Stereoselective synthesis and structure determination of a bicyclo[3.3.2]decapeptide

By analogy to the structural diversity of covalent bond networks between atoms within organic molecules, one can design topologically diverse peptides from mathematical graphs by assigning amino acids to graph nodes and peptide bonds to graph edges. The key is to use diamino acids or amino diacids as equivalents of trivalent graph nodes, which enables a variety of graph topologies beyond the standard linear and monocyclic graphs in natural peptides. Here the bicyclic decapeptide A1FGk2VFPE1AG2 (1b) was prepared and crystallized to assign its bridge stereochemistry. The bridge configuration appears as planned by the chirality of the branching amino acids. Bicyclization furthermore depends on the presence of matched chiralities in the branching amino acids. The stereoselective formation of the second bridge opens the way for the synthesis of a large family of bicyclic peptides as promising new scaffolds for drug design.

VirtualMesh: An Emulation Framework for Wireless Mesh Networks in OMNeT++

Wireless Mesh Networks (WMN) have proven to be a key technology for increased network coverage of Internet infrastructures. The development process for new protocols and architectures in the area of WMN is typically split into evaluation by network simulation and testing of a prototype in a test-bed. Testing a prototype in a real test-bed is time-consuming and expensive. Irrepressible external interferences can occur which makes debugging difficult. Moreover, the test-bed usually supports only a limited number of test topologies. Finally, mobility tests are impractical. Therefore, we propose VirtualMesh as a new testing architecture which can be used before going to a real test-bed. It provides instruments to test the real communication software including the network stack inside a controlled environment. VirtualMesh is implemented by capturing real traffic through a virtual interface at the mesh nodes. The traffic is then redirected to the network simulator OMNeT++. In our experiments, VirtualMesh has proven to be scalable and introduces moderate delays. Therefore, it is suitable for predeployment testing of communication software for WMNs.

Dimension Distortion by Sobolev Mappings in Foliated Metric Spaces

We quantify the extent to which a supercritical Sobolev mapping can increase the dimension of subsets of its domain, in the setting of metric measure spaces supporting a Poincaré inequality. We show that the set of mappings that distort the dimensions of sets by the maximum possible amount is a prevalent subset of the relevant function space. For foliations of a metric space X defined by a David–Semmes regular mapping Π : X → W, we quantitatively estimate, in terms of Hausdorff dimension in W, the size of the set of leaves of the foliation that are mapped onto sets of higher dimension. We discuss key examples of such foliations, including foliations of the Heisenberg group by left and right cosets of horizontal subgroups.

Assessment of a robust opportunistic routing for video transmission in dynamic topologies

Mobile multimedia ad hoc services run on dynamic topologies due to node mobility or failures and wireless channel impairments. A robust routing service must adapt to topology changes with the aim of recovering or maintaining the video quality level and reducing the impact of the user's experience. In those scenarios, beacon-less Opportunistic Routing (OR) increases the robustness by supporting routing decisions in a completely distributed manner based on protocol-specific characteristics. However, the existing beacon-less OR approaches do not efficiently combine multiple metrics for forwarding selection, which cause higher packet loss rate, and consequently reduce the video quality level. In this paper, we assess the robustness and reliability of our recently developed OR protocol under node failures, called cross-layer Link quality and Geographical-aware OR protocol (LinGO). Simulation results show that LinGO achieves multimedia dissemination with QoE support and robustness in scenarios with dynamic topologies.

Optical properties of a nanomatch-like plasmonic structure

The optical properties of a match-like plasmonic nanostructure are numerically investigated using full-wave finite-difference time-domain analysis in conjunction with dispersive material models. This work is mainly motivated by the developed technique enabling reproducible fabrication of nanomatch structures as well as the growing applications that utilize the localized field enhancement in plasmonic nanostructures. Our research revealed that due to the pronounced field enhancement and larger resonance tunabilities, some nanomatch topologies show potentials for various applications in the field of, e.g., sensing as well as a novel scheme for highly reproducible tips in scanning near field optical microscopy, among others. Despite the additional degrees of freedom that are offered by the composite nature of the proposed nanomatch topology, the paper also reflects on a fundamental complication intrinsic to the material interfaces especially in the nanoscale: stoichiometric mixing. We conclude that the specificity in material modeling will become a significant issue in future research on functionalized composite nanostructures.

Evaluating the Impact of the Number of Access Points in Mobile Robots Localization Using Artificial Neural Networks

Localization is information of fundamental importance to carry out various tasks in the mobile robotic area. The exact degree of precision required in the localization depends on the nature of the task. The GPS provides global position estimation but is restricted to outdoor environments and has an inherent imprecision of a few meters. In indoor spaces, other sensors like lasers and cameras are commonly used for position estimation, but these require landmarks (or maps) in the environment and a fair amount of computation to process complex algorithms. These sensors also have a limited field of vision. Currently, Wireless Networks (WN) are widely available in indoor environments and can allow efficient global localization that requires relatively low computing resources. However, the inherent instability in the wireless signal prevents it from being used for very accurate position estimation. The growth in the number of Access Points (AP) increases the overlap signals areas and this could be a useful means of improving the precision of the localization. In this paper we evaluate the impact of the number of Access Points in mobile nodes localization using Artificial Neural Networks (ANN). We use three to eight APs as a source signal and show how the ANNs learn and generalize the data. Added to this, we evaluate the robustness of the ANNs and evaluate a heuristic to try to decrease the error in the localization. In order to validate our approach several ANNs topologies have been evaluated in experimental tests that were conducted with a mobile node in an indoor space.

