these studies due to their high host specificity. In this context, the objective of the present study was to establish whether the relationship between Anacanthorus spp. with their hosts from the upper Paraná River and its tributaries can be explained by means of cospeciation processes. Nine fish species and 14 monogenean species, most of them host specific, were studied. Partial DNA sequences of the genes RAG1, 16S and COI of the fish hosts and of the genes ITS2, COI and 5.8S of the parasite species were used for phylogenetic reconstruction. Maximum likelihood phylogenetic trees of the host and parasite species were built and used for analyses of topological congruence with PACo and ParaFit. The program Jane was used to estimate the nature of cospeciation events. The comparison of the two phylogenies revealed high topological congruence between them. Both PACo and ParaFit supported the hypothesis of global cospeciation. Results from Jane pointed to duplications as the most frequent coevolutionary event, followed by cospeciation, whereas duplications followed by host-switching were the least common event in Anacanthorus spp. studied. Host-sharing (spreading) was also identified but only between congeneric host species. PMID:29538463

Topological congruence between phylogenies of Anacanthorus spp. (Monogenea: Dactylogyridae) and their Characiformes (Actinopterygii) hosts: A case of host-parasite cospeciation.

PubMed

da Graça, Rodrigo J; Fabrin, Thomaz M C; Gasques, Luciano S; Prioli, Sônia M A P; Balbuena, Juan A; Prioli, Alberto J; Takemoto, Ricardo M

2018-01-01

Cophylogenetic studies aim at testing specific hypotheses to understand the nature of coevolving associations between sets of organisms, such as host and parasites. Monogeneans and their hosts provide and interesting platform for these studies due to their high host specificity. In this context, the objective of the present study was to establish whether the relationship between Anacanthorus spp. with their hosts from the upper Paraná River and its tributaries can be explained by means of cospeciation processes. Nine fish species and 14 monogenean species, most of them host specific, were studied. Partial DNA sequences of the genes RAG1, 16S and COI of the fish hosts and of the genes ITS2, COI and 5.8S of the parasite species were used for phylogenetic reconstruction. Maximum likelihood phylogenetic trees of the host and parasite species were built and used for analyses of topological congruence with PACo and ParaFit. The program Jane was used to estimate the nature of cospeciation events. The comparison of the two phylogenies revealed high topological congruence between them. Both PACo and ParaFit supported the hypothesis of global cospeciation. Results from Jane pointed to duplications as the most frequent coevolutionary event, followed by cospeciation, whereas duplications followed by host-switching were the least common event in Anacanthorus spp. studied. Host-sharing (spreading) was also identified but only between congeneric host species.

Observations of energetic particles between a pair of corotating interaction regions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Z.; Chen, Y.; Tang, C. L.

We report observations of the acceleration and trapping of energetic ions and electrons between a pair of corotating interaction regions (CIRs). The event occurred in Carrington Rotation 2060. Observed by the STEREO-B spacecraft, the two CIRs were separated by less than 5 days. In contrast to other CIR events, the fluxes of the energetic ions and electrons in this event reached their maxima between the trailing edge of the first CIR and the leading edge of the second CIR. The radial magnetic field (B{sub r} ) reversed its sense and the anisotropy of the flux also changed from Sunward tomore » anti-Sunward between the two CIRs. Furthermore, there was an extended period of counterstreaming suprathermal electrons between the two CIRs. Similar observations for this event were also obtained with the Advanced Composition Explorer and STEREO-A. We conjecture that these observations were due to a U-shaped, large-scale magnetic field topology connecting the reverse shock of the first CIR and the forward shock of the second CIR. Such a disconnected U-shaped magnetic field topology may have formed due to magnetic reconnection in the upper corona.« less

Ultrafast photocurrents at the surface of the three-dimensional topological insulator Bi2Se3

PubMed Central

Braun, Lukas; Mussler, Gregor; Hruban, Andrzej; Konczykowski, Marcin; Schumann, Thomas; Wolf, Martin; Münzenberg, Markus; Perfetti, Luca; Kampfrath, Tobias

2016-01-01

Three-dimensional topological insulators are fascinating materials with insulating bulk yet metallic surfaces that host highly mobile charge carriers with locked spin and momentum. Remarkably, surface currents with tunable direction and magnitude can be launched with tailored light beams. To better understand the underlying mechanisms, the current dynamics need to be resolved on the timescale of elementary scattering events (∼10 fs). Here, we excite and measure photocurrents in the model topological insulator Bi2Se3 with a time resolution of 20 fs by sampling the concomitantly emitted broadband terahertz (THz) electromagnetic field from 0.3 to 40 THz. Strikingly, the surface current response is dominated by an ultrafast charge transfer along the Se–Bi bonds. In contrast, photon-helicity-dependent photocurrents are found to be orders of magnitude smaller than expected from generation scenarios based on asymmetric depopulation of the Dirac cone. Our findings are of direct relevance for broadband optoelectronic devices based on topological-insulator surface currents. PMID:27796297

Stability of knotted vortices in wave chaos

NASA Astrophysics Data System (ADS)

Taylor, Alexander; Dennis, Mark

Large scale tangles of disordered filaments occur in many diverse physical systems, from turbulent superfluids to optical volume speckle to liquid crystal phases. They can exhibit particular large scale random statistics despite very different local physics. We have previously used the topological statistics of knotting and linking to characterise the large scale tangling, using the vortices of three-dimensional wave chaos as a universal model system whose physical lengthscales are set only by the wavelength. Unlike geometrical quantities, the statistics of knotting depend strongly on the physical system and boundary conditions. Although knotting patterns characterise different systems, the topology of vortices is highly unstable to perturbation, under which they may reconnect with one another. In systems of constructed knots, these reconnections generally rapidly destroy the knot, but for vortex tangles the topological statistics must be stable. Using large scale simulations of chaotic eigenfunctions, we numerically investigate the prevalence and impact of reconnection events, and their effect on the topology of the tangle.

On the Topological Changes of Local Hurst Exponent in Polar Regions

NASA Astrophysics Data System (ADS)

Consolini, G.; De Michelis, P.

2014-12-01

Geomagnetic activity during magnetic substorms and storms is related to the dinamical and topological changes of the current systems flowing in the Earth's magnetosphere-ionosphere. This is particularly true in the case of polar regions where the enhancement of auroral electrojet current system is responsible for the observed geomagnetic perturbations. Here, using the DMA-technique we evaluate the local Hurst exponent (H"older exponent) for a set of 46 geomagnetic observatories, widely distributed in the northern hemisphere, during one of the most famous and strong geomagnetic storm, the Bastille event, and reconstruct a sequence of polar maps showing the dinamical changes of the topology of the local Hurst exponent with the geomagnetic activity level. The topological evolution of local Hurst exponent maps is discussed in relation to the dinamical changes of the current systems flowing in the polar ionosphere. G. Consolini has received funding from the European Community's Seventh Framework Programme (FP7/2007-2013) under Grant agreement no. 313038/STORM for this research.

Phylogenetic study of Class Armophorea (Alveolata, Ciliophora) based on 18S-rDNA data.

PubMed

da Silva Paiva, Thiago; do Nascimento Borges, Bárbara; da Silva-Neto, Inácio Domingos

2013-12-01

The 18S rDNA phylogeny of Class Armophorea, a group of anaerobic ciliates, is proposed based on an analysis of 44 sequences (out of 195) retrieved from the NCBI/GenBank database. Emphasis was placed on the use of two nucleotide alignment criteria that involved variation in the gap-opening and gap-extension parameters and the use of rRNA secondary structure to orientate multiple-alignment. A sensitivity analysis of 76 data sets was run to assess the effect of variations in indel parameters on tree topologies. Bayesian inference, maximum likelihood and maximum parsimony phylogenetic analyses were used to explore how different analytic frameworks influenced the resulting hypotheses. A sensitivity analysis revealed that the relationships among higher taxa of the Intramacronucleata were dependent upon how indels were determined during multiple-alignment of nucleotides. The phylogenetic analyses rejected the monophyly of the Armophorea most of the time and consistently indicated that the Metopidae and Nyctotheridae were related to the Litostomatea. There was no consensus on the placement of the Caenomorphidae, which could be a sister group of the Metopidae + Nyctorheridae, or could have diverged at the base of the Spirotrichea branch or the Intramacronucleata tree.

Phylogenetic study of Class Armophorea (Alveolata, Ciliophora) based on 18S-rDNA data

PubMed Central

da Silva Paiva, Thiago; do Nascimento Borges, Bárbara; da Silva-Neto, Inácio Domingos

2013-01-01

The 18S rDNA phylogeny of Class Armophorea, a group of anaerobic ciliates, is proposed based on an analysis of 44 sequences (out of 195) retrieved from the NCBI/GenBank database. Emphasis was placed on the use of two nucleotide alignment criteria that involved variation in the gap-opening and gap-extension parameters and the use of rRNA secondary structure to orientate multiple-alignment. A sensitivity analysis of 76 data sets was run to assess the effect of variations in indel parameters on tree topologies. Bayesian inference, maximum likelihood and maximum parsimony phylogenetic analyses were used to explore how different analytic frameworks influenced the resulting hypotheses. A sensitivity analysis revealed that the relationships among higher taxa of the Intramacronucleata were dependent upon how indels were determined during multiple-alignment of nucleotides. The phylogenetic analyses rejected the monophyly of the Armophorea most of the time and consistently indicated that the Metopidae and Nyctotheridae were related to the Litostomatea. There was no consensus on the placement of the Caenomorphidae, which could be a sister group of the Metopidae + Nyctorheridae, or could have diverged at the base of the Spirotrichea branch or the Intramacronucleata tree. PMID:24385862

Mirroring co-evolving trees in the light of their topologies.

PubMed

Hajirasouliha, Iman; Schönhuth, Alexander; de Juan, David; Valencia, Alfonso; Sahinalp, S Cenk

2012-05-01

Determining the interaction partners among protein/domain families poses hard computational problems, in particular in the presence of paralogous proteins. Available approaches aim to identify interaction partners among protein/domain families through maximizing the similarity between trimmed versions of their phylogenetic trees. Since maximization of any natural similarity score is computationally difficult, many approaches employ heuristics to evaluate the distance matrices corresponding to the tree topologies in question. In this article, we devise an efficient deterministic algorithm which directly maximizes the similarity between two leaf labeled trees with edge lengths, obtaining a score-optimal alignment of the two trees in question. Our algorithm is significantly faster than those methods based on distance matrix comparison: 1 min on a single processor versus 730 h on a supercomputer. Furthermore, we outperform the current state-of-the-art exhaustive search approach in terms of precision, while incurring acceptable losses in recall. A C implementation of the method demonstrated in this article is available at http://compbio.cs.sfu.ca/mirrort.htm

Self-assembly and electrostriction of arrays and chains of hopfion particles in chiral liquid crystals

PubMed Central

Ackerman, Paul J.; van de Lagemaat, Jao; Smalyukh, Ivan I.

2015-01-01

Some of the most exotic condensed matter phases, such as twist grain boundary and blue phases in liquid crystals and Abrikosov phases in superconductors, contain arrays of topological defects in their ground state. Comprised of a triangular lattice of double-twist tubes of magnetization, the so-called ‘A-phase’ in chiral magnets is an example of a thermodynamically stable phase with topologically nontrivial solitonic field configurations referred to as two-dimensional skyrmions, or baby-skyrmions. Here we report that three-dimensional skyrmions in the form of double-twist tori called ‘hopfions’, or ‘torons’ when accompanied by additional self-compensating defects, self-assemble into periodic arrays and linear chains that exhibit electrostriction. In confined chiral nematic liquid crystals, this self-assembly is similar to that of liquid crystal colloids and originates from long-range elastic interactions between particle-like skyrmionic torus knots of molecular alignment field, which can be tuned from isotropic repulsive to weakly or highly anisotropic attractive by low-voltage electric fields. PMID:25607778

Carrier and photon dynamics in a topological insulator Bi{sub 2}Te{sub 3}/GaN type II staggered heterostructure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chaturvedi, P.; Chouksey, S.; Banerjee, D.

2015-11-09

We have demonstrated a type-II band-aligned heterostructure between pulsed laser deposited topological insulator bismuth telluride and metal organic-chemical-vapour deposited GaN on a sapphire substrate. The heterostructure shows a large valence band-offset of 3.27 eV as determined from x-ray photoelectron spectroscopy, which is close to the bandgap of GaN (3.4 eV). Further investigation using x-ray diffraction, Raman spectroscopy, and energy-dispersive x-ray spectrum reveals the stoichiometric and material properties of bismuth telluride on GaN. Steady state photon emission from GaN is found to be modulated by the charge transfer process due to diffusion across the junction. The time constant involved with the charge transfermore » process is found to be 0.6 ns by transient absorption spectroscopy. The heterostructure can be used for designing devices with different functionalities and improving the performance of the existing devices on GaN.« less

Quantum transport in new two-dimensional heterostructures: Thin films of topological insulators, phosphorene

NASA Astrophysics Data System (ADS)

Majidi, Leyla; Zare, Moslem; Asgari, Reza

2018-06-01

The unusual features of the charge and spin transport characteristics are investigated in new two-dimensional heterostructures. Intraband specular Andreev reflection is realized in a topological insulator thin film normal/superconducting junction in the presence of a gate electric field. Perfect specular electron-hole conversion is shown for different excitation energy values in a wide experimentally available range of the electric field and also for all angles of incidence when the excitation energy has a particular value. It is further demonstrated that the transmission probabilities of the incoming electrons from different spin subbands to the monolayer phosphorene ferromagnetic/normal/ferromagnetic (F/N/F) hybrid structure have different behavior with the angle of incidence and perfect transmission occurs at defined angles of incidence to the proposed structure with different length of the N region, and different alignments of magnetization vectors. Moreover, the sign change of the spin-current density is demonstrated by tuning the chemical potential and exchange field of the F region.

Defects in Nematic Shells: A Γ-Convergence Discrete-to-Continuum Approach

NASA Astrophysics Data System (ADS)

Canevari, Giacomo; Segatti, Antonio

2018-07-01

In this paper we rigorously investigate the emergence of defects on Nematic Shells with a genus different from one. This phenomenon is related to a non-trivial interplay between the topology of the shell and the alignment of the director field. To this end, we consider a discrete XY system on the shell M, described by a tangent vector field with unit norm sitting at the vertices of a triangulation of the shell. Defects emerge when we let the mesh size of the triangulation go to zero, namely in the discrete-to-continuum limit. In this paper we investigate the discrete-to-continuum limit in terms of Γ-convergence in two different asymptotic regimes. The first scaling promotes the appearance of a finite number of defects whose charges are in accordance with the topology of shell M, via the Poincaré-Hopf Theorem. The second scaling produces the so called Renormalized Energy that governs the equilibrium of the configurations with defects.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ackerman, P. J.; van de Lagemaat, J.; Smalyukh, I. I.

Some of the most exotic condensed matter phases, such as twist grain boundary and blue phases in liquid crystals and Abrikosov phases in superconductors, contain arrays of topological defects in their ground state. Comprised of a triangular lattice of double-twist tubes of magnetization, the so-called ‘A-phase’ in chiral magnets is an example of a thermodynamically stable phase with topologically nontrivial solitonic field configurations referred to as two-dimensional skyrmions, or baby-skyrmions. Here we report that three-dimensional skyrmions in the form of double-twist tori called ‘hopfions’, or ‘torons’ when accompanied by additional self-compensating defects, self-assemble into periodic arrays and linear chains thatmore » exhibit electrostriction. In confined chiral nematic liquid crystals, this self-assembly is similar to that of liquid crystal colloids and originates from long-range elastic interactions between particle-like skyrmionic torus knots of molecular alignment field, which can be tuned from isotropic repulsive to weakly or highly anisotropic attractive by low-voltage electric fields.« less

Topological Transformation of Defects in Nematic Liquid Crystals

NASA Astrophysics Data System (ADS)

Pagel, Zachary; Atherton, Timothy; Guasto, Jeffrey; Cebe, Peggy

A topological transformation around silica microsphere inclusions in nematic liquid crystal cells (LCC) is experimentally studied. Silica microspheres are coated to induce homeotropic LC anchoring to the spheres. Parallel rub directions of the alignment polymer during LCC construction create a splay wall that traps the microspheres. Application of an out-of-plane electric field then permits a transformation of hedgehog defects, reversing the orientation of the defect around microspheres. The transformation controllably reverses the microsphere's direction of travel during AC electrophoresis due to defect-dependent velocity anisotropy. A similar transformation is studied on chains of microspheres with hedgehog defects, where the defect orientation is reversed on the entire chain. Polarized and confocal microscopies are used to study the defect structures. Results contribute to recent developments in microsphere electrokinetics in nematic LCs, as the transformation adds an additional degree of control in the electrophoretic motion of microspheres and chains of microspheres with dipolar defects. The author thanks NSF Grant DMR-1608126 for funding reseearch and Tufts University for funding travel.

3D Architecture of Trabecular Bone in the Pig Mandible and Femur: Inter-Trabecular Angle Distributions.

NASA Astrophysics Data System (ADS)

Ben-Zvi, Yehonatan; Reznikov, Natalie; Shahar, Ron; Weiner, Steve

2017-09-01

Cancellous bone is an intricate network of interconnected trabeculae, to which analysis of network topology can be applied. The inter-trabecular angle (ITA) analysis - an analysis of network topological parameters and regularity of network-forming nodes, was previously carried out on human proximal femora and showed that trabecular bone follows two main principles: sparsity of the network connectedness (prevalence of nodes with low connectivity in the network) and maximal space spanning (angular offset of connected elements is maximal for their number and approximates the values of geometrically symmetric shapes). These observations suggest that 3D organization of trabecular bone, irrespective of size and shape of individual elements, reflects a tradeoff between minimal metabolic cost of maintenance and maximal network stability under conditions of multidirectional loading. In this study we validate the ITA application using additional 3D structures (cork and 3D-printed metal lattices), analyze the ITA parameters in porcine proximal femora and mandibles and carry out a spatial analysis of the most common node type in the porcine mandibular condyle. The validation shows that the ITA application reliably detects designed or evolved topological parameters. The ITA parameters of porcine trabecular bones are similar to those of human bones. We demonstrate functional adaptation in the pig mandibular condyle by showing that the planar nodes with 3 edges are preferentially aligned in relation to the muscle forces that are applied to the condyle. We conclude that the ITA topological parameters are remarkable conserved, but locally do adapt to applied stresses.

Environmental constraints shaping constituent order in emerging communication systems: Structural iconicity, interactive alignment and conventionalization.

PubMed

Christensen, Peer; Fusaroli, Riccardo; Tylén, Kristian

2016-01-01

Where does linguistic structure come from? Recent gesture elicitation studies have indicated that constituent order (corresponding to for instance subject-verb-object, or SVO in English) may be heavily influenced by human cognitive biases constraining gesture production and transmission. Here we explore the alternative hypothesis that syntactic patterns are motivated by multiple environmental and social-interactional constraints that are external to the cognitive domain. In three experiments, we systematically investigate different motivations for structure in the gestural communication of simple transitive events. The first experiment indicates that, if participants communicate about different types of events, manipulation events (e.g. someone throwing a cake) and construction events (e.g. someone baking a cake), they spontaneously and systematically produce different constituent orders, SOV and SVO respectively, thus following the principle of structural iconicity. The second experiment shows that participants' choice of constituent order is also reliably influenced by social-interactional forces of interactive alignment, that is, the tendency to re-use an interlocutor's previous choice of constituent order, thus potentially overriding affordances for iconicity. Lastly, the third experiment finds that the relative frequency distribution of referent event types motivates the stabilization and conventionalization of a single constituent order for the communication of different types of events. Together, our results demonstrate that constituent order in emerging gestural communication systems is shaped and stabilized in response to multiple external environmental and social factors: structural iconicity, interactive alignment and distributional frequency. Copyright © 2015 Elsevier B.V. All rights reserved.

SWPhylo - A Novel Tool for Phylogenomic Inferences by Comparison of Oligonucleotide Patterns and Integration of Genome-Based and Gene-Based Phylogenetic Trees.

PubMed

Yu, Xiaoyu; Reva, Oleg N

2018-01-01

Modern phylogenetic studies may benefit from the analysis of complete genome sequences of various microorganisms. Evolutionary inferences based on genome-scale analysis are believed to be more accurate than the gene-based alternative. However, the computational complexity of current phylogenomic procedures, inappropriateness of standard phylogenetic tools to process genome-wide data, and lack of reliable substitution models which correlates with alignment-free phylogenomic approaches deter microbiologists from using these opportunities. For example, the super-matrix and super-tree approaches of phylogenomics use multiple integrated genomic loci or individual gene-based trees to infer an overall consensus tree. However, these approaches potentially multiply errors of gene annotation and sequence alignment not mentioning the computational complexity and laboriousness of the methods. In this article, we demonstrate that the annotation- and alignment-free comparison of genome-wide tetranucleotide frequencies, termed oligonucleotide usage patterns (OUPs), allowed a fast and reliable inference of phylogenetic trees. These were congruent to the corresponding whole genome super-matrix trees in terms of tree topology when compared with other known approaches including 16S ribosomal RNA and GyrA protein sequence comparison, complete genome-based MAUVE, and CVTree methods. A Web-based program to perform the alignment-free OUP-based phylogenomic inferences was implemented at http://swphylo.bi.up.ac.za/. Applicability of the tool was tested on different taxa from subspecies to intergeneric levels. Distinguishing between closely related taxonomic units may be enforced by providing the program with alignments of marker protein sequences, eg, GyrA.

SWPhylo – A Novel Tool for Phylogenomic Inferences by Comparison of Oligonucleotide Patterns and Integration of Genome-Based and Gene-Based Phylogenetic Trees

PubMed Central

Yu, Xiaoyu; Reva, Oleg N

2018-01-01

Modern phylogenetic studies may benefit from the analysis of complete genome sequences of various microorganisms. Evolutionary inferences based on genome-scale analysis are believed to be more accurate than the gene-based alternative. However, the computational complexity of current phylogenomic procedures, inappropriateness of standard phylogenetic tools to process genome-wide data, and lack of reliable substitution models which correlates with alignment-free phylogenomic approaches deter microbiologists from using these opportunities. For example, the super-matrix and super-tree approaches of phylogenomics use multiple integrated genomic loci or individual gene-based trees to infer an overall consensus tree. However, these approaches potentially multiply errors of gene annotation and sequence alignment not mentioning the computational complexity and laboriousness of the methods. In this article, we demonstrate that the annotation- and alignment-free comparison of genome-wide tetranucleotide frequencies, termed oligonucleotide usage patterns (OUPs), allowed a fast and reliable inference of phylogenetic trees. These were congruent to the corresponding whole genome super-matrix trees in terms of tree topology when compared with other known approaches including 16S ribosomal RNA and GyrA protein sequence comparison, complete genome-based MAUVE, and CVTree methods. A Web-based program to perform the alignment-free OUP-based phylogenomic inferences was implemented at http://swphylo.bi.up.ac.za/. Applicability of the tool was tested on different taxa from subspecies to intergeneric levels. Distinguishing between closely related taxonomic units may be enforced by providing the program with alignments of marker protein sequences, eg, GyrA. PMID:29511354

Host and Phenology Shifts in the Evolution of the Social Moth Genus Thaumetopoea

PubMed Central

Simonato, Mauro; Battisti, Andrea; Kerdelhué, Carole; Burban, Christian; Lopez-Vaamonde, Carlos; Pivotto, Isabelle; Salvato, Paola; Negrisolo, Enrico

2013-01-01

The genus Thaumetopoea contains the processionary moths, a group of lepidopteran associated with forest trees, well known for the social behaviour of the larvae and for carrying urticating setae. The taxonomy of the genus is partly unresolved and a phylogenetic approach is lacking. The goal of this work is to produce a phylogeny for Thaumetopoea and to identify the main traits driving the evolution of this group. Eighteen mitochondrial and three nuclear genes were fully/partly sequenced. Markers were aligned and analysed singularly or in various combinations. Phylogenetic analyses were performed according to maximum likelihood and Bayesian inference methods. Trees obtained from largest data sets provided identical topologies that received strong statistical support. Three main clades were identified within Thaumetopoea and were further supported by several signatures located in the mitochondrial tRNAs and intergenic spacers. The reference topology was used to investigate the evolution of life history traits related to biogeography, host plant, ecology, and morphology. A multigenic approach allowed to produce a robust phylogenetic analysis of the genus Thaumetopoea, with the identification of three major clades linked to different ecological and life history traits. The first clade is associated with Angiosperm host plants and has a fast spring development of larvae on young foliage. The other clades have originated by one event of host plant shift to Gymnosperm Pinaceae, which implied a longer larval developmental time due to the lower nutritional quality of leaves. These clades showed different adaptations to such a constraint, the first with a switch of larval feeding to cold season (winter pine processionary moths), and the second with a retraction to high altitude and latitude and a development cycle extended over two years (summer pine processionary moths). Recent global warming is affecting all species and seems able to further shape the evolution of the group. PMID:23460830

Early Verb Learning: How Do Children Learn How to Compare Events?

ERIC Educational Resources Information Center

Childers, Jane B.; Parrish, Rebecca; Olson, Christina V.; Burch, Clare; Fung, Gavin; McIntyre, Kevin P.

2016-01-01

An important problem verb learners must solve is how to extend verbs. Children could use cross-situational information to guide their extensions; however, comparing events is difficult. In 2 studies, researchers tested whether children benefit from initially seeing a pair of similar events ("progressive alignment") while learning new…

Optimization of cw-QC lasers for Doppler and sub-Doppler molecular spectroscopy

NASA Astrophysics Data System (ADS)

Kelly, James F.; Disselkamp, Robert S.; Sams, Robert L.; Blake, Thomas A.; Sharpe, Steven W.; Richter, Dirk A.; Fried, Alan

2002-09-01

Inter-subband (Type I) quantum-cascade (QC) lasers have shown the potential to generate tunable mid-IR radiation with narrow intrinsic linewidths (< 160 KHz in 15 mSec sweeps) and excellent amplitude stability (< 3 ppm averaged over minutes). Our bench-scale efforts to develop the Type I distributed feedback (DFB)-QC lasers for fieldable atmospheric chemistry campaigns, where multipass (Herriot or White) cells are used to enhance path-length, have not yet realized performance to the low intrinsic noise levels seen in these devices. By comparison, many operational systems' levels of noise-equivalent-absorbance (NEA) using Pb-salt lasers can routinely achieve at least one-order of magnitude better cw-performance, and with much lower powers. We have found that instability effets from weak back-scattered laser light -primarily from the Herriot cell- results in feedback-implicated technical noise well above the thermal and shot-noise of standard IR detectors. Of more fundamental concern is the fact that planar-stripe DFB-QC lasers undergo beam steering and transverse spatial-mode competitions during current tuning. It is the development of fully automated sub-ppbV sensitive IR chem-sensors. It is possible to reach low-ppm levels of absorptance change-detection (ΔI/I0) over small wavelength regions with careful alignment to 100 M Herriott cells, but extreme care in spatial filtering is critical. However in the case of optical configurations which preclude significant optical feedback and need for stringent mode coupling alignments, the cw-DFB-QC lasers show great promise to do high resolution sub-Doppler spectroscopy. By serendipitous events, a varient of 'mode- or level-crossing' spectroscopy was probably rediscovered, which may allow very high resolution, sub-Doppler features and/or hyperfine alignments to be probed with 'uni-directional' topologies. We will primarily discuss the basic features of the 'uni-directional' sub-Doppler spectroscopy concept in this report. It shows potential to be exploitable in multi-pass cells or ring configurations. The phenomena of satuation 'dips' in molecular transitions appear to be very accessible with sinusoidally current-modulated DFB-QC lasers. Observations of sub-Doppler structures, either induced by residual AM 'pulsation dips' and/or hyperfine level-crossing effects (due to weak Zeeman splittings by the earth's B-field) can be recovered with good contrast. If this phenomena is indeed implicated with long-lived coherent hyperfine alignments, due perhaps to coherent population trapping in 'dark-states,' then sub-Doppler signals from saturated 'level-crossings' can potentially be seen without recourse to expensive polarization optics, nor elaborate beam shaping and isolation techniques.

Bi-directional streaming of halo electrons in interplanetary plasma clouds observed between 0.3 and 1 AU

NASA Technical Reports Server (NTRS)

Ivory, K.; Schwenn, R.

1995-01-01

The solar wind data obtained from the two Helios solar probes in the years 1974 to 1986 were systematically searched for the occurrence of bi-directional electron events. Most often these events are found in conjunction with shock associated magnetic clouds. The implications of these observations for the topology of interplanetary plasma clouds are discussed.

Flow field topology of transient mixing driven by buoyancy

NASA Technical Reports Server (NTRS)

Duval, Walter M B.

2004-01-01

Transient mixing driven by buoyancy occurs through the birth of a symmetric Rayleigh-Taylor morphology (RTM) structure for large length scales. Beyond its critical bifurcation the RTM structure exhibits self-similarity and occurs on smaller and smaller length scales. The dynamics of the RTM structure, its nonlinear growth and internal collision, show that its genesis occurs from an explosive bifurcation which leads to the overlap of resonance regions in phase space. This event shows the coexistence of regular and chaotic regions in phase space which is corroborated with the existence of horseshoe maps. A measure of local chaos given by the topological entropy indicates that as the system evolves there is growth of uncertainty. Breakdown of the dissipative RTM structure occurs during the transition from explosive to catastrophic bifurcation; this event gives rise to annihilation of the separatrices which drives overlap of resonance regions. The global bifurcation of explosive and catastrophic events in phase space for the large length scale of the RTM structure serves as a template for which mixing occurs on smaller and smaller length scales. Copyright 2004 American Institute of Physics.

Study on field-aligned electrons with Cluster observation in the Earth's cusp

NASA Astrophysics Data System (ADS)

Shi, Jiankui; Torkar, Klaus; Cheng, Zhengwei

2017-04-01

Cusp region is very important to the solar wind-magnetosphere coupling. The solar wind particles, through the cusp, can directly entry into the magnetosphere and ionosphere, and transport the mass, momentum and energy. The gyrating charged particles with field-aligned velocity are significant to perform the transportation. In this study, data from Cluster observation are used to study the characteristics of field-aligned electrons (FAE's) including the downward and the upward FAEs in the cusp. We select FAE event to do analysis. The durations of the FAE event covered a wide range from 6 to 475 seconds. The FAE's were found to occur very commonly in a circumpolar zone in the polar region and the MLT and ILAT distributions showed that most of the FAE events were observed around the cusp (70-80°ILAT, 0900-1500MLT). With the FAE flux the contribution of the electrons to the Field-Aligned Current (FAC) is estimated and the result shows that the FAE was the main carrier to the FAC in the cusp. The physical mechanisms of the FAE are analyzed, namely that the downward electrons were mainly from the solar wind and the upward electrons may originated from accelerated ionospheric up-flowing electrons or mirrored solar wind electrons. The energy transportation into the magnetosphere by the solar wind electrons through the cusp is also investigated.

Galaxy Alignments: Theory, Modelling & Simulations

NASA Astrophysics Data System (ADS)

Kiessling, Alina; Cacciato, Marcello; Joachimi, Benjamin; Kirk, Donnacha; Kitching, Thomas D.; Leonard, Adrienne; Mandelbaum, Rachel; Schäfer, Björn Malte; Sifón, Cristóbal; Brown, Michael L.; Rassat, Anais

2015-11-01

The shapes of galaxies are not randomly oriented on the sky. During the galaxy formation and evolution process, environment has a strong influence, as tidal gravitational fields in the large-scale structure tend to align nearby galaxies. Additionally, events such as galaxy mergers affect the relative alignments of both the shapes and angular momenta of galaxies throughout their history. These "intrinsic galaxy alignments" are known to exist, but are still poorly understood. This review will offer a pedagogical introduction to the current theories that describe intrinsic galaxy alignments, including the apparent difference in intrinsic alignment between early- and late-type galaxies and the latest efforts to model them analytically. It will then describe the ongoing efforts to simulate intrinsic alignments using both N-body and hydrodynamic simulations. Due to the relative youth of this field, there is still much to be done to understand intrinsic galaxy alignments and this review summarises the current state of the field, providing a solid basis for future work.

A software bus for thread objects

NASA Technical Reports Server (NTRS)

Callahan, John R.; Li, Dehuai

1995-01-01

The authors have implemented a software bus for lightweight threads in an object-oriented programming environment that allows for rapid reconfiguration and reuse of thread objects in discrete-event simulation experiments. While previous research in object-oriented, parallel programming environments has focused on direct communication between threads, our lightweight software bus, called the MiniBus, provides a means to isolate threads from their contexts of execution by restricting communications between threads to message-passing via their local ports only. The software bus maintains a topology of connections between these ports. It routes, queues, and delivers messages according to this topology. This approach allows for rapid reconfiguration and reuse of thread objects in other systems without making changes to the specifications or source code. A layered approach that provides the needed transparency to developers is presented. Examples of using the MiniBus are given, and the value of bus architectures in building and conducting simulations of discrete-event systems is discussed.

A Goal Bias in Action: The Boundaries Adults Perceive in Events Align with Sites of Actor Intent

ERIC Educational Resources Information Center

Levine, Dani; Hirsh-Pasek, Kathy; Pace, Amy; Michnick Golinkoff, Roberta

2017-01-01

We live in a dynamic world comprised of continuous events. Remembering our past and predicting future events, however, requires that we segment these ongoing streams of information in a consistent manner. How is this segmentation achieved? This research examines whether the boundaries adults perceive in events, such as the Olympic figure skating…

Aligning observed and modelled behaviour based on workflow decomposition

NASA Astrophysics Data System (ADS)

Wang, Lu; Du, YuYue; Liu, Wei

2017-09-01

When business processes are mostly supported by information systems, the availability of event logs generated from these systems, as well as the requirement of appropriate process models are increasing. Business processes can be discovered, monitored and enhanced by extracting process-related information. However, some events cannot be correctly identified because of the explosion of the amount of event logs. Therefore, a new process mining technique is proposed based on a workflow decomposition method in this paper. Petri nets (PNs) are used to describe business processes, and then conformance checking of event logs and process models is investigated. A decomposition approach is proposed to divide large process models and event logs into several separate parts that can be analysed independently; while an alignment approach based on a state equation method in PN theory enhances the performance of conformance checking. Both approaches are implemented in programmable read-only memory (ProM). The correctness and effectiveness of the proposed methods are illustrated through experiments.

Novel Real-time Alignment and Calibration of the LHCb detector in Run2

NASA Astrophysics Data System (ADS)

Martinelli, Maurizio; LHCb Collaboration

2017-10-01

LHCb has introduced a novel real-time detector alignment and calibration strategy for LHC Run2. Data collected at the start of the fill are processed in a few minutes and used to update the alignment parameters, while the calibration constants are evaluated for each run. This procedure improves the quality of the online reconstruction. For example, the vertex locator is retracted and reinserted for stable beam conditions in each fill to be centred on the primary vertex position in the transverse plane. Consequently its position changes on a fill-by-fill basis. Critically, this new real-time alignment and calibration procedure allows identical constants to be used in the online and offline reconstruction, thus improving the correlation between triggered and offline-selected events. This offers the opportunity to optimise the event selection in the trigger by applying stronger constraints. The required computing time constraints are met thanks to a new dedicated framework using the multi-core farm infrastructure for the trigger. The motivation for a real-time alignment and calibration of the LHCb detector is discussed from both the operational and physics performance points of view. Specific challenges of this novel configuration are discussed, as well as the working procedures of the framework and its performance.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ding, Fei; Jiang, Huaiguang; Tan, Jin

This paper proposes an event-driven approach for reconfiguring distribution systems automatically. Specifically, an optimal synchrophasor sensor placement (OSSP) is used to reduce the number of synchrophasor sensors while keeping the whole system observable. Then, a wavelet-based event detection and location approach is used to detect and locate the event, which performs as a trigger for network reconfiguration. With the detected information, the system is then reconfigured using the hierarchical decentralized approach to seek for the new optimal topology. In this manner, whenever an event happens the distribution network can be reconfigured automatically based on the real-time information that is observablemore » and detectable.« less

Location of long-period events below Kilauea Volcano using seismic amplitudes and accurate relative relocation

USGS Publications Warehouse

Battaglia, J.; Got, J.-L.; Okubo, P.

2003-01-01

We present methods for improving the location of long-period (LP) events, deep and shallow, recorded below Kilauea Volcano by the permanent seismic network. LP events might be of particular interest to understanding eruptive processes as their source mechanism is assumed to directly involve fluid transport. However, it is usually difficult or impossible to locate their source using traditional arrival time methods because of emergent wave arrivals. At Kilauea, similar LP waveform signatures suggest the existence of LP multiplets. The waveform similarity suggests spatially close sources, while catalog solutions using arrival time estimates are widely scattered beneath Kilauea's summit caldera. In order to improve estimates of absolute LP location, we use the distribution of seismic amplitudes corrected for station site effects. The decay of the amplitude as a function of hypocentral distance is used for inferring LP location. In a second stage, we use the similarity of the events to calculate their relative positions. The analysis of the entire LP seismicity recorded between January 1997 and December 1999 suggests that a very large part of the LP event population, both deep and shallow, is generated by a small number of compact sources. Deep events are systematically composed of a weak high-frequency onset followed by a low-frequency wave train. Aligning the low-frequency wave trains does not lead to aligning the onsets indicating the two parts of the signal are dissociated. This observation favors an interpretation in terms of triggering and resonance of a magmatic conduit. Instead of defining fault planes, the precise relocation of similar LP events, based on the alignment of the high-energy low-frequency wave trains, defines limited size volumes. Copyright 2003 by the American Geophysical Union.

Efficient Exploration of the Space of Reconciled Gene Trees

PubMed Central

Szöllősi, Gergely J.; Rosikiewicz, Wojciech; Boussau, Bastien; Tannier, Eric; Daubin, Vincent

2013-01-01

Gene trees record the combination of gene-level events, such as duplication, transfer and loss (DTL), and species-level events, such as speciation and extinction. Gene tree–species tree reconciliation methods model these processes by drawing gene trees into the species tree using a series of gene and species-level events. The reconstruction of gene trees based on sequence alone almost always involves choosing between statistically equivalent or weakly distinguishable relationships that could be much better resolved based on a putative species tree. To exploit this potential for accurate reconstruction of gene trees, the space of reconciled gene trees must be explored according to a joint model of sequence evolution and gene tree–species tree reconciliation. Here we present amalgamated likelihood estimation (ALE), a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. We implement the ALE approach in the context of a reconciliation model (Szöllősi et al. 2013), which allows for the DTL of genes. We use ALE to efficiently approximate the sum of the joint likelihood over amalgamations and to find the reconciled gene tree that maximizes the joint likelihood among all such trees. We demonstrate using simulations that gene trees reconstructed using the joint likelihood are substantially more accurate than those reconstructed using sequence alone. Using realistic gene tree topologies, branch lengths, and alignment sizes, we demonstrate that ALE produces more accurate gene trees even if the model of sequence evolution is greatly simplified. Finally, examining 1099 gene families from 36 cyanobacterial genomes we find that joint likelihood-based inference results in a striking reduction in apparent phylogenetic discord, with respectively. 24%, 59%, and 46% reductions in the mean numbers of duplications, transfers, and losses per gene family. The open source implementation of ALE is available from https://github.com/ssolo/ALE.git. [amalgamation; gene tree reconciliation; gene tree reconstruction; lateral gene transfer; phylogeny.] PMID:23925510

A novel transition pathway of ligand-induced topological conversion from hybrid forms to parallel forms of human telomeric G-quadruplexes

PubMed Central

Wang, Zi-Fu; Li, Ming-Hao; Chen, Wei-Wen; Hsu, Shang-Te Danny; Chang, Ta-Chau

2016-01-01

The folding topology of DNA G-quadruplexes (G4s) depends not only on their nucleotide sequences but also on environmental factors and/or ligand binding. Here, a G4 ligand, 3,6-bis(1-methyl-4-vinylpyridium iodide)-9-(1-(1-methyl-piperidinium iodide)-3,6,9-trioxaundecane) carbazole (BMVC-8C3O), can induce topological conversion of non-parallel to parallel forms in human telomeric DNA G4s. Nuclear magnetic resonance (NMR) spectroscopy with hydrogen-deuterium exchange (HDX) reveals the presence of persistent imino proton signals corresponding to the central G-quartet during topological conversion of Tel23 and Tel25 G4s from hybrid to parallel forms, implying that the transition pathway mainly involves local rearrangements. In contrast, rapid HDX was observed during the transition of 22-CTA G4 from an anti-parallel form to a parallel form, resulting in complete disappearance of all the imino proton signals, suggesting the involvement of substantial unfolding events associated with the topological transition. Site-specific imino proton NMR assignments of Tel23 G4 enable determination of the interconversion rates of individual guanine bases and detection of the presence of intermediate states. Since the rate of ligand binding is much higher than the rate of ligand-induced topological conversion, a three-state kinetic model was evoked to establish the associated energy diagram for the topological conversion of Tel23 G4 induced by BMVC-8C3O. PMID:26975658

Hot spine loops and the nature of a late-phase solar flare

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, Xudong; Todd Hoeksema, J.; Liu, Yang

2013-12-01

The fan-spine magnetic topology is believed to be responsible for many curious features in solar explosive events. A spine field line links distinct flux domains, but direct observation of such a feature has been rare. Here we report a unique event observed by the Solar Dynamic Observatory where a set of hot coronal loops (over 10 MK) connected to a quasi-circular chromospheric ribbon at one end and a remote brightening at the other. Magnetic field extrapolation suggests that these loops are partly tracers of the evolving spine field line. Continuous slipping- and null-point-type reconnections were likely at work, energizing themore » loop plasma and transferring magnetic flux within and across the fan quasi-separatrix layer. We argue that the initial reconnection is of the 'breakout' type, which then transitioned to a more violent flare reconnection with an eruption from the fan dome. Significant magnetic field changes are expected and indeed ensued. This event also features an extreme-ultraviolet (EUV) late phase, i.e., a delayed secondary emission peak in warm EUV lines (about 2-7 MK). We show that this peak comes from the cooling of large post-reconnection loops beside and above the compact fan, a direct product of eruption in such topological settings. The long cooling time of the large arcades contributes to the long delay; additional heating may also be required. Our result demonstrates the critical nature of cross-scale magnetic coupling—topological change in a sub-system may lead to explosions on a much larger scale.« less

RF current distribution and topology of RF sheath potentials in front of ICRF antennae

NASA Astrophysics Data System (ADS)

Colas, L.; Heuraux, S.; Brémond, S.; Bosia, G.

2005-08-01

The 2D (radial/poloidal) spatial topology of RF-induced convective cells developing radially in front of ion cyclotron range of frequency (ICRF) antennae is investigated, in relation to the spatial distribution of RF currents over the metallic structure of the antenna. This is done via a Green's function, determined from the ICRF wave coupling equations, and well-suited to open field lines extending toroidally far away on both sides of the antenna. Using such formalism, combined with a full-wave calculation using the 3D antenna code ICANT (Pécoul S. et al 2000 Comput. Phys. Commun. 146 166-87), two classes of convective cells are analysed. The first one appears in front of phased arrays of straps, and depending on the strap phasing, its topology is interpreted using the poloidal profiles of either the RF current or the RF voltage of the strip line theory. The other class of convective cells is specific to antenna box corners and is evidenced for the first time. Based on such analysis, general design rules are worked out in order to reduce the RF-sheath potentials, which generalize those proposed in the earlier literature, and concrete antenna design options are tested numerically. The merits of aligning all strap centres on the same (tilted) flux tube, and of reducing the antenna box toroidal conductivity in its lower and upper parts, are discussed.

Tunable system for production of mirror and cusp configurations using chassis of permanent magnets

NASA Astrophysics Data System (ADS)

Hyde, Alexander; Bushmelov, Maxim; Batishchev, Oleg

2018-03-01

Compact arrays of permanent magnets have shown promise as replacements for electromagnets in applications requiring magnetic cusps and mirrors. An adjustable system capable of suspending and translating a pair of light, nonmagnetic chassis carrying such sources of magnetic field has been designed and constructed. Using this device to align two cylindrical chassis, strong solenoid-like domains of field, as well as classic biconic cusp and magnetic mirror topologies, are generated. Employing a pair of ring-shaped chassis instead, the superposition of their naturally-emitted cusps is demonstrated to produce sextupolar and octupolar magnetic fields.

Claustrum of the short-tailed fruit bat, Carollia perspicillata: Alignment of cellular orientation and functional connectivity.

