Topological Location Research Articles

Triva: Interactive 3D visualization for performance analysis of parallel applications

The successful execution of parallel applications in grid infrastructures depends directly on a performance analysis that takes into account the grid characteristics, such as the network topology and resources location. This paper presents Triva, a software analysis tool that implements a novel technique to visualize the behavior of parallel applications. The proposed technique explores 3D graphics to show the application behavior together with a description of the resources, highlighting communication patterns, the network topology and a visual representation of a logical organization of the resources. We have used a real grid infrastructure to execute and trace applications composed of thousands of processes.

Converged Optical Network Infrastructures in Support of Future Internet and Grid Services Using IaaS to Reduce GHG Emissions

With the rapid and growing volume of green house gas (GHG) we may soon cross a tipping point where there may be dramatic climatic catastrophes such that governments will be forced to order the shutdown of coal powered electrical production or mandate carbon neutrality across all sectors of society. On the other hand, in the event of such a development, the future Internet and Grid infrastructure may become absolutely essential for communications and a replacement for travel and for the delivery of critical services such as health, education, research, etc. Information and Communication Technologies (ICT) produce 2%-3% of the world's GHG emissions through the consumption of electricity largely produced by coal plants. This rate of GHG is expected to double in the next few years and is clearly unsustainable. Therefore it is critical that any future Internet and Grid infrastructure be designed not only to survive, but also be sustained, through an age where no additional GHG emissions will be allowed. Converged optical networks, Grid and cloud services hosted at zero carbon renewable energy sites using Infrastructure as a Service (IaaS) where each network and computer element is represented to a user as a configurable virtual service will allow for the deployment of what are often referred to as ldquofollow the sun or follow the windrdquo optical network and Grid architectures where the network and Grid topology and Grid resources availability and location are constantly changing depending on local availability states of the wind or sun.

Statistical geometry based prediction of nonsynonymous SNP functional effects using random forest and neuro‐fuzzy classifiers

There is substantial interest in methods designed to predict the effect of nonsynonymous single nucleotide polymorphisms (nsSNPs) on protein function, given their potential relationship to heritable diseases. Current state-of-the-art supervised machine learning algorithms, such as random forest (RF), train models that classify single amino acid mutations in proteins as either neutral or deleterious to function. However, it is frequently the case that the functional effect of a polymorphism on a protein resides between these two extremes. The utilization of classifiers that incorporate fuzzy logic provides a natural extension in order to account for the spectrum of possible functional consequences. We generated a dataset of single amino acid substitutions in human proteins having known three-dimensional structures. Each variant was uniquely represented as a feature vector that included computational geometry and knowledge-based statistical potential predictors obtained though application of Delaunay tessellation of protein structures. Additional attributes consisted of physicochemical properties of the native and replacement amino acids as well as topological location of the mutated residue position in the solved structure. Classification performance of the RF algorithm was evaluated on a training set consisting of the disease-associated and neutral nsSNPs taken from our dataset, and attributes were ranked according to their relative importance. Similarly, we evaluated the performance of adaptive neuro-fuzzy inference system (ANFIS). The utility of statistical geometry predictors was compared with that of traditional structural and evolutionary attributes employed by other researchers, revealing an equally effective yet complementary methodology. Among all attributes in our feature set, the statistical geometry predictors were found to be the most highly ranked. On the basis of the AUC (area under the ROC curve) measure of performance, the ANFIS and RF models were equally effective when only statistical geometry features were utilized. Tenfold cross-validation studies evaluating AUC, balanced error rate (BER), and Matthew's correlation coefficient (MCC) showed that our RF model was at least comparable with the well-established methods of SIFT and PolyPhen. The trained RF and ANFIS models were each subsequently used to predict the disease potential of human nsSNPs in our dataset that are currently unclassified (http://rna.gmu.edu/FuzzySnps/).

Proximal common pathway in the circuit of atrioventricular nodal reentrant tachycardia.

