Backbone dynamics in an intramolecular prolylpeptide-SH3 complex from the diphtheria toxin repressor, DtxR

PubMed Central

Bhattacharya, Nilakshee; Yi, Myunggi; Zhou, Huan-Xiang; Logan, Timothy M.

2008-01-01

Summary The diphtheria toxin repressor contains an SH3-like domain that forms an intramolecular complex with a proline-rich (Pr) peptide segment and stabilizes the inactive state of the repressor. Upon activation of DtxR by transition metals, this intramolecular complex must dissociate as the SH3 domain and Pr segment form different interactions in the active repressor. In this study we investigate the dynamics of this intramolecular complex using backbone amide nuclear spin relaxation rates determined using NMR spectroscopy and molecular dynamics trajectories. The SH3 domain in the unbound and bound states showed typical dynamics in that the secondary structures were fairly ordered with high generalized order parameters and low effective correlation times while residues in the loops connecting β-strands exhibited reduced generalized order parameters and required additional motional terms to adequately model the relaxation rates. Residues forming the Pr segment exhibited low order parameters with internal rotational correlation times on the order of 0.6 – 1 ns. Further analysis showed that the SH3 domain was rich in millisecond timescale motions while the Pr segment was rich in motions on the 100s μs timescale. Molecular dynamics simultations indicated structural rearrangements that may contribute to the observed relaxation rates and, together with the observed relaxation rate data, suggested that the Pr segment exhibits a binding ↔ unbinding equilibrium. The results of this study provide new insights into the nature of the intramolecular complex and provide a better understanding of the biological role of the SH3 domain in regulating DtxR activity. PMID:17976643

Preparation of metallic cation conducting polymers based on sterically hindered phenols containing polymeric systems

DOEpatents

Skotheim, Terje A.; Okamoto, Yoshiyuki; Lee, Hung S.

1989-01-01

The present invention relates to ion-conducting solvent-free polymeric systems characterized as being cationic single ion conductors. The solvent-free polymer electrolytes comprise a flexible polymer backbone to which is attached a metal salt, such as a lithium, sodium or potassium salt, of a sterically hindered phenol. The solid polymer electrolyte may be prepared either by (1) attaching the hindered phenol directly to a flexible polymeric backbone, followed by neutralization of the phenolic OH's or (2) reacting the hindered phenol with a polymer precursor which is then polymerized to form a flexible polymer having phenolic OH's which are subsequently neutralized. Preferably the hindered phenol-modified polymeric backbone contains a polyether segment. The ionic conductivity of these solvent-free polymer electrolytes has been measured to be in the range of 10.sup.-4 to 10.sup.-7 S cm.sup.-1 at room temperature.

Preparation of metallic cation conducting polymers based on sterically hindered phenols containing polymeric systems

DOEpatents

Skotheim, T.A.; Okamoto, Yoshiyuki; Lee, H.S.

1989-11-21

The present invention relates to ion-conducting solvent-free polymeric systems characterized as being cationic single ion conductors. The solvent-free polymer electrolytes comprise a flexible polymer backbone to which is attached a metal salt, such as a lithium, sodium or potassium salt, of a sterically hindered phenol. The solid polymer electrolyte may be prepared either by (1) attaching the hindered phenol directly to a flexible polymeric backbone, followed by neutralization of the phenolic OH's or (2) reacting the hindered phenol with a polymer precursor which is then polymerized to form a flexible polymer having phenolic OH's which are subsequently neutralized. Preferably the hindered phenol-modified polymeric backbone contains a polyether segment. The ionic conductivity of these solvent-free polymer electrolytes has been measured to be in the range of 10[sup [minus]4] to 10[sup [minus]7] S cm[sup [minus]1] at room temperature.

MOSAIC: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level.

PubMed

Chiapello, Hélène; Gendrault, Annie; Caron, Christophe; Blum, Jérome; Petit, Marie-Agnès; El Karoui, Meriem

2008-11-27

The recent availability of complete sequences for numerous closely related bacterial genomes opens up new challenges in comparative genomics. Several methods have been developed to align complete genomes at the nucleotide level but their use and the biological interpretation of results are not straightforward. It is therefore necessary to develop new resources to access, analyze, and visualize genome comparisons. Here we present recent developments on MOSAIC, a generalist comparative bacterial genome database. This database provides the bacteriologist community with easy access to comparisons of complete bacterial genomes at the intra-species level. The strategy we developed for comparison allows us to define two types of regions in bacterial genomes: backbone segments (i.e., regions conserved in all compared strains) and variable segments (i.e., regions that are either specific to or variable in one of the aligned genomes). Definition of these segments at the nucleotide level allows precise comparative and evolutionary analyses of both coding and non-coding regions of bacterial genomes. Such work is easily performed using the MOSAIC Web interface, which allows browsing and graphical visualization of genome comparisons. The MOSAIC database now includes 493 pairwise comparisons and 35 multiple maximal comparisons representing 78 bacterial species. Genome conserved regions (backbones) and variable segments are presented in various formats for further analysis. A graphical interface allows visualization of aligned genomes and functional annotations. The MOSAIC database is available online at http://genome.jouy.inra.fr/mosaic.

LOCAL AND GLOBAL DYNAMICS OF POLYLACTIDES. (R826733)

EPA Science Inventory

Polylactides (PLAs) are a family of degradable plastics having a component of the dipole moment both perpendicular and parallel to the polymer backbone (i.e. is a type-A polymer). We have studied the sub-glass, segmental and global chain dynamics in a series of fully amorphous...

Comparative analysis of pentavalent rotavirus vaccine strains and G8 rotaviruses identified during vaccine trial in Africa.

PubMed

Heylen, Elisabeth; Zeller, Mark; Ciarlet, Max; Lawrence, Jody; Steele, Duncan; Van Ranst, Marc; Matthijnssens, Jelle

2015-10-06

RotaTeqTM is a pentavalent rotavirus vaccine based on a bovine rotavirus genetic backbone in vitro reassorted with human outer capsid genes. During clinical trials of RotaTeqTM in Sub-Saharan Africa, the vaccine efficacy over a 2-year follow-up was lower against the genotypes contained in the vaccine than against the heterotypic G8P[6] and G8P[1] rotavirus strains of which the former is highly prevalent in Africa. Complete genome analyses of 43 complete rotavirus genomes collected during phase III clinical trials of RotaTeqTM in Sub-Saharan Africa, were conducted to gain insight into the high level of cross-protection afforded by RotaTeqTM against these G8 strains. Phylogenetic analysis revealed the presence of a high number of bovine rotavirus gene segments in these human G8 strains. In addition, we performed an in depth analysis on the individual amino acid level which showed that G8 rotaviruses were more similar to the RotaTeqTM vaccine than non-G8 strains. Because RotaTeqTM possesses a bovine genetic backbone, the high vaccine efficacy against G8 strains might be partially explained by the fact that all these strains contain a complete or partial bovine-like backbone. Altogether, this study supports the hypothesis that gene segments other than VP7 and VP4 play a role in vaccine-induced immunity.

Polyether/Polyester Graft Copolymers

NASA Technical Reports Server (NTRS)

Bell, Vernon L., Jr.; Wakelyn, N.; Stoakley, D. M.; Proctor, K. M.

1986-01-01

Higher solvent resistance achieved along with lower melting temperature. New technique provides method of preparing copolymers with polypivalolactone segments grafted onto poly (2,6-dimethyl-phenylene oxide) backbone. Process makes strong materials with improved solvent resistance and crystalline, thermally-reversible crosslinks. Resulting graft copolymers easier to fabricate into useful articles, including thin films, sheets, fibers, foams, laminates, and moldings.

Ambient noise levels in the continental United States

USGS Publications Warehouse

McNamara, D.E.; Buland, R.P.

2004-01-01

The results of our noise analysis are useful for characterizing the performance of existing broadband stations and for detecting operational problems and should be relevant to the future siting of ANSS backbone stations. The noise maps at body-wave frequencies should be useful for estimating the magnitude threshold for the ANSS backbone and regional networks or conversely for optimizing the distribution of regional network stations.

Force Field for Peptides and Proteins based on the Classical Drude Oscillator

PubMed Central

Lopes, Pedro E.M.; Huang, Jing; Shim, Jihyun; Luo, Yun; Li, Hui; Roux, Benoît; MacKerell, Alexander D.

2013-01-01

Presented is a polarizable force field based on a classical Drude oscillator framework, currently implemented in the programs CHARMM and NAMD, for modeling and molecular dynamics (MD) simulation studies of peptides and proteins. Building upon parameters for model compounds representative of the functional groups in proteins, the development of the force field focused on the optimization of the parameters for the polypeptide backbone and the connectivity between the backbone and side chains. Optimization of the backbone electrostatic parameters targeted quantum mechanical conformational energies, interactions with water, molecular dipole moments and polarizabilities and experimental condensed phase data for short polypeptides such as (Ala)5. Additional optimization of the backbone φ, ψ conformational preferences included adjustments of the tabulated two-dimensional spline function through the CMAP term. Validation of the model included simulations of a collection of peptides and proteins. This 1st generation polarizable model is shown to maintain the folded state of the studied systems on the 100 ns timescale in explicit solvent MD simulations. The Drude model typically yields larger RMS differences as compared to the additive CHARMM36 force field (C36) and shows additional flexibility as compared to the additive model. Comparison with NMR chemical shift data shows a small degradation of the polarizable model with respect to the additive, though the level of agreement may be considered satisfactory, while for residues shown to have significantly underestimated S2 order parameters in the additive model, improvements are calculated with the polarizable model. Analysis of dipole moments associated with the peptide backbone and tryptophan side chains show the Drude model to have significantly larger values than those present in C36, with the dipole moments of the peptide backbone enhanced to a greater extent in sheets versus helices and the dipoles of individual moieties observed to undergo significant variations during the MD simulations. Although there are still some limitations, the presented model, termed Drude-2013, is anticipated to yield a molecular picture of peptide and protein structure and function that will be of increased physical validity and internal consistency in a computationally accessible fashion. PMID:24459460

Prediction of Long Loops with Embedded Secondary Structure using the Protein Local Optimization Program

PubMed Central

Miller, Edward B.; Murrett, Colleen S.; Zhu, Kai; Zhao, Suwen; Goldfeld, Dahlia A.; Bylund, Joseph H.; Friesner, Richard A.

2013-01-01

Robust homology modeling to atomic-level accuracy requires in the general case successful prediction of protein loops containing small segments of secondary structure. Further, as loop prediction advances to success with larger loops, the exclusion of loops containing secondary structure becomes awkward. Here, we extend the applicability of the Protein Local Optimization Program (PLOP) to loops up to 17 residues in length that contain either helical or hairpin segments. In general, PLOP hierarchically samples conformational space and ranks candidate loops with a high-quality molecular mechanics force field. For loops identified to possess α-helical segments, we employ an alternative dihedral library composed of (ϕ,ψ) angles commonly found in helices. The alternative library is searched over a user-specified range of residues that define the helical bounds. The source of these helical bounds can be from popular secondary structure prediction software or from analysis of past loop predictions where a propensity to form a helix is observed. Due to the maturity of our energy model, the lowest energy loop across all experiments can be selected with an accuracy of sub-Ångström RMSD in 80% of cases, 1.0 to 1.5 Å RMSD in 14% of cases, and poorer than 1.5 Å RMSD in 6% of cases. The effectiveness of our current methods in predicting hairpin-containing loops is explored with hairpins up to 13 residues in length and again reaching an accuracy of sub-Ångström RMSD in 83% of cases, 1.0 to 1.5 Å RMSD in 10% of cases, and poorer than 1.5 Å RMSD in 7% of cases. Finally, we explore the effect of an imprecise surrounding environment, in which side chains, but not the backbone, are initially in perturbed geometries. In these cases, loops perturbed to 3Å RMSD from the native environment were restored to their native conformation with sub-Ångström RMSD. PMID:23814507

Investigation of structure-property relationships in systematic series of novel polymers

NASA Technical Reports Server (NTRS)

Gillham, J. K.

1976-01-01

Solid state transitions in polymeric materials was associated with the onset of sub-molecular motions of the polymer chains. Although these were considered to be intramolecular in general, the local environment of the polymer molecule exerts a strong influence through, for example, the effects of crystallinity, polarity and diluents. The manner of specimen preparation and previous history also affect transitions. The transitions are considered to arise when sufficient free volume is available to permit the occurrence of these side chain and backbone reorientations. The glass transition is the principal transition of amorphous polymeric materials and is associated with the onset of long range segmental motion of the polymer backbone. The various types of shorter range motion occurring below the glass transition have been catalogued.

What Is the Internet, Who Is Running It and How Is It Used?

ERIC Educational Resources Information Center

Eschbach, Darel

The Internet, for the purposes of this discussion, refers to the network that has the National Science Foundation Network (NSFNET) as its backbone. For this paper, internet is the larger connection of networks that provides a minimum basic connection for electronic mail. The network is made up of many segments structured in a multitiered hierarchy…

Chemical synthesis of membrane proteins by the removable backbone modification method.

PubMed

Tang, Shan; Zuo, Chao; Huang, Dong-Liang; Cai, Xiao-Ying; Zhang, Long-Hua; Tian, Chang-Lin; Zheng, Ji-Shen; Liu, Lei

2017-12-01

Chemical synthesis can produce membrane proteins bearing specifically designed modifications (e.g., phosphorylation, isotope labeling) that are difficult to obtain through recombinant protein expression approaches. The resulting homogeneously modified synthetic membrane proteins are valuable tools for many advanced biochemical and biophysical studies. This protocol describes the chemical synthesis of membrane proteins by condensation of transmembrane peptide segments through native chemical ligation. To avoid common problems encountered due to the poor solubility of transmembrane peptides in almost any solvent, we describe an effective procedure for the chemical synthesis of membrane proteins through the removable-backbone modification (RBM) strategy. Two key steps of this protocol are: (i) installation of solubilizing Arg4-tagged RBM groups into the transmembrane peptides at any primary amino acid through Fmoc (9-fluorenylmethyloxycarbonyl) solid-phase peptide synthesis and (ii) native ligation of the full-length sequence, followed by removal of the RBM tags by TFA (trifluoroacetic acid) cocktails to afford the native protein. The installation of RBM groups is achieved by using 4-methoxy-5-nitrosalicyladehyde by reduction amination to incorporate an activated O-to-N acyl transfer auxiliary. The Arg4-tag-modified membrane-spanning peptide segments behave like water-soluble peptides to facilitate their purification, ligation and mass characterization.

KSC-07pd1423

NASA Image and Video Library

2007-06-08

KENNEDY SPACE CENTER, FLA. -- STS-117 Mission Specialist Patrick Forrester completes his suitup for launch of Space Shuttle Atlantis at 7:38 p.m. EDT from Launch Pad 39A. The shuttle is delivering a new segment to the starboard side of the International Space Station's backbone, known as the truss. Three spacewalks are planned to install the S3/S4 truss segment, deploy a set of solar arrays and prepare them for operation. STS-117 is the 118th space shuttle flight, the 21st flight to the station, the 28th flight for Atlantis and the first of four flights planned for 2007. Photo credit: NASA/Kim Shiflett

Optimization of segmented thermoelectric generator using Taguchi and ANOVA techniques.

PubMed

Kishore, Ravi Anant; Sanghadasa, Mohan; Priya, Shashank

2017-12-01

Recent studies have demonstrated that segmented thermoelectric generators (TEGs) can operate over large thermal gradient and thus provide better performance (reported efficiency up to 11%) as compared to traditional TEGs, comprising of single thermoelectric (TE) material. However, segmented TEGs are still in early stages of development due to the inherent complexity in their design optimization and manufacturability. In this study, we demonstrate physics based numerical techniques along with Analysis of variance (ANOVA) and Taguchi optimization method for optimizing the performance of segmented TEGs. We have considered comprehensive set of design parameters, such as geometrical dimensions of p-n legs, height of segmentation, hot-side temperature, and load resistance, in order to optimize output power and efficiency of segmented TEGs. Using the state-of-the-art TE material properties and appropriate statistical tools, we provide near-optimum TEG configuration with only 25 experiments as compared to 3125 experiments needed by the conventional optimization methods. The effect of environmental factors on the optimization of segmented TEGs is also studied. Taguchi results are validated against the results obtained using traditional full factorial optimization technique and a TEG configuration for simultaneous optimization of power and efficiency is obtained.

Nuclear magnetic resonance investigation of dynamics in poly(ethylene oxide) based polyether-ester-sulfonate ionomers

NASA Astrophysics Data System (ADS)

Roach, David J.

Nuclear magnetic resonance (NMR) spectroscopy has been utilized to investigate the dynamics of poly(ethylene oxide)-based lithium sulfonate ionomer samples that have low glass transition temperatures. 1H and 7Li spin-lattice relaxation times (T1) of the bulk polymer and lithium ions, respectively, were measured and analyzed in samples with a range of ion contents. The temperature dependence of T1 values along with the presence of minima in T1 as a function of temperature enabled correlation times and activation energies to be obtained for both the segmental motion of the polymer backbone and the hopping motion of lithium cations. Similar activation energies for motion of both the polymer and lithium ions in the samples with lower ion content indicate that the polymer segmental motion and lithium ion hopping motion are correlated in these samples, even though lithium hopping is about ten times slower than the segmental motion. A divergent trend is observed for correlation times and activation energies of the highest ion content sample with 100% lithium sulfonation due to the presence of ionic aggregation. Details of the polymer and cation dynamics on the nanosecond timescale are discussed and complement the findings of X-ray scattering and Quasi Elastic Neutron Scattering experiments. Polymer backbone dynamics of single ion conducting poly(ethylene oxide) (PEO)-based ionomer samples with low glass transition temperatures (T g) have been investigated using solid-state nuclear magnetic resonance (NMR). Experiments detecting 13C with 1H decoupling under magic angle spinning (MAS) conditions identified the different components and relative mobilities of the polymer backbone of a suite of. lithium- and sodium-containing ionomer samples with varying cation contents. Variable temperature (203-373 K) 1H-13C cross-polarization MAS (CP-MAS) experiments also provided qualitative assessment of the differences in the motions of the polymer backbone components as a function of cation content. Each of the main backbone components (PEO spacer and isophthalate groups) exhibit distinct motions, following the trends expected for motional characteristics based on earlier Quasi Elastic Neutron Scattering and 1H spin-lattice relaxation rate measurements. The temperature dependences of 13C linewidths were used to both qualitatively and quantitatively examine the effects of cation content on PEO mobility. Variable contact time 1H-13C CP-MAS experiments were used to further assess the motions of the polymer backbone on the microsecond timescale. The motion of the PEO spacer, determined from the rate of magnetization transfer from 1H to 13C nuclei, in all ionic samples becomes similar for T [special characters omitted] 1.1 Tg, indicating that the motions of the polymer backbones on the microsecond timescale become insensitive to ion interactions. These results compliment previous findings and present an improved picture of the dependence of backbone dynamics on cation type and density in these amorphous PEO-based ionomer systems. 7Li PFG NMR experiments provided measurements of the self-diffusion coefficients for Li+ cations in the PEO600-y Li ionomer series over a range of temperatures. When the Tg values are taken into account, the self-diffusion coefficients of Li+ in each sample follow a similar trendline, indicating that lithium diffusion is independent of ion concentration at any given reduced inverse temperature, Tg/T. Ion aggregation increases Tg and slows both lithium cation diffusion and displacement, but there is no further slowing beyond the Tg effect in the PEO600-y Li ionomers samples. The differences in activation energies obtained from diffusion measurements and relaxation times suggest that at least one additional barrier must be overcome for cations emerge from local hopping motion to macroscopic cation transpfort. Using the Nernst- Einstein equation lithium diffusion coefficients were also calculated from conductivity measurements. The differences between the diffusion measured by the two separate techniques indicate the presence of ion pairs. The activation energy of lithium diffusion was found to be nearly identical between the PFG NMR and conductivity, suggesting that the conductivity and ionic diffusion are related to the same ionic dynamics. As the ion content within the PEO600-y Li samples increases the relative concentration of nonconducting ion pairs decrease. Also an increase in temperature causes a fraction of ion pairs to thermally dissociate into positive triple ions.

Rational Design of Orthogonal Multipolar Interactions with Fluorine in Protein–Ligand Complexes

DOE PAGES

Pollock, Jonathan; Borkin, Dmitry; Lund, George; ...

2015-08-19

Multipolar interactions involving fluorine and the protein backbone have been frequently observed in protein–ligand complexes. Such fluorine–backbone interactions may substantially contribute to the high affinity of small molecule inhibitors. Here we found that introduction of trifluoromethyl groups into two different sites in the thienopyrimidine class of menin–MLL inhibitors considerably improved their inhibitory activity. In both cases, trifluoromethyl groups are engaged in short interactions with the backbone of menin. In order to understand the effect of fluorine, we synthesized a series of analogues by systematically changing the number of fluorine atoms, and we determined high-resolution crystal structures of the complexes withmore » menin. Here, we found that introduction of fluorine at favorable geometry for interactions with backbone carbonyls may improve the activity of menin–MLL inhibitors as much as 5- to 10-fold. In order to facilitate the design of multipolar fluorine–backbone interactions in protein–ligand complexes, we developed a computational algorithm named FMAP, which calculates fluorophilic sites in proximity to the protein backbone. We demonstrated that FMAP could be used to rationalize improvement in the activity of known protein inhibitors upon introduction of fluorine. Furthermore, FMAP may also represent a valuable tool for designing new fluorine substitutions and support ligand optimization in drug discovery projects. Analysis of the menin–MLL inhibitor complexes revealed that the backbone in secondary structures is particularly accessible to the interactions with fluorine. Lastly, considering that secondary structure elements are frequently exposed at protein interfaces, we postulate that multipolar fluorine–backbone interactions may represent a particularly attractive approach to improve inhibitors of protein–protein interactions.« less

A local segmentation parameter optimization approach for mapping heterogeneous urban environments using VHR imagery

NASA Astrophysics Data System (ADS)

Grippa, Tais; Georganos, Stefanos; Lennert, Moritz; Vanhuysse, Sabine; Wolff, Eléonore

2017-10-01

Mapping large heterogeneous urban areas using object-based image analysis (OBIA) remains challenging, especially with respect to the segmentation process. This could be explained both by the complex arrangement of heterogeneous land-cover classes and by the high diversity of urban patterns which can be encountered throughout the scene. In this context, using a single segmentation parameter to obtain satisfying segmentation results for the whole scene can be impossible. Nonetheless, it is possible to subdivide the whole city into smaller local zones, rather homogeneous according to their urban pattern. These zones can then be used to optimize the segmentation parameter locally, instead of using the whole image or a single representative spatial subset. This paper assesses the contribution of a local approach for the optimization of segmentation parameter compared to a global approach. Ouagadougou, located in sub-Saharan Africa, is used as case studies. First, the whole scene is segmented using a single globally optimized segmentation parameter. Second, the city is subdivided into 283 local zones, homogeneous in terms of building size and building density. Each local zone is then segmented using a locally optimized segmentation parameter. Unsupervised segmentation parameter optimization (USPO), relying on an optimization function which tends to maximize both intra-object homogeneity and inter-object heterogeneity, is used to select the segmentation parameter automatically for both approaches. Finally, a land-use/land-cover classification is performed using the Random Forest (RF) classifier. The results reveal that the local approach outperforms the global one, especially by limiting confusions between buildings and their bare-soil neighbors.

"Double-Cable" Conjugated Polymers with Linear Backbone toward High Quantum Efficiencies in Single-Component Polymer Solar Cells.

PubMed

Feng, Guitao; Li, Junyu; Colberts, Fallon J M; Li, Mengmeng; Zhang, Jianqi; Yang, Fan; Jin, Yingzhi; Zhang, Fengling; Janssen, René A J; Li, Cheng; Li, Weiwei

2017-12-27

A series of "double-cable" conjugated polymers were developed for application in efficient single-component polymer solar cells, in which high quantum efficiencies could be achieved due to the optimized nanophase separation between donor and acceptor parts. The new double-cable polymers contain electron-donating poly(benzodithiophene) (BDT) as linear conjugated backbone for hole transport and pendant electron-deficient perylene bisimide (PBI) units for electron transport, connected via a dodecyl linker. Sulfur and fluorine substituents were introduced to tune the energy levels and crystallinity of the conjugated polymers. The double-cable polymers adopt a "face-on" orientation in which the conjugated BDT backbone and the pendant PBI units have a preferential π-π stacking direction perpendicular to the substrate, favorable for interchain charge transport normal to the plane. The linear conjugated backbone acts as a scaffold for the crystallization of the PBI groups, to provide a double-cable nanophase separation of donor and acceptor phases. The optimized nanophase separation enables efficient exciton dissociation as well as charge transport as evidenced from the high-up to 80%-internal quantum efficiency for photon-to-electron conversion. In single-component organic solar cells, the double-cable polymers provide power conversion efficiency up to 4.18%. This is one of the highest performances in single-component organic solar cells. The nanophase-separated design can likely be used to achieve high-performance single-component organic solar cells.

The role of molecular structure of sugar-phosphate backbone and nucleic acid bases in the formation of single-stranded and double-stranded DNA structures.

PubMed

Poltev, Valeri; Anisimov, Victor M; Danilov, Victor I; Garcia, Dolores; Sanchez, Carolina; Deriabina, Alexandra; Gonzalez, Eduardo; Rivas, Francisco; Polteva, Nina

2014-06-01

Our previous DFT computations of deoxydinucleoside monophosphate complexes with Na(+)-ions (dDMPs) have demonstrated that the main characteristics of Watson-Crick (WC) right-handed duplex families are predefined in the local energy minima of dDMPs. In this work, we study the mechanisms of contribution of chemically monotonous sugar-phosphate backbone and the bases into the double helix irregularity. Geometry optimization of sugar-phosphate backbone produces energy minima matching the WC DNA conformations. Studying the conformational variability of dDMPs in response to sequence permutation, we found that simple replacement of bases in the previously fully optimized dDMPs, e.g. by constructing Pyr-Pur from Pur-Pyr, and Pur-Pyr from Pyr-Pur sequences, while retaining the backbone geometry, automatically produces the mutual base position characteristic of the target sequence. Based on that, we infer that the directionality and the preferable regions of the sugar-phosphate torsions, combined with the difference of purines from pyrimidines in ring shape, determines the sequence dependence of the structure of WC DNA. No such sequence dependence exists in dDMPs corresponding to other DNA conformations (e.g., Z-family and Hoogsteen duplexes). Unlike other duplexes, WC helix is unique by its ability to match the local energy minima of the free single strand to the preferable conformations of the duplex. Copyright © 2013 Wiley Periodicals, Inc.

Hidden Markov model approach for identifying the modular framework of the protein backbone.

PubMed

Camproux, A C; Tuffery, P; Chevrolat, J P; Boisvieux, J F; Hazout, S

1999-12-01

The hidden Markov model (HMM) was used to identify recurrent short 3D structural building blocks (SBBs) describing protein backbones, independently of any a priori knowledge. Polypeptide chains are decomposed into a series of short segments defined by their inter-alpha-carbon distances. Basically, the model takes into account the sequentiality of the observed segments and assumes that each one corresponds to one of several possible SBBs. Fitting the model to a database of non-redundant proteins allowed us to decode proteins in terms of 12 distinct SBBs with different roles in protein structure. Some SBBs correspond to classical regular secondary structures. Others correspond to a significant subdivision of their bounding regions previously considered to be a single pattern. The major contribution of the HMM is that this model implicitly takes into account the sequential connections between SBBs and thus describes the most probable pathways by which the blocks are connected to form the framework of the protein structures. Validation of the SBBs code was performed by extracting SBB series repeated in recoding proteins and examining their structural similarities. Preliminary results on the sequence specificity of SBBs suggest promising perspectives for the prediction of SBBs or series of SBBs from the protein sequences.

KSC-07pd1420

NASA Image and Video Library

2007-06-08

KENNEDY SPACE CENTER, FLA. -- STS-117 Mission Specialist John "Danny" Olivas signals go for launch as he completes suitup by donning his helmet. The launch of Space Shuttle Atlantis is scheduled for 7:38 p.m. EDT from Launch Pad 39A. The shuttle is delivering a new segment to the starboard side of the International Space Station's backbone, known as the truss. Three spacewalks are planned to install the S3/S4 truss segment, deploy a set of solar arrays and prepare them for operation. STS-117 is the 118th space shuttle flight, the 21st flight to the station, the 28th flight for Atlantis and the first of four flights planned for 2007. Photo credit: NASA/Kim Shiflett

KSC-07pd1445

NASA Image and Video Library

2007-06-08

KENNEDY SPACE CENTER, FLA. -- Space Shuttle Atlantis is poised for flight at liftoff from Launch Pad 39A on mission STS-117 to the International Space Station. Liftoff was on-time at 7:38:04 p.m. EDT. The shuttle is delivering a new segment to the starboard side of the International Space Station's backbone, known as the truss. Three spacewalks are planned to install the S3/S4 truss segment, deploy a set of solar arrays and prepare them for operation. STS-117 is the 118th space shuttle flight, the 21st flight to the station, the 28th flight for Atlantis and the first of four flights planned for 2007. Photo courtesy of Nikon/Scott Andrews

KSC-07pd1437

NASA Image and Video Library

2007-06-08

KENNEDY SPACE CENTER, FLA. -- Billows of smoke surround the mobile launcher platform on Launch Pad 39A as Space Shuttle Atlantis lifts off on mission STS-117 to the International Space Station. Liftoff was on-time at 7:38:04 p.m. EDT. The shuttle is delivering a new segment to the starboard side of the International Space Station's backbone, known as the truss. Three spacewalks are planned to install the S3/S4 truss segment, deploy a set of solar arrays and prepare them for operation. STS-117 is the 118th space shuttle flight, the 21st flight to the station, the 28th flight for Atlantis and the first of four flights planned for 2007. Photo courtesy of Reuters.

KSC-07pd1422

NASA Image and Video Library

2007-06-08

KENNEDY SPACE CENTER, FLA. -- STS-117 Mission Specialist James Reilly is helped with his helmet as he completes suitup for launch of Space Shuttle Atlantis at 7:38 p.m. EDT from Launch Pad 39A. The shuttle is delivering a new segment to the starboard side of the International Space Station's backbone, known as the truss. Three spacewalks are planned to install the S3/S4 truss segment, deploy a set of solar arrays and prepare them for operation. STS-117 is the 118th space shuttle flight, the 21st flight to the station, the 28th flight for Atlantis and the first of four flights planned for 2007. Photo credit: NASA/Kim Shiflett

Theoretical study of the self-assembly of Janus Bottlebrush Polymers from A-Branch-B Diblock Macromonomers

NASA Astrophysics Data System (ADS)

Gadelrab, Karim; Alexander-Katz, Alfredo; LaboratoryTheoretical Soft Materials Team

The self-assembly of block copolymers BCP has provided an impressive control over the nanoscale structure of soft matter. While the main focus of the research in the field has been directed towards simple linear diblocks, the development of advanced polymer architecture provided improved performance and access to new structures. In particular, bottlebrush BCPs (BBCPs) have interesting characteristics due to their dense functionality, high molecular weight, low levels of entanglement, and tendency to efficiently undergo rapid bulk phase separation. In this work, we are interested in theoretically studying the self-assembly of Janus-type ``A-branch-B'' BBCPs where A and B blocks can phase separate with the bottlebrush polymer backbone serving as the interface between the two blocks. Hence, the polymer backbone adds an extra constraint on the equilibrium spacing between neighboring linear diblock chains. In this regard, the segment length of the backbone separating the AB junctions has a direct effect of the observed domain spacing and effective segregation strength of the AB blocks. We employ self-consistent field theoretic SCFT simulations to capture the effect of volume fraction of different constituents and construct a phase diagram of the accessible morphologies of these BBCPs.

Fast approximation for joint optimization of segmentation, shape, and location priors, and its application in gallbladder segmentation.

PubMed

Saito, Atsushi; Nawano, Shigeru; Shimizu, Akinobu

2017-05-01

This paper addresses joint optimization for segmentation and shape priors, including translation, to overcome inter-subject variability in the location of an organ. Because a simple extension of the previous exact optimization method is too computationally complex, we propose a fast approximation for optimization. The effectiveness of the proposed approximation is validated in the context of gallbladder segmentation from a non-contrast computed tomography (CT) volume. After spatial standardization and estimation of the posterior probability of the target organ, simultaneous optimization of the segmentation, shape, and location priors is performed using a branch-and-bound method. Fast approximation is achieved by combining sampling in the eigenshape space to reduce the number of shape priors and an efficient computational technique for evaluating the lower bound. Performance was evaluated using threefold cross-validation of 27 CT volumes. Optimization in terms of translation of the shape prior significantly improved segmentation performance. The proposed method achieved a result of 0.623 on the Jaccard index in gallbladder segmentation, which is comparable to that of state-of-the-art methods. The computational efficiency of the algorithm is confirmed to be good enough to allow execution on a personal computer. Joint optimization of the segmentation, shape, and location priors was proposed, and it proved to be effective in gallbladder segmentation with high computational efficiency.

A Method for Optimizing Non-Axisymmetric Liners for Multimodal Sound Sources

NASA Technical Reports Server (NTRS)

Watson, W. R.; Jones, M. G.; Parrott, T. L.; Sobieski, J.

2002-01-01

Central processor unit times and memory requirements for a commonly used solver are compared to that of a state-of-the-art, parallel, sparse solver. The sparse solver is then used in conjunction with three constrained optimization methodologies to assess the relative merits of non-axisymmetric versus axisymmetric liner concepts for improving liner acoustic suppression. This assessment is performed with a multimodal noise source (with equal mode amplitudes and phases) in a finite-length rectangular duct without flow. The sparse solver is found to reduce memory requirements by a factor of five and central processing time by a factor of eleven when compared with the commonly used solver. Results show that the optimum impedance of the uniform liner is dominated by the least attenuated mode, whose attenuation is maximized by the Cremer optimum impedance. An optimized, four-segmented liner with impedance segments in a checkerboard arrangement is found to be inferior to an optimized spanwise segmented liner. This optimized spanwise segmented liner is shown to attenuate substantially more sound than the optimized uniform liner and tends to be more effective at the higher frequencies. The most important result of this study is the discovery that when optimized, a spanwise segmented liner with two segments gives attenuations equal to or substantially greater than an optimized axially segmented liner with the same number of segments.

DNA Motion Capture Reveals the Mechanical Properties of DNA at the Mesoscale

PubMed Central

Price, Allen C.; Pilkiewicz, Kevin R.; Graham, Thomas G.W.; Song, Dan; Eaves, Joel D.; Loparo, Joseph J.

2015-01-01

Single-molecule studies probing the end-to-end extension of long DNAs have established that the mechanical properties of DNA are well described by a wormlike chain force law, a polymer model where persistence length is the only adjustable parameter. We present a DNA motion-capture technique in which DNA molecules are labeled with fluorescent quantum dots at specific sites along the DNA contour and their positions are imaged. Tracking these positions in time allows us to characterize how segments within a long DNA are extended by flow and how fluctuations within the molecule are correlated. Utilizing a linear response theory of small fluctuations, we extract elastic forces for the different, ∼2-μm-long segments along the DNA backbone. We find that the average force-extension behavior of the segments can be well described by a wormlike chain force law with an anomalously small persistence length. PMID:25992731

Protein Side-Chain Resonance Assignment and NOE Assignment Using RDC-Defined Backbones without TOCSY Data3

PubMed Central

Zeng, Jianyang; Zhou, Pei; Donald, Bruce Randall

2011-01-01

One bottleneck in NMR structure determination lies in the laborious and time-consuming process of side-chain resonance and NOE assignments. Compared to the well-studied backbone resonance assignment problem, automated side-chain resonance and NOE assignments are relatively less explored. Most NOE assignment algorithms require nearly complete side-chain resonance assignments from a series of through-bond experiments such as HCCH-TOCSY or HCCCONH. Unfortunately, these TOCSY experiments perform poorly on large proteins. To overcome this deficiency, we present a novel algorithm, called NASCA (NOE Assignment and Side-Chain Assignment), to automate both side-chain resonance and NOE assignments and to perform high-resolution protein structure determination in the absence of any explicit through-bond experiment to facilitate side-chain resonance assignment, such as HCCH-TOCSY. After casting the assignment problem into a Markov Random Field (MRF), NASCA extends and applies combinatorial protein design algorithms to compute optimal assignments that best interpret the NMR data. The MRF captures the contact map information of the protein derived from NOESY spectra, exploits the backbone structural information determined by RDCs, and considers all possible side-chain rotamers. The complexity of the combinatorial search is reduced by using a dead-end elimination (DEE) algorithm, which prunes side-chain resonance assignments that are provably not part of the optimal solution. Then an A* search algorithm is employed to find a set of optimal side-chain resonance assignments that best fit the NMR data. These side-chain resonance assignments are then used to resolve the NOE assignment ambiguity and compute high-resolution protein structures. Tests on five proteins show that NASCA assigns resonances for more than 90% of side-chain protons, and achieves about 80% correct assignments. The final structures computed using the NOE distance restraints assigned by NASCA have backbone RMSD 0.8 – 1.5 Å from the reference structures determined by traditional NMR approaches. PMID:21706248

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

Bolton, Justin; Rzayev, Javid

Polystyrene–poly(methyl methacrylate)–polylactide (PS–PMMA–PLA) triblock bottlebrush copolymer with nearly symmetric volume fractions was synthesized by grafting from a symmetrical triblock backbone and the resulting melt was characterized by scanning electron microscopy and small-angle X-ray scattering. The copolymer backbone was prepared by sequential reversible addition–fragmentation chain transfer (RAFT) polymerization of solketal methacrylate (SM), 2-(bromoisobutyryl)ethyl methacrylate (BIEM), and 5-(trimethylsilyl)-4-pentyn-1-ol methacrylate (TPYM). PMMA branches were grafted by atom transfer radical polymerization from the poly(BIEM) segment, PS branches were grafted by RAFT polymerization from the poly(TPYM) block after installment of the RAFT agents, while PLA side chains were grafted from the deprotected poly(SM) block. Themore » resulting copolymer was found to exhibit a lamellae morphology with a domain spacing of 79 nm. Differential scanning calorimetry analysis indicated that PMMA was preferentially mixing with PS while phase separating from PLA domains.« less

Using NMR chemical shifts to calculate the propensity for structural order and disorder in proteins.

PubMed

Tamiola, Kamil; Mulder, Frans A A

2012-10-01

NMR spectroscopy offers the unique possibility to relate the structural propensities of disordered proteins and loop segments of folded peptides to biological function and aggregation behaviour. Backbone chemical shifts are ideally suited for this task, provided that appropriate reference data are available and idiosyncratic sensitivity of backbone chemical shifts to structural information is treated in a sensible manner. In the present paper, we describe methods to detect structural protein changes from chemical shifts, and present an online tool [ncSPC (neighbour-corrected Structural Propensity Calculator)], which unites aspects of several current approaches. Examples of structural propensity calculations are given for two well-characterized systems, namely the binding of α-synuclein to micelles and light activation of photoactive yellow protein. These examples spotlight the great power of NMR chemical shift analysis for the quantitative assessment of protein disorder at the atomic level, and further our understanding of biologically important problems.

Genus Ranges of Chord Diagrams

PubMed Central

Burns, Jonathan; Jonoska, Nataša; Saito, Masahico

2015-01-01

A chord diagram consists of a circle, called the backbone, with line segments, called chords, whose endpoints are attached to distinct points on the circle. The genus of a chord diagram is the genus of the orientable surface obtained by thickening the backbone to an annulus and attaching bands to the inner boundary circle at the ends of each chord. Variations of this construction are considered here, where bands are possibly attached to the outer boundary circle of the annulus. The genus range of a chord diagram is the genus values over all such variations of surfaces thus obtained from a given chord diagram. Genus ranges of chord diagrams for a fixed number of chords are studied. Integer intervals that can be, and those that cannot be, realized as genus ranges are investigated. Computer calculations are presented, and play a key role in discovering and proving the properties of genus ranges. PMID:26478650

Genus Ranges of Chord Diagrams.

PubMed

Burns, Jonathan; Jonoska, Nataša; Saito, Masahico

2015-04-01

A chord diagram consists of a circle, called the backbone, with line segments, called chords, whose endpoints are attached to distinct points on the circle. The genus of a chord diagram is the genus of the orientable surface obtained by thickening the backbone to an annulus and attaching bands to the inner boundary circle at the ends of each chord. Variations of this construction are considered here, where bands are possibly attached to the outer boundary circle of the annulus. The genus range of a chord diagram is the genus values over all such variations of surfaces thus obtained from a given chord diagram. Genus ranges of chord diagrams for a fixed number of chords are studied. Integer intervals that can be, and those that cannot be, realized as genus ranges are investigated. Computer calculations are presented, and play a key role in discovering and proving the properties of genus ranges.

The temperature-sensitive and attenuation phenotypes conferred by mutations in the influenza virus PB2, PB1, and NP genes are influenced by the species of origin of the PB2 gene in reassortant viruses derived from influenza A/California/07/2009 and A/WSN/33 viruses.

PubMed

Broadbent, Andrew J; Santos, Celia P; Godbout, Rachel A; Subbarao, Kanta

2014-11-01

Live attenuated influenza vaccines in the United States are derived from a human virus that is temperature sensitive (ts), characterized by restricted (≥ 100-fold) replication at 39 °C. The ts genetic signature (ts sig) has been mapped to 5 loci in 3 genes: PB1 (391 E, 581 G, and 661 T), PB2 (265 S), and NP (34 G). However, when transferred into avian and swine influenza viruses, only partial ts and attenuation phenotypes occur. To investigate the reason for this, we introduced the ts sig into the human origin virus A/WSN/33 (WSN), the avian-origin virus A/Vietnam/1203/04 (VN04), and the swine origin triple-reassortant 2009 pandemic H1N1 virus A/California/07/2009 (CA07), which contains gene segments from human, avian, and swine viruses. The VN04(ts sig) and CA07(ts sig) viruses replicated efficiently in Madin-Darby canine kidney (MDCK) cells at 39 °C, but the replication of WSN(ts sig) was restricted ≥ 100-fold compared to that at 33 °C. Reassortant CA07(ts sig) viruses were generated with individual polymerase gene segments from WSN, and vice versa. Only ts sig viruses with a PB2 gene segment derived from WSN were restricted in replication ≥ 100-fold at 39 °C. In ferrets, the CA07(ts sig) virus replicated in the upper and lower respiratory tract, but the replication of a reassortant CA07(ts sig) virus with a WSN PB2 gene was severely restricted in the lungs. Taken together, these data suggest that the origin of the PB2 gene segment influences the ts phenotype in vitro and attenuation in vivo. This could have implications for the design of novel live vaccines against animal origin influenza viruses. Live attenuated influenza vaccines (LAIVs) on temperature-sensitive (ts) backbones derived from animal origin influenza viruses are being sought for use in the poultry and swine industries and to protect people against animal origin influenza. However, inserting the ts genetic signature from a licensed LAIV backbone fails to fully attenuate these viruses. Our data indicate this is associated with the presence of a PB2 gene segment derived from an avian influenza virus. We show that a reassortant 2009 pandemic H1N1 virus with the ts signature from a licensed LAIV donor virus is ts in vitro and attenuated in vivo when the PB2 gene is derived from a human origin virus but not from an avian virus. Our study provides information that could benefit the rational design of alternative LAIV backbones against animal origin influenza viruses. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

The Temperature-Sensitive and Attenuation Phenotypes Conferred by Mutations in the Influenza Virus PB2, PB1, and NP Genes Are Influenced by the Species of Origin of the PB2 Gene in Reassortant Viruses Derived from Influenza A/California/07/2009 and A/WSN/33 Viruses

PubMed Central

Broadbent, Andrew J.; Santos, Celia P.; Godbout, Rachel A.

2014-01-01

ABSTRACT Live attenuated influenza vaccines in the United States are derived from a human virus that is temperature sensitive (ts), characterized by restricted (≥100-fold) replication at 39°C. The ts genetic signature (ts sig) has been mapped to 5 loci in 3 genes: PB1 (391E, 581G, and 661T), PB2 (265S), and NP (34G). However, when transferred into avian and swine influenza viruses, only partial ts and attenuation phenotypes occur. To investigate the reason for this, we introduced the ts sig into the human origin virus A/WSN/33 (WSN), the avian-origin virus A/Vietnam/1203/04 (VN04), and the swine origin triple-reassortant 2009 pandemic H1N1 virus A/California/07/2009 (CA07), which contains gene segments from human, avian, and swine viruses. The VN04ts sig and CA07ts sig viruses replicated efficiently in Madin-Darby canine kidney (MDCK) cells at 39°C, but the replication of WSNts sig was restricted ≥100-fold compared to that at 33°C. Reassortant CA07ts sig viruses were generated with individual polymerase gene segments from WSN, and vice versa. Only ts sig viruses with a PB2 gene segment derived from WSN were restricted in replication ≥100-fold at 39°C. In ferrets, the CA07ts sig virus replicated in the upper and lower respiratory tract, but the replication of a reassortant CA07ts sig virus with a WSN PB2 gene was severely restricted in the lungs. Taken together, these data suggest that the origin of the PB2 gene segment influences the ts phenotype in vitro and attenuation in vivo. This could have implications for the design of novel live vaccines against animal origin influenza viruses. IMPORTANCE Live attenuated influenza vaccines (LAIVs) on temperature-sensitive (ts) backbones derived from animal origin influenza viruses are being sought for use in the poultry and swine industries and to protect people against animal origin influenza. However, inserting the ts genetic signature from a licensed LAIV backbone fails to fully attenuate these viruses. Our data indicate this is associated with the presence of a PB2 gene segment derived from an avian influenza virus. We show that a reassortant 2009 pandemic H1N1 virus with the ts signature from a licensed LAIV donor virus is ts in vitro and attenuated in vivo when the PB2 gene is derived from a human origin virus but not from an avian virus. Our study provides information that could benefit the rational design of alternative LAIV backbones against animal origin influenza viruses. PMID:25122786

Predicting the helix packing of globular proteins by self-correcting distance geometry.

PubMed

Mumenthaler, C; Braun, W

1995-05-01

A new self-correcting distance geometry method for predicting the three-dimensional structure of small globular proteins was assessed with a test set of 8 helical proteins. With the knowledge of the amino acid sequence and the helical segments, our completely automated method calculated the correct backbone topology of six proteins. The accuracy of the predicted structures ranged from 2.3 A to 3.1 A for the helical segments compared to the experimentally determined structures. For two proteins, the predicted constraints were not restrictive enough to yield a conclusive prediction. The method can be applied to all small globular proteins, provided the secondary structure is known from NMR analysis or can be predicted with high reliability.

KSC-07pd1426

NASA Image and Video Library

2007-06-08

KENNEDY SPACE CENTER, FLA. -- Photographers crowd around the countdown clock and flag post near the NASA News Center to capture the successful on-time launch of Space Shuttle Atlantis from Launch Pad 39A at 7:38:04 p.m. EDT on mission STS-117. The shuttle is delivering a new segment to the starboard side of the International Space Station's backbone, known as the truss. Three spacewalks are planned to install the S3/S4 truss segment, deploy a set of solar arrays and prepare them for operation. STS-117 is the 118th space shuttle flight, the 21st flight to the station, the 28th flight for Atlantis and the first of four flights planned for 2007. Photo credit: NASA/Jim Grossmann

KSC-07pd1454

NASA Image and Video Library

2007-06-08

KENNEDY SPACE CENTER, FLA. -- Twin columns of fire rocket the Space Shuttle Atlantis into the sky above Kennedy Space Center. Liftoff of Atlantis on mission STS-117 to the International Space Station from Launch Pad 39A was on-time at 7:38:04 p.m. EDT. The shuttle is delivering a new segment to the starboard side of the International Space Station's backbone, known as the truss. Three spacewalks are planned to install the S3/S4 truss segment, deploy a set of solar arrays and prepare them for operation. STS-117 is the 118th space shuttle flight, the 21st flight to the station, the 28th flight for Atlantis and the first of four flights planned for 2007. Photo credit: NASA/Chris Lynch

KSC-07pd1443

NASA Image and Video Library

2007-06-08

KENNEDY SPACE CENTER, FLA. -- Branches and leaves frame Space Shuttle Atlantis as it lifts off Launch Pad 39A on mission STS-117 to the International Space Station. Liftoff was on-time at 7:38:04 p.m. EDT. The shuttle is delivering a new segment to the starboard side of the International Space Station's backbone, known as the truss. Three spacewalks are planned to install the S3/S4 truss segment, deploy a set of solar arrays and prepare them for operation. STS-117 is the 118th space shuttle flight, the 21st flight to the station, the 28th flight for Atlantis and the first of four flights planned for 2007. Photo credit: NASA/Sandra Joseph, Robert Murray and Tom Farrar

KSC-07pd1427

NASA Image and Video Library

2007-06-08

KENNEDY SPACE CENTER, FLA. -- Trailing smoke and fire, Space Shuttle Atlantis roars into the sky past the U.S. flag on its journey to the International Space Station on mission STS-117. Liftoff was on-time at 7:38:04 p.m. EDT . The shuttle is delivering a new segment to the starboard side of the International Space Station's backbone, known as the truss. Three spacewalks are planned to install the S3/S4 truss segment, deploy a set of solar arrays and prepare them for operation. STS-117 is the 118th space shuttle flight, the 21st flight to the station, the 28th flight for Atlantis and the first of four flights planned for 2007. Photo credit: NASA/Ken Thornsley

KSC-07pd1438

NASA Image and Video Library

2007-06-08

KENNEDY SPACE CENTER, FLA. -- Trailing fire, Space Shuttle Atlantis roars toward the sky on mission STS-117. Below it can be seen the lighting mast atop the fixed service structure. Liftoff from Launch Pad 39A was on-time at 7:38:04 p.m. EDT. The shuttle is delivering a new segment to the starboard side of the International Space Station's backbone, known as the truss. Three spacewalks are planned to install the S3/S4 truss segment, deploy a set of solar arrays and prepare them for operation. STS-117 is the 118th space shuttle flight, the 21st flight to the station, the 28th flight for Atlantis and the first of four flights planned for 2007. Photo courtesy of Reuters.

KSC-07pd1429

NASA Image and Video Library

2007-06-08

KENNEDY SPACE CENTER, FLA. -- Trailing fire and smoke, Space Shuttle Atlantis races into the sky toward a rendezvous with the International Space Station on mission STS-117. Liftoff from Launch Pad 39A was on-time at 7:38:04 p.m. EDT. The shuttle is delivering a new segment to the starboard side of the International Space Station's backbone, known as the truss. Three spacewalks are planned to install the S3/S4 truss segment, deploy a set of solar arrays and prepare them for operation. STS-117 is the 118th space shuttle flight, the 21st flight to the station, the 28th flight for Atlantis and the first of four flights planned for 2007. Photo credit: NASA/Ken Thornsley

Optimal trajectories for the aeroassisted flight experiment. Part 4: Data, tables, and graphs

NASA Technical Reports Server (NTRS)

Miele, A.; Wang, T.; Lee, W. Y.; Wang, H.; Wu, G. D.

1989-01-01

The determination of optimal trajectories for the aeroassisted flight experiment (AFE) is discussed. Data, tables, and graphs relative to the following transfers are presented: (IA) indirect ascent to a 178 NM perigee via a 197 NM apogee; and (DA) direct ascent to a 178 NM apogee. For both transfers, two cases are investigated: (1) the bank angle is continuously variable; and (2) the trajectory is divided into segments along which the bank angle is constant. For case (2), the following subcases are studied: two segments, three segments, four segments, and five segments; because the time duration of each segment is optimized, the above subcases involve four, six, eight, and ten parameters, respectively. Presented here are systematic data on a total of ten optimal trajectories (OT), five for Transfer IA and five for Transfer DA. For comparison purposes and only for Transfer IA, a five-segment reference trajectory RT is also considered.

Generation of a reassortant avian influenza virus H5N2 vaccine strain capable of protecting chickens against infection with Egyptian H5N1 and H9N2 viruses.

PubMed

Kandeil, Ahmed; Moatasim, Yassmin; Gomaa, Mokhtar R; Shehata, Mahmoud M; El-Shesheny, Rabeh; Barakat, Ahmed; Webby, Richard J; Ali, Mohamed A; Kayali, Ghazi

2016-01-04

Avian influenza H5N1 viruses have been enzootic in Egyptian poultry since 2006. Avian influenza H9N2 viruses which have been circulating in Egyptian poultry since 2011 showed high replication rates in embryonated chicken eggs and mammalian cells. To investigate which gene segment was responsible for increasing replication, we constructed reassortant influenza viruses using the low pathogenic H1N1 PR8 virus as backbone and included individual genes from A/chicken/Egypt/S4456B/2011(H9N2) virus. Then, we invested this finding to improve a PR8-derived H5N1 influenza vaccine strain by incorporation of the NA segment of H9N2 virus instead of the NA of H5N1. The growth properties of this virus and several other forms of reassortant H5 viruses were compared. Finally, we tested the efficacy of this reassortant vaccine strain in chickens. We observed an increase in replication for a reassortant virus expressing the neuraminidase gene (N2) of H9N2 virus relative to that of either parental viruses or reassortant PR8 viruses expressing other genes. Then, we generated an H5N2 vaccine strain based on the H5 from an Egyptian H5N1 virus and the N2 from an Egyptian H9N2 virus on a PR8 backbone. This strain had better replication rates than an H5N2 reassortant strain on an H9N2 backbone and an H5N1 reassortant on a PR8 backbone. This virus was then used to develop a killed, oil-emulsion vaccine and tested for efficacy against H5N1 and H9N2 viruses in chickens. Results showed that this vaccine was immunogenic and reduced mortality and shedding. Our findings suggest that an inactivated PR8-derived H5N2 influenza vaccine is efficacious in poultry against H5N1 and H9N2 viruses and the vaccine seed replicates at a high rate thus improving vaccine production. Copyright © 2015 Elsevier Ltd. All rights reserved.

Information Extraction of High Resolution Remote Sensing Images Based on the Calculation of Optimal Segmentation Parameters

PubMed Central

Zhu, Hongchun; Cai, Lijie; Liu, Haiying; Huang, Wei

2016-01-01

Multi-scale image segmentation and the selection of optimal segmentation parameters are the key processes in the object-oriented information extraction of high-resolution remote sensing images. The accuracy of remote sensing special subject information depends on this extraction. On the basis of WorldView-2 high-resolution data, the optimal segmentation parameters methodof object-oriented image segmentation and high-resolution image information extraction, the following processes were conducted in this study. Firstly, the best combination of the bands and weights was determined for the information extraction of high-resolution remote sensing image. An improved weighted mean-variance method was proposed andused to calculatethe optimal segmentation scale. Thereafter, the best shape factor parameter and compact factor parameters were computed with the use of the control variables and the combination of the heterogeneity and homogeneity indexes. Different types of image segmentation parameters were obtained according to the surface features. The high-resolution remote sensing images were multi-scale segmented with the optimal segmentation parameters. Ahierarchical network structure was established by setting the information extraction rules to achieve object-oriented information extraction. This study presents an effective and practical method that can explain expert input judgment by reproducible quantitative measurements. Furthermore the results of this procedure may be incorporated into a classification scheme. PMID:27362762

Information Extraction of High Resolution Remote Sensing Images Based on the Calculation of Optimal Segmentation Parameters.

PubMed

Zhu, Hongchun; Cai, Lijie; Liu, Haiying; Huang, Wei

2016-01-01

Multi-scale image segmentation and the selection of optimal segmentation parameters are the key processes in the object-oriented information extraction of high-resolution remote sensing images. The accuracy of remote sensing special subject information depends on this extraction. On the basis of WorldView-2 high-resolution data, the optimal segmentation parameters methodof object-oriented image segmentation and high-resolution image information extraction, the following processes were conducted in this study. Firstly, the best combination of the bands and weights was determined for the information extraction of high-resolution remote sensing image. An improved weighted mean-variance method was proposed andused to calculatethe optimal segmentation scale. Thereafter, the best shape factor parameter and compact factor parameters were computed with the use of the control variables and the combination of the heterogeneity and homogeneity indexes. Different types of image segmentation parameters were obtained according to the surface features. The high-resolution remote sensing images were multi-scale segmented with the optimal segmentation parameters. Ahierarchical network structure was established by setting the information extraction rules to achieve object-oriented information extraction. This study presents an effective and practical method that can explain expert input judgment by reproducible quantitative measurements. Furthermore the results of this procedure may be incorporated into a classification scheme.