PubMed

Orman, Rena; Kollmar, Richard; Stewart, Mark

2017-04-15

The claustrum is a gray-matter structure that underlies neocortex and reciprocates connections with cortical and subcortical targets. In lower mammals, the claustrum is directly adjacent to neocortex, making the definition of claustral boundaries challenging. Latexin, an endogenous inhibitor of metallocarboxypeptidases, localizes to claustral cells, enabling a clear delineation of claustrum. Given its proportionately large claustrum, we hypothesized that the short-tailed fruit bat, Carollia perspicillata, can be a useful model for claustral structure-function relations. We used latexin immunohistochemistry to identify claustral boundaries and intrinsic structure and multielectrode recordings from brain slices to explore intrinsic excitatory connectivity of the claustrum. Carollia's claustrum contains cells whose intrinsic connectivity and alignment permit the generation of spontaneous, synchronous population events and mirror their pattern of spread in disinhibited brain slices over millimeters. Carollia shows cellular alignment and spontaneous population-activity spread along both horizontal and dorsoventral axes. Carollia claustrum possesses intrinsic excitatory connectivity sufficient to: 1) generate single, spontaneous, synchronized burst discharges, 2) support activity spread along axes where claustral cells are aligned, and 3), because of multiple axes for cell alignment, support activity spread along both rostrocaudal and dorsoventral axes. The smaller event sizes in bat claustrum compared with rat claustrum are consistent with events occurring in population subsets rather than the full claustral cell population. The overall size of claustrum, its pronounced vascularity, and its more complex intrinsic connectivity than rat suggest that the bat is an animal model for claustral structure and function that will permit unique access to claustrum's processing capabilities. J. Comp. Neurol. 525:1459-1474, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Phylogenetics of Pinus (Pinaceae) based on nuclear ribosomal DNA internal transcribed spacer region sequences.

PubMed

Liston, A; Robinson, W A; Piñero, D; Alvarez-Buylla, E R

1999-02-01

A 650-bp portion of the nuclear ribosomal DNA internal transcribed spacer region was sequenced in 47 species of Pinus, representing all recognized subsections of the genus, and 2 species of Picea and Cathaya as outgroups. Parsimony analyses of these length variable sequences were conducted using a manual alignment, 13 different automated alignments, elision of the automated alignments, and exclusion of all alignment ambiguous sites. High and moderately supported clades were consistently resolved across the different analyses, while poorly supported clades were inconsistently recovered. Comparison of the topologies highlights taxa of particularly problematic placement including Pinus nelsonii and P. aristata. Within subgenus Pinus, there is moderate support for the monophyly of a narrowly circumscribed subsect. Pinus (=subsect. Sylvestres) and strong support for a clade of North and Central American hard pines. The Himalayan P. roxburghii may be sister species to these "New World hard pines," which have two well-supported subgroups, subsect. Ponderosae and a clade of the remaining five subsections. The position of subsect. Contortae conflicts with its placement in a chloroplast DNA restriction site study. Within subgenus Strobus there is consistent support for the monophyly of a broadly circumscribed subsect. Strobi (including P. krempfii and a polyphyletic subsect. Cembrae) derived from a paraphyletic grade of the remaining soft pines. Relationships among subsects. Gerardianae, Cembroides, and Balfourianae are poorly resolved. Support for the monophyly of subgenus Pinus and subgenus Strobus is not consistently obtained. Copyright 1999 Academic Press.

Multidimensional oriented solid-state NMR experiments enable the sequential assignment of uniformly 15N labeled integral membrane proteins in magnetically aligned lipid bilayers.

PubMed

Mote, Kaustubh R; Gopinath, T; Traaseth, Nathaniel J; Kitchen, Jason; Gor'kov, Peter L; Brey, William W; Veglia, Gianluigi

2011-11-01

Oriented solid-state NMR is the most direct methodology to obtain the orientation of membrane proteins with respect to the lipid bilayer. The method consists of measuring (1)H-(15)N dipolar couplings (DC) and (15)N anisotropic chemical shifts (CSA) for membrane proteins that are uniformly aligned with respect to the membrane bilayer. A significant advantage of this approach is that tilt and azimuthal (rotational) angles of the protein domains can be directly derived from analytical expression of DC and CSA values, or, alternatively, obtained by refining protein structures using these values as harmonic restraints in simulated annealing calculations. The Achilles' heel of this approach is the lack of suitable experiments for sequential assignment of the amide resonances. In this Article, we present a new pulse sequence that integrates proton driven spin diffusion (PDSD) with sensitivity-enhanced PISEMA in a 3D experiment ([(1)H,(15)N]-SE-PISEMA-PDSD). The incorporation of 2D (15)N/(15)N spin diffusion experiments into this new 3D experiment leads to the complete and unambiguous assignment of the (15)N resonances. The feasibility of this approach is demonstrated for the membrane protein sarcolipin reconstituted in magnetically aligned lipid bicelles. Taken with low electric field probe technology, this approach will propel the determination of sequential assignment as well as structure and topology of larger integral membrane proteins in aligned lipid bilayers. © Springer Science+Business Media B.V. 2011

Investigation of the Large Scale Evolution and Topology of Coronal Mass Ejections in the Solar Wind

NASA Technical Reports Server (NTRS)

Riley, Peter

1999-01-01

This investigation is concerned with the large-scale evolution and topology of Coronal Mass Ejections (CMEs) in the solar wind. During this reporting period we have analyzed a series of low density intervals in the ACE (Advanced Composition Explorer) plasma data set that bear many similarities to CMEs. We have begun a series of 3D, MHD (Magnetohydrodynamics) coronal models to probe potential causes of these events. We also edited two manuscripts concerning the properties of CMEs in the solar wind. One was re-submitted to the Journal of Geophysical Research.

Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L. (Pinaceae)

PubMed Central

2012-01-01

Background Through next-generation sequencing, the amount of sequence data potentially available for phylogenetic analyses has increased exponentially in recent years. Simultaneously, the risk of incorporating ‘noisy’ data with misleading phylogenetic signal has also increased, and may disproportionately influence the topology of weakly supported nodes and lineages featuring rapid radiations and/or elevated rates of evolution. Results We investigated the influence of phylogenetic noise in large data sets by applying two fundamental strategies, variable site removal and long-branch exclusion, to the phylogenetic analysis of a full plastome alignment of 107 species of Pinus and six Pinaceae outgroups. While high overall phylogenetic resolution resulted from inclusion of all data, three historically recalcitrant nodes remained conflicted with previous analyses. Close investigation of these nodes revealed dramatically different responses to data removal. Whereas topological resolution and bootstrap support for two clades peaked with removal of highly variable sites, the third clade resolved most strongly when all sites were included. Similar trends were observed using long-branch exclusion, but patterns were neither as strong nor as clear. When compared to previous phylogenetic analyses of nuclear loci and morphological data, the most highly supported topologies seen in Pinus plastome analysis are congruent for the two clades gaining support from variable site removal and long-branch exclusion, but in conflict for the clade with highest support from the full data set. Conclusions These results suggest that removal of misleading signal in phylogenomic datasets can result not only in increased resolution for poorly supported nodes, but may serve as a tool for identifying erroneous yet highly supported topologies. For Pinus chloroplast genomes, removal of variable sites appears to be more effective than long-branch exclusion for clarifying phylogenetic hypotheses. PMID:22731878

A High-resolution Model of Field-aligned Currents Through Empirical Orthogonal Functions Analysis (MFACE)

NASA Technical Reports Server (NTRS)

He, Maosheng; Vogt, Joachim; Luehr, Hermann; Sorbalo, Eugen; Blagau, Adrian; Le, Guan; Lu, Gang

2012-01-01

Ten years of CHAMP magnetic field measurements are integrated into MFACE, a model of field-aligned currents (FACs) using empirical orthogonal functions (EOFs). EOF1 gives the basic Region-1/Region-2 pattern varying mainly with the interplanetary magnetic field Bz component. EOF2 captures separately the cusp current signature and By-related variability. Compared to existing models, MFACE yields significantly better spatial resolution, reproduces typically observed FAC thickness and intensity, improves on the magnetic local time (MLT) distribution, and gives the seasonal dependence of FAC latitudes and the NBZ current signature. MFACE further reveals systematic dependences on By, including 1) Region-1/Region-2 topology modifications around noon; 2) imbalance between upward and downward maximum current density; 3) MLT location of the Harang discontinuity. Furthermore, our procedure allows quantifying response times of FACs to solar wind driving at the bow shock nose: we obtain 20 minutes and 35-40 minutes lags for the FAC density and latitude, respectively.

Recombination Proteins Mediate Meiotic Spatial Chromosome Organization and Pairing

PubMed Central

Storlazzi, Aurora; Gargano, Silvana; Ruprich-Robert, Gwenael; Falque, Matthieu; David, Michelle; Kleckner, Nancy; Zickler, Denise

2010-01-01

SUMMARY Meiotic chromosome pairing involves not only recognition of homology but also juxtaposition of entire chromosomes in a topologically regular way. Analysis of filamentous fungus Sordaria macrospora reveals that recombination proteins Mer3, Msh4 and Mlh1 play direct roles in all of these aspects, in advance of their known roles in recombination. Absence of Mer3 helicase results in interwoven chromosomes, thereby revealing the existence of features that specifically ensure “entanglement avoidance”. Entanglements that remain at zygotene, i.e. “interlockings”, require Mlh1 for resolution, likely to eliminate constraining recombinational connections. Patterns of Mer3 and Msh4 foci along aligned chromosomes show that the double-strand breaks mediating homologous alignment have spatially separated ends, one localized to each partner axis, and that pairing involves interference among developing interhomolog interactions. We propose that Mer3, Msh4 and Mlh1 execute all of these roles during pairing by modulating the state of nascent double-strand break/partner DNA contacts within axis-associated recombination complexes. PMID:20371348

Wet etch methods for InAs nanowire patterning and self-aligned electrical contacts

NASA Astrophysics Data System (ADS)

Fülöp, G.; d'Hollosy, S.; Hofstetter, L.; Baumgartner, A.; Nygård, J.; Schönenberger, C.; Csonka, S.

2016-05-01

Advanced synthesis of semiconductor nanowires (NWs) enables their application in diverse fields, notably in chemical and electrical sensing, photovoltaics, or quantum electronic devices. In particular, indium arsenide (InAs) NWs are an ideal platform for quantum devices, e.g. they may host topological Majorana states. While the synthesis has been continously perfected, only a few techniques have been developed to tailor individual NWs after growth. Here we present three wet chemical etch methods for the post-growth morphological engineering of InAs NWs on the sub-100 nm scale. The first two methods allow the formation of self-aligned electrical contacts to etched NWs, while the third method results in conical shaped NW profiles ideal for creating smooth electrical potential gradients and shallow barriers. Low temperature experiments show that NWs with etched segments have stable transport characteristics and can serve as building blocks of quantum electronic devices. As an example we report the formation of a single electrically stable quantum dot between two etched NW segments.

Power law tails in phylogenetic systems.

PubMed

Qin, Chongli; Colwell, Lucy J

2018-01-23

Covariance analysis of protein sequence alignments uses coevolving pairs of sequence positions to predict features of protein structure and function. However, current methods ignore the phylogenetic relationships between sequences, potentially corrupting the identification of covarying positions. Here, we use random matrix theory to demonstrate the existence of a power law tail that distinguishes the spectrum of covariance caused by phylogeny from that caused by structural interactions. The power law is essentially independent of the phylogenetic tree topology, depending on just two parameters-the sequence length and the average branch length. We demonstrate that these power law tails are ubiquitous in the large protein sequence alignments used to predict contacts in 3D structure, as predicted by our theory. This suggests that to decouple phylogenetic effects from the interactions between sequence distal sites that control biological function, it is necessary to remove or down-weight the eigenvectors of the covariance matrix with largest eigenvalues. We confirm that truncating these eigenvectors improves contact prediction.

Beam based alignment and its relevance in Indus-2.

PubMed

Jena, Saroj Kumar; Husain, Riyasat; Gandhi, M L; Agrawal, R K; Yadav, S; Ghodke, A D

2015-09-01

Initially in the Indus-2 storage ring, the closed orbit distortion (COD) could be best corrected to 1.3 mm rms in the horizontal and 0.43 mm rms in the vertical plane. The strength of the corrector magnets required high values for COD correction. This revealed that offsets in COD readout by the beam position monitors (BPMs) played a role in not achieving a rms COD lower than the above value. Thus, the offset between the electrical center of BPMs and the magnetic center of the nearest quadrupole magnet could be estimated using the beam based alignment (BBA) method. It prefers that the quadrupole magnet is able to be controlled individually and active shunt power supply (ASPS) system was designed for this purpose that works efficiently. This paper describes the methodology of BBA, topology of ASPS and its performance, and COD minimization using the measured BPM offsets. After BBA, the COD could be reduced to 0.45 mm rms and 0.2 mm rms in horizontal and vertical planes, respectively.

Beam based alignment and its relevance in Indus-2

NASA Astrophysics Data System (ADS)

Jena, Saroj Kumar; Husain, Riyasat; Gandhi, M. L.; Agrawal, R. K.; Yadav, S.; Ghodke, A. D.

2015-09-01

Initially in the Indus-2 storage ring, the closed orbit distortion (COD) could be best corrected to 1.3 mm rms in the horizontal and 0.43 mm rms in the vertical plane. The strength of the corrector magnets required high values for COD correction. This revealed that offsets in COD readout by the beam position monitors (BPMs) played a role in not achieving a rms COD lower than the above value. Thus, the offset between the electrical center of BPMs and the magnetic center of the nearest quadrupole magnet could be estimated using the beam based alignment (BBA) method. It prefers that the quadrupole magnet is able to be controlled individually and active shunt power supply (ASPS) system was designed for this purpose that works efficiently. This paper describes the methodology of BBA, topology of ASPS and its performance, and COD minimization using the measured BPM offsets. After BBA, the COD could be reduced to 0.45 mm rms and 0.2 mm rms in horizontal and vertical planes, respectively.

76 FR 43267 - Takes of Marine Mammals Incidental to Specified Activities; Taking Marine Mammals Incidental To...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-20

... optical and electronic sensors are also employed for target clearance. If any marine mammals are detected... events: (1) 30 min for take-off and to perform airborne sensor alignment, align electro- optical sensors... viewing window. The AC-130's optical and electronic sensors will also be employed for target clearance. If...

An alternative view of protein fold space.

PubMed

Shindyalov, I N; Bourne, P E

2000-02-15

Comparing and subsequently classifying protein structures information has received significant attention concurrent with the increase in the number of experimentally derived 3-dimensional structures. Classification schemes have focused on biological function found within protein domains and on structure classification based on topology. Here an alternative view is presented that groups substructures. Substructures are long (50-150 residue) highly repetitive near-contiguous pieces of polypeptide chain that occur frequently in a set of proteins from the PDB defined as structurally non-redundant over the complete polypeptide chain. The substructure classification is based on a previously reported Combinatorial Extension (CE) algorithm that provides a significantly different set of structure alignments than those previously described, having, for example, only a 40% overlap with FSSP. Qualitatively the algorithm provides longer contiguous aligned segments at the price of a slightly higher root-mean-square deviation (rmsd). Clustering these alignments gives a discreet and highly repetitive set of substructures not detectable by sequence similarity alone. In some cases different substructures represent all or different parts of well known folds indicative of the Russian doll effect--the continuity of protein fold space. In other cases they fall into different structure and functional classifications. It is too early to determine whether these newly classified substructures represent new insights into the evolution of a structural framework important to many proteins. What is apparent from on-going work is that these substructures have the potential to be useful probes in finding remote sequence homology and in structure prediction studies. The characteristics of the complete all-by-all comparison of the polypeptide chains present in the PDB and details of the filtering procedure by pair-wise structure alignment that led to the emergent substructure gallery are discussed. Substructure classification, alignments, and tools to analyze them are available at http://cl.sdsc.edu/ce.html.

Identification of true EST alignments for recognising transcribed regions.

PubMed

Ma, Chuang; Wang, Jia; Li, Lun; Duan, Mo-Jie; Zhou, Yan-Hong

2011-01-01

Transcribed regions can be determined by aligning Expressed Sequence Tags (ESTs) with genome sequences. The kernel of this strategy is to effectively distinguish true EST alignments from spurious ones. In this study, three measures including Direction Check, Identity Check and Terminal Check were introduced to more effectively eliminate spurious EST alignments. On the basis of these introduced measures and other widely used measures, a computational tool, named ESTCleanser, has been developed to identify true EST alignments for obtaining reliable transcribed regions. The performance of ESTCleanser has been evaluated on the well-annotated human ENCyclopedia of DNA Elements (ENCODE) regions using human ESTs in the dbEST database. The evaluation results show that the accuracy of ESTCleanser at exon and intron levels is more remarkably enhanced than that of UCSC-spliced EST alignments. This work would be helpful to EST-based researches on finding new genes, complementing genome annotation, recognising alternative splicing events and Single Nucleotide Polymorphisms (SNPs), etc.

Probing the Pathways and Interactions Controlling Crystallization by Particle Attachment

NASA Astrophysics Data System (ADS)

De Yoreo, J. J.; Li, D.; Chun, J.; Schenter, G.; Mundy, C.; Rosso, K. M.

2016-12-01

Crystallization by particle attachment appears to be a widespread mechanism of mineralization. Yet many long-standing questions surrounding nucleation and assembly of precursor particles remain unanswered, due in part to a lack of tools to probe mineralization dynamics with adequate spatial and temporal resolution. Here we report results of liquid phase TEM studies of nucleation and particle assembly in a number of mineral systems. We interpret the results within a framework that considers the impact of both the complexity of free energy landscapes and kinetic factors associated with high supersaturation or slow dynamics. In the calcium carbonate system, the need for high supersturations to overcome the high barrier to nucleation of calcite leads to simultaneous occurrence of multiple pathways, including direct formation of all the common ploymorphs, as well as two-step pathways through which initial precursors, particularly ACC, undergo a direct transformation to a more stable phase. Introduction of highly charged polymers that bind calcium inhibits nucleation, but directs the pathway to a metastable amorphous phase that no longer transforms to more stable polymorphs. Experiments in the iron oxide and oxyhydroxide systems show that, when high supersaturations lead to nucleation of many nanoprticles, further growth occurs through a combination of particle aggregation events and Ostwald ripening. In some cases, aggregation occurs only through oriented attachment on lattice matched faces, leading to single crystals with complex topologies and internal twin boundaries, while in others aggregation results initially in poor co-alignment, but over time the particles undergo atomic rearrangements to achieve a single crystal structure. AFM-based measurements of forces between phyllosilicate surfaces reveal the importance of long-range dispersion interactions in driving alignment, as well as the impact of electrolyte concentration and temperature on the competition of those attractive forces with repulsive electrostatic interactions. Taken together, the results help to define an emerging framework for understanding crystallization by particle attachment.

FAST/Polar Conjunction Study of Field-Aligned Auroral Acceleration and Corresponding Magnetotail Drivers

NASA Technical Reports Server (NTRS)

Schriver, D.; Ashour-Abdalla, M.; Strangeway, R. J.; Richard, R. L.; Klezting, C.; Dotan, Y.; Wygant, J.

2003-01-01

The discrete aurora results when energized electrons bombard the Earth's atmosphere at high latitudes. This paper examines the physical processes that can cause field-aligned acceleration of plasma particles in the auroral region. A data and theoretical study has been carried out to examine the acceleration mechanisms that operate in the auroral zone and to identi@ the magnetospheric drivers of these acceleration mechanisms. The observations used in the study were collected by the Fast Auroral Snapshot (FAST) and Polar satellites when the two satellites were in approximate magnetic conjunction in the auroral region. During these events FAST was in the middle of the auroral zone and Polar was above the auroral zone in the near-Earth plasma sheet. Polar data were used to determine the conditions in the magnetotail at the time field-aligned acceleration was measured by FAST in the auroral zone. For each of the magnetotail drivers identified in the data study, the physics of field-aligned acceleration in the auroral region was examined using existing theoretical efforts and/or a long-system particle in cell simulation to model the magnetically connected region between the two satellites. Results from the study indicate that there are three main drivers of auroral acceleration: (1) field-aligned currents that lead to quasistatic parallel potential drops (parallel electric fields), (2) earthward flow of high-energy plasma beams from the magnetotail into the auroral zone that lead to quasistatic parallel potential drops, and (3) large-amplitude Alfven waves that propagate into the auroral region from the magnetotail. The events examined thus far confm the previously established invariant latitudinal dependence of the drivers and show a strong dependence on magnetic activity. Alfven waves tend to occur primarily at the poleward edge of the auroral region during more magnetically active times and are correlated with intense electron precipitation. At lower latitudes away from the poleward edge of the auroral zone is the primary field-aligned current region which results in the classical field- aligned acceleration associated with the auroral zone (electrons earthward and ion beams tailward). During times of high magnetic activity, high-energy ion beams originating from the magnetotail are observed within, and overlapping, the regions of primary and return field-aligned current. Along the field lines where the high-energy magnetotail ion beams are located, field-aligned acceleration can occur in the auroral zone leading to precipitating electrons and upwelling ionospheric ion beams. Field-aligned currents are present during both quiet and active times, while the Alfven waves and magnetotail ion beams were observed only during more magnetically active events.

Visualizing Internet routing changes.

PubMed

Lad, Mohit; Massey, Dan; Zhang, Lixia

2006-01-01

Today's Internet provides a global data delivery service to millions of end users and routing protocols play a critical role in this service. It is important to be able to identify and diagnose any problems occurring in Internet routing. However, the Internet's sheer size makes this task difficult. One cannot easily extract out the most important or relevant routing information from the large amounts of data collected from multiple routers. To tackle this problem, we have developed Link-Rank, a tool to visualize Internet routing changes at the global scale. Link-Rank weighs links in a topological graph by the number of routes carried over each link and visually captures changes in link weights in the form of a topological graph with adjustable size. Using Link-Rank, network operators can easily observe important routing changes from massive amounts of routing data, discover otherwise unnoticed routing problems, understand the impact of topological events, and infer root causes of observed routing changes.

Analyses of the radiation of birnaviruses from diverse host phyla and of their evolutionary affinities with other double-stranded RNA and positive strand RNA viruses using robust structure-based multiple sequence alignments and advanced phylogenetic methods

PubMed Central

2013-01-01

Background Birnaviruses form a distinct family of double-stranded RNA viruses infecting animals as different as vertebrates, mollusks, insects and rotifers. With such a wide host range, they constitute a good model for studying the adaptation to the host. Additionally, several lines of evidence link birnaviruses to positive strand RNA viruses and suggest that phylogenetic analyses may provide clues about transition. Results We characterized the genome of a birnavirus from the rotifer Branchionus plicalitis. We used X-ray structures of RNA-dependent RNA polymerases and capsid proteins to obtain multiple structure alignments that allowed us to obtain reliable multiple sequence alignments and we employed “advanced” phylogenetic methods to study the evolutionary relationships between some positive strand and double-stranded RNA viruses. We showed that the rotifer birnavirus genome exhibited an organization remarkably similar to other birnaviruses. As this host was phylogenetically very distant from the other known species targeted by birnaviruses, we revisited the evolutionary pathways within the Birnaviridae family using phylogenetic reconstruction methods. We also applied a number of phylogenetic approaches based on structurally conserved domains/regions of the capsid and RNA-dependent RNA polymerase proteins to study the evolutionary relationships between birnaviruses, other double-stranded RNA viruses and positive strand RNA viruses. Conclusions We show that there is a good correlation between the phylogeny of the birnaviruses and that of their hosts at the phylum level using the RNA-dependent RNA polymerase (genomic segment B) on the one hand and a concatenation of the capsid protein, protease and ribonucleoprotein (genomic segment A) on the other hand. This correlation tends to vanish within phyla. The use of advanced phylogenetic methods and robust structure-based multiple sequence alignments allowed us to obtain a more accurate picture (in terms of probability of the tree topologies) of the evolutionary affinities between double-stranded RNA and positive strand RNA viruses. In particular, we were able to show that there exists a good statistical support for the claims that dsRNA viruses are not monophyletic and that viruses with permuted RdRps belong to a common evolution lineage as previously proposed by other groups. We also propose a tree topology with a good statistical support describing the evolutionary relationships between the Picornaviridae, Caliciviridae, Flaviviridae families and a group including the Alphatetraviridae, Nodaviridae, Permutotretraviridae, Birnaviridae, and Cystoviridae families. PMID:23865988

Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets

PubMed Central

Zhou, Xiaofan; Shen, Xing-Xing; Hittinger, Chris Todd

2018-01-01

Abstract The sizes of the data matrices assembled to resolve branches of the tree of life have increased dramatically, motivating the development of programs for fast, yet accurate, inference. For example, several different fast programs have been developed in the very popular maximum likelihood framework, including RAxML/ExaML, PhyML, IQ-TREE, and FastTree. Although these programs are widely used, a systematic evaluation and comparison of their performance using empirical genome-scale data matrices has so far been lacking. To address this question, we evaluated these four programs on 19 empirical phylogenomic data sets with hundreds to thousands of genes and up to 200 taxa with respect to likelihood maximization, tree topology, and computational speed. For single-gene tree inference, we found that the more exhaustive and slower strategies (ten searches per alignment) outperformed faster strategies (one tree search per alignment) using RAxML, PhyML, or IQ-TREE. Interestingly, single-gene trees inferred by the three programs yielded comparable coalescent-based species tree estimations. For concatenation-based species tree inference, IQ-TREE consistently achieved the best-observed likelihoods for all data sets, and RAxML/ExaML was a close second. In contrast, PhyML often failed to complete concatenation-based analyses, whereas FastTree was the fastest but generated lower likelihood values and more dissimilar tree topologies in both types of analyses. Finally, data matrix properties, such as the number of taxa and the strength of phylogenetic signal, sometimes substantially influenced the programs’ relative performance. Our results provide real-world gene and species tree phylogenetic inference benchmarks to inform the design and execution of large-scale phylogenomic data analyses. PMID:29177474

Event-triggered consensus tracking of multi-agent systems with Lur'e nonlinear dynamics

NASA Astrophysics Data System (ADS)

Huang, Na; Duan, Zhisheng; Wen, Guanghui; Zhao, Yu

2016-05-01

In this paper, distributed consensus tracking problem for networked Lur'e systems is investigated based on event-triggered information interactions. An event-triggered control algorithm is designed with the advantages of reducing controller update frequency and sensor energy consumption. By using tools of ?-procedure and Lyapunov functional method, some sufficient conditions are derived to guarantee that consensus tracking is achieved under a directed communication topology. Meanwhile, it is shown that Zeno behaviour of triggering time sequences is excluded for the proposed event-triggered rule. Finally, some numerical simulations on coupled Chua's circuits are performed to illustrate the effectiveness of the theoretical algorithms.

Parallel discrete event simulation using shared memory

NASA Technical Reports Server (NTRS)

Reed, Daniel A.; Malony, Allen D.; Mccredie, Bradley D.

1988-01-01

With traditional event-list techniques, evaluating a detailed discrete-event simulation-model can often require hours or even days of computation time. By eliminating the event list and maintaining only sufficient synchronization to ensure causality, parallel simulation can potentially provide speedups that are linear in the numbers of processors. A set of shared-memory experiments, using the Chandy-Misra distributed-simulation algorithm, to simulate networks of queues is presented. Parameters of the study include queueing network topology and routing probabilities, number of processors, and assignment of network nodes to processors. These experiments show that Chandy-Misra distributed simulation is a questionable alternative to sequential-simulation of most queueing network models.

Using ProMED-Mail and MedWorm blogs for cross-domain pattern analysis in epidemic intelligence.

PubMed

Stewart, Avaré; Denecke, Kerstin

2010-01-01

In this work we motivate the use of medical blog user generated content for gathering facts about disease reporting events to support biosurveillance investigation. Given the characteristics of blogs, the extraction of such events is made more difficult due to noise and data abundance. We address the problem of automatically inferring disease reporting event extraction patterns in this more noisy setting. The sublanguage used in outbreak reports is exploited to align with the sequences of disease reporting sentences in blogs. Based our Cross Domain Pattern Analysis Framework, experimental results show that Phase-Level sequences tend to produce more overlap across the domains than Word-Level sequences. The cross domain alignment process is effective at filtering noisy sequences from blogs and extracting good candidate sequence patterns from an abundance of text.

Hydromagnetic vortices. I - The 11 December 1977 event

NASA Technical Reports Server (NTRS)

Saunders, M. A.; Southwood, D. J.; Fritz, T. A.; Hones, E. W., Jr.

1983-01-01

Through a synthesis of magnetometer, plasma, energetic particle and electric field data from the ISEE satellite pair, the characteristics of the initial (11 December 1977) magnetotail plasma vortex event reported by Hones et al. (1978), are described. The event is associated with a hot (beta is approximately unity) compressional hydromagnetic wave and apparent vortical motion is seen because at two points in the flow cycle the flow is field-aligned. The behavior of the energetic ions receives special study: when combined with the thermal flow measurements energy dispersion is evident in the field-aligned flow, while the large pitch angle energetic ions reveal the presence of gradients. It is argued that these gradients are wave-induced, and the data are used to determine the perpendicular wave wavelength together with the speed and direction of transverse wave propagation.

Nucleon Alignment and Shape Competition at High Spin in ^180Hf

NASA Astrophysics Data System (ADS)

Tandel, U. S.; Chowdhury, P.; Tandel, S. K.; Sheppard, S.; Cline, D.; Wu, C. Y.; Carpenter, M. P.; Janssens, R. V. F.; Khoo, T. L.; Lauritsen, T.; Lister, C. J.; Seweryniak, D.; Zhu, S.

2006-10-01

In light even-N Hf isotopes (N = 96-106), the first i13/2 neutron alignment occurs at hφ< 0.3 MeV. In contrast, no alignment was observed up to ˜ 0.4 MeV in ^180,182Hf (N = 108,110) [1]. Theoretical calculations predict that oblate collective rotation becomes yrast at high spins in ^180Hf [2, 3]. In the present work, the yrast band of ^180Hf has been extended to high spins, via inelastic excitation, using a 1300 MeV ^180Hf beam incident on a thin ^232Th target. The γ rays were detected by Gammasphere, with event by event Doppler correction and Q-value selectivity provided by CHICO. The data reveal onset of the first nucleon alignment in ^180Hf at hφ ˜ 0.43 MeV, which is significantly higher than predictions (˜ 0.35 MeV). Interestingly, the γ-vibrational band is crossed by a band with apparent high moment-of-inertia at ˜ 0.25 MeV. This structure, which becomes near yrast at the highest observed spins will be discussed in the context of nucleon alignment and shape competition at high spin in ^180Hf. [1] E. Ngijoi-Yogo, Ph.D. thesis, U.Mass. Lowell (2004) [2] R.R. Hilton and H.J. Mang, Phys. Rev. Lett. 43, 1979 (1979). [3] F.R. Xu et al., Phys. Rev. C62, 014301 (2000).

Temperature-driven massless Kane fermions in HgCdTe crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Teppe, F.; Marcinkiewicz, M.; Krishtopenko, S. S.

2016-08-30

It has recently been shown that electronic states in bulk gapless HgCdTe offer another realization of pseudo-relativistic three-dimensional particles in condensed matter systems. These single valley relativistic states, massless Kane fermions, cannot be described by any other relativistic particles. Furthermore, the HgCdTe band structure can be continuously tailored by modifying cadmium content or temperature. At critical concentration or temperature, the bandgap collapses as the system undergoes a semimetal-to-semiconductor topological phase transition between the inverted and normal alignments. Here, using far-infrared magneto-spectroscopy we explore the continuous evolution of band structure of bulk HgCdTe as temperature is tuned across the topological phasemore » transition. We demonstrate that the rest mass of Kane fermions changes sign at critical temperature, whereas their velocity remains constant. The velocity universal value of (1.07±0.05) × 106 m s -1 remains valid in a broad range of temperatures and Cd concentrations, indicating a striking universality of the pseudo-relativistic description of the Kane fermions in HgCdTe.« less

Self-Assembly and Electrostriction of Arrays and Chains of Hopfion Particles in Chiral Liquid Crystals

DOE PAGES

Ackerman, P. J.; van de Lagemaat, J.; Smalyukh, I. I.

2015-01-21

Some of the most exotic condensed matter phases, such as twist grain boundary and blue phases in liquid crystals and Abrikosov phases in superconductors, contain arrays of topological defects in their ground state. Comprised of a triangular lattice of double-twist tubes of magnetization, the so-called ‘A-phase’ in chiral magnets is an example of a thermodynamically stable phase with topologically nontrivial solitonic field configurations referred to as two-dimensional skyrmions, or baby-skyrmions. Here we report that three-dimensional skyrmions in the form of double-twist tori called ‘hopfions’, or ‘torons’ when accompanied by additional self-compensating defects, self-assemble into periodic arrays and linear chains thatmore » exhibit electrostriction. In confined chiral nematic liquid crystals, this self-assembly is similar to that of liquid crystal colloids and originates from long-range elastic interactions between particle-like skyrmionic torus knots of molecular alignment field, which can be tuned from isotropic repulsive to weakly or highly anisotropic attractive by low-voltage electric fields.« less

Rapid Ordering in "Wet Brush" Block Copolymer/Homopolymer Ternary Blends.

PubMed

Doerk, Gregory S; Yager, Kevin G

2017-12-26

The ubiquitous presence of thermodynamically unfavored but kinetically trapped topological defects in nanopatterns formed via self-assembly of block copolymer thin films may prevent their use for many envisioned applications. Here, we demonstrate that lamellae patterns formed by symmetric polystyrene-block-poly(methyl methacrylate) diblock copolymers self-assemble and order extremely rapidly when the diblock copolymers are blended with low molecular weight homopolymers of the constituent blocks. Being in the "wet brush" regime, the homopolymers uniformly distribute within their respective self-assembled microdomains, preventing increases in domain widths. An order-of-magnitude increase in topological grain size in blends over the neat (unblended) diblock copolymer is achieved within minutes of thermal annealing as a result of the significantly higher power law exponent for ordering kinetics in the blends. Moreover, the blends are demonstrated to be capable of rapid and robust domain alignment within micrometer-scale trenches, in contrast to the corresponding neat diblock copolymer. These results can be attributed to the lowering of energy barriers associated with domain boundaries by bringing the system closer to an order-disorder transition through low molecular weight homopolymer blending.

T-RMSD: a web server for automated fine-grained protein structural classification.

PubMed

Magis, Cedrik; Di Tommaso, Paolo; Notredame, Cedric

2013-07-01

This article introduces the T-RMSD web server (tree-based on root-mean-square deviation), a service allowing the online computation of structure-based protein classification. It has been developed to address the relation between structural and functional similarity in proteins, and it allows a fine-grained structural clustering of a given protein family or group of structurally related proteins using distance RMSD (dRMSD) variations. These distances are computed between all pairs of equivalent residues, as defined by the ungapped columns within a given multiple sequence alignment. Using these generated distance matrices (one per equivalent position), T-RMSD produces a structural tree with support values for each cluster node, reminiscent of bootstrap values. These values, associated with the tree topology, allow a quantitative estimate of structural distances between proteins or group of proteins defined by the tree topology. The clusters thus defined have been shown to be structurally and functionally informative. The T-RMSD web server is a free website open to all users and available at http://tcoffee.crg.cat/apps/tcoffee/do:trmsd.

T-RMSD: a web server for automated fine-grained protein structural classification

PubMed Central

Magis, Cedrik; Di Tommaso, Paolo; Notredame, Cedric

2013-01-01

This article introduces the T-RMSD web server (tree-based on root-mean-square deviation), a service allowing the online computation of structure-based protein classification. It has been developed to address the relation between structural and functional similarity in proteins, and it allows a fine-grained structural clustering of a given protein family or group of structurally related proteins using distance RMSD (dRMSD) variations. These distances are computed between all pairs of equivalent residues, as defined by the ungapped columns within a given multiple sequence alignment. Using these generated distance matrices (one per equivalent position), T-RMSD produces a structural tree with support values for each cluster node, reminiscent of bootstrap values. These values, associated with the tree topology, allow a quantitative estimate of structural distances between proteins or group of proteins defined by the tree topology. The clusters thus defined have been shown to be structurally and functionally informative. The T-RMSD web server is a free website open to all users and available at http://tcoffee.crg.cat/apps/tcoffee/do:trmsd. PMID:23716642

Designed topology and site-selective metal composition in tetranuclear [MM'...M'M] linear complexes.

PubMed

Barrios, Leoní A; Aguilà, David; Roubeau, Olivier; Gamez, Patrick; Ribas-Ariño, Jordi; Teat, Simon J; Aromí, Guillem

2009-10-26

The ligand 1,3-bis[3-oxo-3-(2-hydroxyphenyl)propionyl]benzene (H(4)L), designed to align transition metals into tetranuclear linear molecules, reacts with M(II) salts (M=Ni, Co, Cu) to yield complexes with the expected [MMMM] topology. The novel complexes [Co(4)L(2)(py)(6)] (2; py=pyridine) and [Na(py)(2)][Cu(4)L(2)(py)(4)](ClO(4)) (3) have been crystallographically characterised. The metal sites in complexes 2 and 3, together with previously characterised [Ni(4)L(2)(py)(6)] (1), favour different coordination geometries. These have been exploited for the deliberate synthesis of the heterometallic complex [Cu(2)Ni(2)L(2)(py)(6)] (4). Complexes 1, 2, 3 and 4 exhibit antiferromagnetic interactions between pairs of metals within each cluster, leading to S=0 spin ground states, except for the latter cluster, which features two quasi-independent S=1/2 moieties within the molecule. Complex 4 gathers the structural and physical conditions, thus allowing it to be considered as prototype of a two-qbit quantum gate.

HiTAD: detecting the structural and functional hierarchies of topologically associating domains from chromatin interactions

PubMed Central

Wang, Xiao-Tao; Cui, Wang

2017-01-01

Abstract A current question in the high-order organization of chromatin is whether topologically associating domains (TADs) are distinct from other hierarchical chromatin domains. However, due to the unclear TAD definition in tradition, the structural and functional uniqueness of TAD is not well studied. In this work, we refined TAD definition by further constraining TADs to the optimal separation on global intra-chromosomal interactions. Inspired by this constraint, we developed a novel method, called HiTAD, to detect hierarchical TADs from Hi-C chromatin interactions. HiTAD performs well in domain sensitivity, replicate reproducibility and inter cell-type conservation. With a novel domain-based alignment proposed by us, we defined several types of hierarchical TAD changes which were not systematically studied previously, and subsequently used them to reveal that TADs and sub-TADs differed statistically in correlating chromosomal compartment, replication timing and gene transcription. Finally, our work also has the implication that the refinement of TAD definition could be achieved by only utilizing chromatin interactions, at least in part. HiTAD is freely available online. PMID:28977529

Representation of molecular structure using quantum topology with inductive logic programming in structure-activity relationships.

PubMed

Buttingsrud, Bård; Ryeng, Einar; King, Ross D; Alsberg, Bjørn K

2006-06-01

The requirement of aligning each individual molecule in a data set severely limits the type of molecules which can be analysed with traditional structure activity relationship (SAR) methods. A method which solves this problem by using relations between objects is inductive logic programming (ILP). Another advantage of this methodology is its ability to include background knowledge as 1st-order logic. However, previous molecular ILP representations have not been effective in describing the electronic structure of molecules. We present a more unified and comprehensive representation based on Richard Bader's quantum topological atoms in molecules (AIM) theory where critical points in the electron density are connected through a network. AIM theory provides a wealth of chemical information about individual atoms and their bond connections enabling a more flexible and chemically relevant representation. To obtain even more relevant rules with higher coverage, we apply manual postprocessing and interpretation of ILP rules. We have tested the usefulness of the new representation in SAR modelling on classifying compounds of low/high mutagenicity and on a set of factor Xa inhibitors of high and low affinity.

Filamentary field-aligned currents at the polar cap region during northward interplanetary magnetic field derived with the Swarm constellation

PubMed Central

Lühr, Hermann; Huang, Tao; Wing, Simon; Kervalishvili, Guram; Rauberg, Jan; Korth, Haje

2017-01-01

ESA’s Swarm constellation mission makes it possible for the first time to determine field-aligned currents (FACs) in the ionosphere uniquely. In particular at high latitudes, the dual-satellite approach can reliably detect some FAC structures which are missed by the traditional single-satellite technique. These FAC events occur preferentially poleward of the auroral oval and during times of northward interplanetary magnetic field (IMF) orientation. Most events appear on the nightside. They are not related to the typical FAC structures poleward of the cusp, commonly termed NBZ. Simultaneously observed precipitating particle spectrograms and auroral images from Defense Meteorological Satellite Program (DMSP) satellites are consistent with the detected FACs and indicate that they occur on closed field lines mostly adjacent to the auroral oval. We suggest that the FACs are associated with Sun-aligned filamentary auroral arcs. Here we introduce in an initial study features of the high-latitude FAC structures which have been observed during the early phase of the Swarm mission. A more systematic survey over longer times is required to fully characterize the so far undetected field aligned currents. PMID:29056833

Score distributions of gapped multiple sequence alignments down to the low-probability tail

NASA Astrophysics Data System (ADS)

Fieth, Pascal; Hartmann, Alexander K.

2016-08-01

Assessing the significance of alignment scores of optimally aligned DNA or amino acid sequences can be achieved via the knowledge of the score distribution of random sequences. But this requires obtaining the distribution in the biologically relevant high-scoring region, where the probabilities are exponentially small. For gapless local alignments of infinitely long sequences this distribution is known analytically to follow a Gumbel distribution. Distributions for gapped local alignments and global alignments of finite lengths can only be obtained numerically. To obtain result for the small-probability region, specific statistical mechanics-based rare-event algorithms can be applied. In previous studies, this was achieved for pairwise alignments. They showed that, contrary to results from previous simple sampling studies, strong deviations from the Gumbel distribution occur in case of finite sequence lengths. Here we extend the studies to multiple sequence alignments with gaps, which are much more relevant for practical applications in molecular biology. We study the distributions of scores over a large range of the support, reaching probabilities as small as 10-160, for global and local (sum-of-pair scores) multiple alignments. We find that even after suitable rescaling, eliminating the sequence-length dependence, the distributions for multiple alignment differ from the pairwise alignment case. Furthermore, we also show that the previously discussed Gaussian correction to the Gumbel distribution needs to be refined, also for the case of pairwise alignments.

Crystals for krypton helium-alpha line emission microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koch, Jeffrey A.; Haugh, Michael J.

2018-04-17

A system for reflecting and recording x-ray radiation from an x-ray emitting event to characterize the event. A crystal is aligned to receive radiation along a first path from an x-ray emitting event. Upon striking the crystal, the x-ray reflects from the crystal along a second path due to a reflection plane of the crystal defined by one of the following Miller indices: (9,7,3) or (11,3,3). Exemplary crystalline material is germanium. The x-rays are reflected to a detector aligned to receive reflected x-rays that are reflected from the crystal along the second path and the detector generates a detector signalmore » in response to x-rays impacting the detector. The detector may include a CCD electronic detector, film plates, or any other detector type. A processor receives and processes the detector signal to generate reflection data representing the x-rays emitted from the x-ray emitting event.« less

Microseismic Event Grouping Based on PageRank Linkage at the Newberry Volcano Geothermal Site

NASA Astrophysics Data System (ADS)

Aguiar, A. C.; Myers, S. C.

2016-12-01

The Newberry Volcano DOE FORGE site in Central Oregon has been stimulated two times using high-pressure fluid injection to study the Enhanced Geothermal Systems (EGS) technology. Several hundred microseismic events were generated during the first stimulation in the fall of 2012. Initial locations of this microseismicity do not show well defined subsurface structure in part because event location uncertainties are large (Foulger and Julian, 2013). We focus on this stimulation to explore the spatial and temporal development of microseismicity, which is key to understanding how subsurface stimulation modifies stress, fractures rock, and increases permeability. We use PageRank, Google's initial search algorithm, to determine connectivity within the events (Aguiar and Beroza, 2014) and assess signal-correlation topology for the micro-earthquakes. We then use this information to create signal families and compare these to the spatial and temporal proximity of associated earthquakes. We relocate events within families (identified by PageRank linkage) using the Bayesloc approach (Myers et al., 2007). Preliminary relocations show tight spatial clustering of event families as well as evidence of events relocating to a different cluster than originally reported. We also find that signal similarity (linkage) at several stations, not just one or two, is needed in order to determine that events are in close proximity to one another. We show that indirect linkage of signals using PageRank is a reliable way to increase the number of events that are confidently determined to be similar to one another, which may lead to efficient and effective grouping of earthquakes with similar physical characteristics, such as focal mechanisms and stress drop. Our ultimate goal is to determine whether changes in the state of stress and/or changes in the generation of subsurface fracture networks can be detected using PageRank topology as well as aid in the event relocation to obtain more accurate subsurface structure. Prepared by LLNL under Contract DE-AC52-07NA27344. LLNL-ABS-699142.

Characteristics of ionospheric convection and field-aligned current in the dayside cusp region

NASA Technical Reports Server (NTRS)

Lu, G.; Lyons, L. R.; Reiff, P. H.; Denig, W. F.; Beaujardiere, O. De LA; Kroehl, H. W.; Newell, P. T.; Rich, F. J.; Opgenoorth, H.; Persson, M. A. L.