Whether atrium tissue is involved in the reentrant circuit of atrioventricular nodal reentrant tachycardia (AVNRT) has been debated for decades. Animal models, clinical electrophysiological studies, surgery and catheter ablation have all documented that the perinodal tissue forms part of the tachycardia circuit. However, the occasional clinical finding of AVNRT with ventriculoatrial block suggests the presence of a proximal common pathway. We describe a 43-year-old woman who developed recurrent AVNRT with new onset of complete ventriculoatrial block after an attempted radiofrequency ablation at the posterior septal area. This case demonstrates the anatomical existence of a proximal common pathway and the topological location of such a pathway for typical AVNRT. This case also demonstrates the isolated nature of the AVNRT circuit and the delicate nature of the responsible reentrant substrate.

A scalable explicit multicast protocol for MANETs

Group oriented multicast applications are becoming increasingly popular in mobile ad hoc networks (MANETs). Due to dynamic topology of MANETs, stateless multicast protocols are finding increased acceptance since they do not require maintenance of state information at intermediate nodes. Recently, several multicast schemes have been proposed which scale better with the number of multicast sessions than traditional multicast strategies. These schemes are also known as explicit multicast (Xcast; explicit list of destinations in the packet header) or small group multicast (SGM). In this paper, we propose a new scheme for small group multicast in MANETs named extended explicit multicast (E2M), which is implemented on top of Xcast and introduces mechanisms to make it scalable with number of group members for a given multicast session. Unlike other schemes, E2M does not make any assumptions related to network topology or node location. It is based on the novel concept of dynamic selection of Xcast forwarders (XFs) between a source and its potential destinations. The XF selection is based on group membership and the processing overhead involved in supporting the Xcast protocol at a given node. If the number of members in a given session is small, E2M behaves just like the basic Xcast scheme with no intermediate XFs. As group membership increases, nodes may dynamically decide to become an XF. This scheme, which can work with few E2M aware nodes in the network, provides transparency of stateless multicast, reduces header processing overhead, minimizes Xcast control traffic, and makes Xcast scalable with the number of group members.

The Topology of Bulges in the Long Stem of the Flavivirus 3′ Stem-Loop Is a Major Determinant of RNA Replication Competence

All flavivirus genomes contain a 3'terminal stem-loop secondary structure (3'SL) formed by the most downstream approximately 100 nucleotides (nt) of the viral RNA. The 3'SL is required for virus replication and has been shown to bind both virus-coded and cellular proteins. Results of the present study using an infectious DNA for WN virus strain 956 initially demonstrated that the dengue virus serotype 2 (DEN2) 3'SL nucleotide sequence could not substitute for that of the WN 3'SL to support WN genome replication. To determine what WN virus-specific 3'SL nucleotide sequences were required for WN virus replication, WN virus 3'SL nucleotide sequences were selectively deleted and replaced by analogous segments of the DEN2 3'SL nucleotide sequence such that the overall 3'SL secondary structure was not disrupted. Top and bottom portions of the WN virus 3'SL were defined according to previous studies (J. L. Blackwell and M. A. Brinton, J. Virol. 71:6433-6444, 1997; L. Zeng, L., B. Falgout, and L. Markoff, J. Virol. 72:7510-7522, 1998). A bulge in the top portion of the long stem of the WN 3'SL was essential for replication of mutant WN RNAs, and replication-defective RNAs failed to produce negative strands in transfected cells. Introduction of a second bulge into the bottom portion of the long stem of the wild-type WN 3'SL markedly enhanced the replication competence of WN virus in mosquito cells but had no effect on replication in mammalian cells. This second bulge was identified as a host cell-specific enhancer of flavivirus replication. Results suggested that bulges and their topological location within the long stem of the 3'SL are primary determinants of replication competence for flavivirus genomes.