Development of optimized segmentation map in dual energy computed tomography

NASA Astrophysics Data System (ADS)

Yamakawa, Keisuke; Ueki, Hironori

2012-03-01

Dual energy computed tomography (DECT) has been widely used in clinical practice and has been particularly effective for tissue diagnosis. In DECT the difference of two attenuation coefficients acquired by two kinds of X-ray energy enables tissue segmentation. One problem in conventional DECT is that the segmentation deteriorates in some cases, such as bone removal. This is due to two reasons. Firstly, the segmentation map is optimized without considering the Xray condition (tube voltage and current). If we consider the tube voltage, it is possible to create an optimized map, but unfortunately we cannot consider the tube current. Secondly, the X-ray condition is not optimized. The condition can be set empirically, but this means that the optimized condition is not used correctly. To solve these problems, we have developed methods for optimizing the map (Method-1) and the condition (Method-2). In Method-1, the map is optimized to minimize segmentation errors. The distribution of the attenuation coefficient is modeled by considering the tube current. In Method-2, the optimized condition is decided to minimize segmentation errors depending on tube voltagecurrent combinations while keeping the total exposure constant. We evaluated the effectiveness of Method-1 by performing a phantom experiment under the fixed condition and of Method-2 by performing a phantom experiment under different combinations calculated from the total exposure constant. When Method-1 was followed with Method-2, the segmentation error was reduced from 37.8 to 13.5 %. These results demonstrate that our developed methods can achieve highly accurate segmentation while keeping the total exposure constant.

Retinal imaging in uveitis

PubMed Central

Gupta, Vishali; Al-Dhibi, Hassan A.; Arevalo, J. Fernando

2014-01-01

Ancillary investigations are the backbone of uveitis workup for posterior segment inflammations. They help in establishing the differential diagnosis and making certain diagnosis by ruling out certain pathologies and are a useful aid in monitoring response to therapy during follow-up. These investigations include fundus photography including ultra wide field angiography, fundus autofluorescence imaging, fluorescein angiography, optical coherence tomography and multimodal imaging. This review aims to be an overview describing the role of these retinal investigations for posterior uveitis. PMID:24843301

Energies and 2'-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations.

PubMed

Mládek, Arnošt; Banáš, Pavel; Jurečka, Petr; Otyepka, Michal; Zgarbová, Marie; Šponer, Jiří

2014-01-14

Sugar-phosphate backbone is an electronically complex molecular segment imparting RNA molecules high flexibility and architectonic heterogeneity necessary for their biological functions. The structural variability of RNA molecules is amplified by the presence of the 2'-hydroxyl group, capable of forming multitude of intra- and intermolecular interactions. Bioinformatics studies based on X-ray structure database revealed that RNA backbone samples at least 46 substates known as rotameric families. The present study provides a comprehensive analysis of RNA backbone conformational preferences and 2'-hydroxyl group orientations. First, we create a benchmark database of estimated CCSD(T)/CBS relative energies of all rotameric families and test performance of dispersion-corrected DFT-D3 methods and molecular mechanics in vacuum and in continuum solvent. The performance of the DFT-D3 methods is in general quite satisfactory. The B-LYP-D3 method provides the best trade-off between accuracy and computational demands. B3-LYP-D3 slightly outperforms the new PW6B95-D3 and MPW1B95-D3 and is the second most accurate density functional of the study. The best agreement with CCSD(T)/CBS is provided by DSD-B-LYP-D3 double-hybrid functional, although its large-scale applications may be limited by high computational costs. Molecular mechanics does not reproduce the fine energy differences between the RNA backbone substates. We also demonstrate that the differences in the magnitude of the hyperconjugation effect do not correlate with the energy ranking of the backbone conformations. Further, we investigated the 2'-hydroxyl group orientation preferences. For all families, we conducted a QM and MM hydroxyl group rigid scan in gas phase and solvent. We then carried out set of explicit solvent MD simulations of folded RNAs and analyze 2'-hydroxyl group orientations of different backbone families in MD. The solvent energy profiles determined primarily by the sugar pucker match well with the distribution data derived from the simulations. The QM and MM energy profiles predict the same 2'-hydroxyl group orientation preferences. Finally, we demonstrate that the high energy of unfavorable and rarely sampled 2'-hydroxyl group orientations can be attributed to clashes between occupied orbitals.

Finite grade pheromone ant colony optimization for image segmentation

NASA Astrophysics Data System (ADS)

Yuanjing, F.; Li, Y.; Liangjun, K.

2008-06-01

By combining the decision process of ant colony optimization (ACO) with the multistage decision process of image segmentation based on active contour model (ACM), an algorithm called finite grade ACO (FACO) for image segmentation is proposed. This algorithm classifies pheromone into finite grades and updating of the pheromone is achieved by changing the grades and the updated quantity of pheromone is independent from the objective function. The algorithm that provides a new approach to obtain precise contour is proved to converge to the global optimal solutions linearly by means of finite Markov chains. The segmentation experiments with ultrasound heart image show the effectiveness of the algorithm. Comparing the results for segmentation of left ventricle images shows that the ACO for image segmentation is more effective than the GA approach and the new pheromone updating strategy appears good time performance in optimization process.

Conformational analysis investigation into the influence of nano-porosity of ultra-permeable ultra-selective polyimides on its diffusivity as potential membranes for use in the "green" separation of natural gases

NASA Astrophysics Data System (ADS)

Madkour, Tarek M.

2013-08-01

Nano-porous polymers of intrinsic microporosity, PIM, have exhibited excellent permeability and selectivity characteristics that could be utilized in an environmentally friendly gas separation process. A full understanding of the mechanism through which these membranes effectively and selectively allow for the permeation of specific gases will lead to further development of these membranes. Three factors obviously influenced the conformational behavior of these polymers, which are the presence of electronegative atoms, the presence of non-linearity in the polymeric backbones (backbone kinks) and the presence of bulky side groups on the polymeric chains. The dipole moment increased sharply with the presence of backbone kinks more than any other factor. Replacing the fluorine atoms with bulky alkyl groups didn't influence the dipole moment greatly indicating that the size of the side chains had much less dramatic influence on the dipole moment than having a bent backbone. Similarly, the presence of the backbone kinks in the polymeric chains influenced the polymeric chains to assume less extended configuration causing the torsional angles around the interconnecting bonds unable to cross the high potential energy barriers. The presence of the bulky side groups also caused the energy barriers of the cis-configurations to increase dramatically, which prevented the polymeric segments from experiencing full rotation about the connecting bonds. For these polymers, it was clear that the fully extended configurations are the preferred configurations in the absence of strong electronegative atoms, backbones kinks or bulky side groups. The addition of any of these factors to the polymeric structures resulted in the polymeric chains being forced to assume less extended configurations. Rather interestingly, the length or bulkiness of the side groups didn't affect the end-to-end distance distribution to a great deal since the presence of quite large bulky side chain such as the pentyl group has caused the polymeric chains to revert back to the fully extended configurations possibly due to the quite high potential energy barriers that the chains have to cross to reach the less extended configurational states.

Proline-Rich Salivary Proteins Have Extended Conformations

PubMed Central

Boze, Hélène; Marlin, Thérèse; Durand, Dominique; Pérez, Javier; Vernhet, Aude; Canon, Francis; Sarni-Manchado, Pascale; Cheynier, Véronique; Cabane, Bernard

2010-01-01

Abstract Three basic proline-rich salivary proteins have been produced through the recombinant route. IB5 is a small basic proline-rich protein that is involved in the binding of plant tannins in the oral cavity. II-1 is a larger protein with a closely related backbone; it is glycosylated, and it is also able to bind plant tannins. II-1ng has the same polypeptidic backbone as II-1, but it is not glycosylated. Small angle x-ray scattering experiments on dilute solutions of these proteins confirm that they are intrinsically disordered. IB5 and II-1ng can be described through a chain model including a persistence length and cross section. The measured radii of gyration (Rg = 27.9 and 41.0 ± 1 Å respectively) and largest distances (rmax = 110 and 155 ± 10 Å respectively) show that their average conformations are rather extended. The length of the statistical segment (twice the persistence length) is b = 30 Å, which is larger than the usual value (18 Å − 20 Å) for unstructured polypeptide chains. These characteristics are presumably related to the presence of polyproline helices within the polypeptidic backbones. For both proteins, the radius of gyration of the chain cross-section is Rc = 2.7 ± 0.2Å. The glycosylated protein II-1 has similar conformations but the presence of large polyoside sidegroups yields the structure of a branched macromolecule with the same hydrophobic backbone and hydrophilic branches. It is proposed that the unusually extended conformations of these proteins in solution facilitate the capture of plant tannins in the oral cavity. PMID:20643086

Vanishing amplitude of backbone dynamics causes a true protein dynamical transition: H2 NMR studies on perdeuterated C-phycocyanin

NASA Astrophysics Data System (ADS)

Kämpf, Kerstin; Kremmling, Beke; Vogel, Michael

2014-03-01

Using a combination of H2 nuclear magnetic resonance (NMR) methods, we study internal rotational dynamics of the perdeuterated protein C-phycocyanin (CPC) in dry and hydrated states over broad temperature and dynamic ranges with high angular resolution. Separating H2 NMR signals from methyl deuterons, we show that basically all backbone deuterons exhibit highly restricted motion occurring on time scales faster than microseconds. The amplitude of this motion increases when a hydration shell exists, while it decreases upon cooling and vanishes near 175 K. We conclude that the vanishing of the highly restricted motion marks a dynamical transition, which is independent of the time window and of a fundamental importance. This conclusion is supported by results from experimental and computational studies of the proteins myoglobin and elastin. In particular, we argue based on findings in molecular dynamics simulations that the behavior of the highly restricted motion of proteins at the dynamical transition resembles that of a characteristic secondary relaxation of liquids at the glass transition, namely the nearly constant loss. Furthermore, H2 NMR studies on perdeuterated CPC reveal that, in addition to highly restricted motion, small fractions of backbone segments exhibit weakly restricted dynamics when temperature and hydration are sufficiently high.

Inventory of system operations data collection and use in the Virginia Department of Transportation.

DOT National Transportation Integrated Search

2006-01-01

Accurate data describing the status of the transportation network is the backbone of system operations management. Without accurate data, traffic engineers cannot optimize signal phasing and timing, effective incident management cannot be undertaken,...

Optimal segmentation and packaging process

DOEpatents

Kostelnik, Kevin M.; Meservey, Richard H.; Landon, Mark D.

1999-01-01

A process for improving packaging efficiency uses three dimensional, computer simulated models with various optimization algorithms to determine the optimal segmentation process and packaging configurations based on constraints including container limitations. The present invention is applied to a process for decontaminating, decommissioning (D&D), and remediating a nuclear facility involving the segmentation and packaging of contaminated items in waste containers in order to minimize the number of cuts, maximize packaging density, and reduce worker radiation exposure. A three-dimensional, computer simulated, facility model of the contaminated items are created. The contaminated items are differentiated. The optimal location, orientation and sequence of the segmentation and packaging of the contaminated items is determined using the simulated model, the algorithms, and various constraints including container limitations. The cut locations and orientations are transposed to the simulated model. The contaminated items are actually segmented and packaged. The segmentation and packaging may be simulated beforehand. In addition, the contaminated items may be cataloged and recorded.

Knowledge-Guided Docking of WW Domain Proteins and Flexible Ligands

NASA Astrophysics Data System (ADS)

Lu, Haiyun; Li, Hao; Banu Bte Sm Rashid, Shamima; Leow, Wee Kheng; Liou, Yih-Cherng

Studies of interactions between protein domains and ligands are important in many aspects such as cellular signaling. We present a knowledge-guided approach for docking protein domains and flexible ligands. The approach is applied to the WW domain, a small protein module mediating signaling complexes which have been implicated in diseases such as muscular dystrophy and Liddle’s syndrome. The first stage of the approach employs a substring search for two binding grooves of WW domains and possible binding motifs of peptide ligands based on known features. The second stage aligns the ligand’s peptide backbone to the two binding grooves using a quasi-Newton constrained optimization algorithm. The backbone-aligned ligands produced serve as good starting points to the third stage which uses any flexible docking algorithm to perform the docking. The experimental results demonstrate that the backbone alignment method in the second stage performs better than conventional rigid superposition given two binding constraints. It is also shown that using the backbone-aligned ligands as initial configurations improves the flexible docking in the third stage. The presented approach can also be applied to other protein domains that involve binding of flexible ligand to two or more binding sites.

Structural test of the parameterized-backbone method for protein design.

PubMed

Plecs, Joseph J; Harbury, Pehr B; Kim, Peter S; Alber, Tom

2004-09-03

Designing new protein folds requires a method for simultaneously optimizing the conformation of the backbone and the side-chains. One approach to this problem is the use of a parameterized backbone, which allows the systematic exploration of families of structures. We report the crystal structure of RH3, a right-handed, three-helix coiled coil that was designed using a parameterized backbone and detailed modeling of core packing. This crystal structure was determined using another rationally designed feature, a metal-binding site that permitted experimental phasing of the X-ray data. RH3 adopted the intended fold, which has not been observed previously in biological proteins. Unanticipated structural asymmetry in the trimer was a principal source of variation within the RH3 structure. The sequence of RH3 differs from that of a previously characterized right-handed tetramer, RH4, at only one position in each 11 amino acid sequence repeat. This close similarity indicates that the design method is sensitive to the core packing interactions that specify the protein structure. Comparison of the structures of RH3 and RH4 indicates that both steric overlap and cavity formation provide strong driving forces for oligomer specificity.

Dual-threshold segmentation using Arimoto entropy based on chaotic bee colony optimization

NASA Astrophysics Data System (ADS)

Li, Li

2018-03-01

In order to extract target from complex background more quickly and accurately, and to further improve the detection effect of defects, a method of dual-threshold segmentation using Arimoto entropy based on chaotic bee colony optimization was proposed. Firstly, the method of single-threshold selection based on Arimoto entropy was extended to dual-threshold selection in order to separate the target from the background more accurately. Then intermediate variables in formulae of Arimoto entropy dual-threshold selection was calculated by recursion to eliminate redundant computation effectively and to reduce the amount of calculation. Finally, the local search phase of artificial bee colony algorithm was improved by chaotic sequence based on tent mapping. The fast search for two optimal thresholds was achieved using the improved bee colony optimization algorithm, thus the search could be accelerated obviously. A large number of experimental results show that, compared with the existing segmentation methods such as multi-threshold segmentation method using maximum Shannon entropy, two-dimensional Shannon entropy segmentation method, two-dimensional Tsallis gray entropy segmentation method and multi-threshold segmentation method using reciprocal gray entropy, the proposed method can segment target more quickly and accurately with superior segmentation effect. It proves to be an instant and effective method for image segmentation.

KSC-06pd1670

NASA Image and Video Library

2006-07-26

KENNEDY SPACE CENTER, FLA. - Shortly after midnight, the payload canister makes a slow journey to Launch Pad 39B. Inside the canister is the payload for Atlantis and mission STS-115, the Port 3/4 truss segment with two large solar arrays. The payload changeout room provides an environmentally clean or "white room" condition in which to receive a payload transferred from a protective payload canister. After the shuttle arrives at the pad, the rotating service structure will close around it and the payload will then be transferred into Atlantis' payload bay. Atlantis' launch window begins Aug. 28. During its 11-day mission to the International Space Station, the STS-115 crew of six astronauts will install the truss, a 17-ton segment of the space station's truss backbone. Photo credit: NASA/George Shelton

KSC-07pd1450

NASA Image and Video Library

2007-06-08

KENNEDY SPACE CENTER, FLA. -- Smoke and steam billow across Launch Pad 39A as Space Shuttle Atlantis, trailing columns of fire from the solid rocket boosters, hurtles into the sky on mission STS-117 to the International Space Station. Liftoff was on-time at 7:38:04 p.m. EDT. The shuttle is delivering a new segment to the starboard side of the International Space Station's backbone, known as the truss. Three spacewalks are planned to install the S3/S4 truss segment, deploy a set of solar arrays and prepare them for operation. STS-117 is the 118th space shuttle flight, the 21st flight to the station, the 28th flight for Atlantis and the first of four flights planned for 2007. Photo courtesy of Nikon/Scott Andrews

KSC-07pd1439

NASA Image and Video Library

2007-06-08

KENNEDY SPACE CENTER, FLA. -- Viewed from the top of the Vehicle Assembly Building, Space Shuttle Atlantis is a small tip on the trailing column of fire and smoke after launching on mission STS-117. Liftoff from Launch Pad 39A was on-time at 7:38:04 p.m. EDT. The shuttle is delivering a new segment to the starboard side of the International Space Station's backbone, known as the truss. Three spacewalks are planned to install the S3/S4 truss segment, deploy a set of solar arrays and prepare them for operation. STS-117 is the 118th space shuttle flight, the 21st flight to the station, the 28th flight for Atlantis and the first of four flights planned for 2007. Photo courtesy of Nikon/Scott Andrews

DNA motion capture reveals the mechanical properties of DNA at the mesoscale.

PubMed

Price, Allen C; Pilkiewicz, Kevin R; Graham, Thomas G W; Song, Dan; Eaves, Joel D; Loparo, Joseph J

2015-05-19

Single-molecule studies probing the end-to-end extension of long DNAs have established that the mechanical properties of DNA are well described by a wormlike chain force law, a polymer model where persistence length is the only adjustable parameter. We present a DNA motion-capture technique in which DNA molecules are labeled with fluorescent quantum dots at specific sites along the DNA contour and their positions are imaged. Tracking these positions in time allows us to characterize how segments within a long DNA are extended by flow and how fluctuations within the molecule are correlated. Utilizing a linear response theory of small fluctuations, we extract elastic forces for the different, ∼2-μm-long segments along the DNA backbone. We find that the average force-extension behavior of the segments can be well described by a wormlike chain force law with an anomalously small persistence length. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Regulating Molecular Aggregations of Polymers via Ternary Copolymerization Strategy for Efficient Solar Cells.

PubMed

Wang, Qian; Wang, Yingying; Zheng, Wei; Shahid, Bilal; Qiu, Meng; Wang, Di; Zhu, Dangqiang; Yang, Renqiang

2017-09-20

For many high-performance photovoltaic materials in polymer solar cells (PSCs), the active layers usually need to be spin-coated at high temperature due to the strong intermolecular aggregation of donor polymers, which is unfavorable in device repeatability and large-scale PSC printing. In this work, we adopted a ternary copolymerization strategy to regulate polymer solubility and molecular aggregation. A series of D-A 1 -D-A 2 random polymers based on different acceptors, strong electron-withdrawing unit ester substituted thieno[3,4-b]thiophene (TT-E), and highly planar dithiazole linked TT-E (DTzTT) were constructed to realize the regulation of molecular aggregation and simplification of device fabrication. The results showed that as the relative proportion of TT-E segment in the backbone increased, the absorption evidently red-shifted with a gradually decreased aggregation in solution, eventually leading to the active layers that can be fabricated at low temperature. Furthermore, due to the excellent phase separation and low recombination, the optimized solar cells based on the terpolymer P1 containing 30% of TT-E segment exhibit high power conversion efficiency (PCE) of 9.09% with a significantly enhanced fill factor up to 72.86%. Encouragingly, the photovoltaic performance is insensitive to the fabrication temperature of the active layer, and it still could maintain high PCE of 8.82%, even at room temperature. This work not only develops the highly efficient photovoltaic materials for low temperature processed PSCs through ternary copolymerization strategy but also preliminarily constructs the relationship between aggregation and photovoltaic performance.

Backbone conformational preferences of an intrinsically disordered protein in solution.

PubMed

Espinoza-Fonseca, L Michel; Ilizaliturri-Flores, Ian; Correa-Basurto, José

2012-06-01

We have performed a 4-μs molecular dynamics simulation to investigate the native conformational preferences of the intrinsically disordered kinase-inducible domain (KID) of the transcription factor CREB in solution. There is solid experimental evidence showing that KID does not possess a bound-like structure in solution; however, it has been proposed that coil-to-helix transitions upon binding to its binding partner (CBP) are template-driven. While these studies indicate that IDPs possess a bias towards the bound structure, they do not provide direct evidence on the time-dependent conformational preferences of IDPs in atomic detail. Our simulation captured intrinsic conformational characteristics of KID that are in good agreement with experimental data such as a very small percentage of helical structure in its segment α(B) and structural disorder in solution. We used dihedral principal component analysis dPCA to map the conformations of KID in the microsecond timescale. By using principal components as reaction coordinates, we further constructed dPCA-based free energy landscapes of KID. Analysis of the free energy landscapes showed that KID is best characterized as a conformational ensemble of rapidly interconverting conformations. Interestingly, we found that despite the conformational heterogeneity of the backbone and the absence of substantial secondary structure, KID does not randomly sample the conformational space in solution: analysis of the (Φ, Ψ) dihedral angles showed that several individual residues of KID possess a strong bias toward the helical region of the Ramachandran plot. We suggest that the intrinsic conformational preferences of KID provide a bias toward the folded state without having to populate bound-like conformations before binding. Furthermore, we argue that these conformational preferences do not represent actual structural constraints which drive binding through a single pathway, which allows for specific interactions with multiple binding partners. Based on this evidence, we propose that the backbone conformational preferences of KID provide a thermodynamic advantage for folding and binding without negatively affecting the kinetics of binding. We further discuss the relation of our results to previous studies to rationalize the functional implications of the conformational preferences of IDPs, such as the optimization of structural disorder in protein-protein interactions. This study illustrates the importance in obtaining atomistic information of intrinsically disordered proteins in real time to reveal functional features arising from their complex conformational space.

Design and Optimization of the SPOT Primary Mirror Segment

NASA Technical Reports Server (NTRS)

Budinoff, Jason G.; Michaels, Gregory J.

2005-01-01

The 3m Spherical Primary Optical Telescope (SPOT) will utilize a single ring of 0.86111 point-to-point hexagonal mirror segments. The f2.85 spherical mirror blanks will be fabricated by the same replication process used for mass-produced commercial telescope mirrors. Diffraction-limited phasing will require segment-to-segment radius of curvature (ROC) variation of approx.1 micron. Low-cost, replicated segment ROC variations are estimated to be almost 1 mm, necessitating a method for segment ROC adjustment & matching. A mechanical architecture has been designed that allows segment ROC to be adjusted up to 400 microns while introducing a minimum figure error, allowing segment-to-segment ROC matching. A key feature of the architecture is the unique back profile of the mirror segments. The back profile of the mirror was developed with shape optimization in MSC.Nastran(TradeMark) using optical performance response equations written with SigFit. A candidate back profile was generated which minimized ROC-adjustment-induced surface error while meeting the constraints imposed by the fabrication method. Keywords: optimization, radius of curvature, Pyrex spherical mirror, Sigfit

Local Structure and Ion Transport in Glassy Poly(ethylene oxide styrene) Copolymers

NASA Astrophysics Data System (ADS)

Yang, Han-Chang; Mays, Jimmy; Sokolov, Alexei P.; Winey, Karen I.

2014-03-01

Polymer electrolytes have attracted attention for a wide variety of applications in energy production such as lithium-ion batteries and fuel cells. The concept of free volume provides important information about ion mobility and chain dynamics in the polymer matrix. Researchers have recently demonstrated that ion transport in glassy polymer can be improved by designing a system with high free volume. We have studied the effect of temperature and humidity on the intermolecular correlations of poly(ethylene oxide styrene-block-styrene) (PEOSt- b-St) block copolymer and poly(ethylene oxide styrene) (PEOSt) homopolymer using in situ multi-angle x-ray scattering across a wide range of scattering angles (q = 0.007-1.5 Å-1) . An increase in backbone-to-backbone distance is observed, indicating an increase in free volume between different polymer main chains. Structural characterization of the polymer segments will be discussed together with conductivity and dielectric results to better understand the ion transport mechanism in the local environment of the polymer system. Department of Chemistry, University of Tennessee.

Correlating morphology to dc conductivity in polymerized ionic liquids

NASA Astrophysics Data System (ADS)

Iacob, Ciprian; Matusmoto, Atsushi; Inoue, Tadashi; Runt, James

Polymerized ionic liquids (PILs) combine the attractive mechanical characteristics of polymers and unique physico-chemical properties of low molecular weight ionic liquids in the same material. PILs have shown remarkable advantages when employed in electrochemical devices such as dye-sensitized solar cells and lithium batteries, among others. Understanding their ionic transport mechanism is the key for designing highly conductive PILs. In the current study, the correlation between morphology and charge transport in two homologous series of PILs with systematic variation of the alkyl chain length and anions is investigated using broadband dielectric spectroscopy, rheology, differential scanning calorimetry and X-ray scattering. As the alkyl chain length increases, the backbone-to-backbone separation increases, and dc-conductivity consequently decreases. The cations dominate structural dynamics since they are attached to the polymer chains, while the anions are smaller and more mobile ionic species thereby controlling the ionic conductivity. Further interpretation of decoupling of dc conductivity from the segmental relaxation enabled the correlation between polymer morphology and dc conductivity. Supported by the National Science Foundation, Polymers Program.

Influence of proline upon the folding and geometry of the WALP19 transmembrane peptide.

PubMed

Thomas, Rachel; Vostrikov, Vitaly V; Greathouse, Denise V; Koeppe, Roger E

2009-12-22

The orientations, geometries, and lipid interactions of designed transmembrane (TM) peptides have attracted significant experimental and theoretical interest. Because the amino acid proline will introduce a known discontinuity into an alpha helix, we have sought to measure the extent of helix kinking caused by a single proline within the isolated TM helical domain of WALP19. For this purpose, we synthesized acetyl-GWWLALALAP(10)ALALALWWA-ethanolamide and included pairs of deuterated alanines by using 60-100% Fmoc-l-Ala-d(4) at selected sequence positions. Solid-state deuterium ((2)H) magnetic resonance spectra from oriented, hydrated samples (1/40, peptide/lipid; using several lipids) reveal signals from many of the alanine backbone C(alpha) deuterons as well as the alanine side-chain C(beta) methyl groups, whereas signals from C(alpha) deuterons generally have not been observed for similar peptides without proline. It is conceivable that altered peptide dynamics may be responsible for the apparent "unmasking" of the backbone resonances in the presence of the proline. Data analysis using the geometric analysis of labeled alanines (GALA) method reveals that the peptide helix is distorted due to the presence of the proline. To provide additional data points for evaluating the segmental tilt angles of the two halves of the peptide, we substituted selected leucines with l-Ala-d(4). Using this approach, we were able to deduce that the apparent average tilt of the C-terminal increases from approximately 4 degrees to approximately 12 degrees when Pro(10) is introduced. The segment N-terminal to proline is more complex and possibly is more dynamically flexible; Leu to Ala mutations within the N-terminal segment alter the average orientations of alanines in both segments. Nevertheless, in DOPC, we could estimate an apparent kink angle of approximately 19 degrees . Together, the results suggest that the central proline influences not only the geometry but also the dynamics of the membrane-spanning peptide. The results make up an important basis for understanding the functional role of proline in several families of membrane proteins.

Optimal segmentation and packaging process

DOEpatents

Kostelnik, K.M.; Meservey, R.H.; Landon, M.D.

1999-08-10

A process for improving packaging efficiency uses three dimensional, computer simulated models with various optimization algorithms to determine the optimal segmentation process and packaging configurations based on constraints including container limitations. The present invention is applied to a process for decontaminating, decommissioning (D and D), and remediating a nuclear facility involving the segmentation and packaging of contaminated items in waste containers in order to minimize the number of cuts, maximize packaging density, and reduce worker radiation exposure. A three-dimensional, computer simulated, facility model of the contaminated items are created. The contaminated items are differentiated. The optimal location, orientation and sequence of the segmentation and packaging of the contaminated items is determined using the simulated model, the algorithms, and various constraints including container limitations. The cut locations and orientations are transposed to the simulated model. The contaminated items are actually segmented and packaged. The segmentation and packaging may be simulated beforehand. In addition, the contaminated items may be cataloged and recorded. 3 figs.

Fast Appearance Modeling for Automatic Primary Video Object Segmentation.

PubMed

Yang, Jiong; Price, Brian; Shen, Xiaohui; Lin, Zhe; Yuan, Junsong

2016-02-01

Automatic segmentation of the primary object in a video clip is a challenging problem as there is no prior knowledge of the primary object. Most existing techniques thus adapt an iterative approach for foreground and background appearance modeling, i.e., fix the appearance model while optimizing the segmentation and fix the segmentation while optimizing the appearance model. However, these approaches may rely on good initialization and can be easily trapped in local optimal. In addition, they are usually time consuming for analyzing videos. To address these limitations, we propose a novel and efficient appearance modeling technique for automatic primary video object segmentation in the Markov random field (MRF) framework. It embeds the appearance constraint as auxiliary nodes and edges in the MRF structure, and can optimize both the segmentation and appearance model parameters simultaneously in one graph cut. The extensive experimental evaluations validate the superiority of the proposed approach over the state-of-the-art methods, in both efficiency and effectiveness.

Conjugated-Backbone Effect of Organic Small Molecules for n-Type Thermoelectric Materials with ZT over 0.2.

PubMed

Huang, Dazhen; Yao, Huiying; Cui, Yutao; Zou, Ye; Zhang, Fengjiao; Wang, Chao; Shen, Hongguang; Jin, Wenlong; Zhu, Jia; Diao, Ying; Xu, Wei; Di, Chong-An; Zhu, Daoben

2017-09-20

Conjugated backbones play a fundamental role in determining the electronic properties of organic semiconductors. On the basis of two solution-processable dihydropyrrolo[3,4-c]pyrrole-1,4-diylidenebis(thieno[3,2-b]thiophene) derivatives with aromatic and quinoid structures, we have carried out a systematic study of the relationship between the conjugated-backbone structure and the thermoelectric properties. In particular, a combination of UV-vis-NIR spectra, photoemission spectroscopy, and doping optimization are utilized to probe the interplay between energy levels, chemical doping, and thermoelectric performance. We found that a moderate change in the conjugated backbone leads to varied doping mechanisms and contributes to dramatic changes in the thermoelectric performance. Notably, the chemically doped A-DCV-DPPTT, a small molecule with aromatic structure, exhibits an electrical conductivity of 5.3 S cm -1 and a high power factor (PF 373 K ) up to 236 μW m -1 K -2 , which is 50 times higher than that of Q-DCM-DPPTT with a quinoid structure. More importantly, the low thermal conductivity enables A-DCV-DPPTT to possess a figure of merit (ZT) of 0.23 ± 0.03, which is the highest value reported to date for thermoelectric materials based on organic small molecules. These results demonstrate that the modulation of the conjugated backbone represents a powerful strategy for tuning the electronic structure and mobility of organic semiconductors toward a maximum thermoelectric performance.

Estimating the concentration of gold nanoparticles incorporated on natural rubber membranes using multi-level starlet optimal segmentation

NASA Astrophysics Data System (ADS)

de Siqueira, A. F.; Cabrera, F. C.; Pagamisse, A.; Job, A. E.

2014-12-01

This study consolidates multi-level starlet segmentation (MLSS) and multi-level starlet optimal segmentation (MLSOS) techniques for photomicrograph segmentation, based on starlet wavelet detail levels to separate areas of interest in an input image. Several segmentation levels can be obtained using MLSS; after that, Matthews correlation coefficient is used to choose an optimal segmentation level, giving rise to MLSOS. In this paper, MLSOS is employed to estimate the concentration of gold nanoparticles with diameter around 47 nm, reduced on natural rubber membranes. These samples were used for the construction of SERS/SERRS substrates and in the study of the influence of natural rubber membranes with incorporated gold nanoparticles on the physiology of Leishmania braziliensis. Precision, recall, and accuracy are used to evaluate the segmentation performance, and MLSOS presents an accuracy greater than 88 % for this application.

Effect of Chain Rigidity on the Decoupling of Ion Motion from Segmental Relaxation in Polymerized Ionic Liquids: Ambient and Elevated Pressure Studies

DOE PAGES

Wojnarowska, Zaneta; Feng, Hongbo; Fu, Yao; ...

2017-08-21

Conductivity in polymer electrolytes has been generally discussed with the assumption that the segmental motions control charge transport. However, much less attention has been paid to the mechanism of ion conductivity where the motions of ions are less dependent (decoupled) on segmental dynamics. We present that this phenomenon is observed in ionic materials as they approach their glass transition temperature and becomes essential for design and development of highly conducting solid polymer electrolytes. In this paper, we study the effect of chain rigidity on the decoupling of ion transport from segmental motion in three polymerized ionic liquids (polyILs) containing themore » same cation–anion pair but differing in flexibility of the polymer backbones and side groups. Analysis of dielectric and rheology data reveals that decoupling is strong in vinyl-based rigid polymers while almost negligible in novel siloxane-based flexible polyILs. To explain this behavior, we investigated ion and chain dynamics at ambient and elevated pressure. Our results suggest that decoupling has a direct relationship to the frustration in chain packing and free volume. Finally, these conclusions are also supported by coarse-grained molecular dynamics simulations.« less

Effect of Chain Rigidity on the Decoupling of Ion Motion from Segmental Relaxation in Polymerized Ionic Liquids: Ambient and Elevated Pressure Studies

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

Wojnarowska, Zaneta; Feng, Hongbo; Fu, Yao

Conductivity in polymer electrolytes has been generally discussed with the assumption that the segmental motions control charge transport. However, much less attention has been paid to the mechanism of ion conductivity where the motions of ions are less dependent (decoupled) on segmental dynamics. We present that this phenomenon is observed in ionic materials as they approach their glass transition temperature and becomes essential for design and development of highly conducting solid polymer electrolytes. In this paper, we study the effect of chain rigidity on the decoupling of ion transport from segmental motion in three polymerized ionic liquids (polyILs) containing themore » same cation–anion pair but differing in flexibility of the polymer backbones and side groups. Analysis of dielectric and rheology data reveals that decoupling is strong in vinyl-based rigid polymers while almost negligible in novel siloxane-based flexible polyILs. To explain this behavior, we investigated ion and chain dynamics at ambient and elevated pressure. Our results suggest that decoupling has a direct relationship to the frustration in chain packing and free volume. Finally, these conclusions are also supported by coarse-grained molecular dynamics simulations.« less

Mixed pyruvate labeling enables backbone resonance assignment of large proteins using a single experiment.

PubMed

Robson, Scott A; Takeuchi, Koh; Boeszoermenyi, Andras; Coote, Paul W; Dubey, Abhinav; Hyberts, Sven; Wagner, Gerhard; Arthanari, Haribabu

2018-01-24

Backbone resonance assignment is a critical first step in the investigation of proteins by NMR. This is traditionally achieved with a standard set of experiments, most of which are not optimal for large proteins. Of these, HNCA is the most sensitive experiment that provides sequential correlations. However, this experiment suffers from chemical shift degeneracy problems during the assignment procedure. We present a strategy that increases the effective resolution of HNCA and enables near-complete resonance assignment using this single HNCA experiment. We utilize a combination of 2- 13 C and 3- 13 C pyruvate as the carbon source for isotope labeling, which suppresses the one bond ( 1 J αβ ) coupling providing enhanced resolution for the Cα resonance and amino acid-specific peak shapes that arise from the residual coupling. Using this approach, we can obtain near-complete (>85%) backbone resonance assignment of a 42 kDa protein using a single HNCA experiment.

Image Segmentation Method Using Fuzzy C Mean Clustering Based on Multi-Objective Optimization

NASA Astrophysics Data System (ADS)

Chen, Jinlin; Yang, Chunzhi; Xu, Guangkui; Ning, Li

2018-04-01

Image segmentation is not only one of the hottest topics in digital image processing, but also an important part of computer vision applications. As one kind of image segmentation algorithms, fuzzy C-means clustering is an effective and concise segmentation algorithm. However, the drawback of FCM is that it is sensitive to image noise. To solve the problem, this paper designs a novel fuzzy C-mean clustering algorithm based on multi-objective optimization. We add a parameter λ to the fuzzy distance measurement formula to improve the multi-objective optimization. The parameter λ can adjust the weights of the pixel local information. In the algorithm, the local correlation of neighboring pixels is added to the improved multi-objective mathematical model to optimize the clustering cent. Two different experimental results show that the novel fuzzy C-means approach has an efficient performance and computational time while segmenting images by different type of noises.

Automatic multi-organ segmentation using learning-based segmentation and level set optimization.

PubMed

Kohlberger, Timo; Sofka, Michal; Zhang, Jingdan; Birkbeck, Neil; Wetzl, Jens; Kaftan, Jens; Declerck, Jérôme; Zhou, S Kevin

2011-01-01

We present a novel generic segmentation system for the fully automatic multi-organ segmentation from CT medical images. Thereby we combine the advantages of learning-based approaches on point cloud-based shape representation, such a speed, robustness, point correspondences, with those of PDE-optimization-based level set approaches, such as high accuracy and the straightforward prevention of segment overlaps. In a benchmark on 10-100 annotated datasets for the liver, the lungs, and the kidneys we show that the proposed system yields segmentation accuracies of 1.17-2.89 mm average surface errors. Thereby the level set segmentation (which is initialized by the learning-based segmentations) contributes with an 20%-40% increase in accuracy.

Frequency Assignment for Joint Aerial Layer Network High-Capacity Backbone

DTIC Science & Technology

2017-08-11

Department of the Army position unless so designated by other authorized documents. Citation of manufacturer’s or trade names does not constitute an...performance of the proposed approach. Frequency Assignment, JALN, Resource Allocation, Network Optimization, Performance Evaluation 24 Peng Wang 410-278

Optimized multisectioned acoustic liners

NASA Technical Reports Server (NTRS)

Baumeister, K. J.

1979-01-01

New calculations show that segmenting is most efficient at high frequencies with relatively long duct lengths where the attenuation is low for both uniform and segmented liners. Statistical considerations indicate little advantage in using optimized liners with more than two segments while the bandwidth of an optimized two-segment liner is shown to be nearly equal to that of a uniform liner. Multielement liner calculations show a large degradation in performance due to changes in assumed input modal structure. Computer programs are used to generate theoretical attenuations for a number of liner configurations for liners in a rectangular duct with no mean flow. Overall, the use of optimized multisectioned liners fails to offer sufficient advantage over a uniform liner to warrant their use except in low frequency single mode application.

KSC-06pd1671

NASA Image and Video Library

2006-07-26

KENNEDY SPACE CENTER, FLA. - Shortly after midnight, the payload canister and convoy negotiate the turn on the Saturn Causeway, heading for Launch Pad 39B. Inside the canister is the payload for Atlantis and mission STS-115, the Port 3/4 truss segment with two large solar arrays. The payload changeout room provides an environmentally clean or "white room" condition in which to receive a payload transferred from a protective payload canister. After the shuttle arrives at the pad, the rotating service structure will close around it and the payload will then be transferred into Atlantis' payload bay. Atlantis' launch window begins Aug. 28. During its 11-day mission to the International Space Station, the STS-115 crew of six astronauts will install the truss, a 17-ton segment of the space station's truss backbone. Photo credit: NASA/George Shelton

KSC-06pd1673

NASA Image and Video Library

2006-07-26

KENNEDY SPACE CENTER, FLA. - On Launch Pad 39B, the payload canister is moved into position beneath the payload changeout room (PCR) for transfer of its cargo into the PCR. The canister holds the payload for Atlantis and mission STS-115, the Port 3/4 truss segment with two large solar arrays. The payload changeout room provides an environmentally clean or "white room" condition in which to receive a payload transferred from a protective payload canister. After the shuttle arrives at the pad, the rotating service structure will close around it and the payload will then be transferred into Atlantis' payload bay. Atlantis' launch window begins Aug. 28. During its 11-day mission to the International Space Station, the STS-115 crew of six astronauts will install the truss, a 17-ton segment of the space station's truss backbone. Photo credit: NASA/George Shelton

KSC-07pd1449

NASA Image and Video Library

2007-06-08

KENNEDY SPACE CENTER, FLA. -- Columns of fire flow from the solid rocket boosters launching Space Shuttle Atlantis on mission STS-117 while masses of smoke and steam billow across Launch Pad 39A. Atlantis passes the fixed service structure at left, topped by the 80-foot-tall lightning mast. Liftoff was on-time at 7:38:04 p.m. EDT. The shuttle is delivering a new segment to the starboard side of the International Space Station's backbone, known as the truss. Three spacewalks are planned to install the S3/S4 truss segment, deploy a set of solar arrays and prepare them for operation. STS-117 is the 118th space shuttle flight, the 21st flight to the station, the 28th flight for Atlantis and the first of four flights planned for 2007. Photo courtesy of Nikon/Scott Andrews

KSC-07pp1467

NASA Image and Video Library

2007-06-08

KENNEDY SPACE CENTER, FLA. -- With solid rocket boosters firing, Space Shuttle Atlantis leaps toward the heavens in a near-perfect launch on mission STS-117 to the International Space Station. The clouds of smoke and steam roll across Launch Pad 39A and surround the rotating service structure at left. Liftoff was on-time at 7:38:04 p.m. EDT. The shuttle is delivering a new segment to the starboard side of the International Space Station's backbone, known as the truss. Three spacewalks are planned to install the S3/S4 truss segment, deploy a set of solar arrays and prepare them for operation. STS-117 is the 118th space shuttle flight, the 21st flight to the station, the 28th flight for Atlantis and the first of four flights planned for 2007. Photo credit: NASA/Jerry Cannon & Mike Kerley

Identifying the optimal segmentors for mass classification in mammograms

NASA Astrophysics Data System (ADS)

Zhang, Yu; Tomuro, Noriko; Furst, Jacob; Raicu, Daniela S.

2015-03-01

In this paper, we present the results of our investigation on identifying the optimal segmentor(s) from an ensemble of weak segmentors, used in a Computer-Aided Diagnosis (CADx) system which classifies suspicious masses in mammograms as benign or malignant. This is an extension of our previous work, where we used various parameter settings of image enhancement techniques to each suspicious mass (region of interest (ROI)) to obtain several enhanced images, then applied segmentation to each image to obtain several contours of a given mass. Each segmentation in this ensemble is essentially a "weak segmentor" because no single segmentation can produce the optimal result for all images. Then after shape features are computed from the segmented contours, the final classification model was built using logistic regression. The work in this paper focuses on identifying the optimal segmentor(s) from an ensemble mix of weak segmentors. For our purpose, optimal segmentors are those in the ensemble mix which contribute the most to the overall classification rather than the ones that produced high precision segmentation. To measure the segmentors' contribution, we examined weights on the features in the derived logistic regression model and computed the average feature weight for each segmentor. The result showed that, while in general the segmentors with higher segmentation success rates had higher feature weights, some segmentors with lower segmentation rates had high classification feature weights as well.

KSC-08pd2048

NASA Image and Video Library

2008-07-21

CAPE CANAVERAL, Fla. – In the Space Station Processing Facility at NASA's Kennedy Space Center, workers prepare to install the final solar array wing for the International Space Station onto the S6 truss element. Scheduled to launch on the STS-119 mission, space shuttle Discovery will carry the S6 truss segment to complete the 361-foot-long backbone of the International Space Station. The truss includes the fourth pair of solar array wings and electronics that convert sunlight to power for the orbiting laboratory. Launch is targeted for Feb. 12, 2009. Photo credit: NASA/Troy Cryder

XUNET experimental high-speed network testbed CRADA 1136, DOE TTI No. 92-MULT-020-B2

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

Palmer, R.E.

1996-04-01

XUNET is a research program with AT&T and other partners to study high-speed wide area communication between local area networks over a backbone using Asynchronous Transfer Mode (ATM) switches. Important goals of the project are to develop software techniques for network control and management, and applications for high-speed networks. The project entails building a testbed between member sites to explore performance issues for mixed network traffic such as congestion control, multimedia communications protocols, segmentation and reassembly of ATM cells, and overall data throughput rates.

A new bead-spring model for simulation of semi-flexible macromolecules

NASA Astrophysics Data System (ADS)

Saadat, Amir; Khomami, Bamin

2016-11-01

A bead-spring model for semi-flexible macromolecules is developed to overcome the deficiencies of the current coarse-grained bead-spring models. Specifically, model improvements are achieved through incorporation of a bending potential. The new model is designed to accurately describe the correlation along the backbone of the chain, segmental length, and force-extension behavior of the macromolecule even at the limit of 1 Kuhn step per spring. The relaxation time of different Rouse modes is used to demonstrate the capabilities of the new model in predicting chain dynamics.

Optimal Dynamic Advertising Strategy Under Age-Specific Market Segmentation

NASA Astrophysics Data System (ADS)

Krastev, Vladimir

2011-12-01

We consider the model proposed by Faggian and Grosset for determining the advertising efforts and goodwill in the long run of a company under age segmentation of consumers. Reducing this model to optimal control sub problems we find the optimal advertising strategy and goodwill.

Semi-automatic segmentation of brain tumors using population and individual information.

PubMed

Wu, Yao; Yang, Wei; Jiang, Jun; Li, Shuanqian; Feng, Qianjin; Chen, Wufan

2013-08-01

Efficient segmentation of tumors in medical images is of great practical importance in early diagnosis and radiation plan. This paper proposes a novel semi-automatic segmentation method based on population and individual statistical information to segment brain tumors in magnetic resonance (MR) images. First, high-dimensional image features are extracted. Neighborhood components analysis is proposed to learn two optimal distance metrics, which contain population and patient-specific information, respectively. The probability of each pixel belonging to the foreground (tumor) and the background is estimated by the k-nearest neighborhood classifier under the learned optimal distance metrics. A cost function for segmentation is constructed through these probabilities and is optimized using graph cuts. Finally, some morphological operations are performed to improve the achieved segmentation results. Our dataset consists of 137 brain MR images, including 68 for training and 69 for testing. The proposed method overcomes segmentation difficulties caused by the uneven gray level distribution of the tumors and even can get satisfactory results if the tumors have fuzzy edges. Experimental results demonstrate that the proposed method is robust to brain tumor segmentation.

Segmentation of the Clustered Cells with Optimized Boundary Detection in Negative Phase Contrast Images

PubMed Central

Wang, Yuliang; Zhang, Zaicheng; Wang, Huimin; Bi, Shusheng

2015-01-01

Cell image segmentation plays a central role in numerous biology studies and clinical applications. As a result, the development of cell image segmentation algorithms with high robustness and accuracy is attracting more and more attention. In this study, an automated cell image segmentation algorithm is developed to get improved cell image segmentation with respect to cell boundary detection and segmentation of the clustered cells for all cells in the field of view in negative phase contrast images. A new method which combines the thresholding method and edge based active contour method was proposed to optimize cell boundary detection. In order to segment clustered cells, the geographic peaks of cell light intensity were utilized to detect numbers and locations of the clustered cells. In this paper, the working principles of the algorithms are described. The influence of parameters in cell boundary detection and the selection of the threshold value on the final segmentation results are investigated. At last, the proposed algorithm is applied to the negative phase contrast images from different experiments. The performance of the proposed method is evaluated. Results show that the proposed method can achieve optimized cell boundary detection and highly accurate segmentation for clustered cells. PMID:26066315

Molecular mechanical studies of DNA flexibility: Coupled backbone torsion angles and base-pair openings

PubMed Central

Keepers, Joe W.; Kollman, Peter A.; Weiner, Paul K.; James, Thomas L.

1982-01-01

Molecular mechanics studies have been carried out on “B-DNA-like” structures of [d(C-G-C-G-A-A-T-T-C-G-C-G)]2 and [d(A)]12·[d(T)]12. Each of the backbone torsion angles (ψ, φ, ω, ω′, φ′) has been “forced” to alternative values from the normal B-DNA values (g+, t, g-, g-, t conformations). Compensating torsion angle changes preserve most of the base stacking energy in the double helix. In a second part of the study, one purine N3-pyrimidine N1 distance at a time has been forced to a value of 6 Å in an attempt to simulate the base opening motions required to rationalize proton exchange data for DNA. When the 6-Å constraint is removed, many of the structures revert to the normal Watson-Crick hydrogen-bonded structure, but a number are trapped in structures ≈5 kcal/mol higher in energy than the starting B-DNA structure. The relative energy of these structures, some of which involve a non-Watson-Crick thymine C2(carbonyl)[unk]adenine 6NH2 hydrogen bond, are qualitatively consistent with the ΔH for a “base pair-open state” suggested by Mandal et al. of 4-6 kcal/mol [Mandal, C., Kallenbach, N. R. & Englander, S. W. (1979) J. Mol. Biol. 135, 391-411]. The picture of DNA flexibility emerging from this study depicts the backbone as undergoing rapid motion between local torsional minima on a nanosecond time scale. Backbone motion is mainly localized within a dinucleoside segment and generally not conformationally coupled along the chain or across the base pairs. Base motions are much smaller in magnitude than backbone motions. Base sliding allows imino N—H exchange, but it is localized, and only a small fraction of the N—H groups is exposed at any one time. Stacking and hydrogen bonding cause a rigid core of bases in the center of the molecule accounting for the hydrodynamic properties of DNA. PMID:6957879

Optimization of Process Conditions for Enzymatic Modification of Alternan using Dextranase from Chaetomium erraticum

USDA-ARS?s Scientific Manuscript database

Alternan is a unique branched glucan with alternating a-(1 ' 6) and a-(1 ' 3) backbone linkages. We previously described the modification of alternan to a reduced molecular weight form using dextranase from Penicillium sp. The solution viscosity properties of this modified alternan resemble those ...

Lung Segmentation Refinement based on Optimal Surface Finding Utilizing a Hybrid Desktop/Virtual Reality User Interface

PubMed Central

Sun, Shanhui; Sonka, Milan; Beichel, Reinhard R.

2013-01-01

Recently, the optimal surface finding (OSF) and layered optimal graph image segmentation of multiple objects and surfaces (LOGISMOS) approaches have been reported with applications to medical image segmentation tasks. While providing high levels of performance, these approaches may locally fail in the presence of pathology or other local challenges. Due to the image data variability, finding a suitable cost function that would be applicable to all image locations may not be feasible. This paper presents a new interactive refinement approach for correcting local segmentation errors in the automated OSF-based segmentation. A hybrid desktop/virtual reality user interface was developed for efficient interaction with the segmentations utilizing state-of-the-art stereoscopic visualization technology and advanced interaction techniques. The user interface allows a natural and interactive manipulation on 3-D surfaces. The approach was evaluated on 30 test cases from 18 CT lung datasets, which showed local segmentation errors after employing an automated OSF-based lung segmentation. The performed experiments exhibited significant increase in performance in terms of mean absolute surface distance errors (2.54 ± 0.75 mm prior to refinement vs. 1.11 ± 0.43 mm post-refinement, p ≪ 0.001). Speed of the interactions is one of the most important aspects leading to the acceptance or rejection of the approach by users expecting real-time interaction experience. The average algorithm computing time per refinement iteration was 150 ms, and the average total user interaction time required for reaching complete operator satisfaction per case was about 2 min. This time was mostly spent on human-controlled manipulation of the object to identify whether additional refinement was necessary and to approve the final segmentation result. The reported principle is generally applicable to segmentation problems beyond lung segmentation in CT scans as long as the underlying segmentation utilizes the OSF framework. The two reported segmentation refinement tools were optimized for lung segmentation and might need some adaptation for other application domains. PMID:23415254

Alternative reverse genetics system for influenza viruses based on a synthesized swine 45S rRNA promoter.

PubMed

Wang, Kai; Huang, Qi; Yang, Zhiwei; Qi, Kezong; Liu, Hongmei; Chen, Hongjun

2017-08-01

We generated an alternative reverse genetics (RG) system based on a synthesized swine 45S rRNA promoter to rescue the H3N2 subtype swine influenza virus. All eight flanking segment cassettes of A/swine/Henan/7/2010 (H3N2) were amplified with ambisense expression elements from RG plasmids. All segments were then recombined with the pHC2014 vector, which contained the synthesized swine 45S rRNA promoter (spol1) and its terminal sequence (t1) in a pcDNA3 backbone. As a result, we obtained a set of RG plasmids carrying the corresponding eight-segment cassettes. We efficiently generated the H3N2 virus after transfection into 293T/PK15, PK15, and 293T cells. The efficiency of spol1-driven influenza virus rescue in PK15 cells was similar to that in 293T cells by titration using the human pol1 RG system. Our approach suggests that an alternative spol1-based RG system can produce influenza viruses.

Expanding the peptide beta-turn in alphagamma hybrid sequences: 12 atom hydrogen bonded helical and hairpin turns.

PubMed

Chatterjee, Sunanda; Vasudev, Prema G; Raghothama, Srinivasarao; Ramakrishnan, Chandrasekharan; Shamala, Narayanaswamy; Balaram, Padmanabhan

2009-04-29

Hybrid peptide segments containing contiguous alpha and gamma amino acid residues can form C(12) hydrogen bonded turns which may be considered as backbone expanded analogues of C(10) (beta-turns) found in alphaalpha segments. Exploration of the regular hydrogen bonded conformations accessible for hybrid alphagamma sequences is facilitated by the use of a stereochemically constrained gamma amino acid residue gabapentin (1-aminomethylcyclohexaneacetic acid, Gpn), in which the two torsion angles about C(gamma)-C(beta) (theta(1)) and C(beta)-C(alpha) (theta(2)) are predominantly restricted to gauche conformations. The crystal structures of the octapeptides Boc-Gpn-Aib-Gpn-Aib-Gpn-Aib-Gpn-Aib-OMe (1) and Boc-Leu-Phe-Val-Aib-Gpn-Leu-Phe-Val-OMe (2) reveal two distinct conformations for the Aib-Gpn segment. Peptide 1 forms a continuous helix over the Aib(2)-Aib(6) segment, while the peptide 2 forms a beta-hairpin structure stabilized by four cross-strand hydrogen bonds with the Aib-Gpn segment forming a nonhelical C(12) turn. The robustness of the helix in peptide 1 in solution is demonstrated by NMR methods. Peptide 2 is conformationally fragile in solution with evidence of beta-hairpin conformations being obtained in methanol. Theoretical calculations permit delineation of the various C(12) hydrogen bonded structures which are energetically feasible in alphagamma and gammaalpha sequences.

Optimization-based interactive segmentation interface for multiregion problems

PubMed Central

Baxter, John S. H.; Rajchl, Martin; Peters, Terry M.; Chen, Elvis C. S.

2016-01-01

Abstract. Interactive segmentation is becoming of increasing interest to the medical imaging community in that it combines the positive aspects of both manual and automated segmentation. However, general-purpose tools have been lacking in terms of segmenting multiple regions simultaneously with a high degree of coupling between groups of labels. Hierarchical max-flow segmentation has taken advantage of this coupling for individual applications, but until recently, these algorithms were constrained to a particular hierarchy and could not be considered general-purpose. In a generalized form, the hierarchy for any given segmentation problem is specified in run-time, allowing different hierarchies to be quickly explored. We present an interactive segmentation interface, which uses generalized hierarchical max-flow for optimization-based multiregion segmentation guided by user-defined seeds. Applications in cardiac and neonatal brain segmentation are given as example applications of its generality. PMID:27335892

Efficient Algorithms for Segmentation of Item-Set Time Series

NASA Astrophysics Data System (ADS)

Chundi, Parvathi; Rosenkrantz, Daniel J.

We propose a special type of time series, which we call an item-set time series, to facilitate the temporal analysis of software version histories, email logs, stock market data, etc. In an item-set time series, each observed data value is a set of discrete items. We formalize the concept of an item-set time series and present efficient algorithms for segmenting a given item-set time series. Segmentation of a time series partitions the time series into a sequence of segments where each segment is constructed by combining consecutive time points of the time series. Each segment is associated with an item set that is computed from the item sets of the time points in that segment, using a function which we call a measure function. We then define a concept called the segment difference, which measures the difference between the item set of a segment and the item sets of the time points in that segment. The segment difference values are required to construct an optimal segmentation of the time series. We describe novel and efficient algorithms to compute segment difference values for each of the measure functions described in the paper. We outline a dynamic programming based scheme to construct an optimal segmentation of the given item-set time series. We use the item-set time series segmentation techniques to analyze the temporal content of three different data sets—Enron email, stock market data, and a synthetic data set. The experimental results show that an optimal segmentation of item-set time series data captures much more temporal content than a segmentation constructed based on the number of time points in each segment, without examining the item set data at the time points, and can be used to analyze different types of temporal data.

Mapping multivalency and differential affinities within large intrinsically disordered protein complexes with segmental motion analysis.