1995-01-01

The assimilative mapping of ionospheric electrodynamics (AMIE) technique has been used to estimate global distributions of high-latitude ionospheric convection and field-aligned current by combining data obtained nearly simultaneously both from ground and from space. Therefore, unlike the statistical patterns, the 'snapshot' distributions derived by AMIE allow us to examine in more detail the distinctions between field-aligned current systems associated with separate magnetospheric processes, especially in the dayside cusp region. By comparing the field-aligned current and ionospheric convection patterns with the corresponding spectrograms of precipitating particles, the following signatures have been identified: (1) For the three cases studied, which all had an IMF with negative y and z components, the cusp precipitation was encountered by the DMSP satellites in the postnoon sector in the northern hemisphere and in the prenoon sector in the southern hemisphere. The equatorward part of the cusp in both hemispheres is in the sunward flow region and marks the beginning of the flow rotation from sunward to antisunward. (2) The pair of field-aligned currents near local noon, i.e., the cusp/mantle currents, are coincident with the cusp or mantle particle precipitation. In distinction, the field-aligned currents on the dawnside and duskside, i.e., the normal region 1 currents, are usually associated with the plasma sheet particle precipitation. Thus the cusp/mantle currents are generated on open field lines and the region 1 currents mainly on closed field lines. (3) Topologically, the cusp/mantle currents appear as an expansion of the region 1 currents from the dawnside and duskside and they overlap near local noon. When B(sub y) is negative, in the northern hemisphere the downward field-aligned current is located poleward of the upward current; whereas in the southern hemisphere the upward current is located poleward of the downward current. (4) Under the assumption of quasi-steady state reconnection, the location of the separatrix in the ionosphere is estimated and the reconnection velocity is calculated to be between 400 and 550 m/s. The dayside separatrix lies equatorward of the dayside convection throat in the two cases examined.

A greedy, graph-based algorithm for the alignment of multiple homologous gene lists.

PubMed

Fostier, Jan; Proost, Sebastian; Dhoedt, Bart; Saeys, Yvan; Demeester, Piet; Van de Peer, Yves; Vandepoele, Klaas

2011-03-15

Many comparative genomics studies rely on the correct identification of homologous genomic regions using accurate alignment tools. In such case, the alphabet of the input sequences consists of complete genes, rather than nucleotides or amino acids. As optimal multiple sequence alignment is computationally impractical, a progressive alignment strategy is often employed. However, such an approach is susceptible to the propagation of alignment errors in early pairwise alignment steps, especially when dealing with strongly diverged genomic regions. In this article, we present a novel accurate and efficient greedy, graph-based algorithm for the alignment of multiple homologous genomic segments, represented as ordered gene lists. Based on provable properties of the graph structure, several heuristics are developed to resolve local alignment conflicts that occur due to gene duplication and/or rearrangement events on the different genomic segments. The performance of the algorithm is assessed by comparing the alignment results of homologous genomic segments in Arabidopsis thaliana to those obtained by using both a progressive alignment method and an earlier graph-based implementation. Especially for datasets that contain strongly diverged segments, the proposed method achieves a substantially higher alignment accuracy, and proves to be sufficiently fast for large datasets including a few dozens of eukaryotic genomes. http://bioinformatics.psb.ugent.be/software. The algorithm is implemented as a part of the i-ADHoRe 3.0 package.

Skin-Friction Measurements in a 3-D, Supersonic Shock-Wave/Boundary-Layer Interaction

NASA Technical Reports Server (NTRS)

Wideman, J. K.; Brown, J. L.; Miles, J. B.; Ozcan, O.

1994-01-01

The experimental documentation of a three-dimensional shock-wave/boundary-layer interaction in a nominal Mach 3 cylinder, aligned with the free-stream flow, and 20 deg. half-angle conical flare offset 1.27 cm from the cylinder centerline. Surface oil flow, laser light sheet illumination, and schlieren were used to document the flow topology. The data includes surface-pressure and skin-friction measurements. A laser interferometric skin friction data. Included in the skin-friction data are measurements within separated regions and three-dimensional measurements in highly-swept regions. The skin-friction data will be particularly valuable in turbulence modeling and computational fluid dynamics validation.

Outflow off the Beaten Path: Low Energy (< keV) O+ Outflow Directly Into the Inner Magnetosphere as Observed by the Van Allen Probes and the Implications for Mid- and Low-Latitude Magnetosphere-Ionosphere Coupling

NASA Astrophysics Data System (ADS)

Gkioulidou, M.; Mitchell, D. G.; Ukhorskiy, S.; Ohtani, S.; Takahashi, K.

2017-12-01

The low-energy (eV to hundreds of eV) ion population in the inner magnetosphere, the warm plasma cloak, and in particular its heavy ion component, the O+ torus, is crucial to magnetospheric dynamics. Yet, although the effects of high latitude and cusp ionospheric O+ outflow and its subsequent transport and acceleration within the magnetotail and plasma sheet have been extensively studied, the source of low-energy O+ within the inner magnetosphere (already observed by the DE1 spacecraft in the 80s) remains a compelling open question. The HOPE instrument aboard each of the Van Allen Probes, moving in highly elliptical, equatorial orbits with apogee of 5.8 RE, has repeatedly detected low-energy O+ field-aligned enhancements. We present a comprehensive study of one such event, where low energy O+ field-aligned intensity enhancements were observed, both at small and large pitch angles, during a geomagnetic storm. The energy spectrogram exhibited a dispersive signature and a banded structure, features that our simple particle tracing simulation demonstrated are due to O+ ions outflowing from both hemispheres of the night-side ionosphere directly into the magnetosphere within L = 4, and subsequently bouncing from one hemisphere to the other. These outflows are associated with field-aligned Poynting flux enhancements and field-aligned electron beams, as observed at the Van Allen Probes location, revealing energy transport from the magnetosphere to ionosphere as well as simultaneous field-aligned electron heating. We also incorporate ionospheric measurements, such as field-aligned currents, as those are inferred by AMPERE data. The combination of unprecedented simultaneous magnetospheric and ionospheric observations allow us to investigate the processes that lead to an O+ outflow event from the low-latitude, night-side ionosphere directly into the inner magnetosphere. The ubiquity of such events in the Van Allen Probes data might reveal one of the sources for the O+ torus.

On the mechanism of elasto-inertial turbulence.

PubMed

Dubief, Yves; Terrapon, Vincent E; Soria, Julio

2013-11-01

Elasto-inertial turbulence (EIT) is a new state of turbulence found in inertial flows with polymer additives. The dynamics of turbulence generated and controlled by such additives is investigated from the perspective of the coupling between polymer dynamics and flow structures. Direct numerical simulations of channel flow with Reynolds numbers ranging from 1000 to 6000 (based on the bulk and the channel height) are used to study the formation and dynamics of elastic instabilities and their effects on the flow. The flow topology of EIT is found to differ significantly from Newtonian wall-turbulence. Structures identified by positive (rotational flow topology) and negative (extensional/compressional flow topology) second invariant Q a isosurfaces of the velocity gradient are cylindrical and aligned in the spanwise direction. Polymers are significantly stretched in sheet-like regions that extend in the streamwise direction with a small upward tilt. The Q a cylindrical structures emerge from the sheets of high polymer extension, in a mechanism of energy transfer from the fluctuations of the polymer stress work to the turbulent kinetic energy. At subcritical Reynolds numbers, EIT is observed at modest Weissenberg number ( Wi , ratio polymer relaxation time to viscous time scale). For supercritical Reynolds numbers, flows approach EIT at large Wi . EIT provides new insights on the nature of the asymptotic state of polymer drag reduction (maximum drag reduction), and explains the phenomenon of early turbulence, or onset of turbulence at lower Reynolds numbers than for Newtonian flows observed in some polymeric flows.

On the mechanism of elasto-inertial turbulence

NASA Astrophysics Data System (ADS)

Dubief, Yves; Terrapon, Vincent E.; Soria, Julio

2013-11-01

Elasto-inertial turbulence (EIT) is a new state of turbulence found in inertial flows with polymer additives. The dynamics of turbulence generated and controlled by such additives is investigated from the perspective of the coupling between polymer dynamics and flow structures. Direct numerical simulations of channel flow with Reynolds numbers ranging from 1000 to 6000 (based on the bulk and the channel height) are used to study the formation and dynamics of elastic instabilities and their effects on the flow. The flow topology of EIT is found to differ significantly from Newtonian wall-turbulence. Structures identified by positive (rotational flow topology) and negative (extensional/compressional flow topology) second invariant Qa isosurfaces of the velocity gradient are cylindrical and aligned in the spanwise direction. Polymers are significantly stretched in sheet-like regions that extend in the streamwise direction with a small upward tilt. The Qa cylindrical structures emerge from the sheets of high polymer extension, in a mechanism of energy transfer from the fluctuations of the polymer stress work to the turbulent kinetic energy. At subcritical Reynolds numbers, EIT is observed at modest Weissenberg number (Wi, ratio polymer relaxation time to viscous time scale). For supercritical Reynolds numbers, flows approach EIT at large Wi. EIT provides new insights on the nature of the asymptotic state of polymer drag reduction (maximum drag reduction), and explains the phenomenon of early turbulence, or onset of turbulence at lower Reynolds numbers than for Newtonian flows observed in some polymeric flows.

On the mechanism of elasto-inertial turbulence

PubMed Central

Dubief, Yves; Terrapon, Vincent E.; Soria, Julio

2013-01-01

Elasto-inertial turbulence (EIT) is a new state of turbulence found in inertial flows with polymer additives. The dynamics of turbulence generated and controlled by such additives is investigated from the perspective of the coupling between polymer dynamics and flow structures. Direct numerical simulations of channel flow with Reynolds numbers ranging from 1000 to 6000 (based on the bulk and the channel height) are used to study the formation and dynamics of elastic instabilities and their effects on the flow. The flow topology of EIT is found to differ significantly from Newtonian wall-turbulence. Structures identified by positive (rotational flow topology) and negative (extensional/compressional flow topology) second invariant Qa isosurfaces of the velocity gradient are cylindrical and aligned in the spanwise direction. Polymers are significantly stretched in sheet-like regions that extend in the streamwise direction with a small upward tilt. The Qa cylindrical structures emerge from the sheets of high polymer extension, in a mechanism of energy transfer from the fluctuations of the polymer stress work to the turbulent kinetic energy. At subcritical Reynolds numbers, EIT is observed at modest Weissenberg number (Wi, ratio polymer relaxation time to viscous time scale). For supercritical Reynolds numbers, flows approach EIT at large Wi. EIT provides new insights on the nature of the asymptotic state of polymer drag reduction (maximum drag reduction), and explains the phenomenon of early turbulence, or onset of turbulence at lower Reynolds numbers than for Newtonian flows observed in some polymeric flows. PMID:24170968

Optical and x-ray alignment approaches for off-plane reflection gratings

NASA Astrophysics Data System (ADS)

Allured, Ryan; Donovan, Benjamin D.; DeRoo, Casey T.; Marlowe, Hannah R.; McEntaffer, Randall L.; Tutt, James H.; Cheimets, Peter N.; Hertz, Edward; Smith, Randall K.; Burwitz, Vadim; Hartner, Gisela; Menz, Benedikt

2015-09-01

Off-plane reflection gratings offer the potential for high-resolution, high-throughput X-ray spectroscopy on future missions. Typically, the gratings are placed in the path of a converging beam from an X-ray telescope. In the off-plane reflection grating case, these gratings must be co-aligned such that their diffracted spectra overlap at the focal plane. Misalignments degrade spectral resolution and effective area. In-situ X-ray alignment of a pair of off-plane reflection gratings in the path of a silicon pore optics module has been performed at the MPE PANTER beamline in Germany. However, in-situ X-ray alignment may not be feasible when assembling all of the gratings required for a satellite mission. In that event, optical methods must be developed to achieve spectral alignment. We have developed an alignment approach utilizing a Shack-Hartmann wavefront sensor and diffraction of an ultraviolet laser. We are fabricating the necessary hardware, and will be taking a prototype grating module to an X-ray beamline for performance testing following assembly and alignment.

Deterministic ripple-spreading model for complex networks.

PubMed

Hu, Xiao-Bing; Wang, Ming; Leeson, Mark S; Hines, Evor L; Di Paolo, Ezequiel

2011-04-01

This paper proposes a deterministic complex network model, which is inspired by the natural ripple-spreading phenomenon. The motivations and main advantages of the model are the following: (i) The establishment of many real-world networks is a dynamic process, where it is often observed that the influence of a few local events spreads out through nodes, and then largely determines the final network topology. Obviously, this dynamic process involves many spatial and temporal factors. By simulating the natural ripple-spreading process, this paper reports a very natural way to set up a spatial and temporal model for such complex networks. (ii) Existing relevant network models are all stochastic models, i.e., with a given input, they cannot output a unique topology. Differently, the proposed ripple-spreading model can uniquely determine the final network topology, and at the same time, the stochastic feature of complex networks is captured by randomly initializing ripple-spreading related parameters. (iii) The proposed model can use an easily manageable number of ripple-spreading related parameters to precisely describe a network topology, which is more memory efficient when compared with traditional adjacency matrix or similar memory-expensive data structures. (iv) The ripple-spreading model has a very good potential for both extensions and applications.

Search for signatures of magnetically-induced alignment in the arrival directions measured by the Pierre Auger Observatory

NASA Astrophysics Data System (ADS)

Pierre Auger Collaboration; Abreu, P.; Aglietta, M.; Ahn, E. J.; Albuquerque, I. F. M.; Allard, D.; Allekotte, I.; Allen, J.; Allison, P.; Alvarez Castillo, J.; Alvarez-Muñiz, J.; Ambrosio, M.; Aminaei, A.; Anchordoqui, L.; Andringa, S.; Antičić, T.; Anzalone, A.; Aramo, C.; Arganda, E.; Arqueros, F.; Asorey, H.; Assis, P.; Aublin, J.; Ave, M.; Avenier, M.; Avila, G.; Bäcker, T.; Balzer, M.; Barber, K. B.; Barbosa, A. F.; Bardenet, R.; Barroso, S. L. C.; Baughman, B.; Bäuml, J.; Beatty, J. J.; Becker, B. R.; Becker, K. H.; Bellétoile, A.; Bellido, J. A.; Benzvi, S.; Berat, C.; Bertou, X.; Biermann, P. L.; Billoir, P.; Blanco, F.; Blanco, M.; Bleve, C.; Blümer, H.; Boháčová, M.; Boncioli, D.; Bonifazi, C.; Bonino, R.; Borodai, N.; Brack, J.; Brogueira, P.; Brown, W. C.; Bruijn, R.; Buchholz, P.; Bueno, A.; Burton, R. E.; Caballero-Mora, K. S.; Caramete, L.; Caruso, R.; Castellina, A.; Catalano, O.; Cataldi, G.; Cazon, L.; Cester, R.; Chauvin, J.; Cheng, S. H.; Chiavassa, A.; Chinellato, J. A.; Chou, A.; Chudoba, J.; Clay, R. W.; Coluccia, M. R.; Conceição, R.; Contreras, F.; Cook, H.; Cooper, M. J.; Coppens, J.; Cordier, A.; Coutu, S.; Covault, C. E.; Creusot, A.; Criss, A.; Cronin, J.; Curutiu, A.; Dagoret-Campagne, S.; Dallier, R.; Dasso, S.; Daumiller, K.; Dawson, B. R.; de Almeida, R. M.; de Domenico, M.; de Donato, C.; de Jong, S. J.; de La Vega, G.; de Mello Junior, W. J. M.; de Mello Neto, J. R. T.; de Mitri, I.; de Souza, V.; de Vries, K. D.; Decerprit, G.; Del Peral, L.; Del Río, M.; Deligny, O.; Dembinski, H.; Dhital, N.; di Giulio, C.; Diaz, J. C.; Díaz Castro, M. L.; Diep, P. N.; Dobrigkeit, C.; Docters, W.; D'Olivo, J. C.; Dong, P. N.; Dorofeev, A.; Dos Anjos, J. C.; Dova, M. T.; D'Urso, D.; Dutan, I.; Ebr, J.; Engel, R.; Erdmann, M.; Escobar, C. O.; Espadanal, J.; Etchegoyen, A.; Facal San Luis, P.; Fajardo Tapia, I.; Falcke, H.; Farrar, G.; Fauth, A. C.; Fazzini, N.; Ferguson, A. P.; Ferrero, A.; Fick, B.; Filevich, A.; Filipčič, A.; Fliescher, S.; Fracchiolla, C. E.; Fraenkel, E. D.; Fröhlich, U.; Fuchs, B.; Gaior, R.; Gamarra, R. F.; Gambetta, S.; García, B.; García Gámez, D.; Garcia-Pinto, D.; Gascon, A.; Gemmeke, H.; Gesterling, K.; Ghia, P. L.; Giaccari, U.; Giller, M.; Glass, H.; Gold, M. S.; Golup, G.; Gomez Albarracin, F.; Gómez Berisso, M.; Gonçalves, P.; Gonzalez, D.; Gonzalez, J. G.; Gookin, B.; Góra, D.; Gorgi, A.; Gouffon, P.; Gozzini, S. R.; Grashorn, E.; Grebe, S.; Griffith, N.; Grigat, M.; Grillo, A. F.; Guardincerri, Y.; Guarino, F.; Guedes, G. P.; Guzman, A.; Hague, J. D.; Hansen, P.; Harari, D.; Harmsma, S.; Harton, J. L.; Haungs, A.; Hebbeker, T.; Heck, D.; Herve, A. E.; Hojvat, C.; Hollon, N.; Holmes, V. C.; Homola, P.; Hörandel, J. R.; Horneffer, A.; Hrabovský, M.; Huege, T.; Insolia, A.; Ionita, F.; Italiano, A.; Jarne, C.; Jiraskova, S.; Josebachuili, M.; Kadija, K.; Kampert, K. H.; Karhan, P.; Kasper, P.; Kégl, B.; Keilhauer, B.; Keivani, A.; Kelley, J. L.; Kemp, E.; Kieckhafer, R. M.; Klages, H. O.; Kleifges, M.; Kleinfeller, J.; Knapp, J.; Koang, D.-H.; Kotera, K.; Krohm, N.; Krömer, O.; Kruppke-Hansen, D.; Kuehn, F.; Kuempel, D.; Kulbartz, J. K.; Kunka, N.; La Rosa, G.; Lachaud, C.; Lautridou, P.; Leão, M. S. A. B.; Lebrun, D.; Lebrun, P.; Leigui de Oliveira, M. A.; Lemiere, A.; Letessier-Selvon, A.; Lhenry-Yvon, I.; Link, K.; López, R.; Lopez Agüera, A.; Louedec, K.; Lozano Bahilo, J.; Lu, L.; Lucero, A.; Ludwig, M.; Lyberis, H.; Maccarone, M. C.; Macolino, C.; Maldera, S.; Mandat, D.; Mantsch, P.; Mariazzi, A. G.; Marin, J.; Marin, V.; Maris, I. C.; Marquez Falcon, H. R.; Marsella, G.; Martello, D.; Martin, L.; Martinez, H.; Martínez Bravo, O.; Mathes, H. J.; Matthews, J.; Matthews, J. A. J.; Matthiae, G.; Maurizio, D.; Mazur, P. O.; Medina-Tanco, G.; Melissas, M.; Melo, D.; Menichetti, E.; Menshikov, A.; Mertsch, P.; Meurer, C.; Mićanović, S.; Micheletti, M. I.; Miller, W.; Miramonti, L.; Molina-Bueno, L.; Mollerach, S.; Monasor, M.; Monnier Ragaigne, D.; Montanet, F.; Morales, B.; Morello, C.; Moreno, E.; Moreno, J. C.; Morris, C.; Mostafá, M.; Moura, C. A.; Mueller, S.; Muller, M. A.; Müller, G.; Münchmeyer, M.; Mussa, R.; Navarra, G.; Navarro, J. L.; Navas, S.; Necesal, P.; Nellen, L.; Nelles, A.; Neuser, J.; Nhung, P. T.; Niemietz, L.; Nierstenhoefer, N.; Nitz, D.; Nosek, D.; Nožka, L.; Nyklicek, M.; Oehlschläger, J.; Olinto, A.; Oliva, P.; Olmos-Gilbaja, V. M.; Ortiz, M.; Pacheco, N.; Pakk Selmi-Dei, D.; Palatka, M.; Pallotta, J.; Palmieri, N.; Parente, G.; Parizot, E.; Parra, A.; Parsons, R. D.; Pastor, S.; Paul, T.; Pech, M.; PeĶala, J.; Pelayo, R.; Pepe, I. M.; Perrone, L.; Pesce, R.; Petermann, E.; Petrera, S.; Petrinca, P.; Petrolini, A.; Petrov, Y.; Petrovic, J.; Pfendner, C.; Phan, N.; Piegaia, R.; Pierog, T.; Pieroni, P.; Pimenta, M.; Pirronello, V.; Platino, M.; Ponce, V. H.; Pontz, M.; Privitera, P.; Prouza, M.; Quel, E. J.; Querchfeld, S.; Rautenberg, J.; Ravel, O.; Ravignani, D.; Revenu, B.; Ridky, J.; Riggi, S.; Risse, M.; Ristori, P.; Rivera, H.; Rizi, V.; Roberts, J.; Robledo, C.; Rodrigues de Carvalho, W.; Rodriguez, G.; Rodriguez Martino, J.; Rodriguez Rojo, J.; Rodriguez-Cabo, I.; Rodríguez-Frías, M. D.; Ros, G.; Rosado, J.; Rossler, T.; Roth, M.; Rouillé-D'Orfeuil, B.; Roulet, E.; Rovero, A. C.; Rühle, C.; Salamida, F.; Salazar, H.; Salina, G.; Sánchez, F.; Santo, C. E.; Santos, E.; Santos, E. M.; Sarazin, F.; Sarkar, B.; Sarkar, S.; Sato, R.; Scharf, N.; Scherini, V.; Schieler, H.; Schiffer, P.; Schmidt, A.; Schmidt, F.; Scholten, O.; Schoorlemmer, H.; Schovancova, J.; Schovánek, P.; Schröder, F.; Schulte, S.; Schuster, D.; Sciutto, S. J.; Scuderi, M.; Segreto, A.; Settimo, M.; Shadkam, A.; Shellard, R. C.; Sidelnik, I.; Sigl, G.; Silva Lopez, H. H.; Śmiałkowski, A.; Šmída, R.; Snow, G. R.; Sommers, P.; Sorokin, J.; Spinka, H.; Squartini, R.; Stanic, S.; Stapleton, J.; Stasielak, J.; Stephan, M.; Strazzeri, E.; Stutz, A.; Suarez, F.; Suomijärvi, T.; Supanitsky, A. D.; Šuša, T.; Sutherland, M. S.; Swain, J.; Szadkowski, Z.; Szuba, M.; Tamashiro, A.; Tapia, A.; Tartare, M.; Taşcău, O.; Tavera Ruiz, C. G.; Tcaciuc, R.; Tegolo, D.; Thao, N. T.; Thomas, D.; Tiffenberg, J.; Timmermans, C.; Tiwari, D. K.; Tkaczyk, W.; Todero Peixoto, C. J.; Tomé, B.; Tonachini, A.; Travnicek, P.; Tridapalli, D. B.; Tristram, G.; Trovato, E.; Tueros, M.; Ulrich, R.; Unger, M.; Urban, M.; Valdés Galicia, J. F.; Valiño, I.; Valore, L.; van den Berg, A. M.; Varela, E.; Vargas Cárdenas, B.; Vázquez, J. R.; Vázquez, R. A.; Veberič, D.; Verzi, V.; Vicha, J.; Videla, M.; Villaseñor, L.; Wahlberg, H.; Wahrlich, P.; Wainberg, O.; Walz, D.; Warner, D.; Watson, A. A.; Weber, M.; Weidenhaupt, K.; Weindl, A.; Westerhoff, S.; Whelan, B. J.; Wieczorek, G.; Wiencke, L.; Wilczyńska, B.; Wilczyński, H.; Will, M.; Williams, C.; Winchen, T.; Winnick, M. G.; Wommer, M.; Wundheiler, B.; Yamamoto, T.; Yapici, T.; Younk, P.; Yuan, G.; Yushkov, A.; Zamorano, B.; Zas, E.; Zavrtanik, D.; Zavrtanik, M.; Zaw, I.; Zepeda, A.; Zimbres Silva, M.; Ziolkowski, M.

2012-01-01

We present the results of an analysis of data recorded at the Pierre Auger Observatory in which we search for groups of directionally-aligned events (or 'multiplets') which exhibit a correlation between arrival direction and the inverse of the energy. These signatures are expected from sets of events coming from the same source after having been deflected by intervening coherent magnetic fields. The observation of several events from the same source would open the possibility to accurately reconstruct the position of the source and also measure the integral of the component of the magnetic field orthogonal to the trajectory of the cosmic rays. We describe the largest multiplets found and compute the probability that they appeared by chance from an isotropic distribution. We find no statistically significant evidence for the presence of multiplets arising from magnetic deflections in the present data.

Search for signatures of magnetically-induced alignment in the arrival directions measured by the Pierre Auger Observatory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abreu, P.; /Lisbon, IST; Aglietta, M.

2011-11-01

We present the results of an analysis of data recorded at the Pierre Auger Observatory in which we search for groups of directionally-aligned events (or ''multiplets'') which exhibit a correlation between arrival direction and the inverse of the energy. These signatures are expected from sets of events coming from the same source after having been deflected by intervening coherent magnetic fields. The observation of several events from the same source would open the possibility to accurately reconstruct the position of the source and also measure the integral of the component of the magnetic field orthogonal to the trajectory of themore » cosmic rays. We describe the largest multiplets found and compute the probability that they appeared by chance from an isotropic distribution. We find no statistically significant evidence for the presence of multiplets arising from magnetic deflections in the present data.« less

Field-aligned currents associated with multiple arc systems

NASA Astrophysics Data System (ADS)

Wu, J.; Knudsen, D. J.; Gillies, D. M.; Donovan, E.; Burchill, J. K.

2016-12-01

It is often thought that auroral arcs are a direct consequence of upward field-aligned currents. In fact, the relation between currents and brightness is more complicated. Multiple auroral arc systems provide and opportunity to study this relation in detail; this information can be used as a test of models for quasi-static arc formation. In this study, we have identified two types of FAC configurations in multiple parallel arc systems using ground-based optical data from the THEMIS all-sky imagers (ASIs), magnetometers and electric field instruments onboard the Swarm satellites during the period from December 2013 to March 2015. In type 1 events, each arc is an intensification within a broad, unipolar current sheet and downward currents only exist outside the upward current sheet. In type 2 events, multiple arc systems represent a collection of multiple up/down current pairs. By collecting 12 events for type 1 and 17 events for type 2, we find that (1) Type 1 events are mainly located between 22-23MLT. Type 2 events are mainly located around midnight. (2) The typical size of upward and downward FAC in type 2 events are comparable, while upward FAC in type 1 events are larger than downward FAC. (3) Upward currents with more arcs embedded have larger intensities and widths. (4) There is no significant difference between the characteristic widths of multiple arcs and single arcs.

Eddy correlation measurements of size-dependent cloud droplet turbulent fluxes to complex terrain

NASA Astrophysics Data System (ADS)

Vong, Richard J.; Kowalski, Andrew S.

1995-07-01

An eddy correlation technique was used to measure the turbulent flux of cloud droplets to complex, forested terrain near the coast of Washington State during the spring of 1993. Excellent agreement was achieved for cloud liquid water content measured by two instruments. Substantial downward liquid water fluxes of 1mm per 24 h were measured at night during "steady and continuous" cloud events, about twice the magnitude of those measured by Beswick etal. in Scotland. Cloud water chemical fluxes were estimated to represent up to 50% of the chemical deposition associated with precipitation at the site. An observed size-dependence in the turbulent liquid water fluxes suggested that both droplet impaction, which leads to downward fluxes, and phase change processes, which can lead to upward fluxes, consistently are important contributors to the eddy correlation results. The diameter below which phase change processes were important to observed fluxes was shown to depend upon σL, the relative standard deviation of the liquid water content (LWC) within a 30-min averaging period. The crossover from upward to downward LW flux occurs at 8µm for steady and continuous cloud events but at 13µm for events with a larger degree of LWC variability. This comparison of the two types of cloud events suggested that evaporation was the most likely cause of upward droplet fluxes for the smaller droplets (dia<13µm) during cloud with variable LWC (σL>0.3).

High-spin states in 103,105Mo, 103Nb, and the νh11/2 alignment

NASA Astrophysics Data System (ADS)

Hua, H.; Wu, C. Y.; Cline, D.; Hayes, A. B.; Teng, R.; Clark, R. M.; Fallon, P.; Macchiavelli, A. O.; Vetter, K.

2002-06-01

High-spin states in neutron-rich nuclei 103,105Mo,103Nb have been studied using the 238U(α,f) fusion-fission reaction. The deexcitation γ rays were detected by Gammasphere in coincidence with the detection of both fission fragments by the Rochester 4π heavy-ion detector array, CHICO. The measured fission kinematics were used to deduce the masses and velocity vectors for both fission fragments. This allowed Doppler-shift corrections to be applied to the observed γ rays on an event-by-event basis and the origin of γ rays from either fission fragment to be established. With such advantages, the yrast sequences for these nuclei have been extended to the band crossing region. This band crossing is ascribed to the alignment of a pair of h11/2 neutrons, which is supported by the observed blocking effect for the νh11/2 band in 105Mo while there is no evidence for blocking in the alignment measured for either the νd5/2 band in 103Mo or the πg9/2 band in 103Nb. The observed upbend, rather than the sharp backbend seen in the Ru-Pd region, indicates a strong interaction between the ground-state and the aligned h11/2 bands.

Microfluidic impact printer with interchangeable cartridges for versatile non-contact multiplexed micropatterning

PubMed Central

Ding, Yuzhe; Huang, Eric; Lam, Kit S.; Pan, Tingrui

2015-01-01

Biopatterning has been increasingly used for well-defined cellular microenvironment, patterned surface topology, and guided biological cues; however, it meets additional challenges on biocompatibility, temperature and chemical sensitivity and limited reagent volume. In this paper, we target at combining the desired features from the non-contact inkjet printing and the dot-matrix impact printing to establish a versatile multiplexed micropatterning platform, referred to as Microfluidic Impact Printer (MI-Printer), for emerging biomedical applications. Using this platform, we can achieve the distinct features of no cross-contamination, minute volume manipulation with minimal dead volume, high-throughput and biocompatible printing process, multiplexed patterning with automatic alignment, printing availability for complex medium (cell suspension or colloidal solutions), interchangeable/disposable microfluidic cartridge design with out-of-cleanroom microfabrication, simple printing system assembly and configuration, all highly desirable towards biological applications. Specifically, the printing resolution of the MI-printer platform has been experimentally characterized and theoretically analyzed. Printed droplets with 80µm in diameter have been repeatedly obtained. Furthermore, two unique features of MI-printer platform, multiplexed printing and self-alignment printing, have been successfully experimentally demonstrated (less than 10µm misalignment). In addition, combinatorial patterning and biological patterning, which utilizes the multiplexed and self-alignment printing nature of the MI-printer, have been devised to demonstrate the applicability of this robust printing technique for emerging biomedical applications. PMID:23525299

Synergetic effect of topological cue and periodic mechanical tension-stress on osteogenic differentiation of rat bone mesenchymal stem cells.

PubMed

Liu, Yao; Yang, Guang; Ji, Huanzhong; Xiang, Tao; Luo, En; Zhou, Shaobing

2017-06-01

Mesenchymal stem cells (MSCs) are able to self-renew and differentiate into tissues of mesenchymal origin, making them to be significant for cell-based therapies, such as metabolic bone diseases and bone repair. Regulating the differentiation of MSCs is significant for bone regeneration. Electrospun fibers mimicking natural extracellular matrix (ECM), is an effective artificial ECM to regulate the behaviors and fates of MSCs. The aligned electrospun fibers can modulate polar cell pattern of bone mesenchymal stem cells, which leads to more obvious osteogenic differentiation. Apart from the topographic effect of electrospun fibers, mechanical cues can also intervene the cell behaviors. In this study, the osteogenic differentiation of rat bone mesenchymal stem cells was evaluated, which were cultured on aligned/random electrospun fiber mats materials under mechanical tension intervention. Scanning electron microscope and immune-fluorescent staining were used to directly observe the polarity changing of cellular morphology and cytoskeleton. The results proved that aligned electrospun fibers could be more conducive to promote osteogenic differentiation of rat bone mesenchymal stem cells and this promotion of osteogenic differentiation was enhanced by tension intervention. These results were correlated to the quantitative real-time PCR assay. In general, culturing rat bone mesenchymal stem cells on electrospun fibers under the intervention of mechanical tension is an effective way to mimic a more real cellular microenvironment. Copyright © 2017 Elsevier B.V. All rights reserved.

Positional Influences on Information Packaging: Insights from Topological Fields in German

ERIC Educational Resources Information Center

Schumacher, Petra B.; Hung, Yu-Chen

2012-01-01

We present three event-related potential studies that investigated the contribution of givenness and position-induced topicality (what a sentence is about) to information processing. The studies compared two types of referential expressions (given and inferred noun phrases (NPs)) in distinct sentential positions. The data revealed…

Early Detection of Lightning Caused Wildfires and Prediction of Wildfire Behavior through Energy Distribution, Atmospherics, Geophysics, the Sun's Azimuth, and Topology

NASA Astrophysics Data System (ADS)

Giesige, C.; Nava, E.

2016-12-01

In the midst of a changing climate we have seen extremes in weather events: lightning, wildfires, hurricanes, tornadoes, and earthquakes. All of these ride on an imbalance of magnetic and electrical distribution about the earth including what goes on from the atmospheric and geophysic levels. There is relevance to the important role the sun plays in developing and feeding of the extreme weather events along with the sun's role helping to create a separation of charges on earth furthering climactic extremes. Focusing attention in North America and on how the sun, atmospheric and geophysic winds come together producing lightning events, there are connections between energy distribution in the environment, lightning caused wildfires, and extreme wildfire behavior. Lightning caused wildfires and extreme fire behavior have become enhanced with the changing climate conditions. Even with strong developments in wildfire science, there remains a lack in full understanding of connections that create a lightning caused wildfire event and lack of monitoring advancements in predicting extreme fire behavior. Several connections have been made in our research allowing us to connect multiple facets of the environment in regards to electric and magnetic influences on wildfires. Among them include: irradiance, winds, pressure systems, humidity, and topology. The connections can be made to develop better detection systems of wildfires, establish with more accuracy areas of highest risk for wildfire and extreme wildfire behavior, and prediction of wildfire behavior. A platform found within the environment can also lead to further understanding and monitoring of other extreme weather events in the future.

Molecular phylogeny and larval morphological diversity of the lanternfish genus Hygophum (Teleostei: Myctophidae).

PubMed

Yamaguchi, M; Miya, M; Okiyama, M; Nishida, M

2000-04-01

Larvae of the deep-sea lanternfish genus Hygophum (Myctophidae) exhibit a remarkable morphological diversity that is quite unexpected, considering their homogeneous adult morphology. In an attempt to elucidate the evolutionary patterns of such larval morphological diversity, nucleotide sequences of a portion of the mitochondrially encoded 16S ribosomal RNA gene were determined for seven Hygophum species and three outgroup taxa. Secondary structure-based alignment resulted in a character matrix consisting of 1172 bp of unambiguously aligned sequences, which were subjected to phylogenetic analyses using maximum-parsimony, maximum-likelihood, and neighbor-joining methods. The resultant tree topologies from the three methods were congruent, with most nodes, including that of the genus Hygophum, being strongly supported by various tree statistics. The most parsimonious reconstruction of the three previously recognized, distinct larval morphs onto the molecular phylogeny revealed that one of the morphs had originated as the common ancestor of the genus, the other two having diversified separately in two subsequent major clades. The patterns of such diversification are discussed in terms of the unusual larval eye morphology and geographic distribution. Copyright 2000 Academic Press.

Beam based alignment and its relevance in Indus-2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jena, Saroj Kumar; Husain, Riyasat; Gandhi, M. L.

2015-09-15

Initially in the Indus-2 storage ring, the closed orbit distortion (COD) could be best corrected to 1.3 mm rms in the horizontal and 0.43 mm rms in the vertical plane. The strength of the corrector magnets required high values for COD correction. This revealed that offsets in COD readout by the beam position monitors (BPMs) played a role in not achieving a rms COD lower than the above value. Thus, the offset between the electrical center of BPMs and the magnetic center of the nearest quadrupole magnet could be estimated using the beam based alignment (BBA) method. It prefers thatmore » the quadrupole magnet is able to be controlled individually and active shunt power supply (ASPS) system was designed for this purpose that works efficiently. This paper describes the methodology of BBA, topology of ASPS and its performance, and COD minimization using the measured BPM offsets. After BBA, the COD could be reduced to 0.45 mm rms and 0.2 mm rms in horizontal and vertical planes, respectively.« less

Swarm observation of field-aligned current and electric field in multiple arc systems

NASA Astrophysics Data System (ADS)

Wu, J.; Knudsen, D. J.; Gillies, M.; Donovan, E.; Burchill, J. K.

2017-12-01

It is often thought that auroral arcs are a direct consequence of upward field-aligned currents. In fact, the relation between currents and brightness is more complicated. Multiple auroral arc systems provide and opportunity to study this relation in detail. In this study, we have identified two types of FAC configurations in multiple parallel arc systems using ground-based optical data from the THEMIS all-sky imagers (ASIs), magnetometers and electric field instruments onboard the Swarm satellites during the period from December 2013 to March 2015. In type 1 events, each arc is an intensification within a broad, unipolar current sheet and downward currents only exist outside the upward current sheet. These types of events are termed "unipolar FAC" events. In type 2 events, multiple arc systems represent a collection of multiple up/down current pairs, which are termed as "multipolar FAC" events. Comparisons of these two types of FAC events are presented with 17 "unipolar FAC" events and 12 "multipolar FAC" events. The results show that "unipolar FAC" and "multipolar FAC" events have systematic differences in terms of MLT, arc width and separation, and dependence on substorm onset time. For "unipolar FAC" events, significant electric field enhancements are shown on the edges of the broad upward current sheet. Electric field fluctuations inside the multiple arc system can be large or small. For "multipolar FAC" events, a strong correlation between magnetic and electric field indicate uniform conductance within each upward current sheet. The electrodynamical structures of multiple arc systems presented in this paper represents a step toward understanding arc generation.

Counterstreaming solar wind halo electron events on open field lines?

NASA Technical Reports Server (NTRS)

Gosling, J. T.; Mccomas, D. J.; Phillips, J. L.

1992-01-01

Counterstreaming solar wind halo electron events have been identified as a common 1 AU signature of coronal mass ejection events, and have generally been interpreted as indicative of closed magnetic field topologies, i.e., magnetic loops or flux ropes rooted at both ends in the Sun, or detached plasmoids. In this paper we examine the possibility that these events may instead occur preferentially on open field lines, and that counterstreaming results from reflection or injection behind interplanetary shocks or from mirroring from regions of compressed magnetic field farther out in the heliosphere. We conclude that neither of these suggested sources of counterstreaming electron beams is viable and that the best interpretation of observed counterstreaming electron events in the solar wind remains that of passage of closed field structures.

Reconstructing particle masses in events with displaced vertices

NASA Astrophysics Data System (ADS)

Cottin, Giovanna

2018-03-01

We propose a simple way to extract particle masses given a displaced vertex signature in event topologies where two long-lived mother particles decay to visible particles and an invisible daughter. The mother could be either charged or neutral and the neutral daughter could correspond to a dark matter particle in different models. The method allows to extract the parent and daughter masses by using on-shell conditions and energy-momentum conservation, in addition to the displaced decay positions of the parents, which allows to solve the kinematic equations fully on an event-by-event basis. We show the validity of the method by means of simulations including detector effects. If displaced events are seen in discovery searches at the Large Hadron Collider (LHC), this technique can be applied.

Real-time calibration and alignment of the LHCb RICH detectors

NASA Astrophysics Data System (ADS)

HE, Jibo

2017-12-01

In 2015, the LHCb experiment established a new and unique software trigger strategy with the purpose of increasing the purity of the signal events by applying the same algorithms online and offline. To achieve this, real-time calibration and alignment of all LHCb sub-systems is needed to provide vertexing, tracking, and particle identification of the best possible quality. The calibration of the refractive index of the RICH radiators, the calibration of the Hybrid Photon Detector image, and the alignment of the RICH mirror system, are reported in this contribution. The stability of the RICH performance and the particle identification performance are also discussed.

Site-directed fluorescence labeling reveals a revised N-terminal membrane topology and functional periplasmic residues in the Escherichia coli cell division protein FtsK.

PubMed

Berezuk, Alison M; Goodyear, Mara; Khursigara, Cezar M

2014-08-22

In Escherichia coli, FtsK is a large integral membrane protein that coordinates chromosome segregation and cell division. The N-terminal domain of FtsK (FtsKN) is essential for division, and the C terminus (FtsKC) is a well characterized DNA translocase. Although the function of FtsKN is unknown, it is suggested that FtsK acts as a checkpoint to ensure DNA is properly segregated before septation. This may occur through modulation of protein interactions between FtsKN and other division proteins in both the periplasm and cytoplasm; thus, a clear understanding of how FtsKN is positioned in the membrane is required to characterize these interactions. The membrane topology of FtsKN was initially determined using site-directed reporter fusions; however, questions regarding this topology persist. Here, we report a revised membrane topology generated by site-directed fluorescence labeling. The revised topology confirms the presence of four transmembrane segments and reveals a newly identified periplasmic loop between the third and fourth transmembrane domains. Within this loop, four residues were identified that, when mutated, resulted in the appearance of cellular voids. High resolution transmission electron microscopy of these voids showed asymmetric division of the cytoplasm in the absence of outer membrane invagination or visible cell wall ingrowth. This uncoupling reveals a novel role for FtsK in linking cell envelope septation events and yields further evidence for FtsK as a critical checkpoint of cell division. The revised topology of FtsKN also provides an important platform for future studies on essential interactions required for this process. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Final Report: Nanoscale Dynamical Heterogeneity in Complex Magnetic Materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kevan, Stephen

2016-05-27

A magnetic object can be demagnetized by dropping it on a hard surface, but what does ‘demagnetized’ actually mean? In 1919 Heinrich Barkhausen proved the existence of magnetic domains, which are regions of uniform magnetization that are much larger than atoms but much smaller than a macroscopic object. A material is fully magnetized when domain magnetizations are aligned, while it is demagnetized when the domain magnetizations are randomly oriented and the net magnetization is zero. The heterogeneity of a demagnetized object leads to interesting questions. Magnets are unstable when their poles align, and stable when their poles anti-align, so whymore » is the magnetized state ever stable? What do domains look like? What is the structure of a domain wall? How does the magnetized state transform to the demagnetized state? How do domains appear and disappear? What are the statistical properties of domains and how do these vary as the domain pattern evolves? Some of these questions remain the focus of intense study nearly a century after Barkhausen’s discovery. For example, just a few years ago a new kind of magnetic texture called a skyrmion was discovered. A skyrmion is a magnetic domain that is a nanometer-scale, topologically protected vortex. ‘Topologically protected’ means that skyrmions are hard to destroy and so are stable for extended periods. Skyrmions are characterized by integral quantum numbers and are observed to move with little dissipation and so could store and process information with very low power input. Our research project uses soft x-rays, which offer very high magnetic contrast, to probe magnetic heterogeneity and to measure how it evolves in time under external influences. We will condition a soft x-ray beam so that the wave fronts will be coherent, that is, they will be smooth and well-defined. When coherent soft x-ray beam interacts with a magnetic material, the magnetic heterogeneity is imprinted onto the wave fronts and projected into a diffraction pattern. These patterns will be analyzed to understand the structure, motion, and statistical properties of magnetic textures and their boundaries. Over the period covered by this grant we will study a) the structure, phase behaviors, and motion of skyrmions in various thin film materials, and 2) the statistical properties of Barkhausen cascades, which are a key factor in how magnetization varies.« less

Low-altitude ion heating with downflowing and upflowing ions

NASA Astrophysics Data System (ADS)

Shen, Y.; Knudsen, D. J.; Burchill, J. K.; Howarth, A. D.; Yau, A. W.; James, G.; Miles, D.; Cogger, L. L.; Perry, G. W.

2017-12-01

Mechanisms that energize ions at the initial stage of ion upflow are still not well understood. We statistically investigate ionospheric ion energization and field-aligned motion at very low altitudes (330-730 km) using simultaneous plasma, magnetic field, wave electric field and optical data from the e-POP satellite. The high-time-resolution (10 ms) dataset enables us to study the micro-structures of ion heating and field-aligned ion motion. The ion temperature and field-aligned bulk flow velocity are derived from 2-D ion distribution functions measured by the SEI instrument. From March 2015 to March 2016, we've found 17 orbits (in total 24 ion heating periods) with clear ion heating signatures passing across the dayside cleft or the nightside auroral regions. Most of these events have consistent ion heating and flow velocity characteristics observed from both the SEI and IRM instruments. The perpendicular ion temperature goes up to 4.5 eV within a 2 km-wide region in some cases, in which the Radio Receiver Instrument (RRI) sees broadband extremely low frequency (BBELF) waves, demonstrating significant wave-ion heating down to as low as 350 km. The e-POP Fast Auroral Imager (FAI) and Magnetic Field (MGF) instruments show that many events are associated with active aurora and are within downward current regions. Contrary to what would be expected from mirror-force acceleration of heated ions, the majority of these heating events (17 out of 24) are associated with the core ion downflow rather than upflow. These statistical results provide us with new sights into ion heating and field-aligned flow processes at very low altitudes.