Synchronism of Leaf and Tiller Emergence Relative to Position and to Main Stem Development Stage in a Rice Cultivar

Tillering is an essential factor when estimating yield, but investigations rarely include both the temporal and spatial changes that occur in tillers. This study analyses the morphology and development dynamics of each tiller, based on its topological location, the timing of appearance and main stem development stage. An indica cultivar of rice, 'Ir64', glasshouse-grown (25/20 degrees C, 12 h photoperiod), was used to examine the emergence, phenology and morphology of each axis starting at the third leaf stage up to heading. Little variability was observed in the structural and morphological characteristics of the tillers, and the rice population appeared to be hierarchical. Blade length initially increased with leaf rank and then decreased sharply for the last three leaves. The number of phytomers per axis decreased with branching order and rank. An analysis of plant dynamics showed synchronous emergence of the leaves on the main stem and on the tillers up to flowering. Axillary bud development into tillers depended on their topological location and plant developmental stage. The timing and frequency of flowering tillers complied with rules of priority depending on their order, rank and emergence time. Precise description of plant topology in grasses is a useful tool that can be used to quantify growth events and predict tillering in terms of location, structure and fate according to growing conditions.

Human acyl-coenzyme A:cholesterol acyltransferase expressed in chinese hamster ovary cells: membrane topology and active site location.

Acyl-CoA:cholesterol acyltransferase (ACAT) is a membrane-bound enzyme that produces cholesteryl esters intracellularly. Two ACAT genes (ACAT1 and ACAT2) have been identified. The expression of ACAT1 is ubiquitous, whereas that of ACAT2 is tissue restricted. Previous research indicates that ACAT1 may contain seven transmembrane domains (TMDs). To study ACAT2 topology, we inserted two different antigenic tags (hemagglutinin, monoclonal antibody Mab1) at various hydrophilic regions flanking each of its predicted TMDs, and expressed the recombinant proteins in mutant Chinese hamster ovary cells lacking endogenous ACAT. Each tagged ACAT2 was expressed in the endoplasmic reticulum as a single undegraded protein band and was at least partially active enzymatically. We then used cytoimmunofluorescence and protease protection assays to monitor the sidedness of the hemagglutinin and Mab1 tags along the ER membranes. The results indicated that ACAT2 contains only two detectable TMDs, located near the N terminal region. We also show that a conserved serine (S245), a candidate active site residue, is not essential for ACAT catalysis. Instead, a conserved histidine (H434) present within a hydrophobic peptide segment, may be essential for ACAT catalysis. H434 may be located at the cytoplasmic side of the membrane.

The terminal nerve in turbot, Psetta maxima: : A developmental immunocytochemical study

The ontogeny and organization of the terminal nerve (TN) during turbot development was studied using an antiserum to neuropeptide Y. First immunoreactive cells were detected in the olfactory placode at hatching time. At 1 day after hatching, a loose group of labeled neurons form an extracranial primordial ganglion of the TN. During the subsequent larval development, more perikarya displaying increased immunoreactivity were found along the course of the olfactory nerve. Moreover, labeled cells cross the meninx of the forebrain gathering in the olfactory bulb of larval turbot. Projections from these cells, directed both to the caudal brain and to the retina, develop when the cells become established in the olfactory bulb. The generation of immunoreactive cells in the olfactory organ extends into the metamorphic period, when a pronounced asymmetry affects the turbot morphology. At this time, the topological location of the immunoreactive cells in the TN becomes distorted. This developmental pattern was compared with those found in other teleosts and in other vertebrates. Preabsorption experiments of anti-neuropeptide Y serum with neuropeptide Y and FMRF-amide suggests that immunoreactive material observed in TN cells was not neuropeptide Y, and raises the possibility that other peptides, e.g. FMRF-amide-like peptides, exist in this neural system.