PubMed

Milles, Sigrid; Lemke, Edward A

2014-07-07

Intrinsically disordered proteins (IDPs) can bind to multiple interaction partners. Numerous binding regions in the IDP that act in concert through complex cooperative effects facilitate such interactions, but complicate studying IDP complexes. To address this challenge we developed a combined fluorescence correlation and time-resolved polarization spectroscopy approach to study the binding properties of the IDP nucleoporin153 (Nup153) to nuclear transport receptors (NTRs). The detection of segmental backbone mobility of Nup153 within the unperturbed complex provided a readout of local, region-specific binding properties that are usually masked in measurements of the whole IDP. The binding affinities of functionally and structurally diverse NTRs to distinct regions of Nup153 can differ by orders of magnitudes-a result with implications for the diversity of transport routes in nucleocytoplasmic transport. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

KSC-07pp1461

NASA Image and Video Library

2007-06-08

KENNEDY SPACE CENTER, FLA. -- Space Shuttle Atlantis rockets into the blue sky above Launch Pad 39A after liftoff. Beneath Atlantis' main engines are blue cones of light, known as shock or mach diamonds. They are a formation of shock waves in the exhaust plume of an aerospace propulsion system. Liftoff of Atlantis on mission STS-117 to the International Space Station was on time at 7:38:04 p.m. EDT. The shuttle is delivering a new segment to the starboard side of the International Space Station's backbone, known as the truss. Three spacewalks are planned to install the S3/S4 truss segment, deploy a set of solar arrays and prepare them for operation. STS-117 is the 118th space shuttle flight, the 21st flight to the station, the 28th flight for Atlantis and the first of four flights planned for 2007. Photo Credit: NASA/Tony Gray & Don Kight

KSC-06pd1674

NASA Image and Video Library

2006-07-26

KENNEDY SPACE CENTER, FLA. - Nearing dawn on Launch Pad 39B, the payload canister is in position to be lifted into the payload changeout room (PCR) for transfer of its cargo into the PCR. The canister holds the payload for Atlantis and mission STS-115, the Port 3/4 truss segment with two large solar arrays. The payload changeout room provides an environmentally clean or "white room" condition in which to receive a payload transferred from a protective payload canister. After the shuttle arrives at the pad, the rotating service structure will close around it and the payload will then be transferred into Atlantis' payload bay. Atlantis' launch window begins Aug. 28. During its 11-day mission to the International Space Station, the STS-115 crew of six astronauts will install the truss, a 17-ton segment of the space station's truss backbone. Photo credit: NASA/George Shelton

KSC-06pd1676

NASA Image and Video Library

2006-07-26

KENNEDY SPACE CENTER, FLA. - On Launch Pad 39B, the payload canister is lifted toward the payload changeout room (PCR) for transfer of its cargo into the PCR. The canister holds the payload for Atlantis and mission STS-115, the Port 3/4 truss segment with two large solar arrays. The red umbilical lines are still attached to the transporter, lower right. The payload changeout room provides an environmentally clean or "white room" condition in which to receive a payload transferred from a protective payload canister. After the shuttle arrives at the pad, the rotating service structure will close around it and the payload will then be transferred into Atlantis' payload bay. Atlantis' launch window begins Aug. 28. During its 11-day mission to the International Space Station, the STS-115 crew of six astronauts will install the truss, a 17-ton segment of the space station's truss backbone. Photo credit: NASA/George Shelton

KSC-06pd1672

NASA Image and Video Library

2006-07-26

KENNEDY SPACE CENTER, FLA. - After a several-hour trip from the Canister Rotation Facility, the payload canister arrives on Launch Pad 39B. Inside the canister is the payload for Atlantis and mission STS-115, the Port 3/4 truss segment with two large solar arrays. The canister will be positioned alongside the rotating service structure and beneath the payload changeout room (PCR) for transfer of the truss into the PCR. The payload changeout room provides an environmentally clean or "white room" condition in which to receive a payload transferred from a protective payload canister. After the shuttle arrives at the pad, the rotating service structure will close around it and the payload will then be transferred into Atlantis' payload bay. Atlantis' launch window begins Aug. 28. During its 11-day mission to the International Space Station, the STS-115 crew of six astronauts will install the truss, a 17-ton segment of the space station's truss backbone. Photo credit: NASA/George Shelton

KSC-06pd1675

NASA Image and Video Library

2006-07-26

KENNEDY SPACE CENTER, FLA. - On Launch Pad 39B, the payload canister is lifted toward the payload changeout room (PCR) for transfer of its cargo into the PCR. The canister holds the payload for Atlantis and mission STS-115, the Port 3/4 truss segment with two large solar arrays. The red umbilical lines are still attached, lower right. The payload changeout room provides an environmentally clean or "white room" condition in which to receive a payload transferred from a protective payload canister. After the shuttle arrives at the pad, the rotating service structure will close around it and the payload will then be transferred into Atlantis' payload bay. Atlantis' launch window begins Aug. 28. During its 11-day mission to the International Space Station, the STS-115 crew of six astronauts will install the truss, a 17-ton segment of the space station's truss backbone. Photo credit: NASA/George Shelton

KSC-07pp1456

NASA Image and Video Library

2007-06-08

KENNEDY SPACE CENTER, FLA. -- Moments after liftoff, Space Shuttle Atlantis rises on columns of fire from the solid rocket boosters to leap into the sky and a rendezvous with the International Space Station on mission STS-117. Below Atlantis is the mobile launcher platform. At upper left is the fixed service structure with the 80-foot-tall lightning mast on top. Liftoff of Atlantis was on-time at 7:38:04 p.m. EDT. The shuttle is delivering a new segment to the starboard side of the International Space Station's backbone, known as the truss. Three spacewalks are planned to install the S3/S4 truss segment, deploy a set of solar arrays and prepare them for operation. STS-117 is the 118th space shuttle flight, the 21st flight to the station, the 28th flight for Atlantis and the first of four flights planned for 2007. Photo Credit: NASA/Sandra Joseph and Robert Murray

KSC-07pp1468

NASA Image and Video Library

2007-06-08

KENNEDY SPACE CENTER, FLA. -- Smoke and steam billow across Launch Pad 39A as Space Shuttle Atlantis, trailing columns of fire from the solid rocket boosters, hurtles into the sky on mission STS-117 to the International Space Station. At left is the fixed service structure with the 80-foot-tall lightning mast on top. Liftoff was on-time at 7:38:04 p.m. EDT. The shuttle is delivering a new segment to the starboard side of the International Space Station's backbone, known as the truss. Three spacewalks are planned to install the S3/S4 truss segment, deploy a set of solar arrays and prepare them for operation. STS-117 is the 118th space shuttle flight, the 21st flight to the station, the 28th flight for Atlantis and the first of four flights planned for 2007. Photo credit: NASA/Tony Gray & Don Kight

KSC-07pd1440

NASA Image and Video Library

2007-06-08

KENNEDY SPACE CENTER, FLA. -- Space Shuttle Atlantis is barely visible above the column of fire and smoke as it soars into the sky after launching on mission STS-117. Liftoff from Launch Pad 39A was on-time at 7:38:04 p.m. EDT. At right is the viewing area on top of the buildings used by the Florida Today newspaper at the NASA News Center. The shuttle is delivering a new segment to the starboard side of the International Space Station's backbone, known as the truss. Three spacewalks are planned to install the S3/S4 truss segment, deploy a set of solar arrays and prepare them for operation. STS-117 is the 118th space shuttle flight, the 21st flight to the station, the 28th flight for Atlantis and the first of four flights planned for 2007. Photo courtesy of Nikon/Scott Andrews

KSC-07pd1451

NASA Image and Video Library

2007-06-08

KENNEDY SPACE CENTER, FLA. -- Smoke and steam billow across Launch Pad 39A as Space Shuttle Atlantis, trailing columns of fire from the solid rocket boosters, hurtles into the sky on mission STS-117 to the International Space Station. At right is the water tank that provides the deluge over the mobile launcher platform for sound suppression during liftoff. Liftoff was on-time at 7:38:04 p.m. EDT.The shuttle is delivering a new segment to the starboard side of the International Space Station's backbone, known as the truss. Three spacewalks are planned to install the S3/S4 truss segment, deploy a set of solar arrays and prepare them for operation. STS-117 is the 118th space shuttle flight, the 21st flight to the station, the 28th flight for Atlantis and the first of four flights planned for 2007. Photo courtesy of Nikon/Scott Andrews

KSC-07pp1465

NASA Image and Video Library

2007-06-08

KENNEDY SPACE CENTER, FLA. -- Smoke and steam billow across Launch Pad 39A as Space Shuttle Atlantis, trailing columns of fire from the solid rocket boosters, hurtles into the sky on mission STS-117 to the International Space Station. At left is the fixed service structure with the 80-foot-tall lightning mast on top. Liftoff was on-time at 7:38:04 p.m. EDT. The shuttle is delivering a new segment to the starboard side of the International Space Station's backbone, known as the truss. Three spacewalks are planned to install the S3/S4 truss segment, deploy a set of solar arrays and prepare them for operation. STS-117 is the 118th space shuttle flight, the 21st flight to the station, the 28th flight for Atlantis and the first of four flights planned for 2007. Photo Credit: NASA/Tony Gray & Don Kight

Segmented media and medium damping in microwave assisted magnetic recording

NASA Astrophysics Data System (ADS)

Bai, Xiaoyu; Zhu, Jian-Gang

2018-05-01

In this paper, we present a methodology of segmented media stack design for microwave assisted magnetic recording. Through micro-magnetic modeling, it is demonstrated that an optimized media segmentation is able to yield high signal-to-noise ratio even with limited ac field power. With proper segmentation, the ac field power could be utilized more efficiently and this can alleviate the requirement for medium damping which has been previously considered a critical limitation. The micro-magnetic modeling also shows that with segmentation optimization, recording signal-to-noise ratio can have very little dependence on damping for different recording linear densities.

Graphical user interface to optimize image contrast parameters used in object segmentation - biomed 2009.

PubMed

Anderson, Jeffrey R; Barrett, Steven F

2009-01-01

Image segmentation is the process of isolating distinct objects within an image. Computer algorithms have been developed to aid in the process of object segmentation, but a completely autonomous segmentation algorithm has yet to be developed [1]. This is because computers do not have the capability to understand images and recognize complex objects within the image. However, computer segmentation methods [2], requiring user input, have been developed to quickly segment objects in serial sectioned images, such as magnetic resonance images (MRI) and confocal laser scanning microscope (CLSM) images. In these cases, the segmentation process becomes a powerful tool in visualizing the 3D nature of an object. The user input is an important part of improving the performance of many segmentation methods. A double threshold segmentation method has been investigated [3] to separate objects in gray scaled images, where the gray level of the object is among the gray levels of the background. In order to best determine the threshold values for this segmentation method the image must be manipulated for optimal contrast. The same is true of other segmentation and edge detection methods as well. Typically, the better the image contrast, the better the segmentation results. This paper describes a graphical user interface (GUI) that allows the user to easily change image contrast parameters that will optimize the performance of subsequent object segmentation. This approach makes use of the fact that the human brain is extremely effective in object recognition and understanding. The GUI provides the user with the ability to define the gray scale range of the object of interest. These lower and upper bounds of this range are used in a histogram stretching process to improve image contrast. Also, the user can interactively modify the gamma correction factor that provides a non-linear distribution of gray scale values, while observing the corresponding changes to the image. This interactive approach gives the user the power to make optimal choices in the contrast enhancement parameters.

Assessment of Multiresolution Segmentation for Extracting Greenhouses from WORLDVIEW-2 Imagery

NASA Astrophysics Data System (ADS)

Aguilar, M. A.; Aguilar, F. J.; García Lorca, A.; Guirado, E.; Betlej, M.; Cichon, P.; Nemmaoui, A.; Vallario, A.; Parente, C.

2016-06-01

The latest breed of very high resolution (VHR) commercial satellites opens new possibilities for cartographic and remote sensing applications. In this way, object based image analysis (OBIA) approach has been proved as the best option when working with VHR satellite imagery. OBIA considers spectral, geometric, textural and topological attributes associated with meaningful image objects. Thus, the first step of OBIA, referred to as segmentation, is to delineate objects of interest. Determination of an optimal segmentation is crucial for a good performance of the second stage in OBIA, the classification process. The main goal of this work is to assess the multiresolution segmentation algorithm provided by eCognition software for delineating greenhouses from WorldView- 2 multispectral orthoimages. Specifically, the focus is on finding the optimal parameters of the multiresolution segmentation approach (i.e., Scale, Shape and Compactness) for plastic greenhouses. The optimum Scale parameter estimation was based on the idea of local variance of object heterogeneity within a scene (ESP2 tool). Moreover, different segmentation results were attained by using different combinations of Shape and Compactness values. Assessment of segmentation quality based on the discrepancy between reference polygons and corresponding image segments was carried out to identify the optimal setting of multiresolution segmentation parameters. Three discrepancy indices were used: Potential Segmentation Error (PSE), Number-of-Segments Ratio (NSR) and Euclidean Distance 2 (ED2).

Automatic optimal filament segmentation with sub-pixel accuracy using generalized linear models and B-spline level-sets

PubMed Central

Xiao, Xun; Geyer, Veikko F.; Bowne-Anderson, Hugo; Howard, Jonathon; Sbalzarini, Ivo F.

2016-01-01

Biological filaments, such as actin filaments, microtubules, and cilia, are often imaged using different light-microscopy techniques. Reconstructing the filament curve from the acquired images constitutes the filament segmentation problem. Since filaments have lower dimensionality than the image itself, there is an inherent trade-off between tracing the filament with sub-pixel accuracy and avoiding noise artifacts. Here, we present a globally optimal filament segmentation method based on B-spline vector level-sets and a generalized linear model for the pixel intensity statistics. We show that the resulting optimization problem is convex and can hence be solved with global optimality. We introduce a simple and efficient algorithm to compute such optimal filament segmentations, and provide an open-source implementation as an ImageJ/Fiji plugin. We further derive an information-theoretic lower bound on the filament segmentation error, quantifying how well an algorithm could possibly do given the information in the image. We show that our algorithm asymptotically reaches this bound in the spline coefficients. We validate our method in comprehensive benchmarks, compare with other methods, and show applications from fluorescence, phase-contrast, and dark-field microscopy. PMID:27104582

Optimal reinforcement of training datasets in semi-supervised landmark-based segmentation

NASA Astrophysics Data System (ADS)

Ibragimov, Bulat; Likar, Boštjan; Pernuš, Franjo; Vrtovec, Tomaž

2015-03-01

During the last couple of decades, the development of computerized image segmentation shifted from unsupervised to supervised methods, which made segmentation results more accurate and robust. However, the main disadvantage of supervised segmentation is a need for manual image annotation that is time-consuming and subjected to human error. To reduce the need for manual annotation, we propose a novel learning approach for training dataset reinforcement in the area of landmark-based segmentation, where newly detected landmarks are optimally combined with reference landmarks from the training dataset and therefore enriches the training process. The approach is formulated as a nonlinear optimization problem, where the solution is a vector of weighting factors that measures how reliable are the detected landmarks. The detected landmarks that are found to be more reliable are included into the training procedure with higher weighting factors, whereas the detected landmarks that are found to be less reliable are included with lower weighting factors. The approach is integrated into the landmark-based game-theoretic segmentation framework and validated against the problem of lung field segmentation from chest radiographs.

Multitask assessment of roads and vehicles network (MARVN)

NASA Astrophysics Data System (ADS)

Yang, Fang; Yi, Meng; Cai, Yiran; Blasch, Erik; Sullivan, Nichole; Sheaff, Carolyn; Chen, Genshe; Ling, Haibin

2018-05-01

Vehicle detection in wide area motion imagery (WAMI) has drawn increasing attention from the computer vision research community in recent decades. In this paper, we present a new architecture for vehicle detection on road using multi-task network, which is able to detect and segment vehicles, estimate their pose, and meanwhile yield road isolation for a given region. The multi-task network consists of three components: 1) vehicle detection, 2) vehicle and road segmentation, and 3) detection screening. Segmentation and detection components share the same backbone network and are trained jointly in an end-to-end way. Unlike background subtraction or frame differencing based methods, the proposed Multitask Assessment of Roads and Vehicles Network (MARVN) method can detect vehicles which are slowing down, stopped, and/or partially occluded in a single image. In addition, the method can eliminate the detections which are located at outside road using yielded road segmentation so as to decrease the false positive rate. As few WAMI datasets have road mask and vehicles bounding box anotations, we extract 512 frames from WPAFB 2009 dataset and carefully refine the original annotations. The resulting dataset is thus named as WAMI512. We extensively compare the proposed method with state-of-the-art methods on WAMI512 dataset, and demonstrate superior performance in terms of efficiency and accuracy.

Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting

PubMed Central

2016-01-01

Molecular dynamics simulations depend critically on the accuracy of the underlying force fields in properly representing biomolecules. Hence, it is crucial to validate the force-field parameter sets in this respect. In the context of the GROMOS force field, this is usually achieved by comparing simulation data to experimental observables for small molecules. In this study, we develop new amino acid backbone dihedral angle potential energy parameters based on the widely used 54A7 parameter set by matching to experimental J values and secondary structure propensity scales. In order to find the most appropriate backbone parameters, close to 100 000 different combinations of parameters have been screened. However, since the sheer number of combinations considered prohibits actual molecular dynamics simulations for each of them, we instead predicted the values for every combination using Hamiltonian reweighting. While the original 54A7 parameter set fails to reproduce the experimental data, we are able to provide parameters that match significantly better. However, to ensure applicability in the context of larger peptides and full proteins, further studies have to be undertaken. PMID:27559757

Di-Isocyanate Crosslinked Aerogels with 1, 6-Bis (Trimethoxysilyl) Hexane Incorporated in Silica Backbone

NASA Technical Reports Server (NTRS)

Vivod, Stephanie L.; Meador, Mary Ann B.; Nguyen, Baochau N.; Quade, Derek; Randall, Jason; Perry, Renee

2008-01-01

Silica aerogels are desirable materials for many applications that take advantage of their light weight and low thermal conductivity. Addition of a conformal polymer coating which bonds with the amine decorated surface of the silica network improves the strength of the aerogels by as much as 200 times. Even with vast improvement in strength they still tend to undergo brittle failure due to the rigid silica backbone. We hope to increase the flexibility and elastic recovery of the silica based aerogel by altering the silica back-bone by incorporation of more flexible hexane links. To this end, we investigated the use of 1,6-bis(trimethoxysilyl)hexane (BTMSH), a polysilsesquioxane precursor3, as an additional co-reactant to prepare silica gels which were subsequently cross-linked with di-isocyanate. Previously, this approach of adding flexibility by BTMSH incorporation was demonstrated with styrene cross-linked aerogels. In our study, we varied silane concentration, mol % of silicon from BTMSH and di-isocyanate concentration by weight percent to attempt to optimize both the flexibility and the strength of the aerogels.

Multi-source micro-friction identification for a class of cable-driven robots with passive backbone

NASA Astrophysics Data System (ADS)

Tjahjowidodo, Tegoeh; Zhu, Ke; Dailey, Wayne; Burdet, Etienne; Campolo, Domenico

2016-12-01

This paper analyses the dynamics of cable-driven robots with a passive backbone and develops techniques for their dynamic identification, which are tested on the H-Man, a planar cabled differential transmission robot for haptic interaction. The mechanism is optimized for human-robot interaction by accounting for the cost-benefit-ratio of the system, specifically by eliminating the necessity of an external force sensor to reduce the overall cost. As a consequence, this requires an effective dynamic model for accurate force feedback applications which include friction behavior in the system. We first consider the significance of friction in both the actuator and backbone spaces. Subsequently, we study the required complexity of the stiction model for the application. Different models representing different levels of complexity are investigated, ranging from the conventional approach of Coulomb to an advanced model which includes hysteresis. The results demonstrate each model's ability to capture the dynamic behavior of the system. In general, it is concluded that there is a trade-off between model accuracy and the model cost.

Two-subunit DNA escort mechanism and inactive subunit bypass in an ultra-fast ring ATPase

DOE PAGES

Liu, Ninning; Chistol, Gheorghe; Bustamante, Carlos

2015-10-09

SpoIIIE is a homo-hexameric dsDNA translocase responsible for completing chromosome segregation in Bacillus subtilis. Here in this study, we use a single-molecule approach to monitor SpoIIIE translocation when challenged with neutral-backbone DNA and non-hydrolyzable ATP analogs. We show that SpoIIIE makes multiple essential contacts with phosphates on the 5'→3' strand in the direction of translocation. Using DNA constructs with two neutral-backbone segments separated by a single charged base pair, we deduce that SpoIIIE’s step size is 2 bp. Finally, experiments with non-hydrolyzable ATP analogs suggest that SpoIIIE can operate with non-consecutive inactive subunits. We propose a two-subunit escort translocation mechanismmore » that is strict enough to enable SpoIIIE to track one DNA strand, yet sufficiently compliant to permit the motor to bypass inactive subunits without arrest. We speculate that such a flexible mechanism arose for motors that, like SpoIIIE, constitute functional bottlenecks where the inactivation of even a single motor can be lethal for the cell.« less

Two-subunit DNA escort mechanism and inactive subunit bypass in an ultra-fast ring ATPase

DOE PAGES

Liu, Ninning; Chistol, Gheorghe; Bustamante, Carlos

2015-10-09

SpoIIIE is a homo-hexameric dsDNA translocase responsible for completing chromosome segregation in Bacillus subtilis . Here, we use a single-molecule approach to monitor SpoIIIE translocation when challenged with neutral-backbone DNA and non-hydrolyzable ATP analogs. We show that SpoIIIE makes multiple essential contacts with phosphates on the 5'→3' strand in the direction of translocation. Using DNA constructs with two neutral-backbone segments separated by a single charged base pair, we deduce that SpoIIIE’s step size is 2 bp. Finally, experiments with non-hydrolyzable ATP analogs suggest that SpoIIIE can operate with non-consecutive inactive subunits. We propose a two-subunit escort translocation mechanism that ismore » strict enough to enable SpoIIIE to track one DNA strand, yet sufficiently compliant to permit the motor to bypass inactive subunits without arrest. We speculate that such a flexible mechanism arose for motors that, like SpoIIIE, constitute functional bottlenecks where the inactivation of even a single motor can be lethal for the cell.« less

Deriving high-resolution protein backbone structure propensities from all crystal data using the information maximization device.

PubMed

Solis, Armando D

2014-01-01

The most informative probability distribution functions (PDFs) describing the Ramachandran phi-psi dihedral angle pair, a fundamental descriptor of backbone conformation of protein molecules, are derived from high-resolution X-ray crystal structures using an information-theoretic approach. The Information Maximization Device (IMD) is established, based on fundamental information-theoretic concepts, and then applied specifically to derive highly resolved phi-psi maps for all 20 single amino acid and all 8000 triplet sequences at an optimal resolution determined by the volume of current data. The paper shows that utilizing the latent information contained in all viable high-resolution crystal structures found in the Protein Data Bank (PDB), totaling more than 77,000 chains, permits the derivation of a large number of optimized sequence-dependent PDFs. This work demonstrates the effectiveness of the IMD and the superiority of the resulting PDFs by extensive fold recognition experiments and rigorous comparisons with previously published triplet PDFs. Because it automatically optimizes PDFs, IMD results in improved performance of knowledge-based potentials, which rely on such PDFs. Furthermore, it provides an easy computational recipe for empirically deriving other kinds of sequence-dependent structural PDFs with greater detail and precision. The high-resolution phi-psi maps derived in this work are available for download.

A Multi-Objective Decision Making Approach for Solving the Image Segmentation Fusion Problem.

PubMed

Khelifi, Lazhar; Mignotte, Max

2017-08-01

Image segmentation fusion is defined as the set of methods which aim at merging several image segmentations, in a manner that takes full advantage of the complementarity of each one. Previous relevant researches in this field have been impeded by the difficulty in identifying an appropriate single segmentation fusion criterion, providing the best possible, i.e., the more informative, result of fusion. In this paper, we propose a new model of image segmentation fusion based on multi-objective optimization which can mitigate this problem, to obtain a final improved result of segmentation. Our fusion framework incorporates the dominance concept in order to efficiently combine and optimize two complementary segmentation criteria, namely, the global consistency error and the F-measure (precision-recall) criterion. To this end, we present a hierarchical and efficient way to optimize the multi-objective consensus energy function related to this fusion model, which exploits a simple and deterministic iterative relaxation strategy combining the different image segments. This step is followed by a decision making task based on the so-called "technique for order performance by similarity to ideal solution". Results obtained on two publicly available databases with manual ground truth segmentations clearly show that our multi-objective energy-based model gives better results than the classical mono-objective one.

Simultaneous segmentation of the bone and cartilage surfaces of a knee joint in 3D

NASA Astrophysics Data System (ADS)

Yin, Y.; Zhang, X.; Anderson, D. D.; Brown, T. D.; Hofwegen, C. Van; Sonka, M.

2009-02-01

We present a novel framework for the simultaneous segmentation of multiple interacting surfaces belonging to multiple mutually interacting objects. The method is a non-trivial extension of our previously reported optimal multi-surface segmentation. Considering an example application of knee-cartilage segmentation, the framework consists of the following main steps: 1) Shape model construction: Building a mean shape for each bone of the joint (femur, tibia, patella) from interactively segmented volumetric datasets. Using the resulting mean-shape model - identification of cartilage, non-cartilage, and transition areas on the mean-shape bone model surfaces. 2) Presegmentation: Employment of iterative optimal surface detection method to achieve approximate segmentation of individual bone surfaces. 3) Cross-object surface mapping: Detection of inter-bone equidistant separating sheets to help identify corresponding vertex pairs for all interacting surfaces. 4) Multi-object, multi-surface graph construction and final segmentation: Construction of a single multi-bone, multi-surface graph so that two surfaces (bone and cartilage) with zero and non-zero intervening distances can be detected for each bone of the joint, according to whether or not cartilage can be locally absent or present on the bone. To define inter-object relationships, corresponding vertex pairs identified using the separating sheets were interlinked in the graph. The graph optimization algorithm acted on the entire multiobject, multi-surface graph to yield a globally optimal solution. The segmentation framework was tested on 16 MR-DESS knee-joint datasets from the Osteoarthritis Initiative database. The average signed surface positioning error for the 6 detected surfaces ranged from 0.00 to 0.12 mm. When independently initialized, the signed reproducibility error of bone and cartilage segmentation ranged from 0.00 to 0.26 mm. The results showed that this framework provides robust, accurate, and reproducible segmentation of the knee joint bone and cartilage surfaces of the femur, tibia, and patella. As a general segmentation tool, the developed framework can be applied to a broad range of multi-object segmentation problems.

Multiple-Optimizing Dynamic Sensor Networks with MIMO Technology (PREPRINT)

DTIC Science & Technology

2010-06-01

a) where PAP is the power consumption dependent on the transmit power , cP is the power consumption dependent on the transceiver circuit...w’s parent p received new’s request, p adds new into its backbone list and sets d(p, new) = 2d; p sends the kowledge it holds to new

A convex optimization method for self-organization in dynamic (FSO/RF) wireless networks

NASA Astrophysics Data System (ADS)

Llorca, Jaime; Davis, Christopher C.; Milner, Stuart D.

2008-08-01

Next generation communication networks are becoming increasingly complex systems. Previously, we presented a novel physics-based approach to model dynamic wireless networks as physical systems which react to local forces exerted on network nodes. We showed that under clear atmospheric conditions the network communication energy can be modeled as the potential energy of an analogous spring system and presented a distributed mobility control algorithm where nodes react to local forces driving the network to energy minimizing configurations. This paper extends our previous work by including the effects of atmospheric attenuation and transmitted power constraints in the optimization problem. We show how our new formulation still results in a convex energy minimization problem. Accordingly, an updated force-driven mobility control algorithm is presented. Forces on mobile backbone nodes are computed as the negative gradient of the new energy function. Results show how in the presence of atmospheric obscuration stronger forces are exerted on network nodes that make them move closer to each other, avoiding loss of connectivity. We show results in terms of network coverage and backbone connectivity and compare the developed algorithms for different scenarios.

Supply chain optimization: a practitioner's perspective on the next logistics breakthrough.

PubMed

Schlegel, G L

2000-08-01

The objective of this paper is to profile a practitioner's perspective on supply chain optimization and highlight the critical elements of this potential new logistics breakthrough idea. The introduction will briefly describe the existing distribution network, and business environment. This will include operational statistics, manufacturing software, and hardware configurations. The first segment will cover the critical success factors or foundations elements that are prerequisites for success. The second segment will give you a glimpse of a "working game plan" for successful migration to supply chain optimization. The final segment will briefly profile "bottom-line" benefits to be derived from the use of supply chain optimization as a strategy, tactical tool, and competitive advantage.

Use of Binary Partition Tree and energy minimization for object-based classification of urban land cover

NASA Astrophysics Data System (ADS)

Li, Mengmeng; Bijker, Wietske; Stein, Alfred

2015-04-01

Two main challenges are faced when classifying urban land cover from very high resolution satellite images: obtaining an optimal image segmentation and distinguishing buildings from other man-made objects. For optimal segmentation, this work proposes a hierarchical representation of an image by means of a Binary Partition Tree (BPT) and an unsupervised evaluation of image segmentations by energy minimization. For building extraction, we apply fuzzy sets to create a fuzzy landscape of shadows which in turn involves a two-step procedure. The first step is a preliminarily image classification at a fine segmentation level to generate vegetation and shadow information. The second step models the directional relationship between building and shadow objects to extract building information at the optimal segmentation level. We conducted the experiments on two datasets of Pléiades images from Wuhan City, China. To demonstrate its performance, the proposed classification is compared at the optimal segmentation level with Maximum Likelihood Classification and Support Vector Machine classification. The results show that the proposed classification produced the highest overall accuracies and kappa coefficients, and the smallest over-classification and under-classification geometric errors. We conclude first that integrating BPT with energy minimization offers an effective means for image segmentation. Second, we conclude that the directional relationship between building and shadow objects represented by a fuzzy landscape is important for building extraction.

KSC-08pd2049

NASA Image and Video Library

2008-07-21

CAPE CANAVERAL, Fla. – In the Space Station Processing Facility at NASA's Kennedy Space Center, workers prepare to move the final solar array wing for the International Space Station for installation on the S6 truss element. Scheduled to launch on the STS-119 mission, space shuttle Discovery will carry the S6 truss segment to complete the 361-foot-long backbone of the International Space Station. The truss includes the fourth pair of solar array wings and electronics that convert sunlight to power for the orbiting laboratory. Launch is targeted for Feb. 12, 2009. Photo credit: NASA/Troy Cryder

Lung segmentation refinement based on optimal surface finding utilizing a hybrid desktop/virtual reality user interface.

PubMed

Sun, Shanhui; Sonka, Milan; Beichel, Reinhard R

2013-01-01

Recently, the optimal surface finding (OSF) and layered optimal graph image segmentation of multiple objects and surfaces (LOGISMOS) approaches have been reported with applications to medical image segmentation tasks. While providing high levels of performance, these approaches may locally fail in the presence of pathology or other local challenges. Due to the image data variability, finding a suitable cost function that would be applicable to all image locations may not be feasible. This paper presents a new interactive refinement approach for correcting local segmentation errors in the automated OSF-based segmentation. A hybrid desktop/virtual reality user interface was developed for efficient interaction with the segmentations utilizing state-of-the-art stereoscopic visualization technology and advanced interaction techniques. The user interface allows a natural and interactive manipulation of 3-D surfaces. The approach was evaluated on 30 test cases from 18 CT lung datasets, which showed local segmentation errors after employing an automated OSF-based lung segmentation. The performed experiments exhibited significant increase in performance in terms of mean absolute surface distance errors (2.54±0.75 mm prior to refinement vs. 1.11±0.43 mm post-refinement, p≪0.001). Speed of the interactions is one of the most important aspects leading to the acceptance or rejection of the approach by users expecting real-time interaction experience. The average algorithm computing time per refinement iteration was 150 ms, and the average total user interaction time required for reaching complete operator satisfaction was about 2 min per case. This time was mostly spent on human-controlled manipulation of the object to identify whether additional refinement was necessary and to approve the final segmentation result. The reported principle is generally applicable to segmentation problems beyond lung segmentation in CT scans as long as the underlying segmentation utilizes the OSF framework. The two reported segmentation refinement tools were optimized for lung segmentation and might need some adaptation for other application domains. Copyright © 2013 Elsevier Ltd. All rights reserved.

Sequestration of dyes from artificially prepared textile effluent using RSM-CCD optimized hybrid backbone based adsorbent-kinetic and equilibrium studies.

PubMed

Sukriti; Sharma, Jitender; Chadha, Amritpal Singh; Pruthi, Vaishali; Anand, Prerna; Bhatia, Jaspreet; Kaith, B S

2017-04-01

Present work reports the synthesis of semi-Interpenetrating Network Polymer (semi-IPN) using Gelatin-Gum xanthan hybrid backbone and polyvinyl alcohol in presence of l-tartaric acid and ammonium persulphate as the crosslinker-initiator system. Reaction parameters were optimized with Response Surface Methodology (RSM) in order to maximize the percent gel fraction of the synthesized sample. Polyvinyl alcohol, l-Tartaric acid, ammonium persulphate, reaction temperature, time and pH of the reaction medium were found to make an impact on the percentage gel fraction obtained. Incorporation of polyvinyl alcohol chains onto hybrid backbone and crosslinking between the different polymer chains were confirmed through techniques like FTIR, SEM-EDX and XRD. Semi-IPN was found to be very efficient in the removal of cationic dyes rhodamine-B (70%) and auramine-O (63%) from a mixture with an adsorbent dose of 700 mg, initial concentration of rhodamine-B 6 mgL -1 and auramine-O 26 mgL -1 , at an time interval of 22-25 h and 30 °C temp. Further to determine the nature of adsorption Langmuir and Freundlich adsorption isotherm models were studied and it was found that Langmuir adsorption isotherm was the best fit model for the removal of mixture of dyes. Kinetic studies for the sorption of dyes favored the reaction mechanism to occur via a pseudo second order pathway with R 2 value about 0.99. Copyright © 2017 Elsevier Ltd. All rights reserved.

Left-ventricle segmentation in real-time 3D echocardiography using a hybrid active shape model and optimal graph search approach

NASA Astrophysics Data System (ADS)

Zhang, Honghai; Abiose, Ademola K.; Campbell, Dwayne N.; Sonka, Milan; Martins, James B.; Wahle, Andreas

2010-03-01

Quantitative analysis of the left ventricular shape and motion patterns associated with left ventricular mechanical dyssynchrony (LVMD) is essential for diagnosis and treatment planning in congestive heart failure. Real-time 3D echocardiography (RT3DE) used for LVMD analysis is frequently limited by heavy speckle noise or partially incomplete data, thus a segmentation method utilizing learned global shape knowledge is beneficial. In this study, the endocardial surface of the left ventricle (LV) is segmented using a hybrid approach combining active shape model (ASM) with optimal graph search. The latter is used to achieve landmark refinement in the ASM framework. Optimal graph search translates the 3D segmentation into the detection of a minimum-cost closed set in a graph and can produce a globally optimal result. Various information-gradient, intensity distributions, and regional-property terms-are used to define the costs for the graph search. The developed method was tested on 44 RT3DE datasets acquired from 26 LVMD patients. The segmentation accuracy was assessed by surface positioning error and volume overlap measured for the whole LV as well as 16 standard LV regions. The segmentation produced very good results that were not achievable using ASM or graph search alone.

Automatic optimal filament segmentation with sub-pixel accuracy using generalized linear models and B-spline level-sets.

PubMed

Xiao, Xun; Geyer, Veikko F; Bowne-Anderson, Hugo; Howard, Jonathon; Sbalzarini, Ivo F

2016-08-01

Biological filaments, such as actin filaments, microtubules, and cilia, are often imaged using different light-microscopy techniques. Reconstructing the filament curve from the acquired images constitutes the filament segmentation problem. Since filaments have lower dimensionality than the image itself, there is an inherent trade-off between tracing the filament with sub-pixel accuracy and avoiding noise artifacts. Here, we present a globally optimal filament segmentation method based on B-spline vector level-sets and a generalized linear model for the pixel intensity statistics. We show that the resulting optimization problem is convex and can hence be solved with global optimality. We introduce a simple and efficient algorithm to compute such optimal filament segmentations, and provide an open-source implementation as an ImageJ/Fiji plugin. We further derive an information-theoretic lower bound on the filament segmentation error, quantifying how well an algorithm could possibly do given the information in the image. We show that our algorithm asymptotically reaches this bound in the spline coefficients. We validate our method in comprehensive benchmarks, compare with other methods, and show applications from fluorescence, phase-contrast, and dark-field microscopy. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Shape complexes: the intersection of label orderings and star convexity constraints in continuous max-flow medical image segmentation

PubMed Central

Baxter, John S. H.; Inoue, Jiro; Drangova, Maria; Peters, Terry M.

2016-01-01

Abstract. Optimization-based segmentation approaches deriving from discrete graph-cuts and continuous max-flow have become increasingly nuanced, allowing for topological and geometric constraints on the resulting segmentation while retaining global optimality. However, these two considerations, topological and geometric, have yet to be combined in a unified manner. The concept of “shape complexes,” which combine geodesic star convexity with extendable continuous max-flow solvers, is presented. These shape complexes allow more complicated shapes to be created through the use of multiple labels and super-labels, with geodesic star convexity governed by a topological ordering. These problems can be optimized using extendable continuous max-flow solvers. Previous approaches required computationally expensive coordinate system warping, which are ill-defined and ambiguous in the general case. These shape complexes are demonstrated in a set of synthetic images as well as vessel segmentation in ultrasound, valve segmentation in ultrasound, and atrial wall segmentation from contrast-enhanced CT. Shape complexes represent an extendable tool alongside other continuous max-flow methods that may be suitable for a wide range of medical image segmentation problems. PMID:28018937

Automated segmentation of the lungs from high resolution CT images for quantitative study of chronic obstructive pulmonary diseases

NASA Astrophysics Data System (ADS)

Garg, Ishita; Karwoski, Ronald A.; Camp, Jon J.; Bartholmai, Brian J.; Robb, Richard A.

2005-04-01

Chronic obstructive pulmonary diseases (COPD) are debilitating conditions of the lung and are the fourth leading cause of death in the United States. Early diagnosis is critical for timely intervention and effective treatment. The ability to quantify particular imaging features of specific pathology and accurately assess progression or response to treatment with current imaging tools is relatively poor. The goal of this project was to develop automated segmentation techniques that would be clinically useful as computer assisted diagnostic tools for COPD. The lungs were segmented using an optimized segmentation threshold and the trachea was segmented using a fixed threshold characteristic of air. The segmented images were smoothed by a morphological close operation using spherical elements of different sizes. The results were compared to other segmentation approaches using an optimized threshold to segment the trachea. Comparison of the segmentation results from 10 datasets showed that the method of trachea segmentation using a fixed air threshold followed by morphological closing with spherical element of size 23x23x5 yielded the best results. Inclusion of greater number of pulmonary vessels in the lung volume is important for the development of computer assisted diagnostic tools because the physiological changes of COPD can result in quantifiable anatomic changes in pulmonary vessels. Using a fixed threshold to segment the trachea removed airways from the lungs to a better extent as compared to using an optimized threshold. Preliminary measurements gathered from patient"s CT scans suggest that segmented images can be used for accurate analysis of total lung volume and volumes of regional lung parenchyma. Additionally, reproducible segmentation allows for quantification of specific pathologic features, such as lower intensity pixels, which are characteristic of abnormal air spaces in diseases like emphysema.

PepComposer: computational design of peptides binding to a given protein surface

PubMed Central

Obarska-Kosinska, Agnieszka; Iacoangeli, Alfredo; Lepore, Rosalba; Tramontano, Anna

2016-01-01

There is a wide interest in designing peptides able to bind to a specific region of a protein with the aim of interfering with a known interaction or as starting point for the design of inhibitors. Here we describe PepComposer, a new pipeline for the computational design of peptides binding to a given protein surface. PepComposer only requires the target protein structure and an approximate definition of the binding site as input. We first retrieve a set of peptide backbone scaffolds from monomeric proteins that harbor the same backbone arrangement as the binding site of the protein of interest. Next, we design optimal sequences for the identified peptide scaffolds. The method is fully automatic and available as a web server at http://biocomputing.it/pepcomposer/webserver. PMID:27131789

Optimal field-splitting algorithm in intensity-modulated radiotherapy: Evaluations using head-and-neck and female pelvic IMRT cases

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

Dou, Xin; Kim, Yusung, E-mail: yusung-kim@uiowa.edu; Bayouth, John E.

2013-04-01

To develop an optimal field-splitting algorithm of minimal complexity and verify the algorithm using head-and-neck (H and N) and female pelvic intensity-modulated radiotherapy (IMRT) cases. An optimal field-splitting algorithm was developed in which a large intensity map (IM) was split into multiple sub-IMs (≥2). The algorithm reduced the total complexity by minimizing the monitor units (MU) delivered and segment number of each sub-IM. The algorithm was verified through comparison studies with the algorithm as used in a commercial treatment planning system. Seven IMRT, H and N, and female pelvic cancer cases (54 IMs) were analyzed by MU, segment numbers, andmore » dose distributions. The optimal field-splitting algorithm was found to reduce both total MU and the total number of segments. We found on average a 7.9 ± 11.8% and 9.6 ± 18.2% reduction in MU and segment numbers for H and N IMRT cases with an 11.9 ± 17.4% and 11.1 ± 13.7% reduction for female pelvic cases. The overall percent (absolute) reduction in the numbers of MU and segments were found to be on average −9.7 ± 14.6% (−15 ± 25 MU) and −10.3 ± 16.3% (−3 ± 5), respectively. In addition, all dose distributions from the optimal field-splitting method showed improved dose distributions. The optimal field-splitting algorithm shows considerable improvements in both total MU and total segment number. The algorithm is expected to be beneficial for the radiotherapy treatment of large-field IMRT.« less

New synthesis of maleic anhydride modified polyolefins and their applications

NASA Astrophysics Data System (ADS)

Lu, Bing

Maleic anhydride (MA) modified polyolefins are the most useful commercial functional polyolefins. The current technology of producing MA modified polyolefins, mainly free radical modification, usually results in low MA graft contents, extensive side reactions, and poor control of graft structures. In this thesis, we show a new synthetic route for preparing MA modified polyolefins with excellent control of polymer structures and MA concentrations. The synthesis is based on the "reactive" polyolefin copolymers, i.e. polyolefins containing p-methylstyrene or alkylborane groups. The p-methylstyrene copolymers lead to selectively grafting reactions on the p-methyl groups, greatly reducing the side reactions on the polyolefin backbone. The MA graft content was proportional to the concentration of p-methylstyrene. In the borane approach, under controlled selective oxidation, the alkylborane containing PP polymers formed the "stable" polymeric radical in situ which initiated the graft-from reaction. By varying the monomer concentrations of MA and styrene, reaction time and temperature, a broad range of MA modified PP polymers were prepared from a single MA terminated or grafted PP to a very long SMA segment blocked or grafted PP, and there is no detectable side reaction on the PP backbone. MA modified polyolefins were investigated in the applications of glass fiber reinforced PP, elastomer toughened Nylon, and polyolefin/Nylon blends. The MA modified polyolefin compatibilizers showed the significant improved mechanical properties and morphology of the blends. The effectiveness of compatibilization depends on the MA concentration, molecular weight of the polyolefin segments, the structure of the compatibilizers, and the composition of the blend. By amidation or imidation reaction of MA modified PP with amine terminated PP, long chain branched PP polymers were also prepared. The results of IR, GPC, intrinsic viscosity and DSC studies clearly indicate the formation of long chain branched PP.

Impact of oxidation on protein therapeutics: Conformational dynamics of intact and oxidized acid-β-glucocerebrosidase at near-physiological pH

PubMed Central

Bobst, Cedric E; Thomas, John J; Salinas, Paul A; Savickas, Philip; Kaltashov, Igor A

2010-01-01

The solution dynamics of an enzyme acid-β-glucocerebrosidase (GCase) probed at a physiologically relevant (lysosomal) pH by hydrogen/deuterium exchange mass spectrometry (HDX-MS) reveals very uneven distribution of backbone amide protection across the polypeptide chain. Highly mobile segments are observed even within the catalytic cavity alongside highly protective segments, highlighting the importance of the balance between conformational stability and flexibility for enzymatic activity. Forced oxidation of GCase that resulted in a 40–60% reduction in in vitro biological activity affects the stability of some key structural elements within the catalytic site. These changes in dynamics occur on a longer time scale that is irrelevant for catalysis, effectively ruling out loss of structure in the catalytic site as a major factor contributing to the reduction of the catalytic activity. Oxidation also leads to noticeable destabilization of conformation in remote protein segments on a much larger scale, which is likely to increase the aggregation propensity of GCase and affect its bioavailability. Therefore, it appears that oxidation exerts its negative impact on the biological activity of GCase indirectly, primarily through accelerated aggregation and impaired trafficking. PMID:20945356

Optimal graph search segmentation using arc-weighted graph for simultaneous surface detection of bladder and prostate.

PubMed

Song, Qi; Wu, Xiaodong; Liu, Yunlong; Smith, Mark; Buatti, John; Sonka, Milan

2009-01-01

We present a novel method for globally optimal surface segmentation of multiple mutually interacting objects, incorporating both edge and shape knowledge in a 3-D graph-theoretic approach. Hard surface interacting constraints are enforced in the interacting regions, preserving the geometric relationship of those partially interacting surfaces. The soft smoothness a priori shape compliance is introduced into the energy functional to provide shape guidance. The globally optimal surfaces can be simultaneously achieved by solving a maximum flow problem based on an arc-weighted graph representation. Representing the segmentation problem in an arc-weighted graph, one can incorporate a wider spectrum of constraints into the formulation, thus increasing segmentation accuracy and robustness in volumetric image data. To the best of our knowledge, our method is the first attempt to introduce the arc-weighted graph representation into the graph-searching approach for simultaneous segmentation of multiple partially interacting objects, which admits a globally optimal solution in a low-order polynomial time. Our new approach was applied to the simultaneous surface detection of bladder and prostate. The result was quite encouraging in spite of the low saliency of the bladder and prostate in CT images.

An improved wavelet neural network medical image segmentation algorithm with combined maximum entropy

NASA Astrophysics Data System (ADS)

Hu, Xiaoqian; Tao, Jinxu; Ye, Zhongfu; Qiu, Bensheng; Xu, Jinzhang

2018-05-01

In order to solve the problem of medical image segmentation, a wavelet neural network medical image segmentation algorithm based on combined maximum entropy criterion is proposed. Firstly, we use bee colony algorithm to optimize the network parameters of wavelet neural network, get the parameters of network structure, initial weights and threshold values, and so on, we can quickly converge to higher precision when training, and avoid to falling into relative extremum; then the optimal number of iterations is obtained by calculating the maximum entropy of the segmented image, so as to achieve the automatic and accurate segmentation effect. Medical image segmentation experiments show that the proposed algorithm can reduce sample training time effectively and improve convergence precision, and segmentation effect is more accurate and effective than traditional BP neural network (back propagation neural network : a multilayer feed forward neural network which trained according to the error backward propagation algorithm.

Modified Discrete Grey Wolf Optimizer Algorithm for Multilevel Image Thresholding

PubMed Central

Sun, Lijuan; Guo, Jian; Xu, Bin; Li, Shujing

2017-01-01

The computation of image segmentation has become more complicated with the increasing number of thresholds, and the option and application of the thresholds in image thresholding fields have become an NP problem at the same time. The paper puts forward the modified discrete grey wolf optimizer algorithm (MDGWO), which improves on the optimal solution updating mechanism of the search agent by the weights. Taking Kapur's entropy as the optimized function and based on the discreteness of threshold in image segmentation, the paper firstly discretizes the grey wolf optimizer (GWO) and then proposes a new attack strategy by using the weight coefficient to replace the search formula for optimal solution used in the original algorithm. The experimental results show that MDGWO can search out the optimal thresholds efficiently and precisely, which are very close to the result examined by exhaustive searches. In comparison with the electromagnetism optimization (EMO), the differential evolution (DE), the Artifical Bee Colony (ABC), and the classical GWO, it is concluded that MDGWO has advantages over the latter four in terms of image segmentation quality and objective function values and their stability. PMID:28127305

Fast globally optimal segmentation of 3D prostate MRI with axial symmetry prior.

PubMed

Qiu, Wu; Yuan, Jing; Ukwatta, Eranga; Sun, Yue; Rajchl, Martin; Fenster, Aaron

2013-01-01

We propose a novel global optimization approach to segmenting a given 3D prostate T2w magnetic resonance (MR) image, which enforces the inherent axial symmetry of the prostate shape and simultaneously performs a sequence of 2D axial slice-wise segmentations with a global 3D coherence prior. We show that the proposed challenging combinatorial optimization problem can be solved globally and exactly by means of convex relaxation. With this regard, we introduce a novel coupled continuous max-flow model, which is dual to the studied convex relaxed optimization formulation and leads to an efficient multiplier augmented algorithm based on the modern convex optimization theory. Moreover, the new continuous max-flow based algorithm was implemented on GPUs to achieve a substantial improvement in computation. Experimental results using public and in-house datasets demonstrate great advantages of the proposed method in terms of both accuracy and efficiency.

A new synthesis route for Os-complex modified redox polymers for potential biofuel cell applications.

PubMed

Pöller, Sascha; Beyl, Yvonne; Vivekananthan, Jeevanthi; Guschin, Dmitrii A; Schuhmann, Wolfgang

2012-10-01

A new synthesis route for Os-complex modified redox polymers was developed. Instead of ligand exchange reactions for coordinative binding of suitable precursor Os-complexes at the polymer, Os-complexes already exhibiting the final ligand shell containing a suitable functional group were bound to the polymer via an epoxide opening reaction. By separation of the polymer synthesis from the ligand exchange reaction at the Os-complex, the modification of the same polymer backbone with different Os-complexes or the binding of the same Os-complex to a number of different polymer backbones becomes feasible. In addition, the Os-complex can be purified and characterized prior to its binding to the polymer. In order to further understand and optimize suitable enzyme/redox polymer systems concerning their potential application in biosensors or biofuel cells, a series of redox polymers was synthesized and used as immobilization matrix for Trametes hirsuta laccase. The properties of the obtained biofuel cell cathodes were compared with similar biocatalytic interfaces derived from redox polymers obtained via ligand exchange reaction of the parent Os-complex with a ligand integrated into the polymer backbone during the polymer synthesis. Copyright © 2011 Elsevier B.V. All rights reserved.

LOGISMOS—Layered Optimal Graph Image Segmentation of Multiple Objects and Surfaces: Cartilage Segmentation in the Knee Joint

PubMed Central

Zhang, Xiangmin; Williams, Rachel; Wu, Xiaodong; Anderson, Donald D.; Sonka, Milan

2011-01-01

A novel method for simultaneous segmentation of multiple interacting surfaces belonging to multiple interacting objects, called LOGISMOS (layered optimal graph image segmentation of multiple objects and surfaces), is reported. The approach is based on the algorithmic incorporation of multiple spatial inter-relationships in a single n-dimensional graph, followed by graph optimization that yields a globally optimal solution. The LOGISMOS method’s utility and performance are demonstrated on a bone and cartilage segmentation task in the human knee joint. Although trained on only a relatively small number of nine example images, this system achieved good performance. Judged by dice similarity coefficients (DSC) using a leave-one-out test, DSC values of 0.84 ± 0.04, 0.80 ± 0.04 and 0.80 ± 0.04 were obtained for the femoral, tibial, and patellar cartilage regions, respectively. These are excellent DSC values, considering the narrow-sheet character of the cartilage regions. Similarly, low signed mean cartilage thickness errors were obtained when compared to a manually-traced independent standard in 60 randomly selected 3-D MR image datasets from the Osteoarthritis Initiative database—0.11 ± 0.24, 0.05 ± 0.23, and 0.03 ± 0.17 mm for the femoral, tibial, and patellar cartilage thickness, respectively. The average signed surface positioning errors for the six detected surfaces ranged from 0.04 ± 0.12 mm to 0.16 ± 0.22 mm. The reported LOGISMOS framework provides robust and accurate segmentation of the knee joint bone and cartilage surfaces of the femur, tibia, and patella. As a general segmentation tool, the developed framework can be applied to a broad range of multiobject multisurface segmentation problems. PMID:20643602

Performance analysis of unsupervised optimal fuzzy clustering algorithm for MRI brain tumor segmentation.

PubMed

Blessy, S A Praylin Selva; Sulochana, C Helen

2015-01-01

Segmentation of brain tumor from Magnetic Resonance Imaging (MRI) becomes very complicated due to the structural complexities of human brain and the presence of intensity inhomogeneities. To propose a method that effectively segments brain tumor from MR images and to evaluate the performance of unsupervised optimal fuzzy clustering (UOFC) algorithm for segmentation of brain tumor from MR images. Segmentation is done by preprocessing the MR image to standardize intensity inhomogeneities followed by feature extraction, feature fusion and clustering. Different validation measures are used to evaluate the performance of the proposed method using different clustering algorithms. The proposed method using UOFC algorithm produces high sensitivity (96%) and low specificity (4%) compared to other clustering methods. Validation results clearly show that the proposed method with UOFC algorithm effectively segments brain tumor from MR images.

Direct aperture optimization using an inverse form of back-projection.

PubMed

Zhu, Xiaofeng; Cullip, Timothy; Tracton, Gregg; Tang, Xiaoli; Lian, Jun; Dooley, John; Chang, Sha X

2014-03-06

Direct aperture optimization (DAO) has been used to produce high dosimetric quality intensity-modulated radiotherapy (IMRT) treatment plans with fast treatment delivery by directly modeling the multileaf collimator segment shapes and weights. To improve plan quality and reduce treatment time for our in-house treatment planning system, we implemented a new DAO approach without using a global objective function (GFO). An index concept is introduced as an inverse form of back-projection used in the CT multiplicative algebraic reconstruction technique (MART). The index, introduced for IMRT optimization in this work, is analogous to the multiplicand in MART. The index is defined as the ratio of the optima over the current. It is assigned to each voxel and beamlet to optimize the fluence map. The indices for beamlets and segments are used to optimize multileaf collimator (MLC) segment shapes and segment weights, respectively. Preliminary data show that without sacrificing dosimetric quality, the implementation of the DAO reduced average IMRT treatment time from 13 min to 8 min for the prostate, and from 15 min to 9 min for the head and neck using our in-house treatment planning system PlanUNC. The DAO approach has also shown promise in optimizing rotational IMRT with burst mode in a head and neck test case.

Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling.

PubMed

Arnautova, Yelena A; Abagyan, Ruben A; Totrov, Maxim

2011-02-01

We report the development of internal coordinate mechanics force field (ICMFF), new force field parameterized using a combination of experimental data for crystals of small molecules and quantum mechanics calculations. The main features of ICMFF include: (a) parameterization for the dielectric constant relevant to the condensed state (ε = 2) instead of vacuum, (b) an improved description of hydrogen-bond interactions using duplicate sets of van der Waals parameters for heavy atom-hydrogen interactions, and (c) improved backbone covalent geometry and energetics achieved using novel backbone torsional potentials and inclusion of the bond angles at the C(α) atoms into the internal variable set. The performance of ICMFF was evaluated through loop modeling simulations for 4-13 residue loops. ICMFF was combined with a solvent-accessible surface area solvation model optimized using a large set of loop decoys. Conformational sampling was carried out using the biased probability Monte Carlo method. Average/median backbone root-mean-square deviations of the lowest energy conformations from the native structures were 0.25/0.21 Å for four residues loops, 0.84/0.46 Å for eight residue loops, and 1.16/0.73 Å for 12 residue loops. To our knowledge, these results are significantly better than or comparable with those reported to date for any loop modeling method that does not take crystal packing into account. Moreover, the accuracy of our method is on par with the best previously reported results obtained considering the crystal environment. We attribute this success to the high accuracy of the new ICM force field achieved by meticulous parameterization, to the optimized solvent model, and the efficiency of the search method. © 2010 Wiley-Liss, Inc.

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

Li, Dengwang; Wang, Jie; Kapp, Daniel S.

Purpose: The aim of this work is to develop a robust algorithm for accurate segmentation of liver with special attention paid to the problems with fuzzy edges and tumor. Methods: 200 CT images were collected from radiotherapy treatment planning system. 150 datasets are selected as the panel data for shape dictionary and parameters estimation. The remaining 50 datasets were used as test images. In our study liver segmentation was formulated as optimization process of implicit function. The liver region was optimized via local and global optimization during iterations. Our method consists five steps: 1)The livers from the panel data weremore » segmented manually by physicians, and then We estimated the parameters of GMM (Gaussian mixture model) and MRF (Markov random field). Shape dictionary was built by utilizing the 3D liver shapes. 2)The outlines of chest and abdomen were located according to rib structure in the input images, and the liver region was initialized based on GMM. 3)The liver shape for each 2D slice was adjusted using MRF within the neighborhood of liver edge for local optimization. 4)The 3D liver shape was corrected by employing SSR (sparse shape representation) based on liver shape dictionary for global optimization. Furthermore, H-PSO(Hybrid Particle Swarm Optimization) was employed to solve the SSR equation. 5)The corrected 3D liver was divided into 2D slices as input data of the third step. The iteration was repeated within the local optimization and global optimization until it satisfied the suspension conditions (maximum iterations and changing rate). Results: The experiments indicated that our method performed well even for the CT images with fuzzy edge and tumors. Comparing with physician delineated results, the segmentation accuracy with the 50 test datasets (VOE, volume overlap percentage) was on average 91%–95%. Conclusion: The proposed automatic segmentation method provides a sensible technique for segmentation of CT images. This work is supported by NIH/NIBIB (1R01-EB016777), National Natural Science Foundation of China (No.61471226 and No.61201441), Research funding from Shandong Province (No.BS2012DX038 and No.J12LN23), and Research funding from Jinan City (No.201401221 and No.20120109)« less

Conservation of high-flux backbone in alternate optimal and near-optimal flux distributions of metabolic networks.