Sequence of events from the onset to the demise of the Last Interglacial: Evaluating strengths and limitations of chronologies used in climatic archives

NASA Astrophysics Data System (ADS)

Govin, A.; Capron, E.; Tzedakis, P. C.; Verheyden, S.; Ghaleb, B.; Hillaire-Marcel, C.; St-Onge, G.; Stoner, J. S.; Bassinot, F.; Bazin, L.; Blunier, T.; Combourieu-Nebout, N.; El Ouahabi, A.; Genty, D.; Gersonde, R.; Jimenez-Amat, P.; Landais, A.; Martrat, B.; Masson-Delmotte, V.; Parrenin, F.; Seidenkrantz, M.-S.; Veres, D.; Waelbroeck, C.; Zahn, R.

2015-12-01

The Last Interglacial (LIG) represents an invaluable case study to investigate the response of components of the Earth system to global warming. However, the scarcity of absolute age constraints in most archives leads to extensive use of various stratigraphic alignments to different reference chronologies. This feature sets limitations to the accuracy of the stratigraphic assignment of the climatic sequence of events across the globe during the LIG. Here, we review the strengths and limitations of the methods that are commonly used to date or develop chronologies in various climatic archives for the time span (∼140-100 ka) encompassing the penultimate deglaciation, the LIG and the glacial inception. Climatic hypotheses underlying record alignment strategies and the interpretation of tracers are explicitly described. Quantitative estimates of the associated absolute and relative age uncertainties are provided. Recommendations are subsequently formulated on how best to define absolute and relative chronologies. Future climato-stratigraphic alignments should provide (1) a clear statement of climate hypotheses involved, (2) a detailed understanding of environmental parameters controlling selected tracers and (3) a careful evaluation of the synchronicity of aligned paleoclimatic records. We underscore the need to (1) systematically report quantitative estimates of relative and absolute age uncertainties, (2) assess the coherence of chronologies when comparing different records, and (3) integrate these uncertainties in paleoclimatic interpretations and comparisons with climate simulations. Finally, we provide a sequence of major climatic events with associated age uncertainties for the period 140-105 ka, which should serve as a new benchmark to disentangle mechanisms of the Earth system's response to orbital forcing and evaluate transient climate simulations.

The Voronoi spatio-temporal data structure

NASA Astrophysics Data System (ADS)

Mioc, Darka

2002-04-01

Current GIS models cannot integrate the temporal dimension of spatial data easily. Indeed, current GISs do not support incremental (local) addition and deletion of spatial objects, and they can not support the temporal evolution of spatial data. Spatio-temporal facilities would be very useful in many GIS applications: harvesting and forest planning, cadastre, urban and regional planning, and emergency planning. The spatio-temporal model that can overcome these problems is based on a topological model---the Voronoi data structure. Voronoi diagrams are irregular tessellations of space, that adapt to spatial objects and therefore they are a synthesis of raster and vector spatial data models. The main advantage of the Voronoi data structure is its local and sequential map updates, which allows us to automatically record each event and performed map updates within the system. These map updates are executed through map construction commands that are composed of atomic actions (geometric algorithms for addition, deletion, and motion of spatial objects) on the dynamic Voronoi data structure. The formalization of map commands led to the development of a spatial language comprising a set of atomic operations or constructs on spatial primitives (points and lines), powerful enough to define the complex operations. This resulted in a new formal model for spatio-temporal change representation, where each update is uniquely characterized by the numbers of newly created and inactivated Voronoi regions. This is used for the extension of the model towards the hierarchical Voronoi data structure. In this model, spatio-temporal changes induced by map updates are preserved in a hierarchical data structure that combines events and corresponding changes in topology. This hierarchical Voronoi data structure has an implicit time ordering of events visible through changes in topology, and it is equivalent to an event structure that can support temporal data without precise temporal information. This formal model of spatio-temporal change representation is currently applied to retroactive map updates and visualization of map evolution. It offers new possibilities in the domains of temporal GIS, transaction processing, spatio-temporal queries, spatio-temporal analysis, map animation and map visualization.

Parallel discrete event simulation: A shared memory approach

NASA Technical Reports Server (NTRS)

Reed, Daniel A.; Malony, Allen D.; Mccredie, Bradley D.

1987-01-01

With traditional event list techniques, evaluating a detailed discrete event simulation model can often require hours or even days of computation time. Parallel simulation mimics the interacting servers and queues of a real system by assigning each simulated entity to a processor. By eliminating the event list and maintaining only sufficient synchronization to insure causality, parallel simulation can potentially provide speedups that are linear in the number of processors. A set of shared memory experiments is presented using the Chandy-Misra distributed simulation algorithm to simulate networks of queues. Parameters include queueing network topology and routing probabilities, number of processors, and assignment of network nodes to processors. These experiments show that Chandy-Misra distributed simulation is a questionable alternative to sequential simulation of most queueing network models.

A discussion of IceCube neutrino events, circa 2015

NASA Astrophysics Data System (ADS)

Esmaili, Arman; Palladino, Andrea; Vissani, Francesco

2016-04-01

IceCube has changed the rules of the game and continues to progress. Their observations are compatible with cosmic neutrinos undergoing 3 flavor oscillations. The topologies of the events have been used to probe ordinary and exotic physics. Still, we need independent confirmations of this assumption; the astrophysical connections heavily rely on speculations (excepting special cases, such as GRB); the amount of prompt events is not known precisely; double bang and/or Glashow resonance events are still to be seen; the energy and the angular distributions are not well-known, even if the simplest picture (isotropic flux, power law distributed in energy) is still compatible with the data. In this talk, we select specific topics concerning expectations, inferences and prospects.

Rapid Ordering in “Wet Brush” Block Copolymer/Homopolymer Ternary Blends

DOE Office of Scientific and Technical Information (OSTI.GOV)

Doerk, Gregory S.; Yager, Kevin G.

The ubiquitous presence of thermodynamically unfavored but kinetically trapped topological defects in nanopatterns formed via self-assembly of block copolymer thin films may prevent their use for many envisioned applications. Here, we demonstrate that lamellae patterns formed by symmetric polystyrene-block-poly(methyl methacrylate) diblock copolymers self-assemble and order extremely rapidly when the diblock copolymers are blended with low molecular weight homopolymers of the constituent blocks. Being in the “wet brush” regime, the homopolymers uniformly distribute within their respective self-assembled microdomains, preventing increases in domain widths. An order-of-magnitude increase in topological grain size in blends over the neat (unblended) diblock copolymer is achieved withinmore » minutes of thermal annealing as a result of the significantly higher power law exponent for ordering kinetics in the blends. Moreover, the blends are demonstrated to be capable of rapid and robust domain alignment within micrometer-scale trenches, in contrast to the corresponding neat diblock copolymer. Furthermore, these results can be attributed to the lowering of energy barriers associated with domain boundaries by bringing the system closer to an order–disorder transition through low molecular weight homopolymer blending.« less

Rapid Ordering in “Wet Brush” Block Copolymer/Homopolymer Ternary Blends

DOE PAGES

Doerk, Gregory S.; Yager, Kevin G.

2017-12-01

The ubiquitous presence of thermodynamically unfavored but kinetically trapped topological defects in nanopatterns formed via self-assembly of block copolymer thin films may prevent their use for many envisioned applications. Here, we demonstrate that lamellae patterns formed by symmetric polystyrene-block-poly(methyl methacrylate) diblock copolymers self-assemble and order extremely rapidly when the diblock copolymers are blended with low molecular weight homopolymers of the constituent blocks. Being in the “wet brush” regime, the homopolymers uniformly distribute within their respective self-assembled microdomains, preventing increases in domain widths. An order-of-magnitude increase in topological grain size in blends over the neat (unblended) diblock copolymer is achieved withinmore » minutes of thermal annealing as a result of the significantly higher power law exponent for ordering kinetics in the blends. Moreover, the blends are demonstrated to be capable of rapid and robust domain alignment within micrometer-scale trenches, in contrast to the corresponding neat diblock copolymer. Furthermore, these results can be attributed to the lowering of energy barriers associated with domain boundaries by bringing the system closer to an order–disorder transition through low molecular weight homopolymer blending.« less

Predicting the transmembrane secondary structure of ligand-gated ion channels.

PubMed

Bertaccini, E; Trudell, J R

2002-06-01

Recent mutational analyses of ligand-gated ion channels (LGICs) have demonstrated a plausible site of anesthetic action within their transmembrane domains. Although there is a consensus that the transmembrane domain is formed from four membrane-spanning segments, the secondary structure of these segments is not known. We utilized 10 state-of-the-art bioinformatics techniques to predict the transmembrane topology of the tetrameric regions within six members of the LGIC family that are relevant to anesthetic action. They are the human forms of the GABA alpha 1 receptor, the glycine alpha 1 receptor, the 5HT3 serotonin receptor, the nicotinic AChR alpha 4 and alpha 7 receptors and the Torpedo nAChR alpha 1 receptor. The algorithms utilized were HMMTOP, TMHMM, TMPred, PHDhtm, DAS, TMFinder, SOSUI, TMAP, MEMSAT and TOPPred2. The resulting predictions were superimposed on to a multiple sequence alignment of the six amino acid sequences created using the CLUSTAL W algorithm. There was a clear statistical consensus for the presence of four alpha helices in those regions experimentally thought to span the membrane. The consensus of 10 topology prediction techniques supports the hypothesis that the transmembrane subunits of the LGICs are tetrameric bundles of alpha helices.

Exotic quantum properties under high magnetic fields and pressure-induced superconductivity in layered ZrTe5 and pyrite PtBi2

NASA Astrophysics Data System (ADS)

Tian, Mingliang; Tian, Zhaorong; Ning, Wei; Mingliang Tian Team

Topological Dirac semimetal is a newly discovered class of materials which has attracted intense attention. This material can be viewed as a three-dimensional (3D) analog of graphene and has linear energy dispersion in bulk, leading to a range of exotic transport properties. Here we report direct quantum transport evidence of the 3D Dirac semimetal phase of semimetallic materials ZrTe5 and pyrite PtBi2 by angular-dependent magnetoresistance measurements under high magnetic fields up to 35 T, as well as the pressure-induced superconductivity. We observed very clear negative longitudinal magnetoresistance in ZrTe5 induced by chiral anomaly under the condition of the magnetic field aligned only along the current direction, and the extreme large unsaturated magnetoresistance in pyrite PtBi2 up to 11.2 million percent at T = 1.8 K and 33 T, which surpasses the previously reported Dirac materials, such as LaSb, WTe2 and NbP. Analysis of the Shubnikov de Haas oscillations suggest that both ZrTe5 and PtBi2\\ are likely a new topological semimetals.

PhyloTreePruner: A Phylogenetic Tree-Based Approach for Selection of Orthologous Sequences for Phylogenomics.

PubMed

Kocot, Kevin M; Citarella, Mathew R; Moroz, Leonid L; Halanych, Kenneth M

2013-01-01

Molecular phylogenetics relies on accurate identification of orthologous sequences among the taxa of interest. Most orthology inference programs available for use in phylogenomics rely on small sets of pre-defined orthologs from model organisms or phenetic approaches such as all-versus-all sequence comparisons followed by Markov graph-based clustering. Such approaches have high sensitivity but may erroneously include paralogous sequences. We developed PhyloTreePruner, a software utility that uses a phylogenetic approach to refine orthology inferences made using phenetic methods. PhyloTreePruner checks single-gene trees for evidence of paralogy and generates a new alignment for each group containing only sequences inferred to be orthologs. Importantly, PhyloTreePruner takes into account support values on the tree and avoids unnecessarily deleting sequences in cases where a weakly supported tree topology incorrectly indicates paralogy. A test of PhyloTreePruner on a dataset generated from 11 completely sequenced arthropod genomes identified 2,027 orthologous groups sampled for all taxa. Phylogenetic analysis of the concatenated supermatrix yielded a generally well-supported topology that was consistent with the current understanding of arthropod phylogeny. PhyloTreePruner is freely available from http://sourceforge.net/projects/phylotreepruner/.

A Native Intelligence Metric for Artificial Systems

DTIC Science & Technology

2002-08-01

an example to help clarify the GCEA. Say we are S and we stumble upon Stonehenge . We don’t wonder whether humans carried the stones (some...stones S encounters that may be exhibiting alignment with celestial bodies at certain seasonal times. S determines that the designer of Stonehenge had...matching of the stones with particular celestial events. The various celestial events and our prehistoric Stonehenge designer’s awareness of these events

Evolutionary profiles derived from the QR factorization of multiple structural alignments gives an economy of information.

PubMed

O'Donoghue, Patrick; Luthey-Schulten, Zaida

2005-02-25

We present a new algorithm, based on the multidimensional QR factorization, to remove redundancy from a multiple structural alignment by choosing representative protein structures that best preserve the phylogenetic tree topology of the homologous group. The classical QR factorization with pivoting, developed as a fast numerical solution to eigenvalue and linear least-squares problems of the form Ax=b, was designed to re-order the columns of A by increasing linear dependence. Removing the most linear dependent columns from A leads to the formation of a minimal basis set which well spans the phase space of the problem at hand. By recasting the problem of redundancy in multiple structural alignments into this framework, in which the matrix A now describes the multiple alignment, we adapted the QR factorization to produce a minimal basis set of protein structures which best spans the evolutionary (phase) space. The non-redundant and representative profiles obtained from this procedure, termed evolutionary profiles, are shown in initial results to outperform well-tested profiles in homology detection searches over a large sequence database. A measure of structural similarity between homologous proteins, Q(H), is presented. By properly accounting for the effect and presence of gaps, a phylogenetic tree computed using this metric is shown to be congruent with the maximum-likelihood sequence-based phylogeny. The results indicate that evolutionary information is indeed recoverable from the comparative analysis of protein structure alone. Applications of the QR ordering and this structural similarity metric to analyze the evolution of structure among key, universally distributed proteins involved in translation, and to the selection of representatives from an ensemble of NMR structures are also discussed.

Analyzing and synthesizing phylogenies using tree alignment graphs.

PubMed

Smith, Stephen A; Brown, Joseph W; Hinchliff, Cody E

2013-01-01

Phylogenetic trees are used to analyze and visualize evolution. However, trees can be imperfect datatypes when summarizing multiple trees. This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer, incomplete lineage sorting, and hybridization, as well as topological conflict between datasets. Additionally, researchers may want to combine information from sets of trees that have partially overlapping taxon sets. To address the problem of analyzing sets of trees with conflicting relationships and partially overlapping taxon sets, we introduce methods for aligning, synthesizing and analyzing rooted phylogenetic trees within a graph, called a tree alignment graph (TAG). The TAG can be queried and analyzed to explore uncertainty and conflict. It can also be synthesized to construct trees, presenting an alternative to supertrees approaches. We demonstrate these methods with two empirical datasets. In order to explore uncertainty, we constructed a TAG of the bootstrap trees from the Angiosperm Tree of Life project. Analysis of the resulting graph demonstrates that areas of the dataset that are unresolved in majority-rule consensus tree analyses can be understood in more detail within the context of a graph structure, using measures incorporating node degree and adjacency support. As an exercise in synthesis (i.e., summarization of a TAG constructed from the alignment trees), we also construct a TAG consisting of the taxonomy and source trees from a recent comprehensive bird study. We synthesized this graph into a tree that can be reconstructed in a repeatable fashion and where the underlying source information can be updated. The methods presented here are tractable for large scale analyses and serve as a basis for an alternative to consensus tree and supertree methods. Furthermore, the exploration of these graphs can expose structures and patterns within the dataset that are otherwise difficult to observe.

Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs

PubMed Central

Smith, Stephen A.; Brown, Joseph W.; Hinchliff, Cody E.

2013-01-01

Phylogenetic trees are used to analyze and visualize evolution. However, trees can be imperfect datatypes when summarizing multiple trees. This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer, incomplete lineage sorting, and hybridization, as well as topological conflict between datasets. Additionally, researchers may want to combine information from sets of trees that have partially overlapping taxon sets. To address the problem of analyzing sets of trees with conflicting relationships and partially overlapping taxon sets, we introduce methods for aligning, synthesizing and analyzing rooted phylogenetic trees within a graph, called a tree alignment graph (TAG). The TAG can be queried and analyzed to explore uncertainty and conflict. It can also be synthesized to construct trees, presenting an alternative to supertrees approaches. We demonstrate these methods with two empirical datasets. In order to explore uncertainty, we constructed a TAG of the bootstrap trees from the Angiosperm Tree of Life project. Analysis of the resulting graph demonstrates that areas of the dataset that are unresolved in majority-rule consensus tree analyses can be understood in more detail within the context of a graph structure, using measures incorporating node degree and adjacency support. As an exercise in synthesis (i.e., summarization of a TAG constructed from the alignment trees), we also construct a TAG consisting of the taxonomy and source trees from a recent comprehensive bird study. We synthesized this graph into a tree that can be reconstructed in a repeatable fashion and where the underlying source information can be updated. The methods presented here are tractable for large scale analyses and serve as a basis for an alternative to consensus tree and supertree methods. Furthermore, the exploration of these graphs can expose structures and patterns within the dataset that are otherwise difficult to observe. PMID:24086118

Hippocampal Replay Captures the Unique Topological Structure of a Novel Environment

PubMed Central

Wu, Xiaojing

2014-01-01

Hippocampal place-cell replay has been proposed as a fundamental mechanism of learning and memory, which might support navigational learning and planning. An important hypothesis of relevance to these proposed functions is that the information encoded in replay should reflect the topological structure of experienced environments; that is, which places in the environment are connected with which others. Here we report several attributes of replay observed in rats exploring a novel forked environment that support the hypothesis. First, we observed that overlapping replays depicting divergent trajectories through the fork recruited the same population of cells with the same firing rates to represent the common portion of the trajectories. Second, replay tended to be directional and to flip the represented direction at the fork. Third, replay-associated sharp-wave–ripple events in the local field potential exhibited substructure that mapped onto the maze topology. Thus, the spatial complexity of our recording environment was accurately captured by replay: the underlying neuronal activities reflected the bifurcating shape, and both directionality and associated ripple structure reflected the segmentation of the maze. Finally, we observed that replays occurred rapidly after small numbers of experiences. Our results suggest that hippocampal replay captures learned information about environmental topology to support a role in navigation. PMID:24806672

NOBAI: a web server for character coding of geometrical and statistical features in RNA structure

PubMed Central

Knudsen, Vegeir; Caetano-Anollés, Gustavo

2008-01-01

The Numeration of Objects in Biology: Alignment Inferences (NOBAI) web server provides a web interface to the applications in the NOBAI software package. This software codes topological and thermodynamic information related to the secondary structure of RNA molecules as multi-state phylogenetic characters, builds character matrices directly in NEXUS format and provides sequence randomization options. The web server is an effective tool that facilitates the search for evolutionary history embedded in the structure of functional RNA molecules. The NOBAI web server is accessible at ‘http://www.manet.uiuc.edu/nobai/nobai.php’. This web site is free and open to all users and there is no login requirement. PMID:18448469

Vortex dynamics in the wake of a pivoted cylinder undergoing vortex-induced vibrations with elliptic trajectories

NASA Astrophysics Data System (ADS)

Marble, Erik; Morton, Christopher; Yarusevych, Serhiy

2018-05-01

Vortex-induced vibrations of a pivoted cylinder are investigated experimentally at a fixed Reynolds number of 3100, a mass ratio of 10.8, and a range of reduced velocities, 4.42 ≤ U^* ≤ 9.05. For these conditions, the cylinder traces elliptic trajectories, with the experimental conditions producing three out of four possible combinations of orbiting direction and primary axis alignment relative to the incoming flow. The study focuses on the quantitative analysis of wake topology and its relation to this type of structural response. Velocity fields were measured using time-resolved, two-component particle image velocimetry (TR-PIV). These results show that phase-averaged wake topology generally agrees with the Morse and Williamson (J Fluids Struct 25(4):697-712, 2009) shedding map for one-degree-of-freedom vortex-induced vibrations, with 2S, 2{P}o, and 2P shedding patterns observed within the range of reduced velocities studied here. Vortex tracking and vortex strength quantification are used to analyze the vortex shedding process and how it relates to cylinder response. In the case of 2S vortex shedding, vortices are shed when the cylinder is approaching the maximum transverse displacement and reaches the streamwise equilibrium. 2P vortices are shed approximately half a period earlier in the cylinder's elliptic trajectory. Leading vortices shed immediately after the peak in transverse oscillation and trailing vortices shed near the equilibrium of transverse oscillation. The orientation and direction of the cylinder's elliptic trajectory are shown to influence the timing of vortex shedding, inducing changes in the 2P wake topology.

MAGNETIC TOPOLOGY OF BUBBLES IN QUIESCENT PROMINENCES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dudik, J.; Aulanier, G.; Schmieder, B.

We study a polar-crown prominence with a bubble and its plume observed in several coronal filters by the SDO/AIA and in H{alpha} by the MSDP spectrograph in Bialkow (Poland) to address the following questions: what is the brightness of prominence bubbles in EUV with respect to the corona outside of the prominence and the prominence coronal cavity? What is the geometry and topology of the magnetic field in the bubble? What is the nature of the vertical threads seen within prominences? We find that the brightness of the bubble and plume is lower than the brightness of the corona outsidemore » of the prominence, and is similar to that of the coronal cavity. We constructed linear force-free models of prominences with bubbles, where the flux rope is perturbed by inclusion of parasitic bipoles. The arcade field lines of the bipole create the bubble, which is thus devoid of magnetic dips. Shearing the bipole or adding a second one can lead to cusp-shaped prominences with bubbles similar to the observed ones. The bubbles have complex magnetic topology, with a pair of coronal magnetic null points linked by a separator outlining the boundary between the bubble and the prominence body. We conjecture that plume formation involves magnetic reconnection at the separator. Depending on the viewing angle, the prominence can appear either anvil-shaped with predominantly horizontal structures, or cusp-shaped with predominantly vertical structuring. The latter is an artifact of the alignment of magnetic dips with respect to the prominence axis and the line of sight.« less

Alignment-free detection of horizontal gene transfer between closely related bacterial genomes.

PubMed

Domazet-Lošo, Mirjana; Haubold, Bernhard

2011-09-01

Bacterial epidemics are often caused by strains that have acquired their increased virulence through horizontal gene transfer. Due to this association with disease, the detection of horizontal gene transfer continues to receive attention from microbiologists and bioinformaticians alike. Most software for detecting transfer events is based on alignments of sets of genes or of entire genomes. But despite great advances in the design of algorithms and computer programs, genome alignment remains computationally challenging. We have therefore developed an alignment-free algorithm for rapidly detecting horizontal gene transfer between closely related bacterial genomes. Our implementation of this algorithm is called alfy for "ALignment Free local homologY" and is freely available from http://guanine.evolbio.mpg.de/alfy/. In this comment we demonstrate the application of alfy to the genomes of Staphylococcus aureus. We also argue that-contrary to popular belief and in spite of increasing computer speed-algorithmic optimization is becoming more, not less, important if genome data continues to accumulate at the present rate.

Measurements of spin alignment of vector mesons and global polarization of hyperons with ALICE at the LHC

NASA Astrophysics Data System (ADS)

Mohanty, Bedangadas

2018-02-01

We present the measurements related to global polarization of Λ hyperons and spin alignment of K*0 vector mesons at mid-rapidity for Pb-Pb collisions at = 2.76 TeV using the ALICE detector at the LHC. The global polarization measurements are carried out with respect to the first order event plane while the spin alignment measurements are carried out with respect to the production plane. No global polarization signal for Λ is observed for 5-15% and 15-50% central Pb-Pb collisions. The spin density matrix element ρ00 is found to have values slightly below ⅓ at low transverse momentum (pT) for K*0 mesons, while it is consistent with ⅓ (no spin alignment) at higher pT. No spin alignment is observed for K*0 in pp collisions at √s = 13 TeV and for the spin zero hadron K0S in 20-40% Pb-Pb collisions at = 2.76 TeV.

A Lossy Compression Technique Enabling Duplication-Aware Sequence Alignment

PubMed Central

Freschi, Valerio; Bogliolo, Alessandro

2012-01-01

In spite of the recognized importance of tandem duplications in genome evolution, commonly adopted sequence comparison algorithms do not take into account complex mutation events involving more than one residue at the time, since they are not compliant with the underlying assumption of statistical independence of adjacent residues. As a consequence, the presence of tandem repeats in sequences under comparison may impair the biological significance of the resulting alignment. Although solutions have been proposed, repeat-aware sequence alignment is still considered to be an open problem and new efficient and effective methods have been advocated. The present paper describes an alternative lossy compression scheme for genomic sequences which iteratively collapses repeats of increasing length. The resulting approximate representations do not contain tandem duplications, while retaining enough information for making their comparison even more significant than the edit distance between the original sequences. This allows us to exploit traditional alignment algorithms directly on the compressed sequences. Results confirm the validity of the proposed approach for the problem of duplication-aware sequence alignment. PMID:22518086

Data Day: Highlighting the Geographic Skills in a Schoolwide Event

ERIC Educational Resources Information Center

Lewis, Lydia

2010-01-01

Data Day, an event that is the culmination of a multiple-week unit, is the perfect opportunity to work across disciplines and, in particular, aligns beautifully with skills and objectives geography teachers work on with their students. Bruce Jones at The Blake School in Hopkins, Minnesota, was the originator of Data Day. Jones described the…

Multipoint connectivity analysis of the May 2007 solar energetic particle events

NASA Astrophysics Data System (ADS)

Chollet, E. E.; Mewaldt, R. A.; Cummings, A. C.; Gosling, J. T.; Haggerty, D. K.; Hu, Q.; Larson, D.; Lavraud, B.; Leske, R. A.; Opitz, A.; Roelof, E. C.; Russell, C. T.; Sauvaud, J.-A.

2010-12-01

In May of 2007, the STEREO Ahead and Behind spacecraft, along with the ACE spacecraft situated between the two STEREO spacecraft, observed two small solar energetic particle (SEP) events. STEREO-A and -B observed nearly identical time profiles in the 19 May event, but in the 23 May event, the protons arrived significantly earlier at STEREO-A than at STEREO-B and the time-intensity profiles were markedly different. We present SEP anisotropy, suprathermal electron pitch angle and solar wind data to demonstrate distortion in the magnetic field topology produced by the passage of multiple interplanetary coronal mass ejections on 22 and 23 May, causing the two spacecraft to magnetically connect to different points back at the Sun. This pair of events illustrates the power of multipoint observations in detailed interpretation of complex events, since only a small shift in observer location results in different magnetic field line connections and different SEP time-intensity profiles.

Generating functions and stability study of multivariate self-excited epidemic processes

NASA Astrophysics Data System (ADS)

Saichev, A. I.; Sornette, D.

2011-09-01

We present a stability study of the class of multivariate self-excited Hawkes point processes, that can model natural and social systems, including earthquakes, epileptic seizures and the dynamics of neuron assemblies, bursts of exchanges in social communities, interactions between Internet bloggers, bank network fragility and cascading of failures, national sovereign default contagion, and so on. We present the general theory of multivariate generating functions to derive the number of events over all generations of various types that are triggered by a mother event of a given type. We obtain the stability domains of various systems, as a function of the topological structure of the mutual excitations across different event types. We find that mutual triggering tends to provide a significant extension of the stability (or subcritical) domain compared with the case where event types are decoupled, that is, when an event of a given type can only trigger events of the same type.

Fluoride export (FEX) proteins from fungi, plants and animals are 'single barreled' channels containing one functional and one vestigial ion pore

PubMed Central

Berbasova, Tetyana; Nallur, Sunitha; Sells, Taylor; Smith, Kathryn D.; Gordon, Patricia B.; Tausta, Susan Lori

2017-01-01

The fluoride export protein (FEX) in yeast and other fungi provides tolerance to fluoride (F-), an environmentally ubiquitous anion. FEX efficiently eliminates intracellular fluoride that otherwise would accumulate at toxic concentrations. The FEX homolog in bacteria, Fluc, is a ‘double-barreled’ channel formed by dimerization of two identical or similar subunits. FEX in yeast and other eukaryotes is a monomer resulting from covalent fusion of the two subunits. As a result, both potential fluoride pores are created from different parts of the same protein. Here we identify FEX proteins from two multicellular eukaryotes, a plant Arabidopsis thaliana and an animal Amphimedon queenslandica, by demonstrating significant fluoride tolerance when these proteins are heterologously expressed in the yeast Saccharomyces cerevisiae. Residues important for eukaryotic FEX function were determined by phylogenetic sequence alignment and functional analysis using a yeast growth assay. Key residues of the fluoride channel are conserved in only one of the two potential fluoride-transporting pores. FEX activity is abolished upon mutation of residues in this conserved pore, suggesting that only one of the pores is functional. The same topology is conserved for the newly identified FEX proteins from plant and animal. These data suggest that FEX family of fluoride channels in eukaryotes are ‘single-barreled’ transporters containing one functional pore and a second non-functional vestigial remnant of a homologous gene fusion event. PMID:28472134

A new yeti crab phylogeny: Vent origins with indications of regional extinction in the East Pacific

PubMed Central

Liu, Xinming; Lin, Rongcheng; Li, Xinzheng; Won, Yong-Jin

2018-01-01

The recent discovery of two new species of kiwaid squat lobsters on hydrothermal vents in the Pacific Ocean and in the Pacific sector of the Southern Ocean has prompted a re-analysis of Kiwaid biogeographical history. Using a larger alignment with more fossil calibrated nodes than previously, we consider the precise relationship between Kiwaidae, Chirostylidae and Eumunididae within Chirostyloidea (Decapoda: Anomura) to be still unresolved at present. Additionally, the placement of both new species within a new “Bristly” clade along with the seep-associated Kiwa puravida is most parsimoniously interpreted as supporting a vent origin for the family, rather than a seep-to-vent progression. Fossil-calibrated divergence analysis indicates an origin for the clade around the Eocene-Oligocene boundary in the eastern Pacific ~33–38 Ma, coincident with a lowering of bottom temperatures and increased ventilation in the Pacific deep sea. Likewise, the mid-Miocene (~10–16 Ma) rapid radiation of the new Bristly clade also coincides with a similar cooling event in the tropical East Pacific. The distribution, diversity, tree topology and divergence timing of Kiwaidae in the East Pacific is most consistent with a pattern of extinctions, recolonisations and radiations along fast-spreading ridges in this region and may have been punctuated by large-scale fluctuations in deep-water ventilation and temperature during the Cenozoic; further affecting the viability of Kiwaidae populations along portions of mid-ocean ridge. PMID:29547631

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abe, Toshinori

We present a measurement of the rate of gluon splitting into bottom quarks, g --> b anti-b, in hadronic Z 0 decays collected by SLD from 1996 to 1998. The analysis was performed by looking for secondary bottom production in 4-jet events of any primary avor. A topological vertex mass technique was used to tag the two jets with the smallest angle between them as b/anti-b. We obtained a rate of g --> b anti-b per hadronic event to be (3.07 ± 0.71(stat:) ± 0.66(syst:)) × 10³ (preliminary).

Experiment Pamir-3. Coplanar emission of high energy gamma-quanta at interaction of hadrons with nuclei of air atoms at energies above 10 to the 7th power GeV

NASA Technical Reports Server (NTRS)

Asatiani, T. L.; Genina, L. E.; Zatsepin, G. T.

1985-01-01

A systematic analysis of large gamma families, detected in X-ray emulsion chambers, cases of multicore halos have been observed, and among them five events in which the halo is divided into three of four separate cores with their alignment observed in the target diagram (coplanarity of axes of corresponding electron photon cascades). The halo alignment (tendency to the straight line) leads to the aximuthal asymmetry (thrust). The analysis of lateral and momentum distributions of particles in these families shows that they also have thrust that correlates with the direction of the halo core alignment.

Polar cap particle precipitation and aurora: Review and commentary

NASA Astrophysics Data System (ADS)

Newell, Patrick T.; Liou, Kan; Wilson, Gordon R.

2009-02-01

Polar rain has a beautiful set of symmetry properties, individually established, but not previously discussed collectively, which can be organized by a single unifying principle. The key polar rain properties are favored hemisphere (controlled by the interplanetary magnetic field Bx), dawn/dusk gradient (IMF By), merging rate (IMF Bz or more generally d[Phi]MP/dt), nightside/dayside gradient, and seasonal effect. We argue that all five properties involve variants on a single theme: the further downstream a field line exits the magnetosphere (or less directly points toward the solar wind electron heat flux), the weaker the polar rain. This effect is the result of the requirements of charge quasi-neutrality, and because the ion thermal velocity declines and the tailward ion bulk flow velocity rises moving down tail from the frontside magnetopause. Polar cap arcs (or more properly, high-latitude sun-aligned arcs) are largely complementary to the polar rain, occurring most frequently when the dayside merging rate is low, and thus when polar rain is weak. Sun-aligned arcs are often considered as originating either in the polar rain or the expansion of the plasma sheet into the polar cap. In fact three quite distinct types of sun-aligned high-latitude arcs exist, two common, and one rare. One type of arc occurs as intensifications of the polar rain, and is common, but weak, typically <0.1 ergs/cm2 s, and lacks associated ion precipitation. A second category of Sun-aligned arcs with energy flux >0.1 ergs/cm2 s usually occurs adjacent to the auroral oval, and includes ion precipitation. The plasma regime of these common, and at times intense, arcs is often distinct from the oval which they abut. Convection alone does not specify the open/closed nature of these arcs, because multiple narrow convection reversals are common around such arcs, and the arcs themselves can be embedded within flows that are either sunward or anti-sunward. These observational facts do not neatly fit into either a plasma sheet origin or a polar rain origin (e.g., the necessity to abut the auroral oval, and the presence of ions does not fit the properties of polar rain, which can in any event be nearly absent for northward interplanetary magnetic field). One theory is that such arcs are associated with merging tailward of the cusp. Both of these common types of sun-aligned arcs fade within about 30 min of a southward IMF turning. The third, and rarest, category of sun-aligned arcs are intense, well detached from the auroral oval, contain plasma sheet origin ion precipitation as well as electrons, and persist for hours after a southward turning. These intense detached sun-aligned arcs can rapidly cross the polar cap, sometimes multiple times. Most events discussed in the literature as "theta-aurora" do not fit into this category (for example, although they may appear detached in images, they abut the oval in particle data, and do not have the persistence of detached events under southward IMF turnings). It is possible that no single theory can account for all three types of sun-aligned arcs. Solar energetic particle (SEP) events are at times used to demarcate polar cap open/closed boundaries. Although this works at times, examples exist where this method fails (e.g., very quiet conditions for which SEP reaches below L=4), and the method should be used with caution. Finally, it is shown that, although it is rare, the polar cap can at times completely close.

Dynamics of Genome Rearrangement in Bacterial Populations

PubMed Central

Darling, Aaron E.; Miklós, István; Ragan, Mark A.

2008-01-01

Genome structure variation has profound impacts on phenotype in organisms ranging from microbes to humans, yet little is known about how natural selection acts on genome arrangement. Pathogenic bacteria such as Yersinia pestis, which causes bubonic and pneumonic plague, often exhibit a high degree of genomic rearrangement. The recent availability of several Yersinia genomes offers an unprecedented opportunity to study the evolution of genome structure and arrangement. We introduce a set of statistical methods to study patterns of rearrangement in circular chromosomes and apply them to the Yersinia. We constructed a multiple alignment of eight Yersinia genomes using Mauve software to identify 78 conserved segments that are internally free from genome rearrangement. Based on the alignment, we applied Bayesian statistical methods to infer the phylogenetic inversion history of Yersinia. The sampling of genome arrangement reconstructions contains seven parsimonious tree topologies, each having different histories of 79 inversions. Topologies with a greater number of inversions also exist, but were sampled less frequently. The inversion phylogenies agree with results suggested by SNP patterns. We then analyzed reconstructed inversion histories to identify patterns of rearrangement. We confirm an over-representation of “symmetric inversions”—inversions with endpoints that are equally distant from the origin of chromosomal replication. Ancestral genome arrangements demonstrate moderate preference for replichore balance in Yersinia. We found that all inversions are shorter than expected under a neutral model, whereas inversions acting within a single replichore are much shorter than expected. We also found evidence for a canonical configuration of the origin and terminus of replication. Finally, breakpoint reuse analysis reveals that inversions with endpoints proximal to the origin of DNA replication are nearly three times more frequent. Our findings represent the first characterization of genome arrangement evolution in a bacterial population evolving outside laboratory conditions. Insight into the process of genomic rearrangement may further the understanding of pathogen population dynamics and selection on the architecture of circular bacterial chromosomes. PMID:18650965

Pitfalls in alignment of observation models resolved using PROV as an upper ontology

NASA Astrophysics Data System (ADS)

Cox, S. J. D.

2015-12-01

A number of models for observation metadata have been developed in the earth and environmental science communities, including OGC's Observations and Measurements (O&M), the ecosystems community's Extensible Observation Ontology (OBOE), the W3C's Semantic Sensor Network Ontology (SSNO), and the CUAHSI/NSF Observations Data Model v2 (ODM2). In order to combine data formalized in the various models, mappings between these must be developed. In some cases this is straightforward: since ODM2 took O&M as its starting point, their terminology is almost completely aligned. In the eco-informatics world observations are almost never made in isolation of other observations, so OBOE pays particular attention to groupings, with multiple atomic 'Measurements' in each oboe:Observation which does not have a result of its own and thus plays a different role to an om:Observation. And while SSN also adopted terminology from O&M, mapping is confounded by the fact that SSN uses DOLCE as its foundation and places ssn:Observations as 'Social Objects' which are explicitly disjoint from 'Events', while O&M is formalized as part of the ISO/TC 211 harmonised (UML) model and sees om:Observations as value assignment activities. Foundational ontologies (such as BFO, GFO, UFO or DOLCE) can provide a framework for alignment, but different upper ontologies can be based in profoundly different worldviews and use of incommensurate frameworks can confound rather than help. A potential resolution is provided by comparing recent studies that align SSN and O&M, respectively, with the PROV-O ontology. PROV-O provides just three base classes: Entity, Activity and Agent. om:Observation is sub-classed from prov:Activity, while ssn:Observation is sub-classed from prov:Entity. This confirms that, despite the same name, om:Observation and ssn:Observation denote different aspects of the observation process: the observation event, and the record of the observation event, respectively. Alignment with the simple PROV-O classes has clarified this issue in a way that had previously proved difficult to resolve. The simple 3-class base model from PROV appears to provide just enough logic to serve as a lightweight upper ontology, particularly for workflow or process-based information.

2010 August 1–2 Sympathetic Eruptions. II. Magnetic Topology of the MHD Background Field

DOE Office of Scientific and Technical Information (OSTI.GOV)

Titov, Viacheslav S.; Mikić, Zoran; Török, Tibor

Using a potential field source-surface (PFSS) model, we recently analyzed the global topology of the background coronal magnetic field for a sequence of coronal mass ejections (CMEs) that occurred on 2010 August 1–2. Here we repeat this analysis for the background field reproduced by a magnetohydrodynamic (MHD) model that incorporates plasma thermodynamics. As for the PFSS model, we find that all three CME source regions contain a coronal hole (CH) that is separated from neighboring CHs by topologically very similar pseudo-streamer structures. However, the two models yield very different results for the size, shape, and flux of the CHs. Wemore » find that the helmet-streamer cusp line, which corresponds to a source-surface null line in the PFSS model, is structurally unstable and does not form in the MHD model. Our analysis indicates that, generally, in MHD configurations, this line instead consists of a multiple-null separator passing along the edge of disconnected-flux regions. Some of these regions are transient and may be the origin of the so-called streamer blobs. We show that the core topological structure of such blobs is a three-dimensional “plasmoid” consisting of two conjoined flux ropes of opposite handedness, which connect at a spiral null point of the magnetic field. Our analysis reveals that such plasmoids also appear in pseudo-streamers on much smaller scales. These new insights into the coronal magnetic topology provide some intriguing implications for solar energetic particle events and for the properties of the slow solar wind.« less

2010 August 1-2 Sympathetic Eruptions. II. Magnetic Topology of the MHD Background Field

NASA Astrophysics Data System (ADS)

Titov, Viacheslav S.; Mikić, Zoran; Török, Tibor; Linker, Jon A.; Panasenco, Olga

2017-08-01

Using a potential field source-surface (PFSS) model, we recently analyzed the global topology of the background coronal magnetic field for a sequence of coronal mass ejections (CMEs) that occurred on 2010 August 1-2. Here we repeat this analysis for the background field reproduced by a magnetohydrodynamic (MHD) model that incorporates plasma thermodynamics. As for the PFSS model, we find that all three CME source regions contain a coronal hole (CH) that is separated from neighboring CHs by topologically very similar pseudo-streamer structures. However, the two models yield very different results for the size, shape, and flux of the CHs. We find that the helmet-streamer cusp line, which corresponds to a source-surface null line in the PFSS model, is structurally unstable and does not form in the MHD model. Our analysis indicates that, generally, in MHD configurations, this line instead consists of a multiple-null separator passing along the edge of disconnected-flux regions. Some of these regions are transient and may be the origin of the so-called streamer blobs. We show that the core topological structure of such blobs is a three-dimensional “plasmoid” consisting of two conjoined flux ropes of opposite handedness, which connect at a spiral null point of the magnetic field. Our analysis reveals that such plasmoids also appear in pseudo-streamers on much smaller scales. These new insights into the coronal magnetic topology provide some intriguing implications for solar energetic particle events and for the properties of the slow solar wind.

Multiwavelength Characteristics of Microflares

NASA Astrophysics Data System (ADS)

Poduval, Bala; Schmelz, J. T.

2016-10-01

We present the multiwavelength characteristic of microflare detected in the SDO/AIA and IRIS images using the Automated Microevent-finding Code (AMC). We have catalogued independent events with information such as location on the disk, size, lifetime and peak flux, and obtained their frequency distribution. We mapped these events to other wavelengths, using their location information, to study their associated features, and infer the temperature characteristics and evolution. Moreover, we obtained their magnetic topologies by mapping the microflare locations on to the HMI photospheric magnetic field synoptic maps. Further, we analyzed the filtered brightness profiles and light curves for each event to classify them. Finally, we carried out a differential emission measure (DEM) analysis to study their temperature characteristics.

A novel flexible field-aligned coordinate system for tokamak edge plasma simulation

NASA Astrophysics Data System (ADS)

Leddy, J.; Dudson, B.; Romanelli, M.; Shanahan, B.; Walkden, N.

2017-03-01

Tokamak plasmas are confined by a magnetic field that limits the particle and heat transport perpendicular to the field. Parallel to the field the ionised particles can move freely, so to obtain confinement the field lines are "closed" (i.e. form closed surfaces of constant poloidal flux) in the core of a tokamak. Towards, the edge, however, the field lines intersect physical surfaces, leading to interaction between neutral and ionised particles, and the potential melting of the material surface. Simulation of this interaction is important for predicting the performance and lifetime of future tokamak devices such as ITER. Field-aligned coordinates are commonly used in the simulation of tokamak plasmas due to the geometry and magnetic topology of the system. However, these coordinates are limited in the geometry they allow in the poloidal plane due to orthogonality requirements. A novel 3D coordinate system is proposed herein that relaxes this constraint so that any arbitrary, smoothly varying geometry can be matched in the poloidal plane while maintaining a field-aligned coordinate. This system is implemented in BOUT++ and tested for accuracy using the method of manufactured solutions. A MAST edge cross-section is simulated using a fluid plasma model and the results show expected behaviour for density, temperature, and velocity. Finally, simulations of an isolated divertor leg are conducted with and without neutrals to demonstrate the ion-neutral interaction near the divertor plate and the corresponding beneficial decrease in plasma temperature.

Using Information Communication Technologies to Develop Dynamic Curriculum Frameworks for Diverse Cohorts: A Case Study from Event Management

ERIC Educational Resources Information Center

Hadley, Bree Jamila

2012-01-01

This article investigates the role of information communication technologies (ICTs) in establishing a well-aligned, authentic learning environment for a diverse cohort of non-cognate and cognate students studying event management in a higher education context. Based on a case study which examined the way ICTs assisted in accommodating diverse…

Spatio-temporal Event Classification using Time-series Kernel based Structured Sparsity

PubMed Central

Jeni, László A.; Lőrincz, András; Szabó, Zoltán; Cohn, Jeffrey F.; Kanade, Takeo

2016-01-01

In many behavioral domains, such as facial expression and gesture, sparse structure is prevalent. This sparsity would be well suited for event detection but for one problem. Features typically are confounded by alignment error in space and time. As a consequence, high-dimensional representations such as SIFT and Gabor features have been favored despite their much greater computational cost and potential loss of information. We propose a Kernel Structured Sparsity (KSS) method that can handle both the temporal alignment problem and the structured sparse reconstruction within a common framework, and it can rely on simple features. We characterize spatio-temporal events as time-series of motion patterns and by utilizing time-series kernels we apply standard structured-sparse coding techniques to tackle this important problem. We evaluated the KSS method using both gesture and facial expression datasets that include spontaneous behavior and differ in degree of difficulty and type of ground truth coding. KSS outperformed both sparse and non-sparse methods that utilize complex image features and their temporal extensions. In the case of early facial event classification KSS had 10% higher accuracy as measured by F1 score over kernel SVM methods1. PMID:27830214

Magnetically aligned phospholipid bilayers in weak magnetic fields: optimization, mechanism, and advantages for X-band EPR studies.