Correspondence establishment in statistical modeling of shapes with arbitrary topology

Correspondence establishment is a key step in statistical shape model building. There are several automated methods for solving this problem in 3D, but they usually can only handle objects with simple topology, like that of a sphere or a disc. We propose an extension to correspondence establishment over a population based on the optimization of the minimal description length function, allowing considering objects with arbitrary topology. Instead of using a fixed structure of kernel placement on a sphere for the systematic manipulation of point landmark positions, we rely on an adaptive, hierarchical organization of surface patches. This hierarchy can be built on surfaces of arbitrary topology and the resulting patches are used as a basis for a consistent, multi-scale modification of the surfaces' parameterization, based on point distribution models. The feasibility of the approach is demonstrated on synthetic models with different topologies.

Parameter-free extraction of the functional network topology from intracranial EEG recordings: a time-resolved study of graph properties in focal onset seizures

Rationale: Focal onset epileptic seizures are due to abnormal interactions between distributed brain areas. By estimating the cross-correlation matrix of multi-site intra-cerebral EEG recordings (iEEG), one can quantify these interactions. To assess the topology of the underlying functional network, the binary connectivity matrix has to be derived from the cross-correlation matrix by use of a threshold. Classically, a unique threshold is used that constrains the topology [1]. Our method aims to set the threshold in a data-driven way by separating genuine from random cross-correlation. We compare our approach to the fixed threshold method and study the dynamics of the functional topology. Methods: We investigate the iEEG of patients suffering from focal onset seizures who underwent evaluation for the possibility of surgery. The equal-time cross-correlation matrices are evaluated using a sliding time window. We then compare 3 approaches assessing the corresponding binary networks. For each time window: * Our parameter-free method derives from the cross-correlation strength matrix (CCS)[2]. It aims at disentangling genuine from random correlations (due to finite length and varying frequency content of the signals). In practice, a threshold is evaluated for each pair of channels independently, in a data-driven way. * The fixed mean degree (FMD) uses a unique threshold on the whole connectivity matrix so as to ensure a user defined mean degree. * The varying mean degree (VMD) uses the mean degree of the CCS network to set a unique threshold for the entire connectivity matrix. * Finally, the connectivity (c), connectedness (given by k, the number of disconnected sub-networks), mean global and local efficiencies (Eg, El, resp.) are computed from FMD, CCS, VMD, and their corresponding random and lattice networks. Results: Compared to FMD and VMD, CCS networks present: *topologies that are different in terms of c, k, Eg and El. *from the pre-ictal to the ictal and then post-ictal period, topological features time courses that are more stable within a period, and more contrasted from one period to the next. For CCS, pre-ictal connectivity is low, increases to a high level during the seizure, then decreases at offset. k shows a ‘‘U-curve’’ underlining the synchronization of all electrodes during the seizure. Eg and El time courses fluctuate between the corresponding random and lattice networks values in a reproducible manner. Conclusions: The definition of a data-driven threshold provides new insights into the topology of the epileptic functional networks.

Genetic relationships of Aeromonas strains inferred from 16S rRNA, gyrB and rpoB gene sequences

Genetic relationships among bacterial strains belonging to the genus Aeromonas were inferred from 16S rRNA, gyrB and rpoB gene sequences. Twenty-eight type or collection strains of the recognized species or subspecies and 33 Aeromonas strains isolated from human and animal specimens as well as from environmental samples were included in the study. As reported previously, the 16S rRNA gene sequence is highly conserved within the genus Aeromonas, having only limited resolution for this very tight group of species. Analysis of a 1.1 kb gyrB sequence confirmed that this gene has high resolving power, with maximal interspecies divergence of 15.2 %. Similar results were obtained by sequencing only 517 bp of the rpoB gene, which showed maximal interspecies divergence of 13 %. The topologies of the gyrB- and rpoB-derived trees were similar. The results confirm the close relationship of species within the genus Aeromonas and show that a phylogenetic approach including several genes is suitable for improving the complicated taxonomy of the genus.

Frequency of Sobolev and quasiconformal dimension distortion

We study Hausdorff and Minkowski dimension distortion for images of generic affine subspaces of Euclidean space under Sobolev and quasiconformal maps. For a supercritical Sobolev map f defined on a domain in RnRn, we estimate from above the Hausdorff dimension of the set of affine subspaces parallel to a fixed m-dimensional linear subspace, whose image under f has positive HαHα measure for some fixed α>mα>m. As a consequence, we obtain new dimension distortion and absolute continuity statements valid for almost every affine subspace. Our results hold for mappings taking values in arbitrary metric spaces, yet are new even for quasiconformal maps of the plane. We illustrate our results with numerous examples.