PubMed

Samal, Areejit

2008-12-01

Constraint-based flux balance analysis (FBA) has proven successful in predicting the flux distribution of metabolic networks in diverse environmental conditions. FBA finds one of the alternate optimal solutions that maximizes the biomass production rate. Almaas et al. have shown that the flux distribution follows a power law, and it is possible to associate with most metabolites two reactions which maximally produce and consume a given metabolite, respectively. This observation led to the concept of high-flux backbone (HFB) in metabolic networks. In previous work, the HFB has been computed using a particular optima obtained using FBA. In this paper, we investigate the conservation of HFB of a particular solution for a given medium across different alternate optima and near-optima in metabolic networks of E. coli and S. cerevisiae. Using flux variability analysis (FVA), we propose a method to determine reactions that are guaranteed to be in HFB regardless of alternate solutions. We find that the HFB of a particular optima is largely conserved across alternate optima in E. coli, while it is only moderately conserved in S. cerevisiae. However, the HFB of a particular near-optima shows a large variation across alternate near-optima in both organisms. We show that the conserved set of reactions in HFB across alternate near-optima has a large overlap with essential reactions and reactions which are both uniquely consuming (UC) and uniquely producing (UP). Our findings suggest that the structure of the metabolic network admits a high degree of redundancy and plasticity in near-optimal flow patterns enhancing system robustness for a given environmental condition.

Developing hybrid approaches to predict pKa values of ionizable groups

PubMed Central

Witham, Shawn; Talley, Kemper; Wang, Lin; Zhang, Zhe; Sarkar, Subhra; Gao, Daquan; Yang, Wei

2011-01-01

Accurate predictions of pKa values of titratable groups require taking into account all relevant processes associated with the ionization/deionization. Frequently, however, the ionization does not involve significant structural changes and the dominating effects are purely electrostatic in origin allowing accurate predictions to be made based on the electrostatic energy difference between ionized and neutral forms alone using a static structure. On another hand, if the change of the charge state is accompanied by a structural reorganization of the target protein, then the relevant conformational changes have to be taken into account in the pKa calculations. Here we report a hybrid approach that first predicts the titratable groups, which ionization is expected to cause conformational changes, termed “problematic” residues, then applies a special protocol on them, while the rest of the pKa’s are predicted with rigid backbone approach as implemented in multi-conformation continuum electrostatics (MCCE) method. The backbone representative conformations for “problematic” groups are generated with either molecular dynamics simulations with charged and uncharged amino acid or with ab-initio local segment modeling. The corresponding ensembles are then used to calculate the pKa of the “problematic” residues and then the results are averaged. PMID:21744395

The influence of ion content on mobility and ion aggregation in PEO-based single-ion conductors

NASA Astrophysics Data System (ADS)

Caldwell, David; Maranas, Janna

2013-03-01

PEO-based ionomers reduce concentration polarization in solid polymer electrolytes by binding the anion to the polymer backbone. Ionomers have significant ion aggregation compared to PEO/salt systems, and the influence of these aggregates is unclear. When ion transport is coupled to the segmental dynamics of the polymer, aggregation will always reduce ion motion and conductivity. However, the conductivity of PEO ionomers is not sensitive to the degree of aggregation. We present results of molecular dynamics simulations where ion content is systematically varied. We consider the influence of ion content on ion aggregation, polymer mobility and cation motion.

A Novel Mechanism of Sugar Selection Utilized by a Human X-family DNA Polymerase†

PubMed Central

Brown, Jessica A.; Fiala, Kevin A.; Fowler, Jason D.; Sherrer, Shanen M.; Newmister, Sean A.; Dyum, Wade W.; Suo, Zucai

2009-01-01

During DNA synthesis, most DNA polymerases and reverse transcriptases select against ribonucleotides via a steric clash between the ribose 2′-hydroxyl group and the bulky side chain of an active site residue. Here, we demonstrated that human DNA polymerase λ used a novel sugar selection mechanism to discriminate against ribonucleotides, whereby the ribose 2′-hydroxyl group was excluded mostly by a backbone segment and slightly by the side chain of Y505. Such a steric clash was further demonstrated to be dependent on the size and orientation of the substituent covalently attached at the ribonucleotide C2′ position. PMID:19900463

Simulation study of poled low-water ionomers with different architectures

NASA Astrophysics Data System (ADS)

Allahyarov, Elshad; Taylor, Philip L.; Löwen, Hartmut

2011-11-01

The role of the ionomer architecture in the formation of ordered structures in poled membranes is investigated by molecular dynamics computer simulations. It is shown that the length of the sidechain Ls controls both the areal density of cylindrical aggregates Nc and the diameter of these cylinders in the poled membrane. The backbone segment length Lb tunes the average diameter Ds of cylindrical clusters and the average number of sulfonates Ns in each cluster. A simple empirical formula is noted for the dependence of the number density of induced rod-like aggregates on the sidechain length Ls within the parameter range considered in this study.

KSC-06pd1677

NASA Image and Video Library

2006-07-26

KENNEDY SPACE CENTER, FLA. - On Launch Pad 39B, the payload canister is lifted toward the payload changeout room (PCR) for transfer of its cargo into the PCR. The canister holds the payload for Atlantis and mission STS-115, the Port 3/4 truss segment with two large solar arrays. The red umbilical lines are still attached to the transporter, below it. To the right of the rotating structure is the fixed service structure with the 80-foot lightning mast on top. The payload changeout room provides an environmentally clean or "white room" condition in which to receive a payload transferred from a protective payload canister. After the shuttle arrives at the pad, the rotating service structure will close around it and the payload will then be transferred into Atlantis' payload bay. Atlantis' launch window begins Aug. 28. During its 11-day mission to the International Space Station, the STS-115 crew of six astronauts will install the truss, a 17-ton segment of the space station's truss backbone. Photo credit: NASA/George Shelton

Building the backbone: the development and evolution of vertebral patterning.

PubMed

Fleming, Angeleen; Kishida, Marcia G; Kimmel, Charles B; Keynes, Roger J

2015-05-15

The segmented vertebral column comprises a repeat series of vertebrae, each consisting of two key components: the vertebral body (or centrum) and the vertebral arches. Despite being a defining feature of the vertebrates, much remains to be understood about vertebral development and evolution. Particular controversy surrounds whether vertebral component structures are homologous across vertebrates, how somite and vertebral patterning are connected, and the developmental origin of vertebral bone-mineralizing cells. Here, we assemble evidence from ichthyologists, palaeontologists and developmental biologists to consider these issues. Vertebral arch elements were present in early stem vertebrates, whereas centra arose later. We argue that centra are homologous among jawed vertebrates, and review evidence in teleosts that the notochord plays an instructive role in segmental patterning, alongside the somites, and contributes to mineralization. By clarifying the evolutionary relationship between centra and arches, and their varying modes of skeletal mineralization, we can better appreciate the detailed mechanisms that regulate and diversify vertebral patterning. © 2015. Published by The Company of Biologists Ltd.

Structure and mechanisms underlying ion transport in ternary polymer electrolytes containing ionic liquids

NASA Astrophysics Data System (ADS)

Mogurampelly, Santosh; Ganesan, Venkat

2017-02-01

We use all atom molecular dynamics simulations to investigate the influence of 1-butyl-3-methylimidazolium hexafluorophosphate (BMIMPF6) ionic liquid on the structure and transport properties of poly(ethylene oxide) (PEO) polymer electrolytes doped with LiPF6 salt. We observe enhanced diffusivities of the Li+, PF6-, and BMIM+ ions with increasing loading of the ionic liquid. Interplay between the different ion-ion and ion-polymer interactions is seen to lead to a destabilization of the Li-PF6 coordination and increase in the strength of association between the Li+ cations and the polymer backbone. As a consequence, the polymer segmental relaxation times are shown to be only moderately affected by the addition of ionic liquids. The ionic-liquid induced changes in the mobilities of Li+ ions are seen to be correlated to polymer segmental relaxation times. However, the mobilities of BMIM+ ions are seen to be more strongly correlated to the BMIM-PF6 ion-pair relaxation times.

Facile preparation of mussel-inspired polyurethane hydrogel and its rapid curing behavior.

PubMed

Sun, Peiyu; Wang, Jing; Yao, Xiong; Peng, Ying; Tu, Xiaoxiong; Du, Pengfei; Zheng, Zhen; Wang, Xinling

2014-08-13

A facile method was found to incorporate a mussel-inspired adhesive moiety into synthetic polymers, and mussel mimetic polyurethanes were developed as adhesive hydrogels. In these polymers, a urethane backbone was substituted for the polyamide chain of mussel adhesive proteins, and dopamine was appended to mimic the adhesive moiety of adhesive proteins. A series of mussel mimetic polyurethanes were created through a step-growth polymerization based on hexamethylene diisocyanate as a hard segment, PEG having different molecular weights as a soft segment, and lysine-dopamine as a chain extender. Upon a treatment with Fe(3+), the aqueous mussel mimetic polyurethane solutions can be triggered by pH adjustment to form adhesive hydrogels instantaneously; these materials can be used as injectable adhesive hydrogels. Upon a treatment with NaIO4, the mussel mimetic polyurethane solutions can be cured in a controllable period of time. The successful combination of the unique mussel-inspired adhesive moiety with a tunable polyurethane structure can result in a new kind of mussel-inspired adhesive polymers.

KSC-07pp1466

NASA Image and Video Library

2007-06-08

KENNEDY SPACE CENTER, FLA. -- Smoke and steam billow across Launch Pad 39A as Space Shuttle Atlantis, trailing columns of fire from the solid rocket boosters, hurtles into the sky on mission STS-117 to the International Space Station. At left is the fixed service structure with the 80-foot-tall lightning mast on top. At right is the 290-foot-high water tower that supplies the water for sound suppression. Liftoff was on-time at 7:38:04 p.m. EDT. The shuttle is delivering a new segment to the starboard side of the International Space Station's backbone, known as the truss. Three spacewalks are planned to install the S3/S4 truss segment, deploy a set of solar arrays and prepare them for operation. STS-117 is the 118th space shuttle flight, the 21st flight to the station, the 28th flight for Atlantis and the first of four flights planned for 2007. Photo credit: NASA/Tony Gray & Don Kight

On Inertial Body Tracking in the Presence of Model Calibration Errors

PubMed Central

Miezal, Markus; Taetz, Bertram; Bleser, Gabriele

2016-01-01

In inertial body tracking, the human body is commonly represented as a biomechanical model consisting of rigid segments with known lengths and connecting joints. The model state is then estimated via sensor fusion methods based on data from attached inertial measurement units (IMUs). This requires the relative poses of the IMUs w.r.t. the segments—the IMU-to-segment calibrations, subsequently called I2S calibrations—to be known. Since calibration methods based on static poses, movements and manual measurements are still the most widely used, potentially large human-induced calibration errors have to be expected. This work compares three newly developed/adapted extended Kalman filter (EKF) and optimization-based sensor fusion methods with an existing EKF-based method w.r.t. their segment orientation estimation accuracy in the presence of model calibration errors with and without using magnetometer information. While the existing EKF-based method uses a segment-centered kinematic chain biomechanical model and a constant angular acceleration motion model, the newly developed/adapted methods are all based on a free segments model, where each segment is represented with six degrees of freedom in the global frame. Moreover, these methods differ in the assumed motion model (constant angular acceleration, constant angular velocity, inertial data as control input), the state representation (segment-centered, IMU-centered) and the estimation method (EKF, sliding window optimization). In addition to the free segments representation, the optimization-based method also represents each IMU with six degrees of freedom in the global frame. In the evaluation on simulated and real data from a three segment model (an arm), the optimization-based method showed the smallest mean errors, standard deviations and maximum errors throughout all tests. It also showed the lowest dependency on magnetometer information and motion agility. Moreover, it was insensitive w.r.t. I2S position and segment length errors in the tested ranges. Errors in the I2S orientations were, however, linearly propagated into the estimated segment orientations. In the absence of magnetic disturbances, severe model calibration errors and fast motion changes, the newly developed IMU centered EKF-based method yielded comparable results with lower computational complexity. PMID:27455266

A general framework for multicharacter segmentation and its application in recognizing multilingual Asian documents

NASA Astrophysics Data System (ADS)

Wen, Di; Ding, Xiaoqing

2003-12-01

In this paper we propose a general framework for character segmentation in complex multilingual documents, which is an endeavor to combine the traditionally separated segmentation and recognition processes into a cooperative system. The framework contains three basic steps: Dissection, Local Optimization and Global Optimization, which are designed to fuse various properties of the segmentation hypotheses hierarchically into a composite evaluation to decide the final recognition results. Experimental results show that this framework is general enough to be applied in variety of documents. A sample system based on this framework to recognize Chinese, Japanese and Korean documents and experimental performance is reported finally.

A bioluminescent imaging mouse model for Marburg virus based on a pseudovirus system.

PubMed

Zhang, Li; Li, Qianqian; Liu, Qiang; Huang, Weijin; Nie, Jianhui; Wang, Youchun

2017-08-03

Marburg virus (MARV) can cause lethal hemorrhagic fever in humans. Handling of MARV is restricted to high-containment biosafety level 4 (BSL-4) facilities, which greatly impedes research into this virus. In this study, a high titer of MARV pseudovirus was generated through optimization of the HIV backbone vectors, the ratio of backbone vector to MARV glycoprotein expression vector, and the transfection reagents. An in vitro neutralization assay and an in vivo bioluminescent imaging mouse model for MARV were developed based on the pseudovirus. Protective serum against MARV was successfully induced in guinea pigs, which showed high neutralization activity in vitro and could also protect Balb/c mice from MARV pseudovirus infection in vivo. This system could be a convenient tool to enable the evaluation of vaccines and therapeutic drugs against MARV in non-BSL-4 laboratories.

SU-F-T-387: A Novel Optimization Technique for Field in Field (FIF) Chestwall Radiation Therapy Using a Single Plan to Improve Delivery Safety and Treatment Planning Efficiency

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

Tabibian, A; Kim, A; Rose, J

Purpose: A novel optimization technique was developed for field-in-field (FIF) chestwall radiotherapy using bolus every other day. The dosimetry was compared to currently used optimization. Methods: The prior five patients treated at our clinic to the chestwall and supraclavicular nodes with a mono-isocentric four-field arrangement were selected for this study. The prescription was 5040 cGy in 28 fractions, 5 mm bolus every other day on the tangent fields, 6 and/or 10 MV x-rays, and multileaf collimation.Novelly, tangents FIF segments were forward planned optimized based on the composite bolus and non-bolus dose distribution simultaneously. The prescription was spilt into 14 fractionsmore » for both bolus and non-bolus tangents. The same segments and monitor units were used for the bolus and non-bolus treatment. The plan was optimized until the desired coverage was achieved, minimized 105% hotspots, and a maximum dose of less than 108%. Each tangential field had less than 5 segments.Comparison plans were generated using FIF optimization with the same dosimetric goals, but using only the non-bolus calculation for FIF optimization. The non-bolus fields were then copied and bolus was applied. The same segments and monitor units were used for the bolus and non-bolus segments. Results: The prescription coverage of the chestwall, as defined by RTOG guidelines, was on average 51.8% for the plans that optimized bolus and non-bolus treatments simultaneous (SB) and 43.8% for the plans optimized to the non-bolus treatments (NB). Chestwall coverage of 90% prescription averaged to 80.4% for SB and 79.6% for NB plans. The volume receiving 105% of the prescription was 1.9% for SB and 0.8% for NB plans on average. Conclusion: Simultaneously optimizing for bolus and non-bolus treatments noticeably improves prescription coverage of the chestwall while maintaining similar hotspots and 90% prescription coverage in comparison to optimizing only to non-bolus treatments.« less

Software for Alignment of Segments of a Telescope Mirror

NASA Technical Reports Server (NTRS)

Hall, Drew P.; Howard, Richard T.; Ly, William C.; Rakoczy, John M.; Weir, John M.

2006-01-01

The Segment Alignment Maintenance System (SAMS) software is designed to maintain the overall focus and figure of the large segmented primary mirror of the Hobby-Eberly Telescope. This software reads measurements made by sensors attached to the segments of the primary mirror and from these measurements computes optimal control values to send to actuators that move the mirror segments.

Adaptive distance metric learning for diffusion tensor image segmentation.

PubMed

Kong, Youyong; Wang, Defeng; Shi, Lin; Hui, Steve C N; Chu, Winnie C W

2014-01-01

High quality segmentation of diffusion tensor images (DTI) is of key interest in biomedical research and clinical application. In previous studies, most efforts have been made to construct predefined metrics for different DTI segmentation tasks. These methods require adequate prior knowledge and tuning parameters. To overcome these disadvantages, we proposed to automatically learn an adaptive distance metric by a graph based semi-supervised learning model for DTI segmentation. An original discriminative distance vector was first formulated by combining both geometry and orientation distances derived from diffusion tensors. The kernel metric over the original distance and labels of all voxels were then simultaneously optimized in a graph based semi-supervised learning approach. Finally, the optimization task was efficiently solved with an iterative gradient descent method to achieve the optimal solution. With our approach, an adaptive distance metric could be available for each specific segmentation task. Experiments on synthetic and real brain DTI datasets were performed to demonstrate the effectiveness and robustness of the proposed distance metric learning approach. The performance of our approach was compared with three classical metrics in the graph based semi-supervised learning framework.

Adaptive Distance Metric Learning for Diffusion Tensor Image Segmentation

PubMed Central

Kong, Youyong; Wang, Defeng; Shi, Lin; Hui, Steve C. N.; Chu, Winnie C. W.

2014-01-01

High quality segmentation of diffusion tensor images (DTI) is of key interest in biomedical research and clinical application. In previous studies, most efforts have been made to construct predefined metrics for different DTI segmentation tasks. These methods require adequate prior knowledge and tuning parameters. To overcome these disadvantages, we proposed to automatically learn an adaptive distance metric by a graph based semi-supervised learning model for DTI segmentation. An original discriminative distance vector was first formulated by combining both geometry and orientation distances derived from diffusion tensors. The kernel metric over the original distance and labels of all voxels were then simultaneously optimized in a graph based semi-supervised learning approach. Finally, the optimization task was efficiently solved with an iterative gradient descent method to achieve the optimal solution. With our approach, an adaptive distance metric could be available for each specific segmentation task. Experiments on synthetic and real brain DTI datasets were performed to demonstrate the effectiveness and robustness of the proposed distance metric learning approach. The performance of our approach was compared with three classical metrics in the graph based semi-supervised learning framework. PMID:24651858

Topology optimization for design of segmented permanent magnet arrays with ferromagnetic materials

NASA Astrophysics Data System (ADS)

Lee, Jaewook; Yoon, Minho; Nomura, Tsuyoshi; Dede, Ercan M.

2018-03-01

This paper presents multi-material topology optimization for the co-design of permanent magnet segments and iron material. Specifically, a co-design methodology is proposed to find an optimal border of permanent magnet segments, a pattern of magnetization directions, and an iron shape. A material interpolation scheme is proposed for material property representation among air, permanent magnet, and iron materials. In this scheme, the permanent magnet strength and permeability are controlled by density design variables, and permanent magnet magnetization directions are controlled by angle design variables. In addition, a scheme to penalize intermediate magnetization direction is proposed to achieve segmented permanent magnet arrays with discrete magnetization directions. In this scheme, permanent magnet strength is controlled depending on magnetization direction, and consequently the final permanent magnet design converges into permanent magnet segments having target discrete directions. To validate the effectiveness of the proposed approach, three design examples are provided. The examples include the design of a dipole Halbach cylinder, magnetic system with arbitrarily-shaped cavity, and multi-objective problem resembling a magnetic refrigeration device.

Stability Mechanisms of a Thermophilic Laccase Probed by Molecular Dynamics

PubMed Central

Christensen, Niels J.; Kepp, Kasper P.

2013-01-01

Laccases are highly stable, industrially important enzymes capable of oxidizing a large range of substrates. Causes for their stability are, as for other proteins, poorly understood. In this work, multiple-seed molecular dynamics (MD) was applied to a Trametes versicolor laccase in response to variable ionic strengths, temperatures, and glycosylation status. Near-physiological conditions provided excellent agreement with the crystal structure (average RMSD ∼0.92 Å) and residual agreement with experimental B-factors. The persistence of backbone hydrogen bonds was identified as a key descriptor of structural response to environment, whereas solvent-accessibility, radius of gyration, and fluctuations were only locally relevant. Backbone hydrogen bonds decreased systematically with temperature in all simulations (∼9 per 50 K), probing structural changes associated with enthalpy-entropy compensation. Approaching T opt (∼350 K) from 300 K, this change correlated with a beginning “unzipping” of critical β-sheets. 0 M ionic strength triggered partial denucleation of the C-terminal (known experimentally to be sensitive) at 400 K, suggesting a general salt stabilization effect. In contrast, F− (but not Cl−) specifically impaired secondary structure by formation of strong hydrogen bonds with backbone NH, providing a mechanism for experimentally observed small anion destabilization, potentially remedied by site-directed mutagenesis at critical intrusion sites. N-glycosylation was found to support structural integrity by increasing persistent backbone hydrogen bonds by ∼4 across simulations, mainly via prevention of F− intrusion. Hydrogen-bond loss in distinct loop regions and ends of critical β-sheets suggest potential strategies for laboratory optimization of these industrially important enzymes. PMID:23658618

Multi-segment detector array for hybrid reflection-mode ultrasound and optoacoustic tomography (Conference Presentation)

NASA Astrophysics Data System (ADS)

Merčep, Elena; Burton, Neal C.; Deán-Ben, Xosé Luís.; Razansky, Daniel

2017-02-01

The complementary contrast of the optoacoustic (OA) and pulse-echo ultrasound (US) modalities makes the combined usage of these imaging technologies highly advantageous. Due to the different physical contrast mechanisms development of a detector array optimally suited for both modalities is one of the challenges to efficient implementation of a single OA-US imaging device. We demonstrate imaging performance of the first hybrid detector array whose novel design, incorporating array segments of linear and concave geometry, optimally supports image acquisition in both reflection-mode ultrasonography and optoacoustic tomography modes. Hybrid detector array has a total number of 256 elements and three segments of different geometry and variable pitch size: a central 128-element linear segment with pitch of 0.25mm, ideally suited for pulse-echo US imaging, and two external 64-elements segments with concave geometry and 0.6mm pitch optimized for OA image acquisition. Interleaved OA and US image acquisition with up to 25 fps is facilitated through a custom-made multiplexer unit. Spatial resolution of the transducer was characterized in numerical simulations and validated in phantom experiments and comprises 230 and 300 μm in the respective OA and US imaging modes. Imaging performance of the multi-segment detector array was experimentally shown in a series of imaging sessions with healthy volunteers. Employing mixed array geometries allows at the same time achieving excellent OA contrast with a large field of view, and US contrast for complementary structural features with reduced side-lobes and improved resolution. The newly designed hybrid detector array that comprises segments of linear and concave geometries optimally fulfills requirements for efficient US and OA imaging and may expand the applicability of the developed hybrid OPUS imaging technology and accelerate its clinical translation.

Performance Evaluation of the NASA/KSC Transmission System

NASA Technical Reports Server (NTRS)

Christensen, Kenneth J.

2000-01-01

NASA-KSC currently uses three bridged 100-Mbps FDDI segments as its backbone for data traffic. The FDDI Transmission System (FTXS) connects the KSC industrial area, KSC launch complex 39 area, and the Cape Canaveral Air Force Station. The report presents a performance modeling study of the FTXS and the proposed ATM Transmission System (ATXS). The focus of the study is on performance of MPEG video transmission on these networks. Commercial modeling tools - the CACI Predictor and Comnet tools - were used. In addition, custom software tools were developed to characterize conversation pairs in Sniffer trace (capture) files to use as input to these tools. A baseline study of both non-launch and launch day data traffic on the FTXS is presented. MPEG-1 and MPEG-2 video traffic was characterized and the shaping of it evaluated. It is shown that the characteristics of a video stream has a direct effect on its performance in a network. It is also shown that shaping of video streams is necessary to prevent overflow losses and resulting poor video quality. The developed models can be used to predict when the existing FTXS will 'run out of room' and for optimizing the parameters of ATM links used for transmission of MPEG video. Future work with these models can provide useful input and validation to set-top box projects within the Advanced Networks Development group in NASA-KSC Development Engineering.

Utilizing Benzotriazole and Indacenodithiophene Units to Construct both Polymeric Donor and Small Molecular Acceptors to Realize Organic Solar Cells with High Open-Circuit Voltages beyond 1.2 V

NASA Astrophysics Data System (ADS)

Tang, Ailing; Chen, Fan; Xiao, Bo; Yang, Jing; Li, Jianfeng; Wang, Xiaochen; Zhou, Erjun

2018-05-01

Devolopment of organic solar cells with high open-circuit voltage (VOC) and power conversion efficiency (PCE) simutaniously plays a significant role, but there is no guideline how to choose the suitable photovoltaic material combinations. In this study, we adopted a simple and feasible strategy by utilizing the same electron-donating unit and electron-accepting segment to construct both polymeric donor and small molecular acceptors. The p-type polymer of PIDT-DTffBTA is designed by inserting conjugated bridge between indacenodithiophene (IDT) and fluorinated benzotriazole (BTA), while the n-type small molecules of BTAx (x = 1, 2, 3) are obtained by introducing different end-capped groups to BTA-IDT-BTA backbone. PIDT-DTffBTA: BTAx (x = 1-3) based photovolatic devices can realize high VOC of 1.21-1.37 V with the very small voltage loss (0.55-0.60 V), while only the PIDT-DTffBTA: BTA3 based device possesses the enough driving force for efficient hole and electron transfer and yields the optimal PCE of 5.67%, which is among the highest value for organic solar cells with a VOC beyond 1.20 V reported so far. Our results provide a simple and effective method to obtain fullerene-free organic solar cells with a high VOC and PCE.

Globally optimal tumor segmentation in PET-CT images: a graph-based co-segmentation method.

PubMed

Han, Dongfeng; Bayouth, John; Song, Qi; Taurani, Aakant; Sonka, Milan; Buatti, John; Wu, Xiaodong

2011-01-01

Tumor segmentation in PET and CT images is notoriously challenging due to the low spatial resolution in PET and low contrast in CT images. In this paper, we have proposed a general framework to use both PET and CT images simultaneously for tumor segmentation. Our method utilizes the strength of each imaging modality: the superior contrast of PET and the superior spatial resolution of CT. We formulate this problem as a Markov Random Field (MRF) based segmentation of the image pair with a regularized term that penalizes the segmentation difference between PET and CT. Our method simulates the clinical practice of delineating tumor simultaneously using both PET and CT, and is able to concurrently segment tumor from both modalities, achieving globally optimal solutions in low-order polynomial time by a single maximum flow computation. The method was evaluated on clinically relevant tumor segmentation problems. The results showed that our method can effectively make use of both PET and CT image information, yielding segmentation accuracy of 0.85 in Dice similarity coefficient and the average median hausdorff distance (HD) of 6.4 mm, which is 10% (resp., 16%) improvement compared to the graph cuts method solely using the PET (resp., CT) images.

Segmentation of deformable organs from medical images using particle swarm optimization and nonlinear shape priors

NASA Astrophysics Data System (ADS)

Afifi, Ahmed; Nakaguchi, Toshiya; Tsumura, Norimichi

2010-03-01

In many medical applications, the automatic segmentation of deformable organs from medical images is indispensable and its accuracy is of a special interest. However, the automatic segmentation of these organs is a challenging task according to its complex shape. Moreover, the medical images usually have noise, clutter, or occlusion and considering the image information only often leads to meager image segmentation. In this paper, we propose a fully automated technique for the segmentation of deformable organs from medical images. In this technique, the segmentation is performed by fitting a nonlinear shape model with pre-segmented images. The kernel principle component analysis (KPCA) is utilized to capture the complex organs deformation and to construct the nonlinear shape model. The presegmentation is carried out by labeling each pixel according to its high level texture features extracted using the overcomplete wavelet packet decomposition. Furthermore, to guarantee an accurate fitting between the nonlinear model and the pre-segmented images, the particle swarm optimization (PSO) algorithm is employed to adapt the model parameters for the novel images. In this paper, we demonstrate the competence of proposed technique by implementing it to the liver segmentation from computed tomography (CT) scans of different patients.

Optimal Design of General Stiffened Composite Circular Cylinders for Global Buckling with Strength Constraints

NASA Technical Reports Server (NTRS)

Jaunky, N.; Ambur, D. R.; Knight, N. F., Jr.

1998-01-01

A design strategy for optimal design of composite grid-stiffened cylinders subjected to global and local buckling constraints and strength constraints was developed using a discrete optimizer based on a genetic algorithm. An improved smeared stiffener theory was used for the global analysis. Local buckling of skin segments were assessed using a Rayleigh-Ritz method that accounts for material anisotropy. The local buckling of stiffener segments were also assessed. Constraints on the axial membrane strain in the skin and stiffener segments were imposed to include strength criteria in the grid-stiffened cylinder design. Design variables used in this study were the axial and transverse stiffener spacings, stiffener height and thickness, skin laminate stacking sequence and stiffening configuration, where stiffening configuration is a design variable that indicates the combination of axial, transverse and diagonal stiffener in the grid-stiffened cylinder. The design optimization process was adapted to identify the best suited stiffening configurations and stiffener spacings for grid-stiffened composite cylinder with the length and radius of the cylinder, the design in-plane loads and material properties as inputs. The effect of having axial membrane strain constraints in the skin and stiffener segments in the optimization process is also studied for selected stiffening configurations.

Optimal Design of General Stiffened Composite Circular Cylinders for Global Buckling with Strength Constraints

NASA Technical Reports Server (NTRS)

Jaunky, Navin; Knight, Norman F., Jr.; Ambur, Damodar R.

1998-01-01

A design strategy for optimal design of composite grid-stiffened cylinders subjected to global and local buckling constraints and, strength constraints is developed using a discrete optimizer based on a genetic algorithm. An improved smeared stiffener theory is used for the global analysis. Local buckling of skin segments are assessed using a Rayleigh-Ritz method that accounts for material anisotropy. The local buckling of stiffener segments are also assessed. Constraints on the axial membrane strain in the skin and stiffener segments are imposed to include strength criteria in the grid-stiffened cylinder design. Design variables used in this study are the axial and transverse stiffener spacings, stiffener height and thickness, skin laminate stacking sequence, and stiffening configuration, where herein stiffening configuration is a design variable that indicates the combination of axial, transverse, and diagonal stiffener in the grid-stiffened cylinder. The design optimization process is adapted to identify the best suited stiffening configurations and stiffener spacings for grid-stiffened composite cylinder with the length and radius of the cylinder, the design in-plane loads, and material properties as inputs. The effect of having axial membrane strain constraints in the skin and stiffener segments in the optimization process is also studied for selected stiffening configuration.

Renal cortex segmentation using optimal surface search with novel graph construction.

PubMed

Li, Xiuli; Chen, Xinjian; Yao, Jianhua; Zhang, Xing; Tian, Jie

2011-01-01

In this paper, we propose a novel approach to solve the renal cortex segmentation problem, which has rarely been studied. In this study, the renal cortex segmentation problem is handled as a multiple-surfaces extraction problem, which is solved using the optimal surface search method. We propose a novel graph construction scheme in the optimal surface search to better accommodate multiple surfaces. Different surface sub-graphs are constructed according to their properties, and inter-surface relationships are also modeled in the graph. The proposed method was tested on 17 clinical CT datasets. The true positive volume fraction (TPVF) and false positive volume fraction (FPVF) are 74.10% and 0.08%, respectively. The experimental results demonstrate the effectiveness of the proposed method.

Chemical crosslinking and mass spectrometry studies of the structure and dynamics of membrane proteins and receptors.

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

Haskins, William E.; Leavell, Michael D.; Lane, Pamela

2005-03-01

Membrane proteins make up a diverse and important subset of proteins for which structural information is limited. In this study, chemical cross-linking and mass spectrometry were used to explore the structure of the G-protein-coupled photoreceptor bovine rhodopsin in the dark-state conformation. All experiments were performed in rod outer segment membranes using amino acid 'handles' in the native protein sequence and thus minimizing perturbations to the native protein structure. Cysteine and lysine residues were covalently cross-linked using commercially available reagents with a range of linker arm lengths. Following chemical digestion of cross-linked protein, cross-linked peptides were identified by accurate mass measurementmore » using liquid chromatography-fourier transform mass spectrometry and an automated data analysis pipeline. Assignments were confirmed and, if necessary, resolved, by tandem MS. The relative reactivity of lysine residues participating in cross-links was evaluated by labeling with NHS-esters. A distinct pattern of cross-link formation within the C-terminal domain, and between loop I and the C-terminal domain, emerged. Theoretical distances based on cross-linking were compared to inter-atomic distances determined from the energy-minimized X-ray crystal structure and Monte Carlo conformational search procedures. In general, the observed cross-links can be explained by re-positioning participating side-chains without significantly altering backbone structure. One exception, between C3 16 and K325, requires backbone motion to bring the reactive atoms into sufficient proximity for cross-linking. Evidence from other studies suggests that residues around K325 for a region of high backbone mobility. These findings show that cross-linking studies can provide insight into the structural dynamics of membrane proteins in their native environment.« less

Ion transport mechanisms in lamellar phases of salt-doped PS-PEO block copolymer electrolytes.

PubMed

Sethuraman, Vaidyanathan; Mogurampelly, Santosh; Ganesan, Venkat

2017-11-01

We use a multiscale simulation strategy to elucidate, at an atomistic level, the mechanisms underlying ion transport in the lamellar phase of polystyrene-polyethylene oxide (PS-PEO) block copolymer (BCP) electrolytes doped with LiPF 6 salts. Explicitly, we compare the results obtained for ion transport in the microphase separated block copolymer melts to those for salt-doped PEO homopolymer melts. In addition, we also present results for dynamics of the ions individually in the PEO and PS domains of the BCP melt, and locally as a function of the distance from the lamellar interfaces. When compared to the PEO homopolymer melt, ions were found to exhibit slower dynamics in both the block copolymer (overall) and in the PEO phase of the BCP melt. Such results are shown to arise from the effects of slower polymer segmental dynamics in the BCP melt and the coordination characteristics of the ions. Polymer backbone-ion residence times analyzed as a function of distance from the interface indicate that ions have a larger residence time near the interface compared to that near the bulk of lamella, and demonstrates the influence of the glassy PS blocks and microphase segregation on the ion transport properties. Ion transport mechanisms in BCP melts reveal that there exist five distinct mechanisms for ion transport along the backbone of the chain and exhibit qualitative differences from the behavior in homopolymer melts. We also present results as a function of salt concentration which show that the mean-squared displacements of the ions decrease with increasing salt concentration, and that the ion residence times near the polymer backbone increase with increasing salt concentration.

A Complete NMR Spectral Assignment of the Lipid-free Mouse Apolipoprotein A-I (ApoAI) C-terminal Truncation Mutant, ApoAI(1-216)

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

Yang, Yunhuang; Hoyt, David W.; Wang, Jianjun

2007-07-28

Apolipoprotein A-I (apoAI) is the major protein component of the high-density lipoprotein (HDL) that has been a hot subject of interests because of its anti-atherogenic properties. Upon lipid-binding, apoAI undergoes conformational changes from lipid-free to several different HDL-associated states (1). These different conformational states regulate HDL formation, maturation and transportation. Recent crystal structure of lipid-free human apoAI represents a major progress of structural study of lipid-free apoAI (2). However, no structural is available for lipid-free mouse apoAI (240-residues). Since mouse HDL is homogenous with only HDL2-like size, whereas human HDL is heterogeneous, containing HDL2/HDL3 as its main species, a structuralmore » comparison between human and mouse apoAI may allow us to identify structure basis of HDL size distribution difference between human and mouse. We carried out an NMR structure determination of lipid-free mouse apoAI (1-216) and completely assigned backbone atoms (except backbone amide proton and nitrogen atoms for residues D1, N48, W107, K108, K132, E135, F147, R148, M169 and K203). Secondary structure prediction using backbone NMR parameters indicates that lipid-free mouse apoAI consists of a four helical segments in the N-terminal domain, residues 1-180. In addition, two short helices are also observed between residues 190-195 and 210-215. The helix locations are significantly different from those in the crystal structure of human apoAI, suggesting that mouse apoAI may have a different conformational adaptation upon lipid-binding. BMRB deposit with accession number: 15091.« less

Synthesis and Characterization of a Chondroitin Sulfate Based Hybrid Bio/Synthetic Biomimetic Aggrecan Macromolecule

NASA Astrophysics Data System (ADS)

Sarkar, Sumona

Lower back pain resulting from intervertebral disc degeneration is one of the leading musculoskeletal disorders confronting our health system. In order to mechanically stabilize the disc early in the degenerative cascade and prevent the need for spinal fusion surgeries, we have proposed the development of a hybrid-bio/synthetic biomimetic proteoglycan macromolecule for injection into the disc in the early stages of degeneration. The goal of this thesis was to incorporate natural chondroitin sulfate (CS) chains into bottle brush polymer synthesis strategies for the fabrication of CS-macromolecules which mimic the proteoglycan structure and function while resisting enzymatic degradation. Both the "grafting-to" and "grafting-through" techniques of bottle brush synthesis were explored. CS was immobilized via a terminal primary amine onto a model polymeric backbone (polyacrylic acid) for investigation of the "grafting-to" strategy and an epoxy-amine step-growth polymerization technique was utilized for the "grafting-through" synthesis of CS-macromolecules with polyethylene glycol backbone segments. Incorporation of a synthetic polymeric backbone at the terminal amine of CS was confirmed via biochemical assays, 1H-NMR and FTIR spectroscopy, and CS-macromolecule size was demonstrated to be higher than that of natural CS via gel permeation chromatography, transmission electron microscopy and viscosity measurements. Further analysis of CS-macromolecule functionality indicated maintenance of natural CS properties such as high fixed charge density, high osmotic potential and low cytotoxicity with nucleus pulposus cells. These studies are the first attempt at the incorporation of natural CS into biomimetic bottle brush structures. CS-macromolecules synthesized via the methods developed in these studies may be utilized in the treatment and prevention of debilitating back pain as well as act as mimetics for other proteoglycans implicated in cartilage, heart valve, and nervous system tissue function.

Bayesian segmentation of atrium wall using globally-optimal graph cuts on 3D meshes.

PubMed

Veni, Gopalkrishna; Fu, Zhisong; Awate, Suyash P; Whitaker, Ross T

2013-01-01

Efficient segmentation of the left atrium (LA) wall from delayed enhancement MRI is challenging due to inconsistent contrast, combined with noise, and high variation in atrial shape and size. We present a surface-detection method that is capable of extracting the atrial wall by computing an optimal a-posteriori estimate. This estimation is done on a set of nested meshes, constructed from an ensemble of segmented training images, and graph cuts on an associated multi-column, proper-ordered graph. The graph/mesh is a part of a template/model that has an associated set of learned intensity features. When this mesh is overlaid onto a test image, it produces a set of costs which lead to an optimal segmentation. The 3D mesh has an associated weighted, directed multi-column graph with edges that encode smoothness and inter-surface penalties. Unlike previous graph-cut methods that impose hard constraints on the surface properties, the proposed method follows from a Bayesian formulation resulting in soft penalties on spatial variation of the cuts through the mesh. The novelty of this method also lies in the construction of proper-ordered graphs on complex shapes for choosing among distinct classes of base shapes for automatic LA segmentation. We evaluate the proposed segmentation framework on simulated and clinical cardiac MRI.

Automatic 3D liver segmentation based on deep learning and globally optimized surface evolution

NASA Astrophysics Data System (ADS)

Hu, Peijun; Wu, Fa; Peng, Jialin; Liang, Ping; Kong, Dexing

2016-12-01

The detection and delineation of the liver from abdominal 3D computed tomography (CT) images are fundamental tasks in computer-assisted liver surgery planning. However, automatic and accurate segmentation, especially liver detection, remains challenging due to complex backgrounds, ambiguous boundaries, heterogeneous appearances and highly varied shapes of the liver. To address these difficulties, we propose an automatic segmentation framework based on 3D convolutional neural network (CNN) and globally optimized surface evolution. First, a deep 3D CNN is trained to learn a subject-specific probability map of the liver, which gives the initial surface and acts as a shape prior in the following segmentation step. Then, both global and local appearance information from the prior segmentation are adaptively incorporated into a segmentation model, which is globally optimized in a surface evolution way. The proposed method has been validated on 42 CT images from the public Sliver07 database and local hospitals. On the Sliver07 online testing set, the proposed method can achieve an overall score of 80.3+/- 4.5 , yielding a mean Dice similarity coefficient of 97.25+/- 0.65 % , and an average symmetric surface distance of 0.84+/- 0.25 mm. The quantitative validations and comparisons show that the proposed method is accurate and effective for clinical application.

Automatic Segmenting Structures in MRI's Based on Texture Analysis and Fuzzy Logic

NASA Astrophysics Data System (ADS)

Kaur, Mandeep; Rattan, Munish; Singh, Pushpinder

2017-12-01

The purpose of this paper is to present the variational method for geometric contours which helps the level set function remain close to the sign distance function, therefor it remove the need of expensive re-initialization procedure and thus, level set method is applied on magnetic resonance images (MRI) to track the irregularities in them as medical imaging plays a substantial part in the treatment, therapy and diagnosis of various organs, tumors and various abnormalities. It favors the patient with more speedy and decisive disease controlling with lesser side effects. The geometrical shape, the tumor's size and tissue's abnormal growth can be calculated by the segmentation of that particular image. It is still a great challenge for the researchers to tackle with an automatic segmentation in the medical imaging. Based on the texture analysis, different images are processed by optimization of level set segmentation. Traditionally, optimization was manual for every image where each parameter is selected one after another. By applying fuzzy logic, the segmentation of image is correlated based on texture features, to make it automatic and more effective. There is no initialization of parameters and it works like an intelligent system. It segments the different MRI images without tuning the level set parameters and give optimized results for all MRI's.

Validation tools for image segmentation

NASA Astrophysics Data System (ADS)

Padfield, Dirk; Ross, James

2009-02-01

A large variety of image analysis tasks require the segmentation of various regions in an image. For example, segmentation is required to generate accurate models of brain pathology that are important components of modern diagnosis and therapy. While the manual delineation of such structures gives accurate information, the automatic segmentation of regions such as the brain and tumors from such images greatly enhances the speed and repeatability of quantifying such structures. The ubiquitous need for such algorithms has lead to a wide range of image segmentation algorithms with various assumptions, parameters, and robustness. The evaluation of such algorithms is an important step in determining their effectiveness. Therefore, rather than developing new segmentation algorithms, we here describe validation methods for segmentation algorithms. Using similarity metrics comparing the automatic to manual segmentations, we demonstrate methods for optimizing the parameter settings for individual cases and across a collection of datasets using the Design of Experiment framework. We then employ statistical analysis methods to compare the effectiveness of various algorithms. We investigate several region-growing algorithms from the Insight Toolkit and compare their accuracy to that of a separate statistical segmentation algorithm. The segmentation algorithms are used with their optimized parameters to automatically segment the brain and tumor regions in MRI images of 10 patients. The validation tools indicate that none of the ITK algorithms studied are able to outperform with statistical significance the statistical segmentation algorithm although they perform reasonably well considering their simplicity.

Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: Improved backbone hydration and interactions between charged side chains

PubMed Central

Han, Wei; Schulten, Klaus

2012-01-01

PACE, a hybrid force field which couples united-atom protein models with coarse-grained (CG) solvent, has been further optimized, aiming to improve itse ciency for folding simulations. Backbone hydration parameters have been re-optimized based on hydration free energies of polyalanyl peptides through atomistic simulations. Also, atomistic partial charges from all-atom force fields were combined with PACE in order to provide a more realistic description of interactions between charged groups. Using replica exchange molecular dynamics (REMD), ab initio folding using the new PACE has been achieved for seven small proteins (16 – 23 residues) with different structural motifs. Experimental data about folded states, such as their stability at room temperature, melting point and NMR NOE constraints, were also well reproduced. Moreover, a systematic comparison of folding kinetics at room temperature has been made with experiments, through standard MD simulations, showing that the new PACE may speed up the actual folding kinetics 5-10 times. Together with the computational speedup benefited from coarse-graining, the force field provides opportunities to study folding mechanisms. In particular, we used the new PACE to fold a 73-residue protein, 3D, in multiple 10 – 30 μs simulations, to its native states (Cα RMSD ~ 0.34 nm). Our results suggest the potential applicability of the new PACE for the study of folding and dynamics of proteins. PMID:23204949

Improvements to robotics-inspired conformational sampling in rosetta.

PubMed

Stein, Amelie; Kortemme, Tanja

2013-01-01

To accurately predict protein conformations in atomic detail, a computational method must be capable of sampling models sufficiently close to the native structure. All-atom sampling is difficult because of the vast number of possible conformations and extremely rugged energy landscapes. Here, we test three sampling strategies to address these difficulties: conformational diversification, intensification of torsion and omega-angle sampling and parameter annealing. We evaluate these strategies in the context of the robotics-based kinematic closure (KIC) method for local conformational sampling in Rosetta on an established benchmark set of 45 12-residue protein segments without regular secondary structure. We quantify performance as the fraction of sub-Angstrom models generated. While improvements with individual strategies are only modest, the combination of intensification and annealing strategies into a new "next-generation KIC" method yields a four-fold increase over standard KIC in the median percentage of sub-Angstrom models across the dataset. Such improvements enable progress on more difficult problems, as demonstrated on longer segments, several of which could not be accurately remodeled with previous methods. Given its improved sampling capability, next-generation KIC should allow advances in other applications such as local conformational remodeling of multiple segments simultaneously, flexible backbone sequence design, and development of more accurate energy functions.

Improvements to Robotics-Inspired Conformational Sampling in Rosetta

PubMed Central

Stein, Amelie; Kortemme, Tanja

2013-01-01

To accurately predict protein conformations in atomic detail, a computational method must be capable of sampling models sufficiently close to the native structure. All-atom sampling is difficult because of the vast number of possible conformations and extremely rugged energy landscapes. Here, we test three sampling strategies to address these difficulties: conformational diversification, intensification of torsion and omega-angle sampling and parameter annealing. We evaluate these strategies in the context of the robotics-based kinematic closure (KIC) method for local conformational sampling in Rosetta on an established benchmark set of 45 12-residue protein segments without regular secondary structure. We quantify performance as the fraction of sub-Angstrom models generated. While improvements with individual strategies are only modest, the combination of intensification and annealing strategies into a new “next-generation KIC” method yields a four-fold increase over standard KIC in the median percentage of sub-Angstrom models across the dataset. Such improvements enable progress on more difficult problems, as demonstrated on longer segments, several of which could not be accurately remodeled with previous methods. Given its improved sampling capability, next-generation KIC should allow advances in other applications such as local conformational remodeling of multiple segments simultaneously, flexible backbone sequence design, and development of more accurate energy functions. PMID:23704889

Megasupramolecules for safer, cleaner fuel by end association of long telechelic polymers

NASA Astrophysics Data System (ADS)

Wei, Ming-Hsin; Li, Boyu; David, R. L. Ameri; Jones, Simon C.; Sarohia, Virendra; Schmitigal, Joel A.; Kornfield, Julia A.

2015-10-01

We used statistical mechanics to design polymers that defy conventional wisdom by self-assembling into “megasupramolecules” (≥5000 kg/mol) at low concentration (≤0.3 weight percent). Theoretical treatment of the distribution of individual subunits—end-functional polymers—among cyclic and linear supramolecules (ring-chain equilibrium) predicts that megasupramolecules can form at low total polymer concentration if, and only if, the backbones are long (>400 kg/mol) and end-association strength is optimal. Viscometry and scattering measurements of long telechelic polymers having polycyclooctadiene backbones and acid or amine end groups verify the formation of megasupramolecules. They control misting and reduce drag in the same manner as ultralong covalent polymers. With individual building blocks short enough to avoid hydrodynamic chain scission (weight-average molecular weights of 400 to 1000 kg/mol) and reversible linkages that protect covalent bonds, these megasupramolecules overcome the obstacles of shear degradation and engine incompatibility.

Improved Force Fields for Peptide Nucleic Acids with Optimized Backbone Torsion Parameters.

PubMed

Jasiński, Maciej; Feig, Michael; Trylska, Joanna

2018-06-06

Peptide nucleic acids are promising nucleic acid analogs for antisense therapies as they can form stable duplex and triplex structures with DNA and RNA. Computational studies of PNA-containing duplexes and triplexes are an important component for guiding their design, yet existing force fields have not been well validated and parametrized with modern computational capabilities. We present updated CHARMM and Amber force fields for PNA that greatly improve the stability of simulated PNA-containing duplexes and triplexes in comparison with experimental structures and allow such systems to be studied on microsecond time scales. The force field modifications focus on reparametrized PNA backbone torsion angles to match high-level quantum mechanics reference energies for a model compound. The microsecond simulations of PNA-PNA, PNA-DNA, PNA-RNA, and PNA-DNA-PNA complexes also allowed a comprehensive analysis of hydration and ion interactions with such systems.

A proposal of optimal sampling design using a modularity strategy

NASA Astrophysics Data System (ADS)

Simone, A.; Giustolisi, O.; Laucelli, D. B.

2016-08-01

In real water distribution networks (WDNs) are present thousands nodes and optimal placement of pressure and flow observations is a relevant issue for different management tasks. The planning of pressure observations in terms of spatial distribution and number is named sampling design and it was faced considering model calibration. Nowadays, the design of system monitoring is a relevant issue for water utilities e.g., in order to manage background leakages, to detect anomalies and bursts, to guarantee service quality, etc. In recent years, the optimal location of flow observations related to design of optimal district metering areas (DMAs) and leakage management purposes has been faced considering optimal network segmentation and the modularity index using a multiobjective strategy. Optimal network segmentation is the basis to identify network modules by means of optimal conceptual cuts, which are the candidate locations of closed gates or flow meters creating the DMAs. Starting from the WDN-oriented modularity index, as a metric for WDN segmentation, this paper proposes a new way to perform the sampling design, i.e., the optimal location of pressure meters, using newly developed sampling-oriented modularity index. The strategy optimizes the pressure monitoring system mainly based on network topology and weights assigned to pipes according to the specific technical tasks. A multiobjective optimization minimizes the cost of pressure meters while maximizing the sampling-oriented modularity index. The methodology is presented and discussed using the Apulian and Exnet networks.

Interleaved segment correction achieves higher improvement factors in using genetic algorithm to optimize light focusing through scattering media

NASA Astrophysics Data System (ADS)

Li, Runze; Peng, Tong; Liang, Yansheng; Yang, Yanlong; Yao, Baoli; Yu, Xianghua; Min, Junwei; Lei, Ming; Yan, Shaohui; Zhang, Chunmin; Ye, Tong

2017-10-01

Focusing and imaging through scattering media has been proved possible with high resolution wavefront shaping. A completely scrambled scattering field can be corrected by applying a correction phase mask on a phase only spatial light modulator (SLM) and thereby the focusing quality can be improved. The correction phase is often found by global searching algorithms, among which Genetic Algorithm (GA) stands out for its parallel optimization process and high performance in noisy environment. However, the convergence of GA slows down gradually with the progression of optimization, causing the improvement factor of optimization to reach a plateau eventually. In this report, we propose an interleaved segment correction (ISC) method that can significantly boost the improvement factor with the same number of iterations comparing with the conventional all segment correction method. In the ISC method, all the phase segments are divided into a number of interleaved groups; GA optimization procedures are performed individually and sequentially among each group of segments. The final correction phase mask is formed by applying correction phases of all interleaved groups together on the SLM. The ISC method has been proved significantly useful in practice because of its ability to achieve better improvement factors when noise is present in the system. We have also demonstrated that the imaging quality is improved as better correction phases are found and applied on the SLM. Additionally, the ISC method lowers the demand of dynamic ranges of detection devices. The proposed method holds potential in applications, such as high-resolution imaging in deep tissue.

VirSSPA- a virtual reality tool for surgical planning workflow.

PubMed

Suárez, C; Acha, B; Serrano, C; Parra, C; Gómez, T

2009-03-01

A virtual reality tool, called VirSSPA, was developed to optimize the planning of surgical processes. Segmentation algorithms for Computed Tomography (CT) images: a region growing procedure was used for soft tissues and a thresholding algorithm was implemented to segment bones. The algorithms operate semiautomati- cally since they only need seed selection with the mouse on each tissue segmented by the user. The novelty of the paper is the adaptation of an enhancement method based on histogram thresholding applied to CT images for surgical planning, which simplifies subsequent segmentation. A substantial improvement of the virtual reality tool VirSSPA was obtained with these algorithms. VirSSPA was used to optimize surgical planning, to decrease the time spent on surgical planning and to improve operative results. The success rate increases due to surgeons being able to see the exact extent of the patient's ailment. This tool can decrease operating room time, thus resulting in reduced costs. Virtual simulation was effective for optimizing surgical planning, which could, consequently, result in improved outcomes with reduced costs.

Integrative image segmentation optimization and machine learning approach for high quality land-use and land-cover mapping using multisource remote sensing data

NASA Astrophysics Data System (ADS)

Gibril, Mohamed Barakat A.; Idrees, Mohammed Oludare; Yao, Kouame; Shafri, Helmi Zulhaidi Mohd

2018-01-01

The growing use of optimization for geographic object-based image analysis and the possibility to derive a wide range of information about the image in textual form makes machine learning (data mining) a versatile tool for information extraction from multiple data sources. This paper presents application of data mining for land-cover classification by fusing SPOT-6, RADARSAT-2, and derived dataset. First, the images and other derived indices (normalized difference vegetation index, normalized difference water index, and soil adjusted vegetation index) were combined and subjected to segmentation process with optimal segmentation parameters obtained using combination of spatial and Taguchi statistical optimization. The image objects, which carry all the attributes of the input datasets, were extracted and related to the target land-cover classes through data mining algorithms (decision tree) for classification. To evaluate the performance, the result was compared with two nonparametric classifiers: support vector machine (SVM) and random forest (RF). Furthermore, the decision tree classification result was evaluated against six unoptimized trials segmented using arbitrary parameter combinations. The result shows that the optimized process produces better land-use land-cover classification with overall classification accuracy of 91.79%, 87.25%, and 88.69% for SVM and RF, respectively, while the results of the six unoptimized classifications yield overall accuracy between 84.44% and 88.08%. Higher accuracy of the optimized data mining classification approach compared to the unoptimized results indicates that the optimization process has significant impact on the classification quality.

A novel mechanism of sugar selection utilized by a human X-family DNA polymerase.

PubMed

Brown, Jessica A; Fiala, Kevin A; Fowler, Jason D; Sherrer, Shanen M; Newmister, Sean A; Duym, Wade W; Suo, Zucai

2010-01-15

During DNA synthesis, most DNA polymerases and reverse transcriptases select against ribonucleotides via a steric clash between the ribose 2'-hydroxyl group and the bulky side chain of an active-site residue. In this study, we demonstrated that human DNA polymerase lambda used a novel sugar selection mechanism to discriminate against ribonucleotides, whereby the ribose 2'-hydroxyl group was excluded mostly by a backbone segment and slightly by the side chain of Y505. Such steric clash was further demonstrated to be dependent on the size and orientation of the substituent covalently attached at the ribonucleotide C2'-position. Copyright 2009 Elsevier Ltd. All rights reserved.