PubMed

Cardon, Thomas B; Tiburu, Elvis K; Lorigan, Gary A

2003-03-01

Our lab is developing a spin-labeled EPR spectroscopic technique complementary to solid-state NMR studies to study the structure, orientation, and dynamics of uniaxially aligned integral membrane proteins inserted into magnetically aligned discotic phospholipid bilayers, or bicelles. The focus of this study is to optimize and understand the mechanisms involved in the magnetic alignment process of bicelle disks in weak magnetic fields. Developing experimental conditions for optimized magnetic alignment of bicelles in low magnetic fields may prove useful to study the dynamics of membrane proteins and its interactions with lipids, drugs, steroids, signaling events, other proteins, etc. In weak magnetic fields, the magnetic alignment of Tm(3+)-doped bicelle disks was thermodynamically and kinetically very sensitive to experimental conditions. Tm(3+)-doped bicelles were magnetically aligned using the following optimized procedure: the temperature was slowly raised at a rate of 1.9K/min from an initial temperature being between 298 and 307K to a final temperature of 318K in the presence of a static magnetic field of 6300G. The spin probe 3beta-doxyl-5alpha-cholestane (cholestane) was inserted into the bicelle disks and utilized to monitor bicelle alignment by analyzing the anisotropic hyperfine splitting for the corresponding EPR spectra. The phases of the bicelles were determined using solid-state 2H NMR spectroscopy and compared with the corresponding EPR spectra. Macroscopic alignment commenced in the liquid crystalline nematic phase (307K), continued to increase upon slowly raising the temperature, and was well-aligned in the liquid crystalline lamellar smectic phase (318K).

Hadronic interactions in the MINOS detectors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kordosky, Michael Alan

2004-08-01

MINOS, the Main Injector Neutrino Oscillation Search, will study neutrino flavor transformations using a Near detector at the Fermi National Accelerator Laboratory and a Far detector located in the Soudan Underground Laboratory in northern Minnesota. The MINOS collaboration also constructed the CalDet (calibration detector), a smaller version of the Near and Far detectors, to determine the topological and signal response to hadrons, electrons and muons. The detector was exposed to test-beams in the CERN Proton Synchrotron East Hall during 2001-2003, where it collected events at momentum settings between 200 MeV/c and 10 GeV/c. In this dissertation we present results ofmore » the CalDet experiment, focusing on the topological and signal response to hadrons. We briefly describe the MINOS experiment and its iron-scintillator tracking-sampling calorimters as a motivation for the CalDet experiment. We discuss the operation of the CalDet in the beamlines as well as the trigger and particle identification systems used to isolate the hadron sample. The method used to calibrate the MINOS detector is described and validated with test-beam data. The test-beams were simulated to model the muon flux, energy loss upstream of the detector and the kaon background. We describe the procedure used to discriminate between pions and muons on the basis of the event topology. The hadron samples were used to benchmark the existing GEANT3 based hadronic shower codes and determine the detector response and resolution for pions and protons. We conclude with comments on the response to single hadrons and to neutrino induced hadronic showers.« less

Evolution of the nuclear receptor superfamily: early diversification from an ancestral orphan receptor.

PubMed

Laudet, V

1997-12-01

From a database containing the published nuclear hormone receptor (NR) sequences I constructed an alignment of the C, D and E domains of these molecules. Using this alignment, I have performed tree reconstruction using both distance matrix and parsimony analysis. The robustness of each branch was estimated using bootstrap resampling methods. The trees constructed by these two methods gave congruent topologies. From these analyses I defined six NR subfamilies: (i) a large one clustering thyroid hormone receptors (TRs), retinoic acid receptors (RARs), peroxisome proliferator-activated receptors (PPARs), vitamin D receptors (VDRs) and ecdysone receptors (EcRs) as well as numerous orphan receptors such as RORs or Rev-erbs; (ii) one containing retinoid X receptors (RXRs) together with COUP, HNF4, tailless, TR2 and TR4 orphan receptors; (iii) one containing steroid receptors; (iv) one containing the NGFIB orphan receptors; (v) one containing FTZ-F1 orphan receptors; and finally (vi) one containing to date only one gene, the GCNF1 orphan receptor. The relationships between the six subfamilies are not known except for subfamilies I and IV which appear to be related. Interestingly, most of the liganded receptors appear to be derived when compared with orphan receptors. This suggests that the ligand-binding ability of NRs has been gained by orphan receptors during the course of evolution to give rise to the presently known receptors. The distribution into six subfamilies correlates with the known abilities of the various NRs to bind to DNA as homo- or heterodimers. For example, receptors heterodimerizing efficiently with RXR belong to the first or the fourth subfamilies. I suggest that the ability to heterodimerize evolved once, just before the separation of subfamilies I and IV and that the first NR was able to bind to DNA as a homodimer. From the study of NR sequences existing in vertebrates, arthropods and nematodes, I define two major steps of NR diversification: one that took place very early, probably during the multicellularization event leading to all the metazoan phyla, and a second occurring later on, corresponding to the advent of vertebrates. Finally, I show that in vertebrate species the various groups of NRs accumulated mutations at very different rates.

Big words, halved brains and small worlds: complex brain networks of figurative language comprehension.

PubMed

Arzouan, Yossi; Solomon, Sorin; Faust, Miriam; Goldstein, Abraham

2011-04-27

Language comprehension is a complex task that involves a wide network of brain regions. We used topological measures to qualify and quantify the functional connectivity of the networks used under various comprehension conditions. To that aim we developed a technique to represent functional networks based on EEG recordings, taking advantage of their excellent time resolution in order to capture the fast processes that occur during language comprehension. Networks were created by searching for a specific causal relation between areas, the negative feedback loop, which is ubiquitous in many systems. This method is a simple way to construct directed graphs using event-related activity, which can then be analyzed topologically. Brain activity was recorded while subjects read expressions of various types and indicated whether they found them meaningful. Slightly different functional networks were obtained for event-related activity evoked by each expression type. The differences reflect the special contribution of specific regions in each condition and the balance of hemispheric activity involved in comprehending different types of expressions and are consistent with the literature in the field. Our results indicate that representing event-related brain activity as a network using a simple temporal relation, such as the negative feedback loop, to indicate directional connectivity is a viable option for investigation which also derives new information about aspects not reflected in the classical methods for investigating brain activity.

A new era of emergency care: planning and design consideration.

PubMed

Zilm, Frank

2007-01-01

Emergency care is one of the most complex, rapidly growing areas of ambulatory care. Providers need to consider new issues related to management of low-acuity patients, capacity for surge events, and the need to integrate patient focused care into the emergency department environment. This article explores these issues and discusses basic organizational topologies for facilities.

Communication: Gas-phase structural isomer identification by Coulomb explosion of aligned molecules

NASA Astrophysics Data System (ADS)

Burt, Michael; Amini, Kasra; Lee, Jason W. L.; Christiansen, Lars; Johansen, Rasmus R.; Kobayashi, Yuki; Pickering, James D.; Vallance, Claire; Brouard, Mark; Stapelfeldt, Henrik

2018-03-01

The gas-phase structures of four difluoroiodobenzene and two dihydroxybromobenzene isomers were identified by correlating the emission angles of atomic fragment ions created, following femtosecond laser-induced Coulomb explosion. The structural determinations were facilitated by confining the most polarizable axis of each molecule to the detection plane prior to the Coulomb explosion event using one-dimensional laser-induced adiabatic alignment. For a molecular target consisting of two difluoroiodobenzene isomers, each constituent structure could additionally be singled out and distinguished.

B-cell Ligand Processing Pathways Detected by Large-scale Comparative Analysis

PubMed Central

Towfic, Fadi; Gupta, Shakti; Honavar, Vasant; Subramaniam, Shankar

2012-01-01

The initiation of B-cell ligand recognition is a critical step for the generation of an immune response against foreign bodies. We sought to identify the biochemical pathways involved in the B-cell ligand recognition cascade and sets of ligands that trigger similar immunological responses. We utilized several comparative approaches to analyze the gene coexpression networks generated from a set of microarray experiments spanning 33 different ligands. First, we compared the degree distributions of the generated networks. Second, we utilized a pairwise network alignment algorithm, BiNA, to align the networks based on the hubs in the networks. Third, we aligned the networks based on a set of KEGG pathways. We summarized our results by constructing a consensus hierarchy of pathways that are involved in B cell ligand recognition. The resulting pathways were further validated through literature for their common physiological responses. Collectively, the results based on our comparative analyses of degree distributions, alignment of hubs, and alignment based on KEGG pathways provide a basis for molecular characterization of the immune response states of B-cells and demonstrate the power of comparative approaches (e.g., gene coexpression network alignment algorithms) in elucidating biochemical pathways involved in complex signaling events in cells. PMID:22917187

Convection and electrodynamic signatures in the vicinity of a Sun-aligned arc: Results from the Polar Acceleration Regions and Convection Study (Polar ARCS)

NASA Technical Reports Server (NTRS)

Weiss, L. A.; Weber, E. J.; Reiff, P. H.; Sharber, J. R.; Winningham, J. D.; Primdahl, F.; Mikkelsen, I. S.; Seifring, C.; Wescott, Eugene M.

1994-01-01

An experimental campaign designed to study high-latitude auroral arcs was conducted in Sondre Stromfjord, Greenland, on February 26, 1987. The Polar Acceleration Regions and Convection Study (Polar ARCS) consisted of a coordinated set of ground-based, airborne, and sounding rocket measurements of a weak, sun-aligned arc system within the duskside polar cap. A rocket-borne barium release experiment, two DMSP satellite overflights, all-sky photography, and incoherent scatter radar measurements provided information on the large-scale plasma convection over the polar cap region while a second rocket instrumented with a DC magnetometer, Langmuir and electric field probes, and an electron spectrometer provided measurements of small-scale electrodynamics. The large-scale data indicate that small, sun-aligned precipitation events formed within a region of antisunward convection between the duskside auroral oval and a large sun-aligned arc further poleward. This convection signature, used to assess the relationship of the sun-aligned arc to the large-scale magnetospheric configuration, is found to be consistent with either a model in which the arc formed on open field lines on the dusk side of a bifurcated polar cap or on closed field lines threading an expanded low-latitude boundary layer, but not a model in which the polar cap arc field lines map to an expanded plasma sheet. The antisunward convection signature may also be explained by a model in which the polar cap arc formed on long field lines recently reconnected through a highly skewed plasma sheet. The small-scale measurements indicate the rocket passed through three narrow (less than 20 km) regions of low-energy (less than 100 eV) electron precipitation in which the electric and magnetic field perturbations were well correlated. These precipitation events are shown to be associated with regions of downward Poynting flux and small-scale upward and downward field-aligned currents of 1-2 micro-A/sq m. The paired field-aligned currents are associated with velocity shears (higher and lower speed streams) embedded in the region of antisunward flow.

Cross-sections and maps showing double-difference relocated earthquakes from 1984-2000 along the Hayward and Calaveras faults, California

USGS Publications Warehouse

Simpson, Robert W.; Graymer, Russell W.; Jachens, Robert C.; Ponce, David A.; Wentworth, Carl M.

2004-01-01

We present cross-section and map views of earthquakes that occurred from 1984 to 2000 in the vicinity of the Hayward and Calaveras faults in the San Francisco Bay region, California. These earthquakes came from a catalog of events relocated using the double-difference technique, which provides superior relative locations of nearby events. As a result, structures such as fault surfaces and alignments of events along these surfaces are more sharply defined than in previous catalogs.

Planck 2013 results. XXVI. Background geometry and topology of the Universe

NASA Astrophysics Data System (ADS)

Planck Collaboration; Ade, P. A. R.; Aghanim, N.; Armitage-Caplan, C.; Arnaud, M.; Ashdown, M.; Atrio-Barandela, F.; Aumont, J.; Baccigalupi, C.; Banday, A. J.; Barreiro, R. B.; Bartlett, J. G.; Battaner, E.; Benabed, K.; Benoît, A.; Benoit-Lévy, A.; Bernard, J.-P.; Bersanelli, M.; Bielewicz, P.; Bobin, J.; Bock, J. J.; Bonaldi, A.; Bonavera, L.; Bond, J. R.; Borrill, J.; Bouchet, F. R.; Bridges, M.; Bucher, M.; Burigana, C.; Butler, R. C.; Cardoso, J.-F.; Catalano, A.; Challinor, A.; Chamballu, A.; Chiang, H. C.; Chiang, L.-Y.; Christensen, P. R.; Church, S.; Clements, D. L.; Colombi, S.; Colombo, L. P. L.; Couchot, F.; Coulais, A.; Crill, B. P.; Curto, A.; Cuttaia, F.; Danese, L.; Davies, R. D.; Davis, R. J.; de Bernardis, P.; de Rosa, A.; de Zotti, G.; Delabrouille, J.; Delouis, J.-M.; Désert, F.-X.; Diego, J. M.; Dole, H.; Donzelli, S.; Doré, O.; Douspis, M.; Dupac, X.; Efstathiou, G.; Enßlin, T. A.; Eriksen, H. K.; Fabre, O.; Finelli, F.; Forni, O.; Frailis, M.; Franceschi, E.; Galeotta, S.; Ganga, K.; Giard, M.; Giardino, G.; Giraud-Héraud, Y.; González-Nuevo, J.; Górski, K. M.; Gratton, S.; Gregorio, A.; Gruppuso, A.; Hansen, F. K.; Hanson, D.; Harrison, D. L.; Henrot-Versillé, S.; Hernández-Monteagudo, C.; Herranz, D.; Hildebrandt, S. R.; Hivon, E.; Hobson, M.; Holmes, W. A.; Hornstrup, A.; Hovest, W.; Huffenberger, K. M.; Jaffe, A. H.; Jaffe, T. R.; Jones, W. C.; Juvela, M.; Keihänen, E.; Keskitalo, R.; Kisner, T. S.; Knoche, J.; Knox, L.; Kunz, M.; Kurki-Suonio, H.; Lagache, G.; Lähteenmäki, A.; Lamarre, J.-M.; Lasenby, A.; Laureijs, R. J.; Lawrence, C. R.; Leahy, J. P.; Leonardi, R.; Leroy, C.; Lesgourgues, J.; Liguori, M.; Lilje, P. B.; Linden-Vørnle, M.; López-Caniego, M.; Lubin, P. M.; Macías-Pérez, J. F.; Maffei, B.; Maino, D.; Mandolesi, N.; Maris, M.; Marshall, D. J.; Martin, P. G.; Martínez-González, E.; Masi, S.; Massardi, M.; Matarrese, S.; Matthai, F.; Mazzotta, P.; McEwen, J. D.; Melchiorri, A.; Mendes, L.; Mennella, A.; Migliaccio, M.; Mitra, S.; Miville-Deschênes, M.-A.; Moneti, A.; Montier, L.; Morgante, G.; Mortlock, D.; Moss, A.; Munshi, D.; Murphy, J. A.; Naselsky, P.; Nati, F.; Natoli, P.; Netterfield, C. B.; Nørgaard-Nielsen, H. U.; Noviello, F.; Novikov, D.; Novikov, I.; Osborne, S.; Oxborrow, C. A.; Paci, F.; Pagano, L.; Pajot, F.; Paoletti, D.; Pasian, F.; Patanchon, G.; Peiris, H. V.; Perdereau, O.; Perotto, L.; Perrotta, F.; Piacentini, F.; Piat, M.; Pierpaoli, E.; Pietrobon, D.; Plaszczynski, S.; Pogosyan, D.; Pointecouteau, E.; Polenta, G.; Ponthieu, N.; Popa, L.; Poutanen, T.; Pratt, G. W.; Prézeau, G.; Prunet, S.; Puget, J.-L.; Rachen, J. P.; Rebolo, R.; Reinecke, M.; Remazeilles, M.; Renault, C.; Riazuelo, A.; Ricciardi, S.; Riller, T.; Ristorcelli, I.; Rocha, G.; Rosset, C.; Roudier, G.; Rowan-Robinson, M.; Rusholme, B.; Sandri, M.; Santos, D.; Savini, G.; Scott, D.; Seiffert, M. D.; Shellard, E. P. S.; Spencer, L. D.; Starck, J.-L.; Stolyarov, V.; Stompor, R.; Sudiwala, R.; Sureau, F.; Sutton, D.; Suur-Uski, A.-S.; Sygnet, J.-F.; Tauber, J. A.; Tavagnacco, D.; Terenzi, L.; Toffolatti, L.; Tomasi, M.; Tristram, M.; Tucci, M.; Tuovinen, J.; Valenziano, L.; Valiviita, J.; Van Tent, B.; Varis, J.; Vielva, P.; Villa, F.; Vittorio, N.; Wade, L. A.; Wandelt, B. D.; Yvon, D.; Zacchei, A.; Zonca, A.

2014-11-01

The new cosmic microwave background (CMB) temperature maps from Planck provide the highest-quality full-sky view of the surface of last scattering available to date. This allows us to detect possible departures from the standard model of a globally homogeneous and isotropic cosmology on the largest scales. We search for correlations induced by a possible non-trivial topology with a fundamental domain intersecting, or nearly intersecting, the last scattering surface (at comoving distance χrec), both via a direct search for matched circular patterns at the intersections and by an optimal likelihood search for specific topologies. For the latter we consider flat spaces with cubic toroidal (T3), equal-sided chimney (T2) and slab (T1) topologies, three multi-connected spaces of constant positive curvature (dodecahedral, truncated cube and octahedral) and two compact negative-curvature spaces. These searches yield no detection of the compact topology with the scale below the diameter of the last scattering surface. For most compact topologies studied the likelihood maximized over the orientation of the space relative to the observed map shows some preference for multi-connected models just larger than the diameter of the last scattering surface. Since this effect is also present in simulated realizations of isotropic maps, we interpret it as the inevitable alignment of mild anisotropic correlations with chance features in a single sky realization; such a feature can also be present, in milder form, when the likelihood is marginalized over orientations. Thus marginalized, the limits on the radius ℛi of the largest sphere inscribed in topological domain (at log-likelihood-ratio Δln ℒ > -5 relative to a simply-connected flat Planck best-fit model) are: in a flat Universe, ℛi> 0.92χrec for the T3 cubic torus; ℛi> 0.71χrec for the T2 chimney; ℛi> 0.50χrec for the T1 slab; and in a positively curved Universe, ℛi> 1.03χrec for the dodecahedral space; ℛi> 1.0χrec for the truncated cube; and ℛi> 0.89χrec for the octahedral space. The limit for a wider class of topologies, i.e., those predicting matching pairs of back-to-back circles, among them tori and the three spherical cases listed above, coming from the matched-circles search, is ℛi> 0.94χrec at 99% confidence level. Similar limits apply to a wide, although not exhaustive, range of topologies. We also perform a Bayesian search for an anisotropic global Bianchi VIIh geometry. In the non-physical setting where the Bianchi cosmology is decoupled from the standard cosmology, Planck data favour the inclusion of a Bianchi component with a Bayes factor of at least 1.5 units of log-evidence. Indeed, the Bianchi pattern is quite efficient at accounting for some of the large-scale anomalies found in Planck data. However, the cosmological parameters that generate this pattern are in strong disagreement with those found from CMB anisotropy data alone. In the physically motivated setting where the Bianchi parameters are coupled and fitted simultaneously with the standard cosmological parameters, we find no evidence for a Bianchi VIIh cosmology and constrain the vorticity of such models to (ω/H)0< 8.1 × 10-10 (95% confidence level).

Separator Reconnection at Earth's Dayside Magnetopause and the Tail: MMS Observations Compared to Global 3D Simulations

NASA Astrophysics Data System (ADS)

Buzulukova, N.; Dorelli, J.; Glocer, A.

2017-12-01

We present the results of global high resolution resistive magnetohydrodynamics (MHD BATS-R-US) simulations of Earth's magnetosphere. We extract location of magnetic separators with RECONX tool and compare the results with observations from the Magnetospheric Multiscale (MMS). A few cases are analysed including a southward IMF magnetopause crossing during October 16, 2015 that was previously identified as an electron diffusion region (EDR) event. The simulation predicts a complex time-dependent magnetic topology consisting of multiple separators and flux ropes. Despite the topological complexity, the predicted distance between MMS and the primary separator is less than 0.5 Earth radii. The simulation shows that the existence of IMF Bx results in a duskward shift of the location of the topological separator. The results are explained by a combined effect of solar wind draping and pile-up effect that modify the current density across the magnetopause and affect the location of the separator. The RECONX tool also is used to extract the separator location in the geomagnetic tail, and relate transient tail structures (bursty bulk flows) to the location of separator. These results suggest that global magnetic topology, rather than local magnetic geometry alone, determines the location of the separator reconnection both at the dayside magnetopause and in the tail. We show that the resistive MHD model helps to understand the global context of local MMS observations.

Measurement of the underlying event activity in inclusive Z boson production in proton-proton collisions at $$\\sqrt{s} = $$ 13 TeV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sirunyan, Albert M; et al.

This paper presents a measurement of the underlying event activity in proton-proton collisions at a center-of-mass energy of 13 TeV, performed using inclusive Z boson production events collected with the CMS experiment at the LHC. The analyzed data correspond to an integrated luminosity of 2.1 fbmore » $$^{-1}$$. The underlying event activity is quantified in terms of the charged particle multiplicity, as well as of the scalar sum of the charged particles' transverse momenta in different topological regions defined with respect to the Z boson direction. The distributions are unfolded to the stable particle level and compared with predictions from various Monte Carlo event generators, as well as with similar CDF and CMS measurements at center-of-mass energies of 1.96 and 7 TeV respectively.« less

Phylogenetic Analyses of Meloidogyne Small Subunit rDNA.

PubMed

De Ley, Irma Tandingan; De Ley, Paul; Vierstraete, Andy; Karssen, Gerrit; Moens, Maurice; Vanfleteren, Jacques

2002-12-01

Phylogenies were inferred from nearly complete small subunit (SSU) 18S rDNA sequences of 12 species of Meloidogyne and 4 outgroup taxa (Globodera pallida, Nacobbus abberans, Subanguina radicicola, and Zygotylenchus guevarai). Alignments were generated manually from a secondary structure model, and computationally using ClustalX and Treealign. Trees were constructed using distance, parsimony, and likelihood algorithms in PAUP* 4.0b4a. Obtained tree topologies were stable across algorithms and alignments, supporting 3 clades: clade I = [M. incognita (M. javanica, M. arenaria)]; clade II = M. duytsi and M. maritima in an unresolved trichotomy with (M. hapla, M. microtyla); and clade III = (M. exigua (M. graminicola, M. chitwoodi)). Monophyly of [(clade I, clade II) clade III] was given maximal bootstrap support (mbs). M. artiellia was always a sister taxon to this joint clade, while M. ichinohei was consistently placed with mbs as a basal taxon within the genus. Affinities with the outgroup taxa remain unclear, although G. pallida and S. radicicola were never placed as closest relatives of Meloidogyne. Our results show that SSU sequence data are useful in addressing deeper phylogeny within Meloidogyne, and that both M. ichinohei and M. artiellia are credible outgroups for phylogenetic analysis of speciations among the major species.

A similarity measure for partially folded proteins: application to unfolded and native-like conformational fluctuations

NASA Astrophysics Data System (ADS)

Larios, Edgar; Yang, Wei Y.; Schulten, K.; Gruebele, M.

2004-12-01

Computing the root-mean-square deviation (RMSD) of a partially folded protein structure from the folded state requires the two structures to be translationally and rotationally aligned. We examine the constraint matrix L that preserves orthogonality of the rotation matrix during minimization of the RMSD. L is proportional to the sensitivity of the RMSD to the rotational alignment matrix. Its trace yields an isotropic reaction coordinate, while its off-diagonal matrix elements are related to the moment of inertia derivative tensor that encodes anisotropic information about the structure. We use L to compare λ-repressor fragment 6-85 (λ 6-85) to several partially folded structures obtained from molecular dynamics simulation (MD), and find that L as a reaction coordinate indeed encodes some information about protein topology. We also apply C α RMSD, L and tryptophan sidechain mobility as criteria for native state structural fluctuations of several λ 6-85 mutants. The mutants' denaturation curves and fluorescence quenching are measured experimentally for comparison. The results are in accord with a recent proposal that structural fluctuations near the chromophore can induce increased native state fluorescence or hyperfluorescence during unfolding of proteins.

DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics

PubMed Central

Laurens, Niels; Rusling, David A.; Pernstich, Christian; Brouwer, Ineke; Halford, Stephen E.; Wuite, Gijs J. L.

2012-01-01

Protein-induced DNA looping is crucial for many genetic processes such as transcription, gene regulation and DNA replication. Here, we use tethered-particle motion to examine the impact of DNA bending and twisting rigidity on loop capture and release, using the restriction endonuclease FokI as a test system. To cleave DNA efficiently, FokI bridges two copies of an asymmetric sequence, invariably aligning the sites in parallel. On account of the fixed alignment, the topology of the DNA loop is set by the orientation of the sites along the DNA. We show that both the separation of the FokI sites and their orientation, altering, respectively, the twisting and the bending of the DNA needed to juxtapose the sites, have profound effects on the dynamics of the looping interaction. Surprisingly, the presence of a nick within the loop does not affect the observed rigidity of the DNA. In contrast, the introduction of a 4-nt gap fully relaxes all of the torque present in the system but does not necessarily enhance loop stability. FokI therefore employs torque to stabilise its DNA-looping interaction by acting as a ‘torsional’ catch bond. PMID:22373924

Evaluation of body-wise and organ-wise registrations for abdominal organs

NASA Astrophysics Data System (ADS)

Xu, Zhoubing; Panjwani, Sahil A.; Lee, Christopher P.; Burke, Ryan P.; Baucom, Rebeccah B.; Poulose, Benjamin K.; Abramson, Richard G.; Landman, Bennett A.

2016-03-01

Identifying cross-sectional and longitudinal correspondence in the abdomen on computed tomography (CT) scans is necessary for quantitatively tracking change and understanding population characteristics, yet abdominal image registration is a challenging problem. The key difficulty in solving this problem is huge variations in organ dimensions and shapes across subjects. The current standard registration method uses the global or body-wise registration technique, which is based on the global topology for alignment. This method (although producing decent results) has substantial influence of outliers, thus leaving room for significant improvement. Here, we study a new image registration approach using local (organ-wise registration) by first creating organ-specific bounding boxes and then using these regions of interest (ROIs) for aligning references to target. Based on Dice Similarity Coefficient (DSC), Mean Surface Distance (MSD) and Hausdorff Distance (HD), the organ-wise approach is demonstrated to have significantly better results by minimizing the distorting effects of organ variations. This paper compares exclusively the two registration methods by providing novel quantitative and qualitative comparison data and is a subset of the more comprehensive problem of improving the multi-atlas segmentation by using organ normalization.

Phylogenetic Analyses of Meloidogyne Small Subunit rDNA

PubMed Central

De Ley, Irma Tandingan; De Ley, Paul; Vierstraete, Andy; Karssen, Gerrit; Moens, Maurice; Vanfleteren, Jacques

2002-01-01

Phylogenies were inferred from nearly complete small subunit (SSU) 18S rDNA sequences of 12 species of Meloidogyne and 4 outgroup taxa (Globodera pallida, Nacobbus abberans, Subanguina radicicola, and Zygotylenchus guevarai). Alignments were generated manually from a secondary structure model, and computationally using ClustalX and Treealign. Trees were constructed using distance, parsimony, and likelihood algorithms in PAUP* 4.0b4a. Obtained tree topologies were stable across algorithms and alignments, supporting 3 clades: clade I = [M. incognita (M. javanica, M. arenaria)]; clade II = M. duytsi and M. maritima in an unresolved trichotomy with (M. hapla, M. microtyla); and clade III = (M. exigua (M. graminicola, M. chitwoodi)). Monophyly of [(clade I, clade II) clade III] was given maximal bootstrap support (mbs). M. artiellia was always a sister taxon to this joint clade, while M. ichinohei was consistently placed with mbs as a basal taxon within the genus. Affinities with the outgroup taxa remain unclear, although G. pallida and S. radicicola were never placed as closest relatives of Meloidogyne. Our results show that SSU sequence data are useful in addressing deeper phylogeny within Meloidogyne, and that both M. ichinohei and M. artiellia are credible outgroups for phylogenetic analysis of speciations among the major species. PMID:19265950

WNV Typer: a server for genotyping of West Nile viruses using an alignment-free method based on a return time distribution.

PubMed

Kolekar, Pandurang; Hake, Nilesh; Kale, Mohan; Kulkarni-Kale, Urmila

2014-03-01

West Nile virus (WNV), genus Flavivirus, family Flaviviridae, is a major cause of viral encephalitis with broad host range and global spread. The virus has undergone a series of evolutionary changes with emergence of various genotypic lineages that are known to differ in type and severity of the diseases caused. Currently, genotyping is carried out using molecular phylogeny of complete coding sequences and genotype is assigned based on proximity to reference genotypes in tree topology. Efficient epidemiological surveillance of WNVs demands development of objective criteria for typing. An alignment-free approach based on return time distribution (RTD) of k-mers has been validated for genotyping of WNVs. The RTDs of complete genome sequences at k=7 were found to be optimum for classification of the known lineages of WNVs as well as for genotyping. It provides time and computationally efficient alternative for genome based annotation of WNV lineages. The development of a WNV Typer server based on RTD is described (http://bioinfo.net.in/wnv/homepage.html). Both the method and the server have 100% sensitivity and specificity. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

The UAH Spinning Terrella Experiment: A Laboratory Analog for the Earth's Magnetosphere

NASA Technical Reports Server (NTRS)

Sheldon, R. B.; Gallagher, D. L.; Craven, P. D.; Whitaker, Ann F. (Technical Monitor)

2001-01-01

The UAH Spinning Terrella Experiment has been modified to include the effect of a second magnet. This is a simple laboratory demonstration of the well-known double-dipole approximation to the Earth's magnetosphere. In addition, the magnet has been biassed $\\sim$-400V which generates a DC glow discharge and traps it in a ring current around the magnet. This ring current is easily imaged with a digital camera and illustrates several significant topological properties of a dipole field. In particular, when the two dipoles are aligned, and therefore repel, they emulate a northward IMF Bz magnetosphere. Such a geometry traps plasma in the high latitude cusps as can be clearly seen in the movies. Likewise, when the two magnets are anti-aligned, they emulate a southward IMF Bz magnetosphere with direct feeding of plasma through the x-line. We present evidence for trapping and heating of the plasma, comparing the dipole-trapped ring current to the cusp-trapped population. We also present a peculiar asymmetric ring current produced in by the plasma at low plasma densities. We discuss the similarities and dissimilarities of the laboratory analog to the collisionless Earth plasma, and implications for the interpretation of IMAGE data.

Bunker probe: A plasma potential probe almost insensitive to its orientation with the magnetic field

DOE Office of Scientific and Technical Information (OSTI.GOV)

Costea, S., E-mail: stefan.costea@uibk.ac.at; Schneider, B. S.; Schrittwieser, R.

Due to their ability to suppress a large part of the electron current and thus measuring directly the plasma potential, ion sensitive probes have begun to be widely tested and used in fusion devices. For these probes to work, almost perfect alignment with the total magnetic field is necessary. This condition cannot always be fulfilled due to the curvature of magnetic fields, complex magnetic structure, or magnetic field reconnection. In this perspective, we have developed a plasma potential probe (named Bunker probe) based on the principle of the ion sensitive probe but almost insensitive to its orientation with the totalmore » magnetic field. Therefore it can be used to measure the plasma potential inside fusion devices, especially in regions with complex magnetic field topology. Experimental results are presented and compared with Ball-Pen probe measurements taken under identical conditions. We have observed that the floating potential of the Bunker probe is indeed little affected by its orientation with the magnetic field for angles ranging from 90° to 30°, in contrast to the Ball-Pen probe whose floating potential decreases towards that of a Langmuir probe if not properly aligned with the magnetic field.« less

Initial experience with custom-fit total knee replacement: intra-operative events and long-leg coronal alignment.

PubMed

Spencer, Brian A; Mont, Michael A; McGrath, Mike S; Boyd, Bradley; Mitrick, Michael F

2009-12-01

New technology using magnetic resonance imaging (MRI) allows the surgeon to place total knee replacement components into each patient's pre-arthritic natural alignment. This study evaluated the initial intra-operative experience using this technique. Twenty-one patients had a sagittal MRI of their arthritic knee to determine component placement for a total knee replacement. Cutting guides were machined to control all intra-operative cuts. Intra-operative events were recorded and these knees were compared to a matching cohort of the senior surgeon's previous 30 conventional total knee replacements. Post-operative scanograms were obtained from each patient and coronal alignment was compared to previous studies using conventional and computer-assisted techniques. There were no intra-operative or acute post-operative complications. There were no differences in blood loss and there was a mean decrease in operative time of 14% compared to a cohort of patients with conventional knee replacements. The average deviation from the mechanical axis was 1.2 degrees of varus, which was comparable to previously reported conventional and computer-assisted techniques. Custom-fit total knee replacement appeared to be a safe procedure for uncomplicated cases of osteoarthritis.

ISEE 1 charged particle observations indicative of open magnetospheric field lines near the subsolar region

NASA Technical Reports Server (NTRS)

Williams, D. J.; Frank, L. A.

1980-01-01

On November 20, 1977, at 0230-0300 UT, ISEE 1 encountered unusual charged particle distributions within the magnetosphere. The three-dimensional distribution observations for energetic (greater than 24 keV) ions and plasma show the development of field-aligned asymmetries in the energetic ion distributions simultaneously with a marked change in plasma flow. It is concluded that the most likely explanation for these observations is that ISEE 1 encountered open magnetospheric field lines at its position within the magnetosphere (1030 LT and 1200 plus or minus 300 km from the magnetopause). Field lines were open near the geomagnetic equator, and the geometry was spatially or temporally variable. Other features of the field line topology are presented.

Global problems in magnetospheric plasma physics and prospects for their solution

NASA Technical Reports Server (NTRS)

Roederer, J. G.

1977-01-01

Selected problems in magnetospheric plasma physics are critically reviewed. The discussion is restricted to questions that are 'global' in nature (i.e., involve the magnetosphere as a whole) and that are beyond the stage of systematic survey or isolated study requirements. Only low-energy particle aspects are discussed. The article focuses on the following subjects: (1) the effect of the interplanetary magnetic field on the topography, topology, and stability of the magnetospheric boundary; (2) solar-wind plasma entry into the magnetosphere; (3) plasma storage and release mechanisms in the magnetospheric tail; and (4) magnetic-field-aligned currents and magnetosphere-ionosphere interactions. A brief discussion of the prospects for the solution of these problems during and after the International Magnetospheric Study is given.

The Topology of the Growing Human Interactome Data.

PubMed

Janjić, Vuk; Pržulj, Nataša

2014-06-01

We have long moved past the one-gene-one-function concept originally proposed by Beadle and Tatum back in 1941; but the full understanding of genotype-phenotype relations still largely relies on the analysis of static, snapshot-like, interaction data sets. Here, we look at what global patterns can be uncovered if we simply trace back the human interactome network over the last decade of protein-protein interaction (PPI) screening. We take a purely topological approach and find that as the human interactome is getting denser, it is not only gaining in structure (in terms of now being better fit by structured network models than before), but also there are patterns in the way in which it is growing: (a) newly added proteins tend to get linked to existing proteins in the interactome that are not know to interact; and (b) new proteins tend to link to already well connected proteins. Moreover, the alignment between human and yeast interactomes spanning over 40% of yeast's proteins - that are involved in regulation of transcription, RNA splicing and other cellcycle- related processes-suggests the existence of a part of the interactome which remains topologically and functionally unaffected through evolution. Furthermore, we find a small sub-network, specific to the "core" of the human interactome and involved in regulation of transcription and cancer development, whose wiring has not changed within the human interactome over the last 10 years of interacome data acquisition. Finally, we introduce a generalisation of the clustering coefficient of a network as a new measure called the cycle coefficient, and use it to show that PPI networks of human and model organisms are wired in a tight way which forbids the occurrence large cycles.

The topology of the growing human interactome data.

PubMed

Janjić, Vuk; Pržulj, Nataša

2014-06-23

We have long moved past the one-gene–one-function concept originally proposed by Beadle and Tatum back in 1941; but the full understanding of genotype–phenotype relations still largely relies on the analysis of static, snapshot-like, interaction data sets. Here, we look at what global patterns can be uncovered if we simply trace back the human interactome network over the last decade of protein- protein interaction (PPI) screening. We take a purely topological approach and find that as the human interactome is getting denser, it is not only gaining in structure (in terms of now being better fit by structured network models than before), but also there are patterns in the way in which it is growing: (a) newly added proteins tend to get linked to existing proteins in the interactome that are not know to interact; and (b) new proteins tend to link to already well connected proteins. Moreover, the alignment between human and yeast interactomes spanning over 40% of yeast’s proteins — that are involved in regulation of transcription, RNA splicing and other cellcycle-related processes—suggests the existence of a part of the interactome which remains topologically and functionally unaffected through evolution. Furthermore, we find a small sub-network, specific to the “core” of the human interactome and involved in regulation of transcription and cancer development, whose wiring has not changed within the human interactome over the last 10 years of interacome data acquisition. Finally, we introduce a generalisation of the clustering coefficient of a network as a new measure called the cycle coefficient, and use it to show that PPI networks of human and model organisms are wired in a tight way which forbids the occurrence large cycles.

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

PubMed

Guindon, Stéphane; Dufayard, Jean-François; Lefort, Vincent; Anisimova, Maria; Hordijk, Wim; Gascuel, Olivier

2010-05-01

PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.

Functional units and lead topologies: a hierarchical framework for observing and modeling the interplay of structures, storage dynamics and integral mass and energy flows in lower mesoscale catchments

NASA Astrophysics Data System (ADS)

Zehe, Erwin; Jackisch, Conrad; Blume, Theresa; Haßler, Sibylle; Allroggen, Niklas; Tronicke, Jens

2013-04-01

The CAOS Research Unit recently proposed a hierarchical classification scheme to subdivide a catchment into what we vaguely name classes of functional entities that puts the gradients driving mass and energy flows and their controls on top of the hierarchy and the arrangement of landscape attributes controlling flow resistances along these driving gradients (for instance soil types and apparent preferential pathways) at the second level. We name these functional entities lead topology classes, to highlight that they are characterized by a spatially ordered arrangement of landscape elements along a superordinate driving gradient. Our idea is that these lead topology classes have a distinct way how their structural and textural architecture controls the interplay of storage dynamics and integral response behavior that is typical for all members of a class, but is dissimilar between different classes. This implies that we might gain exemplary understanding of the typical dynamic behavior of the class, when thoroughly studying a few class members. We propose that the main integral catchment functions mass export and drainage, mass redistribution and storage, energy exchange with the atmosphere, as well as energy redistribution and storage - result from spatially organized interactions of processes within lead topologies that operate at different scale levels and partly dominate during different conditions. We distinguish: 1) Lead topologies controlling the land surface energy balance during radiation driven conditions at the plot/pedon scale level. In this case energy fluxes dominate and deplete a vertical temperature gradient that is build up by depleting a gradient in radiation fluxes. Water is a facilitator in this concert due to the high specific heat of vaporization. Slow vertical water fluxes in soil dominate, which are driven by vertical gradients in atmospheric water potential, chemical potential in the plant and in soil hydraulic potentials. 2) Lead topologies controlling fast drainage and generation stream flow during rainfall events at the hillslope scale level: Fast vertical and lateral mass fluxes dominate. They are driven by vertical and lateral gradients in pressure heads which build up by depleting the kinetic energy/velocity gradient of rainfall when it hits the ground or of vertical subsurface flows that "hit" a layer of low permeability. 3) Lead topologies controlling slow drainage and its supply, and thus creating memory at the catchment scale level: These are the groundwater system and the stream including the riparian zone. Permanent lateral water flows dominate that are driven by permanently active lateral gradients in pressure heads. Event scale stream flow generation and energy exchange with the atmospheric boundary layer are organized by the first two types of lead topologies, and their dominance changes with prevailing type of boundary conditions. We furthermore propose that lead topologies at the plot and the hillslope scale levels can be further subdivided into least functional entities we name call classes of elementary functional units. These classes of elementary functional units co-evolved being exposed to similar superordinate vertical gradients in a self-reinforcing manner. Being located either at the hilltop (sediment source area), midslope (sediment transport area) or hillfoot/riparian zone (sediment deposit area) they experienced similar weathering processes (past water, energy and nutrient flows), causing formation of similar soil texture in different horizons. This implies, depending on hillslope position and aspect, formation of distinct niches (with respect to water, nutrient and sun light availability) and thus "similar filters" to select distinct natural communities of animal and vegetation species. This in turn implies similarity with respect to formation of biotic flow networks (ant-, worm-, mole- and whole burrow systems, as well as root systems), which feeds back on vertical and lateral water/mass and thermal energy flows and so on. The idea is that members of EFU classes interact within lead topologies along a hierarchy of driving potential gradients and that these interactions are mediated by a hierarchy of connected flow networks like macropores, root networks or lateral pipe systems. We hypothesize that members of a functional unit class are similar with respect to the time invariant controls of the vertical gradients (soil hydraulic potentials, soil temperature, plant water potential) and the flow resistances in vertical direction (plant and soil albedo, soil hydraulic and thermal conductivity, vertical macropore networks). This implies that members of an EFU class behave functionally similar at least with respect to vertical flows of water and heat: we may gain exemplary understanding of the typical dynamic behavior of the class, by thoroughly studying a few class members. In the following we will thus use the term "elementary functional units, EFUs" and "elementary functional unit class, EFU class" as synonyms. We propose that a thorough understanding of the behavior of a few representatives of the most important EFU classes and of their interactions within a hierarchy of lead topology classes is sufficient for understanding and distributed modeling of event scale stream flow production under rainfall driven conditions and energy exchange with the atmosphere under radiation driven conditions. Good and not surprising news is that lead topologies controlling stream flow contribution, are an interconnected, ordered arrangement of the lead topologies that control energy exchange. We suggests that a combination of the related model approaches which simplified but physical based approaches to simulate dynamics in the saturated zone, riparian zone and the river network results in a structurally more adequate model framework for catchments of organized complexity. The feasibility of this concept is currently tested in the Attert catchment by setting up pseudo replica of field experiments and a distributed monitoring network in several members of first guess EFUs and superordinate lead topology classes. We combine geophysical and soil physical survey, artificial tracer tests and analysis of stable isotopes and ecological survey with distributed sensor clusters that permanently monitor meteorological variables, soil moisture and matric potential, piezometric heads etc. Within the proposed study we will present first results especially from the sensor clusters and geophysical survey. By using geostatistical methods we will work out to which extend members within a candidate EFU class are similar with respect to subsurface structures like depth to bedrock and soil properties as well as with respect to soil moisture/storage dynamics. Secondly, we will work out whether structurally similar hillslopes produce a similar event scale stream flow contribution, which of course is dependent on the degree of similarity of a) the rainfall forcing they receive and b) of their wetness state. To this end we will perform virtual experiments with the physically based model CATFLOW by perturbing behavioral model structures. These have been shown to portray system behavior and its architecture in a sense that they reproduce distributed observations of soil moisture and subsurface storm flow and represent the observed structural and textural signatures of soils, flow networks and vegetation.

Multiple photon emission in heavy particle decays

NASA Technical Reports Server (NTRS)

Asakimori, K.; Burnett, T. H.; Cherry, M. L.; Christl, M. J.; Dake, S.; Derrickson, J. H.; Fountain, W. F.; Fuki, M.; Gregory, J. C.; Hayashi, T.

1994-01-01

Cosmic ray interactions, at energies above 1 TeV/nucleon, in emulsion chambers flown on high altitude balloons have yielded two events showing apparent decays of a heavy particle into one charged particle and four photons. The photons converted into electron pairs very close to the decay vertex. Attempts to explain this decay topology with known particle decays are presented. Unless both events represent a b yields u transition, which is statistically unlikely, then other known decay modes for charmed or bottom particles do not account satisfactorily for these observations. This could indicate, possibly, a new decay channel.

IRiS: construction of ARG networks at genomic scales.

PubMed

Javed, Asif; Pybus, Marc; Melé, Marta; Utro, Filippo; Bertranpetit, Jaume; Calafell, Francesc; Parida, Laxmi

2011-09-01

Given a set of extant haplotypes IRiS first detects high confidence recombination events in their shared genealogy. Next using the local sequence topology defined by each detected event, it integrates these recombinations into an ancestral recombination graph. While the current system has been calibrated for human population data, it is easily extendible to other species as well. IRiS (Identification of Recombinations in Sequences) binary files are available for non-commercial use in both Linux and Microsoft Windows, 32 and 64 bit environments from https://researcher.ibm.com/researcher/view_project.php?id = 2303 parida@us.ibm.com.

