On The Topology Of Manifolds With Positive Isotropic Curvature

We show that a closed orientable Riemannian n-manifold, n >= 5, with positive isotropic curvature and free fundamental group is homeomorphic to the connected sum of copies of Sn-1 x S-1.

Combining ganglion cell topology and data of patients with glaucoma to determine a structure-function map

PURPOSE: To introduce techniques for deriving a map that relates visual field locations to optic nerve head (ONH) sectors and to use the techniques to derive a map relating Medmont perimetric data to data from the Heidelberg Retinal Tomograph. METHODS: Spearman correlation coefficients were calculated relating each visual field location (Medmont M700) to rim area and volume measures for 10 degrees ONH sectors (HRT III software) for 57 participants: 34 with glaucoma, 18 with suspected glaucoma, and 5 with ocular hypertension. Correlations were constrained to be anatomically plausible with a computational model of the axon growth of retinal ganglion cells (Algorithm GROW). GROW generated a map relating field locations to sectors of the ONH. The sector with the maximum statistically significant (P < 0.05) correlation coefficient within 40 degrees of the angle predicted by GROW for each location was computed. Before correlation, both functional and structural data were normalized by either normative data or the fellow eye in each participant. RESULTS: The model of axon growth produced a 24-2 map that is qualitatively similar to existing maps derived from empiric data. When GROW was used in conjunction with normative data, 31% of field locations exhibited a statistically significant relationship. This significance increased to 67% (z-test, z = 4.84; P < 0.001) when both field and rim area data were normalized with the fellow eye. CONCLUSIONS: A computational model of axon growth and normalizing data by the fellow eye can assist in constructing an anatomically plausible map connecting visual field data and sectoral ONH data.

Multi-output DC-DC converters based on diode-clamped converters configuration : topology and control strategy

This paper presents a new DC-DC Multi-Output Boost (MOB) converter which can share its total output between different series of output voltages for low and high power applications. This configuration can be utilised instead of several single output power supplies. This is a compatible topology for a diode-clamed inverter in the grid connection systems, where boosting low rectified output-voltage and series DC link capacitors is required. To verify the proposed topology, steady state and dynamic analysis of a MOB converter are examined. A simple control strategy has been proposed to demonstrate the performance of the proposed topology for a double-output boost converter. The topology and its control strategy can easily be extended to offer multiple outputs. Simulation and experimental results are presented to show the validity of the control strategy for the proposed converter.

Cojoined Irregular Topology and Routing Table Generation for Network-on-Chip

Scalable Networks on Chips (NoCs) are needed to match the ever-increasing communication demands of large-scale Multi-Processor Systems-on-chip (MPSoCs) for multi media communication applications. The heterogeneous nature of application specific on-chip cores along with the specific communication requirements among the cores calls for the design of application-specific NoCs for improved performance in terms of communication energy, latency, and throughput. In this work, we propose a methodology for the design of customized irregular networks-on-chip. The proposed method exploits a priori knowledge of the applications communication characteristic to generate an optimized network topology and corresponding routing tables.

Sensitivity of Water Dynamics to Biologically Significant Surfaces of Monomeric Insulin: Role of Topology and Electrostatic Interactions

In addition to the biologically active monomer of the protein insulin circulating in human blood, the molecule also exists in dimeric and hexameric forms that are used as storage. The insulin monomer contains two distinct surfaces, namely, the dimer forming surface (DFS) and the hexamer forming surface (HFS), that are specifically designed to facilitate the formation of the dimer and the hexamer, respectively. In order to characterize the structural and dynamical behavior of interfacial water molecules near these two surfaces (DFS and HFS), we performed atomistic molecular dynamics simulations of insulin with explicit water. Dynamical characterization reveals that the structural relaxation of the hydrogen bonds formed between the residues of DFS and the interfacial water molecules is faster than those formed between water and that of the HFS. Furthermore, the residence times of water molecules in the protein hydration layer for both the DFS and HFS are found to be significantly higher than those for some of the other proteins studied so far, such as HP-36 and lysozyme. In particular, we find that more structured water molecules, with higher residence times (similar to 300-500 ps), are present near HFS than those near DFS. A significant slowing down is observed in the decay of associated rotational auto time correlation functions of O-H bond vector of water in the vicinity of HFS. The surface topography and the arrangement of amino acid residues work together to organize the water molecules in the hydration layer in order to provide them with a preferred orientation. HFS having a large polar solvent accessible surface area and a convex extensive nonpolar region, drives the surrounding water molecules to acquire predominantly an outward H-atoms directed, clathrate-like structure. In contrast, near the DFS, the surrounding water molecules acquire an inward H-atoms directed orientation owing to the flat curvature of hydrophobic surface and the interrupted hydrophilic residual alignment. We have followed escape trajectory of several such quasi-bound water molecules from both the surfaces that reveal the significant differences between the two hydration layers.

Streamline topology and dilute particle dynamics in a Karman vortex street flow

Three types of streamline topology in a Karman vortex street flow are shown under the variation of spatial parameters. For the motion of dilute particles in the Karman vortex street flow, there exist a route of bifurcation to a chaotic orbit and more attractors in a bifurcation diagram for the proportion of particle density to fluid density. Along with the increase of spatial parameters in the flow field, the bifurcation process is suspended, as well as more and more attractors emerge. In the motion of dilute particles, a drag term and gravity term dominate and result in the bifurcation phenomenon.

Influence of network topology and data collection on network inference.