KSC-2009-1096

NASA Image and Video Library

2009-01-11

CAPE CANAVERAL, Fla. -- With red umbilical lines attached, the payload containing space shuttle Discovery's S6 truss and solar arrays is lifted up to the Payload Changeout Room, or PCR, on Launch Pad 39A at NASA's Kennedy Space Center in Florida. The payload will be transferred inside the PCR where it will wait until Discovery rolls out to the pad. Then the payload will be installed in the shuttle's payload bay. Launch of Discovery on the STS-119 mission is scheduled for Feb. 12. During Discovery's 14-day mission, the crew will install the S6 truss segment and its solar arrays to the starboard side of the station, completing the station's backbone, or truss. Photo credit: NASA/Jim Grossmann

KSC-2009-1097

NASA Image and Video Library

2009-01-11

CAPE CANAVERAL, Fla. -- With red umbilical lines attached, the payload containing space shuttle Discovery's S6 truss and solar arrays is lifted up to the Payload Changeout Room, or PCR, on Launch Pad 39A at NASA's Kennedy Space Center in Florida. The payload will be transferred inside the PCR where it will wait until Discovery rolls out to the pad. Then the payload will be installed in the shuttle's payload bay. Launch of Discovery on the STS-119 mission is scheduled for Feb. 12. During Discovery's 14-day mission, the crew will install the S6 truss segment and its solar arrays to the starboard side of the station, completing the station's backbone, or truss Photo credit: NASA/Jim Grossmann

KSC-2009-1098

NASA Image and Video Library

2009-01-11

CAPE CANAVERAL, Fla. -- With red umbilical lines attached, the payload containing space shuttle Discovery's S6 truss and solar arrays is lifted up to the Payload Changeout Room, or PCR, on Launch Pad 39A at NASA's Kennedy Space Center in Florida. The payload will be transferred inside the PCR where it will wait until Discovery rolls out to the pad. Then the payload will be installed in the shuttle's payload bay. Launch of Discovery on the STS-119 mission is scheduled for Feb. 12. During Discovery's 14-day mission, the crew will install the S6 truss segment and its solar arrays to the starboard side of the station, completing the station's backbone, or truss Photo credit: NASA/Jim Grossmann

Hybrid Active/Passive Jet Engine Noise Suppression System

NASA Technical Reports Server (NTRS)

Parente, C. A.; Arcas, N.; Walker, B. E.; Hersh, A. S.; Rice, E. J.

1999-01-01

A novel adaptive segmented liner concept has been developed that employs active control elements to modify the in-duct sound field to enhance the tone-suppressing performance of passive liner elements. This could potentially allow engine designs that inherently produce more tone noise but less broadband noise, or could allow passive liner designs to more optimally address high frequency broadband noise. A proof-of-concept validation program was undertaken, consisting of the development of an adaptive segmented liner that would maximize attenuation of two radial modes in a circular or annular duct. The liner consisted of a leading active segment with dual annuli of axially spaced active Helmholtz resonators, followed by an optimized passive liner and then an array of sensing microphones. Three successively complex versions of the adaptive liner were constructed and their performances tested relative to the performance of optimized uniform passive and segmented passive liners. The salient results of the tests were: The adaptive segmented liner performed well in a high flow speed model fan inlet environment, was successfully scaled to a high sound frequency and successfully attenuated three radial modes using sensor and active resonator arrays that were designed for a two mode, lower frequency environment.

Ultra-short beam expander with segmented curvature control: the emergence of a semi-lens

DOE PAGES

Abbaslou, Siamak; Gatdula, Robert; Lu, Ming; ...

2017-01-01

We introduce direct curvature control in designing a segmented beam expander, and explore novel design possibilities for ultra-compact beam expanders. Assisted by the particle swarm optimization algorithm, we search for an optimal curvature-controlled multi-segment taper that maintains width continuity. Counterintuitively, the optimization yields a structure with abrupt width discontinuity and width compression features. Through spatial phase and parameterized analysis, a semi-lens feature is revealed that helps to flatten the wavefront at the output end for higher coupling efficiency. Such functionality cannot be achieved by normal tapers in a short distance. The structure is fabricated and characterized experimentally. By a figuremore » of merit that accounts for expansion ratio, length, and efficiency, this structure outperforms an adiabatic taper by 9 times.« less

A Novel Segmentation Approach Combining Region- and Edge-Based Information for Ultrasound Images

PubMed Central

Luo, Yaozhong; Liu, Longzhong; Li, Xuelong

2017-01-01

Ultrasound imaging has become one of the most popular medical imaging modalities with numerous diagnostic applications. However, ultrasound (US) image segmentation, which is the essential process for further analysis, is a challenging task due to the poor image quality. In this paper, we propose a new segmentation scheme to combine both region- and edge-based information into the robust graph-based (RGB) segmentation method. The only interaction required is to select two diagonal points to determine a region of interest (ROI) on the original image. The ROI image is smoothed by a bilateral filter and then contrast-enhanced by histogram equalization. Then, the enhanced image is filtered by pyramid mean shift to improve homogeneity. With the optimization of particle swarm optimization (PSO) algorithm, the RGB segmentation method is performed to segment the filtered image. The segmentation results of our method have been compared with the corresponding results obtained by three existing approaches, and four metrics have been used to measure the segmentation performance. The experimental results show that the method achieves the best overall performance and gets the lowest ARE (10.77%), the second highest TPVF (85.34%), and the second lowest FPVF (4.48%). PMID:28536703

Spatio-Temporal Video Segmentation with Shape Growth or Shrinkage Constraint

NASA Technical Reports Server (NTRS)

Tarabalka, Yuliya; Charpiat, Guillaume; Brucker, Ludovic; Menze, Bjoern H.

2014-01-01

We propose a new method for joint segmentation of monotonously growing or shrinking shapes in a time sequence of noisy images. The task of segmenting the image time series is expressed as an optimization problem using the spatio-temporal graph of pixels, in which we are able to impose the constraint of shape growth or of shrinkage by introducing monodirectional infinite links connecting pixels at the same spatial locations in successive image frames. The globally optimal solution is computed with a graph cut. The performance of the proposed method is validated on three applications: segmentation of melting sea ice floes and of growing burned areas from time series of 2D satellite images, and segmentation of a growing brain tumor from sequences of 3D medical scans. In the latter application, we impose an additional intersequences inclusion constraint by adding directed infinite links between pixels of dependent image structures.

Improved Modeling of Side-Chain–Base Interactions and Plasticity in Protein–DNA Interface Design

PubMed Central

Thyme, Summer B.; Baker, David; Bradley, Philip

2012-01-01

Combinatorial sequence optimization for protein design requires libraries of discrete side-chain conformations. The discreteness of these libraries is problematic, particularly for long, polar side chains, since favorable interactions can be missed. Previously, an approach to loop remodeling where protein backbone movement is directed by side-chain rotamers predicted to form interactions previously observed in native complexes (termed “motifs”) was described. Here, we show how such motif libraries can be incorporated into combinatorial sequence optimization protocols and improve native complex recapitulation. Guided by the motif rotamer searches, we made improvements to the underlying energy function, increasing recapitulation of native interactions. To further test the methods, we carried out a comprehensive experimental scan of amino acid preferences in the I-AniI protein–DNA interface and found that many positions tolerated multiple amino acids. This sequence plasticity is not observed in the computational results because of the fixed-backbone approximation of the model. We improved modeling of this diversity by introducing DNA flexibility and reducing the convergence of the simulated annealing algorithm that drives the design process. In addition to serving as a benchmark, this extensive experimental data set provides insight into the types of interactions essential to maintain the function of this potential gene therapy reagent. PMID:22426128

Improved modeling of side-chain--base interactions and plasticity in protein--DNA interface design.

PubMed

Thyme, Summer B; Baker, David; Bradley, Philip

2012-06-08

Combinatorial sequence optimization for protein design requires libraries of discrete side-chain conformations. The discreteness of these libraries is problematic, particularly for long, polar side chains, since favorable interactions can be missed. Previously, an approach to loop remodeling where protein backbone movement is directed by side-chain rotamers predicted to form interactions previously observed in native complexes (termed "motifs") was described. Here, we show how such motif libraries can be incorporated into combinatorial sequence optimization protocols and improve native complex recapitulation. Guided by the motif rotamer searches, we made improvements to the underlying energy function, increasing recapitulation of native interactions. To further test the methods, we carried out a comprehensive experimental scan of amino acid preferences in the I-AniI protein-DNA interface and found that many positions tolerated multiple amino acids. This sequence plasticity is not observed in the computational results because of the fixed-backbone approximation of the model. We improved modeling of this diversity by introducing DNA flexibility and reducing the convergence of the simulated annealing algorithm that drives the design process. In addition to serving as a benchmark, this extensive experimental data set provides insight into the types of interactions essential to maintain the function of this potential gene therapy reagent. Published by Elsevier Ltd.

Toward a web-based real-time radiation treatment planning system in a cloud computing environment.

PubMed

Na, Yong Hum; Suh, Tae-Suk; Kapp, Daniel S; Xing, Lei

2013-09-21

To exploit the potential dosimetric advantages of intensity modulated radiation therapy (IMRT) and volumetric modulated arc therapy (VMAT), an in-depth approach is required to provide efficient computing methods. This needs to incorporate clinically related organ specific constraints, Monte Carlo (MC) dose calculations, and large-scale plan optimization. This paper describes our first steps toward a web-based real-time radiation treatment planning system in a cloud computing environment (CCE). The Amazon Elastic Compute Cloud (EC2) with a master node (named m2.xlarge containing 17.1 GB of memory, two virtual cores with 3.25 EC2 Compute Units each, 420 GB of instance storage, 64-bit platform) is used as the backbone of cloud computing for dose calculation and plan optimization. The master node is able to scale the workers on an 'on-demand' basis. MC dose calculation is employed to generate accurate beamlet dose kernels by parallel tasks. The intensity modulation optimization uses total-variation regularization (TVR) and generates piecewise constant fluence maps for each initial beam direction in a distributed manner over the CCE. The optimized fluence maps are segmented into deliverable apertures. The shape of each aperture is iteratively rectified to be a sequence of arcs using the manufacture's constraints. The output plan file from the EC2 is sent to the simple storage service. Three de-identified clinical cancer treatment plans have been studied for evaluating the performance of the new planning platform with 6 MV flattening filter free beams (40 × 40 cm(2)) from the Varian TrueBeam(TM) STx linear accelerator. A CCE leads to speed-ups of up to 14-fold for both dose kernel calculations and plan optimizations in the head and neck, lung, and prostate cancer cases considered in this study. The proposed system relies on a CCE that is able to provide an infrastructure for parallel and distributed computing. The resultant plans from the cloud computing are identical to PC-based IMRT and VMAT plans, confirming the reliability of the cloud computing platform. This cloud computing infrastructure has been established for a radiation treatment planning. It substantially improves the speed of inverse planning and makes future on-treatment adaptive re-planning possible.

Toward a web-based real-time radiation treatment planning system in a cloud computing environment

NASA Astrophysics Data System (ADS)

Hum Na, Yong; Suh, Tae-Suk; Kapp, Daniel S.; Xing, Lei

2013-09-01

To exploit the potential dosimetric advantages of intensity modulated radiation therapy (IMRT) and volumetric modulated arc therapy (VMAT), an in-depth approach is required to provide efficient computing methods. This needs to incorporate clinically related organ specific constraints, Monte Carlo (MC) dose calculations, and large-scale plan optimization. This paper describes our first steps toward a web-based real-time radiation treatment planning system in a cloud computing environment (CCE). The Amazon Elastic Compute Cloud (EC2) with a master node (named m2.xlarge containing 17.1 GB of memory, two virtual cores with 3.25 EC2 Compute Units each, 420 GB of instance storage, 64-bit platform) is used as the backbone of cloud computing for dose calculation and plan optimization. The master node is able to scale the workers on an ‘on-demand’ basis. MC dose calculation is employed to generate accurate beamlet dose kernels by parallel tasks. The intensity modulation optimization uses total-variation regularization (TVR) and generates piecewise constant fluence maps for each initial beam direction in a distributed manner over the CCE. The optimized fluence maps are segmented into deliverable apertures. The shape of each aperture is iteratively rectified to be a sequence of arcs using the manufacture’s constraints. The output plan file from the EC2 is sent to the simple storage service. Three de-identified clinical cancer treatment plans have been studied for evaluating the performance of the new planning platform with 6 MV flattening filter free beams (40 × 40 cm2) from the Varian TrueBeamTM STx linear accelerator. A CCE leads to speed-ups of up to 14-fold for both dose kernel calculations and plan optimizations in the head and neck, lung, and prostate cancer cases considered in this study. The proposed system relies on a CCE that is able to provide an infrastructure for parallel and distributed computing. The resultant plans from the cloud computing are identical to PC-based IMRT and VMAT plans, confirming the reliability of the cloud computing platform. This cloud computing infrastructure has been established for a radiation treatment planning. It substantially improves the speed of inverse planning and makes future on-treatment adaptive re-planning possible.

Spherical cloaking using nonlinear transformations for improved segmentation into concentric isotropic coatings.

PubMed

Qiu, Cheng-Wei; Hu, Li; Zhang, Baile; Wu, Bae-Ian; Johnson, Steven G; Joannopoulos, John D

2009-08-03

Two novel classes of spherical invisibility cloaks based on nonlinear transformation have been studied. The cloaking characteristics are presented by segmenting the nonlinear transformation based spherical cloak into concentric isotropic homogeneous coatings. Detailed investigations of the optimal discretization (e.g., thickness control of each layer, nonlinear factor, etc.) are presented for both linear and nonlinear spherical cloaks and their effects on invisibility performance are also discussed. The cloaking properties and our choice of optimal segmentation are verified by the numerical simulation of not only near-field electric-field distribution but also the far-field radar cross section (RCS).

Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design.

PubMed

Smith, Colin A; Kortemme, Tanja

2011-01-01

Predicting the set of sequences that are tolerated by a protein or protein interface, while maintaining a desired function, is useful for characterizing protein interaction specificity and for computationally designing sequence libraries to engineer proteins with new functions. Here we provide a general method, a detailed set of protocols, and several benchmarks and analyses for estimating tolerated sequences using flexible backbone protein design implemented in the Rosetta molecular modeling software suite. The input to the method is at least one experimentally determined three-dimensional protein structure or high-quality model. The starting structure(s) are expanded or refined into a conformational ensemble using Monte Carlo simulations consisting of backrub backbone and side chain moves in Rosetta. The method then uses a combination of simulated annealing and genetic algorithm optimization methods to enrich for low-energy sequences for the individual members of the ensemble. To emphasize certain functional requirements (e.g. forming a binding interface), interactions between and within parts of the structure (e.g. domains) can be reweighted in the scoring function. Results from each backbone structure are merged together to create a single estimate for the tolerated sequence space. We provide an extensive description of the protocol and its parameters, all source code, example analysis scripts and three tests applying this method to finding sequences predicted to stabilize proteins or protein interfaces. The generality of this method makes many other applications possible, for example stabilizing interactions with small molecules, DNA, or RNA. Through the use of within-domain reweighting and/or multistate design, it may also be possible to use this method to find sequences that stabilize particular protein conformations or binding interactions over others.

Template-free modeling by LEE and LEER in CASP11.

PubMed

Joung, InSuk; Lee, Sun Young; Cheng, Qianyi; Kim, Jong Yun; Joo, Keehyoung; Lee, Sung Jong; Lee, Jooyoung

2016-09-01

For the template-free modeling of human targets of CASP11, we utilized two of our modeling protocols, LEE and LEER. The LEE protocol took CASP11-released server models as the input and used some of them as templates for 3D (three-dimensional) modeling. The template selection procedure was based on the clustering of the server models aided by a community detection method of a server-model network. Restraining energy terms generated from the selected templates together with physical and statistical energy terms were used to build 3D models. Side-chains of the 3D models were rebuilt using target-specific consensus side-chain library along with the SCWRL4 rotamer library, which completed the LEE protocol. The first success factor of the LEE protocol was due to efficient server model screening. The average backbone accuracy of selected server models was similar to that of top 30% server models. The second factor was that a proper energy function along with our optimization method guided us, so that we successfully generated better quality models than the input template models. In 10 out of 24 cases, better backbone structures than the best of input template structures were generated. LEE models were further refined by performing restrained molecular dynamics simulations to generate LEER models. CASP11 results indicate that LEE models were better than the average template models in terms of both backbone structures and side-chain orientations. LEER models were of improved physical realism and stereo-chemistry compared to LEE models, and they were comparable to LEE models in the backbone accuracy. Proteins 2016; 84(Suppl 1):118-130. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Toward optimal feature and time segment selection by divergence method for EEG signals classification.

PubMed

Wang, Jie; Feng, Zuren; Lu, Na; Luo, Jing

2018-06-01

Feature selection plays an important role in the field of EEG signals based motor imagery pattern classification. It is a process that aims to select an optimal feature subset from the original set. Two significant advantages involved are: lowering the computational burden so as to speed up the learning procedure and removing redundant and irrelevant features so as to improve the classification performance. Therefore, feature selection is widely employed in the classification of EEG signals in practical brain-computer interface systems. In this paper, we present a novel statistical model to select the optimal feature subset based on the Kullback-Leibler divergence measure, and automatically select the optimal subject-specific time segment. The proposed method comprises four successive stages: a broad frequency band filtering and common spatial pattern enhancement as preprocessing, features extraction by autoregressive model and log-variance, the Kullback-Leibler divergence based optimal feature and time segment selection and linear discriminate analysis classification. More importantly, this paper provides a potential framework for combining other feature extraction models and classification algorithms with the proposed method for EEG signals classification. Experiments on single-trial EEG signals from two public competition datasets not only demonstrate that the proposed method is effective in selecting discriminative features and time segment, but also show that the proposed method yields relatively better classification results in comparison with other competitive methods. Copyright © 2018 Elsevier Ltd. All rights reserved.

Hybrid Artificial Root Foraging Optimizer Based Multilevel Threshold for Image Segmentation

PubMed Central

Liu, Yang; Liu, Junfei

2016-01-01

This paper proposes a new plant-inspired optimization algorithm for multilevel threshold image segmentation, namely, hybrid artificial root foraging optimizer (HARFO), which essentially mimics the iterative root foraging behaviors. In this algorithm the new growth operators of branching, regrowing, and shrinkage are initially designed to optimize continuous space search by combining root-to-root communication and coevolution mechanism. With the auxin-regulated scheme, various root growth operators are guided systematically. With root-to-root communication, individuals exchange information in different efficient topologies, which essentially improve the exploration ability. With coevolution mechanism, the hierarchical spatial population driven by evolutionary pressure of multiple subpopulations is structured, which ensure that the diversity of root population is well maintained. The comparative results on a suit of benchmarks show the superiority of the proposed algorithm. Finally, the proposed HARFO algorithm is applied to handle the complex image segmentation problem based on multilevel threshold. Computational results of this approach on a set of tested images show the outperformance of the proposed algorithm in terms of optimization accuracy computation efficiency. PMID:27725826

Hybrid Artificial Root Foraging Optimizer Based Multilevel Threshold for Image Segmentation.

PubMed

Liu, Yang; Liu, Junfei; Tian, Liwei; Ma, Lianbo

2016-01-01

This paper proposes a new plant-inspired optimization algorithm for multilevel threshold image segmentation, namely, hybrid artificial root foraging optimizer (HARFO), which essentially mimics the iterative root foraging behaviors. In this algorithm the new growth operators of branching, regrowing, and shrinkage are initially designed to optimize continuous space search by combining root-to-root communication and coevolution mechanism. With the auxin-regulated scheme, various root growth operators are guided systematically. With root-to-root communication, individuals exchange information in different efficient topologies, which essentially improve the exploration ability. With coevolution mechanism, the hierarchical spatial population driven by evolutionary pressure of multiple subpopulations is structured, which ensure that the diversity of root population is well maintained. The comparative results on a suit of benchmarks show the superiority of the proposed algorithm. Finally, the proposed HARFO algorithm is applied to handle the complex image segmentation problem based on multilevel threshold. Computational results of this approach on a set of tested images show the outperformance of the proposed algorithm in terms of optimization accuracy computation efficiency.

Optimal Co-segmentation of Tumor in PET-CT Images with Context Information

PubMed Central

Song, Qi; Bai, Junjie; Han, Dongfeng; Bhatia, Sudershan; Sun, Wenqing; Rockey, William; Bayouth, John E.; Buatti, John M.

2014-01-01

PET-CT images have been widely used in clinical practice for radiotherapy treatment planning of the radiotherapy. Many existing segmentation approaches only work for a single imaging modality, which suffer from the low spatial resolution in PET or low contrast in CT. In this work we propose a novel method for the co-segmentation of the tumor in both PET and CT images, which makes use of advantages from each modality: the functionality information from PET and the anatomical structure information from CT. The approach formulates the segmentation problem as a minimization problem of a Markov Random Field (MRF) model, which encodes the information from both modalities. The optimization is solved using a graph-cut based method. Two sub-graphs are constructed for the segmentation of the PET and the CT images, respectively. To achieve consistent results in two modalities, an adaptive context cost is enforced by adding context arcs between the two subgraphs. An optimal solution can be obtained by solving a single maximum flow problem, which leads to simultaneous segmentation of the tumor volumes in both modalities. The proposed algorithm was validated in robust delineation of lung tumors on 23 PET-CT datasets and two head-and-neck cancer subjects. Both qualitative and quantitative results show significant improvement compared to the graph cut methods solely using PET or CT. PMID:23693127

An efficient global energy optimization approach for robust 3D plane segmentation of point clouds

NASA Astrophysics Data System (ADS)

Dong, Zhen; Yang, Bisheng; Hu, Pingbo; Scherer, Sebastian

2018-03-01

Automatic 3D plane segmentation is necessary for many applications including point cloud registration, building information model (BIM) reconstruction, simultaneous localization and mapping (SLAM), and point cloud compression. However, most of the existing 3D plane segmentation methods still suffer from low precision and recall, and inaccurate and incomplete boundaries, especially for low-quality point clouds collected by RGB-D sensors. To overcome these challenges, this paper formulates the plane segmentation problem as a global energy optimization because it is robust to high levels of noise and clutter. First, the proposed method divides the raw point cloud into multiscale supervoxels, and considers planar supervoxels and individual points corresponding to nonplanar supervoxels as basic units. Then, an efficient hybrid region growing algorithm is utilized to generate initial plane set by incrementally merging adjacent basic units with similar features. Next, the initial plane set is further enriched and refined in a mutually reinforcing manner under the framework of global energy optimization. Finally, the performances of the proposed method are evaluated with respect to six metrics (i.e., plane precision, plane recall, under-segmentation rate, over-segmentation rate, boundary precision, and boundary recall) on two benchmark datasets. Comprehensive experiments demonstrate that the proposed method obtained good performances both in high-quality TLS point clouds (i.e., http://SEMANTIC3D.NET)

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

Jones, Brad H.; Wheeler, David R.; Black, Hayden T.

Physical stress relaxation in rubbery, thermoset polymers is limited by cross-links, which impede segmental motion and restrict relaxation to network defects, such as chain ends. In parallel, the cure shrinkage associated with thermoset polymerizations leads to the development of internal residual stress that cannot be effectively relaxed. Recent strategies have reduced or eliminated such cure stress in thermoset polymers largely by exploiting chemical relaxation processes, wherein temporary cross-links or otherwise transient bonds are incorporated into the polymer network. In this paper, we explore an alternative approach, wherein physical relaxation is enhanced by the incorporation of organometallic sandwich moieties into themore » backbone of the polymer network. A standard epoxy resin is cured with a diamine derivative of ferrocene and compared to conventional diamine curing agents. The ferrocene-based thermoset is clearly distinguished from the conventional materials by reduced cure stress with increasing cure temperature as well as unique stress relaxation behavior above its glass transition in the fully cured state. The relaxation experiments exhibit features characteristic of a physical relaxation process. Furthermore, the cure stress is observed to vanish precipitously upon deliberate introduction of network defects through an increasing imbalance of epoxy and amine functional groups. Finally, we postulate that these beneficial properties arise from fluxional motion of the cyclopentadienyl ligands on the polymer backbone.« less

Ser/Thr Motifs in Transmembrane Proteins: Conservation Patterns and Effects on Local Protein Structure and Dynamics

PubMed Central

del Val, Coral; White, Stephen H.

2014-01-01

We combined systematic bioinformatics analyses and molecular dynamics simulations to assess the conservation patterns of Ser and Thr motifs in membrane proteins, and the effect of such motifs on the structure and dynamics of α-helical transmembrane (TM) segments. We find that Ser/Thr motifs are often present in β-barrel TM proteins. At least one Ser/Thr motif is present in almost half of the sequences of α-helical proteins analyzed here. The extensive bioinformatics analyses and inspection of protein structures led to the identification of molecular transporters with noticeable numbers of Ser/Thr motifs within the TM region. Given the energetic penalty for burying multiple Ser/Thr groups in the membrane hydrophobic core, the observation of transporters with multiple membrane-embedded Ser/Thr is intriguing and raises the question of how the presence of multiple Ser/Thr affects protein local structure and dynamics. Molecular dynamics simulations of four different Ser-containing model TM peptides indicate that backbone hydrogen bonding of membrane-buried Ser/Thr hydroxyl groups can significantly change the local structure and dynamics of the helix. Ser groups located close to the membrane interface can hydrogen bond to solvent water instead of protein backbone, leading to an enhanced local solvation of the peptide. PMID:22836667

Rational design of cyclopropane-based chiral PHOX ligands for intermolecular asymmetric Heck reaction

PubMed Central

Rubina, Marina; Sherrill, William M; Barkov, Alexey Yu

2014-01-01

Summary A novel class of chiral phosphanyl-oxazoline (PHOX) ligands with a conformationally rigid cyclopropyl backbone was synthesized and tested in the intermolecular asymmetric Heck reaction. Mechanistic modelling and crystallographic studies were used to predict the optimal ligand structure and helped to design a very efficient and highly selective catalytic system. Employment of the optimized ligands in the asymmetric arylation of cyclic olefins allowed for achieving high enantioselectivities and significantly suppressing product isomerization. Factors affecting the selectivity and the rate of the isomerization were identified. It was shown that the nature of this isomerization is different from that demonstrated previously using chiral diphosphine ligands. PMID:25161709

BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization

PubMed Central

Ryu, Joonghyun; Lee, Mokwon; Cha, Jehyun; Laskowski, Roman A.; Ryu, Seong Eon; Kim, Deok-Soo

2016-01-01

Many applications, such as protein design, homology modeling, flexible docking, etc. require the prediction of a protein's optimal side-chain conformations from just its amino acid sequence and backbone structure. Side-chain prediction (SCP) is an NP-hard energy minimization problem. Here, we present BetaSCPWeb which efficiently computes a conformation close to optimal using a geometry-prioritization method based on the Voronoi diagram of spherical atoms. Its outputs are visual, textual and PDB file format. The web server is free and open to all users at http://voronoi.hanyang.ac.kr/betascpweb with no login requirement. PMID:27151195

The matrix gene segment destabilizes the acid and thermal stability of the hemagglutinin of pandemic live attenuated influenza virus vaccines.

PubMed

O'Donnell, Christopher D; Vogel, Leatrice; Matsuoka, Yumiko; Jin, Hong; Subbarao, Kanta

2014-11-01

The threat of future influenza pandemics and their potential for rapid spread, morbidity, and mortality has led to the development of pandemic vaccines. We generated seven reassortant pandemic live attenuated influenza vaccines (pLAIVs) with the hemagglutinin (HA) and neuraminidase (NA) genes derived from animal influenza viruses on the backbone of the six internal protein gene segments of the temperature sensitive, cold-adapted (ca) A/Ann Arbor/60 (H2N2) virus (AA/60 ca) of the licensed seasonal LAIV. The pLAIV viruses were moderately to highly restricted in replication in seronegative adults; we sought to determine the biological basis for this restriction. Avian influenza viruses generally replicate at higher temperatures than human influenza viruses and, although they shared the same backbone, the pLAIV viruses had a lower shutoff temperature than seasonal LAIV viruses, suggesting that the HA and NA influence the degree of temperature sensitivity. The pH of HA activation of highly pathogenic avian influenza viruses was greater than human and low-pathogenicity avian influenza viruses, as reported by others. However, pLAIV viruses had a consistently higher pH of HA activation and reduced HA thermostability compared to the corresponding wild-type parental viruses. From studies with single-gene reassortant viruses bearing one gene segment from the AA/60 ca virus in recombinant H5N1 or pH1N1 viruses, we found that the lower HA thermal stability and increased pH of HA activation were associated with the AA/60 M gene. Together, the impaired HA acid and thermal stability and temperature sensitivity likely contributed to the restricted replication of the pLAIV viruses we observed in seronegative adults. There is increasing evidence that the HA stability of influenza viruses depends on the virus strain and host species and that HA stability can influence replication, virulence, and transmission of influenza A viruses in different species. We investigated the HA stability of pandemic live attenuated influenza vaccine (pLAIV) viruses and observed that the pLAIV viruses consistently had a less stable HA than the corresponding wild-type influenza viruses. The reduced HA stability and temperature sensitivity of the pLAIV viruses may account for their restricted replication in clinical trials. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

The Matrix Gene Segment Destabilizes the Acid and Thermal Stability of the Hemagglutinin of Pandemic Live Attenuated Influenza Virus Vaccines

PubMed Central

O'Donnell, Christopher D.; Vogel, Leatrice; Matsuoka, Yumiko; Jin, Hong

2014-01-01

ABSTRACT The threat of future influenza pandemics and their potential for rapid spread, morbidity, and mortality has led to the development of pandemic vaccines. We generated seven reassortant pandemic live attenuated influenza vaccines (pLAIVs) with the hemagglutinin (HA) and neuraminidase (NA) genes derived from animal influenza viruses on the backbone of the six internal protein gene segments of the temperature sensitive, cold-adapted (ca) A/Ann Arbor/60 (H2N2) virus (AA/60 ca) of the licensed seasonal LAIV. The pLAIV viruses were moderately to highly restricted in replication in seronegative adults; we sought to determine the biological basis for this restriction. Avian influenza viruses generally replicate at higher temperatures than human influenza viruses and, although they shared the same backbone, the pLAIV viruses had a lower shutoff temperature than seasonal LAIV viruses, suggesting that the HA and NA influence the degree of temperature sensitivity. The pH of HA activation of highly pathogenic avian influenza viruses was greater than human and low-pathogenicity avian influenza viruses, as reported by others. However, pLAIV viruses had a consistently higher pH of HA activation and reduced HA thermostability compared to the corresponding wild-type parental viruses. From studies with single-gene reassortant viruses bearing one gene segment from the AA/60 ca virus in recombinant H5N1 or pH1N1 viruses, we found that the lower HA thermal stability and increased pH of HA activation were associated with the AA/60 M gene. Together, the impaired HA acid and thermal stability and temperature sensitivity likely contributed to the restricted replication of the pLAIV viruses we observed in seronegative adults. IMPORTANCE There is increasing evidence that the HA stability of influenza viruses depends on the virus strain and host species and that HA stability can influence replication, virulence, and transmission of influenza A viruses in different species. We investigated the HA stability of pandemic live attenuated influenza vaccine (pLAIV) viruses and observed that the pLAIV viruses consistently had a less stable HA than the corresponding wild-type influenza viruses. The reduced HA stability and temperature sensitivity of the pLAIV viruses may account for their restricted replication in clinical trials. PMID:25122789

3D conformal planning using low segment multi-criteria IMRT optimization

PubMed Central

Khan, Fazal; Craft, David

2014-01-01

Purpose To evaluate automated multicriteria optimization (MCO) – designed for intensity modulated radiation therapy (IMRT), but invoked with limited segmentation – to efficiently produce high quality 3D conformal radiation therapy (3D-CRT) plans. Methods Ten patients previously planned with 3D-CRT to various disease sites (brain, breast, lung, abdomen, pelvis), were replanned with a low-segment inverse multicriteria optimized technique. The MCO-3D plans used the same beam geometry of the original 3D plans, but were limited to an energy of 6 MV. The MCO-3D plans were optimized using fluence-based MCO IMRT and then, after MCO navigation, segmented with a low number of segments. The 3D and MCO-3D plans were compared by evaluating mean dose for all structures, D95 (dose that 95% of the structure receives) and homogeneity indexes for targets, D1 and clinically appropriate dose volume objectives for individual organs at risk (OARs), monitor units (MUs), and physician preference. Results The MCO-3D plans reduced the OAR mean doses (41 out of a total of 45 OARs had a mean dose reduction, p<<0.01) and monitor units (seven out of ten plans have reduced MUs; the average reduction is 17%, p=0.08) while maintaining clinical standards on coverage and homogeneity of target volumes. All MCO-3D plans were preferred by physicians over their corresponding 3D plans. Conclusion High quality 3D plans can be produced using MCO-IMRT optimization, resulting in automated field-in-field type plans with good monitor unit efficiency. Adopting this technology in a clinic could improve plan quality, and streamline treatment plan production by utilizing a single system applicable to both IMRT and 3D planning. PMID:25413405

Segmentation of MRI Brain Images with an Improved Harmony Searching Algorithm.

PubMed

Yang, Zhang; Shufan, Ye; Li, Guo; Weifeng, Ding

2016-01-01

The harmony searching (HS) algorithm is a kind of optimization search algorithm currently applied in many practical problems. The HS algorithm constantly revises variables in the harmony database and the probability of different values that can be used to complete iteration convergence to achieve the optimal effect. Accordingly, this study proposed a modified algorithm to improve the efficiency of the algorithm. First, a rough set algorithm was employed to improve the convergence and accuracy of the HS algorithm. Then, the optimal value was obtained using the improved HS algorithm. The optimal value of convergence was employed as the initial value of the fuzzy clustering algorithm for segmenting magnetic resonance imaging (MRI) brain images. Experimental results showed that the improved HS algorithm attained better convergence and more accurate results than those of the original HS algorithm. In our study, the MRI image segmentation effect of the improved algorithm was superior to that of the original fuzzy clustering method.

Segmentation of MRI Brain Images with an Improved Harmony Searching Algorithm

PubMed Central

Yang, Zhang; Li, Guo; Weifeng, Ding

2016-01-01

The harmony searching (HS) algorithm is a kind of optimization search algorithm currently applied in many practical problems. The HS algorithm constantly revises variables in the harmony database and the probability of different values that can be used to complete iteration convergence to achieve the optimal effect. Accordingly, this study proposed a modified algorithm to improve the efficiency of the algorithm. First, a rough set algorithm was employed to improve the convergence and accuracy of the HS algorithm. Then, the optimal value was obtained using the improved HS algorithm. The optimal value of convergence was employed as the initial value of the fuzzy clustering algorithm for segmenting magnetic resonance imaging (MRI) brain images. Experimental results showed that the improved HS algorithm attained better convergence and more accurate results than those of the original HS algorithm. In our study, the MRI image segmentation effect of the improved algorithm was superior to that of the original fuzzy clustering method. PMID:27403428

Optimal reconstruction interval in dual source CT coronary angiography: a single-center experience in 285 patients

PubMed Central

Akgöz, Ayça; Akata, Deniz; Hazırolan, Tuncay; Karçaaltıncaba, Muşturay

2014-01-01

PURPOSE We aimed to evaluate the visibility of coronary arteries and bypass-grafts in patients who underwent dual source computed tomography (DSCT) angiography without heart rate (HR) control and to determine optimal intervals for image reconstruction. MATERIALS AND METHODS A total of 285 consecutive cases who underwent coronary (n=255) and bypass-graft (n=30) DSCT angiography at our institution were identified retrospectively. Patients with atrial fibrillation were excluded. Ten datasets in 10% increments were reconstructed in all patients. On each dataset, the visibility of coronary arteries was evaluated using the 15-segment American Heart Association classification by two radiologists in consensus. RESULTS Mean HR was 76±16.3 bpm, (range, 46–127 bpm). All coronary segments could be visualized in 277 patients (97.19%). On a segment-basis, 4265 of 4275 (99.77%) coronary artery segments were visible. All segments of 56 bypass-grafts in 30 patients were visible (100%). Total mean segment visibility scores of all coronary arteries were highest at 70%, 40%, and 30% intervals for all HRs. The optimal reconstruction intervals to visualize the segments of all three coronary arteries in descending order were 70%, 60%, 80%, and 30% intervals in patients with a mean HR <70 bpm; 40%, 70%, and 30% intervals in patients with a mean HR 70–100 bpm; and 40%, 50%, and 30% in patients with a mean HR >100 bpm. CONCLUSION Without beta-blocker administration, DSCT coronary angiography offers excellent visibility of vascular segments using both end-systolic and mid-late diastolic reconstructions at HRs up to 100 bpm, and only end-systolic reconstructions at HRs over 100 bpm. PMID:24834490

Shape-driven 3D segmentation using spherical wavelets.

PubMed

Nain, Delphine; Haker, Steven; Bobick, Aaron; Tannenbaum, Allen

2006-01-01

This paper presents a novel active surface segmentation algorithm using a multiscale shape representation and prior. We define a parametric model of a surface using spherical wavelet functions and learn a prior probability distribution over the wavelet coefficients to model shape variations at different scales and spatial locations in a training set. Based on this representation, we derive a parametric active surface evolution using the multiscale prior coefficients as parameters for our optimization procedure to naturally include the prior in the segmentation framework. Additionally, the optimization method can be applied in a coarse-to-fine manner. We apply our algorithm to the segmentation of brain caudate nucleus, of interest in the study of schizophrenia. Our validation shows our algorithm is computationally efficient and outperforms the Active Shape Model algorithm by capturing finer shape details.

Automated main-chain model building by template matching and iterative fragment extension.

PubMed

Terwilliger, Thomas C

2003-01-01

An algorithm for the automated macromolecular model building of polypeptide backbones is described. The procedure is hierarchical. In the initial stages, many overlapping polypeptide fragments are built. In subsequent stages, the fragments are extended and then connected. Identification of the locations of helical and beta-strand regions is carried out by FFT-based template matching. Fragment libraries of helices and beta-strands from refined protein structures are then positioned at the potential locations of helices and strands and the longest segments that fit the electron-density map are chosen. The helices and strands are then extended using fragment libraries consisting of sequences three amino acids long derived from refined protein structures. The resulting segments of polypeptide chain are then connected by choosing those which overlap at two or more C(alpha) positions. The fully automated procedure has been implemented in RESOLVE and is capable of model building at resolutions as low as 3.5 A. The algorithm is useful for building a preliminary main-chain model that can serve as a basis for refinement and side-chain addition.

The basic helix-loop-helix region of the transcriptional repressor hairy and enhancer of split 1 is preorganized to bind DNA.

PubMed

Popovic, Matija; Wienk, Hans; Coglievina, Maristella; Boelens, Rolf; Pongor, Sándor; Pintar, Alessandro

2014-04-01

Hairy and enhancer of split 1, one of the main downstream effectors in Notch signaling, is a transcriptional repressor of the basic helix-loop-helix (bHLH) family. Using nuclear magnetic resonance methods, we have determined the structure and dynamics of a recombinant protein, H1H, which includes an N-terminal segment, b1, containing functionally important phosphorylation sites, the basic region b2, required for binding to DNA, and the HLH domain. We show that a proline residue in the sequence divides the protein in two parts, a flexible and disordered N-terminal region including b1 and a structured, mainly helical region comprising b2 and the HLH domain. Binding of H1H to a double strand DNA oligonucleotide was monitored through the chemical shift perturbation of backbone amide resonances, and showed that the interaction surface involves not only the b2 segment but also several residues in the b1 and HLH regions. Copyright © 2014 Wiley Periodicals, Inc.

Single gene reassortment of highly pathogenic avian influenza A H5N1 in the low pathogenic H9N2 backbone and its impact on pathogenicity and infectivity of novel reassortant viruses.

PubMed

Moatasim, Yassmin; Kandeil, Ahmed; Mostafa, Ahmed; Elghaffar, Sary Khaleel Abd; El Shesheny, Rabeh; Elwahy, Ahmed Helmy M; Ali, Mohamed Ahmed

2017-10-01

Avian influenza A H5N1 and H9N2 viruses have been extensively circulating in various avian species and frequently infect mammals, including humans. The synchronous circulation of both viruses in Egypt provides an opportunity for possible genetic assortment, posing a probable threat to global public health. To assess the potential risk of the IAV reassortants derived from co-circulation of these two AI subtypes, reverse genetics technology was used to generate a set of IAV reassortants carrying single genetic segments of clade 2.2.1.2 virus A/duck/Egypt/Q4596D/2012 (H5N1), a representative of the most prevalent H5N1 clade in Egypt, in the genetic backbone of A/chicken/Egypt/S4456B/2011 (H9N2), a representative of G1-like H9N2 lineage which is widely circulating in Egypt. Furthermore, the genetic compatibility, growth kinetics and virulence were evaluated in vitro in mammalian systems using the MDCK cell line and avian system using SPF embryonated chicken eggs. Pathogenicity and virus shedding were further tested using SPF chickens. Out of the eight desired H9-reassortants, we could rescue only 5 reassortant viruses, either due to difficulty in cloning (PB1 of H5N1 virus) or genetic incompatibility (NP-H5/H9 and NA-H5/H9). Results revealed higher replication rates for the H9N2 virus having the NS segment of H5N1 virus. The lowest survival rate in both SPF eggs and SPF chickens was associated with the H5N1 parent virus infection, followed by the HA-H5/H9 virus. Our findings also suggest that all other reassortant viruses were of lower pathogenicity than the wild type H5N1 virus.

Memoryless cooperative graph search based on the simulated annealing algorithm

NASA Astrophysics Data System (ADS)

Hou, Jian; Yan, Gang-Feng; Fan, Zhen

2011-04-01

We have studied the problem of reaching a globally optimal segment for a graph-like environment with a single or a group of autonomous mobile agents. Firstly, two efficient simulated-annealing-like algorithms are given for a single agent to solve the problem in a partially known environment and an unknown environment, respectively. It shows that under both proposed control strategies, the agent will eventually converge to a globally optimal segment with probability 1. Secondly, we use multi-agent searching to simultaneously reduce the computation complexity and accelerate convergence based on the algorithms we have given for a single agent. By exploiting graph partition, a gossip-consensus method based scheme is presented to update the key parameter—radius of the graph, ensuring that the agents spend much less time finding a globally optimal segment.

Spectral optimized asymmetric segmented phase-only correlation filter.

PubMed

Leonard, I; Alfalou, A; Brosseau, C

2012-05-10

We suggest a new type of optimized composite filter, i.e., the asymmetric segmented phase-only filter (ASPOF), for improving the effectiveness of a VanderLugt correlator (VLC) when used for face identification. Basically, it consists in merging several reference images after application of a specific spectral optimization method. After segmentation of the spectral filter plane to several areas, each area is assigned to a single winner reference according to a new optimized criterion. The point of the paper is to show that this method offers a significant performance improvement on standard composite filters for face identification. We first briefly revisit composite filters [adapted, phase-only, inverse, compromise optimal, segmented, minimum average correlation energy, optimal trade-off maximum average correlation, and amplitude-modulated phase-only (AMPOF)], which are tools of choice for face recognition based on correlation techniques, and compare their performances with those of the ASPOF. We illustrate some of the drawbacks of current filters for several binary and grayscale image identifications. Next, we describe the optimization steps and introduce the ASPOF that can overcome these technical issues to improve the quality and the reliability of the correlation-based decision. We derive performance measures, i.e., PCE values and receiver operating characteristic curves, to confirm consistency of the results. We numerically find that this filter increases the recognition rate and decreases the false alarm rate. The results show that the discrimination of the ASPOF is comparable to that of the AMPOF, but the ASPOF is more robust than the trade-off maximum average correlation height against rotation and various types of noise sources. Our method has several features that make it amenable to experimental implementation using a VLC.

Multiscale approach to contour fitting for MR images

NASA Astrophysics Data System (ADS)

Rueckert, Daniel; Burger, Peter

1996-04-01

We present a new multiscale contour fitting process which combines information about the image and the contour of the object at different levels of scale. The algorithm is based on energy minimizing deformable models but avoids some of the problems associated with these models. The segmentation algorithm starts by constructing a linear scale-space of an image through convolution of the original image with a Gaussian kernel at different levels of scale, where the scale corresponds to the standard deviation of the Gaussian kernel. At high levels of scale large scale features of the objects are preserved while small scale features, like object details as well as noise, are suppressed. In order to maximize the accuracy of the segmentation, the contour of the object of interest is then tracked in scale-space from coarse to fine scales. We propose a hybrid multi-temperature simulated annealing optimization to minimize the energy of the deformable model. At high levels of scale the SA optimization is started at high temperatures, enabling the SA optimization to find a global optimal solution. At lower levels of scale the SA optimization is started at lower temperatures (at the lowest level the temperature is close to 0). This enforces a more deterministic behavior of the SA optimization at lower scales and leads to an increasingly local optimization as high energy barriers cannot be crossed. The performance and robustness of the algorithm have been tested on spin-echo MR images of the cardiovascular system. The task was to segment the ascending and descending aorta in 15 datasets of different individuals in order to measure regional aortic compliance. The results show that the algorithm is able to provide more accurate segmentation results than the classic contour fitting process and is at the same time very robust to noise and initialization.

Thermodynamics of Gas Turbine Cycles with Analytic Derivatives in OpenMDAO

NASA Technical Reports Server (NTRS)

Gray, Justin; Chin, Jeffrey; Hearn, Tristan; Hendricks, Eric; Lavelle, Thomas; Martins, Joaquim R. R. A.

2016-01-01

A new equilibrium thermodynamics analysis tool was built based on the CEA method using the OpenMDAO framework. The new tool provides forward and adjoint analytic derivatives for use with gradient based optimization algorithms. The new tool was validated against the original CEA code to ensure an accurate analysis and the analytic derivatives were validated against finite-difference approximations. Performance comparisons between analytic and finite difference methods showed a significant speed advantage for the analytic methods. To further test the new analysis tool, a sample optimization was performed to find the optimal air-fuel equivalence ratio, , maximizing combustion temperature for a range of different pressures. Collectively, the results demonstrate the viability of the new tool to serve as the thermodynamic backbone for future work on a full propulsion modeling tool.

Combinations of various CpG motifs cloned into plasmid backbone modulate and enhance protective immunity of viral replicon DNA anthrax vaccines.

PubMed

Yu, Yun-Zhou; Ma, Yao; Xu, Wen-Hui; Wang, Shuang; Sun, Zhi-Wei

2015-08-01

DNA vaccines are generally weak stimulators of the immune system. Fortunately, their efficacy can be improved using a viral replicon vector or by the addition of immunostimulatory CpG motifs, although the design of these engineered DNA vectors requires optimization. Our results clearly suggest that multiple copies of three types of CpG motifs or combinations of various types of CpG motifs cloned into a viral replicon vector backbone with strong immunostimulatory activities on human PBMC are efficient adjuvants for these DNA vaccines to modulate and enhance protective immunity against anthrax, although modifications with these different CpG forms in vivo elicited inconsistent immune response profiles. Modification with more copies of CpG motifs elicited more potent adjuvant effects leading to the generation of enhanced immunity, which indicated a CpG motif dose-dependent enhancement of antigen-specific immune responses. Notably, the enhanced and/or synchronous adjuvant effects were observed in modification with combinations of two different types of CpG motifs, which provides not only a contribution to the knowledge base on the adjuvant activities of CpG motifs combinations but also implications for the rational design of optimal DNA vaccines with combinations of CpG motifs as "built-in" adjuvants. We describe an efficient strategy to design and optimize DNA vaccines by the addition of combined immunostimulatory CpG motifs in a viral replicon DNA plasmid to produce strong immune responses, which indicates that the CpG-modified viral replicon DNA plasmid may be desirable for use as vector of DNA vaccines.

Electric field theory based approach to search-direction line definition in image segmentation: application to optimal femur-tibia cartilage segmentation in knee-joint 3-D MR

NASA Astrophysics Data System (ADS)

Yin, Y.; Sonka, M.

2010-03-01

A novel method is presented for definition of search lines in a variety of surface segmentation approaches. The method is inspired by properties of electric field direction lines and is applicable to general-purpose n-D shapebased image segmentation tasks. Its utility is demonstrated in graph construction and optimal segmentation of multiple mutually interacting objects. The properties of the electric field-based graph construction guarantee that inter-object graph connecting lines are non-intersecting and inherently covering the entire object-interaction space. When applied to inter-object cross-surface mapping, our approach generates one-to-one and all-to-all vertex correspondent pairs between the regions of mutual interaction. We demonstrate the benefits of the electric field approach in several examples ranging from relatively simple single-surface segmentation to complex multiobject multi-surface segmentation of femur-tibia cartilage. The performance of our approach is demonstrated in 60 MR images from the Osteoarthritis Initiative (OAI), in which our approach achieved a very good performance as judged by surface positioning errors (average of 0.29 and 0.59 mm for signed and unsigned cartilage positioning errors, respectively).

Left ventricle segmentation via graph cut distribution matching.

PubMed

Ben Ayed, Ismail; Punithakumar, Kumaradevan; Li, Shuo; Islam, Ali; Chong, Jaron

2009-01-01

We present a discrete kernel density matching energy for segmenting the left ventricle cavity in cardiac magnetic resonance sequences. The energy and its graph cut optimization based on an original first-order approximation of the Bhattacharyya measure have not been proposed previously, and yield competitive results in nearly real-time. The algorithm seeks a region within each frame by optimization of two priors, one geometric (distance-based) and the other photometric, each measuring a distribution similarity between the region and a model learned from the first frame. Based on global rather than pixelwise information, the proposed algorithm does not require complex training and optimization with respect to geometric transformations. Unlike related active contour methods, it does not compute iterative updates of computationally expensive kernel densities. Furthermore, the proposed first-order analysis can be used for other intractable energies and, therefore, can lead to segmentation algorithms which share the flexibility of active contours and computational advantages of graph cuts. Quantitative evaluations over 2280 images acquired from 20 subjects demonstrated that the results correlate well with independent manual segmentations by an expert.

Hierarchical image segmentation via recursive superpixel with adaptive regularity

NASA Astrophysics Data System (ADS)

Nakamura, Kensuke; Hong, Byung-Woo

2017-11-01

A fast and accurate segmentation algorithm in a hierarchical way based on a recursive superpixel technique is presented. We propose a superpixel energy formulation in which the trade-off between data fidelity and regularization is dynamically determined based on the local residual in the energy optimization procedure. We also present an energy optimization algorithm that allows a pixel to be shared by multiple regions to improve the accuracy and appropriate the number of segments. The qualitative and quantitative evaluations demonstrate that our algorithm, combining the proposed energy and optimization, outperforms the conventional k-means algorithm by up to 29.10% in F-measure. We also perform comparative analysis with state-of-the-art algorithms in the hierarchical segmentation. Our algorithm yields smooth regions throughout the hierarchy as opposed to the others that include insignificant details. Our algorithm overtakes the other algorithms in terms of balance between accuracy and computational time. Specifically, our method runs 36.48% faster than the region-merging approach, which is the fastest of the comparing algorithms, while achieving a comparable accuracy.

Surface-region context in optimal multi-object graph-based segmentation: robust delineation of pulmonary tumors.

PubMed

Song, Qi; Chen, Mingqing; Bai, Junjie; Sonka, Milan; Wu, Xiaodong

2011-01-01

Multi-object segmentation with mutual interaction is a challenging task in medical image analysis. We report a novel solution to a segmentation problem, in which target objects of arbitrary shape mutually interact with terrain-like surfaces, which widely exists in the medical imaging field. The approach incorporates context information used during simultaneous segmentation of multiple objects. The object-surface interaction information is encoded by adding weighted inter-graph arcs to our graph model. A globally optimal solution is achieved by solving a single maximum flow problem in a low-order polynomial time. The performance of the method was evaluated in robust delineation of lung tumors in megavoltage cone-beam CT images in comparison with an expert-defined independent standard. The evaluation showed that our method generated highly accurate tumor segmentations. Compared with the conventional graph-cut method, our new approach provided significantly better results (p < 0.001). The Dice coefficient obtained by the conventional graph-cut approach (0.76 +/- 0.10) was improved to 0.84 +/- 0.05 when employing our new method for pulmonary tumor segmentation.

Automated Sperm Head Detection Using Intersecting Cortical Model Optimised by Particle Swarm Optimization.

PubMed

Tan, Weng Chun; Mat Isa, Nor Ashidi

2016-01-01

In human sperm motility analysis, sperm segmentation plays an important role to determine the location of multiple sperms. To ensure an improved segmentation result, the Laplacian of Gaussian filter is implemented as a kernel in a pre-processing step before applying the image segmentation process to automatically segment and detect human spermatozoa. This study proposes an intersecting cortical model (ICM), which was derived from several visual cortex models, to segment the sperm head region. However, the proposed method suffered from parameter selection; thus, the ICM network is optimised using particle swarm optimization where feature mutual information is introduced as the new fitness function. The final results showed that the proposed method is more accurate and robust than four state-of-the-art segmentation methods. The proposed method resulted in rates of 98.14%, 98.82%, 86.46% and 99.81% in accuracy, sensitivity, specificity and precision, respectively, after testing with 1200 sperms. The proposed algorithm is expected to be implemented in analysing sperm motility because of the robustness and capability of this algorithm.

Improving Antibody-Based Cancer Therapeutics Through Glycan Engineering.

PubMed

Yu, Xiaojie; Marshall, Michael J E; Cragg, Mark S; Crispin, Max

2017-06-01

Antibody-based therapeutics has emerged as a major tool in cancer treatment. Guided by the superb specificity of the antibody variable domain, it allows the precise targeting of tumour markers. Recently, eliciting cellular effector functions, mediated by the Fc domain, has gained traction as a means by which to generate more potent antibody therapeutics. Extensive mutagenesis studies of the Fc protein backbone has enabled the generation of Fc variants that more optimally engage the Fcγ receptors known to mediate cellular effector functions such as antibody-dependent cellular cytotoxicity (ADCC) and cellular phagocytosis. In addition to the protein backbone, the homodimeric Fc domain contains two opposing N-linked glycans, which represent a further point of potential immunomodulation, independent of the Fc protein backbone. For example, a lack of core fucose usually attached to the IgG Fc glycan leads to enhanced ADCC activity, whereas a high level of terminal sialylation is associated with reduced inflammation. Significant growth in knowledge of Fc glycosylation over the last decade, combined with advancement in genetic engineering, has empowered glyco-engineering to fine-tune antibody therapeutics. This has culminated in the approval of two glyco-engineered antibodies for cancer therapy: the anti-CCR4 mogamulizumab approved in 2012 and the anti-CD20 obinutuzumab in 2013. We discuss here the technological platforms for antibody glyco-engineering and review the current clinical landscape of glyco-engineered antibodies.

Myocardial Infarct Segmentation from Magnetic Resonance Images for Personalized Modeling of Cardiac Electrophysiology

PubMed Central

Ukwatta, Eranga; Arevalo, Hermenegild; Li, Kristina; Yuan, Jing; Qiu, Wu; Malamas, Peter; Wu, Katherine C.

2016-01-01

Accurate representation of myocardial infarct geometry is crucial to patient-specific computational modeling of the heart in ischemic cardiomyopathy. We have developed a methodology for segmentation of left ventricular (LV) infarct from clinically acquired, two-dimensional (2D), late-gadolinium enhanced cardiac magnetic resonance (LGE-CMR) images, for personalized modeling of ventricular electrophysiology. The infarct segmentation was expressed as a continuous min-cut optimization problem, which was solved using its dual formulation, the continuous max-flow (CMF). The optimization objective comprised of a smoothness term, and a data term that quantified the similarity between image intensity histograms of segmented regions and those of a set of training images. A manual segmentation of the LV myocardium was used to initialize and constrain the developed method. The three-dimensional geometry of infarct was reconstructed from its segmentation using an implicit, shape-based interpolation method. The proposed methodology was extensively evaluated using metrics based on geometry, and outcomes of individualized electrophysiological simulations of cardiac dys(function). Several existing LV infarct segmentation approaches were implemented, and compared with the proposed method. Our results demonstrated that the CMF method was more accurate than the existing approaches in reproducing expert manual LV infarct segmentations, and in electrophysiological simulations. The infarct segmentation method we have developed and comprehensively evaluated in this study constitutes an important step in advancing clinical applications of personalized simulations of cardiac electrophysiology. PMID:26731693

Physical–chemical determinants of coil conformations in globular proteins

PubMed Central

Perskie, Lauren L; Rose, George D

2010-01-01

We present a method with the potential to generate a library of coil segments from first principles. Proteins are built from α-helices and/or β-strands interconnected by these coil segments. Here, we investigate the conformational determinants of short coil segments, with particular emphasis on chain turns. Toward this goal, we extracted a comprehensive set of two-, three-, and four-residue turns from X-ray–elucidated proteins and classified them by conformation. A remarkably small number of unique conformers account for most of this experimentally determined set, whereas remaining members span a large number of rare conformers, many occurring only once in the entire protein database. Factors determining conformation were identified via Metropolis Monte Carlo simulations devised to test the effectiveness of various energy terms. Simulated structures were validated by comparison to experimental counterparts. After filtering rare conformers, we found that 98% of the remaining experimentally determined turn population could be reproduced by applying a hydrogen bond energy term to an exhaustively generated ensemble of clash-free conformers in which no backbone polar group lacks a hydrogen-bond partner. Further, at least 90% of longer coil segments, ranging from 5- to 20 residues, were found to be structural composites of these shorter primitives. These results are pertinent to protein structure prediction, where approaches can be divided into either empirical or ab initio methods. Empirical methods use database-derived information; ab initio methods rely on physical–chemical principles exclusively. Replacing the database-derived coil library with one generated from first principles would transform any empirically based method into its corresponding ab initio homologue. PMID:20512968

Discriminative spatial-frequency-temporal feature extraction and classification of motor imagery EEG: An sparse regression and Weighted Naïve Bayesian Classifier-based approach.