From Gene Trees to a Dated Allopolyploid Network: Insights from the Angiosperm Genus Viola (Violaceae)

PubMed Central

Marcussen, Thomas; Heier, Lise; Brysting, Anne K.; Oxelman, Bengt; Jakobsen, Kjetill S.

2015-01-01

Allopolyploidization accounts for a significant fraction of speciation events in many eukaryotic lineages. However, existing phylogenetic and dating methods require tree-like topologies and are unable to handle the network-like phylogenetic relationships of lineages containing allopolyploids. No explicit framework has so far been established for evaluating competing network topologies, and few attempts have been made to date phylogenetic networks. We used a four-step approach to generate a dated polyploid species network for the cosmopolitan angiosperm genus Viola L. (Violaceae Batch.). The genus contains ca 600 species and both recent (neo-) and more ancient (meso-) polyploid lineages distributed over 16 sections. First, we obtained DNA sequences of three low-copy nuclear genes and one chloroplast region, from 42 species representing all 16 sections. Second, we obtained fossil-calibrated chronograms for each nuclear gene marker. Third, we determined the most parsimonious multilabeled genome tree and its corresponding network, resolved at the section (not the species) level. Reconstructing the “correct” network for a set of polyploids depends on recovering all homoeologs, i.e., all subgenomes, in these polyploids. Assuming the presence of Viola subgenome lineages that were not detected by the nuclear gene phylogenies (“ghost subgenome lineages”) significantly reduced the number of inferred polyploidization events. We identified the most parsimonious network topology from a set of five competing scenarios differing in the interpretation of homoeolog extinctions and lineage sorting, based on (i) fewest possible ghost subgenome lineages, (ii) fewest possible polyploidization events, and (iii) least possible deviation from expected ploidy as inferred from available chromosome counts of the involved polyploid taxa. Finally, we estimated the homoploid and polyploid speciation times of the most parsimonious network. Homoploid speciation times were estimated by coalescent analysis of gene tree node ages. Polyploid speciation times were estimated by comparing branch lengths and speciation rates of lineages with and without ploidy shifts. Our analyses recognize Viola as an old genus (crown age 31 Ma) whose evolutionary history has been profoundly affected by allopolyploidy. Between 16 and 21 allopolyploidizations are necessary to explain the diversification of the 16 major lineages (sections) of Viola, suggesting that allopolyploidy has accounted for a high percentage—between 67% and 88%—of the speciation events at this level. The theoretical and methodological approaches presented here for (i) constructing networks and (ii) dating speciation events within a network, have general applicability for phylogenetic studies of groups where allopolyploidization has occurred. They make explicit use of a hitherto underexplored source of ploidy information from chromosome counts to help resolve phylogenetic cases where incomplete sequence data hampers network inference. Importantly, the coalescent-based method used herein circumvents the assumption of tree-like evolution required by most techniques for dating speciation events. PMID:25281848

Putting A Face On Rare Diseases | NIH MedlinePlus the Magazine

MedlinePlus

... NIH's event has been "Patients & Researchers—Partners for Life." This slogan aligns with NCATS' philosophy that researchers must work closely with patients, families, caregivers, and advocacy groups to maximize the chances ...

Topological properties of flat electroencephalography's state space

NASA Astrophysics Data System (ADS)

Ken, Tan Lit; Ahmad, Tahir bin; Mohd, Mohd Sham bin; Ngien, Su Kong; Suwa, Tohru; Meng, Ong Sie

2016-02-01

Neuroinverse problem are often associated with complex neuronal activity. It involves locating problematic cell which is highly challenging. While epileptic foci localization is possible with the aid of EEG signals, it relies greatly on the ability to extract hidden information or pattern within EEG signals. Flat EEG being an enhancement of EEG is a way of viewing electroencephalograph on the real plane. In the perspective of dynamical systems, Flat EEG is equivalent to epileptic seizure hence, making it a great platform to study epileptic seizure. Throughout the years, various mathematical tools have been applied on Flat EEG to extract hidden information that is hardly noticeable by traditional visual inspection. While these tools have given worthy results, the journey towards understanding seizure process completely is yet to be succeeded. Since the underlying structure of Flat EEG is dynamic and is deemed to contain wealthy information regarding brainstorm, it would certainly be appealing to explore in depth its structures. To better understand the complex seizure process, this paper studies the event of epileptic seizure via Flat EEG in a more general framework by means of topology, particularly, on the state space where the event of Flat EEG lies.

Effect of molecular topology on the transport properties of dendrimers in dilute solution at Θ temperature: A Brownian dynamics study

NASA Astrophysics Data System (ADS)

Bosko, Jaroslaw T.; Ravi Prakash, J.

2008-01-01

Structure and transport properties of dendrimers in dilute solution are studied with the aid of Brownian dynamics simulations. To investigate the effect of molecular topology on the properties, linear chain, star, and dendrimer molecules of comparable molecular weights are studied. A bead-spring chain model with finitely extensible springs and fluctuating hydrodynamic interactions is used to represent polymer molecules under Θ conditions. Structural properties as well as the diffusivity and zero-shear-rate intrinsic viscosity of polymers with varied degrees of branching are analyzed. Results for the free-draining case are compared to and found in very good agreement with the Rouse model predictions. Translational diffusivity is evaluated and the difference between the short-time and long-time behavior due to dynamic correlations is observed. Incorporation of hydrodynamic interactions is found to be sufficient to reproduce the maximum in the intrinsic viscosity versus molecular weight observed experimentally for dendrimers. Results of the nonequilibrium Brownian dynamics simulations of dendrimers and linear chain polymers subjected to a planar shear flow in a wide range of strain rates are also reported. The flow-induced molecular deformation of molecules is found to decrease hydrodynamic interactions and lead to the appearance of shear thickening. Further, branching is found to suppress flow-induced molecular alignment and deformation.

Effects of Substrate Surface Topology on NiFe/Cu/Co Spin Valve Characteristics

NASA Astrophysics Data System (ADS)

Kim, Hyeong-Jun; Jeong, Won-Cheol; Cho, Kwon-Ku; Kim, Young-Keun; Joo, Seung-Ki

2000-08-01

In order to control the crystallinity of sputter-deposited NiFe/Cu/Co spin valve thin films, surface topology of 4°tilt-cut Si(111) substrates was modified in various ways prior to formation of the spin valves. In case of the mirror polished substrate, NiFe and Co showed fcc (110) preferred orientation with in-plane uniaxial magnetic anisotropy. The easy axes of these magnetic layers were aligned in 90° to each other and giant magnetoresistance (GMR) was measured to be 4.5% at room temperature. The spin valves formed on the amorphized substrate by Ar ion mass doping, however, did not show magnetic anisotropy due to the loss of crystallinity and no appreciable GMR could be observed. The spin valves deposited on the unpolished substrate, of which the average surface roughness was measured to be a few microns, turned out to show a sound multilayeredness as well as crystallinity, but GMR was reduced to 3.5%. Tailing in the magnetoresistance (R-H) curve occurred in the spin valves formed on the unpolished substrate, and it was thought to be attributed to the shape anisotropy related to the interface roughness of the films. Detailed discussion on the relationship between GMR and crystallinity of the magnetic layers has been made with the results of simple simulation.

Topological defects in confined populations of spindle-shaped cells

NASA Astrophysics Data System (ADS)

Duclos, Guillaume; Erlenkämper, Christoph; Joanny, Jean-François; Silberzan, Pascal

2017-01-01

Most spindle-shaped cells (including smooth muscles and sarcomas) organize in vivo into well-aligned `nematic’ domains, creating intrinsic topological defects that may be used to probe the behaviour of these active nematic systems. Active non-cellular nematics have been shown to be dominated by activity, yielding complex chaotic flows. However, the regime in which live spindle-shaped cells operate, and the importance of cell-substrate friction in particular, remains largely unexplored. Using in vitro experiments, we show that these active cellular nematics operate in a regime in which activity is effectively damped by friction, and that the interaction between defects is controlled by the system’s elastic nematic energy. Due to the activity of the cells, these defects behave as self-propelled particles and pairwise annihilate until all displacements freeze as cell crowding increases. When confined in mesoscopic circular domains, the system evolves towards two identical +1/2 disclinations facing each other. The most likely reduced positions of these defects are independent of the size of the disk, the cells’ activity or even the cell type, but are well described by equilibrium liquid crystal theory. These cell-based systems thus operate in a regime more stable than other active nematics, which may be necessary for their biological function.

BlastNeuron for Automated Comparison, Retrieval and Clustering of 3D Neuron Morphologies.

PubMed

Wan, Yinan; Long, Fuhui; Qu, Lei; Xiao, Hang; Hawrylycz, Michael; Myers, Eugene W; Peng, Hanchuan

2015-10-01

Characterizing the identity and types of neurons in the brain, as well as their associated function, requires a means of quantifying and comparing 3D neuron morphology. Presently, neuron comparison methods are based on statistics from neuronal morphology such as size and number of branches, which are not fully suitable for detecting local similarities and differences in the detailed structure. We developed BlastNeuron to compare neurons in terms of their global appearance, detailed arborization patterns, and topological similarity. BlastNeuron first compares and clusters 3D neuron reconstructions based on global morphology features and moment invariants, independent of their orientations, sizes, level of reconstruction and other variations. Subsequently, BlastNeuron performs local alignment between any pair of retrieved neurons via a tree-topology driven dynamic programming method. A 3D correspondence map can thus be generated at the resolution of single reconstruction nodes. We applied BlastNeuron to three datasets: (1) 10,000+ neuron reconstructions from a public morphology database, (2) 681 newly and manually reconstructed neurons, and (3) neurons reconstructions produced using several independent reconstruction methods. Our approach was able to accurately and efficiently retrieve morphologically and functionally similar neuron structures from large morphology database, identify the local common structures, and find clusters of neurons that share similarities in both morphology and molecular profiles.

ISEE 3 observations of low-energy proton bidirectional events and their relation to isolated interplanetary magnetic structures

NASA Technical Reports Server (NTRS)

Marsden, R. G.; Sanderson, T. R.; Tranquille, C.; Wenzel, K.-P.; Smith, E. J.

1987-01-01

The paper represents the results of a comprehensive survey of low-energy proton bidirectional anisotropies and associated transient magnetic structures as observed in the 35-1600 keV energy range on ISEE-3 during the last solar maximum. The majority of observed bidirectional flow (BDF) events (more than 70 percent) are associated with isolated magnetic structures which are postulated to be an interplanetary manifestation of coronal mass ejection (CME) events. The observed BDF events can be qualitatively grouped into five classes depending on the field signature of the related magnetic structure and the association (or lack of association) with an interplanetary shock. Concerning the topology of the CME-related magnetic structures, the observations are interpreted as being consistent with a detached bubble, comprising closed loops or tightly wound helices.

Universal scattering response across the type-II Weyl semimetal phase diagram

NASA Astrophysics Data System (ADS)

Rüßmann, P.; Weber, A. P.; Glott, F.; Xu, N.; Fanciulli, M.; Muff, S.; Magrez, A.; Bugnon, P.; Berger, H.; Bode, M.; Dil, J. H.; Blügel, S.; Mavropoulos, P.; Sessi, P.

2018-02-01

The discovery of Weyl semimetals represents a significant advance in topological band theory. They paradigmatically enlarged the classification of topological materials to gapless systems while simultaneously providing experimental evidence for the long-sought Weyl fermions. Beyond fundamental relevance, their high mobility, strong magnetoresistance, and the possible existence of even more exotic effects, such as the chiral anomaly, make Weyl semimetals a promising platform to develop radically new technology. Fully exploiting their potential requires going beyond the mere identification of materials and calls for a detailed characterization of their functional response, which is severely complicated by the coexistence of surface- and bulk-derived topologically protected quasiparticles, i.e., Fermi arcs and Weyl points, respectively. Here, we focus on the type-II Weyl semimetal class in which we find a stoichiometry-dependent phase transition from a trivial to a nontrivial regime. By exploring the two extreme cases of the phase diagram, we demonstrate the existence of a universal response of both surface and bulk states to perturbations. We show that quasiparticle interference patterns originate from scattering events among surface arcs. Analysis reveals that topologically nontrivial contributions are strongly suppressed by spin texture. We also show that scattering at localized impurities can generate defect-induced quasiparticles sitting close to the Weyl point energy. These give rise to strong peaks in the local density of states, which lift the Weyl node, significantly altering the pristine low-energy spectrum. Remarkably, by comparing the WTe2 and the MoTe2 cases we found that scattering response and topological transition are not directly linked. Visualizing the existence of a universal microscopic response to scattering has important consequences for understanding the unusual transport properties of this class of materials. Overall, our observations provide a unifying picture of the type-II Weyl phase diagram.

W-curve alignments for HIV-1 genomic comparisons.

PubMed

Cork, Douglas J; Lembark, Steven; Tovanabutra, Sodsai; Robb, Merlin L; Kim, Jerome H

2010-06-01

The W-curve was originally developed as a graphical visualization technique for viewing DNA and RNA sequences. Its ability to render features of DNA also makes it suitable for computational studies. Its main advantage in this area is utilizing a single-pass algorithm for comparing the sequences. Avoiding recursion during sequence alignments offers advantages for speed and in-process resources. The graphical technique also allows for multiple models of comparison to be used depending on the nucleotide patterns embedded in similar whole genomic sequences. The W-curve approach allows us to compare large numbers of samples quickly. We are currently tuning the algorithm to accommodate quirks specific to HIV-1 genomic sequences so that it can be used to aid in diagnostic and vaccine efforts. Tracking the molecular evolution of the virus has been greatly hampered by gap associated problems predominantly embedded within the envelope gene of the virus. Gaps and hypermutation of the virus slow conventional string based alignments of the whole genome. This paper describes the W-curve algorithm itself, and how we have adapted it for comparison of similar HIV-1 genomes. A treebuilding method is developed with the W-curve that utilizes a novel Cylindrical Coordinate distance method and gap analysis method. HIV-1 C2-V5 env sequence regions from a Mother/Infant cohort study are used in the comparison. The output distance matrix and neighbor results produced by the W-curve are functionally equivalent to those from Clustal for C2-V5 sequences in the mother/infant pairs infected with CRF01_AE. Significant potential exists for utilizing this method in place of conventional string based alignment of HIV-1 genomes, such as Clustal X. With W-curve heuristic alignment, it may be possible to obtain clinically useful results in a short time-short enough to affect clinical choices for acute treatment. A description of the W-curve generation process, including a comparison technique of aligning extremes of the curves to effectively phase-shift them past the HIV-1 gap problem, is presented. Besides yielding similar neighbor-joining phenogram topologies, most Mother and Infant C2-V5 sequences in the cohort pairs geometrically map closest to each other, indicating that W-curve heuristics overcame any gap problem.

Next generation data harmonization

NASA Astrophysics Data System (ADS)

Armstrong, Chandler; Brown, Ryan M.; Chaves, Jillian; Czerniejewski, Adam; Del Vecchio, Justin; Perkins, Timothy K.; Rudnicki, Ron; Tauer, Greg

2015-05-01

Analysts are presented with a never ending stream of data sources. Often, subsets of data sources to solve problems are easily identified but the process to align data sets is time consuming. However, many semantic technologies do allow for fast harmonization of data to overcome these problems. These include ontologies that serve as alignment targets, visual tools and natural language processing that generate semantic graphs in terms of the ontologies, and analytics that leverage these graphs. This research reviews a developed prototype that employs all these approaches to perform analysis across disparate data sources documenting violent, extremist events.

A Formal Methodology to Design and Deploy Dependable Wireless Sensor Networks

PubMed Central

Testa, Alessandro; Cinque, Marcello; Coronato, Antonio; Augusto, Juan Carlos

2016-01-01

Wireless Sensor Networks (WSNs) are being increasingly adopted in critical applications, where verifying the correct operation of sensor nodes is a major concern. Undesired events may undermine the mission of the WSNs. Hence, their effects need to be properly assessed before deployment, to obtain a good level of expected performance; and during the operation, in order to avoid dangerous unexpected results. In this paper, we propose a methodology that aims at assessing and improving the dependability level of WSNs by means of an event-based formal verification technique. The methodology includes a process to guide designers towards the realization of a dependable WSN and a tool (“ADVISES”) to simplify its adoption. The tool is applicable to homogeneous WSNs with static routing topologies. It allows the automatic generation of formal specifications used to check correctness properties and evaluate dependability metrics at design time and at runtime for WSNs where an acceptable percentage of faults can be defined. During the runtime, we can check the behavior of the WSN accordingly to the results obtained at design time and we can detect sudden and unexpected failures, in order to trigger recovery procedures. The effectiveness of the methodology is shown in the context of two case studies, as proof-of-concept, aiming to illustrate how the tool is helpful to drive design choices and to check the correctness properties of the WSN at runtime. Although the method scales up to very large WSNs, the applicability of the methodology may be compromised by the state space explosion of the reasoning model, which must be faced by partitioning large topologies into sub-topologies. PMID:28025568

Orbs Align

NASA Image and Video Library

2006-05-23

Dione and Rhea pair up for an occultation, or mutual event, as seen by Cassini. While the lit portion of each moon is but a crescent, the dark side of Dione has begun to take a bite out of its distant sibling moon

78 FR 54469 - Solicitation of Written Comments on Draft National Action Plan for Adverse Drug Event Prevention

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-04

... developed with the expectation and understanding that outlining ADE prevention goals and, more importantly... coordinated federal partnerships, as well as public and private sector collaborations and aligned approaches...

Operational Alignment in Predator Training Research

DTIC Science & Technology

2014-04-21

to the SO and, down the road, the Mission Intelligence Coordinator ( MIC ). 2. X-Plane 9 is COTS software and serves as the aeronautical simulation...uses to communicate with ground forces, command and control (C2) elements, and the Mission Intelligence Coordinator ( MIC ), among others. 10. LNCS...because key events can be scripted and initiated as appropriate, while distractor events like a villager walking around a market can be controlled by

Quantifying Discrete Fracture Network Connectivity in Hydraulic Fracturing Stimulation

NASA Astrophysics Data System (ADS)

Urbancic, T.; Ardakani, E. P.; Baig, A.

2017-12-01

Hydraulic fracture stimulations generally result in microseismicity that is associated with the activation or extension of pre-existing microfractures and discontinuities. Microseismic events acquired under 3D downhole sensor coverage provide accurate event locations outlining hydraulic fracture growth. Combined with source characteristics, these events provide a high quality input for seismic moment tensor inversion and eventually constructing the representative discrete fracture network (DFN). In this study, we investigate the strain and stress state, identified fracture orientation, and DFN connectivity and performance for example stages in a multistage perf and plug completion in a North American shale play. We use topology, the familiar concept in many areas of structural geology, to further describe the relationships between the activated fractures and their effectiveness in enhancing permeability. We explore how local perturbations of stress state lead to the activation of different fractures sets and how that effects the DFN interaction and complexity. In particular, we observe that a more heterogeneous stress state shows a higher percentage of sub-horizontal fractures or bedding plane slips. Based on topology, the fractures are evenly distributed from the injection point, with decreasing numbers of connections by distance. The dimensionless measure of connection per branch and connection per line are used for quantifying the DFN connectivity. In order to connect the concept of connectivity back to productive volume and stimulation efficiency, the connectivity is compared with the character of deformation in the reservoir as deduced from the collective behavior of microseismicity using robustly determined source parameters.

The statistical analysis of energy release in small-scale coronal structures

NASA Astrophysics Data System (ADS)

Ulyanov, Artyom; Kuzin, Sergey; Bogachev, Sergey

We present the results of statistical analysis of impulsive flare-like brightenings, which numerously occur in the quiet regions of solar corona. For our study, we utilized high-cadence observations performed with two EUV-telescopes - TESIS/Coronas-Photon and AIA/SDO. In total, we processed 6 sequences of images, registered throughout the period between 2009 and 2013, covering the rising phase of the 24th solar cycle. Based on high-speed DEM estimation method, we developed a new technique to evaluate the main parameters of detected events (geometrical sizes, duration, temperature and thermal energy). We then obtained the statistical distributions of these parameters and examined their variations depending on the level of solar activity. The results imply that near the minimum of the solar cycle the energy release in quiet corona is mainly provided by small-scale events (nanoflares), whereas larger events (microflares) prevail on the peak of activity. Furthermore, we investigated the coronal conditions that had specified the formation and triggering of registered flares. By means of photospheric magnetograms obtained with MDI/SoHO and HMI/SDO instruments, we examined the topology of local magnetic fields at different stages: the pre-flare phase, the peak of intensity and the ending phase. To do so, we introduced a number of topological parameters including the total magnetic flux, the distance between magnetic sources and their mutual arrangement. The found correlation between the change of these parameters and the formation of flares may offer an important tool for application of flare forecasting.

DE 1 observations of type 1 counterstreaming electrons and field-aligned currents

NASA Technical Reports Server (NTRS)

Lin, C. S.; Burch, J. L.; Barfield, J. N.; Sugiura, M.; Nielsen, E.

1984-01-01

Dynamics Explorer 1 satellite observations of plasma and magnetic fields during type one counterstreaming electron events are presented. Counterstreaming electrons are observed at high altitudes in the region of field-aligned current. The total current density computed from the plasma data in the 18-10,000 eV energy range is generally about 1-2 micro-A/sq m. For the downward current, low-energy electrons contribute more than 40 percent of the total plasma current density integrated above 18 eV. For the upward current, such electrons contribute less than 50 percent of that current density. Electron beams in the field-aligned direction are occasionally detected. The pitch angle distributions of counterstreaming electrons are generally enhanced at both small and large pitch angles. STARE simultaneous observations for one DE 1 pass indicated that the field-aligned current was closed through Pedersen currents in the ionosphere. The directions of the ionospheric current systems are consistent with the DE 1 observations at high altitudes.

Test-electron analysis of the magnetic reconnection topology

NASA Astrophysics Data System (ADS)

Borgogno, D.; Perona, A.; Grasso, D.

2017-12-01

Three-dimensional (3D) investigations of the magnetic reconnection field topology in space and laboratory plasmas have identified the abidance of magnetic coherent structures in the stochastic region, which develop during the nonlinear stage of the reconnection process. Further analytical and numerical analyses highlighted the efficacy of some of these structures in limiting the magnetic transport. The question then arises as to what is the possible role played by these patterns in the dynamics of the plasma particles populating the chaotic region. In order to explore this aspect, we provide a detailed description of the nonlinear 3D magnetic field topology in a collisionless magnetic reconnection event with a strong guide field. In parallel, we study the evolution of a population of test electrons in the guiding-center approximation all along the reconnection process. In particular, we focus on the nonlinear spatial redistribution of the initially thermal electrons and show how the electron dynamics in the stochastic region depends on the sign and on the value of their velocities. While the particles with the highest positive speed populate the coherent current structures that survive in the chaotic sea, the presence of the manifolds calculated in the stochastic region defines the confinement area for the electrons with the largest negative velocity. These results stress the link between the magnetic topology and the electron motion and contribute to the overall picture of a non-stationary fluid magnetic reconnection description in a geometry proper to physical systems where the effects of the curvature can be neglected.

Topological evolution of the internet public opinion

NASA Astrophysics Data System (ADS)

Lian, Ying; Dong, Xuefan; Liu, Yijun

2017-11-01

The Internet forms a platform featured with high liquidity, accessibility and concealment for the public to express their respective views on certain events, thus leading to a large network graph. Due to such environmental features, the public opinions formed on the Internet are different from those on traditional media. Studies focusing on the former area are relatively fewer. In addition, the majority of existing methods proposed for constructing the Internet public opinion topological structure are based on the classic BA model, thus resulting in drawbacks in the range of simplicity and a lack of strict deduction. Therefore, based on the complex networks theory, a model applied to describe the topology of the Internet public opinion is deduced with rigorous derivation in the present paper. Results show that the proposed expression could well reflect the degree distribution of Internet public opinion which follows an analogous power law distribution, and that the peak value and the degree distribution are not correlative to each other. Moreover, it has been also proved that compared to the classic BA model, the proposed model has better accuracy performance in the description of the degree distribution of the Internet public opinion, which contributes to future studies focusing on this area. Thus, an attempt has been made to give the first theoretical description of the Internet public opinion topology in the present paper. In addition, it is also the first paper focusing on the solution of networks degree distribution with an exponential growth form.

MemAxes Visualization Software

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hardware advancements such as Intel's PEBS and AMD's IBS, as well as software developments such as the perf_event API in Linux have made available the acquisition of memory access samples with performance information. MemAxes is a visualization and analysis tool for memory access sample data. By mapping the samples to their associated code, variables, node topology, and application dataset, MemAxes provides intuitive views of the data.

On Connection Between Topology and Memory Loss in Sheared Granular Materials

NASA Astrophysics Data System (ADS)

Kovalcinova, Lenka; Kramar, Miro; Mischaikow, Konstantin; Kondic, Lou

We present combined results of discrete element simulations and topological data analysis that allows us to characterize the geometrical properties of force networks. Our numerical setup consists of the system of cylindrical particles placed inside rectangular box with periodic boundary conditions along the horizontal direction. System dynamics is driven by constant shearing speed of the top and bottom walls (in the opposite directions) and pressure applied on the top wall in a dense flow regime. Our study reveals the origin of memory loss in granular systems through local rapid changes in force networks. To understand these rapid events we analyze the evolution of the largest Lyapunov exponent in a simpler case of granular system without inter-particle friction and explore a correlation with topological measures. Surprisingly, our results suggest that the memory loss is driven mainly by pressure even in the case of fixed inertial number. We conclude that the interplay between physical properties of the granular system and force network geometry is a key to understand the dynamics of the sheared systems. This research was supported by NSF Grant No. DMS-1521717 and DARPA No. HR0011-16-2-0033.

Short-Term Load Forecasting Based Automatic Distribution Network Reconfiguration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, Huaiguang; Ding, Fei; Zhang, Yingchen

In a traditional dynamic network reconfiguration study, the optimal topology is determined at every scheduled time point by using the real load data measured at that time. The development of the load forecasting technique can provide an accurate prediction of the load power that will happen in a future time and provide more information about load changes. With the inclusion of load forecasting, the optimal topology can be determined based on the predicted load conditions during a longer time period instead of using a snapshot of the load at the time when the reconfiguration happens; thus, the distribution system operatormore » can use this information to better operate the system reconfiguration and achieve optimal solutions. This paper proposes a short-term load forecasting approach to automatically reconfigure distribution systems in a dynamic and pre-event manner. Specifically, a short-term and high-resolution distribution system load forecasting approach is proposed with a forecaster based on support vector regression and parallel parameters optimization. The network reconfiguration problem is solved by using the forecasted load continuously to determine the optimal network topology with the minimum amount of loss at the future time. The simulation results validate and evaluate the proposed approach.« less

Short-Term Load Forecasting Based Automatic Distribution Network Reconfiguration: Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, Huaiguang; Ding, Fei; Zhang, Yingchen

In the traditional dynamic network reconfiguration study, the optimal topology is determined at every scheduled time point by using the real load data measured at that time. The development of load forecasting technique can provide accurate prediction of load power that will happen in future time and provide more information about load changes. With the inclusion of load forecasting, the optimal topology can be determined based on the predicted load conditions during the longer time period instead of using the snapshot of load at the time when the reconfiguration happens, and thus it can provide information to the distribution systemmore » operator (DSO) to better operate the system reconfiguration to achieve optimal solutions. Thus, this paper proposes a short-term load forecasting based approach for automatically reconfiguring distribution systems in a dynamic and pre-event manner. Specifically, a short-term and high-resolution distribution system load forecasting approach is proposed with support vector regression (SVR) based forecaster and parallel parameters optimization. And the network reconfiguration problem is solved by using the forecasted load continuously to determine the optimal network topology with the minimum loss at the future time. The simulation results validate and evaluate the proposed approach.« less

Short-Term Load Forecasting-Based Automatic Distribution Network Reconfiguration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, Huaiguang; Ding, Fei; Zhang, Yingchen

In a traditional dynamic network reconfiguration study, the optimal topology is determined at every scheduled time point by using the real load data measured at that time. The development of the load forecasting technique can provide an accurate prediction of the load power that will happen in a future time and provide more information about load changes. With the inclusion of load forecasting, the optimal topology can be determined based on the predicted load conditions during a longer time period instead of using a snapshot of the load at the time when the reconfiguration happens; thus, the distribution system operatormore » can use this information to better operate the system reconfiguration and achieve optimal solutions. This paper proposes a short-term load forecasting approach to automatically reconfigure distribution systems in a dynamic and pre-event manner. Specifically, a short-term and high-resolution distribution system load forecasting approach is proposed with a forecaster based on support vector regression and parallel parameters optimization. The network reconfiguration problem is solved by using the forecasted load continuously to determine the optimal network topology with the minimum amount of loss at the future time. The simulation results validate and evaluate the proposed approach.« less

Decomposing the Site Frequency Spectrum: The Impact of Tree Topology on Neutrality Tests.

PubMed

Ferretti, Luca; Ledda, Alice; Wiehe, Thomas; Achaz, Guillaume; Ramos-Onsins, Sebastian E

2017-09-01

We investigate the dependence of the site frequency spectrum on the topological structure of genealogical trees. We show that basic population genetic statistics, for instance, estimators of θ or neutrality tests such as Tajima's D , can be decomposed into components of waiting times between coalescent events and of tree topology. Our results clarify the relative impact of the two components on these statistics. We provide a rigorous interpretation of positive or negative values of an important class of neutrality tests in terms of the underlying tree shape. In particular, we show that values of Tajima's D and Fay and Wu's H depend in a direct way on a peculiar measure of tree balance, which is mostly determined by the root balance of the tree. We present a new test for selection in the same class as Fay and Wu's H and discuss its interpretation and power. Finally, we determine the trees corresponding to extreme expected values of these neutrality tests and present formulas for these extreme values as a function of sample size and number of segregating sites. Copyright © 2017 by the Genetics Society of America.

Evolutionary relationships in Panicoid grasses based on plastome phylogenomics (Panicoideae; Poaceae).

PubMed

Burke, Sean V; Wysocki, William P; Zuloaga, Fernando O; Craine, Joseph M; Pires, J Chris; Edger, Patrick P; Mayfield-Jones, Dustin; Clark, Lynn G; Kelchner, Scot A; Duvall, Melvin R

2016-06-18

Panicoideae are the second largest subfamily in Poaceae (grass family), with 212 genera and approximately 3316 species. Previous studies have begun to reveal relationships within the subfamily, but largely lack resolution and/or robust support for certain tribal and subtribal groups. This study aims to resolve these relationships, as well as characterize a putative mitochondrial insert in one linage. 35 newly sequenced Panicoideae plastomes were combined in a phylogenomic study with 37 other species: 15 Panicoideae and 22 from outgroups. A robust Panicoideae topology largely congruent with previous studies was obtained, but with some incongruences with previously reported subtribal relationships. A mitochondrial DNA (mtDNA) to plastid DNA (ptDNA) transfer was discovered in the Paspalum lineage. The phylogenomic analysis returned a topology that largely supports previous studies. Five previously recognized subtribes appear on the topology to be non-monophyletic. Additionally, evidence for mtDNA to ptDNA transfer was identified in both Paspalum fimbriatum and P. dilatatum, and suggests a single rare event that took place in a common progenitor. Finally, the framework from this study can guide larger whole plastome sampling to discern the relationships in Cyperochloeae, Steyermarkochloeae, Gynerieae, and other incertae sedis taxa that are weakly supported or unresolved.

Different phylogenomic approaches to resolve the evolutionary relationships among model fish species.

PubMed

Negrisolo, Enrico; Kuhl, Heiner; Forcato, Claudio; Vitulo, Nicola; Reinhardt, Richard; Patarnello, Tomaso; Bargelloni, Luca

2010-12-01

Comparative genomics holds the promise to magnify the information obtained from individual genome sequencing projects, revealing common features conserved across genomes and identifying lineage-specific characteristics. To implement such a comparative approach, a robust phylogenetic framework is required to accurately reconstruct evolution at the genome level. Among vertebrate taxa, teleosts represent the second best characterized group, with high-quality draft genome sequences for five model species (Danio rerio, Gasterosteus aculeatus, Oryzias latipes, Takifugu rubripes, and Tetraodon nigroviridis), and several others are in the finishing lane. However, the relationships among the acanthomorph teleost model fishes remain an unresolved taxonomic issue. Here, a genomic region spanning over 1.2 million base pairs was sequenced in the teleost fish Dicentrarchus labrax. Together with genomic data available for the above fish models, the new sequence was used to identify unique orthologous genomic regions shared across all target taxa. Different strategies were applied to produce robust multiple gene and genomic alignments spanning from 11,802 to 186,474 amino acid/nucleotide positions. Ten data sets were analyzed according to Bayesian inference, maximum likelihood, maximum parsimony, and neighbor joining methods. Extensive analyses were performed to explore the influence of several factors (e.g., alignment methodology, substitution model, data set partitions, and long-branch attraction) on the tree topology. Although a general consensus was observed for a closer relationship between G. aculeatus (Gasterosteidae) and Di. labrax (Moronidae) with the atherinomorph O. latipes (Beloniformes) sister taxon of this clade, with the tetraodontiform group Ta. rubripes and Te. nigroviridis (Tetraodontiformes) representing a more distantly related taxon among acanthomorph model fish species, conflicting results were obtained between data sets and methods, especially with respect to the choice of alignment methodology applied to noncoding parts of the genomic region under study. This may limit the use of intergenic/noncoding sequences in phylogenomics until more robust alignment algorithms are developed.

Event-based cluster synchronization of coupled genetic regulatory networks

NASA Astrophysics Data System (ADS)

Yue, Dandan; Guan, Zhi-Hong; Li, Tao; Liao, Rui-Quan; Liu, Feng; Lai, Qiang

2017-09-01

In this paper, the cluster synchronization of coupled genetic regulatory networks with a directed topology is studied by using the event-based strategy and pinning control. An event-triggered condition with a threshold consisting of the neighbors' discrete states at their own event time instants and a state-independent exponential decay function is proposed. The intra-cluster states information and extra-cluster states information are involved in the threshold in different ways. By using the Lyapunov function approach and the theories of matrices and inequalities, we establish the cluster synchronization criterion. It is shown that both the avoidance of continuous transmission of information and the exclusion of the Zeno behavior are ensured under the presented triggering condition. Explicit conditions on the parameters in the threshold are obtained for synchronization. The stability criterion of a single GRN is also given under the reduced triggering condition. Numerical examples are provided to validate the theoretical results.

A Model Independent General Search for new physics in ATLAS

NASA Astrophysics Data System (ADS)

Amoroso, S.; ATLAS Collaboration

2016-04-01

We present results of a model-independent general search for new phenomena in proton-proton collisions at a centre-of-mass energy of 8 TeV with the ATLAS detector at the LHC. The data set corresponds to a total integrated luminosity of 20.3 fb-1. Event topologies involving isolated electrons, photons and muons, as well as jets, including those identified as originating from b-quarks (b-jets) and missing transverse momentum are investigated. The events are subdivided according to their final states into exclusive event classes. For the 697 classes with a Standard Model expectation greater than 0.1 events, a search algorithm tests the compatibility of data against the Monte Carlo simulated background in three kinematic variables sensitive to new physics effects. No significant deviation is found in data. The number and size of the observed deviations follow the Standard Model expectation obtained from simulated pseudo-experiments.

Event Reconstruction Techniques in NOvA

NASA Astrophysics Data System (ADS)

Baird, M.; Bian, J.; Messier, M.; Niner, E.; Rocco, D.; Sachdev, K.

2015-12-01

The NOvA experiment is a long-baseline neutrino oscillation experiment utilizing the NuMI beam generated at Fermilab. The experiment will measure the oscillations within a muon neutrino beam in a 300 ton Near Detector located underground at Fermilab and a functionally-identical 14 kiloton Far Detector placed 810 km away. The detectors are liquid scintillator tracking calorimeters with a fine-grained cellular structure that provides a wealth of information for separating the different particle track and shower topologies. Each detector has its own challenges with the Near Detector seeing multiple overlapping neutrino interactions in each event and the Far Detector having a large background of cosmic rays due to being located on the surface. A series of pattern recognition techniques have been developed to go from event records, to spatially and temporally separating individual interactions, to vertexing and tracking, and particle identification. This combination of methods to achieve the full event reconstruction will be discussed.

The galactic contribution to IceCube's astrophysical neutrino flux

DOE Office of Scientific and Technical Information (OSTI.GOV)

Denton, Peter B.; Marfatia, Danny; Weiler, Thomas J., E-mail: peterbd1@gmail.com, E-mail: dmarf8@hawaii.edu, E-mail: tom.weiler@vanderbilt.edu

2017-08-01

High energy neutrinos have been detected by IceCube, but their origin remains a mystery. Determining the sources of this flux is a crucial first step towards multi-messenger studies. In this work we systematically compare two classes of sources with the data: galactic and extragalactic. We assume that the neutrino sources are distributed according to a class of Galactic models. We build a likelihood function on an event by event basis including energy, event topology, absorption, and direction information. We present the probability that each high energy event with deposited energy E {sub dep}>60 TeV in the HESE sample is Galactic,more » extragalactic, or background. For Galactic models considered the Galactic fraction of the astrophysical flux has a best fit value of 1.3% and is <9.5% at 90% CL. A zero Galactic flux is allowed at <1σ.« less

Screening synteny blocks in pairwise genome comparisons through integer programming.

PubMed

Tang, Haibao; Lyons, Eric; Pedersen, Brent; Schnable, James C; Paterson, Andrew H; Freeling, Michael

2011-04-18

It is difficult to accurately interpret chromosomal correspondences such as true orthology and paralogy due to significant divergence of genomes from a common ancestor. Analyses are particularly problematic among lineages that have repeatedly experienced whole genome duplication (WGD) events. To compare multiple "subgenomes" derived from genome duplications, we need to relax the traditional requirements of "one-to-one" syntenic matchings of genomic regions in order to reflect "one-to-many" or more generally "many-to-many" matchings. However this relaxation may result in the identification of synteny blocks that are derived from ancient shared WGDs that are not of interest. For many downstream analyses, we need to eliminate weak, low scoring alignments from pairwise genome comparisons. Our goal is to objectively select subset of synteny blocks whose total scores are maximized while respecting the duplication history of the genomes in comparison. We call this "quota-based" screening of synteny blocks in order to appropriately fill a quota of syntenic relationships within one genome or between two genomes having WGD events. We have formulated the synteny block screening as an optimization problem known as "Binary Integer Programming" (BIP), which is solved using existing linear programming solvers. The computer program QUOTA-ALIGN performs this task by creating a clear objective function that maximizes the compatible set of synteny blocks under given constraints on overlaps and depths (corresponding to the duplication history in respective genomes). Such a procedure is useful for any pairwise synteny alignments, but is most useful in lineages affected by multiple WGDs, like plants or fish lineages. For example, there should be a 1:2 ploidy relationship between genome A and B if genome B had an independent WGD subsequent to the divergence of the two genomes. We show through simulations and real examples using plant genomes in the rosid superorder that the quota-based screening can eliminate ambiguous synteny blocks and focus on specific genomic evolutionary events, like the divergence of lineages (in cross-species comparisons) and the most recent WGD (in self comparisons). The QUOTA-ALIGN algorithm screens a set of synteny blocks to retain only those compatible with a user specified ploidy relationship between two genomes. These blocks, in turn, may be used for additional downstream analyses such as identifying true orthologous regions in interspecific comparisons. There are two major contributions of QUOTA-ALIGN: 1) reducing the block screening task to a BIP problem, which is novel; 2) providing an efficient software pipeline starting from all-against-all BLAST to the screened synteny blocks with dot plot visualizations. Python codes and full documentations are publicly available http://github.com/tanghaibao/quota-alignment. QUOTA-ALIGN program is also integrated as a major component in SynMap http://genomevolution.com/CoGe/SynMap.pl, offering easier access to thousands of genomes for non-programmers. © 2011 Tang et al; licensee BioMed Central Ltd.

Improvement of the relaxation time and the order parameter of nematic liquid crystal using a hybrid alignment mixture of carbon nanotube and polyimide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Hyojin; Yang, Seungbin; Lee, Ji-Hoon, E-mail: jihoonlee@jbnu.ac.kr

2014-05-12

We examined the electrooptical properties of a nematic liquid crystal (LC) sample whose substrates were coated with a mixture of carbon nanotube (CNT) and polyimide (PI). The relaxation time of the sample coated with 1.5 wt. % CNT mixture was about 35% reduced compared to the pure polyimide sample. The elastic constant and the order parameter of the CNT-mixture sample were increased and the fast relaxation of LC could be approximated to the mean-field theory. We found the CNT-mixed polyimide formed more smooth surface than the pure PI from atomic force microscopy images, indicating the increased order parameter is related to themore » smooth surface topology of the CNT-polyimide mixture.« less

Andreev reflection without Fermi surface alignment in high- T c van der Waals heterostructures

DOE PAGES

Zareapour, Parisa; Hayat, Alex; Zhao, Shu Yang F.; ...

2017-04-05

We address the controversy over the proximity effect between topological materials and high-T c superconductors. Junctions are produced between Bi 2Sr 2CaCu 2Omore » $${}_{8+\\delta }$$ and materials with different Fermi surfaces (Bi 2Te 3 and graphite). Both cases reveal tunneling spectra that are consistent with Andreev reflection. This is confirmed by a magnetic field that shifts features via the Doppler effect. This is modeled with a single parameter that accounts for tunneling into a screening supercurrent. Thus the tunneling involves Cooper pairs crossing the heterostructure, showing that the Fermi surface mismatch does not hinder the ability to form transparent interfaces, which is accounted for by the extended Brillouin zone and different lattice symmetries.« less

The Størmer problem for an aligned rotator

NASA Astrophysics Data System (ADS)

Epp, V.; Pervukhina, O. N.

2018-03-01

The effective potential energy of the particles in the field of rotating uniformly magnetized celestial body is investigated. The axis of rotation coincides with the axis of the magnetic field. Electromagnetic field of the body is composed of a dipole magnetic and quadrupole electric fields. The geometry of the trapping regions is studied as a function of the magnetic field magnitude and the rotation speed of the body. Examples of the potential energy topology for different values of these parameters are given. The main difference from the classical Størmer problem is that the single toroidal trapping region predicted by Størmer is divided into equatorial and off-equatorial trapping regions. Applicability of the idealized model of a rotating uniformly magnetized sphere with a vacuum magnetosphere to real celestial bodies is discussed.

Swarm Observation of Field-Aligned Currents Associated With Multiple Auroral Arc Systems

NASA Astrophysics Data System (ADS)

Wu, J.; Knudsen, D. J.; Gillies, D. M.; Donovan, E. F.; Burchill, J. K.

2017-10-01

Auroral arcs occur in regions of upward field-aligned currents (FACs); however, the relation is not one to one, since kinetic energy of the current-carrying electrons is also important in the production of auroral luminosity. Multiple auroral arc systems provide an opportunity to study the relation between FACs and auroral brightness in detail. In this study, we have identified two types of FAC configurations in multiple parallel arc systems using ground-based optical data from the Time History of Events and Macroscale Interactions during Substorms all-sky imagers, magnetometers and electric field instruments on board the Swarm satellites. In "unipolar FAC" events, each arc is an intensification within a broad, unipolar current sheet and downward return currents occur outside of this broad sheet. In "multipolar FAC" events, multiple arc systems represent a collection of multiple up/down current pairs. By collecting 17 events with unipolar FAC and 12 events with multipolar FACs, we find that (1) unipolar FAC events occur most frequently between 20 and 21 magnetic local time and multipolar FAC events tend to occur around local midnight and within 1 h after substorm onset. (2) Arcs in unipolar FAC systems have a typical width of 10-20 km and a spacing of 25-50 km. Arcs in multipolar FAC systems are wider and more separated. (3) Upward currents with more arcs embedded have larger intensities and widths. (4) Electric fields are strong and highly structured on the edges of multiple arc system with unipolar FAC. The fact that arcs with unipolar FAC are much more highly structured than the associated currents suggests that arc multiplicity is indicative not of a structured generator deep in the magnetosphere, but rather of the magnetosphere-ionosphere coupling process.