Neutral biodiversity theory can explain the imbalance of phylogenetic trees but not the tempo of their diversification

Numerous evolutionary studies have sought to explain the distribution of diversity across the limbs of the tree of life. At the same time, ecological studies have sought to explain differences in diversity and relative abundance within and among ecological communities. Traditionally, these patterns have been considered separately, but models that consider processes operating at the level of individuals, such as neutral biodiversity theory (NBT), can provide a link between them. Here, we compare evolutionary dynamics across a suite of NBT models. We show that NBT can yield phylogenetic tree topologies with imbalance closely resembling empirical observations. In general, metacommunities that exhibit greater disparity in abundance are characterized by more imbalanced phylogenetic trees. However, NBT fails to capture the tempo of diversification as represented by the distribution of branching events through time. We suggest that population-level processes might therefore help explain the asymmetry of phylogenetic trees, but that tree shape might mislead estimates of evolutionary rates unless the diversification process is modeled explicitly.

A Comparative Analysis of Beaconless Opportunistic Routing Protocols for Video Dissemination over Flying Ad-Hoc Networks

A reliable and robust routing service for Flying Ad-Hoc Networks (FANETs) must be able to adapt to topology changes, and also to recover the quality level of the delivered multiple video flows under dynamic network topologies. The user experience on watching live videos must also be satisfactory even in scenarios with network congestion, buffer overflow, and packet loss ratio, as experienced in many FANET multimedia applications. In this paper, we perform a comparative simulation study to assess the robustness, reliability, and quality level of videos transmitted via well-known beaconless opportunistic routing protocols. Simulation results shows that our developed protocol XLinGO achieves multimedia dissemination with Quality of Experience (QoE) support and robustness in a multi-hop, multi-flow, and mobile networks, as required in many multimedia FANET scenarios.

Cross-Layer Optimizations for Multimedia Distribution over Wireless Multimedia Sensor Networks and Flying Ad-Hoc Networks with Quality of Experience Support

The proliferation of multimedia content and the demand for new audio or video services have fostered the development of a new era based on multimedia information, which allowed the evolution of Wireless Multimedia Sensor Networks (WMSNs) and also Flying Ad-Hoc Networks (FANETs). In this way, live multimedia services require real-time video transmissions with a low frame loss rate, tolerable end-to-end delay, and jitter to support video dissemination with Quality of Experience (QoE) support. Hence, a key principle in a QoE-aware approach is the transmission of high priority frames (protect them) with a minimum packet loss ratio, as well as network overhead. Moreover, multimedia content must be transmitted from a given source to the destination via intermediate nodes with high reliability in a large scale scenario. The routing service must cope with dynamic topologies caused by node failure or mobility, as well as wireless channel changes, in order to continue to operate despite dynamic topologies during multimedia transmission. Finally, understanding user satisfaction on watching a video sequence is becoming a key requirement for delivery of multimedia content with QoE support. With this goal in mind, solutions involving multimedia transmissions must take into account the video characteristics to improve video quality delivery. The main research contributions of this thesis are driven by the research question how to provide multimedia distribution with high energy-efficiency, reliability, robustness, scalability, and QoE support over wireless ad hoc networks. The thesis addresses several problem domains with contributions on different layers of the communication stack. At the application layer, we introduce a QoE-aware packet redundancy mechanism to reduce the impact of the unreliable and lossy nature of wireless environment to disseminate live multimedia content. At the network layer, we introduce two routing protocols, namely video-aware Multi-hop and multi-path hierarchical routing protocol for Efficient VIdeo transmission for static WMSN scenarios (MEVI), and cross-layer link quality and geographical-aware beaconless OR protocol for multimedia FANET scenarios (XLinGO). Both protocols enable multimedia dissemination with energy-efficiency, reliability and QoE support. This is achieved by combining multiple cross-layer metrics for routing decision in order to establish reliable routes.

Performance of jet substructure techniques for large-ℝ jets in proton-proton collisions at sqrts = 7 TeV using the ATLAS detector

This paper presents the application of a variety of techniques to study jet substructure. The performance of various modified jet algorithms, or jet grooming techniques, for several jet types and event topologies is investigated for jets with transverse momentum larger than 300 GeV. Properties of jets subjected to the mass-drop filtering, trimming, and pruning algorithms are found to have reduced sensitivity to multiple proton-proton interactions, are more stable at high luminosity and improve the physics potential of searches for heavy boosted objects. Studies of the expected discrimination power of jet mass and jet substructure observables in searches for new physics are also presented. Event samples enriched in boosted W and Z bosons and top-quark pairs are used to study both the individual jet invariant mass scales and the efficacy of algorithms to tag boosted hadronic objects. The analyses presented use the full 2011 ATLAS dataset, corresponding to an integrated luminosity of 4.7 +/- 0.1 /fb from proton-proton collisions produced by the Large Hadron Collider at a center-of-mass energy of sqrt(s) = 7 TeV.