PubMed

Miao, Minmin; Zeng, Hong; Wang, Aimin; Zhao, Changsen; Liu, Feixiang

2017-02-15

Common spatial pattern (CSP) is most widely used in motor imagery based brain-computer interface (BCI) systems. In conventional CSP algorithm, pairs of the eigenvectors corresponding to both extreme eigenvalues are selected to construct the optimal spatial filter. In addition, an appropriate selection of subject-specific time segments and frequency bands plays an important role in its successful application. This study proposes to optimize spatial-frequency-temporal patterns for discriminative feature extraction. Spatial optimization is implemented by channel selection and finding discriminative spatial filters adaptively on each time-frequency segment. A novel Discernibility of Feature Sets (DFS) criteria is designed for spatial filter optimization. Besides, discriminative features located in multiple time-frequency segments are selected automatically by the proposed sparse time-frequency segment common spatial pattern (STFSCSP) method which exploits sparse regression for significant features selection. Finally, a weight determined by the sparse coefficient is assigned for each selected CSP feature and we propose a Weighted Naïve Bayesian Classifier (WNBC) for classification. Experimental results on two public EEG datasets demonstrate that optimizing spatial-frequency-temporal patterns in a data-driven manner for discriminative feature extraction greatly improves the classification performance. The proposed method gives significantly better classification accuracies in comparison with several competing methods in the literature. The proposed approach is a promising candidate for future BCI systems. Copyright © 2016 Elsevier B.V. All rights reserved.

A novel software and conceptual design of the hardware platform for intensity modulated radiation therapy

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

Nguyen, Dan; Ruan, Dan; O’Connor, Daniel

Purpose: To deliver high quality intensity modulated radiotherapy (IMRT) using a novel generalized sparse orthogonal collimators (SOCs), the authors introduce a novel direct aperture optimization (DAO) approach based on discrete rectangular representation. Methods: A total of seven patients—two glioblastoma multiforme, three head & neck (including one with three prescription doses), and two lung—were included. 20 noncoplanar beams were selected using a column generation and pricing optimization method. The SOC is a generalized conventional orthogonal collimators with N leaves in each collimator bank, where N = 1, 2, or 4. SOC degenerates to conventional jaws when N = 1. For SOC-basedmore » IMRT, rectangular aperture optimization (RAO) was performed to optimize the fluence maps using rectangular representation, producing fluence maps that can be directly converted into a set of deliverable rectangular apertures. In order to optimize the dose distribution and minimize the number of apertures used, the overall objective was formulated to incorporate an L2 penalty reflecting the difference between the prescription and the projected doses, and an L1 sparsity regularization term to encourage a low number of nonzero rectangular basis coefficients. The optimization problem was solved using the Chambolle–Pock algorithm, a first-order primal–dual algorithm. Performance of RAO was compared to conventional two-step IMRT optimization including fluence map optimization and direct stratification for multileaf collimator (MLC) segmentation (DMS) using the same number of segments. For the RAO plans, segment travel time for SOC delivery was evaluated for the N = 1, N = 2, and N = 4 SOC designs to characterize the improvement in delivery efficiency as a function of N. Results: Comparable PTV dose homogeneity and coverage were observed between the RAO and the DMS plans. The RAO plans were slightly superior to the DMS plans in sparing critical structures. On average, the maximum and mean critical organ doses were reduced by 1.94% and 1.44% of the prescription dose. The average number of delivery segments was 12.68 segments per beam for both the RAO and DMS plans. The N = 2 and N = 4 SOC designs were, on average, 1.56 and 1.80 times more efficient than the N = 1 SOC design to deliver. The mean aperture size produced by the RAO plans was 3.9 times larger than that of the DMS plans. Conclusions: The DAO and dose domain optimization approach enabled high quality IMRT plans using a low-complexity collimator setup. The dosimetric quality is comparable or slightly superior to conventional MLC-based IMRT plans using the same number of delivery segments. The SOC IMRT delivery efficiency can be significantly improved by increasing the leaf numbers, but the number is still significantly lower than the number of leaves in a typical MLC.« less

A novel software and conceptual design of the hardware platform for intensity modulated radiation therapy.

PubMed

Nguyen, Dan; Ruan, Dan; O'Connor, Daniel; Woods, Kaley; Low, Daniel A; Boucher, Salime; Sheng, Ke

2016-02-01

To deliver high quality intensity modulated radiotherapy (IMRT) using a novel generalized sparse orthogonal collimators (SOCs), the authors introduce a novel direct aperture optimization (DAO) approach based on discrete rectangular representation. A total of seven patients-two glioblastoma multiforme, three head & neck (including one with three prescription doses), and two lung-were included. 20 noncoplanar beams were selected using a column generation and pricing optimization method. The SOC is a generalized conventional orthogonal collimators with N leaves in each collimator bank, where N = 1, 2, or 4. SOC degenerates to conventional jaws when N = 1. For SOC-based IMRT, rectangular aperture optimization (RAO) was performed to optimize the fluence maps using rectangular representation, producing fluence maps that can be directly converted into a set of deliverable rectangular apertures. In order to optimize the dose distribution and minimize the number of apertures used, the overall objective was formulated to incorporate an L2 penalty reflecting the difference between the prescription and the projected doses, and an L1 sparsity regularization term to encourage a low number of nonzero rectangular basis coefficients. The optimization problem was solved using the Chambolle-Pock algorithm, a first-order primal-dual algorithm. Performance of RAO was compared to conventional two-step IMRT optimization including fluence map optimization and direct stratification for multileaf collimator (MLC) segmentation (DMS) using the same number of segments. For the RAO plans, segment travel time for SOC delivery was evaluated for the N = 1, N = 2, and N = 4 SOC designs to characterize the improvement in delivery efficiency as a function of N. Comparable PTV dose homogeneity and coverage were observed between the RAO and the DMS plans. The RAO plans were slightly superior to the DMS plans in sparing critical structures. On average, the maximum and mean critical organ doses were reduced by 1.94% and 1.44% of the prescription dose. The average number of delivery segments was 12.68 segments per beam for both the RAO and DMS plans. The N = 2 and N = 4 SOC designs were, on average, 1.56 and 1.80 times more efficient than the N = 1 SOC design to deliver. The mean aperture size produced by the RAO plans was 3.9 times larger than that of the DMS plans. The DAO and dose domain optimization approach enabled high quality IMRT plans using a low-complexity collimator setup. The dosimetric quality is comparable or slightly superior to conventional MLC-based IMRT plans using the same number of delivery segments. The SOC IMRT delivery efficiency can be significantly improved by increasing the leaf numbers, but the number is still significantly lower than the number of leaves in a typical MLC.

Shape-Driven 3D Segmentation Using Spherical Wavelets

PubMed Central

Nain, Delphine; Haker, Steven; Bobick, Aaron; Tannenbaum, Allen

2013-01-01

This paper presents a novel active surface segmentation algorithm using a multiscale shape representation and prior. We define a parametric model of a surface using spherical wavelet functions and learn a prior probability distribution over the wavelet coefficients to model shape variations at different scales and spatial locations in a training set. Based on this representation, we derive a parametric active surface evolution using the multiscale prior coefficients as parameters for our optimization procedure to naturally include the prior in the segmentation framework. Additionally, the optimization method can be applied in a coarse-to-fine manner. We apply our algorithm to the segmentation of brain caudate nucleus, of interest in the study of schizophrenia. Our validation shows our algorithm is computationally efficient and outperforms the Active Shape Model algorithm by capturing finer shape details. PMID:17354875

Incorporation of physical constraints in optimal surface search for renal cortex segmentation

NASA Astrophysics Data System (ADS)

Li, Xiuli; Chen, Xinjian; Yao, Jianhua; Zhang, Xing; Tian, Jie

2012-02-01

In this paper, we propose a novel approach for multiple surfaces segmentation based on the incorporation of physical constraints in optimal surface searching. We apply our new approach to solve the renal cortex segmentation problem, an important but not sufficiently researched issue. In this study, in order to better restrain the intensity proximity of the renal cortex and renal column, we extend the optimal surface search approach to allow for varying sampling distance and physical separation constraints, instead of the traditional fixed sampling distance and numerical separation constraints. The sampling distance of each vertex-column is computed according to the sparsity of the local triangular mesh. Then the physical constraint learned from a priori renal cortex thickness is applied to the inter-surface arcs as the separation constraints. Appropriate varying sampling distance and separation constraints were learnt from 6 clinical CT images. After training, the proposed approach was tested on a test set of 10 images. The manual segmentation of renal cortex was used as the reference standard. Quantitative analysis of the segmented renal cortex indicates that overall segmentation accuracy was increased after introducing the varying sampling distance and physical separation constraints (the average true positive volume fraction (TPVF) and false positive volume fraction (FPVF) were 83.96% and 2.80%, respectively, by using varying sampling distance and physical separation constraints compared to 74.10% and 0.18%, respectively, by using fixed sampling distance and numerical separation constraints). The experimental results demonstrated the effectiveness of the proposed approach.

Compatibility of segmented thermoelectric generators

NASA Technical Reports Server (NTRS)

Snyder, J.; Ursell, T.

2002-01-01

It is well known that power generation efficiency improves when materials with appropriate properties are combined either in a cascaded or segmented fashion across a temperature gradient. Past methods for determining materials used in segmentation weremainly concerned with materials that have the highest figure of merit in the temperature range. However, the example of SiGe segmented with Bi2Te3 and/or various skutterudites shows a marked decline in device efficiency even though SiGe has the highest figure of merit in the temperature range. The origin of the incompatibility of SiGe with other thermoelectric materials leads to a general definition of compatibility and intrinsic efficiency. The compatibility factor derived as = (Jl+zr - 1) a is a function of only intrinsic material properties and temperature, which is represented by a ratio of current to conduction heat. For maximum efficiency the compatibility factor should not change with temperature both within a single material, and in the segmented leg as a whole. This leads to a measure of compatibility not only between segments, but also within a segment. General temperature trends show that materials are more self compatible at higher temperatures, and segmentation is more difficult across a larger -T. The compatibility factor can be used as a quantitative guide for deciding whether a material is better suited for segmentation orcascading. Analysis of compatibility factors and intrinsic efficiency for optimal segmentation are discussed, with intent to predict optimal material properties, temperature interfaces, and/or currentheat ratios.

On a distinctive feature of problems of calculating time-average characteristics of nuclear reactor optimal control sets

NASA Astrophysics Data System (ADS)

Trifonenkov, A. V.; Trifonenkov, V. P.

2017-01-01

This article deals with a feature of problems of calculating time-average characteristics of nuclear reactor optimal control sets. The operation of a nuclear reactor during threatened period is considered. The optimal control search problem is analysed. The xenon poisoning causes limitations on the variety of statements of the problem of calculating time-average characteristics of a set of optimal reactor power off controls. The level of xenon poisoning is limited. There is a problem of choosing an appropriate segment of the time axis to ensure that optimal control problem is consistent. Two procedures of estimation of the duration of this segment are considered. Two estimations as functions of the xenon limitation were plot. Boundaries of the interval of averaging are defined more precisely.

Caution is required in interpretation of mutations in the voltage sensing domain of voltage gated channels as evidence for gating mechanisms.

PubMed

Kariev, Alisher M; Green, Michael E

2015-01-12

The gating mechanism of voltage sensitive ion channels is generally considered to be the motion of the S4 transmembrane segment of the voltage sensing domains (VSD). The primary supporting evidence came from R → C mutations on the S4 transmembrane segment of the VSD, followed by reaction with a methanethiosulfonate (MTS) reagent. The cys side chain is -SH (reactive form -S-); the arginine side chain is much larger, leaving space big enough to accommodate the MTS sulfonate head group. The cavity created by the mutation has space for up to seven more water molecules than were present in wild type, which could be displaced irreversibly by the MTS reagent. Our quantum calculations show there is major reorientation of three aromatic residues that face into the cavity in response to proton displacement within the VSD. Two phenylalanines reorient sufficiently to shield/unshield the cysteine from the intracellular and extracellular ends, depending on the proton positions, and a tyrosine forms a hydrogen bond to the cysteine sulfur with its side chain -OH. These could produce the results of the experiments that have been interpreted as evidence for physical motion of the S4 segment, without physical motion of the S4 backbone. The computations strongly suggest that the interpretation of cysteine substitution reaction experiments be re-examined in the light of these considerations.

Magnet system optimization for segmented adaptive-gap in-vacuum undulator

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

Kitegi, C., E-mail: ckitegi@bnl.gov; Chubar, O.; Eng, C.

2016-07-27

Segmented Adaptive Gap in-vacuum Undulator (SAGU), in which different segments have different gaps and periods, promises a considerable spectral performance gain over a conventional undulator with uniform gap and period. According to calculations, this gain can be comparable to the gain achievable with a superior undulator technology (e.g. a room-temperature in-vacuum hybrid SAGU would perform as a cryo-cooled hybrid in-vacuum undulator with uniform gap and period). However, for reaching the high spectral performance, SAGU magnetic design has to include compensation of kicks experienced by the electron beam at segment junctions because of different deflection parameter values in the segments. Wemore » show that such compensation to large extent can be accomplished by using a passive correction, however, simple correction coils are nevertheless required as well to reach perfect compensation over a whole SAGU tuning range. Magnetic optimizations performed with Radia code, and the resulting undulator radiation spectra calculated using SRW code, demonstrating a possibility of nearly perfect correction, are presented.« less

Quadrature amplitude modulation (QAM) using binary-driven coupling-modulated rings

NASA Astrophysics Data System (ADS)

Karimelahi, Samira; Sheikholeslami, Ali

2016-05-01

We propose and fully analyze a compact structure for DAC-free pure optical QAM modulation. The proposed structure is the first ring resonator-based DAC-free QAM modulator reported in the literature, to the best of our knowledge. The device consists of two segmented add-drop Mach Zehnder interferometer-assisted ring modulators (MZIARM) in an IQ configuration. The proposed architecture is investigated based on the parameters from SOI technology where various key design considerations are discussed. We have included the loss in the MZI arms in our analysis of phase and amplitude modulation using MZIARM for the first time and show that the imbalanced loss results in a phase error. The output level linearity is also studied for both QAM-16 and QAM-64 not only based on optimizing RF segment lengths but also by optimizing the number of segments. In QAM-16, linearity among levels is achievable with two segments while in QAM-64 an additional segment may be required.

High Efficiency Thermoelectric Radioisotope Power Systems

NASA Technical Reports Server (NTRS)

El-Genk, Mohamed; Saber, Hamed; Caillat, Thierry

2004-01-01

The work performed and whose results presented in this report is a joint effort between the University of New Mexico s Institute for Space and Nuclear Power Studies (ISNPS) and the Jet Propulsion Laboratory (JPL), California Institute of Technology. In addition to the development, design, and fabrication of skutterudites and skutterudites-based segmented unicouples this effort included conducting performance tests of these unicouples for hundreds of hours to verify theoretical predictions of the conversion efficiency. The performance predictions of these unicouples are obtained using 1-D and 3-D models developed for that purpose and for estimating the actual performance and side heat losses in the tests conducted at ISNPS. In addition to the performance tests, the development of the 1-D and 3-D models and the development of Advanced Radioisotope Power systems for Beginning-Of-Life (BOM) power of 108 We are carried out at ISNPS. The materials synthesis and fabrication of the unicouples are carried out at JPL. The research conducted at ISNPS is documented in chapters 2-5 and that conducted at JP, in documented in chapter 5. An important consideration in the design and optimization of segmented thermoelectric unicouples (STUs) is determining the relative lengths, cross-section areas, and the interfacial temperatures of the segments of the different materials in the n- and p-legs. These variables are determined using a genetic algorithm (GA) in conjunction with one-dimensional analytical model of STUs that is developed in chapter 2. Results indicated that when optimized for maximum conversion efficiency, the interfacial temperatures between various segments in a STU are close to those at the intersections of the Figure-Of-Merit (FOM), ZT, curves of the thermoelectric materials of the adjacent segments. When optimizing the STUs for maximum electrical power density, however, the interfacial temperatures are different from those at the intersections of the ZT curves, but close to those at the intersections the characteristic power, CP, curves of the thermoelectric materials of the adjacent segments (CP = T(sup 2)Zk and has a unit of W/m). Results also showed that the number of the segments in the n- and p-legs of the STUs optimized for maximum power density are generally fewer than when the same unicouples are optimized for maximum efficiency. These results are obtained using the 1-D optimization model of STUs that is detailed in chapter 2. A three-dimensional model of STUs is developed and incorporated into the ANSYS commercial software (chapter 3). The governing equations are solved, subject to the prescribed

Low-thrust trajectory optimization of asteroid sample return mission with multiple revolutions and moon gravity assists

NASA Astrophysics Data System (ADS)

Tang, Gao; Jiang, FanHuag; Li, JunFeng

2015-11-01

Near-Earth asteroids have gained a lot of interest and the development in low-thrust propulsion technology makes complex deep space exploration missions possible. A mission from low-Earth orbit using low-thrust electric propulsion system to rendezvous with near-Earth asteroid and bring sample back is investigated. By dividing the mission into five segments, the complex mission is solved separately. Then different methods are used to find optimal trajectories for every segment. Multiple revolutions around the Earth and multiple Moon gravity assists are used to decrease the fuel consumption to escape from the Earth. To avoid possible numerical difficulty of indirect methods, a direct method to parameterize the switching moment and direction of thrust vector is proposed. To maximize the mass of sample, optimal control theory and homotopic approach are applied to find the optimal trajectory. Direct methods of finding proper time to brake the spacecraft using Moon gravity assist are also proposed. Practical techniques including both direct and indirect methods are investigated to optimize trajectories for different segments and they can be easily extended to other missions and more precise dynamic model.

Medial-based deformable models in nonconvex shape-spaces for medical image segmentation.

PubMed

McIntosh, Chris; Hamarneh, Ghassan

2012-01-01

We explore the application of genetic algorithms (GA) to deformable models through the proposition of a novel method for medical image segmentation that combines GA with nonconvex, localized, medial-based shape statistics. We replace the more typical gradient descent optimizer used in deformable models with GA, and the convex, implicit, global shape statistics with nonconvex, explicit, localized ones. Specifically, we propose GA to reduce typical deformable model weaknesses pertaining to model initialization, pose estimation and local minima, through the simultaneous evolution of a large number of models. Furthermore, we constrain the evolution, and thus reduce the size of the search-space, by using statistically-based deformable models whose deformations are intuitive (stretch, bulge, bend) and are driven in terms of localized principal modes of variation, instead of modes of variation across the entire shape that often fail to capture localized shape changes. Although GA are not guaranteed to achieve the global optima, our method compares favorably to the prevalent optimization techniques, convex/nonconvex gradient-based optimizers and to globally optimal graph-theoretic combinatorial optimization techniques, when applied to the task of corpus callosum segmentation in 50 mid-sagittal brain magnetic resonance images.

Image segmentation using local shape and gray-level appearance models

NASA Astrophysics Data System (ADS)

Seghers, Dieter; Loeckx, Dirk; Maes, Frederik; Suetens, Paul

2006-03-01

A new generic model-based segmentation scheme is presented, which can be trained from examples akin to the Active Shape Model (ASM) approach in order to acquire knowledge about the shape to be segmented and about the gray-level appearance of the object in the image. Because in the ASM approach the intensity and shape models are typically applied alternately during optimizing as first an optimal target location is selected for each landmark separately based on local gray-level appearance information only to which the shape model is fitted subsequently, the ASM may be misled in case of wrongly selected landmark locations. Instead, the proposed approach optimizes for shape and intensity characteristics simultaneously. Local gray-level appearance information at the landmark points extracted from feature images is used to automatically detect a number of plausible candidate locations for each landmark. The shape information is described by multiple landmark-specific statistical models that capture local dependencies between adjacent landmarks on the shape. The shape and intensity models are combined in a single cost function that is optimized non-iteratively using dynamic programming which allows to find the optimal landmark positions using combined shape and intensity information, without the need for initialization.

Continuous intensity map optimization (CIMO): A novel approach to leaf sequencing in step and shoot IMRT

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

Cao Daliang; Earl, Matthew A.; Luan, Shuang

2006-04-15

A new leaf-sequencing approach has been developed that is designed to reduce the number of required beam segments for step-and-shoot intensity modulated radiation therapy (IMRT). This approach to leaf sequencing is called continuous-intensity-map-optimization (CIMO). Using a simulated annealing algorithm, CIMO seeks to minimize differences between the optimized and sequenced intensity maps. Two distinguishing features of the CIMO algorithm are (1) CIMO does not require that each optimized intensity map be clustered into discrete levels and (2) CIMO is not rule-based but rather simultaneously optimizes both the aperture shapes and weights. To test the CIMO algorithm, ten IMRT patient cases weremore » selected (four head-and-neck, two pancreas, two prostate, one brain, and one pelvis). For each case, the optimized intensity maps were extracted from the Pinnacle{sup 3} treatment planning system. The CIMO algorithm was applied, and the optimized aperture shapes and weights were loaded back into Pinnacle. A final dose calculation was performed using Pinnacle's convolution/superposition based dose calculation. On average, the CIMO algorithm provided a 54% reduction in the number of beam segments as compared with Pinnacle's leaf sequencer. The plans sequenced using the CIMO algorithm also provided improved target dose uniformity and a reduced discrepancy between the optimized and sequenced intensity maps. For ten clinical intensity maps, comparisons were performed between the CIMO algorithm and the power-of-two reduction algorithm of Xia and Verhey [Med. Phys. 25(8), 1424-1434 (1998)]. When the constraints of a Varian Millennium multileaf collimator were applied, the CIMO algorithm resulted in a 26% reduction in the number of segments. For an Elekta multileaf collimator, the CIMO algorithm resulted in a 67% reduction in the number of segments. An average leaf sequencing time of less than one minute per beam was observed.« less

Megasupramolecules for safer, cleaner fuel by end association of long telechelic polymers.

PubMed

Wei, Ming-Hsin; Li, Boyu; David, R L Ameri; Jones, Simon C; Sarohia, Virendra; Schmitigal, Joel A; Kornfield, Julia A

2015-10-02

We used statistical mechanics to design polymers that defy conventional wisdom by self-assembling into "megasupramolecules" (≥5000 kg/mol) at low concentration (≤0.3 weight percent). Theoretical treatment of the distribution of individual subunits—end-functional polymers—among cyclic and linear supramolecules (ring-chain equilibrium) predicts that megasupramolecules can form at low total polymer concentration if, and only if, the backbones are long (>400 kg/mol) and end-association strength is optimal. Viscometry and scattering measurements of long telechelic polymers having polycyclooctadiene backbones and acid or amine end groups verify the formation of megasupramolecules. They control misting and reduce drag in the same manner as ultralong covalent polymers. With individual building blocks short enough to avoid hydrodynamic chain scission (weight-average molecular weights of 400 to 1000 kg/mol) and reversible linkages that protect covalent bonds, these megasupramolecules overcome the obstacles of shear degradation and engine incompatibility. Copyright © 2015, American Association for the Advancement of Science.

Metabolic engineering for the microbial production of carotenoids and related products with a focus on the rare C50 carotenoids.

PubMed

Heider, Sabine A E; Peters-Wendisch, Petra; Wendisch, Volker F; Beekwilder, Jules; Brautaset, Trygve

2014-05-01

Carotenoids, a subfamily of terpenoids, are yellow- to red-colored pigments synthesized by plants, fungi, algae, and bacteria. They are ubiquitous in nature and take over crucial roles in many biological processes as for example photosynthesis, vision, and the quenching of free radicals and singlet oxygen. Due to their color and their potential beneficial effects on human health, carotenoids receive increasing attention. Carotenoids can be classified due to the length of their carbon backbone. Most carotenoids have a C40 backbone, but also C30 and C50 carotenoids are known. All carotenoids are derived from isopentenyl pyrophosphate (IPP) as a common precursor. Pathways leading to IPP as well as metabolic engineering of IPP synthesis and C40 carotenoid production have been reviewed expertly elsewhere. Since C50 carotenoids are synthesized from the C40 carotenoid lycopene, we will summarize common strategies for optimizing lycopene production and we will focus our review on the characteristics, biosynthesis, glycosylation, and overproduction of C50 carotenoids.

Dextran Nanoparticle Synthesis and Properties

PubMed Central

Wasiak, Iga; Kulikowska, Aleksandra; Janczewska, Magdalena; Michalak, Magdalena; Cymerman, Iwona A.; Nagalski, Andrzej; Kallinger, Peter; Szymanski, Wladyslaw W.; Ciach, Tomasz

2016-01-01

Dextran is widely exploited in medical products and as a component of drug-delivering nanoparticles (NPs). Here, we tested whether dextran can serve as the main substrate of NPs and form a stable backbone. We tested dextrans with several molecular masses under several synthesis conditions to optimize NP stability. The analysis of the obtained nanoparticles showed that dextran NPs that were synthesized from 70 kDa dextran with a 5% degree of oxidation of the polysaccharide chain and 50% substitution with dodecylamine formed a NP backbone composed of modified dextran subunits, the mean diameter of which in an aqueous environment was around 100 nm. Dextran NPs could be stored in a dry state and reassembled in water. Moreover, we found that different chemical moieties (e.g., drugs such as doxorubicin) can be attached to the dextran NPs via a pH-dependent bond that allows release of the drug with lowering pH. We conclude that dextran NPs are a promising nano drug carrier. PMID:26752182

Dextran Nanoparticle Synthesis and Properties.

PubMed

Wasiak, Iga; Kulikowska, Aleksandra; Janczewska, Magdalena; Michalak, Magdalena; Cymerman, Iwona A; Nagalski, Andrzej; Kallinger, Peter; Szymanski, Wladyslaw W; Ciach, Tomasz

2016-01-01

Dextran is widely exploited in medical products and as a component of drug-delivering nanoparticles (NPs). Here, we tested whether dextran can serve as the main substrate of NPs and form a stable backbone. We tested dextrans with several molecular masses under several synthesis conditions to optimize NP stability. The analysis of the obtained nanoparticles showed that dextran NPs that were synthesized from 70 kDa dextran with a 5% degree of oxidation of the polysaccharide chain and 50% substitution with dodecylamine formed a NP backbone composed of modified dextran subunits, the mean diameter of which in an aqueous environment was around 100 nm. Dextran NPs could be stored in a dry state and reassembled in water. Moreover, we found that different chemical moieties (e.g., drugs such as doxorubicin) can be attached to the dextran NPs via a pH-dependent bond that allows release of the drug with lowering pH. We conclude that dextran NPs are a promising nano drug carrier.

Strong liquid-crystalline polymeric compositions

DOEpatents

Dowell, Flonnie

1993-01-01

Strong liquid-crystalline polymeric (LCP) compositions of matter. LCP backbones are combined with liquid crystalline (LC) side chains in a manner which maximizes molecular ordering through interdigitation of the side chains, thereby yielding materials which are predicted to have superior mechanical properties over existing LCPs. The theoretical design of LCPs having such characteristics includes consideration of the spacing distance between side chains along the backbone, the need for rigid sections in the backbone and in the side chains, the degree of polymerization, the length of the side chains, the regularity of the spacing of the side chains along the backbone, the interdigitation of side chains in sub-molecular strips, the packing of the side chains on one or two sides of the backbone to which they are attached, the symmetry of the side chains, the points of attachment of the side chains to the backbone, the flexibility and size of the chemical group connecting each side chain to the backbone, the effect of semiflexible sections in the backbone and the side chains, and the choice of types of dipolar and/or hydrogen bonding forces in the backbones and the side chains for easy alignment.

BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization.

PubMed

Ryu, Joonghyun; Lee, Mokwon; Cha, Jehyun; Laskowski, Roman A; Ryu, Seong Eon; Kim, Deok-Soo

2016-07-08

Many applications, such as protein design, homology modeling, flexible docking, etc. require the prediction of a protein's optimal side-chain conformations from just its amino acid sequence and backbone structure. Side-chain prediction (SCP) is an NP-hard energy minimization problem. Here, we present BetaSCPWeb which efficiently computes a conformation close to optimal using a geometry-prioritization method based on the Voronoi diagram of spherical atoms. Its outputs are visual, textual and PDB file format. The web server is free and open to all users at http://voronoi.hanyang.ac.kr/betascpweb with no login requirement. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

A model-based approach for estimation of changes in lumbar segmental kinematics associated with alterations in trunk muscle forces.

PubMed

Shojaei, Iman; Arjmand, Navid; Meakin, Judith R; Bazrgari, Babak

2018-03-21

The kinematics information from imaging, if combined with optimization-based biomechanical models, may provide a unique platform for personalized assessment of trunk muscle forces (TMFs). Such a method, however, is feasible only if differences in lumbar spine kinematics due to differences in TMFs can be captured by the current imaging techniques. A finite element model of the spine within an optimization procedure was used to estimate segmental kinematics of lumbar spine associated with five different sets of TMFs. Each set of TMFs was associated with a hypothetical trunk neuromuscular strategy that optimized one aspect of lower back biomechanics. For each set of TMFs, the segmental kinematics of lumbar spine was estimated for a single static trunk flexed posture involving, respectively, 40° and 10° of thoracic and pelvic rotations. Minimum changes in the angular and translational deformations of a motion segment with alterations in TMFs ranged from 0° to 0.7° and 0 mm to 0.04 mm, respectively. Maximum changes in the angular and translational deformations of a motion segment with alterations in TMFs ranged from 2.4° to 7.6° and 0.11 mm to 0.39 mm, respectively. The differences in kinematics of lumbar segments between each combination of two sets of TMFs in 97% of cases for angular deformation and 55% of cases for translational deformation were within the reported accuracy of current imaging techniques. Therefore, it might be possible to use image-based kinematics of lumbar segments along with computational modeling for personalized assessment of TMFs. Copyright © 2017 Elsevier Ltd. All rights reserved.

Image segmentation using fuzzy LVQ clustering networks

NASA Technical Reports Server (NTRS)

Tsao, Eric Chen-Kuo; Bezdek, James C.; Pal, Nikhil R.

1992-01-01

In this note we formulate image segmentation as a clustering problem. Feature vectors extracted from a raw image are clustered into subregions, thereby segmenting the image. A fuzzy generalization of a Kohonen learning vector quantization (LVQ) which integrates the Fuzzy c-Means (FCM) model with the learning rate and updating strategies of the LVQ is used for this task. This network, which segments images in an unsupervised manner, is thus related to the FCM optimization problem. Numerical examples on photographic and magnetic resonance images are given to illustrate this approach to image segmentation.

Computational wing optimization and comparisons with experiment for a semi-span wing model

NASA Technical Reports Server (NTRS)

Waggoner, E. G.; Haney, H. P.; Ballhaus, W. F.

1978-01-01

A computational wing optimization procedure was developed and verified by an experimental investigation of a semi-span variable camber wing model in the NASA Ames Research Center 14 foot transonic wind tunnel. The Bailey-Ballhaus transonic potential flow analysis and Woodward-Carmichael linear theory codes were linked to Vanderplaats constrained minimization routine to optimize model configurations at several subsonic and transonic design points. The 35 deg swept wing is characterized by multi-segmented leading and trailing edge flaps whose hinge lines are swept relative to the leading and trailing edges of the wing. By varying deflection angles of the flap segments, camber and twist distribution can be optimized for different design conditions. Results indicate that numerical optimization can be both an effective and efficient design tool. The optimized configurations had as good or better lift to drag ratios at the design points as the best designs previously tested during an extensive parametric study.

EuroFlow antibody panels for standardized n-dimensional flow cytometric immunophenotyping of normal, reactive and malignant leukocytes

PubMed Central

van Dongen, J J M; Lhermitte, L; Böttcher, S; Almeida, J; van der Velden, V H J; Flores-Montero, J; Rawstron, A; Asnafi, V; Lécrevisse, Q; Lucio, P; Mejstrikova, E; Szczepański, T; Kalina, T; de Tute, R; Brüggemann, M; Sedek, L; Cullen, M; Langerak, A W; Mendonça, A; Macintyre, E; Martin-Ayuso, M; Hrusak, O; Vidriales, M B; Orfao, A

2012-01-01

Most consensus leukemia & lymphoma antibody panels consist of lists of markers based on expert opinions, but they have not been validated. Here we present the validated EuroFlow 8-color antibody panels for immunophenotyping of hematological malignancies. The single-tube screening panels and multi-tube classification panels fit into the EuroFlow diagnostic algorithm with entries defined by clinical and laboratory parameters. The panels were constructed in 2–7 sequential design–evaluation–redesign rounds, using novel Infinicyt software tools for multivariate data analysis. Two groups of markers are combined in each 8-color tube: (i) backbone markers to identify distinct cell populations in a sample, and (ii) markers for characterization of specific cell populations. In multi-tube panels, the backbone markers were optimally placed at the same fluorochrome position in every tube, to provide identical multidimensional localization of the target cell population(s). The characterization markers were positioned according to the diagnostic utility of the combined markers. Each proposed antibody combination was tested against reference databases of normal and malignant cells from healthy subjects and WHO-based disease entities, respectively. The EuroFlow studies resulted in validated and flexible 8-color antibody panels for multidimensional identification and characterization of normal and aberrant cells, optimally suited for immunophenotypic screening and classification of hematological malignancies. PMID:22552007

Guiding automated left ventricular chamber segmentation in cardiac imaging using the concept of conserved myocardial volume.

PubMed

Garson, Christopher D; Li, Bing; Acton, Scott T; Hossack, John A

2008-06-01

The active surface technique using gradient vector flow allows semi-automated segmentation of ventricular borders. The accuracy of the algorithm depends on the optimal selection of several key parameters. We investigated the use of conservation of myocardial volume for quantitative assessment of each of these parameters using synthetic and in vivo data. We predicted that for a given set of model parameters, strong conservation of volume would correlate with accurate segmentation. The metric was most useful when applied to the gradient vector field weighting and temporal step-size parameters, but less effective in guiding an optimal choice of the active surface tension and rigidity parameters.

Seamline Determination Based on PKGC Segmentation for Remote Sensing Image Mosaicking

PubMed Central

Dong, Qiang; Liu, Jinghong

2017-01-01

This paper presents a novel method of seamline determination for remote sensing image mosaicking. A two-level optimization strategy is applied to determine the seamline. Object-level optimization is executed firstly. Background regions (BRs) and obvious regions (ORs) are extracted based on the results of parametric kernel graph cuts (PKGC) segmentation. The global cost map which consists of color difference, a multi-scale morphological gradient (MSMG) constraint, and texture difference is weighted by BRs. Finally, the seamline is determined in the weighted cost from the start point to the end point. Dijkstra’s shortest path algorithm is adopted for pixel-level optimization to determine the positions of seamline. Meanwhile, a new seamline optimization strategy is proposed for image mosaicking with multi-image overlapping regions. The experimental results show the better performance than the conventional method based on mean-shift segmentation. Seamlines based on the proposed method bypass the obvious objects and take less time in execution. This new method is efficient and superior for seamline determination in remote sensing image mosaicking. PMID:28749446

Pulmonary vessel segmentation utilizing curved planar reformation and optimal path finding (CROP) in computed tomographic pulmonary angiography (CTPA) for CAD applications

NASA Astrophysics Data System (ADS)

Zhou, Chuan; Chan, Heang-Ping; Kuriakose, Jean W.; Chughtai, Aamer; Wei, Jun; Hadjiiski, Lubomir M.; Guo, Yanhui; Patel, Smita; Kazerooni, Ella A.

2012-03-01

Vessel segmentation is a fundamental step in an automated pulmonary embolism (PE) detection system. The purpose of this study is to improve the segmentation scheme for pulmonary vessels affected by PE and other lung diseases. We have developed a multiscale hierarchical vessel enhancement and segmentation (MHES) method for pulmonary vessel tree extraction based on the analysis of eigenvalues of Hessian matrices. However, it is difficult to segment the pulmonary vessels accurately under suboptimal conditions, such as vessels occluded by PEs, surrounded by lymphoid tissues or lung diseases, and crossing with other vessels. In this study, we developed a new vessel refinement method utilizing curved planar reformation (CPR) technique combined with optimal path finding method (MHES-CROP). The MHES segmented vessels straightened in the CPR volume was refined using adaptive gray level thresholding where the local threshold was obtained from least-square estimation of a spline curve fitted to the gray levels of the vessel along the straightened volume. An optimal path finding method based on Dijkstra's algorithm was finally used to trace the correct path for the vessel of interest. Two and eight CTPA scans were randomly selected as training and test data sets, respectively. Forty volumes of interest (VOIs) containing "representative" vessels were manually segmented by a radiologist experienced in CTPA interpretation and used as reference standard. The results show that, for the 32 test VOIs, the average percentage volume error relative to the reference standard was improved from 32.9+/-10.2% using the MHES method to 9.9+/-7.9% using the MHES-CROP method. The accuracy of vessel segmentation was improved significantly (p<0.05). The intraclass correlation coefficient (ICC) of the segmented vessel volume between the automated segmentation and the reference standard was improved from 0.919 to 0.988. Quantitative comparison of the MHES method and the MHES-CROP method with the reference standard was also evaluated by the Bland-Altman plot. This preliminary study indicates that the MHES-CROP method has the potential to improve PE detection.

Accurate and Fully Automatic Hippocampus Segmentation Using Subject-Specific 3D Optimal Local Maps Into a Hybrid Active Contour Model

PubMed Central

Gkontra, Polyxeni; Daras, Petros; Maglaveras, Nicos

2014-01-01

Assessing the structural integrity of the hippocampus (HC) is an essential step toward prevention, diagnosis, and follow-up of various brain disorders due to the implication of the structural changes of the HC in those disorders. In this respect, the development of automatic segmentation methods that can accurately, reliably, and reproducibly segment the HC has attracted considerable attention over the past decades. This paper presents an innovative 3-D fully automatic method to be used on top of the multiatlas concept for the HC segmentation. The method is based on a subject-specific set of 3-D optimal local maps (OLMs) that locally control the influence of each energy term of a hybrid active contour model (ACM). The complete set of the OLMs for a set of training images is defined simultaneously via an optimization scheme. At the same time, the optimal ACM parameters are also calculated. Therefore, heuristic parameter fine-tuning is not required. Training OLMs are subsequently combined, by applying an extended multiatlas concept, to produce the OLMs that are anatomically more suitable to the test image. The proposed algorithm was tested on three different and publicly available data sets. Its accuracy was compared with that of state-of-the-art methods demonstrating the efficacy and robustness of the proposed method. PMID:27170866

Semi-automated segmentation of a glioblastoma multiforme on brain MR images for radiotherapy planning.

PubMed

Hori, Daisuke; Katsuragawa, Shigehiko; Murakami, Ryuuji; Hirai, Toshinori

2010-04-20

We propose a computerized method for semi-automated segmentation of the gross tumor volume (GTV) of a glioblastoma multiforme (GBM) on brain MR images for radiotherapy planning (RTP). Three-dimensional (3D) MR images of 28 cases with a GBM were used in this study. First, a sphere volume of interest (VOI) including the GBM was selected by clicking a part of the GBM region in the 3D image. Then, the sphere VOI was transformed to a two-dimensional (2D) image by use of a spiral-scanning technique. We employed active contour models (ACM) to delineate an optimal outline of the GBM in the transformed 2D image. After inverse transform of the optimal outline to the 3D space, a morphological filter was applied to smooth the shape of the 3D segmented region. For evaluation of our computerized method, we compared the computer output with manually segmented regions, which were obtained by a therapeutic radiologist using a manual tracking method. In evaluating our segmentation method, we employed the Jaccard similarity coefficient (JSC) and the true segmentation coefficient (TSC) in volumes between the computer output and the manually segmented region. The mean and standard deviation of JSC and TSC were 74.2+/-9.8% and 84.1+/-7.1%, respectively. Our segmentation method provided a relatively accurate outline for GBM and would be useful for radiotherapy planning.

[Object-oriented segmentation and classification of forest gap based on QuickBird remote sensing image.

PubMed

Mao, Xue Gang; Du, Zi Han; Liu, Jia Qian; Chen, Shu Xin; Hou, Ji Yu

2018-01-01

Traditional field investigation and artificial interpretation could not satisfy the need of forest gaps extraction at regional scale. High spatial resolution remote sensing image provides the possibility for regional forest gaps extraction. In this study, we used object-oriented classification method to segment and classify forest gaps based on QuickBird high resolution optical remote sensing image in Jiangle National Forestry Farm of Fujian Province. In the process of object-oriented classification, 10 scales (10-100, with a step length of 10) were adopted to segment QuickBird remote sensing image; and the intersection area of reference object (RA or ) and intersection area of segmented object (RA os ) were adopted to evaluate the segmentation result at each scale. For segmentation result at each scale, 16 spectral characteristics and support vector machine classifier (SVM) were further used to classify forest gaps, non-forest gaps and others. The results showed that the optimal segmentation scale was 40 when RA or was equal to RA os . The accuracy difference between the maximum and minimum at different segmentation scales was 22%. At optimal scale, the overall classification accuracy was 88% (Kappa=0.82) based on SVM classifier. Combining high resolution remote sensing image data with object-oriented classification method could replace the traditional field investigation and artificial interpretation method to identify and classify forest gaps at regional scale.

Rigid shape matching by segmentation averaging.

PubMed

Wang, Hongzhi; Oliensis, John

2010-04-01

We use segmentations to match images by shape. The new matching technique does not require point-to-point edge correspondence and is robust to small shape variations and spatial shifts. To address the unreliability of segmentations computed bottom-up, we give a closed form approximation to an average over all segmentations. Our method has many extensions, yielding new algorithms for tracking, object detection, segmentation, and edge-preserving smoothing. For segmentation, instead of a maximum a posteriori approach, we compute the "central" segmentation minimizing the average distance to all segmentations of an image. For smoothing, instead of smoothing images based on local structures, we smooth based on the global optimal image structures. Our methods for segmentation, smoothing, and object detection perform competitively, and we also show promising results in shape-based tracking.

Optimal graph based segmentation using flow lines with application to airway wall segmentation.

PubMed

Petersen, Jens; Nielsen, Mads; Lo, Pechin; Saghir, Zaigham; Dirksen, Asger; de Bruijne, Marleen

2011-01-01

This paper introduces a novel optimal graph construction method that is applicable to multi-dimensional, multi-surface segmentation problems. Such problems are often solved by refining an initial coarse surface within the space given by graph columns. Conventional columns are not well suited for surfaces with high curvature or complex shapes but the proposed columns, based on properly generated flow lines, which are non-intersecting, guarantee solutions that do not self-intersect and are better able to handle such surfaces. The method is applied to segment human airway walls in computed tomography images. Comparison with manual annotations on 649 cross-sectional images from 15 different subjects shows significantly smaller contour distances and larger area of overlap than are obtained with recently published graph based methods. Airway abnormality measurements obtained with the method on 480 scan pairs from a lung cancer screening trial are reproducible and correlate significantly with lung function.

Automated separation of merged Langerhans islets

NASA Astrophysics Data System (ADS)

Švihlík, Jan; Kybic, Jan; Habart, David

2016-03-01

This paper deals with separation of merged Langerhans islets in segmentations in order to evaluate correct histogram of islet diameters. A distribution of islet diameters is useful for determining the feasibility of islet transplantation in diabetes. First, the merged islets at training segmentations are manually separated by medical experts. Based on the single islets, the merged islets are identified and the SVM classifier is trained on both classes (merged/single islets). The testing segmentations were over-segmented using watershed transform and the most probable back merging of islets were found using trained SVM classifier. Finally, the optimized segmentation is compared with ground truth segmentation (correctly separated islets).

Leaf position optimization for step-and-shoot IMRT.

PubMed

De Gersem, W; Claus, F; De Wagter, C; Van Duyse, B; De Neve, W

2001-12-01

To describe the theoretical basis, the algorithm, and implementation of a tool that optimizes segment shapes and weights for step-and-shoot intensity-modulated radiation therapy delivered by multileaf collimators. The tool, called SOWAT (Segment Outline and Weight Adapting Tool) is applied to a set of segments, segment weights, and corresponding dose distribution, computed by an external dose computation engine. SOWAT evaluates the effects of changing the position of each collimating leaf of each segment on an objective function, as follows. Changing a leaf position causes a change in the segment-specific dose matrix, which is calculated by a fast dose computation algorithm. A weighted sum of all segment-specific dose matrices provides the dose distribution and allows computation of the value of the objective function. Only leaf position changes that comply with the multileaf collimator constraints are evaluated. Leaf position changes that tend to decrease the value of the objective function are retained. After several possible positions have been evaluated for all collimating leaves of all segments, an external dose engine recomputes the dose distribution, based on the adapted leaf positions and weights. The plan is evaluated. If the plan is accepted, a segment sequencer is used to make the prescription files for the treatment machine. Otherwise, the user can restart SOWAT using the new set of segments, segment weights, and corresponding dose distribution. The implementation was illustrated using two example cases. The first example is a T1N0M0 supraglottic cancer case that was distributed as a multicenter planning exercise by investigators from Rotterdam, The Netherlands. The exercise involved a two-phase plan. Phase 1 involved the delivery of 46 Gy to a concave-shaped planning target volume (PTV) consisting of the primary tumor volume and the elective lymph nodal regions II-IV on both sides of the neck. Phase 2 involved a boost of 24 Gy to the primary tumor region only. SOWAT was applied to the Phase 1 plan. Parotid sparing was a planning goal. The second implementation example is an ethmoid sinus cancer case, planned with the intent of bilateral visus sparing. The median PTV prescription dose was 70 Gy with a maximum dose constraint to the optic pathway structures of 60 Gy. The initial set of segments, segment weights, and corresponding dose distribution were obtained, respectively, by an anatomy-based segmentation tool, a segment weight optimization tool, and a differential scatter-air ratio dose computation algorithm as external dose engine. For the supraglottic case, this resulted in a plan that proved to be comparable to the plans obtained at the other institutes by forward or inverse planning techniques. After using SOWAT, the minimum PTV dose and PTV dose homogeneity increased; the maximum dose to the spinal cord decreased from 38 Gy to 32 Gy. The left parotid mean dose decreased from 22 Gy to 19 Gy and the right parotid mean dose from 20 to 18 Gy. For the ethmoid sinus case, the target homogeneity increased by leaf position optimization, together with a better sparing of the optical tracts. By using SOWAT, the plans improved with respect to all plan evaluation end points. Compliance with the multileaf collimator constraints is guaranteed. The treatment delivery time remains almost unchanged, because no additional segments are created.

SU-E-T-250: New IMRT Sequencing Strategy: Towards Intra-Fraction Plan Adaptation for the MR-Linac

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

Kontaxis, C; Bol, G; Lagendijk, J

2014-06-01

Purpose: To develop a new sequencer for IMRT planning that during treatment makes the inclusion of external factors possible and by doing so accounts for intra-fraction anatomy changes. Given a real-time imaging modality that will provide the updated patient anatomy during delivery, this sequencer is able to take these changes into account during the calculation of subsequent segments. Methods: Pencil beams are generated for each beam angle of the treatment and a fluence optimization is performed. The pencil beams, together with the patient anatomy and the above optimal fluence form the input of our algorithm. During each iteration the followingmore » steps are performed: A fluence optimization is done and each beam's fluence is then split to discrete intensity levels. Deliverable segments are calculated for each one of these. Each segment's area multiplied by its intensity describes its efficiency. The most efficient segment among all beams is then chosen to deliver a part of the calculated fluence and the dose that will be delivered by this segment is calculated. This delivered dose is then subtracted from the remaining dose. This loop is repeated until 90% of the dose has been delivered and a final segment weight optimization is performed to reach full convergence. Results: This algorithm was tested in several prostate cases yielding results that meet all clinical constraints. Quality assurance was performed on Delta4 and film phantoms for one of these prostate cases and received clinical acceptance after passing both gamma analyses with the 3%/3mm criteria. Conclusion: A new sequencing algorithm was developed to facilitate the needs of intensity modulated treatment. The first results on static anatomy confirm that it can calculate clinical plans equivalent to those of the commercially available planning systems. We are now working towards 100% dose convergence which will allow us to handle anatomy deformations. This work is financially supported by Elekta AB, Stockholm, Sweden.« less

Joint segmentation of lumen and outer wall from femoral artery MR images: Towards 3D imaging measurements of peripheral arterial disease.

PubMed

Ukwatta, Eranga; Yuan, Jing; Qiu, Wu; Rajchl, Martin; Chiu, Bernard; Fenster, Aaron

2015-12-01

Three-dimensional (3D) measurements of peripheral arterial disease (PAD) plaque burden extracted from fast black-blood magnetic resonance (MR) images have shown to be more predictive of clinical outcomes than PAD stenosis measurements. To this end, accurate segmentation of the femoral artery lumen and outer wall is required for generating volumetric measurements of PAD plaque burden. Here, we propose a semi-automated algorithm to jointly segment the femoral artery lumen and outer wall surfaces from 3D black-blood MR images, which are reoriented and reconstructed along the medial axis of the femoral artery to obtain improved spatial coherence between slices of the long, thin femoral artery and to reduce computation time. The developed segmentation algorithm enforces two priors in a global optimization manner: the spatial consistency between the adjacent 2D slices and the anatomical region order between the femoral artery lumen and outer wall surfaces. The formulated combinatorial optimization problem for segmentation is solved globally and exactly by means of convex relaxation using a coupled continuous max-flow (CCMF) model, which is a dual formulation to the convex relaxed optimization problem. In addition, the CCMF model directly derives an efficient duality-based algorithm based on the modern multiplier augmented optimization scheme, which has been implemented on a GPU for fast computation. The computed segmentations from the developed algorithm were compared to manual delineations from experts using 20 black-blood MR images. The developed algorithm yielded both high accuracy (Dice similarity coefficients ≥ 87% for both the lumen and outer wall surfaces) and high reproducibility (intra-class correlation coefficient of 0.95 for generating vessel wall area), while outperforming the state-of-the-art method in terms of computational time by a factor of ≈ 20. Copyright © 2015 Elsevier B.V. All rights reserved.

Optimization of the Ussing chamber setup with excised rat intestinal segments for dissolution/permeation experiments of poorly soluble drugs.

PubMed

Forner, Kristin; Roos, Carl; Dahlgren, David; Kesisoglou, Filippos; Konerding, Moritz A; Mazur, Johanna; Lennernäs, Hans; Langguth, Peter

2017-02-01

Prediction of the in vivo absorption of poorly soluble drugs may require simultaneous dissolution/permeation experiments. In vivo predictive media have been modified for permeation experiments with Caco-2 cells, but not for excised rat intestinal segments. The present study aimed at improving the setup of dissolution/permeation experiments with excised rat intestinal segments by assessing suitable donor and receiver media. The regional compatibility of rat intestine in Ussing chambers with modified Fasted and Fed State Simulated Intestinal Fluids (Fa/FeSSIF mod ) as donor media was evaluated via several parameters that reflect the viability of the excised intestinal segments. Receiver media that establish sink conditions were investigated for their foaming potential and toxicity. Dissolution/permeation experiments with the optimized conditions were then tested for two particle sizes of the BCS class II drug aprepitant. Fa/FeSSIF mod were toxic for excised rat ileal sheets but not duodenal sheets, the compatibility with jejunal segments depended on the bile salt concentration. A non-foaming receiver medium containing bovine serum albumin (BSA) and Antifoam B was nontoxic. With these conditions, the permeation of nanosized aprepitant was higher than of the unmilled drug formulations. The compatibility of Fa/FeSSIF mod depends on the excised intestinal region. The chosen conditions enable dissolution/permeation experiments with excised rat duodenal segments. The experiments correctly predicted the superior permeation of nanosized over unmilled aprepitant that is observed in vivo. The optimized setup uses FaSSIF mod as donor medium, excised rat duodenal sheets as permeation membrane and a receiver medium containing BSA and Antifoam B.

Strong liquid-crystalline polymeric compositions

DOEpatents

Dowell, F.

1993-12-07

Strong liquid-crystalline polymeric (LCP) compositions of matter are described. LCP backbones are combined with liquid crystalline (LC) side chains in a manner which maximizes molecular ordering through interdigitation of the side chains, thereby yielding materials which are predicted to have superior mechanical properties over existing LCPs. The theoretical design of LCPs having such characteristics includes consideration of the spacing distance between side chains along the backbone, the need for rigid sections in the backbone and in the side chains, the degree of polymerization, the length of the side chains, the regularity of the spacing of the side chains along the backbone, the interdigitation of side chains in sub-molecular strips, the packing of the side chains on one or two sides of the backbone to which they are attached, the symmetry of the side chains, the points of attachment of the side chains to the backbone, the flexibility and size of the chemical group connecting each side chain to the backbone, the effect of semiflexible sections in the backbone and the side chains, and the choice of types of dipolar and/or hydrogen bonding forces in the backbones and the side chains for easy alignment. 27 figures.

Stress Relaxation in Epoxy Thermosets via a Ferrocene-Based Amine Curing Agent

DOE PAGES

Jones, Brad H.; Wheeler, David R.; Black, Hayden T.; ...

2017-06-29

Physical stress relaxation in rubbery, thermoset polymers is limited by cross-links, which impede segmental motion and restrict relaxation to network defects, such as chain ends. In parallel, the cure shrinkage associated with thermoset polymerizations leads to the development of internal residual stress that cannot be effectively relaxed. Recent strategies have reduced or eliminated such cure stress in thermoset polymers largely by exploiting chemical relaxation processes, wherein temporary cross-links or otherwise transient bonds are incorporated into the polymer network. In this paper, we explore an alternative approach, wherein physical relaxation is enhanced by the incorporation of organometallic sandwich moieties into themore » backbone of the polymer network. A standard epoxy resin is cured with a diamine derivative of ferrocene and compared to conventional diamine curing agents. The ferrocene-based thermoset is clearly distinguished from the conventional materials by reduced cure stress with increasing cure temperature as well as unique stress relaxation behavior above its glass transition in the fully cured state. The relaxation experiments exhibit features characteristic of a physical relaxation process. Furthermore, the cure stress is observed to vanish precipitously upon deliberate introduction of network defects through an increasing imbalance of epoxy and amine functional groups. Finally, we postulate that these beneficial properties arise from fluxional motion of the cyclopentadienyl ligands on the polymer backbone.« less

Stress Relaxation in Epoxy Thermosets via a Ferrocene-Based Amine Curing Agent

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

Jones, Brad H.; Wheeler, David R.; Black, Hayden T.

Physical stress relaxation in rubbery, thermoset polymers is limited by cross-links, which impede segmental motion and restrict relaxation to network defects, such as chain ends. In parallel, the cure shrinkage associated with thermoset polymerizations leads to the development of internal residual stress that cannot be effectively relaxed. Recent strategies have reduced or eliminated such cure stress in thermoset polymers largely by exploiting chemical relaxation processes, wherein temporary cross-links or otherwise transient bonds are incorporated into the polymer network. In this paper, we explore an alternative approach, wherein physical relaxation is enhanced by the incorporation of organometallic sandwich moieties into themore » backbone of the polymer network. A standard epoxy resin is cured with a diamine derivative of ferrocene and compared to conventional diamine curing agents. The ferrocene-based thermoset is clearly distinguished from the conventional materials by reduced cure stress with increasing cure temperature as well as unique stress relaxation behavior above its glass transition in the fully cured state. The relaxation experiments exhibit features characteristic of a physical relaxation process. Furthermore, the cure stress is observed to vanish precipitously upon deliberate introduction of network defects through an increasing imbalance of epoxy and amine functional groups. Finally, we postulate that these beneficial properties arise from fluxional motion of the cyclopentadienyl ligands on the polymer backbone.« less

Structure-Functional Basis of Ion Transport in Sodium–Calcium Exchanger (NCX) Proteins

PubMed Central

Giladi, Moshe; Shor, Reut; Lisnyansky, Michal; Khananshvili, Daniel

2016-01-01

The membrane-bound sodium–calcium exchanger (NCX) proteins shape Ca2+ homeostasis in many cell types, thus participating in a wide range of physiological and pathological processes. Determination of the crystal structure of an archaeal NCX (NCX_Mj) paved the way for a thorough and systematic investigation of ion transport mechanisms in NCX proteins. Here, we review the data gathered from the X-ray crystallography, molecular dynamics simulations, hydrogen–deuterium exchange mass-spectrometry (HDX-MS), and ion-flux analyses of mutants. Strikingly, the apo NCX_Mj protein exhibits characteristic patterns in the local backbone dynamics at particular helix segments, thereby possessing characteristic HDX profiles, suggesting structure-dynamic preorganization (geometric arrangements of catalytic residues before the transition state) of conserved α1 and α2 repeats at ion-coordinating residues involved in transport activities. Moreover, dynamic preorganization of local structural entities in the apo protein predefines the status of ion-occlusion and transition states, even though Na+ or Ca2+ binding modifies the preceding backbone dynamics nearby functionally important residues. Future challenges include resolving the structural-dynamic determinants governing the ion selectivity, functional asymmetry and ion-induced alternating access. Taking into account the structural similarities of NCX_Mj with the other proteins belonging to the Ca2+/cation exchanger superfamily, the recent findings can significantly improve our understanding of ion transport mechanisms in NCX and similar proteins. PMID:27879668

Structure-Functional Basis of Ion Transport in Sodium-Calcium Exchanger (NCX) Proteins.