Application of multivariate analysis for recognition of organic patinas on stone monuments

Black organic films, which had accumulated over ages on stone monuments in ancient villages located in the Apennines in central Italy, were solvent-extracted and the extracts analyzed by capillary gas chromatography. The overall procedure, selection of the monuments and patina extraction followed by chromatographic analysis and processing of the data, was developed with the purpose of establishing a new methodology for clusterization of ancient monuments located in the same geographic area, or even of different parts of the same monument, according to the chemical substances deposited on their surfaces. This concept relies on the assumption that the black crusts present on the monument surface represent a chemical memory of the work of art itself, related to its history, topological location, and exposure to environmental conditions. Selection of the most appropriate extraction solvent, as well as treatment of the chromatographic data, was carried out with the aid of multivariate chemometric methods to obtain classification models.

Application of multivariate analysis for recognition of organic patinas on stone monuments

Black organic films, which had accumulated over ages on stone monuments in ancient villages located in the Apennines in central Italy, were solvent-extracted and the extracts analyzed by capillary gas chromatography. The overall procedure, selection of the monuments and patina extraction followed by chromatographic analysis and processing of the data, was developed with the purpose of establishing a new methodology for clusterization of ancient monuments located in the same geographic area, or even of different parts of the same monument, according to the chemical substances deposited on their surfaces. This concept relies on the assumption that the black crusts present on the monument surface represent a chemical memory of the work of art itself, related to its history, topological location, and exposure to environmental conditions. Selection of the most appropriate extraction solvent, as well as treatment of the chromatographic data, was carried out with the aid of multivariate chemometric methods to obtain classification models.

Developmental Genetics and Evolution of Symbiotic Structures in Nitrogen-fixing Nodules and Arbuscular Mycorrhiza

Genetic and molecular mechanisms of development are compared for two major plant–microbe endosymbioses: N2-fixing nodules (with rhizobia or actinomycetes Frankia) and arbuscular mycorrhiza (with Glomales fungi). Development from the primordia formed de novo in root tissues is common for all known types of N2-fixing nodules. However, their structure varies greatly with respect to: (i) tissue topology (location of vascular bundles is peripherical in legumes or central in non-legumes); (ii) position of nodule primordium (inner or outer cortex in legumes, pericycle in non-legumes); (iii) stability of apical meristem (persistent in the indeterminate nodules, transient in the determinate ones). In addition, legumes vary in ability to form compartments harboring endosymbiotic rhizobia and located intercellularly (infection threads) and intracellularly (symbiosomes). Using pea (Pisum sativum) symbiotic mutants, the nodule developmental program is dissected into a range of spatially and temporarily differentiated steps comprising four sub-programs (development of endosymbiotic compartments; nodule histogenesis; autoregulation of nodulation; bacteroid differentiation). The developmental mutations are suggested in some cases to reverse the endosymbiotic system into the morphologically simpler forms some of which may correspond to the ancestral stages of nodule evolution. The origin of legume–rhizobial and actinorhizal symbioses is suggested to be based on a set of preadaptations many of which had been evolved in angiosperms during coevolution with arbuscular mycorrhizal fungi (e.g., inter- and intracellular maintenance of symbionts, their control via defence-like reactions and recognition of chitin-like molecules). An analysis of parallel morphological variation in symbiotic mutants and wild-growing legume species enables us to reconstruct the major stages of evolution for N2-fixing symbioses.

Provision of guaranteed services in broadband LEO satellite networks

The provision of guaranteed services in low earth orbit (LEO) satellite networks is rather complicated due to the mobility of satellites. Users may be handed-off from one spot beam to another and/or from one satellite to another frequently during the lifetime of their calls. Traffic on inter-satellite links (ISLs) incident on a particular satellite change as the user traffic served by the satellite changes due to satellite mobility. The variation of user traffic over the ISLs may cause violation of quality of service (QoS) requirements of ongoing connections. We propose a novel protocol which we call the predictive routing protocol (PRP), which exploits the deterministic nature of the LEO satellite topology to maximize the total number of users served by the system, while maintaining each user's QoS requirements. PRP predicts the traffic load on the ISLs up to a short time in the future by using the deterministic knowledge of the LEO satellite topology and user location information. PRP determines multiple paths for a particular connection that effectively help avoid possible future bottlenecks as predicted by estimated future traffic on the ISLs. The protocol is compared with other non-predictive routing protocols such as IP routing by simulations and it is shown that PRP can deliver deterministic QoS guarantees (such as delay or delay jitter), without over-reserving channel bandwidth. An admission control curve has also been obtained which may be used to limit the number of users in order to ensure that the desired QoS metrics may be guaranteed.