We recently developed an approach for testing the accuracy of network inference algorithms by applying them to biologically realistic simulations with known network topology. Here, we seek to determine the degree to which the network topology and data sampling regime influence the ability of our Bayesian network inference algorithm, NETWORKINFERENCE, to recover gene regulatory networks. NETWORKINFERENCE performed well at recovering feedback loops and multiple targets of a regulator with small amounts of data, but required more data to recover multiple regulators of a gene. When collecting the same number of data samples at different intervals from the system, the best recovery was produced by sampling intervals long enough such that sampling covered propagation of regulation through the network but not so long such that intervals missed internal dynamics. These results further elucidate the possibilities and limitations of network inference based on biological data.

Interaction strength, food web topology and the relative importance of species in food webs

P>1. We established complex marine communities, consisting of over 100 species, in large subtidal experimental mesocosms. We measured the strength of direct interactions and the net strength of direct and indirect interactions between the species in those communities, using a combination of theoretical and empirical approaches.

Membrane Topology and Identification of Critical Amino Acid Residues in the Wzx O-Antigen Translocase from Escherichia coli O157:H4

Wzx belongs to a family of membrane proteins involved in the translocation of isoprenoid lipid-linked glycans, which is loosely related to members of the major facilitator superfamily. Despite Wzx homologs performing a conserved function, it has been difficult to pinpoint specific motifs of functional significance in their amino acid sequences. Here, we elucidate the topology of the Escherichia coli O157 Wzx (Wzx(EcO157)) by a combination of bioinformatics and substituted cysteine scanning mutagenesis, as well as targeted deletion-fusions to green fluorescent protein and alkaline phosphatase. We conclude that Wzx(EcO157) consists of 12 transmembrane (TM) helices and six periplasmic and five cytosolic loops, with N and C termini facing the cytoplasm. Four TM helices (II, IV, X, and XI) contain polar residues (aspartic acid or lysine), and they may form part of a relatively hydrophilic core. Thirty-five amino acid replacements to alanine or serine were targeted to five native cysteines and most of the aspartic acid, arginine, and lysine residues. From these, only replacements of aspartic acid-85, aspartic acid-326, arginine-298, and lysine-419 resulted in a protein unable to support O-antigen production. Aspartic acid-85 and lysine-419 are located in TM helices II and XI, while arginine-298 and aspartic acid-326 are located in periplasmic and cytosolic loops 4, respectively. Further analysis revealed that the charge at these positions is required for Wzx function since conservative substitutions maintaining the same charge polarity resulted in a functional protein, whereas those reversing or eliminating polarity abolished function. We propose that the functional requirement of charged residues at both sides of the membrane and in two TM helices could be important to allow the passage of the Und-PP-linked saccharide substrate across the membrane.

Controlling Surface Topology and Functionality of Electrospun Fibers on the Nanoscale using Amphiphilic Block Copolymers To Direct Mesenchymal Progenitor Cell Adhesion

Surface patterning in three dimensions is of great importance in biomaterials design for controlling cell behavior. A facile one-step functionalization of biodegradable PDLLA fibers using amphiphilic diblock copolymers is demonstrated here to systematically vary the fiber surface composition. The copolymers comprise a hydrophilic poly[oligo(ethylene glycol) methacrylate] (POEGMA), poly[(2-methacryloyloxy)ethyl phosphorylcholine] (PMPC), or poly[2-(dimethylamino)ethyl methacrylate)] (PDMAEMA) block and a hydrophobic poly(l-lactide) (PLA) block. The block copolymer-modified fibers have increased surface hydrophilicity compared to that of PDLLA fibers. Mixtures of PLAPMPC and PLAPOEGMA copolymers are utilized to exploit microphase separation of the incompatible hydrophilic PMPC and POEGMA blocks at the fiber surface. Conjugation of an RGD cell-adhesive peptide to one hydrophilic block (POEGMA) using thiol-ene chemistry produces fibers with domains of cell-adhesive (POEGMA) and cell-inert (PMPC) sites, mimicking the adhesive properties of the extracellular matrix (ECM). Human mesenchymal progenitor cells (hES-MPs) showed much better adhesion to the fibers with surface-adhesive heterogeneity compared to that to fibers with only adhesive or only inert surface chemistries.

Burkholderia cenocepacia and Salmonella enterica ArnT proteins that transfer 4-amino-4-deoxy-L-arabinose to lipopolysaccharide share membrane topology and functional amino acids

We recently demonstrated that incorporation of 4-amino-4-deoxy-l-arabinose (l-Ara4N) to the lipid A moiety of lipopolysaccharide (LPS) is required for transport of LPS to the outer membrane and viability of the Gram-negative bacterium Burkholderia cenocepacia. ArnT is a membrane protein catalyzing the transfer of l-Ara4N to the LPS molecule at the periplasmic face of the inner membrane, but its topology and mechanism of action are not well characterized. Here, we elucidate the topology of ArnT and identify key amino acids that likely contribute to its enzymatic function. PEGylation assays using a cysteineless version of ArnT support a model of 13 transmembrane helices and a large C-terminal region exposed to the periplasm. The same topological configuration is proposed for the Salmonella enterica serovar Typhimurium ArnT. Four highly conserved periplasmic residues in B. cenocepacia ArnT, tyrosine-43, lysine-69, arginine-254 and glutamic acid-493, were required for activity. Tyrosine-43 and lysine-69 span two highly conserved motifs, 42RYA44 and 66YFEKP70, that are found in ArnT homologues from other species. The same residues in S. enterica ArnT are also needed for function. We propose these aromatic and charged amino acids participate in either undecaprenyl phosphate-l-Ara4N substrate recognition or transfer of l-Ara4N to the LPS.

Combining ganglion cell topology and data of patients with glaucoma to determine a structure-function map

PURPOSE