PubMed

Giladi, Moshe; Shor, Reut; Lisnyansky, Michal; Khananshvili, Daniel

2016-11-22

The membrane-bound sodium-calcium exchanger (NCX) proteins shape Ca 2+ homeostasis in many cell types, thus participating in a wide range of physiological and pathological processes. Determination of the crystal structure of an archaeal NCX (NCX_Mj) paved the way for a thorough and systematic investigation of ion transport mechanisms in NCX proteins. Here, we review the data gathered from the X-ray crystallography, molecular dynamics simulations, hydrogen-deuterium exchange mass-spectrometry (HDX-MS), and ion-flux analyses of mutants. Strikingly, the apo NCX_Mj protein exhibits characteristic patterns in the local backbone dynamics at particular helix segments, thereby possessing characteristic HDX profiles, suggesting structure-dynamic preorganization (geometric arrangements of catalytic residues before the transition state) of conserved α₁ and α₂ repeats at ion-coordinating residues involved in transport activities. Moreover, dynamic preorganization of local structural entities in the apo protein predefines the status of ion-occlusion and transition states, even though Na⁺ or Ca 2+ binding modifies the preceding backbone dynamics nearby functionally important residues. Future challenges include resolving the structural-dynamic determinants governing the ion selectivity, functional asymmetry and ion-induced alternating access. Taking into account the structural similarities of NCX_Mj with the other proteins belonging to the Ca 2+ /cation exchanger superfamily, the recent findings can significantly improve our understanding of ion transport mechanisms in NCX and similar proteins.

Autonomous Unmanned Aerial Vehicle Rendezvous for Automated Aerial Refueling

DTIC Science & Technology

2007-03-01

represents a straight line segment. It can be seen that there are ten possible combinations of arcs and line segments (RSR, RSL, LSR, LSL, LRL, RLR , SLR...SRL, RLS, and LRS). However, L. E. Dubins proved that only these six sequences are possibly optimal: RSR, RSL, LSR, LSL, LRL, and RLR [Dubins 1957...From Figure 2-5 and Figure 2-6, it can be seen that the last two cases, RLR and LRL can only be optimal when the initial point and the terminal

White matter lesion extension to automatic brain tissue segmentation on MRI.

PubMed

de Boer, Renske; Vrooman, Henri A; van der Lijn, Fedde; Vernooij, Meike W; Ikram, M Arfan; van der Lugt, Aad; Breteler, Monique M B; Niessen, Wiro J

2009-05-01

A fully automated brain tissue segmentation method is optimized and extended with white matter lesion segmentation. Cerebrospinal fluid (CSF), gray matter (GM) and white matter (WM) are segmented by an atlas-based k-nearest neighbor classifier on multi-modal magnetic resonance imaging data. This classifier is trained by registering brain atlases to the subject. The resulting GM segmentation is used to automatically find a white matter lesion (WML) threshold in a fluid-attenuated inversion recovery scan. False positive lesions are removed by ensuring that the lesions are within the white matter. The method was visually validated on a set of 209 subjects. No segmentation errors were found in 98% of the brain tissue segmentations and 97% of the WML segmentations. A quantitative evaluation using manual segmentations was performed on a subset of 6 subjects for CSF, GM and WM segmentation and an additional 14 for the WML segmentations. The results indicated that the automatic segmentation accuracy is close to the interobserver variability of manual segmentations.

Delineation and geometric modeling of road networks

NASA Astrophysics Data System (ADS)

Poullis, Charalambos; You, Suya

In this work we present a novel vision-based system for automatic detection and extraction of complex road networks from various sensor resources such as aerial photographs, satellite images, and LiDAR. Uniquely, the proposed system is an integrated solution that merges the power of perceptual grouping theory (Gabor filtering, tensor voting) and optimized segmentation techniques (global optimization using graph-cuts) into a unified framework to address the challenging problems of geospatial feature detection and classification. Firstly, the local precision of the Gabor filters is combined with the global context of the tensor voting to produce accurate classification of the geospatial features. In addition, the tensorial representation used for the encoding of the data eliminates the need for any thresholds, therefore removing any data dependencies. Secondly, a novel orientation-based segmentation is presented which incorporates the classification of the perceptual grouping, and results in segmentations with better defined boundaries and continuous linear segments. Finally, a set of gaussian-based filters are applied to automatically extract centerline information (magnitude, width and orientation). This information is then used for creating road segments and transforming them to their polygonal representations.

A graph-based watershed merging using fuzzy C-means and simulated annealing for image segmentation

NASA Astrophysics Data System (ADS)

Vadiveloo, Mogana; Abdullah, Rosni; Rajeswari, Mandava

2015-12-01

In this paper, we have addressed the issue of over-segmented regions produced in watershed by merging the regions using global feature. The global feature information is obtained from clustering the image in its feature space using Fuzzy C-Means (FCM) clustering. The over-segmented regions produced by performing watershed on the gradient of the image are then mapped to this global information in the feature space. Further to this, the global feature information is optimized using Simulated Annealing (SA). The optimal global feature information is used to derive the similarity criterion to merge the over-segmented watershed regions which are represented by the region adjacency graph (RAG). The proposed method has been tested on digital brain phantom simulated dataset to segment white matter (WM), gray matter (GM) and cerebrospinal fluid (CSF) soft tissues regions. The experiments showed that the proposed method performs statistically better, with average of 95.242% regions are merged, than the immersion watershed and average accuracy improvement of 8.850% in comparison with RAG-based immersion watershed merging using global and local features.

Three validation metrics for automated probabilistic image segmentation of brain tumours

PubMed Central

Zou, Kelly H.; Wells, William M.; Kikinis, Ron; Warfield, Simon K.

2005-01-01

SUMMARY The validity of brain tumour segmentation is an important issue in image processing because it has a direct impact on surgical planning. We examined the segmentation accuracy based on three two-sample validation metrics against the estimated composite latent gold standard, which was derived from several experts’ manual segmentations by an EM algorithm. The distribution functions of the tumour and control pixel data were parametrically assumed to be a mixture of two beta distributions with different shape parameters. We estimated the corresponding receiver operating characteristic curve, Dice similarity coefficient, and mutual information, over all possible decision thresholds. Based on each validation metric, an optimal threshold was then computed via maximization. We illustrated these methods on MR imaging data from nine brain tumour cases of three different tumour types, each consisting of a large number of pixels. The automated segmentation yielded satisfactory accuracy with varied optimal thresholds. The performances of these validation metrics were also investigated via Monte Carlo simulation. Extensions of incorporating spatial correlation structures using a Markov random field model were considered. PMID:15083482

Colony image acquisition and genetic segmentation algorithm and colony analyses

NASA Astrophysics Data System (ADS)

Wang, W. X.

2012-01-01

Colony anaysis is used in a large number of engineerings such as food, dairy, beverages, hygiene, environmental monitoring, water, toxicology, sterility testing. In order to reduce laboring and increase analysis acuracy, many researchers and developers have made efforts for image analysis systems. The main problems in the systems are image acquisition, image segmentation and image analysis. In this paper, to acquire colony images with good quality, an illumination box was constructed. In the box, the distances between lights and dishe, camra lens and lights, and camera lens and dishe are adjusted optimally. In image segmentation, It is based on a genetic approach that allow one to consider the segmentation problem as a global optimization,. After image pre-processing and image segmentation, the colony analyses are perfomed. The colony image analysis consists of (1) basic colony parameter measurements; (2) colony size analysis; (3) colony shape analysis; and (4) colony surface measurements. All the above visual colony parameters can be selected and combined together, used to make a new engineeing parameters. The colony analysis can be applied into different applications.

Intensity inhomogeneity compensation and tissue segmentation for magnetic resonance imaging with noise-suppressed multiplicative intrinsic component optimization

NASA Astrophysics Data System (ADS)

Dong, Huaipeng; Zhang, Qi; Shi, Jun

2017-12-01

Magnetic resonance (MR) images suffer from intensity inhomogeneity. Segmentation-based approaches can simultaneously achieve both intensity inhomogeneity compensation (IIC) and tissue segmentation for MR images with little noise, but they often fail for images polluted by severe noise. Here, we propose a noise-robust algorithm named noise-suppressed multiplicative intrinsic component optimization (NSMICO) for simultaneous IIC and tissue segmentation. Considering the spatial characteristics in an image, an adaptive nonlocal means filtering term is incorporated into the objective function of NSMICO to decrease image deterioration due to noise. Then, a fuzzy local factor term utilizing the spatial and gray-level relationship among local pixels is embedded into the objective function to reach a balance between noise suppression and detail preservation. Experimental results on synthetic natural and MR images with various levels of intensity inhomogeneity and noise, as well as in vivo clinical MR images, have demonstrated the effectiveness of the NSMICO and its superiority to three competing approaches. The NSMICO could be potentially valuable for MR image IIC and tissue segmentation.

Extended capture range for focus-diverse phase retrieval in segmented aperture systems using geometrical optics.

PubMed

Jurling, Alden S; Fienup, James R

2014-03-01

Extending previous work by Thurman on wavefront sensing for segmented-aperture systems, we developed an algorithm for estimating segment tips and tilts from multiple point spread functions in different defocused planes. We also developed methods for overcoming two common modes for stagnation in nonlinear optimization-based phase retrieval algorithms for segmented systems. We showed that when used together, these methods largely solve the capture range problem in focus-diverse phase retrieval for segmented systems with large tips and tilts. Monte Carlo simulations produced a rate of success better than 98% for the combined approach.

Surface Enhanced Raman Scattering Monitoring of Chain Alignment in Freely Suspended Nanomembranes

NASA Astrophysics Data System (ADS)

Jiang, Chaoyang; Lio, Wilber Y.; Tsukruk, Vladimir V.

2005-09-01

The molecular chain reorganization in freely standing membranes with encapsulated gold nanoparticles was studied with surface enhanced Raman scattering (SERS) in the course of their elastic deformations. The efficient SERS was enabled by optimizing the design of gold nanoparticle forming chainlike aggregates, thus creating an exceptional ability to conduct in situ monitoring. Small deformations resulted in the radial orientation of side phenyl rings of polymer backbones while larger deflections led to the polymer chains bridging adjacent nanoparticles within one-dimensional aggregates.

Metric Learning for Hyperspectral Image Segmentation

NASA Technical Reports Server (NTRS)

Bue, Brian D.; Thompson, David R.; Gilmore, Martha S.; Castano, Rebecca

2011-01-01

We present a metric learning approach to improve the performance of unsupervised hyperspectral image segmentation. Unsupervised spatial segmentation can assist both user visualization and automatic recognition of surface features. Analysts can use spatially-continuous segments to decrease noise levels and/or localize feature boundaries. However, existing segmentation methods use tasks-agnostic measures of similarity. Here we learn task-specific similarity measures from training data, improving segment fidelity to classes of interest. Multiclass Linear Discriminate Analysis produces a linear transform that optimally separates a labeled set of training classes. The defines a distance metric that generalized to a new scenes, enabling graph-based segmentation that emphasizes key spectral features. We describe tests based on data from the Compact Reconnaissance Imaging Spectrometer (CRISM) in which learned metrics improve segment homogeneity with respect to mineralogical classes.

Jansen-MIDAS: A multi-level photomicrograph segmentation software based on isotropic undecimated wavelets.

PubMed

de Siqueira, Alexandre Fioravante; Cabrera, Flávio Camargo; Nakasuga, Wagner Massayuki; Pagamisse, Aylton; Job, Aldo Eloizo

2018-01-01

Image segmentation, the process of separating the elements within a picture, is frequently used for obtaining information from photomicrographs. Segmentation methods should be used with reservations, since incorrect results can mislead when interpreting regions of interest (ROI). This decreases the success rate of extra procedures. Multi-Level Starlet Segmentation (MLSS) and Multi-Level Starlet Optimal Segmentation (MLSOS) were developed to be an alternative for general segmentation tools. These methods gave rise to Jansen-MIDAS, an open-source software. A scientist can use it to obtain several segmentations of hers/his photomicrographs. It is a reliable alternative to process different types of photomicrographs: previous versions of Jansen-MIDAS were used to segment ROI in photomicrographs of two different materials, with an accuracy superior to 89%. © 2017 Wiley Periodicals, Inc.

[Structure of crambin in solution, crystal and in the trajectories of molecular dynamics simulations].

PubMed

Abaturov, L V; Nosova, N G

2013-01-01

The mechanisms of the three-dimensional crambin structure alterations in the crystalline environments and in the trajectories of the molecular dynamics simulations in the vacuum and crystal surroundings have been analyzed. In the crystalline state and in the solution the partial regrouping of remote intramolecular packing contacts, involved in the formation and stabilization of the tertiary structure of the crambin molecule, occurs in NMR structures. In the crystalline state it is initiated by the formation of the intermolecular contacts, the conformational influence of its appearance is distributed over the structure. The changes of the conformations and positions of the residues of the loop segments, where the intermolecular contacts of the crystal surroundings are preferably concentrated, are most observable. Under the influence of these contacts the principal change of the regular secondary structure of crambin is taking place: extension of the two-strand beta structure to the three-strand structure with the participation of the single last residue N46 of the C-terminal loop. In comparison with the C-terminal loop the more profound changes are observed in the conformation and the atomic positions of the backbone atoms and in the solvent accessibility of the residues of the interhelical loop. In the solution of the ensemble of the 8 NMR structures relative accessibility to the solvent differs more noticeably also in the region of the loop segments and rather markedly in the interhelical loop. In the crambin cryogenic crystal structures the positions of the atoms of the backbone and/or side chain of 14-18 of 46 residues are discretely disordered. The disorganizations of at least 8 of 14 residues occur directly in the regions of the intermolecular contacts and another 5 residues are disordered indirectly through the intramolecular contacts with the residues of the intermolecular contacts. Upon the molecular dynamics simulation in the vacuum surrounding as in the solution of the crystalline structure of crambin the essential changes of the backbone conformation are caused by the intermolecular contacts absence, but partly masked by the structure changes owing to the nonpolar H atoms absence on the simulated structure. The intermolecular contact absence is partly manifested upon the molecular dynamics simulation of the crambin crystal with one protein molecule. Compared to the crystal structure the lengths of the interpeptide hydrogen bonds and other interresidue contacts in an average solution NMR structure are somewhat shorter and accordingly the energy of the interpeptide hydrogen bonds is better. This length shortening can occur at the stage of the refinement of the NMR structures of the crambin and other proteins by its energy minimizations in the vacuum surroundings and not exist in the solution protein structures.

a Comparison of Simulated Annealing, Genetic Algorithm and Particle Swarm Optimization in Optimal First-Order Design of Indoor Tls Networks

NASA Astrophysics Data System (ADS)

Jia, F.; Lichti, D.

2017-09-01

The optimal network design problem has been well addressed in geodesy and photogrammetry but has not received the same attention for terrestrial laser scanner (TLS) networks. The goal of this research is to develop a complete design system that can automatically provide an optimal plan for high-accuracy, large-volume scanning networks. The aim in this paper is to use three heuristic optimization methods, simulated annealing (SA), genetic algorithm (GA) and particle swarm optimization (PSO), to solve the first-order design (FOD) problem for a small-volume indoor network and make a comparison of their performances. The room is simplified as discretized wall segments and possible viewpoints. Each possible viewpoint is evaluated with a score table representing the wall segments visible from each viewpoint based on scanning geometry constraints. The goal is to find a minimum number of viewpoints that can obtain complete coverage of all wall segments with a minimal sum of incidence angles. The different methods have been implemented and compared in terms of the quality of the solutions, runtime and repeatability. The experiment environment was simulated from a room located on University of Calgary campus where multiple scans are required due to occlusions from interior walls. The results obtained in this research show that PSO and GA provide similar solutions while SA doesn't guarantee an optimal solution within limited iterations. Overall, GA is considered as the best choice for this problem based on its capability of providing an optimal solution and fewer parameters to tune.

Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer

PubMed Central

Dršata, Tomáš; Pérez, Alberto; Orozco, Modesto; Morozov, Alexandre V.; Šponer, Jiřĺ; Lankaš, Filip

2013-01-01

The Dickerson–Drew dodecamer (DD) d-[CGCGAATTCGCG]2 is a prototypic B-DNA molecule whose sequence-specific structure and dynamics have been investigated by many experimental and computational studies. Here, we present an analysis of DD properties based on extensive atomistic molecular dynamics (MD) simulations using different ionic conditions and water models. The 0.6–2.4-µs-long MD trajectories are compared to modern crystallographic and NMR data. In the simulations, the duplex ends can adopt an alternative base-pairing, which influences the oligomer structure. A clear relationship between the BI/BII backbone substates and the basepair step conformation has been identified, extending previous findings and exposing an interesting structural polymorphism in the helix. For a given end pairing, distributions of the basepair step coordinates can be decomposed into Gaussian-like components associated with the BI/BII backbone states. The nonlocal stiffness matrices for a rigid-base mechanical model of DD are reported for the first time, suggesting salient stiffness features of the central A-tract. The Riemann distance and Kullback–Leibler divergence are used for stiffness matrix comparison. The basic structural parameters converge very well within 300 ns, convergence of the BI/BII populations and stiffness matrices is less sharp. Our work presents new findings about the DD structural dynamics, mechanical properties, and the coupling between basepair and backbone configurations, including their statistical reliability. The results may also be useful for optimizing future force fields for DNA. PMID:23976886

Aggregation control in natural brush-printed conjugated polymer films and implications for enhancing charge transport

PubMed Central

Wang, Gang; Huang, Wei; Eastham, Nicholas D.; Fabiano, Simone; Manley, Eric F.; Zeng, Li; Wang, Binghao; Zhang, Xinan; Chen, Zhihua; Li, Ran; Chang, Robert P. H.; Chen, Lin X.; Bedzyk, Michael J.; Melkonyan, Ferdinand S.; Facchetti, Antonio; Marks, Tobin J.

2017-01-01

Shear-printing is a promising processing technique in organic electronics for microstructure/charge transport modification and large-area film fabrication. Nevertheless, the mechanism by which shear-printing can enhance charge transport is not well-understood. In this study, a printing method using natural brushes is adopted as an informative tool to realize direct aggregation control of conjugated polymers and to investigate the interplay between printing parameters, macromolecule backbone alignment and aggregation, and charge transport anisotropy in a conjugated polymer series differing in architecture and electronic structure. This series includes (i) semicrystalline hole-transporting P3HT, (ii) semicrystalline electron-transporting N2200, (iii) low-crystallinity hole-transporting PBDTT-FTTE, and (iv) low-crystallinity conducting PEDOT:PSS. The (semi-)conducting films are characterized by a battery of morphology and microstructure analysis techniques and by charge transport measurements. We report that remarkably enhanced mobilities/conductivities, as high as 5.7×/3.9×, are achieved by controlled growth of nanofibril aggregates and by backbone alignment, with the adjusted R2 (R2adj) correlation between aggregation and charge transport as high as 95%. However, while shear-induced aggregation is important for enhancing charge transport, backbone alignment alone does not guarantee charge transport anisotropy. The correlations between efficient charge transport and aggregation are clearly shown, while mobility and degree of orientation are not always well-correlated. These observations provide insights into macroscopic charge transport mechanisms in conjugated polymers and suggest guidelines for optimization. PMID:29109282

The VSGB 2.0 Model: A Next Generation Energy Model for High Resolution Protein Structure Modeling

PubMed Central

Li, Jianing; Abel, Robert; Zhu, Kai; Cao, Yixiang; Zhao, Suwen; Friesner, Richard A.

2011-01-01

A novel energy model (VSGB 2.0) for high resolution protein structure modeling is described, which features an optimized implicit solvent model as well as physics-based corrections for hydrogen bonding, π-π interactions, self-contact interactions and hydrophobic interactions. Parameters of the VSGB 2.0 model were fit to a crystallographic database of 2239 single side chain and 100 11–13 residue loop predictions. Combined with an advanced method of sampling and a robust algorithm for protonation state assignment, the VSGB 2.0 model was validated by predicting 115 super long loops up to 20 residues. Despite the dramatically increasing difficulty in reconstructing longer loops, a high accuracy was achieved: all of the lowest energy conformations have global backbone RMSDs better than 2.0 Å from the native conformations. Average global backbone RMSDs of the predictions are 0.51, 0.63, 0.70, 0.62, 0.80, 1.41, and 1.59 Å for 14, 15, 16, 17, 18, 19, and 20 residue loop predictions, respectively. When these results are corrected for possible statistical bias as explained in the text, the average global backbone RMSDs are 0.61, 0.71, 0.86, 0.62, 1.06, 1.67, and 1.59 Å. Given the precision and robustness of the calculations, we believe that the VSGB 2.0 model is suitable to tackle “real” problems, such as biological function modeling and structure-based drug discovery. PMID:21905107

Conformational study of the hydroxyproline-O-glycosidic linkage: sugar-peptide orientation and prolyl amide isomerization in (α/β)-galactosylated 4(R/S)-hydroxyproline.

PubMed

Naziga, Emmanuel B; Schweizer, Frank; Wetmore, Stacey D

2012-01-19

Glycosylation is a frequent post-translational modification of proteins that has been shown to influence protein structure and function. Glycosylation of hydroxyproline occurs widely in plants, but is absent in humans and animals. Previous experimental studies on model amides have indicated that α/β-galactosylation of 4R-hydroxyproline (Hyp) has no measurable effect on prolyl amide isomerization, while a 7% increase in the trans isomer population, as well as a 25-50% increase in the isomerization rate, was observed for the 4S stereoisomer (hyp). In this work, molecular dynamics simulations in explicit water and implicit solvent DFT optimizations are used to examine the structure of the hydroxyproline-O-galactosyl linkage and the effect of glycosylation on the structure and cis/trans isomerization of the peptide backbone. The calculations show two major minima with respect to the glycosidic linkage in all compounds. The C(γ)-exo puckering observed in 4R compounds projects the sugar away from the peptide backbone, while a twisted C(γ)-endo/C(β)-exo pucker in the 4S compounds brings the peptide and sugar rings together and leads to an intramolecular hydrogen-bonding interaction that is sometimes bridged by a water molecule. This hydrogen bond changes the conformation of the peptide backbone, inducing a favorable n → π* interaction between the oxygen lone pair from the prolyl N-terminal amide and the C═O, which explains the observed increase in trans isomer population in α/β-galactosylated 4S-hydroxyproline. Our results provide the first molecular level information about this important glycosidic linkage, as well as provide an explanation for the previously observed increase in trans isomer population in 4S-hyp compounds. Moreover, this study provides evidence that sugar-mediated long-range hydrogen bonding between hydroxyl groups and the carbonyl peptide backbone can modify the properties of N-terminal prolyl cis/trans isomerization in peptides.

High-Resolution Crystal Structures of Protein Helices Reconciled with Three-Centered Hydrogen Bonds and Multipole Electrostatics

PubMed Central

Kuster, Daniel J.; Liu, Chengyu; Fang, Zheng; Ponder, Jay W.; Marshall, Garland R.

2015-01-01

Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.613 α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.613/10-, Némethy- or N-helix, is proposed. Due to the use of constraints from monopole force fields and assumed secondary structures used in low-resolution refinement of electron density of proteins, such structures in the PDB often show linear hydrogen bonding. PMID:25894612

High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics.

PubMed

Kuster, Daniel J; Liu, Chengyu; Fang, Zheng; Ponder, Jay W; Marshall, Garland R

2015-01-01

Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.6(13) α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.6(13/10)-, Némethy- or N-helix, is proposed. Due to the use of constraints from monopole force fields and assumed secondary structures used in low-resolution refinement of electron density of proteins, such structures in the PDB often show linear hydrogen bonding.

Recovery and fine structure variability of RGII sub-domains in wine (Vitis vinifera Merlot)

PubMed Central

Buffetto, F.; Ropartz, D.; Zhang, X. J.; Gilbert, H. J.; Guillon, F.; Ralet, M.-C.

2014-01-01

Background and Aims Rhamnogalacturonan II (RGII) is a structurally complex pectic sub-domain composed of more than 12 different sugars and 20 different linkages distributed in five side chains along a homogalacturonan backbone. Although RGII has long been described as highly conserved over plant evolution, recent studies have revealed variations in the structure of the polysaccharide. This study examines the fine structure variability of RGII in wine, focusing on the side chains A and B obtained after sequential mild acid hydrolysis. Specifically, this study aims to differentiate intrinsic structural variations in these RGII side chains from structural variations due to acid hydrolysis. Methods RGII from wine (Vitis vinifera Merlot) was sequentially hydrolysed with trifluoroacetic acid (TFA) and the hydrolysis products were separated by anion-exchange chromatography (AEC). AEC fractions or total hydrolysates were analysed by MALDI-TOF mass spectrometry. Key Results The optimal conditions to recover non-degraded side chain B, side chain A and RGII backbone were 0·1 m TFA at 40 °C for 16 h, 0·48 m TFA at 40 °C for 16 h (or 0·1 m TFA at 60 °C for 8 h) and 0·1 m TFA at 60 °C for 16 h, respectively. Side chain B was particularly prone to acid degradation. Side chain A and the RGII GalA backbone were partly degraded by 0·1 m TFA at 80 °C for 1–4 h. AEC allowed separation of side chain B, methyl-esterified side chain A and non-methyl-esterified side chain A. The structure of side chain A and the GalA backbone were highly variable. Conclusions Several modifications to the RGII structure of wine were identified. The observed dearabinosylation and deacetylation were primarily the consequence of acidic treatment, while variation in methyl-esterification, methyl-ether linkages and oxidation reflect natural diversity. The physiological significance of this variability, however, remains to be determined. PMID:24908680

Optimal Design of Grid-Stiffened Composite Panels Using Global and Local Buckling Analysis

NASA Technical Reports Server (NTRS)

Ambur, Damodar R.; Jaunky, Navin; Knight, Norman F., Jr.

1996-01-01

A design strategy for optimal design of composite grid-stiffened panels subjected to global and local buckling constraints is developed using a discrete optimizer. An improved smeared stiffener theory is used for the global buckling analysis. Local buckling of skin segments is assessed using a Rayleigh-Ritz method that accounts for material anisotropy and transverse shear flexibility. The local buckling of stiffener segments is also assessed. Design variables are the axial and transverse stiffener spacing, stiffener height and thickness, skin laminate, and stiffening configuration. The design optimization process is adapted to identify the lightest-weight stiffening configuration and pattern for grid stiffened composite panels given the overall panel dimensions, design in-plane loads, material properties, and boundary conditions of the grid-stiffened panel.

Conformation-related exciton localization and charge-pair formation in polythiophenes: ensemble and single-molecule study.

PubMed

Sugimoto, Toshikazu; Habuchi, Satoshi; Ogino, Kenji; Vacha, Martin

2009-09-10

We study conformation-dependent photophysical properties of polythiophene (PT) by molecular dynamics simulations and by ensemble and single-molecule optical experiments. We use a graft copolymer consisting of a polythiophene backbone and long polystyrene branches and compare its properties with those obtained on the same polythiophene derivative without the side chains. Coarse-grain molecular dynamics simulations show that in a poor solvent, the PT without the side chains (PT-R) forms a globulelike conformation in which distances between any two conjugated segments on the chain are within the Forster radius for efficient energy transfer. In the PT with the polystyrene branches (PT-PS), the polymer main PT chain retains an extended coillike conformation, even in a poor solvent, and the calculated distances between conjugated segments favor energy transfer only between a few neighboring chromophores. The theoretical predictions are confirmed by measurements of fluorescence anisotropy and fluorescence blinking of the polymers' single chains. High anisotropy ratios and two-state blinking in PT-R are due to localization of the exciton on a single conjugated segment. These signatures of exciton localization are absent in single chains of PT-PS. Electric-field-induced quenching measured as a function of concentration of PT dispersed in an inert matrix showed that in well-isolated chains of PT-PS, the exciton dissociation is an intrachain process and that aggregation of the PT-R chains causes an increase in quenching due to the onset of interchain interactions. Measurements of the field-induced quenching on single chains indicate that in PT-R, the exciton dissociation is a slower process that takes place only after the exciton is localized on one conjugated segment.

Adsorption of normal pentane on the surface of rutile. Experimental results and simulations.

PubMed

Rakhmatkariev, G U; Carvalho, A J Palace; Ramalho, J P Prates

2007-07-03

Adsorption isotherms and differential heats of normal pentane adsorption on microcrystalline rutile were measured at 303 K. The heat of adsorption of n-pentane on rutile at zero occupancy is 64 kJ/mol. The differential heats have three descending segments, corresponding to the adsorption of n-pentane on three types of surfaces. At low coverage (first segment), the adsorption is restricted to the rows A of the (110) faces along the 5-fold coordinatively unsaturated (cus) Ti(4+) ions with differential heat showing a linear decrease with increasing occupancy. The second segment is attributed to bonding with atoms of the rows along the remaining faces exposed, (101) and (100). The third segment is related to a multilayer adsorption. The mean molar adsorption entropy of n-pentane is ca. -25 J/mol K less than the entropy of the bulk liquid, thus revealing a hindered state of motion of the n-pentane molecules on the surface of rutile. Simulations of the adsorption of n-pentane on the three most abundant crystallographic faces of rutile were also performed. The adsorption isotherm obtained from the combination of each face's isotherm weighted by the respective abundance was found to be in a good agreement with the experimental data. A structural characterization of n-pentane near the surface was also conducted, and it was found that the substrate, especially for the (110) face, strongly perturbs the distribution of n-pentane conformations, compared to those found for the gas phase. Adsorbed molecules are predominantly oriented with their long axes and their backbone zigzag planes parallel to the surface and are also characterized by fewer gauche conformations than observed in the bulk phase.

Theory of dynamic barriers, activated hopping, and the glass transition in polymer melts

NASA Astrophysics Data System (ADS)

Schweizer, Kenneth S.; Saltzman, Erica J.

2004-07-01

A statistical mechanical theory of collective dynamic barriers, slow segmental relaxation, and the glass transition of polymer melts is developed by combining, and in some aspects extending, methods of mode coupling, density functional, and activated hopping transport theories. A coarse-grained description of polymer chains is adopted and the melt is treated as a liquid of segments. The theory is built on the idea that collective density fluctuations on length scales considerably longer than the local cage scale are of primary importance in the deeply supercooled regime. The barrier hopping or segmental relaxation time is predicted to be a function primarily of a single parameter that is chemical structure, temperature, and pressure dependent. This parameter depends on the material-specific dimensionless amplitude of thermal density fluctuations (compressibility) and a reduced segmental density determined by the packing length and backbone characteristic ratio. Analytic results are derived for a crossover temperature Tc, collective barrier, and glass transition temperature Tg. The relation of these quantities to structural and thermodynamic properties of the polymer melt is established. A universal power-law scaling behavior of the relaxation time below Tc is predicted based on identification of a reduced temperature variable that quantifies the breadth of the supercooled regime. Connections between the ratio Tc/Tg, two measures of dynamic fragility, and the magnitude of the local relaxation time at Tg logically follow. Excellent agreement with experiment is found for these generic aspects, and the crucial importance of the experimentally observed near universality of the dynamic crossover time is established. Extensions of the theory to treat the full chain dynamics, heterogeneity, barrier fluctuations, and nonpolymeric thermal glass forming liquids are briefly discussed.

Automated bone segmentation from dental CBCT images using patch-based sparse representation and convex optimization

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

Wang, Li; Gao, Yaozong; Shi, Feng

Purpose: Cone-beam computed tomography (CBCT) is an increasingly utilized imaging modality for the diagnosis and treatment planning of the patients with craniomaxillofacial (CMF) deformities. Accurate segmentation of CBCT image is an essential step to generate three-dimensional (3D) models for the diagnosis and treatment planning of the patients with CMF deformities. However, due to the poor image quality, including very low signal-to-noise ratio and the widespread image artifacts such as noise, beam hardening, and inhomogeneity, it is challenging to segment the CBCT images. In this paper, the authors present a new automatic segmentation method to address these problems. Methods: To segmentmore » CBCT images, the authors propose a new method for fully automated CBCT segmentation by using patch-based sparse representation to (1) segment bony structures from the soft tissues and (2) further separate the mandible from the maxilla. Specifically, a region-specific registration strategy is first proposed to warp all the atlases to the current testing subject and then a sparse-based label propagation strategy is employed to estimate a patient-specific atlas from all aligned atlases. Finally, the patient-specific atlas is integrated into amaximum a posteriori probability-based convex segmentation framework for accurate segmentation. Results: The proposed method has been evaluated on a dataset with 15 CBCT images. The effectiveness of the proposed region-specific registration strategy and patient-specific atlas has been validated by comparing with the traditional registration strategy and population-based atlas. The experimental results show that the proposed method achieves the best segmentation accuracy by comparison with other state-of-the-art segmentation methods. Conclusions: The authors have proposed a new CBCT segmentation method by using patch-based sparse representation and convex optimization, which can achieve considerably accurate segmentation results in CBCT segmentation based on 15 patients.« less

An image segmentation method based on fuzzy C-means clustering and Cuckoo search algorithm

NASA Astrophysics Data System (ADS)

Wang, Mingwei; Wan, Youchuan; Gao, Xianjun; Ye, Zhiwei; Chen, Maolin

2018-04-01

Image segmentation is a significant step in image analysis and machine vision. Many approaches have been presented in this topic; among them, fuzzy C-means (FCM) clustering is one of the most widely used methods for its high efficiency and ambiguity of images. However, the success of FCM could not be guaranteed because it easily traps into local optimal solution. Cuckoo search (CS) is a novel evolutionary algorithm, which has been tested on some optimization problems and proved to be high-efficiency. Therefore, a new segmentation technique using FCM and blending of CS algorithm is put forward in the paper. Further, the proposed method has been measured on several images and compared with other existing FCM techniques such as genetic algorithm (GA) based FCM and particle swarm optimization (PSO) based FCM in terms of fitness value. Experimental results indicate that the proposed method is robust, adaptive and exhibits the better performance than other methods involved in the paper.

Multi-organ segmentation from multi-phase abdominal CT via 4D graphs using enhancement, shape and location optimization.

PubMed

Linguraru, Marius George; Pura, John A; Chowdhury, Ananda S; Summers, Ronald M

2010-01-01

The interpretation of medical images benefits from anatomical and physiological priors to optimize computer-aided diagnosis (CAD) applications. Diagnosis also relies on the comprehensive analysis of multiple organs and quantitative measures of soft tissue. An automated method optimized for medical image data is presented for the simultaneous segmentation of four abdominal organs from 4D CT data using graph cuts. Contrast-enhanced CT scans were obtained at two phases: non-contrast and portal venous. Intra-patient data were spatially normalized by non-linear registration. Then 4D erosion using population historic information of contrast-enhanced liver, spleen, and kidneys was applied to multi-phase data to initialize the 4D graph and adapt to patient specific data. CT enhancement information and constraints on shape, from Parzen windows, and location, from a probabilistic atlas, were input into a new formulation of a 4D graph. Comparative results demonstrate the effects of appearance and enhancement, and shape and location on organ segmentation.

Enzootic genotype S of H9N2 avian influenza viruses donates internal genes to emerging zoonotic influenza viruses in China.

PubMed

Gu, Min; Chen, Hongzhi; Li, Qunhui; Huang, Junqing; Zhao, Mingjun; Gu, Xiaobing; Jiang, Kaijun; Wang, Xiaoquan; Peng, Daxin; Liu, Xiufan

2014-12-05

Avian influenza viruses of subtype H9N2 are widely prevalent in poultry in many Asian countries, and the segmented nature of the viral genome results in multiple distinct genotypes via reassortment. In this study, genetic evolution of H9N2 viruses circulating in eastern China during 2007-2013 was analyzed. The results showed that the diversity of the gene constellations generated six distinct genotypes, in which a novel genotype (S) bearing the backbone of A/chicken/Shanghai/F/98-like viruses by acquiring A/quail/Hong Kong/G1/97-like polymerase basic subunit 2 and matrix genes has gradually established its ecological niche and been consistently prevalent in chicken flocks in eastern China since its first detection in 2007. Furthermore, genotype S possessed the peculiarity to donate most of its gene segments to other emerging influenza A viruses in China, including the novel reassortant highly pathogenic avian influenza H5N2, the 2013 novel H7N7, H7N9 and the latest reassortant H10N8 viruses, with potential threat to poultry industry and human health. Copyright © 2014 Elsevier B.V. All rights reserved.

Syntheses and properties of elastic copoly(ester-urethane)s containing a phospholipid moiety and the fabrication of nanosheets.

PubMed

Sirithep, Wariya; Morita, Kohei; Iwano, Atsushi; Komachi, Takuya; Okamura, Yosuke; Nagase, Yu

2014-01-01

In these years, we have investigated the syntheses of novel diamine and diol monomers containing phosphorylcholine (PC) group to obtain biocompatible polymers, the backbone components of which were thermally stable and mechanically strong. In this study, the preparations of elastic copoly(ester-urethane)s containing PC group and polycarbonate segment were carried out by polycondensation and polyaddition using a diol monomer containing PC group and polycarbonate diol. It was found that the obtained polymers exhibited the high-thermal stability up to 200 °C and the elasticity derived from the soft segment. The introduction of PC group was effective to improve the resistance to the adhesions of proteins and platelets on the polymer films, which was the result of surface properties derived from the PC moiety. In addition, we tried to prepare ultra-thin polymer films composed of copoly(ester-urethane)s, so-called nanosheets. As a result, the desired nanosheets were successfully fabricated and the obtained nanosheets exhibited the high adhesive strength, indicating that the nanosheets could conform closely to the desired surfaces due to their exquisite flexibility and low roughness.

Singular-Arc Time-Optimal Trajectory of Aircraft in Two-Dimensional Wind Field

NASA Technical Reports Server (NTRS)

Nguyen, Nhan

2006-01-01

This paper presents a study of a minimum time-to-climb trajectory analysis for aircraft flying in a two-dimensional altitude dependent wind field. The time optimal control problem possesses a singular control structure when the lift coefficient is taken as a control variable. A singular arc analysis is performed to obtain an optimal control solution on the singular arc. Using a time-scale separation with the flight path angle treated as a fast state, the dimensionality of the optimal control solution is reduced by eliminating the lift coefficient control. A further singular arc analysis is used to decompose the original optimal control solution into the flight path angle solution and a trajectory solution as a function of the airspeed and altitude. The optimal control solutions for the initial and final climb segments are computed using a shooting method with known starting values on the singular arc The numerical results of the shooting method show that the optimal flight path angle on the initial and final climb segments are constant. The analytical approach provides a rapid means for analyzing a time optimal trajectory for aircraft performance.

Polyphosphazine-based polymer materials

DOEpatents

Fox, Robert V.; Avci, Recep; Groenewold, Gary S.

2010-05-25

Methods of removing contaminant matter from porous materials include applying a polymer material to a contaminated surface, irradiating the contaminated surface to cause redistribution of contaminant matter, and removing at least a portion of the polymer material from the surface. Systems for decontaminating a contaminated structure comprising porous material include a radiation device configured to emit electromagnetic radiation toward a surface of a structure, and at least one spray device configured to apply a capture material onto the surface of the structure. Polymer materials that can be used in such methods and systems include polyphosphazine-based polymer materials having polyphosphazine backbone segments and side chain groups that include selected functional groups. The selected functional groups may include iminos, oximes, carboxylates, sulfonates, .beta.-diketones, phosphine sulfides, phosphates, phosphites, phosphonates, phosphinates, phosphine oxides, monothio phosphinic acids, and dithio phosphinic acids.

KSC-08pd3288

NASA Image and Video Library

2008-10-20

CAPE CANAVERAL, Fla. - In Orbiter Processing Facility bay 3 at NASA's Kennedy Space Center in Florida, boundary layer transition, or BLT, tile is being affixed to space shuttle Discovery before its launch on the STS-119 mission in February 2009. The specially modified tiles and instrumentation package will monitor the heating effects of early re-entry boundary layer transition at high mach numbers. These data support analytical modeling and design efforts for both the space shuttles and NASA next-generation spacecraft, the Orion crew exploration vehicle. On the STS-119 mission, Discovery also will carry the S6 truss segment to complete the 361-foot-long backbone of the International Space Station. The truss includes the fourth pair of solar array wings and electronics that convert sunlight to power for the orbiting laboratory. Photo credit: NASA/Tim Jacobs

KSC-08pd3291

NASA Image and Video Library

2008-10-20

CAPE CANAVERAL, Fla. - In Orbiter Processing Facility bay 3 at NASA's Kennedy Space Center in Florida, workers attach boundary layer transition, or BLT, tile to space shuttle Discovery before its launch on the STS-119 mission in February 2009. The specially modified tiles and instrumentation package will monitor the heating effects of early re-entry boundary layer transition at high mach numbers. These data support analytical modeling and design efforts for both the space shuttles and NASA next-generation spacecraft, the Orion crew exploration vehicle. On the STS-119 mission, Discovery also will carry the S6 truss segment to complete the 361-foot-long backbone of the International Space Station. The truss includes the fourth pair of solar array wings and electronics that convert sunlight to power for the orbiting laboratory. Photo credit: NASA/Tim Jacobs

KSC-08pd3290

NASA Image and Video Library

2008-10-20

CAPE CANAVERAL, Fla. - In Orbiter Processing Facility bay 3 at NASA's Kennedy Space Center in Florida, workers attach boundary layer transition, or BLT, tile to space shuttle Discovery before its launch on the STS-119 mission in February 2009. The specially modified tiles and instrumentation package will monitor the heating effects of early re-entry boundary layer transition at high mach numbers. These data support analytical modeling and design efforts for both the space shuttles and NASA next-generation spacecraft, the Orion crew exploration vehicle. On the STS-119 mission, Discovery also will carry the S6 truss segment to complete the 361-foot-long backbone of the International Space Station. The truss includes the fourth pair of solar array wings and electronics that convert sunlight to power for the orbiting laboratory. Photo credit: NASA/Tim Jacobs

KSC-08pd3289

NASA Image and Video Library

2008-10-20

CAPE CANAVERAL, Fla. - In Orbiter Processing Facility bay 3 at NASA's Kennedy Space Center in Florida, workers attach boundary layer transition, or BLT, tile to space shuttle Discovery before its launch on the STS-119 mission in February 2009. The specially modified tiles and instrumentation package will monitor the heating effects of early re-entry boundary layer transition at high mach numbers. These data support analytical modeling and design efforts for both the space shuttles and NASA next-generation spacecraft, the Orion crew exploration vehicle. On the STS-119 mission, Discovery also will carry the S6 truss segment to complete the 361-foot-long backbone of the International Space Station. The truss includes the fourth pair of solar array wings and electronics that convert sunlight to power for the orbiting laboratory. Photo credit: NASA/Tim Jacobs

Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH.

PubMed

Volk, Jochen; Herrmann, Torsten; Wüthrich, Kurt

2008-07-01

MATCH (Memetic Algorithm and Combinatorial Optimization Heuristics) is a new memetic algorithm for automated sequence-specific polypeptide backbone NMR assignment of proteins. MATCH employs local optimization for tracing partial sequence-specific assignments within a global, population-based search environment, where the simultaneous application of local and global optimization heuristics guarantees high efficiency and robustness. MATCH thus makes combined use of the two predominant concepts in use for automated NMR assignment of proteins. Dynamic transition and inherent mutation are new techniques that enable automatic adaptation to variable quality of the experimental input data. The concept of dynamic transition is incorporated in all major building blocks of the algorithm, where it enables switching between local and global optimization heuristics at any time during the assignment process. Inherent mutation restricts the intrinsically required randomness of the evolutionary algorithm to those regions of the conformation space that are compatible with the experimental input data. Using intact and artificially deteriorated APSY-NMR input data of proteins, MATCH performed sequence-specific resonance assignment with high efficiency and robustness.

Analysis of image thresholding segmentation algorithms based on swarm intelligence

NASA Astrophysics Data System (ADS)

Zhang, Yi; Lu, Kai; Gao, Yinghui; Yang, Bo

2013-03-01

Swarm intelligence-based image thresholding segmentation algorithms are playing an important role in the research field of image segmentation. In this paper, we briefly introduce the theories of four existing image segmentation algorithms based on swarm intelligence including fish swarm algorithm, artificial bee colony, bacteria foraging algorithm and particle swarm optimization. Then some image benchmarks are tested in order to show the differences of the segmentation accuracy, time consumption, convergence and robustness for Salt & Pepper noise and Gaussian noise of these four algorithms. Through these comparisons, this paper gives qualitative analyses for the performance variance of the four algorithms. The conclusions in this paper would give a significant guide for the actual image segmentation.

Fault tolerant high-performance PACS network design and implementation

NASA Astrophysics Data System (ADS)

Chimiak, William J.; Boehme, Johannes M.

1998-07-01

The Wake Forest University School of Medicine and the Wake Forest University/Baptist Medical Center (WFUBMC) are implementing a second generation PACS. The first generation PACS provided helpful information about the functional and temporal requirements of the system. It highlighted the importance of image retrieval speed, system availability, RIS/HIS integration, the ability to rapidly view images on any PACS workstation, network bandwidth, equipment redundancy, and the ability for the system to evolve using standards-based components. This paper deals with the network design and implementation of the PACS. The physical layout of the hospital areas served by the PACS, the choice of network equipment and installation issues encountered are addressed. Efforts to optimize fault tolerance are discussed. The PACS network is a gigabit, mixed-media network based on LAN emulation over ATM (LANE) with a rapid migration from LANE to Multiple Protocols Over ATM (MPOA) planned. Two fault-tolerant backbone ATM switches serve to distribute network accesses with two load-balancing 622 megabit per second (Mbps) OC-12 interconnections. The switch was sized to be upgradable to provide a 2.54 Gbps OC-48 interconnection with an OC-12 interconnection as a load-balancing backup. Modalities connect with legacy network interface cards to a switched-ethernet device. This device has two 155 Mbps OC-3 load-balancing uplinks to each of the backbone ATM switches of the PACS. This provides a fault-tolerant logical connection to the modality servers which pass verified DICOM images to the PACS servers and proper PACS diagnostic workstations. Where fiber pulls were prohibitively expensive, edge ATM switches were installed with an OC-12 uplink to a backbone ATM switches. The PACS and data base servers are fault-tolerant, hot-swappable Sun Enterprise Servers with an OC-12 connection to a backbone ATM switch and a fast-ethernet connection to a back-up network. The workstations come with 10/100 BASET autosense cards. A redundant switched-ethernet network will be installed to provide yet another degree of network fault-tolerance. The switched-ethernet devices are connected to each of the backbone ATM switches with two-load-balancing OC-3 connections to provide fault-tolerant connectivity in the event of a primary network failure.

A segmentation method for lung nodule image sequences based on superpixels and density-based spatial clustering of applications with noise

PubMed Central

Zhang, Wei; Zhang, Xiaolong; Qiang, Yan; Tian, Qi; Tang, Xiaoxian

2017-01-01

The fast and accurate segmentation of lung nodule image sequences is the basis of subsequent processing and diagnostic analyses. However, previous research investigating nodule segmentation algorithms cannot entirely segment cavitary nodules, and the segmentation of juxta-vascular nodules is inaccurate and inefficient. To solve these problems, we propose a new method for the segmentation of lung nodule image sequences based on superpixels and density-based spatial clustering of applications with noise (DBSCAN). First, our method uses three-dimensional computed tomography image features of the average intensity projection combined with multi-scale dot enhancement for preprocessing. Hexagonal clustering and morphological optimized sequential linear iterative clustering (HMSLIC) for sequence image oversegmentation is then proposed to obtain superpixel blocks. The adaptive weight coefficient is then constructed to calculate the distance required between superpixels to achieve precise lung nodules positioning and to obtain the subsequent clustering starting block. Moreover, by fitting the distance and detecting the change in slope, an accurate clustering threshold is obtained. Thereafter, a fast DBSCAN superpixel sequence clustering algorithm, which is optimized by the strategy of only clustering the lung nodules and adaptive threshold, is then used to obtain lung nodule mask sequences. Finally, the lung nodule image sequences are obtained. The experimental results show that our method rapidly, completely and accurately segments various types of lung nodule image sequences. PMID:28880916

Hybrid region merging method for segmentation of high-resolution remote sensing images

NASA Astrophysics Data System (ADS)

Zhang, Xueliang; Xiao, Pengfeng; Feng, Xuezhi; Wang, Jiangeng; Wang, Zuo

2014-12-01

Image segmentation remains a challenging problem for object-based image analysis. In this paper, a hybrid region merging (HRM) method is proposed to segment high-resolution remote sensing images. HRM integrates the advantages of global-oriented and local-oriented region merging strategies into a unified framework. The globally most-similar pair of regions is used to determine the starting point of a growing region, which provides an elegant way to avoid the problem of starting point assignment and to enhance the optimization ability for local-oriented region merging. During the region growing procedure, the merging iterations are constrained within the local vicinity, so that the segmentation is accelerated and can reflect the local context, as compared with the global-oriented method. A set of high-resolution remote sensing images is used to test the effectiveness of the HRM method, and three region-based remote sensing image segmentation methods are adopted for comparison, including the hierarchical stepwise optimization (HSWO) method, the local-mutual best region merging (LMM) method, and the multiresolution segmentation (MRS) method embedded in eCognition Developer software. Both the supervised evaluation and visual assessment show that HRM performs better than HSWO and LMM by combining both their advantages. The segmentation results of HRM and MRS are visually comparable, but HRM can describe objects as single regions better than MRS, and the supervised and unsupervised evaluation results further prove the superiority of HRM.

Automated MRI segmentation for individualized modeling of current flow in the human head.

PubMed

Huang, Yu; Dmochowski, Jacek P; Su, Yuzhuo; Datta, Abhishek; Rorden, Christopher; Parra, Lucas C

2013-12-01

High-definition transcranial direct current stimulation (HD-tDCS) and high-density electroencephalography require accurate models of current flow for precise targeting and current source reconstruction. At a minimum, such modeling must capture the idiosyncratic anatomy of the brain, cerebrospinal fluid (CSF) and skull for each individual subject. Currently, the process to build such high-resolution individualized models from structural magnetic resonance images requires labor-intensive manual segmentation, even when utilizing available automated segmentation tools. Also, accurate placement of many high-density electrodes on an individual scalp is a tedious procedure. The goal was to develop fully automated techniques to reduce the manual effort in such a modeling process. A fully automated segmentation technique based on Statical Parametric Mapping 8, including an improved tissue probability map and an automated correction routine for segmentation errors, was developed, along with an automated electrode placement tool for high-density arrays. The performance of these automated routines was evaluated against results from manual segmentation on four healthy subjects and seven stroke patients. The criteria include segmentation accuracy, the difference of current flow distributions in resulting HD-tDCS models and the optimized current flow intensities on cortical targets. The segmentation tool can segment out not just the brain but also provide accurate results for CSF, skull and other soft tissues with a field of view extending to the neck. Compared to manual results, automated segmentation deviates by only 7% and 18% for normal and stroke subjects, respectively. The predicted electric fields in the brain deviate by 12% and 29% respectively, which is well within the variability observed for various modeling choices. Finally, optimized current flow intensities on cortical targets do not differ significantly. Fully automated individualized modeling may now be feasible for large-sample EEG research studies and tDCS clinical trials.

Polymers containing nickel(II) complexes of Goedken's macrocycle: optimized synthesis and electrochemical characterization.

PubMed

Paquette, Joseph A; Sauvé, Ethan R; Gilroy, Joe B

2015-04-01

The synthesis and characterization of a new class of nickel-containing polymers is described. The optimized copolymerization of alkyne-bearing nickel(II) complexes of Goedken's macrocycle (4,11-dihydro-5,7,12,14-tetramethyldibenzo[b,i][1,4,8,11]tetraazacyclotetradecine) and brominated 9,9-dihexylfluorene produced polymers with potential application as functional redox-active materials. The title polymers exhibit electrochemically reversible, ligand-centered oxidation events at 0.24 and 0.73 V versus the ferrocene/ferrocenium redox couple. They also display exceptional thermal stability and interesting absorption properties due to the presence of the macrocyclic nickel(II) complexes and π-conjugated units incorporated in their backbones. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An Optimized Handover Scheme with Movement Trend Awareness for Body Sensor Networks

PubMed Central

Sun, Wen; Zhang, Zhiqiang; Ji, Lianying; Wong, Wai-Choong

2013-01-01

When a body sensor network (BSN) that is linked to the backbone via a wireless network interface moves from one coverage zone to another, a handover is required to maintain network connectivity. This paper presents an optimized handover scheme with movement trend awareness for BSNs. The proposed scheme predicts the future position of a BSN user using the movement trend extracted from the historical position, and adjusts the handover decision accordingly. Handover initiation time is optimized when the unnecessary handover rate is estimated to meet the requirement and the outage probability is minimized. The proposed handover scheme is simulated in a BSN deployment area in a hospital environment in UK. Simulation results show that the proposed scheme reduces the outage probability by 22% as compared with the existing hysteresis-based handover scheme under the constraint of acceptable handover rate. PMID:23736852

A hybrid flower pollination algorithm based modified randomized location for multi-threshold medical image segmentation.

PubMed

Wang, Rui; Zhou, Yongquan; Zhao, Chengyan; Wu, Haizhou

2015-01-01

Multi-threshold image segmentation is a powerful image processing technique that is used for the preprocessing of pattern recognition and computer vision. However, traditional multilevel thresholding methods are computationally expensive because they involve exhaustively searching the optimal thresholds to optimize the objective functions. To overcome this drawback, this paper proposes a flower pollination algorithm with a randomized location modification. The proposed algorithm is used to find optimal threshold values for maximizing Otsu's objective functions with regard to eight medical grayscale images. When benchmarked against other state-of-the-art evolutionary algorithms, the new algorithm proves itself to be robust and effective through numerical experimental results including Otsu's objective values and standard deviations.

MRI segmentation using dialectical optimization.

PubMed

dos Santos, Wellington P; de Assis, Francisco M; de Souza, Ricardo E

2009-01-01

Biology, Psychology and Social Sciences are intrinsically connected to the very roots of the development of algorithms and methods in Computational Intelligence, as it is easily seen in approaches like genetic algorithms, evolutionary programming and particle swarm optimization. In this work we propose a new optimization method based on dialectics using fuzzy membership functions to model the influence of interactions between integrating poles in the status of each pole. Poles are the basic units composing dialectical systems. In order to validate our proposal we designed a segmentation method based on the optimization of k-means using dialectics for the segmentation of MR images. As a case study we used 181 MR synthetic multispectral images composed by proton density, T(1)- and T(2)-weighted synthetic brain images of 181 slices with 1 mm, resolution of 1 mm(3), for a normal brain and a noiseless MR tomographic system without field inhomogeneities, amounting a total of 543 images, generated by the simulator BrainWeb [2]. Our principal target here is comparing our proposal to k-means, fuzzy c-means, and Kohonen's self-organized maps, concerning the quantization error, we proved that our method can improved results obtained using k-means.

Caution Is Required in Interpretation of Mutations in the Voltage Sensing Domain of Voltage Gated Channels as Evidence for Gating Mechanisms

PubMed Central

Kariev, Alisher M.; Green, Michael E.

2015-01-01

The gating mechanism of voltage sensitive ion channels is generally considered to be the motion of the S4 transmembrane segment of the voltage sensing domains (VSD). The primary supporting evidence came from R→C mutations on the S4 transmembrane segment of the VSD, followed by reaction with a methanethiosulfonate (MTS) reagent. The cys side chain is –SH (reactive form –S−); the arginine side chain is much larger, leaving space big enough to accommodate the MTS sulfonate head group. The cavity created by the mutation has space for up to seven more water molecules than were present in wild type, which could be displaced irreversibly by the MTS reagent. Our quantum calculations show there is major reorientation of three aromatic residues that face into the cavity in response to proton displacement within the VSD. Two phenylalanines reorient sufficiently to shield/unshield the cysteine from the intracellular and extracellular ends, depending on the proton positions, and a tyrosine forms a hydrogen bond to the cysteine sulfur with its side chain –OH. These could produce the results of the experiments that have been interpreted as evidence for physical motion of the S4 segment, without physical motion of the S4 backbone. The computations strongly suggest that the interpretation of cysteine substitution reaction experiments be re-examined in the light of these considerations. PMID:25588216

MUSE: MUlti-atlas region Segmentation utilizing Ensembles of registration algorithms and parameters, and locally optimal atlas selection

PubMed Central

Ou, Yangming; Resnick, Susan M.; Gur, Ruben C.; Gur, Raquel E.; Satterthwaite, Theodore D.; Furth, Susan; Davatzikos, Christos

2016-01-01

Atlas-based automated anatomical labeling is a fundamental tool in medical image segmentation, as it defines regions of interest for subsequent analysis of structural and functional image data. The extensive investigation of multi-atlas warping and fusion techniques over the past 5 or more years has clearly demonstrated the advantages of consensus-based segmentation. However, the common approach is to use multiple atlases with a single registration method and parameter set, which is not necessarily optimal for every individual scan, anatomical region, and problem/data-type. Different registration criteria and parameter sets yield different solutions, each providing complementary information. Herein, we present a consensus labeling framework that generates a broad ensemble of labeled atlases in target image space via the use of several warping algorithms, regularization parameters, and atlases. The label fusion integrates two complementary sources of information: a local similarity ranking to select locally optimal atlases and a boundary modulation term to refine the segmentation consistently with the target image's intensity profile. The ensemble approach consistently outperforms segmentations using individual warping methods alone, achieving high accuracy on several benchmark datasets. The MUSE methodology has been used for processing thousands of scans from various datasets, producing robust and consistent results. MUSE is publicly available both as a downloadable software package, and as an application that can be run on the CBICA Image Processing Portal (https://ipp.cbica.upenn.edu), a web based platform for remote processing of medical images. PMID:26679328

A musculoskeletal foot model for clinical gait analysis.