Building efficient wireless sensor networks with low-level naming

In most distributed systems, naming of nodes for low-level communication leverages topological location (such as node addresses) and is independent of any application. In this paper, we investigate an emerging class of distributed systems where low-level communication does not rely on network topological location. Rather, low-level communication is based on attributes that are external to the network topology and relevant to the application. When combined with dense deployment of nodes, this kind of named data enables in-network processing for data aggregation, collaborative signal processing, and similar problems. These approaches are essential for emerging applications such as sensor networks where resources such as bandwidth and energy are limited. This paper is the first description of the software architecture that supports named data and in-network processing in an operational, multi-application sensor-network. We show that approaches such as in-network aggregation and nested queries can significantly affect network traffic. In one experiment aggregation reduces traffic by up to 42% and nested queries reduce loss rates by 30%. Although aggregation has been previously studied in simulation, this paper demonstrates nested queries as another form of in-network processing, and it presents the first evaluation of these approaches over an operational testbed.

Structure of Tuberoinfundibular Peptide of 39 Residues

Structure of Tuberoinfundibular Peptide of 39 Residues

3D DIGITIZING BASED ON TREE TOPOLOGY : APPLICATION TO STUDY THE VARIABILITY OF APPLE QUALITY WITHIN THE CANOPY

Two training systems, i.e. bent and not bent, were compared for 'Fuji' variety. The topology was organized into four scales of details, including both fruits and different kinds of vegetative shoots. The geometry of each constituent was described with a few parameters that were measured in the field, and its spatial location was recorded using a 3D digitizer. Geometric parameters and spatial coordinates were considered as constituent properties and were attached to the corresponding constituents in the database. At harvest, the main usual quality parameters were analyzed for each individual fruit, and integrated into the database as variables attached to fruit entities. Three-dimensional representations of the digitized apple trees were reconstructed using AMAPmod software. The fruit quality variability within the canopy was explored a posteriori building fruit samples, according to different criteria (spatial location, topological location, number of leaves of the associated bourse-shoot) and taking advantage of the multiscale description of the tree. This approach highlighted that fruit characteristics at harvest are influenced by the vegetative growth considered at different scales within the canopy

Identification of the catalytic triad in the haloalkane dehalogenase from Sphingomonas paucimobilis UT26

The haloalkane dehalogenase from Sphingomonas paucimobilis UT26 (LinB) is the enzyme involved in the γ-hexachlorocyclohexane degradation. This enzyme hydrolyses a broad range of halogenated aliphatic compounds via an alkyl-enzyme intermediate. LinB is believed to belong to the family of α/β-hydrolases which employ a catalytic triad, i.e. nucleophile-histidine-acid, during the catalytic reaction. The position of the catalytic triad within the sequence of LinB was probed by a site-directed mutagenesis. The catalytic triad residues of the haloalkane dehalogenase LinB are proposed to be D108, H272 and E132. The topological location of the catalytic acid (E132) is after the β-strand six which corresponds to the location of catalytic acid in the pancreatic lipase, but not in the haloalkane dehalogenase of Xanthobacter autotrophicus GJ10 which contains the catalytic acid after the β-strand seven.

Cell wall and secreted proteins of Candida albicans: identification, function, and expression.