Search for Neutrinos in Super-Kamiokande Associated with Gravitational-wave Events GW150914 and GW151226

NASA Astrophysics Data System (ADS)

Abe, K.; Haga, K.; Hayato, Y.; Ikeda, M.; Iyogi, K.; Kameda, J.; Kishimoto, Y.; Miura, M.; Moriyama, S.; Nakahata, M.; Nakajima, T.; Nakano, Y.; Nakayama, S.; Orii, A.; Sekiya, H.; Shiozawa, M.; Takeda, A.; Tanaka, H.; Tasaka, S.; Tomura, T.; Akutsu, R.; Kajita, T.; Kaneyuki, K.; Nishimura, Y.; Richard, E.; Okumura, K.; Labarga, L.; Fernandez, P.; Blaszczyk, F. d. M.; Gustafson, J.; Kachulis, C.; Kearns, E.; Raaf, J. L.; Stone, J. L.; Sulak, L. R.; Berkman, S.; Nantais, C. M.; Tobayama, S.; Goldhaber, M.; Kropp, W. R.; Mine, S.; Weatherly, P.; Smy, M. B.; Sobel, H. W.; Takhistov, V.; Ganezer, K. S.; Hartfiel, B. L.; Hill, J.; Hong, N.; Kim, J. Y.; Lim, I. T.; Park, R. G.; Himmel, A.; Li, Z.; O’Sullivan, E.; Scholberg, K.; Walter, C. W.; Ishizuka, T.; Nakamura, T.; Jang, J. S.; Choi, K.; Learned, J. G.; Matsuno, S.; Smith, S. N.; Friend, M.; Hasegawa, T.; Ishida, T.; Ishii, T.; Kobayashi, T.; Nakadaira, T.; Nakamura, K.; Oyama, Y.; Sakashita, K.; Sekiguchi, T.; Tsukamoto, T.; Suzuki, A. T.; Takeuchi, Y.; Yano, T.; Cao, S. V.; Hiraki, T.; Hirota, S.; Huang, K.; Jiang, M.; Minamino, A.; Nakaya, T.; Patel, N. D.; Wendell, R. A.; Suzuki, K.; Fukuda, Y.; Itow, Y.; Suzuki, T.; Mijakowski, P.; Frankiewicz, K.; Hignight, J.; Imber, J.; Jung, C. K.; Li, X.; Palomino, J. L.; Santucci, G.; Wilking, M. J.; Yanagisawa, C.; Fukuda, D.; Ishino, H.; Kayano, T.; Kibayashi, A.; Koshio, Y.; Mori, T.; Sakuda, M.; Xu, C.; Kuno, Y.; Tacik, R.; Kim, S. B.; Okazawa, H.; Choi, Y.; Nishijima, K.; Koshiba, M.; Totsuka, Y.; Suda, Y.; Yokoyama, M.; Bronner, C.; Calland, R. G.; Hartz, M.; Martens, K.; Marti, Ll.; Suzuki, Y.; Vagins, M. R.; Martin, J. F.; Tanaka, H. A.; Konaka, A.; Chen, S.; Wan, L.; Zhang, Y.; Wilkes, R. J.; The Super-Kamiokande Collaboration

2016-10-01

We report the results from a search in Super-Kamiokande for neutrino signals coincident with the first detected gravitational-wave events, GW150914 and GW151226, as well as LVT151012, using a neutrino energy range from 3.5 MeV to 100 PeV. We searched for coincident neutrino events within a time window of ±500 s around the gravitational-wave detection time. Four neutrino candidates are found for GW150914, and no candidates are found for GW151226. The remaining neutrino candidates are consistent with the expected background events. We calculated the 90% confidence level upper limits on the combined neutrino fluence for both gravitational-wave events, which depends on event energy and topologies. Considering the upward-going muon data set (1.6 GeV–100 PeV), the neutrino fluence limit for each gravitational-wave event is 14–37 (19–50) cm‑2 for muon neutrinos (muon antineutrinos), depending on the zenith angle of the event. In the other data sets, the combined fluence limits for both gravitational-wave events range from 2.4 × 104 to 7.0 × 109 cm‑2.

Experimental characterization of extreme events of inertial dissipation in a turbulent swirling flow

PubMed Central

Saw, E. -W.; Kuzzay, D.; Faranda, D.; Guittonneau, A.; Daviaud, F.; Wiertel-Gasquet, C.; Padilla, V.; Dubrulle, B.

2016-01-01

The three-dimensional incompressible Navier–Stokes equations, which describe the motion of many fluids, are the cornerstones of many physical and engineering sciences. However, it is still unclear whether they are mathematically well posed, that is, whether their solutions remain regular over time or develop singularities. Even though it was shown that singularities, if exist, could only be rare events, they may induce additional energy dissipation by inertial means. Here, using measurements at the dissipative scale of an axisymmetric turbulent flow, we report estimates of such inertial energy dissipation and identify local events of extreme values. We characterize the topology of these extreme events and identify several main types. Most of them appear as fronts separating regions of distinct velocities, whereas events corresponding to focusing spirals, jets and cusps are also found. Our results highlight the non-triviality of turbulent flows at sub-Kolmogorov scales as possible footprints of singularities of the Navier–Stokes equation. PMID:27578459

Optimal simultaneous superpositioning of multiple structures with missing data.

PubMed

Theobald, Douglas L; Steindel, Phillip A

2012-08-01

Superpositioning is an essential technique in structural biology that facilitates the comparison and analysis of conformational differences among topologically similar structures. Performing a superposition requires a one-to-one correspondence, or alignment, of the point sets in the different structures. However, in practice, some points are usually 'missing' from several structures, for example, when the alignment contains gaps. Current superposition methods deal with missing data simply by superpositioning a subset of points that are shared among all the structures. This practice is inefficient, as it ignores important data, and it fails to satisfy the common least-squares criterion. In the extreme, disregarding missing positions prohibits the calculation of a superposition altogether. Here, we present a general solution for determining an optimal superposition when some of the data are missing. We use the expectation-maximization algorithm, a classic statistical technique for dealing with incomplete data, to find both maximum-likelihood solutions and the optimal least-squares solution as a special case. The methods presented here are implemented in THESEUS 2.0, a program for superpositioning macromolecular structures. ANSI C source code and selected compiled binaries for various computing platforms are freely available under the GNU open source license from http://www.theseus3d.org. dtheobald@brandeis.edu Supplementary data are available at Bioinformatics online.

Astrocytes Increase ATP Exocytosis Mediated Calcium Signaling in Response to Microgroove Structures

PubMed Central

Singh, Ajay V.; Raymond, Michael; Pace, Fabiano; Certo, Anthony; Zuidema, Jonathan M.; McKay, Christopher A.; Gilbert, Ryan J.; Lu, X. Lucas; Wan, Leo Q.

2015-01-01

Following central nervous system (CNS) injury, activated astrocytes form glial scars, which inhibit axonal regeneration, leading to long-term functional deficits. Engineered nanoscale scaffolds guide cell growth and enhance regeneration within models of spinal cord injury. However, the effects of micro-/nanosize scaffolds on astrocyte function are not well characterized. In this study, a high throughput (HTP) microscale platform was developed to study astrocyte cell behavior on micropatterned surfaces containing 1 μm spacing grooves with a depth of 250 or 500 nm. Significant changes in cell and nuclear elongation and alignment on patterned surfaces were observed, compared to on flat surfaces. The cytoskeleton components (particularly actin filaments and focal adhesions) and nucleus-centrosome axis were aligned along the grooved direction as well. More interestingly, astrocytes on micropatterned surfaces showed enhanced mitochondrial activity with lysosomes localized at the lamellipodia of the cells, accompanied by enhanced adenosine triphosphate (ATP) release and calcium activities. These data indicate that the lysosome-mediated ATP exocytosis and calcium signaling may play an important role in astrocytic responses to substrate topology. These new findings have furthered our understanding of the biomechanical regulation of astrocyte cell–substrate interactions, and may benefit the optimization of scaffold design for CNS healing. PMID:25597401

Simultaneously precise frequency transfer and time synchronization using feed-forward compensation technique via 120 km fiber link.

PubMed

Chen, Xing; Lu, Jinlong; Cui, Yifan; Zhang, Jian; Lu, Xing; Tian, Xusheng; Ci, Cheng; Liu, Bo; Wu, Hong; Tang, Tingsong; Shi, Kebin; Zhang, Zhigang

2015-12-22

Precision time synchronization between two remote sites is desired in many applications such as global positioning satellite systems, long-baseline interferometry, coherent radar detection and fundamental physics constant measurements. The recently developed frequency dissemination technologies based on optical fiber link have improved the transfer instability to the level of 10(-19)/day at remote location. Therefore it is possible to keep clock oscillation at remote locations continuously corrected, or to reproduce a "virtual" clock on the remote location. However the initial alignment and the correction of 1 pps timing signal from time to time are still required, besides the highly stabilized clock frequency transfer between distant locations. Here we demonstrate a time synchronization based on an ultra-stable frequency transfer system via 120-km commercial fiber link by transferring an optical frequency comb. Both the phase noise compensation in frequency dissemination and temporal basis alignment in time synchronization were implemented by a feed-forward digital compensation (FFDC) technique. The fractional frequency instability was measured to be 6.18 × 10(-20) at 2000 s. The timing deviation of time synchronization was measured to be 0.6 ps in 1500 s. This technique also can be applied in multi-node fiber network topology.

Simultaneously precise frequency transfer and time synchronization using feed-forward compensation technique via 120 km fiber link

PubMed Central

Chen, Xing; Lu, Jinlong; Cui, Yifan; Zhang, Jian; Lu, Xing; Tian, Xusheng; Ci, Cheng; Liu, Bo; Wu, Hong; Tang, Tingsong; Shi, Kebin; Zhang, Zhigang

2015-01-01

Precision time synchronization between two remote sites is desired in many applications such as global positioning satellite systems, long-baseline interferometry, coherent radar detection and fundamental physics constant measurements. The recently developed frequency dissemination technologies based on optical fiber link have improved the transfer instability to the level of 10−19/day at remote location. Therefore it is possible to keep clock oscillation at remote locations continuously corrected, or to reproduce a “virtual” clock on the remote location. However the initial alignment and the correction of 1 pps timing signal from time to time are still required, besides the highly stabilized clock frequency transfer between distant locations. Here we demonstrate a time synchronization based on an ultra-stable frequency transfer system via 120-km commercial fiber link by transferring an optical frequency comb. Both the phase noise compensation in frequency dissemination and temporal basis alignment in time synchronization were implemented by a feed-forward digital compensation (FFDC) technique. The fractional frequency instability was measured to be 6.18 × 10−20 at 2000 s. The timing deviation of time synchronization was measured to be 0.6 ps in 1500 s. This technique also can be applied in multi-node fiber network topology. PMID:26691731

Engineering highly organized and aligned single walled carbon nanotube networks for electronic device applications: Interconnects, chemical sensor, and optoelectronics

NASA Astrophysics Data System (ADS)

Kim, Young Lae

For 20 years, single walled carbon nanotubes (SWNTs) have been studied actively due to their unique one-dimensional nanostructure and superior electrical, thermal, and mechanical properties. For these reasons, they offer the potential to serve as building blocks for future electronic devices such as field effect transistors (FETs), electromechanical devices, and various sensors. In order to realize these applications, it is crucial to develop a simple, scalable, and reliable nanomanufacturing process that controllably places aligned SWNTs in desired locations, orientations, and dimensions. Also electronic properties (semiconducting/metallic) of SWNTs and their organized networks must be controlled for the desired performance of devices and systems. These fundamental challenges are significantly limiting the use of SWNTs for future electronic device applications. Here, we demonstrate a strategy to fabricate highly controlled micro/nanoscale SWNT network structures and present the related assembly mechanism to engineer the SWNT network topology and its electrical transport properties. A method designed to evaluate the electrical reliability of such nano- and microscale SWNT networks is also presented. Moreover, we develop and investigate a robust SWNT based multifunctional selective chemical sensor and a range of multifunctional optoelectronic switches, photo-transistors, optoelectronic logic gates and complex optoelectronic digital circuits.

Self-Assembled Epitaxial Au–Oxide Vertically Aligned Nanocomposites for Nanoscale Metamaterials

DOE PAGES

Li, Leigang; Sun, Liuyang; Gomez-Diaz, Juan Sebastian; ...

2016-05-17

Metamaterials made of nanoscale inclusions or artificial unit cells exhibit exotic optical properties that do not exist in natural materials. Promising applications, such as super-resolution imaging, cloaking, hyperbolic propagation, and ultrafast phase velocities have been demonstrated based on mostly micrometer-scale metamaterials and few nanoscale metamaterials. To date, most metamaterials are created using costly and tedious fabrication techniques with limited paths toward reliable large-scale fabrication. In this work, we demonstrate the one-step direct growth of self-assembled epitaxial metal–oxide nanocomposites as a drastically different approach to fabricating large-area nanostructured metamaterials. Using pulsed laser deposition, we fabricated nanocomposite films with vertically aligned goldmore » (Au) nanopillars (~20 nm in diameter) embedded in various oxide matrices with high epitaxial quality. Strong, broad absorption features in the measured absorbance spectrum are clear signatures of plasmon resonances of Au nanopillars. By tuning their densities on selected substrates, anisotropic optical properties are demonstrated via angular dependent and polarization resolved reflectivity measurements and reproduced by full-wave simulations and effective medium theory. Our model predicts exotic properties, such as zero permittivity responses and topological transitions. In conclusion, our studies suggest that these self-assembled metal–oxide nanostructures provide an exciting new material platform to control and enhance optical response at nanometer scales.« less

Iteratively Refined Guide Trees Help Improving Alignment and Phylogenetic Inference in the Mushroom Family Bolbitiaceae

PubMed Central

Tóth, Annamária; Hausknecht, Anton; Krisai-Greilhuber, Irmgard; Papp, Tamás; Vágvölgyi, Csaba; Nagy, László G.

2013-01-01

Reconciling traditional classifications, morphology, and the phylogenetic relationships of brown-spored agaric mushrooms has proven difficult in many groups, due to extensive convergence in morphological features. Here, we address the monophyly of the Bolbitiaceae, a family with over 700 described species and examine the higher-level relationships within the family using a newly constructed multilocus dataset (ITS, nrLSU rDNA and EF1-alpha). We tested whether the fast-evolving Internal Transcribed Spacer (ITS) sequences can be accurately aligned across the family, by comparing the outcome of two iterative alignment refining approaches (an automated and a manual) and various indel-treatment strategies. We used PRANK to align sequences in both cases. Our results suggest that – although PRANK successfully evades overmatching of gapped sites, referred previously to as alignment overmatching – it infers an unrealistically high number of indel events with natively generated guide-trees. This 'alignment undermatching' could be avoided by using more rigorous (e.g. ML) guide trees. The trees inferred in this study support the monophyly of the core Bolbitiaceae, with the exclusion of Panaeolus, Agrocybe, and some of the genera formerly placed in the family. Bolbitius and Conocybe were found monophyletic, however, Pholiotina and Galerella require redefinition. The phylogeny revealed that stipe coverage type is a poor predictor of phylogenetic relationships, indicating the need for a revision of the intrageneric relationships within Conocybe. PMID:23418526

A Fuzzy-Decision Based Approach for Composite Event Detection in Wireless Sensor Networks

PubMed Central

Zhang, Shukui; Chen, Hao; Zhu, Qiaoming

2014-01-01

The event detection is one of the fundamental researches in wireless sensor networks (WSNs). Due to the consideration of various properties that reflect events status, the Composite event is more consistent with the objective world. Thus, the research of the Composite event becomes more realistic. In this paper, we analyze the characteristics of the Composite event; then we propose a criterion to determine the area of the Composite event and put forward a dominating set based network topology construction algorithm under random deployment. For the unreliability of partial data in detection process and fuzziness of the event definitions in nature, we propose a cluster-based two-dimensional τ-GAS algorithm and fuzzy-decision based composite event decision mechanism. In the case that the sensory data of most nodes are normal, the two-dimensional τ-GAS algorithm can filter the fault node data effectively and reduce the influence of erroneous data on the event determination. The Composite event judgment mechanism which is based on fuzzy-decision holds the superiority of the fuzzy-logic based algorithm; moreover, it does not need the support of a huge rule base and its computational complexity is small. Compared to CollECT algorithm and CDS algorithm, this algorithm improves the detection accuracy and reduces the traffic. PMID:25136690

From gene trees to a dated allopolyploid network: insights from the angiosperm genus Viola (Violaceae).

PubMed

Marcussen, Thomas; Heier, Lise; Brysting, Anne K; Oxelman, Bengt; Jakobsen, Kjetill S

2015-01-01

Allopolyploidization accounts for a significant fraction of speciation events in many eukaryotic lineages. However, existing phylogenetic and dating methods require tree-like topologies and are unable to handle the network-like phylogenetic relationships of lineages containing allopolyploids. No explicit framework has so far been established for evaluating competing network topologies, and few attempts have been made to date phylogenetic networks. We used a four-step approach to generate a dated polyploid species network for the cosmopolitan angiosperm genus Viola L. (Violaceae Batch.). The genus contains ca 600 species and both recent (neo-) and more ancient (meso-) polyploid lineages distributed over 16 sections. First, we obtained DNA sequences of three low-copy nuclear genes and one chloroplast region, from 42 species representing all 16 sections. Second, we obtained fossil-calibrated chronograms for each nuclear gene marker. Third, we determined the most parsimonious multilabeled genome tree and its corresponding network, resolved at the section (not the species) level. Reconstructing the "correct" network for a set of polyploids depends on recovering all homoeologs, i.e., all subgenomes, in these polyploids. Assuming the presence of Viola subgenome lineages that were not detected by the nuclear gene phylogenies ("ghost subgenome lineages") significantly reduced the number of inferred polyploidization events. We identified the most parsimonious network topology from a set of five competing scenarios differing in the interpretation of homoeolog extinctions and lineage sorting, based on (i) fewest possible ghost subgenome lineages, (ii) fewest possible polyploidization events, and (iii) least possible deviation from expected ploidy as inferred from available chromosome counts of the involved polyploid taxa. Finally, we estimated the homoploid and polyploid speciation times of the most parsimonious network. Homoploid speciation times were estimated by coalescent analysis of gene tree node ages. Polyploid speciation times were estimated by comparing branch lengths and speciation rates of lineages with and without ploidy shifts. Our analyses recognize Viola as an old genus (crown age 31 Ma) whose evolutionary history has been profoundly affected by allopolyploidy. Between 16 and 21 allopolyploidizations are necessary to explain the diversification of the 16 major lineages (sections) of Viola, suggesting that allopolyploidy has accounted for a high percentage-between 67% and 88%-of the speciation events at this level. The theoretical and methodological approaches presented here for (i) constructing networks and (ii) dating speciation events within a network, have general applicability for phylogenetic studies of groups where allopolyploidization has occurred. They make explicit use of a hitherto underexplored source of ploidy information from chromosome counts to help resolve phylogenetic cases where incomplete sequence data hampers network inference. Importantly, the coalescent-based method used herein circumvents the assumption of tree-like evolution required by most techniques for dating speciation events. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

Cross-section measurement for quasi-elastic production of charmed baryons in νN interactions

NASA Astrophysics Data System (ADS)

Kayis-Topaksu, A.; Onengüt, G.; van Dantzig, R.; de Jong, M.; Melzer, O.; Oldeman, R. G. C.; Pesen, E.; Spada, F. R.; Visschers, J. L.; Güler, M.; Köse, U.; Serin-Zeyrek, M.; Sever, R.; Tolun, P.; Zeyrek, M. T.; Catanesi, M. G.; de Serio, M.; Ieva, M.; Muciaccia, M. T.; Radicioni, E.; Simone, S.; Bülte, A.; Winter, K.; van de Vyver, B.; Vilain, P.; Wilquet, G.; Pittoni, G. L.; Saitta, B.; di Capua, E.; Ogawa, S.; Shibuya, H.; Artamonov, A.; Chizhov, M.; Doucet, M.; Hristova, I. R.; Kawamura, T.; Kolev, D.; Meinhard, H.; Panman, J.; Papadopoulos, I. M.; Ricciardi, S.; Rozanov, A.; Tsenov, R.; Uiterwijk, J. W. E.; Zucchelli, P.; Goldberg, J.; Chikawa, M.; Arik, E.; Song, J. S.; Yoon, C. S.; Kodama, K.; Ushida, N.; Aoki, S.; Hara, T.; Delbar, T.; Favart, D.; Grégoire, G.; Kalinin, S.; Maklioueva, I.; Gorbunov, P.; Khovansky, V.; Shamanov, V.; Tsukerman, I.; Bruski, N.; Frekers, D.; Hoshino, K.; Kawada, J.; Komatsu, M.; Miyanishi, M.; Nakamura, M.; Nakano, T.; Narita, K.; Niu, K.; Niwa, K.; Nonaka, N.; Sato, O.; Toshito, T.; Buontempo, S.; Cocco, A. G.; D'Ambrosio, N.; de Lellis, G.; De Rosa, G.; di Capua, F.; Ereditato, A.; Fiorillo, G.; Marotta, A.; Messina, M.; Migliozzi, P.; Pistillo, C.; Scotto Lavina, L.; Strolin, P.; Tioukov, V.; Nakamura, K.; Okusawa, T.; Dore, U.; Loverre, P. F.; Ludovici, L.; Righini, P.; Rosa, G.; Santacesaria, R.; Satta, A.; Barbuto, E.; Bozza, C.; Grella, G.; Romano, G.; Sirignano, C.; Sorrentino, S.; Sato, Y.; Tezuka, I.; CHORUS Collaboration

2003-11-01

A study of quasi-elastic production of charmed baryons in charged-current interactions of neutrinos with the nuclear emulsion target of CHORUS is presented. In a sample of about 46 000 interactions located in the emulsion, candidates for decays of short-lived particles were identified by using new automatic scanning systems and later confirmed through visual inspection. Criteria based both on the topological and kinematical characteristics of quasi-elastic charm production allowed a clear separation between events of this type and those in which charm is produced in deep inelastic processes. A final sample containing 13 candidates consistent with quasi-elastic production of a charmed baryon with an estimated background of 1.7 events was obtained. At the average neutrino energy of 27 GeV the cross-section for the total quasi-elastic production of charmed baryons relative to the νN charged-current cross-section was measured to be σ(QE)/σ(CC)=(0.23+0.12-0.06(stat)+0.02-0.03(syst))×10-2. Through an analysis of the topology at the production and decay vertices the relative cross-sections were measured separately for singly (Λc+,Σc+,Σc+∗) and doubly (Σc++,Σc++∗) charged baryons.

Inference of Ancestral Recombination Graphs through Topological Data Analysis

PubMed Central

Cámara, Pablo G.; Levine, Arnold J.; Rabadán, Raúl

2016-01-01

The recent explosion of genomic data has underscored the need for interpretable and comprehensive analyses that can capture complex phylogenetic relationships within and across species. Recombination, reassortment and horizontal gene transfer constitute examples of pervasive biological phenomena that cannot be captured by tree-like representations. Starting from hundreds of genomes, we are interested in the reconstruction of potential evolutionary histories leading to the observed data. Ancestral recombination graphs represent potential histories that explicitly accommodate recombination and mutation events across orthologous genomes. However, they are computationally costly to reconstruct, usually being infeasible for more than few tens of genomes. Recently, Topological Data Analysis (TDA) methods have been proposed as robust and scalable methods that can capture the genetic scale and frequency of recombination. We build upon previous TDA developments for detecting and quantifying recombination, and present a novel framework that can be applied to hundreds of genomes and can be interpreted in terms of minimal histories of mutation and recombination events, quantifying the scales and identifying the genomic locations of recombinations. We implement this framework in a software package, called TARGet, and apply it to several examples, including small migration between different populations, human recombination, and horizontal evolution in finches inhabiting the Galápagos Islands. PMID:27532298

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abe, K.; Haga, K.; Hayato, Y.

We report the results from a search in Super-Kamiokande for neutrino signals coincident with the first detected gravitational-wave events, GW150914 and GW151226, as well as LVT151012, using a neutrino energy range from 3.5 MeV to 100 PeV. We searched for coincident neutrino events within a time window of ±500 s around the gravitational-wave detection time. Four neutrino candidates are found for GW150914, and no candidates are found for GW151226. The remaining neutrino candidates are consistent with the expected background events. We calculated the 90% confidence level upper limits on the combined neutrino fluence for both gravitational-wave events, which depends onmore » event energy and topologies. Considering the upward-going muon data set (1.6 GeV–100 PeV), the neutrino fluence limit for each gravitational-wave event is 14–37 (19–50) cm{sup −2} for muon neutrinos (muon antineutrinos), depending on the zenith angle of the event. In the other data sets, the combined fluence limits for both gravitational-wave events range from 2.4 × 10{sup 4} to 7.0 × 10{sup 9} cm{sup −2}.« less

Review of Findings for Human Performance Contribution to Risk in Operating Events

DTIC Science & Technology

2002-03-01

and loss of DC power. Key to this event was failure to control setpoints on safety-related equipment and failure to maintain the load tap changer...34 Therefore, "to optimize task execution at the job site, it is important to align organizational processes and values." Effective team skills are an...reactor was blocked and the water level rapidly dropped to the automatic low-level scram setpoint . Human Performance Issues Control rods were fully

Alignment of dynamic networks.

PubMed

Vijayan, V; Critchlow, D; Milenkovic, T

2017-07-15

Network alignment (NA) aims to find a node mapping that conserves similar regions between compared networks. NA is applicable to many fields, including computational biology, where NA can guide the transfer of biological knowledge from well- to poorly-studied species across aligned network regions. Existing NA methods can only align static networks. However, most complex real-world systems evolve over time and should thus be modeled as dynamic networks. We hypothesize that aligning dynamic network representations of evolving systems will produce superior alignments compared to aligning the systems' static network representations, as is currently done. For this purpose, we introduce the first ever dynamic NA method, DynaMAGNA ++. This proof-of-concept dynamic NA method is an extension of a state-of-the-art static NA method, MAGNA++. Even though both MAGNA++ and DynaMAGNA++ optimize edge as well as node conservation across the aligned networks, MAGNA++ conserves static edges and similarity between static node neighborhoods, while DynaMAGNA++ conserves dynamic edges (events) and similarity between evolving node neighborhoods. For this purpose, we introduce the first ever measure of dynamic edge conservation and rely on our recent measure of dynamic node conservation. Importantly, the two dynamic conservation measures can be optimized with any state-of-the-art NA method and not just MAGNA++. We confirm our hypothesis that dynamic NA is superior to static NA, on synthetic and real-world networks, in computational biology and social domains. DynaMAGNA++ is parallelized and has a user-friendly graphical interface. http://nd.edu/∼cone/DynaMAGNA++/ . tmilenko@nd.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Alignment of dynamic networks

PubMed Central

Vijayan, V.; Critchlow, D.; Milenković, T.

2017-01-01

Abstract Motivation: Network alignment (NA) aims to find a node mapping that conserves similar regions between compared networks. NA is applicable to many fields, including computational biology, where NA can guide the transfer of biological knowledge from well- to poorly-studied species across aligned network regions. Existing NA methods can only align static networks. However, most complex real-world systems evolve over time and should thus be modeled as dynamic networks. We hypothesize that aligning dynamic network representations of evolving systems will produce superior alignments compared to aligning the systems’ static network representations, as is currently done. Results: For this purpose, we introduce the first ever dynamic NA method, DynaMAGNA ++. This proof-of-concept dynamic NA method is an extension of a state-of-the-art static NA method, MAGNA++. Even though both MAGNA++ and DynaMAGNA++ optimize edge as well as node conservation across the aligned networks, MAGNA++ conserves static edges and similarity between static node neighborhoods, while DynaMAGNA++ conserves dynamic edges (events) and similarity between evolving node neighborhoods. For this purpose, we introduce the first ever measure of dynamic edge conservation and rely on our recent measure of dynamic node conservation. Importantly, the two dynamic conservation measures can be optimized with any state-of-the-art NA method and not just MAGNA++. We confirm our hypothesis that dynamic NA is superior to static NA, on synthetic and real-world networks, in computational biology and social domains. DynaMAGNA++ is parallelized and has a user-friendly graphical interface. Availability and implementation: http://nd.edu/∼cone/DynaMAGNA++/. Contact: tmilenko@nd.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28881980

Geometrical Properties of Coronal Mass Ejections

NASA Astrophysics Data System (ADS)

Cremades, Hebe; Bothmer, Volker

Based on the SOHO/LASCO dataset, a collection of "structured" coronal mass ejections (CMEs) has been compiled within the period 1996-2002, in order to analyze their three-dimensional configuration. These CME events exhibit white-light fine structures, likely indicative of their possible 3D topology. From a detailed investigation of the associated low coronal and photospheric source regions, a generic scheme has been deduced, which considers the white-light topology of a CME projected in the plane of the sky as being primarily dependent on the orientation and position of the source region's neutral line on the solar disk. The obtained results imply that structured CMEs are essentially organized along a symmetry axis, in a cylindrical manner. The measured dimensions of the cylinder's base and length yield a ratio of 1.6. These CMEs seem to be better approximated by elliptic cones, rather than by the classical ice cream cone, characterized by a circular cross section.

Modeling Wildfire Hazard in the Western Hindu Kush-Himalayas

NASA Astrophysics Data System (ADS)

Bylow, D.

2012-12-01

Wildfire regimes are a leading driver of global environmental change affecting a diverse array of global ecosystems. Particulates and aerosols produced by wildfires are a primary source of air pollution making the early detection and monitoring of wildfires crucial. The objectives of this study were to model regional wildfire potential and identify environmental, topological, and sociological factors that contribute to the ignition of wildfire events in the Western Hindu Kush-Himalayas of South Asia. The environmental, topological, and sociological factors were used to model regional wildfire potential through multi-criteria evaluation using a method of weighted linear combination. Moderate Resolution Imaging Spectroradiometer (MODIS) and geographic information systems (GIS) data were integrated to analyze regional wildfires and construct the model. Model validation was performed using a holdout cross validation method. The study produced a significant model of wildfire potential in the Western Hindu Kush-Himalayas.; Western Hindu Kush-Himalayas ; Western Hindu Kush-Himalayas Wildfire Potential

Performance of Social Network Sensors during Hurricane Sandy

PubMed Central

Kryvasheyeu, Yury; Chen, Haohui; Moro, Esteban; Van Hentenryck, Pascal; Cebrian, Manuel

2015-01-01

Information flow during catastrophic events is a critical aspect of disaster management. Modern communication platforms, in particular online social networks, provide an opportunity to study such flow and derive early-warning sensors, thus improving emergency preparedness and response. Performance of the social networks sensor method, based on topological and behavioral properties derived from the “friendship paradox”, is studied here for over 50 million Twitter messages posted before, during, and after Hurricane Sandy. We find that differences in users’ network centrality effectively translate into moderate awareness advantage (up to 26 hours); and that geo-location of users within or outside of the hurricane-affected area plays a significant role in determining the scale of such an advantage. Emotional response appears to be universal regardless of the position in the network topology, and displays characteristic, easily detectable patterns, opening a possibility to implement a simple “sentiment sensing” technique that can detect and locate disasters. PMID:25692690

Performance of social network sensors during Hurricane Sandy.

PubMed

Kryvasheyeu, Yury; Chen, Haohui; Moro, Esteban; Van Hentenryck, Pascal; Cebrian, Manuel

2015-01-01

Information flow during catastrophic events is a critical aspect of disaster management. Modern communication platforms, in particular online social networks, provide an opportunity to study such flow and derive early-warning sensors, thus improving emergency preparedness and response. Performance of the social networks sensor method, based on topological and behavioral properties derived from the "friendship paradox", is studied here for over 50 million Twitter messages posted before, during, and after Hurricane Sandy. We find that differences in users' network centrality effectively translate into moderate awareness advantage (up to 26 hours); and that geo-location of users within or outside of the hurricane-affected area plays a significant role in determining the scale of such an advantage. Emotional response appears to be universal regardless of the position in the network topology, and displays characteristic, easily detectable patterns, opening a possibility to implement a simple "sentiment sensing" technique that can detect and locate disasters.

Optimizing performance of hybrid FSO/RF networks in realistic dynamic scenarios

NASA Astrophysics Data System (ADS)

Llorca, Jaime; Desai, Aniket; Baskaran, Eswaran; Milner, Stuart; Davis, Christopher

2005-08-01

Hybrid Free Space Optical (FSO) and Radio Frequency (RF) networks promise highly available wireless broadband connectivity and quality of service (QoS), particularly suitable for emerging network applications involving extremely high data rate transmissions such as high quality video-on-demand and real-time surveillance. FSO links are prone to atmospheric obscuration (fog, clouds, snow, etc) and are difficult to align over long distances due the use of narrow laser beams and the effect of atmospheric turbulence. These problems can be mitigated by using adjunct directional RF links, which provide backup connectivity. In this paper, methodologies for modeling and simulation of hybrid FSO/RF networks are described. Individual link propagation models are derived using scattering theory, as well as experimental measurements. MATLAB is used to generate realistic atmospheric obscuration scenarios, including moving cloud layers at different altitudes. These scenarios are then imported into a network simulator (OPNET) to emulate mobile hybrid FSO/RF networks. This framework allows accurate analysis of the effects of node mobility, atmospheric obscuration and traffic demands on network performance, and precise evaluation of topology reconfiguration algorithms as they react to dynamic changes in the network. Results show how topology reconfiguration algorithms, together with enhancements to TCP/IP protocols which reduce the network response time, enable the network to rapidly detect and act upon link state changes in highly dynamic environments, ensuring optimized network performance and availability.

High-altitude closed magnetic loops at Mars observed by MAVEN

NASA Astrophysics Data System (ADS)

Xu, Shaosui; Mitchell, David; Luhmann, Janet; Ma, Yingjuan; Fang, Xiaohua; Harada, Yuki; Hara, Takuya; Brain, David; Webber, Tristan; Mazelle, Christian; DiBraccio, Gina A.

2017-10-01

With electron and magnetic field data obtained by the Mars Atmosphere and Volatile EvolutioN (MAVEN) spacecraft, we have identified closed magnetic field lines, with both footpoints embedded in the dayside ionosphere, extending up to 6200 km altitude (2.8 $R_m$) into the Martian tail. This topology is deduced from photoelectrons produced in the dayside ionosphere being observed in both parallel and anti-parallel directions along the magnetic field line. At perpendicular pitch angles, cases with either solar wind electrons or photoelectrons have been found, indicative of different formation mechanisms of these closed loops. These large closed loops are predicted by MHD simulations. The case with field-aligned photoelectrons mixed with perpendicular solar wind electrons is likely to be associated with reconnection, while the case with photoelectrons in all directions are probably due to closed field lines being pulled back down tail. We have developed an automated algorithm for distinguishing photoelectrons from solar wind electrons in pitch angle resolved energy spectra. This allows us to systematically analyze the MAVEN database and map the spatial distribution and occurrence rate of these closed magnetic loops, ranging from a few percent to a few tens percent outside of the optical shadow and less than one percent within the wake. These observations can be used to investigate the general magnetic topology in the tail, which is relevant to ion escape, reconnection, and flux ropes.

Dark matter particle spectroscopy at the LHC: generalizing M T2 to asymmetric event topologies

NASA Astrophysics Data System (ADS)

Konar, Partha; Kong, Kyoungchul; Matchev, Konstantin T.; Park, Myeonghun

2010-04-01

We consider SUSY-like missing energy events at hadron colliders and critically examine the common assumption that the missing energy is the result of two identical missing particles. In order to experimentally test this hypothesis, we generalize the subsystem M T2 variable to the case of asymmetric event topologies, where the two SUSY decay chains terminate in different “children” particles. In this more general approach, the endpoint M T2( max) of the M T2 distribution now gives the mass {tilde M_p}left( {tilde M_c^{(a)},tilde M_c^{(b)}} right) of the parent particles as a function of two input children masses tilde M_c^{(a)} and tilde M_c^{(b)} . We propose two methods for an independent determination of the individual children masses M ( a) c and M ( b) c . First, in the presence of upstream transverse momentum PUTM the corresponding function {tilde M_p}left( {tilde M_c^{(a)},tilde M_c^{(b)},{P_{text{UTM}}}} right) is independent of PUTM at precisely the right values of the children masses. Second, the previously discussed M T2 “kink” is now generalized to a “ridge” on the 2-dimensional surface {tilde M_p}left( {tilde M_c^{(a)},tilde M_c^{(b)}} right) . As we show in several examples, quite often there is a special point along that ridge which marks the true values of the children masses. Our results allow collider experiments to probe a multi-component dark matter sector directly and without any theoretical prejudice.

Event Coverage Detection and Event Source Determination in Underwater Wireless Sensor Networks.

PubMed

Zhou, Zhangbing; Xing, Riliang; Duan, Yucong; Zhu, Yueqin; Xiang, Jianming

2015-12-15

With the advent of the Internet of Underwater Things, smart things are deployed in the ocean space and establish underwater wireless sensor networks for the monitoring of vast and dynamic underwater environments. When events are found to have possibly occurred, accurate event coverage should be detected, and potential event sources should be determined for the enactment of prompt and proper responses. To address this challenge, a technique that detects event coverage and determines event sources is developed in this article. Specifically, the occurrence of possible events corresponds to a set of neighboring sensor nodes whose sensory data may deviate from a normal sensing range in a collective fashion. An appropriate sensor node is selected as the relay node for gathering and routing sensory data to sink node(s). When sensory data are collected at sink node(s), the event coverage is detected and represented as a weighted graph, where the vertices in this graph correspond to sensor nodes and the weight specified upon the edges reflects the extent of sensory data deviating from a normal sensing range. Event sources are determined, which correspond to the barycenters in this graph. The results of the experiments show that our technique is more energy efficient, especially when the network topology is relatively steady.

Event Coverage Detection and Event Source Determination in Underwater Wireless Sensor Networks

PubMed Central

Zhou, Zhangbing; Xing, Riliang; Duan, Yucong; Zhu, Yueqin; Xiang, Jianming

2015-01-01

With the advent of the Internet of Underwater Things, smart things are deployed in the ocean space and establish underwater wireless sensor networks for the monitoring of vast and dynamic underwater environments. When events are found to have possibly occurred, accurate event coverage should be detected, and potential event sources should be determined for the enactment of prompt and proper responses. To address this challenge, a technique that detects event coverage and determines event sources is developed in this article. Specifically, the occurrence of possible events corresponds to a set of neighboring sensor nodes whose sensory data may deviate from a normal sensing range in a collective fashion. An appropriate sensor node is selected as the relay node for gathering and routing sensory data to sink node(s). When sensory data are collected at sink node(s), the event coverage is detected and represented as a weighted graph, where the vertices in this graph correspond to sensor nodes and the weight specified upon the edges reflects the extent of sensory data deviating from a normal sensing range. Event sources are determined, which correspond to the barycenters in this graph. The results of the experiments show that our technique is more energy efficient, especially when the network topology is relatively steady. PMID:26694394

Analysis of field-aligned structure of compressional Pc 5 waves and associated energetic ion modulations observed by Polar at L~9.5

NASA Astrophysics Data System (ADS)

Capman, E.; Engebretson, M. J.; Pilipenko, V.; Russell, C. T.; Peterson, W. K.

2012-12-01

Nearly all previous studies of storm-time compressional Pc 5 waves have used data from low-inclination satellites, so the field-aligned structure of these waves could be determined only statistically or by inference. However, the high inclination of the Polar satellite's orbit allowed it to approximately follow a flux tube across the equator. In this study we present examples of compressional Pc 5 events identified during Polar's 2001-02 and 2002-03 duskside passages. The focus of this presentation is on exploring the field-aligned structure of the observed waves near the geomagnetic equator. At least two frequencies were identified in each event. In many cases these are a 1st (fundamental) harmonic with a node in the field-aligned (Bz) component near the geomagnetic equator, and a 2nd harmonic with an anti-node near the equator. To verify this assumption we applied the analytical signal method, verified by manual hodogram analysis, to monitor the amplitude and phase variations of the radial (Bx) and compressional (Bz) components at certain frequencies. The following transitions occurred near the time when Polar crossed the geomagnetic equator: The phase difference was 0° in the southern hemisphere and then 180° out of phase in the northern hemisphere. The waves were often linearly polarized, and the inclination angle of the polarization ellipse in the Bx-Bz plane was negative in the southern hemisphere and positive in the northern hemisphere. The ellipticity still had a slight positive bias in the southern hemisphere and a slight negative bias in the northern hemisphere. These observational results are compared with the results of modeling of coupled MHD Alfven and slow magnetosonic modes.

Electromagnetic versus Lense-Thirring alignment of black hole accretion discs

NASA Astrophysics Data System (ADS)

Polko, Peter; McKinney, Jonathan C.

2017-01-01

Accretion discs and black holes (BHs) have angular momenta that are generally misaligned, which can lead to warped discs and bends in any jets produced. We examine whether a disc that is misaligned at large radii can be aligned more efficiently by the torque of a Blandford-Znajek (BZ) jet than by Lense-Thirring (LT) precession. To obtain a strong result, we will assume that these torques maximally align the disc, rather than cause precession, or disc tearing. We consider several disc states that include radiatively inefficient thick discs, radiatively efficient thin discs, and super-Eddington accretion discs. The magnetic field strength of the BZ jet is chosen as either from standard equipartition arguments or from magnetically arrested disc (MAD) simulations. We show that standard thin accretion discs can reach spin-disc alignment out to large radii long before LT would play a role, due to the slow infall time that gives even a weak BZ jet time to align the disc. We show that geometrically thick radiatively inefficient discs and super-Eddington discs in the MAD state reach spin-disc alignment near the BH when density profiles are shallow as in magnetohydrodynamical simulations, while the BZ jet aligns discs with steep density profiles (as in advection-dominated accretion flows) out to larger radii. Our results imply that the BZ jet torque should affect the cosmological evolution of BH spin magnitude and direction, spin measurements in active galactic nuclei and X-ray binaries, and the interpretations for Event Horizon Telescope observations of discs or jets in strong-field gravity regimes.

Metabarcoding of marine nematodes – evaluation of reference datasets used in tree-based taxonomy assignment approach

PubMed Central

2016-01-01

Abstract Background Metabarcoding is becoming a common tool used to assess and compare diversity of organisms in environmental samples. Identification of OTUs is one of the critical steps in the process and several taxonomy assignment methods were proposed to accomplish this task. This publication evaluates the quality of reference datasets, alongside with several alignment and phylogeny inference methods used in one of the taxonomy assignment methods, called tree-based approach. This approach assigns anonymous OTUs to taxonomic categories based on relative placements of OTUs and reference sequences on the cladogram and support that these placements receive. New information In tree-based taxonomy assignment approach, reliable identification of anonymous OTUs is based on their placement in monophyletic and highly supported clades together with identified reference taxa. Therefore, it requires high quality reference dataset to be used. Resolution of phylogenetic trees is strongly affected by the presence of erroneous sequences as well as alignment and phylogeny inference methods used in the process. Two preparation steps are essential for the successful application of tree-based taxonomy assignment approach. Curated collections of genetic information do include erroneous sequences. These sequences have detrimental effect on the resolution of cladograms used in tree-based approach. They must be identified and excluded from the reference dataset beforehand. Various combinations of multiple sequence alignment and phylogeny inference methods provide cladograms with different topology and bootstrap support. These combinations of methods need to be tested in order to determine the one that gives highest resolution for the particular reference dataset. Completing the above mentioned preparation steps is expected to decrease the number of unassigned OTUs and thus improve the results of the tree-based taxonomy assignment approach. PMID:27932919

Metabarcoding of marine nematodes - evaluation of reference datasets used in tree-based taxonomy assignment approach.

PubMed

Holovachov, Oleksandr

2016-01-01

Metabarcoding is becoming a common tool used to assess and compare diversity of organisms in environmental samples. Identification of OTUs is one of the critical steps in the process and several taxonomy assignment methods were proposed to accomplish this task. This publication evaluates the quality of reference datasets, alongside with several alignment and phylogeny inference methods used in one of the taxonomy assignment methods, called tree-based approach. This approach assigns anonymous OTUs to taxonomic categories based on relative placements of OTUs and reference sequences on the cladogram and support that these placements receive. In tree-based taxonomy assignment approach, reliable identification of anonymous OTUs is based on their placement in monophyletic and highly supported clades together with identified reference taxa. Therefore, it requires high quality reference dataset to be used. Resolution of phylogenetic trees is strongly affected by the presence of erroneous sequences as well as alignment and phylogeny inference methods used in the process. Two preparation steps are essential for the successful application of tree-based taxonomy assignment approach. Curated collections of genetic information do include erroneous sequences. These sequences have detrimental effect on the resolution of cladograms used in tree-based approach. They must be identified and excluded from the reference dataset beforehand.Various combinations of multiple sequence alignment and phylogeny inference methods provide cladograms with different topology and bootstrap support. These combinations of methods need to be tested in order to determine the one that gives highest resolution for the particular reference dataset.Completing the above mentioned preparation steps is expected to decrease the number of unassigned OTUs and thus improve the results of the tree-based taxonomy assignment approach.

Large developing receptive fields using a distributed and locally reprogrammable address-event receiver.

PubMed

Bamford, Simeon A; Murray, Alan F; Willshaw, David J

2010-02-01

A distributed and locally reprogrammable address-event receiver has been designed, in which incoming address-events are monitored simultaneously by all synapses, allowing for arbitrarily large axonal fan-out without reducing channel capacity. Synapses can change the address of their presynaptic neuron, allowing the distributed implementation of a biologically realistic learning rule, with both synapse formation and elimination (synaptic rewiring). Probabilistic synapse formation leads to topographic map development, made possible by a cross-chip current-mode calculation of Euclidean distance. As well as synaptic plasticity in rewiring, synapses change weights using a competitive Hebbian learning rule (spike-timing-dependent plasticity). The weight plasticity allows receptive fields to be modified based on spatio-temporal correlations in the inputs, and the rewiring plasticity allows these modifications to become embedded in the network topology.

Precise measurement of the top-quark mass in the lepton+jets topology at CDF II.