The cell wall is essential to nearly every aspect of the biology and pathogenicity of Candida albicans. Although it was initially considered an almost inert cellular structure that protected the protoplast against osmotic offense, more recent studies have demonstrated that it is a dynamic organelle. The major components of the cell wall are glucan and chitin, which are associated with structural rigidity, and mannoproteins. The protein component, including both mannoprotein and nonmannoproteins, comprises some 40 or more moieties. Wall proteins may differ in their expression, secretion, or topological location within the wall structure. Proteins may be modified by glycosylation (primarily addition of mannose residues), phosphorylation, and ubiquitination. Among the secreted enzymes are those that are postulated to have substrates within the cell wall and those that find substrates in the extracellular environment. Cell wall proteins have been implicated in adhesion to host tissues and ligands. Fibrinogen, complement fragments, and several extracellular matrix components are among the host proteins bound by cell wall proteins. Proteins related to the hsp70 and hsp90 families of conserved stress proteins and some glycolytic enzyme proteins are also found in the cell wall, apparently as bona fide components. In addition, the expression of some proteins is associated with the morphological growth form of the fungus and may play a role in morphogenesis. Finally, surface mannoproteins are strong immunogens that trigger and modulate the host immune response during candidiasis.

Regiospecificity and Catalytic Triad of Lysophospholipase I

A 25-kDa murine lysophospholipase (LysoPLA I) has been cloned and expressed, and Ser-119 has been shown to be essential for the enzyme activity (Wang, A., Deems, R. A., and Dennis, E. A. (1997) J. Biol. Chem. 272, 12723-12729). In the present study, we show that LysoPLA I represents a new member of the serine hydrolase family with Ser-119, Asp-174, and His-208 composing the catalytic triad. The Asp-174 and His-208 are conserved among several esterases and are demonstrated herein to be essential for LysoPLA I activity as the mutation of either residue to Ala abolished LysoPLA I activity, whereas the global conformation of the mutants remained unchanged. Furthermore, the predicted secondary structure of LysoPLA I resembles that of the alpha/beta-hydrolase fold, with Ser-119, Asp-174, and His-208 occupying the conserved topological location of the catalytic triad in the alpha/beta-hydrolases. Structural modeling of LysoPLA I also indicates that the above three residues orient in such a manner that they would comprise a charge-relay network necessary for catalysis. In addition, the regiospecificity of LysoPLA I was studied using 31P NMR, and the result shows that LysoPLA I has similar LysoPLA1 and LysoPLA2 activity. This finding suggests that LysoPLA I may play an important role in removing lysophospholipids produced by both phospholipase A1 and A2 in vivo.

The nucleotide regulatory sites on the mitochondrial K ATP channel face the cytosol

The mitochondrial K ATP channel (mitoK ATP) is richly endowed with regulatory sites for metabolites and drugs, but the topological location of these sites is unknown. Thus, it is not known whether ATP, GTP and acyl CoA esters regulate mitoK ATP from the matrix or cytosolic side of the inner membrane, nor whether they all act from the same side. The experiments reported in this paper provide an unambiguous answer to these questions. Electrophysiological experiments in bilayer membranes containing purified mitoK ATP showed that current is blocked asymmetrically by ATP. K + flux experiments using proteoliposomes containing purified mitoK ATP showed that mitoK ATP is unipolar with respect to regulation by Mg 2+, ATP, GTP, and palmitoyl CoA and that all of these ligands react on the same pole of the protein. This demonstration was made possible by the new finding that mitoK ATP is 85–90% oriented inward or outward in liposomes, depending on the presence or absence of Mg 2+ in the reconstitution buffer. K + flux experiments in respiring rat liver mitochondria showed that mitoK ATP was inhibited by palmitoyl CoA and activated by GTP when these agents were added to the external medium. Given that the inner membrane is impermeant to these ligands and that mitoK ATP is unipolar with respect to nucleotide regulation, it follows that the regulatory sites on mitoK ATP face the cytosol.