PubMed

Aaltonen, T; Abulencia, A; Adelman, J; Affolder, T; Akimoto, T; Albrow, M G; Amerio, S; Amidei, D; Anastassov, A; Anikeev, K; Annovi, A; Antos, J; Aoki, M; Apollinari, G; Arisawa, T; Artikov, A; Ashmanskas, W; Attal, A; Aurisano, A; Azfar, F; Azzi-Bacchetta, P; Azzurri, P; Bacchetta, N; Badgett, W; Barbaro-Galtieri, A; Barnes, V E; Barnett, B A; Baroiant, S; Bartsch, V; Bauer, G; Beauchemin, P-H; Bedeschi, F; Behari, S; Bellettini, G; Bellinger, J; Belloni, A; Benjamin, D; Beretvas, A; Beringer, J; Berry, T; Bhatti, A; Binkley, M; Bisello, D; Bizjak, I; Blair, R E; Blocker, C; Blumenfeld, B; Bocci, A; Bodek, A; Boisvert, V; Bolla, G; Bolshov, A; Bortoletto, D; Boudreau, J; Boveia, A; Brau, B; Brigliadori, L; Bromberg, C; Brubaker, E; Budagov, J; Budd, H S; Budd, S; Burkett, K; Busetto, G; Bussey, P; Buzatu, A; Byrum, K L; Cabrera, S; Campanelli, M; Campbell, M; Canelli, F; Canepa, A; Carrillo, S; Carlsmith, D; Carosi, R; Carron, S; Casal, B; Casarsa, M; Castro, A; Catastini, P; Cauz, D; Cavalli-Sforza, M; Cerri, A; Cerrito, L; Chang, S H; Chen, Y C; Chertok, M; Chiarelli, G; Chlachidze, G; Chlebana, F; Cho, I; Cho, K; Chokheli, D; Chou, J P; Choudalakis, G; Chuang, S H; Chung, K; Chung, W H; Chung, Y S; Cilijak, M; Ciobanu, C I; Ciocci, M A; Clark, A; Clark, D; Coca, M; Compostella, G; Convery, M E; Conway, J; Cooper, B; Copic, K; Cordelli, M; Cortiana, G; Crescioli, F; Cuenca Almenar, C; Cuevas, J; Culbertson, R; Cully, J C; DaRonco, S; Datta, M; D'Auria, S; Davies, T; Dagenhart, D; de Barbaro, P; De Cecco, S; Deisher, A; De Lentdecker, G; De Lorenzo, G; Dell'Orso, M; Delli Paoli, F; Demortier, L; Deng, J; Deninno, M; De Pedis, D; Derwent, P F; Di Giovanni, G P; Dionisi, C; Di Ruzza, B; Dittmann, J R; D'Onofrio, M; Dörr, C; Donati, S; Dong, P; Donini, J; Dorigo, T; Dube, S; Efron, J; Erbacher, R; Errede, D; Errede, S; Eusebi, R; Fang, H C; Farrington, S; Fedorko, I; Fedorko, W T; Feild, R G; Feindt, M; Fernandez, J P; Field, R; Flanagan, G; Forrest, R; Forrester, S; Franklin, M; Freeman, J C; Furic, I; Gallinaro, M; Galyardt, J; Garcia, J E; Garberson, F; Garfinkel, A F; Gay, C; Gerberich, H; Gerdes, D; Giagu, S; Giannetti, P; Gibson, K; Gimmell, J L; Ginsburg, C; Giokaris, N; Giordani, M; Giromini, P; Giunta, M; Giurgiu, G; Glagolev, V; Glenzinski, D; Gold, M; Goldschmidt, N; Goldstein, J; Golossanov, A; Gomez, G; Gomez-Ceballos, G; Goncharov, M; González, O; Gorelov, I; Goshaw, A T; Goulianos, K; Gresele, A; Grinstein, S; Grosso-Pilcher, C; Group, R C; Grundler, U; Guimaraes da Costa, J; Gunay-Unalan, Z; Haber, C; Hahn, K; Hahn, S R; Halkiadakis, E; Hamilton, A; Han, B-Y; Han, J Y; Handler, R; Happacher, F; Hara, K; Hare, D; Hare, M; Harper, S; Harr, R F; Harris, R M; Hartz, M; Hatakeyama, K; Hauser, J; Hays, C; Heck, M; Heijboer, A; Heinemann, B; Heinrich, J; Henderson, C; Herndon, M; Heuser, J; Hidas, D; Hill, C S; Hirschbuehl, D; Hocker, A; Holloway, A; Hou, S; Houlden, M; Hsu, S-C; Huffman, B T; Hughes, R E; Husemann, U; Huston, J; Incandela, J; Introzzi, G; Iori, M; Ivanov, A; Iyutin, B; James, E; Jang, D; Jayatilaka, B; Jeans, D; Jeon, E J; Jindariani, S; Johnson, W; Jones, M; Joo, K K; Jun, S Y; Jung, J E; Junk, T R; Kamon, T; Karchin, P E; Kato, Y; Kemp, Y; Kephart, R; Kerzel, U; Khotilovich, V; Kilminster, B; Kim, D H; Kim, H S; Kim, J E; Kim, M J; Kim, S B; Kim, S H; Kim, Y K; Kimura, N; Kirsch, L; Klimenko, S; Klute, M; Knuteson, B; Ko, B R; Kondo, K; Kong, D J; Konigsberg, J; Korytov, A; Kotwal, A V; Kraan, A C; Kraus, J; Kreps, M; Kroll, J; Krumnack, N; Kruse, M; Krutelyov, V; Kubo, T; Kuhlmann, S E; Kuhr, T; Kulkarni, N P; Kusakabe, Y; Kwang, S; Laasanen, A T; Lai, S; Lami, S; Lammel, S; Lancaster, M; Lander, R L; Lannon, K; Lath, A; Latino, G; Lazzizzera, I; LeCompte, T; Lee, J; Lee, J; Lee, Y J; Lee, S W; Lefèvre, R; Leonardo, N; Leone, S; Levy, S; Lewis, J D; Lin, C; Lin, C S; Lindgren, M; Lipeles, E; Lister, A; Litvintsev, D O; Liu, T; Lockyer, N S; Loginov, A; Loreti, M; Lu, R-S; Lucchesi, D; Lujan, P; Lukens, P; Lungu, G; Lyons, L; Lys, J; Lysak, R; Lytken, E; Mack, P; MacQueen, D; Madrak, R; Maeshima, K; Makhoul, K; Maki, T; Maksimovic, P; Malde, S; Malik, S; Manca, G; Manousakis, A; Margaroli, F; Marginean, R; Marino, C; Marino, C P; Martin, A; Martin, M; Martin, V; Martínez, M; Martínez-Ballarín, R; Maruyama, T; Mastrandrea, P; Masubuchi, T; Matsunaga, H; Mattson, M E; Mazini, R; Mazzanti, P; McFarland, K S; McIntyre, P; McNulty, R; Mehta, A; Mehtala, P; Menzemer, S; Menzione, A; Merkel, P; Mesropian, C; Messina, A; Miao, T; Miladinovic, N; Miles, J; Miller, R; Mills, C; Milnik, M; Mitra, A; Mitselmakher, G; Miyamoto, A; Moed, S; Moggi, N; Mohr, B; Moon, C S; Moore, R; Morello, M; Movilla Fernandez, P; Mülmenstädt, J; Mukherjee, A; Muller, Th; Mumford, R; Murat, P; Mussini, M; Nachtman, J; Nagano, A; Naganoma, J; Nakamura, K; Nakano, I; Napier, A; Necula, V; Neu, C; Neubauer, M S; Nielsen, J; Nodulman, L; Norniella, O; Nurse, E; Oh, S H; Oh, Y D; Oksuzian, I; Okusawa, T; Oldeman, R; Orava, R; 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Shears, T; Shepard, P F; Sherman, D; Shimojima, M; Shochet, M; Shon, Y; Shreyber, I; Sidoti, A; Sinervo, P; Sisakyan, A; Slaughter, A J; Slaunwhite, J; Sliwa, K; Smith, J R; Snider, F D; Snihur, R; Soderberg, M; Soha, A; Somalwar, S; Sorin, V; Spalding, J; Spinella, F; Spreitzer, T; Squillacioti, P; Stanitzki, M; Staveris-Polykalas, A; St Denis, R; Stelzer, B; Stelzer-Chilton, O; Stentz, D; Strologas, J; Stuart, D; Suh, J S; Sukhanov, A; Sun, H; Suslov, I; Suzuki, T; Taffard, A; Takashima, R; Takeuchi, Y; Tanaka, R; Tecchio, M; Teng, P K; Terashi, K; Thom, J; Thompson, A S; Thomson, E; Tipton, P; Tiwari, V; Tkaczyk, S; Toback, D; Tokar, S; Tollefson, K; Tomura, T; Tonelli, D; Torre, S; Torretta, D; Tourneur, S; Trischuk, W; Tsuno, S; Tu, Y; Turini, N; Ukegawa, F; Uozumi, S; Vallecorsa, S; van Remortel, N; Varganov, A; Vataga, E; Vazquez, F; Velev, G; Vellidis, C; Veramendi, G; Veszpremi, V; Vidal, M; Vidal, R; Vila, I; Vilar, R; Vine, T; Vogel, M; Vollrath, I; Volobouev, I; Volpi, G; Würthwein, F; Wagner, P; Wagner, R G; Wagner, R L; Wagner, J; Wagner, W; Wallny, R; Wang, S M; Warburton, A; Waters, D; Weinberger, M; Wester, W C; Whitehouse, B; Whiteson, D; Wicklund, A B; Wicklund, E; Williams, G; Williams, H H; Wilson, P; Winer, B L; Wittich, P; Wolbers, S; Wolfe, C; Wright, T; Wu, X; Wynne, S M; Yagil, A; Yamamoto, K; Yamaoka, J; Yamashita, T; Yang, C; Yang, U K; Yang, Y C; Yao, W M; Yeh, G P; Yoh, J; Yorita, K; Yoshida, T; Yu, G B; Yu, I; Yu, S S; Yun, J C; Zanello, L; Zanetti, A; Zaw, I; Zhang, X; Zhou, J; Zucchelli, S

2007-11-02

We present a measurement of the mass of the top quark from proton-antiproton collisions recorded at the CDF experiment in Run II of the Fermilab Tevatron. We analyze events from the single lepton plus jets final state (tt-->W(+)bW(-)b-->lnubqq'b). The top-quark mass is extracted using a direct calculation of the probability density that each event corresponds to the tt final state. The probability is a function of both the mass of the top quark and the energy scale of the calorimeter jets, which is constrained in situ by the hadronic W boson mass. Using 167 events observed in 955 pb(-1) of integrated luminosity, we achieve the single most precise measurement of the top-quark mass, 170.8+/-2.2(stat.)+/-1.4(syst.) GeV/c(2).

Field theory in superfluid 3He: what are the lessons for particle physics, gravity, and high-temperature superconductivity?

PubMed

Volovik, G E

1999-05-25

There are several classes of homogeneous Fermi systems that are characterized by the topology of the energy spectrum of fermionic quasiparticles: (i) gapless systems with a Fermi surface, (ii) systems with a gap in their spectrum, (iii) gapless systems with topologically stable point nodes (Fermi points), and (iv) gapless systems with topologically unstable lines of nodes (Fermi lines). Superfluid 3He-A and electroweak vacuum belong to the universality class 3. The fermionic quasiparticles (particles) in this class are chiral: they are left-handed or right-handed. The collective bosonic modes of systems of class 3 are the effective gauge and gravitational fields. The great advantage of superfluid 3He-A is that we can perform experiments by using this condensed matter and thereby simulate many phenomena in high energy physics, including axial anomaly, baryoproduction, and magnetogenesis. 3He-A textures induce a nontrivial effective metrics of the space, where the free quasiparticles move along geodesics. With 3He-A one can simulate event horizons, Hawking radiation, rotating vacuum, etc. High-temperature superconductors are believed to belong to class 4. They have gapless fermionic quasiparticles with a "relativistic" spectrum close to gap nodes, which allows application of ideas developed for superfluid 3He-A.

How the toughness in metallic glasses depends on topological and chemical heterogeneity

PubMed Central

An, Qi; Samwer, Konrad; Demetriou, Marios D.; Floyd, Michael C.; Duggins, Danielle O.; Johnson, William L.; Goddard, William A.

2016-01-01

To gain insight into the large toughness variability observed between metallic glasses (MGs), we examine the origin of fracture toughness through bending experiments and molecular dynamics (MD) simulations for two binary MGs: Pd82Si18 and Cu46Zr54. The bending experiments show that Pd82Si18 is considerably tougher than Cu46Zr54, and the higher toughness of Pd82Si18 is attributed to an ability to deform plastically in the absence of crack nucleation through cavitation. The MD simulations study the initial stages of cavitation in both materials and extract the critical factors controlling cavitation. We find that for the tougher Pd82Si18, cavitation is governed by chemical inhomogeneity in addition to topological structures. In contrast, no such chemical correlations are observed in the more brittle Cu46Zr54, where topological low coordination number polyhedra are still observed around the critical cavity. As such, chemical inhomogeneity leads to more difficult cavitation initiation in Pd82Si18 than in Cu46Zr54, leading to a higher toughness. The absence of chemical separation during cavitation initiation in Cu46Zr54 decreases the energy barrier for a cavitation event, leading to lower toughness. PMID:27307438

Electromagnetic Waves and Bursty Electron Acceleration: Implications from Freja

NASA Technical Reports Server (NTRS)

Andersson, Laila; Ivchenko, N.; Wahlund, J.-E.; Clemmons, J.; Gustavsson, B.; Eliasson, L.

2000-01-01

Dispersive Alfven wave activity is identified in four dayside auroral oval events measured by the Freja satellite. The events are characterized by ion injection, bursty electron precipitation below about I keV, transverse ion heating and broadband extremely low frequency (ELF) emissions below the lower hybrid cutoff frequency (a few kHz). The broadband emissions are observed to become more electrostatic towards higher frequencies. Large-scale density depletions/cavities, as determined by the Langmuir probe measurements, and strong electrostatic emissions are often observed simultaneously. A correlation study has been carried out between the E- and B-field fluctuations below 64 Hz (the dc instrument's upper threshold) and the characteristics of the precipitating electrons. This study revealed that the energization of electrons is indeed related to the broadband ELF emissions and that the electrostatic component plays a predominant role during very active magnetospheric conditions. Furthermore, the effect of the ELF electromagnetic emissions on the larger scale field-aligned current systems has been investigated, and it is found that such an effect cannot be detected. Instead, the Alfvenic activity creates a local region of field-aligned currents. It is suggested that dispersive Alfven waves set up these local field-aligned current regions and in turn trigger more electrostatic emissions during certain conditions. In these regions ions are transversely heated, and large-scale density depletions/cavities may be created during especially active periods.

An Event-Triggered Machine Learning Approach for Accelerometer-Based Fall Detection.

PubMed

Putra, I Putu Edy Suardiyana; Brusey, James; Gaura, Elena; Vesilo, Rein

2017-12-22

The fixed-size non-overlapping sliding window (FNSW) and fixed-size overlapping sliding window (FOSW) approaches are the most commonly used data-segmentation techniques in machine learning-based fall detection using accelerometer sensors. However, these techniques do not segment by fall stages (pre-impact, impact, and post-impact) and thus useful information is lost, which may reduce the detection rate of the classifier. Aligning the segment with the fall stage is difficult, as the segment size varies. We propose an event-triggered machine learning (EvenT-ML) approach that aligns each fall stage so that the characteristic features of the fall stages are more easily recognized. To evaluate our approach, two publicly accessible datasets were used. Classification and regression tree (CART), k -nearest neighbor ( k -NN), logistic regression (LR), and the support vector machine (SVM) were used to train the classifiers. EvenT-ML gives classifier F-scores of 98% for a chest-worn sensor and 92% for a waist-worn sensor, and significantly reduces the computational cost compared with the FNSW- and FOSW-based approaches, with reductions of up to 8-fold and 78-fold, respectively. EvenT-ML achieves a significantly better F-score than existing fall detection approaches. These results indicate that aligning feature segments with fall stages significantly increases the detection rate and reduces the computational cost.

LHCb detector and trigger performance in Run II

NASA Astrophysics Data System (ADS)

Francesca, Dordei

2017-12-01

The LHCb detector is a forward spectrometer at the LHC, designed to perform high precision studies of b- and c- hadrons. In Run II of the LHC, a new scheme for the software trigger at LHCb allows splitting the triggering of events into two stages, giving room to perform the alignment and calibration in real time. In the novel detector alignment and calibration strategy for Run II, data collected at the start of the fill are processed in a few minutes and used to update the alignment, while the calibration constants are evaluated for each run. This allows identical constants to be used in the online and offline reconstruction, thus improving the correlation between triggered and offline selected events. The required computing time constraints are met thanks to a new dedicated framework using the multi-core farm infrastructure for the trigger. The larger timing budget, available in the trigger, allows to perform the same track reconstruction online and offline. This enables LHCb to achieve the best reconstruction performance already in the trigger, and allows physics analyses to be performed directly on the data produced by the trigger reconstruction. The novel real-time processing strategy at LHCb is discussed from both the technical and operational point of view. The overall performance of the LHCb detector on the data of Run II is presented as well.

Efficient Analysis of Simulations of the Sun's Magnetic Field

NASA Astrophysics Data System (ADS)

Scarborough, C. W.; Martínez-Sykora, J.

2014-12-01

Dynamics in the solar atmosphere, including solar flares, coronal mass ejections, micro-flares and different types of jets, are powered by the evolution of the sun's intense magnetic field. 3D Radiative Magnetohydrodnamics (MHD) computer simulations have furthered our understanding of the processes involved: When non aligned magnetic field lines reconnect, the alteration of the magnetic topology causes stored magnetic energy to be converted into thermal and kinetic energy. Detailed analysis of this evolution entails tracing magnetic field lines, an operation which is not time-efficient on a single processor. By utilizing a graphics card (GPU) to trace lines in parallel, conducting such analysis is made feasible. We applied our GPU implementation to the most advanced 3D Radiative-MHD simulations (Bifrost, Gudicksen et al. 2011) of the solar atmosphere in order to better understand the evolution of the modeled field lines.

Web-4D-QSAR: A web-based application to generate 4D-QSAR descriptors.

PubMed

Ataide Martins, João Paulo; Rougeth de Oliveira, Marco Antônio; Oliveira de Queiroz, Mário Sérgio

2018-06-05

A web-based application is developed to generate 4D-QSAR descriptors using the LQTA-QSAR methodology, based on molecular dynamics (MD) trajectories and topology information retrieved from the GROMACS package. The LQTAGrid module calculates the intermolecular interaction energies at each grid point, considering probes and all aligned conformations resulting from MD simulations. These interaction energies are the independent variables or descriptors employed in a QSAR analysis. A friendly front end web interface, built using the Django framework and Python programming language, integrates all steps of the LQTA-QSAR methodology in a way that is transparent to the user, and in the backend, GROMACS and LQTAGrid are executed to generate 4D-QSAR descriptors to be used later in the process of QSAR model building. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

The effect of Birkeland currents on magnetic field topology

NASA Technical Reports Server (NTRS)

Peroomian, Vahe; Lyons, Larry R.; Schulz, Michael

1996-01-01

A technique was developed for the inclusion of large scale magnetospheric current systems in magnetic field models. The region 1 and 2 Birkeland current systems are included in the source surface model of the terrestrial magnetosphere. The region 1 and 2 Birkeland currents are placed in the model using a series of field aligned, infinitely thin wire segments. The normal component of the magnetic field from these currents is calculated on the surface of the magnetopause and shielded using image current carrying wires placed outside of the magnetosphere. It is found that the inclusion of the Birkeland currents in the model results in a northward magnetic field in the near-midnight tail, leading to the closure of previously open flux in the tail, and a southward magnetic field in the flanks. A sunward shift in the separatrix is observed.

Velocity Space Evolution of Dayside Reconnection Outflow

NASA Astrophysics Data System (ADS)

Broll, J. M.; Fuselier, S. A.; Trattner, K. J.

2015-12-01

Magnetic reconnection is a universal phenomenon occurring when energy stored in a complicated magnetic field topology is released into the surrounding plasma as the field simplifies its configuration. At Earth's dayside magnetopause, reconnection is responsible for mass and energy input from the solar wind into the magnetosphere. We describe the evolution of the velocity-space evolution of plasma outflow from a dayside magnetic reconnection region. We analyze Cluster magnetopause crossings between 1 and 10 Earth radii from the reconnection X-line predicted by the maximum magnetic shear model. The effects of nonadiabatic processes, such as deformation of the profile due to finite-gyroradius-induced pitch-angle scattering and wave-particle interactions, are described. We compare observations and simulation results to describe the outflow evolution and infer the field-aligned distance between an observation and the reconnection site producing it.

Running and rotating: modelling the dynamics of migrating cell clusters

NASA Astrophysics Data System (ADS)

Copenhagen, Katherine; Gov, Nir; Gopinathan, Ajay

Collective motion of cells is a common occurrence in many biological systems, including tissue development and repair, and tumor formation. Recent experiments have shown cells form clusters in a chemical gradient, which display three different phases of motion: translational, rotational, and random. We present a model for cell clusters based loosely on other models seen in the literature that involves a Vicsek-like alignment as well as physical collisions and adhesions between cells. With this model we show that a mechanism for driving rotational motion in this kind of system is an increased motility of rim cells. Further, we examine the details of the relationship between rim and core cells, and find that the phases of the cluster as a whole are correlated with the creation and annihilation of topological defects in the tangential component of the velocity field.

Stability of a giant connected component in a complex network

NASA Astrophysics Data System (ADS)

Kitsak, Maksim; Ganin, Alexander A.; Eisenberg, Daniel A.; Krapivsky, Pavel L.; Krioukov, Dmitri; Alderson, David L.; Linkov, Igor

2018-01-01

We analyze the stability of the network's giant connected component under impact of adverse events, which we model through the link percolation. Specifically, we quantify the extent to which the largest connected component of a network consists of the same nodes, regardless of the specific set of deactivated links. Our results are intuitive in the case of single-layered systems: the presence of large degree nodes in a single-layered network ensures both its robustness and stability. In contrast, we find that interdependent networks that are robust to adverse events have unstable connected components. Our results bring novel insights to the design of resilient network topologies and the reinforcement of existing networked systems.

Disclosure of adverse events: a data linkage study reporting patient experiences among Australian adults aged ≥ 45 years.

PubMed

Walton, Merrilyn; Harrison, Reema; Smith-Merry, Jennifer; Kelly, Patrick; Manias, Elizabeth; Jorm, Christine; Iedema, Rick

2018-04-26

Objective Since Australia initiated national open disclosure standards in 2002, open disclosure policies have been adopted in all Australian states and territories. Yet, research evidence regarding their adoption is limited. The aim of the present study was to determine the frequency with which patients who report an adverse event had information disclosed to them about the incident, including whether they participated in a formal open disclosure process, their experiences of the process and the extent to which these align with the current New South Wales (NSW) policy. Methods A cross-sectional survey about patient experiences of disclosure associated with an adverse event was administered to a random sample of 20000 participants in the 45 and Up Study who were hospitalised in NSW, Australia, between January and June 2014. Results Of the 18993 eligible potential participants, completed surveys were obtained from 7661 (40% response rate), with 474 (7%) patients reporting an adverse event. Of those who reported an adverse event, a significant majority reported an informal or bedside disclosure (91%; 430/474). Only 79 patients (17%) participated in a formal open disclosure meeting. Most informal disclosures were provided by nurses, with only 25% provided by medical practitioners. Conclusions Experiences of open disclosure may be enhanced by informing patients of their right to full disclosure in advance of or upon admission to hospital, and recognition of and support for informal or bedside disclosure for appropriate types of incidents. A review of the open disclosure guidelines in relation to the types of adverse events that require formal open disclosure and those more suitable to informal bedside disclosure is indicated. Guidelines for bedside disclosure should be drafted to assist medical practitioners and other health professionals facilitate and improve their communications about adverse events. Alignment of formal disclosure with policy requirements may also be enhanced by training multidisciplinary teams in the process. What is known about the topic? While open disclosure is required in all cases of serious adverse events, patients' experiences are variable, and lack of, or poor quality disclosures are all too common. What does this paper add? This paper presents experiences reported by patients across New South Wales in a large cross-sectional survey. Unlike previous studies of open disclosure, recently hospitalised patients were identified and invited using data linkage with medical records. Findings suggest that most patients receive informal disclosures rather than a process that aligns with the current policy guidance. What are the implications for practitioners? Experiences of open disclosure may be enhanced by informing patients of their right to full disclosure in advance of or upon admission to hospital, and recognition of and support for informal or bedside disclosure for appropriate types of incidents.

Design and prototyping of self-centering optical single-mode fiber alignment structures

NASA Astrophysics Data System (ADS)

Ebraert, Evert; Gao, Fei; Beri, Stefano; Watté, Jan; Thienpont, Hugo; Van Erps, Jürgen

2016-06-01

The European Commission’s goal of providing each European household with at least a 30 Mb s-1 Internet connection by 2020 would be facilitated by a widespread deployment of fibre-to-the-home, which would in turn be sped up by the development of connector essential components, such as high-precision alignment features. Currently, the performance of state-of-the-art physical contact optical fiber connectors is limited by the tolerance on the cladding of standard telecom-grade single-mode fiber (SMF), which is typically smaller than  ±1 μm. We propose to overcome this limit by developing micro-spring-based self-centering alignment structures (SCAS) for SMF-connectors. We design these alignment structures with robustness and low-cost replication in mind, allowing for large-scale deployment. Both theoretical and finite element analysis (FEA) models are used to determine the optimal dimensions of the beams of which the micro-springs of the SCAS are comprised. Two topologies of the SCAS, consisting of three and four micro-springs respectively, are investigated for two materials: polysulfone (PSU) and polyetherimide (PEI). These materials hold great potential for high-performance fiber connectors while being compatible with low-cost production and with the harsh environmental operation conditions of those connectors. The theory and FEA agree well (<3% difference) for a simple micro-spring. When including a pedestal on the micro-spring (to bring it further away from the fiber) and for shorter spring lengths the agreement worsens. This is due to spring compression effects not being taken into account in our theoretical model. Prototypes are successfully fabricated using deep proton writing and subsequently characterized. The controlled insertion of an SMF in the SCAS is investigated and we determine that a force of 0.11 N is required. The fiber insertion also causes an out-of-plane deformation of the micro-springs in the SCAS of about 7 μm, which is no problem for robustness according to the FEA model. Finally connector-assemblies are made with the alignment system and we show that an insertion loss down to 0.1 dB is achievable. The prototypes are subsequently used as a sacrificial master for mould fabrication through electroplating with the goal of low-cost replication through hot embossing.

Flapping current sheet with superposed waves seen in space and on the ground

NASA Astrophysics Data System (ADS)

Wang, G. Q.; Volwerk, M.; Nakamura, R.; Boakes, P.; Zhang, T. L.; Yoshikawa, A.; Baishev, D. G.

2014-12-01

A wavy current sheet event observed on 15 October 2004 between 1235 and 1300 UT has been studied by using Cluster and ground-based magnetometer data. Waves propagating from the tail center to the duskside flank with a period ~30 s and wavelength ~1 RE are superimposed on a flapping current sheet, accompanied with a bursty bulk flow. Three Pi2 pulsations, with onset at ~1236, ~1251, and ~1255 UT, respectively, are observed at the Tixie station located near the foot points of Cluster. The mechanism creating the Pi2 (period ~40 s) onset at ~1236 UT is unclear. The second Pi2 (period ~90 s, onset at ~1251 UT) is associated with a strong field-aligned current, which has a strong transverse component of the magnetic field, observed by Cluster with a time delay ~60 s. We suggest that it is caused by bouncing Alfvén waves between the northern and southern ionosphere which transport the field-aligned current. For the third Pi2 (period ~60 s) there is almost no damping at the first three periods. They occur in conjunction with periodic field-aligned currents one-on-one with 72 s delay. We suggest that it is generated by these periodic field-aligned currents. We conclude that the strong field-aligned currents generated in the plasma sheet during flapping with superimposed higher-frequency waves can drive Pi2 pulsations on the ground, and periodic field-aligned currents can even control the period of the Pi2s.

Method and System for Gamma-Ray Localization Induced Spacecraft Navigation Using Celestial Gamma-Ray Sources

NASA Technical Reports Server (NTRS)

Hisamoto, Chuck (Inventor); Arzoumanian, Zaven (Inventor); Sheikh, Suneel I. (Inventor)

2015-01-01

A method and system for spacecraft navigation using distant celestial gamma-ray bursts which offer detectable, bright, high-energy events that provide well-defined characteristics conducive to accurate time-alignment among spatially separated spacecraft. Utilizing assemblages of photons from distant gamma-ray bursts, relative range between two spacecraft can be accurately computed along the direction to each burst's source based upon the difference in arrival time of the burst emission at each spacecraft's location. Correlation methods used to time-align the high-energy burst profiles are provided. The spacecraft navigation may be carried out autonomously or in a central control mode of operation.

A Framework Phylogeny of the American Oak Clade Based on Sequenced RAD Data

PubMed Central

Hipp, Andrew L.; Eaton, Deren A. R.; Cavender-Bares, Jeannine; Fitzek, Elisabeth; Nipper, Rick; Manos, Paul S.

2014-01-01

Previous phylogenetic studies in oaks (Quercus, Fagaceae) have failed to resolve the backbone topology of the genus with strong support. Here, we utilize next-generation sequencing of restriction-site associated DNA (RAD-Seq) to resolve a framework phylogeny of a predominantly American clade of oaks whose crown age is estimated at 23–33 million years old. Using a recently developed analytical pipeline for RAD-Seq phylogenetics, we created a concatenated matrix of 1.40 E06 aligned nucleotides, constituting 27,727 sequence clusters. RAD-Seq data were readily combined across runs, with no difference in phylogenetic placement between technical replicates, which overlapped by only 43–64% in locus coverage. 17% (4,715) of the loci we analyzed could be mapped with high confidence to one or more expressed sequence tags in NCBI Genbank. A concatenated matrix of the loci that BLAST to at least one EST sequence provides approximately half as many variable or parsimony-informative characters as equal-sized datasets from the non-EST loci. The EST-associated matrix is more complete (fewer missing loci) and has slightly lower homoplasy than non-EST subsampled matrices of the same size, but there is no difference in phylogenetic support or relative attribution of base substitutions to internal versus terminal branches of the phylogeny. We introduce a partitioned RAD visualization method (implemented in the R package RADami; http://cran.r-project.org/web/packages/RADami) to investigate the possibility that suboptimal topologies supported by large numbers of loci—due, for example, to reticulate evolution or lineage sorting—are masked by the globally optimal tree. We find no evidence for strongly-supported alternative topologies in our study, suggesting that the phylogeny we recover is a robust estimate of large-scale phylogenetic patterns in the American oak clade. Our study is one of the first to demonstrate the utility of RAD-Seq data for inferring phylogeny in a 23–33 million year-old clade. PMID:24705617

Integrated Computational System for Aerodynamic Steering and Visualization

NASA Technical Reports Server (NTRS)

Hesselink, Lambertus

1999-01-01

In February of 1994, an effort from the Fluid Dynamics and Information Sciences Divisions at NASA Ames Research Center with McDonnel Douglas Aerospace Company and Stanford University was initiated to develop, demonstrate, validate and disseminate automated software for numerical aerodynamic simulation. The goal of the initiative was to develop a tri-discipline approach encompassing CFD, Intelligent Systems, and Automated Flow Feature Recognition to improve the utility of CFD in the design cycle. This approach would then be represented through an intelligent computational system which could accept an engineer's definition of a problem and construct an optimal and reliable CFD solution. Stanford University's role focused on developing technologies that advance visualization capabilities for analysis of CFD data, extract specific flow features useful for the design process, and compare CFD data with experimental data. During the years 1995-1997, Stanford University focused on developing techniques in the area of tensor visualization and flow feature extraction. Software libraries were created enabling feature extraction and exploration of tensor fields. As a proof of concept, a prototype system called the Integrated Computational System (ICS) was developed to demonstrate CFD design cycle. The current research effort focuses on finding a quantitative comparison of general vector fields based on topological features. Since the method relies on topological information, grid matching and vector alignment is not needed in the comparison. This is often a problem with many data comparison techniques. In addition, since only topology based information is stored and compared for each field, there is a significant compression of information that enables large databases to be quickly searched. This report will (1) briefly review the technologies developed during 1995-1997 (2) describe current technologies in the area of comparison techniques, (4) describe the theory of our new method researched during the grant year (5) summarize a few of the results and finally (6) discuss work within the last 6 months that are direct extensions from the grant.

Topological defects in epithelia govern cell death and extrusion

NASA Astrophysics Data System (ADS)

Saw, Thuan Beng; Doostmohammadi, Amin; Nier, Vincent; Kocgozlu, Leyla; Thampi, Sumesh; Toyama, Yusuke; Marcq, Philippe; Lim, Chwee Teck; Yeomans, Julia M.; Ladoux, Benoit

2017-04-01

Epithelial tissues (epithelia) remove excess cells through extrusion, preventing the accumulation of unnecessary or pathological cells. The extrusion process can be triggered by apoptotic signalling, oncogenic transformation and overcrowding of cells. Despite the important linkage of cell extrusion to developmental, homeostatic and pathological processes such as cancer metastasis, its underlying mechanism and connections to the intrinsic mechanics of the epithelium are largely unexplored. We approach this problem by modelling the epithelium as an active nematic liquid crystal (that has a long range directional order), and comparing numerical simulations to strain rate and stress measurements within monolayers of MDCK (Madin Darby canine kidney) cells. Here we show that apoptotic cell extrusion is provoked by singularities in cell alignments in the form of comet-shaped topological defects. We find a universal correlation between extrusion sites and positions of nematic defects in the cell orientation field in different epithelium types. The results confirm the active nematic nature of epithelia, and demonstrate that defect-induced isotropic stresses are the primary precursors of mechanotransductive responses in cells, including YAP (Yes-associated protein) transcription factor activity, caspase-3-mediated cell death, and extrusions. Importantly, the defect-driven extrusion mechanism depends on intercellular junctions, because the weakening of cell-cell interactions in an α-catenin knockdown monolayer reduces the defect size and increases both the number of defects and extrusion rates, as is also predicted by our model. We further demonstrate the ability to control extrusion hotspots by geometrically inducing defects through microcontact printing of patterned monolayers. On the basis of these results, we propose a mechanism for apoptotic cell extrusion: spontaneously formed topological defects in epithelia govern cell fate. This will be important in predicting extrusion hotspots and dynamics in vivo, with potential applications to tissue regeneration and the suppression of metastasis. Moreover, we anticipate that the analogy between the epithelium and active nematic liquid crystals will trigger further investigations of the link between cellular processes and the material properties of epithelia.

Flux transfer events - Scale size and interior structure

NASA Technical Reports Server (NTRS)

Saunders, M. A.; Russell, C. T.; Sckopke, N.

1984-01-01

The first direct investigation of the spatial properties of flux transfer events (FTEs) at the earth's dayside magnetopause are reported. Simultaneous magnetometer and plasma data from the ISEE 1 and 2 satellites are combined to show that magnetosheath FTEs can have a scale size of the order of an earth radius in the magnetopause normal direction. It is confirmed that the magnetic field within the events appears to be twisted, this twisting corresponding to a core field-aligned current of a magnitude of a few tens of thousands of A. Also shown is evidence for plasma vorticity in FTEs. The transverse flow and field perturbations accompanying the three events studied obey approximately the Walen relation for a propagating Alfven wave.

Online data monitoring in the LHCb experiment

NASA Astrophysics Data System (ADS)

Callot, O.; Cherukuwada, S.; Frank, M.; Gaspar, C.; Graziani, G.; Herwijnen, E. v.; Jost, B.; Neufeld, N.; P-Altarelli, M.; Somogyi, P.; Stoica, R.

2008-07-01

The High Level Trigger and Data Acquisition system selects about 2 kHz of events out of the 40 MHz of beam crossings. The selected events are sent to permanent storage for subsequent analysis. In order to ensure the quality of the collected data, identify possible malfunctions of the detector and perform calibration and alignment checks, a small fraction of the accepted events is sent to a monitoring farm, which consists of a few tens of general purpose processors. This contribution introduces the architecture of the data stream splitting mechanism from the storage system to the monitoring farm, where the raw data are analyzed by dedicated tasks. It describes the collaborating software components that are all based on the Gaudi event processing framework.

Systematics and biogeography of New World sea catfishes (Siluriformes: Ariidae) as inferred from mitochondrial, nuclear, and morphological evidence.

PubMed

Betancur-R, Ricardo; Acero P, Arturo; Bermingham, Eldredge; Cooke, Richard

2007-10-01

Ariid or sea catfishes include around 150 species that inhabit marine, brackish, and freshwater environments along world's tropical and subtropical continental shelves. Phylogenetic relationships for 46 New World and three Old World species of ariids were hypothesized using maximum parsimony and Bayesian inference reconstruction criteria on 2842 mitochondrial (cytochrome b, ATP synthase 8 and 6, ribosomal 12S and 16S) and 978 nuclear (rag2) nucleotide sites. The molecular topologies were compared to a previously compiled morphological dataset that was expanded herein to a total of 25 ariid species and 55 characters. Mitochondrial data yielded clades highly resolved at subfamilial, generic, and intrageneric levels. Nuclear rag2 reconstructions showed poor resolution at supra- and intrageneric levels, but provided support for the monophyly of most genera (except Ariopsis and Cathorops) as well as for the subfamilial clades. The hypothesized phylogeny derived from the morphological data was congruent with the molecular topologies at infrafamilial and generic levels. As indicated by the statistical tests of topological congruence, Kailola's phylogenetic hypothesis of ariids based on anatomical data is significantly different from our molecular trees. All reconstructions agree in the division of the Ariidae into two subfamilies, the Ariinae and the monogeneric Galeichthyinae. Basal ariine resolution was negligible suggesting that early diversification events occurred rapidly. The three Indo-Pacific taxa were grouped into a clade, but New World ariines were never recovered as monophyletic. We provide a revised classification for New World ariines examined, which is consistent with the molecular and the morphological evidence. Our classification scheme includes the genera Ariopsis, Bagre, Cathorops, Notarius, Potamarius, and Sciades, and the description of two new genus-level taxa (Occidentarius n. gen and Precathorops n. subgen.). We also hypothesize plausible biogeographic scenarios that explain distributional patterns of major ariid lineages. Diversification of the predominantly circumtropical ariines likely occurred throughout the Tethys Sea, whereas speciation events in the subtropical galeichthyines were probably tied to the southern coast of Gondwana.

Variola Type IB DNA Topoisomerase: DNA Binding and Supercoil Unwinding Using Engineered DNA Minicircles

PubMed Central

2015-01-01

Type IB topoisomerases unwind positive and negative DNA supercoils and play a key role in removing supercoils that would otherwise accumulate at replication and transcription forks. An interesting question is whether topoisomerase activity is regulated by the topological state of the DNA, thereby providing a mechanism for targeting the enzyme to highly supercoiled DNA domains in genomes. The type IB enzyme from variola virus (vTopo) has proven to be useful in addressing mechanistic questions about topoisomerase function because it forms a reversible 3′-phosphotyrosyl adduct with the DNA backbone at a specific target sequence (5′-CCCTT-3′) from which DNA unwinding can proceed. We have synthesized supercoiled DNA minicircles (MCs) containing a single vTopo target site that provides highly defined substrates for exploring the effects of supercoil density on DNA binding, strand cleavage and ligation, and unwinding. We observed no topological dependence for binding of vTopo to these supercoiled MC DNAs, indicating that affinity-based targeting to supercoiled DNA regions by vTopo is unlikely. Similarly, the cleavage and religation rates of the MCs were not topologically dependent, but topoisomers with low superhelical densities were found to unwind more slowly than highly supercoiled topoisomers, suggesting that reduced torque at low superhelical densities leads to an increased number of cycles of cleavage and ligation before a successful unwinding event. The K271E charge reversal mutant has an impaired interaction with the rotating DNA segment that leads to an increase in the number of supercoils that were unwound per cleavage event. This result provides evidence that interactions of the enzyme with the rotating DNA segment can restrict the number of supercoils that are unwound. We infer that both superhelical density and transient contacts between vTopo and the rotating DNA determine the efficiency of supercoil unwinding. Such determinants are likely to be important in regulating the steady-state superhelical density of DNA domains in the cell. PMID:24945825

A minimal mathematical model combining several regulatory cycles from the budding yeast cell cycle.

PubMed

Sriram, K; Bernot, G; Képès, F

2007-11-01

A novel topology of regulatory networks abstracted from the budding yeast cell cycle is studied by constructing a simple nonlinear model. A ternary positive feedback loop with only positive regulations is constructed with elements that activates the subsequent element in a clockwise fashion. A ternary negative feedback loop with only negative regulations is constructed with the elements that inhibit the subsequent element in an anticlockwise fashion. Positive feedback loop exhibits bistability, whereas the negative feedback loop exhibits limit cycle oscillations. The novelty of the topology is that the corresponding elements in these two homogeneous feedback loops are linked by the binary positive feedback loops with only positive regulations. This results in the emergence of mixed feedback loops in the network that displays complex behaviour like the coexistence of multiple steady states, relaxation oscillations and chaos. Importantly, the arrangement of the feedback loops brings in the notion of checkpoint in the model. The model also exhibits domino-like behaviour, where the limit cycle oscillations take place in a stepwise fashion. As the aforementioned topology is abstracted from the budding yeast cell cycle, the events that govern the cell cycle are considered for the present study. In budding yeast, the sequential activation of the transcription factors, cyclins and their inhibitors form mixed feedback loops. The transcription factors that involve in the positive regulation in a clockwise orientation generates ternary positive feedback loop, while the cyclins and their inhibitors that involve in the negative regulation in an anticlockwise orientation generates ternary negative feedback loop. The mutual regulation between the corresponding elements in the transcription factors and the cyclins and their inhibitors generates binary positive feedback loops. The bifurcation diagram constructed for the whole system can be related to the different events of the cell cycle in terms of dynamical system theory. The checkpoint mechanism that plays an important role in different phases of the cell cycle are accounted for by silencing appropriate feedback loops in the model.

Fast first arrival picking algorithm for noisy microseismic data

NASA Astrophysics Data System (ADS)

Kim, Dowan; Byun, Joongmoo; Lee, Minho; Choi, Jihoon; Kim, Myungsun

2017-01-01

Most microseismic events occur during hydraulic fracturing. Thus microseismic monitoring, by recording seismic waves from microseismic events, is one of the best methods for locating the positions of hydraulic fractures. However, since microseismic events have very low energy, the data often have a low signal-to-noise ratio (S/N ratio) and it is not easy to pick the first arrival time. In this study, we suggest a new fast picking method optimised for noisy data using cross-correlation and stacking. In this method, a reference trace is selected and the time differences between the first arrivals of the reference trace and those of the other traces are computed by cross-correlation. Then, all traces are aligned with the reference trace by time shifting, and the aligned traces are summed together to produce a stacked reference trace that has a considerably improved S/N ratio. After the first arrival time of the stacked reference trace is picked, the first arrival time of each trace is calculated automatically using the time differences obtained in the cross-correlation process. In experiments with noisy synthetic data and field data, this method produces more reliable results than the traditional method, which picks the first arrival time of each noisy trace separately. In addition, the computation time is dramatically reduced.

Resolving combinatorial ambiguities in dilepton t t¯ event topologies with constrained M2 variables

NASA Astrophysics Data System (ADS)

Debnath, Dipsikha; Kim, Doojin; Kim, Jeong Han; Kong, Kyoungchul; Matchev, Konstantin T.

2017-10-01

We advocate the use of on-shell constrained M2 variables in order to mitigate the combinatorial problem in supersymmetry-like events with two invisible particles at the LHC. We show that in comparison to other approaches in the literature, the constrained M2 variables provide superior ansätze for the unmeasured invisible momenta and therefore can be usefully applied to discriminate combinatorial ambiguities. We illustrate our procedure with the example of dilepton t t ¯ events. We critically review the existing methods based on the Cambridge MT 2 variable and MAOS reconstruction of invisible momenta, and show that their algorithm can be simplified without loss of sensitivity, due to a perfect correlation between events with complex solutions for the invisible momenta and events exhibiting a kinematic endpoint violation. Then we demonstrate that the efficiency for selecting the correct partition is further improved by utilizing the M2 variables instead. Finally, we also consider the general case when the underlying mass spectrum is unknown, and no kinematic endpoint information is available.

Deconstructive Misalignment: Archives, Events, and Humanities Approaches in Academic Development

ERIC Educational Resources Information Center

Holmes, Trevor M.; Sutherland, Kathryn A.

2015-01-01

Using poetry, role play, readers' theatre, and creative manipulations of space through yarn and paper weaving, a workshop in 2008 challenged one of educational development's more pervasive and least questioned notions ("constructive alignment" associated most often with the work of John Biggs). This paper describes the reasoning behind…

Paracelsus Outside the Classroom (Beyond the SOT)

EPA Science Inventory