PubMed

Saraswat, Prabhav; Andersen, Michael S; Macwilliams, Bruce A

2010-06-18

Several full body musculoskeletal models have been developed for research applications and these models may potentially be developed into useful clinical tools to assess gait pathologies. Existing full-body musculoskeletal models treat the foot as a single segment and ignore the motions of the intrinsic joints of the foot. This assumption limits the use of such models in clinical cases with significant foot deformities. Therefore, a three-segment musculoskeletal model of the foot was developed to match the segmentation of a recently developed multi-segment kinematic foot model. All the muscles and ligaments of the foot spanning the modeled joints were included. Muscle pathways were adjusted with an optimization routine to minimize the difference between the muscle flexion-extension moment arms from the model and moment arms reported in literature. The model was driven by walking data from five normal pediatric subjects (aged 10.6+/-1.57 years) and muscle forces and activation levels required to produce joint motions were calculated using an inverse dynamic analysis approach. Due to the close proximity of markers on the foot, small marker placement error during motion data collection may lead to significant differences in musculoskeletal model outcomes. Therefore, an optimization routine was developed to enforce joint constraints, optimally scale each segment length and adjust marker positions. To evaluate the model outcomes, the muscle activation patterns during walking were compared with electromyography (EMG) activation patterns reported in the literature. Model-generated muscle activation patterns were observed to be similar to the EMG activation patterns. Published by Elsevier Ltd.

Prostate segmentation: an efficient convex optimization approach with axial symmetry using 3-D TRUS and MR images.

PubMed

Qiu, Wu; Yuan, Jing; Ukwatta, Eranga; Sun, Yue; Rajchl, Martin; Fenster, Aaron

2014-04-01

We propose a novel global optimization-based approach to segmentation of 3-D prostate transrectal ultrasound (TRUS) and T2 weighted magnetic resonance (MR) images, enforcing inherent axial symmetry of prostate shapes to simultaneously adjust a series of 2-D slice-wise segmentations in a "global" 3-D sense. We show that the introduced challenging combinatorial optimization problem can be solved globally and exactly by means of convex relaxation. In this regard, we propose a novel coherent continuous max-flow model (CCMFM), which derives a new and efficient duality-based algorithm, leading to a GPU-based implementation to achieve high computational speeds. Experiments with 25 3-D TRUS images and 30 3-D T2w MR images from our dataset, and 50 3-D T2w MR images from a public dataset, demonstrate that the proposed approach can segment a 3-D prostate TRUS/MR image within 5-6 s including 4-5 s for initialization, yielding a mean Dice similarity coefficient of 93.2%±2.0% for 3-D TRUS images and 88.5%±3.5% for 3-D MR images. The proposed method also yields relatively low intra- and inter-observer variability introduced by user manual initialization, suggesting a high reproducibility, independent of observers.

3D prostate TRUS segmentation using globally optimized volume-preserving prior.

PubMed

Qiu, Wu; Rajchl, Martin; Guo, Fumin; Sun, Yue; Ukwatta, Eranga; Fenster, Aaron; Yuan, Jing

2014-01-01

An efficient and accurate segmentation of 3D transrectal ultrasound (TRUS) images plays an important role in the planning and treatment of the practical 3D TRUS guided prostate biopsy. However, a meaningful segmentation of 3D TRUS images tends to suffer from US speckles, shadowing and missing edges etc, which make it a challenging task to delineate the correct prostate boundaries. In this paper, we propose a novel convex optimization based approach to extracting the prostate surface from the given 3D TRUS image, while preserving a new global volume-size prior. We, especially, study the proposed combinatorial optimization problem by convex relaxation and introduce its dual continuous max-flow formulation with the new bounded flow conservation constraint, which results in an efficient numerical solver implemented on GPUs. Experimental results using 12 patient 3D TRUS images show that the proposed approach while preserving the volume-size prior yielded a mean DSC of 89.5% +/- 2.4%, a MAD of 1.4 +/- 0.6 mm, a MAXD of 5.2 +/- 3.2 mm, and a VD of 7.5% +/- 6.2% in - 1 minute, deomonstrating the advantages of both accuracy and efficiency. In addition, the low standard deviation of the segmentation accuracy shows a good reliability of the proposed approach.

Modelling and Optimization of Four-Segment Shielding Coils of Current Transformers

PubMed Central

Gao, Yucheng; Zhao, Wei; Wang, Qing; Qu, Kaifeng; Li, He; Shao, Haiming; Huang, Songling

2017-01-01

Applying shielding coils is a practical way to protect current transformers (CTs) for large-capacity generators from the intensive magnetic interference produced by adjacent bus-bars. The aim of this study is to build a simple analytical model for the shielding coils, from which the optimization of the shielding coils can be calculated effectively. Based on an existing stray flux model, a new analytical model for the leakage flux of partial coils is presented, and finite element method-based simulations are carried out to develop empirical equations for the core-pickup factors of the models. Using the flux models, a model of the common four-segment shielding coils is derived. Furthermore, a theoretical analysis is carried out on the optimal performance of the four-segment shielding coils in a typical six-bus-bars scenario. It turns out that the “all parallel” shielding coils with a 45° starting position have the best shielding performance, whereas the “separated loop” shielding coils with a 0° starting position feature the lowest heating value. Physical experiments were performed, which verified all the models and the conclusions proposed in the paper. In addition, for shielding coils with other than the four-segment configuration, the analysis process will generally be the same. PMID:28587137

Modelling and Optimization of Four-Segment Shielding Coils of Current Transformers.

PubMed

Gao, Yucheng; Zhao, Wei; Wang, Qing; Qu, Kaifeng; Li, He; Shao, Haiming; Huang, Songling

2017-05-26

Applying shielding coils is a practical way to protect current transformers (CTs) for large-capacity generators from the intensive magnetic interference produced by adjacent bus-bars. The aim of this study is to build a simple analytical model for the shielding coils, from which the optimization of the shielding coils can be calculated effectively. Based on an existing stray flux model, a new analytical model for the leakage flux of partial coils is presented, and finite element method-based simulations are carried out to develop empirical equations for the core-pickup factors of the models. Using the flux models, a model of the common four-segment shielding coils is derived. Furthermore, a theoretical analysis is carried out on the optimal performance of the four-segment shielding coils in a typical six-bus-bars scenario. It turns out that the "all parallel" shielding coils with a 45° starting position have the best shielding performance, whereas the "separated loop" shielding coils with a 0° starting position feature the lowest heating value. Physical experiments were performed, which verified all the models and the conclusions proposed in the paper. In addition, for shielding coils with other than the four-segment configuration, the analysis process will generally be the same.

Computer simulation of storm runoff for three watersheds in Albuquerque, New Mexico

USGS Publications Warehouse

Knutilla, R.L.; Veenhuis, J.E.

1994-01-01

Rainfall-runoff data from three watersheds were selected for calibration and verification of the U.S. Geological Survey's Distributed Routing Rainfall-Runoff Model. The watersheds chosen are residentially developed. The conceptually based model uses an optimization process that adjusts selected parameters to achieve the best fit between measured and simulated runoff volumes and peak discharges. Three of these optimization parameters represent soil-moisture conditions, three represent infiltration, and one accounts for effective impervious area. Each watershed modeled was divided into overland-flow segments and channel segments. The overland-flow segments were further subdivided to reflect pervious and impervious areas. Each overland-flow and channel segment was assigned representative values of area, slope, percentage of imperviousness, and roughness coefficients. Rainfall-runoff data for each watershed were separated into two sets for use in calibration and verification. For model calibration, seven input parameters were optimized to attain a best fit of the data. For model verification, parameter values were set using values from model calibration. The standard error of estimate for calibration of runoff volumes ranged from 19 to 34 percent, and for peak discharge calibration ranged from 27 to 44 percent. The standard error of estimate for verification of runoff volumes ranged from 26 to 31 percent, and for peak discharge verification ranged from 31 to 43 percent.

Adaptive surrogate model based multi-objective transfer trajectory optimization between different libration points

NASA Astrophysics Data System (ADS)

Peng, Haijun; Wang, Wei

2016-10-01

An adaptive surrogate model-based multi-objective optimization strategy that combines the benefits of invariant manifolds and low-thrust control toward developing a low-computational-cost transfer trajectory between libration orbits around the L1 and L2 libration points in the Sun-Earth system has been proposed in this paper. A new structure for a multi-objective transfer trajectory optimization model that divides the transfer trajectory into several segments and gives the dominations for invariant manifolds and low-thrust control in different segments has been established. To reduce the computational cost of multi-objective transfer trajectory optimization, a mixed sampling strategy-based adaptive surrogate model has been proposed. Numerical simulations show that the results obtained from the adaptive surrogate-based multi-objective optimization are in agreement with the results obtained using direct multi-objective optimization methods, and the computational workload of the adaptive surrogate-based multi-objective optimization is only approximately 10% of that of direct multi-objective optimization. Furthermore, the generating efficiency of the Pareto points of the adaptive surrogate-based multi-objective optimization is approximately 8 times that of the direct multi-objective optimization. Therefore, the proposed adaptive surrogate-based multi-objective optimization provides obvious advantages over direct multi-objective optimization methods.

Prognostic validation of a 17-segment score derived from a 20-segment score for myocardial perfusion SPECT interpretation.

PubMed

Berman, Daniel S; Abidov, Aiden; Kang, Xingping; Hayes, Sean W; Friedman, John D; Sciammarella, Maria G; Cohen, Ishac; Gerlach, James; Waechter, Parker B; Germano, Guido; Hachamovitch, Rory

2004-01-01

Recently, a 17-segment model of the left ventricle has been recommended as an optimally weighted approach for interpreting myocardial perfusion single photon emission computed tomography (SPECT). Methods to convert databases from previous 20- to new 17-segment data and criteria for abnormality for the 17-segment scores are needed. Initially, for derivation of the conversion algorithm, 65 patients were studied (algorithm population) (pilot group, n = 28; validation group, n = 37). Three conversion algorithms were derived: algorithm 1, which used mid, distal, and apical scores; algorithm 2, which used distal and apical scores alone; and algorithm 3, which used maximal scores of the distal septal, lateral, and apical segments in the 20-segment model for 3 corresponding segments of the 17-segment model. The prognosis population comprised 16,020 consecutive patients (mean age, 65 +/- 12 years; 41% women) who had exercise or vasodilator stress technetium 99m sestamibi myocardial perfusion SPECT and were followed up for 2.1 +/- 0.8 years. In this population, 17-segment scores were derived from 20-segment scores by use of algorithm 2, which demonstrated the best agreement with expert 17-segment reading in the algorithm population. The prognostic value of the 20- and 17-segment scores was compared by converting the respective summed scores into percent myocardium abnormal. Conversion algorithm 2 was found to be highly concordant with expert visual analysis by the 17-segment model (r = 0.982; kappa = 0.866) in the algorithm population. In the prognosis population, 456 cardiac deaths occurred during follow-up. When the conversion algorithm was applied, extent and severity of perfusion defects were nearly identical by 20- and derived 17-segment scores. The receiver operating characteristic curve areas by 20- and 17-segment perfusion scores were identical for predicting cardiac death (both 0.77 +/- 0.02, P = not significant). The optimal prognostic cutoff value for either 20- or derived 17-segment models was confirmed to be 5% myocardium abnormal, corresponding to a summed stress score greater than 3. Of note, the 17-segment model demonstrated a trend toward fewer mildly abnormal scans and more normal and severely abnormal scans. An algorithm for conversion of 20-segment perfusion scores to 17-segment scores has been developed that is highly concordant with expert visual analysis by the 17-segment model and provides nearly identical prognostic information. This conversion model may provide a mechanism for comparison of studies analyzed by the 17-segment system with previous studies analyzed by the 20-segment approach.

Solution, solid phase and computational structures of apicidin and its backbone-reduced analogs.

PubMed

Kranz, Michael; Murray, Peter John; Taylor, Stephen; Upton, Richard J; Clegg, William; Elsegood, Mark R J

2006-06-01

The recently isolated broad-spectrum antiparasitic apicidin (1) is one of the few naturally occurring cyclic tetrapeptides (CTP). Depending on the solvent, the backbone of 1 exhibits two gamma-turns (in CH(2)Cl(2)) or a beta-turn (in DMSO), differing solely in the rotation of the plane of one of the amide bonds. In the X-ray crystal structure, the peptidic C==Os and NHs are on opposite sides of the backbone plane, giving rise to infinite stacks of cyclotetrapeptides connected by three intermolecular hydrogen bonds between the backbones. Conformational searches (Amber force field) on a truncated model system of 1 confirm all three backbone conformations to be low-energy states. The previously synthesized analogs of 1 containing a reduced amide bond exhibit the same backbone conformation as 1 in DMSO, which is confirmed further by the X-ray crystal structure of a model system of the desoxy analogs of 1. This similarity helps in explaining why the desoxy analogs retain some of the antiprotozoal activities of apicidin. The backbone-reduction approach designed to facilitate the cyclization step of the acyclic precursors of the CTPs seems to retain the conformational preferences of the parent peptide backbone.

An intrinsically shielded hydrogel for the adsorptive recovery of lysozyme.

PubMed

Wang, Lu; Zhang, Rongsheng; Eisenthal, Robert; Hubble, John

2006-07-01

The present paper addresses the selective recovery of lysozyme from egg white using CM-dextran (carboxymethyldextran)-based hydrogels containing Cibacron Blue as an affinity ligand and co-immobilized BSA intended to act as a shielding agent to reduce non-specific adsorption. Initial studies using pure lysozyme were conducted that indicated that the adsorption capacity increased with ligand density and that adsorption was well described by a Langmuir-type isotherm. The inclusion of BSA as a putative shielding agent did not decrease the adsorption capacity for lysozyme in single-adsorbate experiments. To assess the effectiveness of the shielding strategy, subsequent experiments were conducted with both defined lysozyme/ovalbumin mixtures and hen's-egg white. From these studies, the optimal operating conditions for lysozyme recovery have been determined. These include: optimal initial egg-white concentration [a 10% (v/v) solution of native egg white in the chosen buffer], affinity-ligand density (1.86 mM) and ligand-to-shielding-agent ratio (4:1). The purity of lysozyme obtained from egg white was improved from 69% with a non-shielded hydrogel to 94% with an intrinsically shielded hydrogel. Finally, the possibility of using a protein, rather than dextran-backbone-based, hydrogel was investigated. It was found that BSA could take the place of CM-dextran as the gel backbone in a simplified synthesis, producing a gel which also proved effective for lysozyme recovery with a 30% lysozyme in egg-white solution purified to approx. 92% in a single adsorption-desorption cycle.

Design of amine modified polymer dispersants for liquid-phase exfoliation of transition metal dichalcogenide nanosheets and their photodetective nanocomposites

NASA Astrophysics Data System (ADS)

Lee, Jinseong; Hahnkee Kim, Richard; Yu, Seunggun; Babu Velusamy, Dhinesh; Lee, Hyeokjung; Park, Chanho; Cho, Suk Man; Jeong, Beomjin; Sol Kang, Han; Park, Cheolmin

2017-12-01

Liquid-phase exfoliation (LPE) of transition metal dichalcogenide (TMD) nanosheets is a facile, cost-effective approach to large-area photoelectric devices including photodetectors and non-volatile memories. Non-destructive exfoliation of nanosheets using macromolecular dispersing agents is beneficial in rendering the TMD nanocomposite films suitable for mechanically flexible devices. Here, an efficient LPE of molybdenum disulfide (MoS2) with an amine modified poly(styrene-co-maleic anhydride) co-polymer (AM-PSMA) is demonstrated, wherein the maleic anhydrides were converted into maleic imides with primary amines using N-Boc-(CH2) n -NH2. The exfoliation of nanosheets was facilitated through Lewis acid-base interaction between the primary amine and transition metal. The results demonstrate that the exfoliation depends upon both the fraction of primary amines in the polymer chain and their distance from the polymer backbone. Under optimized conditions of primary amine content and its distance from the backbone, AM-PSMA gave rise to a highly concentrated MoS2 nanosheet suspension that was stable for over 10 d. Exfoliation of several other TMDs was also achieved using the optimized AM-PSMA, indicating the scope of AM-PSMA applications. Furthermore, a flexible composite film of AM-PSMA and MoS2 nanosheets fabricated by vacuum-assisted filtration showed excellent photoconductive performances including a high I on/I off ratio of 102 and a fast photocurrent switching of 300 ms.

Quantitative mouse brain phenotyping based on single and multispectral MR protocols

PubMed Central

Badea, Alexandra; Gewalt, Sally; Avants, Brian B.; Cook, James J.; Johnson, G. Allan

2013-01-01

Sophisticated image analysis methods have been developed for the human brain, but such tools still need to be adapted and optimized for quantitative small animal imaging. We propose a framework for quantitative anatomical phenotyping in mouse models of neurological and psychiatric conditions. The framework encompasses an atlas space, image acquisition protocols, and software tools to register images into this space. We show that a suite of segmentation tools (Avants, Epstein et al., 2008) designed for human neuroimaging can be incorporated into a pipeline for segmenting mouse brain images acquired with multispectral magnetic resonance imaging (MR) protocols. We present a flexible approach for segmenting such hyperimages, optimizing registration, and identifying optimal combinations of image channels for particular structures. Brain imaging with T1, T2* and T2 contrasts yielded accuracy in the range of 83% for hippocampus and caudate putamen (Hc and CPu), but only 54% in white matter tracts, and 44% for the ventricles. The addition of diffusion tensor parameter images improved accuracy for large gray matter structures (by >5%), white matter (10%), and ventricles (15%). The use of Markov random field segmentation further improved overall accuracy in the C57BL/6 strain by 6%; so Dice coefficients for Hc and CPu reached 93%, for white matter 79%, for ventricles 68%, and for substantia nigra 80%. We demonstrate the segmentation pipeline for the widely used C57BL/6 strain, and two test strains (BXD29, APP/TTA). This approach appears promising for characterizing temporal changes in mouse models of human neurological and psychiatric conditions, and may provide anatomical constraints for other preclinical imaging, e.g. fMRI and molecular imaging. This is the first demonstration that multiple MR imaging modalities combined with multivariate segmentation methods lead to significant improvements in anatomical segmentation in the mouse brain. PMID:22836174

In-plane structuring of proton exchange membrane fuel cell cathodes: Effect of ionomer equivalent weight structuring on performance and current density distribution

NASA Astrophysics Data System (ADS)

Herden, Susanne; Riewald, Felix; Hirschfeld, Julian A.; Perchthaler, Markus

2017-07-01

Within the active area of a fuel cell inhomogeneous operating conditions occur, however, state of the art electrodes are homogenous over the complete active area. This study uses current density distribution measurements to analyze which ionomer equivalent weight (EW) shows locally the highest current densities. With this information a segmented cathode electrode is manufactured by decal transfer. The segmented electrode shows better performance especially at high current densities compared to homogenous electrodes. Furthermore this segmented catalyst coated membrane (CCM) performs optimal in wet as well as dry conditions, both operating conditions arise in automotive fuel cell applications. Thus, cathode electrodes with an optimized ionomer EW distribution might have a significant impact on future automotive fuel cell development.

High performance photovoltaic applications using solution-processed small molecules.

PubMed

Chen, Yongsheng; Wan, Xiangjian; Long, Guankui

2013-11-19

Energy remains a critical issue for the survival and prosperity of humancivilization. Many experts believe that the eventual solution for sustainable energy is the use of direct solar energy as the main energy source. Among the options for renewable energy, photovoltaic technologies that harness solar energy offer a way to harness an unlimited resource and minimum environment impact in contrast with other alternatives such as water, nuclear, and wind energy. Currently, almost all commercial photovoltaic technologies use Si-based technology, which has a number of disadvantages including high cost, lack of flexibility, and the serious environmental impact of the Si industry. Other technologies, such as organic photovoltaic (OPV) cells, can overcome some of these issues. Today, polymer-based OPV (P-OPV) devices have achieved power conversion efficiencies (PCEs) that exceed 9%. Compared with P-OPV, small molecules based OPV (SM-OPV) offers further advantages, including a defined structure for more reproducible performance, higher mobility and open circuit voltage, and easier synthetic control that leads to more diversified structures. Therefore, while largely undeveloped, SM-OPV is an important emerging technology with performance comparable to P-OPV. In this Account, we summarize our recent results on solution-processed SM-OPV. We believe that solution processing is essential for taking full advantage of OPV technologies. Our work started with the synthesis of oligothiophene derivatives with an acceptor-donor-acceptor (A-D-A) structure. Both the backbone conjugation length and electron withdrawing terminal groups play an important role in the light absorption, energy levels and performance of the devices. Among those molecules, devices using a 7-thiophene-unit backbone and a 3-ethylrhodanine (RD) terminal unit produced a 6.1% PCE. With the optimized conjugation length and terminal unit, we borrowed from the results with P-OPV devices to optimize the backbone. Thus we selected BDT (benzo[1,2-b:4,5-b']dithiophene) and DTS (dithienosilole) to replace the central thiophene unit, leading to a PCE of 8.12%. In addition to our molecules, Bazan and co-workers have developed another excellent system using DTS as the core unit that has also achieved a PCE greater than 8%.

Chemical characteristics and antithrombotic effect of chondroitin sulfates from sturgeon skull and sturgeon backbone.

PubMed

Gui, Meng; Song, Juyi; Zhang, Lu; Wang, Shun; Wu, Ruiyun; Ma, Changwei; Li, Pinglan

2015-06-05

Chondroitin sulfates (CSs) were extracted from sturgeon skull and backbone, and their chemical composition, anticoagulant, anti-platelet and thrombolysis activities were evaluated. The average molecular weights of CS from sturgeon skull and backbone were 38.5kDa and 49.2kDa, respectively. Disaccharide analysis indicated that the sturgeon backbone CS was primarily composed of disaccharide monosulfated in position four of the GalNAc (37.8%) and disaccharide monosulfated in position six of the GalNAc (59.6%) while sturgeon skull CS was primarily composed of nonsulfated disaccharide (74.2%). Sturgeon backbone CS showed stronger antithrombotic effect than sturgeon skull CS. Sturgeon backbone CS could significantly prolong activated partial thromboplastin time (APTT) and thrombin time (TT), inhibited ADP-induced platelet aggregation and dissolved platelet plasma clots in vitro. The results suggested that sturgeon backbone CS can be explored as a functional food with antithrombotic function. Copyright © 2015 Elsevier Ltd. All rights reserved.

A threshold selection method based on edge preserving

NASA Astrophysics Data System (ADS)

Lou, Liantang; Dan, Wei; Chen, Jiaqi

2015-12-01

A method of automatic threshold selection for image segmentation is presented. An optimal threshold is selected in order to preserve edge of image perfectly in image segmentation. The shortcoming of Otsu's method based on gray-level histograms is analyzed. The edge energy function of bivariate continuous function is expressed as the line integral while the edge energy function of image is simulated by discretizing the integral. An optimal threshold method by maximizing the edge energy function is given. Several experimental results are also presented to compare with the Otsu's method.

Triazine-Based Sequence-Defined Polymers with Side-Chain Diversity and Backbone-Backbone Interaction Motifs.

PubMed

Grate, Jay W; Mo, Kai-For; Daily, Michael D

2016-03-14

Sequence control in polymers, well-known in nature, encodes structure and functionality. Here we introduce a new architecture, based on the nucleophilic aromatic substitution chemistry of cyanuric chloride, that creates a new class of sequence-defined polymers dubbed TZPs. Proof of concept is demonstrated with two synthesized hexamers, having neutral and ionizable side chains. Molecular dynamics simulations show backbone-backbone interactions, including H-bonding motifs and pi-pi interactions. This architecture is arguably biomimetic while differing from sequence-defined polymers having peptide bonds. The synthetic methodology supports the structural diversity of side chains known in peptides, as well as backbone-backbone hydrogen-bonding motifs, and will thus enable new macromolecules and materials with useful functions. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Thin Films Formed from Conjugated Polymers with Ionic, Water-Soluble Backbones.

PubMed

Voortman, Thomas P; Chiechi, Ryan C

2015-12-30

This paper compares the morphologies of films of conjugated polymers in which the backbone (main chain) and pendant groups are varied between ionic/hydrophilic and aliphatic/hydrophobic. We observe that conjugated polymers in which the pendant groups and backbone are matched, either ionic-ionic or hydrophobic-hydrophobic, form smooth, structured, homogeneous films from water (ionic) or tetrahydrofuran (hydrophobic). Mismatched conjugated polymers, by contrast, form inhomogeneous films with rough topologies. The polymers with ionic backbone chains are conjugated polyions (conjugated polymers with closed-shell charges in the backbone), which are semiconducting materials with tunable bad-gaps, not unlike uncharged conjugated polymers.

Structure and Dynamics of NBD1 from CFTR Characterized Using Crystallography and Hydrogen/Deuterium Exchange Mass Spectrometry

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

Lewis, H.A.; Wang, C.; Zhao, X.

2012-04-30

The {Delta}F508 mutation in nucleotide-binding domain 1 (NBD1) of the cystic fibrosis transmembrane conductance regulator (CFTR) is the predominant cause of cystic fibrosis. Previous biophysical studies on human F508 and {Delta}F508 domains showed only local structural changes restricted to residues 509-511 and only minor differences in folding rate and stability. These results were remarkable because {Delta}F508 was widely assumed to perturb domain folding based on the fact that it prevents trafficking of CFTR out of the endoplasmic reticulum. However, the previously reported crystal structures did not come from matched F508 and {Delta}F508 constructs, and the {Delta}F508 structure contained additional mutationsmore » that were required to obtain sufficient protein solubility. In this article, we present additional biophysical studies of NBD1 designed to address these ambiguities. Mass spectral measurements of backbone amide {sup 1}H/{sup 2}H exchange rates in matched F508 and {Delta}F508 constructs reveal that {Delta}F508 increases backbone dynamics at residues 509-511 and the adjacent protein segments but not elsewhere in NBD1. These measurements also confirm a high level of flexibility in the protein segments exhibiting variable conformations in the crystal structures. We additionally present crystal structures of a broader set of human NBD1 constructs, including one harboring the native F508 residue and others harboring the {Delta}F508 mutation in the presence of fewer and different solubilizing mutations. The only consistent conformational difference is observed at residues 509-511. The side chain of residue V510 in this loop is mostly buried in all non-{Delta}F508 structures but completely solvent exposed in all {Delta}F508 structures. These results reinforce the importance of the perturbation {Delta}F508 causes in the surface topography of NBD1 in a region likely to mediate contact with the transmembrane domains of CFTR. However, they also suggest that increased exposure of the 509-511 loop and increased dynamics in its vicinity could promote aggregation in vitro and aberrant intermolecular interactions that impede trafficking in vivo.« less

Synthesis, characterization and electroluminescence of two highly-twisted non-doped blue light-emitting materials

NASA Astrophysics Data System (ADS)

Gong, Xiaojie; Pan, Yipeng; Xie, Xiang; Tong, Tong; Chen, Runfeng; Gao, Deqing

2018-04-01

Two pyrene derivatives, substituted with 2-methylnaphthalene units on 1,3-position and 1,6-position of pyrene backbones, were designed and synthesized. DFT calculation confirmed that the two molecules were highly twisted and the dihedral angles between pyrene backbone and naphthalene unit were over 80°, being attributed to the steric hindrance of ortho-methyl group and the substitution position of pyrene itself. As a result, the intermolecular aggregation was greatly inhibited in the solid state, being beneficial for suppressing the fluorescence quenching. By analyzing the optical and thermal properties, it was found that the π-π conjugation extension could be adjusted and a balance for high fluorescent efficiency and avoiding quenching at the same time could be reached, which may guide the molecular design in the future. The electroluminescence properties of the non-doped devices were enhanced with the double hole-transporting layers by optimizing the energy level matching. The stable blue EL emission, with the Commission Internationaled'Eclairage (CIEx,y) color coordinates of (0.15, 0.13) and (0.15, 0.11) at 7, 8, 9 and 10 V respectively, was obtained.

Rational Design of a Highly Potent and Selective Peptide Inhibitor of PACE4 by Salt Bridge Interaction with D160 at Position P3.

PubMed

Dianati, Vahid; Shamloo, Azar; Kwiatkowska, Anna; Desjardins, Roxane; Soldera, Armand; Day, Robert; Dory, Yves L

2017-08-08

PACE4, a member of the proprotein convertases (PCs) family of serine proteases, is a validated target for prostate cancer. Our group has developed a potent and selective PACE4 inhibitor: Ac-LLLLRVKR-NH 2 . In seeking for modifications to increase the selectivity of this ligand toward PACE4, we replaced one of its P3 Val methyl groups with a basic group capable of forming a salt bridge with D160 of PACE4. The resulting inhibitor is eight times more potent than the P3 Val parent inhibitor and two times more selective over furin, because the equivalent salt bridge with furin E257 is not optimal. Moreover, the β-branched nature of the new P3 residue favors the extended β-sheet conformation usually associated with substrates of proteases. This work provides new insight for better understanding of β-sheet backbone-backbone interactions between serine proteases and their peptidic ligands. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Systematic Analysis of Polymer Molecular Weight Influence on the Organic Photovoltaic Performance.

PubMed

Katsouras, Athanasios; Gasparini, Nicola; Koulogiannis, Chrysanthos; Spanos, Michael; Ameri, Tayebeh; Brabec, Christoph J; Chochos, Christos L; Avgeropoulos, Apostolos

2015-10-01

The molecular weight of an electron donor-conjugated polymer is as essential as other well-known parameters in the chemical structure of the polymer, such as length and the nature of any side groups (alkyl chains) positioned on the polymeric backbone, as well as their placement, relative strength, the ratio of the donor and acceptor moieties in the backbone of donor-acceptor (D-A)-conjugated polymers, and the arrangement of their energy levels for organic photovoltaic performance. Finding the "optimal" molecular weight for a specific conjugated polymer is an important aspect for the development of novel photovoltaic polymers. Therefore, it is evident that the chemistry of functional conjugated polymers faces major challenges and materials have to adopt a broad range of specifications in order to be established for high photovoltaic performance. In this review, the approaches followed for enhancing the molecular weight of electron-donor polymers are presented in detail, as well as how this influences the optoelectronic properties, charge transport properties, structural conformation, morphology, and the photovoltaic performance of the active layer. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Coronary artery analysis: Computer-assisted selection of best-quality segments in multiple-phase coronary CT angiography

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

Zhou, Chuan, E-mail: chuan@umich.edu; Chan, Heang-

Purpose: The authors are developing an automated method to identify the best-quality coronary arterial segment from multiple-phase coronary CT angiography (cCTA) acquisitions, which may be used by either interpreting physicians or computer-aided detection systems to optimally and efficiently utilize the diagnostic information available in multiple-phase cCTA for the detection of coronary artery disease. Methods: After initialization with a manually identified seed point, each coronary artery tree is automatically extracted from multiple cCTA phases using our multiscale coronary artery response enhancement and 3D rolling balloon region growing vessel segmentation and tracking method. The coronary artery trees from multiple phases are thenmore » aligned by a global registration using an affine transformation with quadratic terms and nonlinear simplex optimization, followed by a local registration using a cubic B-spline method with fast localized optimization. The corresponding coronary arteries among the available phases are identified using a recursive coronary segment matching method. Each of the identified vessel segments is transformed by the curved planar reformation (CPR) method. Four features are extracted from each corresponding segment as quality indicators in the original computed tomography volume and the straightened CPR volume, and each quality indicator is used as a voting classifier for the arterial segment. A weighted voting ensemble (WVE) classifier is designed to combine the votes of the four voting classifiers for each corresponding segment. The segment with the highest WVE vote is then selected as the best-quality segment. In this study, the training and test sets consisted of 6 and 20 cCTA cases, respectively, each with 6 phases, containing a total of 156 cCTA volumes and 312 coronary artery trees. An observer preference study was also conducted with one expert cardiothoracic radiologist and four nonradiologist readers to visually rank vessel segment quality. The performance of our automated method was evaluated by comparing the automatically identified best-quality segments identified by the computer to those selected by the observers. Results: For the 20 test cases, 254 groups of corresponding vessel segments were identified after multiple phase registration and recursive matching. The AI-BQ segments agreed with the radiologist’s top 2 ranked segments in 78.3% of the 254 groups (Cohen’s kappa 0.60), and with the 4 nonradiologist observers in 76.8%, 84.3%, 83.9%, and 85.8% of the 254 groups. In addition, 89.4% of the AI-BQ segments agreed with at least two observers’ top 2 rankings, and 96.5% agreed with at least one observer’s top 2 rankings. In comparison, agreement between the four observers’ top ranked segment and the radiologist’s top 2 ranked segments were 79.9%, 80.7%, 82.3%, and 76.8%, respectively, with kappa values ranging from 0.56 to 0.68. Conclusions: The performance of our automated method for selecting the best-quality coronary segments from a multiple-phase cCTA acquisition was comparable to the selection made by human observers. This study demonstrates the potential usefulness of the automated method in clinical practice, enabling interpreting physicians to fully utilize the best available information in cCTA for diagnosis of coronary disease, without requiring manual search through the multiple phases and minimizing the variability in image phase selection for evaluation of coronary artery segments across the diversity of human readers with variations in expertise.« less

The magnitude of local immunity in the lungs of mice induced by live attenuated influenza vaccines is determined by local viral replication and induction of cytokines.

PubMed

Lau, Yuk-Fai; Santos, Celia; Torres-Vélez, Fernando J; Subbarao, Kanta

2011-01-01

While live attenuated influenza vaccines (LAIVs) have been shown to be efficacious and have been licensed for human use, the surface glycoproteins hemagglutinin (HA) and neuraminidase (NA) have to be updated for optimal protective efficacy. Little is known about the effect of different HA and NA proteins on the immunogenicity of LAIVs developed using the same backbone. A panel of LAIVs that share the internal protein genes, with unique HA and NA gene segments from different influenza subtypes, was rescued by reverse genetics, and a comparative study of immune responses induced by these vaccines was conducted in mice. The results suggest that the magnitude of lung immunity, including pulmonary IgA antibody and memory CD8(+) T lymphocytes, induced by the vaccines depends on the replication efficiency of the LAIVs, as well as the induction of cytokines/chemokines in the lungs. However, these factors are not important in determining systemic immunity such as serum antibody titers and memory CD8(+) T cells in the spleen. A qualitative analysis of immune responses induced by a single dose of an H5N1 LAIV revealed that the vaccine induced robust systemic and mucosal immunity in mice. In addition, antibodies and memory lymphocytes established in the lungs following vaccination were required for protection against lethal challenge with homologous and heterologous H5N1 viruses. Our results highlight the different requirements for inducing systemic and lung immunity that can be explored for the development of pulmonary immunity for protection against respiratory pathogens.

Agrobacterium-mediated transformation of Mexican lime (Citrus aurantifolia Swingle) using optimized systems for epicotyls and cotelydons

USDA-ARS?s Scientific Manuscript database

Epicotyl and internodal stem segments provide the predominantly used explants for regeneration of transgenic citrus plants following co-cultivation with Agrobacterium. Previous reports using epicotyls segments from Mexican lime have shown low affinity for Agrobacterium tumefaciens infection which re...

Correlation-based discrimination between cardiac tissue and blood for segmentation of 3D echocardiographic images

NASA Astrophysics Data System (ADS)

Saris, Anne E. C. M.; Nillesen, Maartje M.; Lopata, Richard G. P.; de Korte, Chris L.

2013-03-01

Automated segmentation of 3D echocardiographic images in patients with congenital heart disease is challenging, because the boundary between blood and cardiac tissue is poorly defined in some regions. Cardiologists mentally incorporate movement of the heart, using temporal coherence of structures to resolve ambiguities. Therefore, we investigated the merit of temporal cross-correlation for automated segmentation over the entire cardiac cycle. Optimal settings for maximum cross-correlation (MCC) calculation, based on a 3D cross-correlation based displacement estimation algorithm, were determined to obtain the best contrast between blood and myocardial tissue over the entire cardiac cycle. Resulting envelope-based as well as RF-based MCC values were used as additional external force in a deformable model approach, to segment the left-ventricular cavity in entire systolic phase. MCC values were tested against, and combined with, adaptive filtered, demodulated RF-data. Segmentation results were compared with manually segmented volumes using a 3D Dice Similarity Index (3DSI). Results in 3D pediatric echocardiographic images sequences (n = 4) demonstrate that incorporation of temporal information improves segmentation. The use of MCC values, either alone or in combination with adaptive filtered, demodulated RF-data, resulted in an increase of the 3DSI in 75% of the cases (average 3DSI increase: 0.71 to 0.82). Results might be further improved by optimizing MCC-contrast locally, in regions with low blood-tissue contrast. Reducing underestimation of the endocardial volume due to MCC processing scheme (choice of window size) and consequential border-misalignment, could also lead to more accurate segmentations. Furthermore, increasing the frame rate will also increase MCC-contrast and thus improve segmentation.

Hierarchical Image Segmentation of Remotely Sensed Data using Massively Parallel GNU-LINUX Software

NASA Technical Reports Server (NTRS)

Tilton, James C.

2003-01-01

A hierarchical set of image segmentations is a set of several image segmentations of the same image at different levels of detail in which the segmentations at coarser levels of detail can be produced from simple merges of regions at finer levels of detail. In [1], Tilton, et a1 describes an approach for producing hierarchical segmentations (called HSEG) and gave a progress report on exploiting these hierarchical segmentations for image information mining. The HSEG algorithm is a hybrid of region growing and constrained spectral clustering that produces a hierarchical set of image segmentations based on detected convergence points. In the main, HSEG employs the hierarchical stepwise optimization (HSWO) approach to region growing, which was described as early as 1989 by Beaulieu and Goldberg. The HSWO approach seeks to produce segmentations that are more optimized than those produced by more classic approaches to region growing (e.g. Horowitz and T. Pavlidis, [3]). In addition, HSEG optionally interjects between HSWO region growing iterations, merges between spatially non-adjacent regions (i.e., spectrally based merging or clustering) constrained by a threshold derived from the previous HSWO region growing iteration. While the addition of constrained spectral clustering improves the utility of the segmentation results, especially for larger images, it also significantly increases HSEG s computational requirements. To counteract this, a computationally efficient recursive, divide-and-conquer, implementation of HSEG (RHSEG) was devised, which includes special code to avoid processing artifacts caused by RHSEG s recursive subdivision of the image data. The recursive nature of RHSEG makes for a straightforward parallel implementation. This paper describes the HSEG algorithm, its recursive formulation (referred to as RHSEG), and the implementation of RHSEG using massively parallel GNU-LINUX software. Results with Landsat TM data are included comparing RHSEG with classic region growing.

Segment and fit thresholding: a new method for image analysis applied to microarray and immunofluorescence data.

PubMed

Ensink, Elliot; Sinha, Jessica; Sinha, Arkadeep; Tang, Huiyuan; Calderone, Heather M; Hostetter, Galen; Winter, Jordan; Cherba, David; Brand, Randall E; Allen, Peter J; Sempere, Lorenzo F; Haab, Brian B

2015-10-06

Experiments involving the high-throughput quantification of image data require algorithms for automation. A challenge in the development of such algorithms is to properly interpret signals over a broad range of image characteristics, without the need for manual adjustment of parameters. Here we present a new approach for locating signals in image data, called Segment and Fit Thresholding (SFT). The method assesses statistical characteristics of small segments of the image and determines the best-fit trends between the statistics. Based on the relationships, SFT identifies segments belonging to background regions; analyzes the background to determine optimal thresholds; and analyzes all segments to identify signal pixels. We optimized the initial settings for locating background and signal in antibody microarray and immunofluorescence data and found that SFT performed well over multiple, diverse image characteristics without readjustment of settings. When used for the automated analysis of multicolor, tissue-microarray images, SFT correctly found the overlap of markers with known subcellular localization, and it performed better than a fixed threshold and Otsu's method for selected images. SFT promises to advance the goal of full automation in image analysis.

Segment and Fit Thresholding: A New Method for Image Analysis Applied to Microarray and Immunofluorescence Data

PubMed Central

Ensink, Elliot; Sinha, Jessica; Sinha, Arkadeep; Tang, Huiyuan; Calderone, Heather M.; Hostetter, Galen; Winter, Jordan; Cherba, David; Brand, Randall E.; Allen, Peter J.; Sempere, Lorenzo F.; Haab, Brian B.

2016-01-01

Certain experiments involve the high-throughput quantification of image data, thus requiring algorithms for automation. A challenge in the development of such algorithms is to properly interpret signals over a broad range of image characteristics, without the need for manual adjustment of parameters. Here we present a new approach for locating signals in image data, called Segment and Fit Thresholding (SFT). The method assesses statistical characteristics of small segments of the image and determines the best-fit trends between the statistics. Based on the relationships, SFT identifies segments belonging to background regions; analyzes the background to determine optimal thresholds; and analyzes all segments to identify signal pixels. We optimized the initial settings for locating background and signal in antibody microarray and immunofluorescence data and found that SFT performed well over multiple, diverse image characteristics without readjustment of settings. When used for the automated analysis of multi-color, tissue-microarray images, SFT correctly found the overlap of markers with known subcellular localization, and it performed better than a fixed threshold and Otsu’s method for selected images. SFT promises to advance the goal of full automation in image analysis. PMID:26339978

A new method for automated discontinuity trace mapping on rock mass 3D surface model

NASA Astrophysics Data System (ADS)

Li, Xiaojun; Chen, Jianqin; Zhu, Hehua

2016-04-01

This paper presents an automated discontinuity trace mapping method on a 3D surface model of rock mass. Feature points of discontinuity traces are first detected using the Normal Tensor Voting Theory, which is robust to noisy point cloud data. Discontinuity traces are then extracted from feature points in four steps: (1) trace feature point grouping, (2) trace segment growth, (3) trace segment connection, and (4) redundant trace segment removal. A sensitivity analysis is conducted to identify optimal values for the parameters used in the proposed method. The optimal triangular mesh element size is between 5 cm and 6 cm; the angle threshold in the trace segment growth step is between 70° and 90°; the angle threshold in the trace segment connection step is between 50° and 70°, and the distance threshold should be at least 15 times the mean triangular mesh element size. The method is applied to the excavation face trace mapping of a drill-and-blast tunnel. The results show that the proposed discontinuity trace mapping method is fast and effective and could be used as a supplement to traditional direct measurement of discontinuity traces.

Segmentation of a Vibro-Shock Cantilever-Type Piezoelectric Energy Harvester Operating in Higher Transverse Vibration Modes

PubMed Central

Zizys, Darius; Gaidys, Rimvydas; Dauksevicius, Rolanas; Ostasevicius, Vytautas; Daniulaitis, Vytautas

2015-01-01

The piezoelectric transduction mechanism is a common vibration-to-electric energy harvesting approach. Piezoelectric energy harvesters are typically mounted on a vibrating host structure, whereby alternating voltage output is generated by a dynamic strain field. A design target in this case is to match the natural frequency of the harvester to the ambient excitation frequency for the device to operate in resonance mode, thus significantly increasing vibration amplitudes and, as a result, energy output. Other fundamental vibration modes have strain nodes, where the dynamic strain field changes sign in the direction of the cantilever length. The paper reports on a dimensionless numerical transient analysis of a cantilever of a constant cross-section and an optimally-shaped cantilever with the objective to accurately predict the position of a strain node. Total effective strain produced by both cantilevers segmented at the strain node is calculated via transient analysis and compared to the strain output produced by the cantilevers segmented at strain nodes obtained from modal analysis, demonstrating a 7% increase in energy output. Theoretical results were experimentally verified by using open-circuit voltage values measured for the cantilevers segmented at optimal and suboptimal segmentation lines. PMID:26703623

Random walks based multi-image segmentation: Quasiconvexity results and GPU-based solutions

PubMed Central

Collins, Maxwell D.; Xu, Jia; Grady, Leo; Singh, Vikas

2012-01-01

We recast the Cosegmentation problem using Random Walker (RW) segmentation as the core segmentation algorithm, rather than the traditional MRF approach adopted in the literature so far. Our formulation is similar to previous approaches in the sense that it also permits Cosegmentation constraints (which impose consistency between the extracted objects from ≥ 2 images) using a nonparametric model. However, several previous nonparametric cosegmentation methods have the serious limitation that they require adding one auxiliary node (or variable) for every pair of pixels that are similar (which effectively limits such methods to describing only those objects that have high entropy appearance models). In contrast, our proposed model completely eliminates this restrictive dependence –the resulting improvements are quite significant. Our model further allows an optimization scheme exploiting quasiconvexity for model-based segmentation with no dependence on the scale of the segmented foreground. Finally, we show that the optimization can be expressed in terms of linear algebra operations on sparse matrices which are easily mapped to GPU architecture. We provide a highly specialized CUDA library for Cosegmentation exploiting this special structure, and report experimental results showing these advantages. PMID:25278742

Segmentation of a Vibro-Shock Cantilever-Type Piezoelectric Energy Harvester Operating in Higher Transverse Vibration Modes.

PubMed

Zizys, Darius; Gaidys, Rimvydas; Dauksevicius, Rolanas; Ostasevicius, Vytautas; Daniulaitis, Vytautas

2015-12-23

The piezoelectric transduction mechanism is a common vibration-to-electric energy harvesting approach. Piezoelectric energy harvesters are typically mounted on a vibrating host structure, whereby alternating voltage output is generated by a dynamic strain field. A design target in this case is to match the natural frequency of the harvester to the ambient excitation frequency for the device to operate in resonance mode, thus significantly increasing vibration amplitudes and, as a result, energy output. Other fundamental vibration modes have strain nodes, where the dynamic strain field changes sign in the direction of the cantilever length. The paper reports on a dimensionless numerical transient analysis of a cantilever of a constant cross-section and an optimally-shaped cantilever with the objective to accurately predict the position of a strain node. Total effective strain produced by both cantilevers segmented at the strain node is calculated via transient analysis and compared to the strain output produced by the cantilevers segmented at strain nodes obtained from modal analysis, demonstrating a 7% increase in energy output. Theoretical results were experimentally verified by using open-circuit voltage values measured for the cantilevers segmented at optimal and suboptimal segmentation lines.

Graph-Cut Methods for Grain Boundary Segmentation (Preprint)

DTIC Science & Technology

2011-06-01

metals and metal alloys ) are among the strongest determinants of many material properties, such as mechanical strength or fracture resistance. In materials...cropped) Ni-based alloy image (a) using normalized cut (b) and ratio cut (c). Similar to normalized cut is the average-cut approach [11], where the...framework [2]. (a) (b) (c) Figure 3: Segmentation of a (cropped) Ni-based alloy image by optimal labeling. (a) Segmented grain bound- aries in a template

Quantitative assessments of the distinct contributions of polypeptide backbone amides versus sidechain groups to chain expansion via chemical denaturation

PubMed Central

Holehouse, Alex S.; Garai, Kanchan; Lyle, Nicholas; Vitalis, Andreas; Pappu, Rohit V.

2015-01-01

In aqueous solutions with high concentrations of chemical denaturants such as urea and guanidinium chloride (GdmCl) proteins expand to populate heterogeneous conformational ensembles. These denaturing environments are thought to be good solvents for generic protein sequences because properties of conformational distributions align with those of canonical random coils. Previous studies showed that water is a poor solvent for polypeptide backbones and therefore backbones form collapsed globular structures in aqueous solvents. Here, we ask if polypeptide backbones can intrinsically undergo the requisite chain expansion in aqueous solutions with high concentrations of urea and GdmCl. We answer this question using a combination of molecular dynamics simulations and fluorescence correlation spectroscopy. We find that the degree of backbone expansion is minimal in aqueous solutions with high concentrations denaturants. Instead, polypeptide backbones sample conformations that are denaturant-specific mixtures of coils and globules, with a persistent preference for globules. Therefore, typical denaturing environments cannot be classified as good solvents for polypeptide backbones. How then do generic protein sequences expand in denaturing environments? To answer this question, we investigated the effects of sidechains using simulations of two archetypal sequences with amino acid compositions that are mixtures of charged, hydrophobic, and polar groups. We find that sidechains lower the effective concentration of backbone amides in water leading to an intrinsic expansion of polypeptide backbones in the absence of denaturants. Additional dilution of the effective concentration of backbone amides is achieved through preferential interactions with denaturants. These effects lead to conformational statistics in denaturing environments that are congruent with those of canonical random coils. Our results highlight the role of sidechain-mediated interactions as determinants of the conformational properties of unfolded states in water and in influencing chain expansion upon denaturation. PMID:25664638

Cost-effectiveness analysis of dolutegravir plus backbone compared with raltegravir plus backbone, darunavir+ritonavir plus backbone and efavirenz/tenofovir/emtricitabine in treatment naïve and experienced HIV-positive patients.

PubMed

Restelli, Umberto; Rizzardini, Giuliano; Antinori, Andrea; Lazzarin, Adriano; Bonfanti, Marzia; Bonfanti, Paolo; Croce, Davide

2017-01-01

In January 2014, the European Medicines Agency issued a marketing authorization for dolutegravir (DTG), a second-generation integrase strand transfer inhibitor for HIV treatment. The study aimed at determining the incremental cost-effectiveness ratio (ICER) of the use of DTG+backbone compared with raltegravir (RAL)+backbone, darunavir (DRV)+ritonavir(r)+backbone and efavirenz/tenofovir/emtricitabine (EFV/TDF/FTC) in HIV-positive treatment-naïve patients and compared with RAL+backbone in treatment-experienced patients, from the Italian National Health Service's point of view. A published Monte Carlo Individual Simulation Model (ARAMIS-DTG model) was used to perform the analysis. Patients pass through mutually exclusive health states (defined in terms of diagnosis of HIV with or without opportunistic infections [OIs] and cardiovascular disease [CVD]) and successive lines of therapy. The model considers costs (2014) and quality of life per monthly cycle in a lifetime horizon. Costs and quality-adjusted life years (QALYs) are dependent on OI, CVD, AIDS events, adverse events and antiretroviral therapies. In treatment-naïve patients, DTG dominates RAL; compared with DRV/r, the ICER obtained is of 38,586 €/QALY (6,170 €/QALY in patients with high viral load) and over EFV/TDF/FTC, DTG generates an ICER of 33,664 €/QALY. In treatment-experienced patients, DTG compared to RAL leads to an ICER of 12,074 €/QALY. The use of DTG+backbone may be cost effective in treatment-naïve and treatment-experienced patients compared with RAL+backbone and in treatment-naïve patients compared with DRV/r+backbone and EFV/TDF/FTC considering a threshold of 40,000 €/QALY.

Parameterization of Shape and Compactness in Object-based Image Classification Using Quickbird-2 Imagery

NASA Astrophysics Data System (ADS)

Tonbul, H.; Kavzoglu, T.

2016-12-01

In recent years, object based image analysis (OBIA) has spread out and become a widely accepted technique for the analysis of remotely sensed data. OBIA deals with grouping pixels into homogenous objects based on spectral, spatial and textural features of contiguous pixels in an image. The first stage of OBIA, named as image segmentation, is the most prominent part of object recognition. In this study, multiresolution segmentation, which is a region-based approach, was employed to construct image objects. In the application of multi-resolution, three parameters, namely shape, compactness and scale must be set by the analyst. Segmentation quality remarkably influences the fidelity of the thematic maps and accordingly the classification accuracy. Therefore, it is of great importance to search and set optimal values for the segmentation parameters. In the literature, main focus has been on the definition of scale parameter, assuming that the effect of shape and compactness parameters is limited in terms of achieved classification accuracy. The aim of this study is to deeply analyze the influence of shape/compactness parameters by varying their values while using the optimal scale parameter determined by the use of Estimation of Scale Parameter (ESP-2) approach. A pansharpened Qickbird-2 image covering Trabzon, Turkey was employed to investigate the objectives of the study. For this purpose, six different combinations of shape/compactness were utilized to make deductions on the behavior of shape and compactness parameters and optimal setting for all parameters as a whole. Objects were assigned to classes using nearest neighbor classifier in all segmentation observations and equal number of pixels was randomly selected to calculate accuracy metrics. The highest overall accuracy (92.3%) was achieved by setting the shape/compactness criteria to 0.3/0.3. The results of this study indicate that shape/compactness parameters can have significant effect on classification accuracy with 4% change in overall accuracy. Also, statistical significance of differences in accuracy was tested using the McNemar's test and found that the difference between poor and optimal setting of shape/compactness parameters was statistically significant, suggesting a search for optimal parameterization instead of default setting.

Structure and Tectonics of the Saint Elias Orogen

NASA Astrophysics Data System (ADS)

Bruhn, R. L.; Pavlis, T. L.; Plafker, G.; Serpa, L.; Picornell, C.

2001-12-01

The Saint Elias orogen of western Canada and southern Alaska is a complex mountain belt formed by transform faulting and subduction between the Pacific and North American plates, and collision of the Yakutat terrane. The orogen is segmented into three regions of different structural style caused by lateral variations in transpression and processes of terrane accretion. Deformation is strain and displacement partitioned throughout the orogen; transcurrent motion is focused along discrete strike-slip faults, and shortening is distributed among reverse faults and folds with sub-horizontal axes. Plunging folds accommodate horizontal shortening and extension in the western part of the orogen. Segment boundaries extend across the Yakutat terrane where they coincide with the courses of huge piedmont glaciers that flow from the topographic backbone of the range onto the coastal plain. The eastern segment is marked by strike-slip faulting along the Fairweather transform fault and by a narrow belt of reverse faulting where the transpression ratio is 0.4:1 shortening to dextral shear. The transpression ratio is 1.7:1 in the central part of the orogen where a broad thin-skinned fold and thrust belt deforms the Yakutat terrane south of the Chugach-Saint Elias (CSE) suture. Dextral shearing is accommodated by strike-slip faulting beneath the Seward and Bagley glaciers in the hanging wall of the CSE suture, and partly by reverse faulting along a structural belt that cuts across the Yakutat terrane along the western edge of the Malaspina Glacier and links to the Pamplona fold and thrust belt offshore. Deformation along this segment boundary is probably also driven by vertical axis bending of the Yakutat microplate during collision. Subduction & accretion in the western segment of the orogen causes re-folding of previously formed structures when they are emplaced into the upper plate of the Alaska-Aleutian mega-thrust. Second phase folds plunge at moderate to steep angles and accretion is marked by only modest amounts of uplift. The structural boundary between the central and western segments of the orogen localizes the course of the Bering piedmont glacier. The structural segments coincide with subdivisions in historical seismicity, particularly ruptures of great to large magnitude earthquakes. The results of this structural study provide the requisite geological framework to design new-generation geophysical monitoring systems to study active deformation within the orogen.

Optimal Symmetric Multimodal Templates and Concatenated Random Forests for Supervised Brain Tumor Segmentation (Simplified) with ANTsR.

PubMed

Tustison, Nicholas J; Shrinidhi, K L; Wintermark, Max; Durst, Christopher R; Kandel, Benjamin M; Gee, James C; Grossman, Murray C; Avants, Brian B

2015-04-01

Segmenting and quantifying gliomas from MRI is an important task for diagnosis, planning intervention, and for tracking tumor changes over time. However, this task is complicated by the lack of prior knowledge concerning tumor location, spatial extent, shape, possible displacement of normal tissue, and intensity signature. To accommodate such complications, we introduce a framework for supervised segmentation based on multiple modality intensity, geometry, and asymmetry feature sets. These features drive a supervised whole-brain and tumor segmentation approach based on random forest-derived probabilities. The asymmetry-related features (based on optimal symmetric multimodal templates) demonstrate excellent discriminative properties within this framework. We also gain performance by generating probability maps from random forest models and using these maps for a refining Markov random field regularized probabilistic segmentation. This strategy allows us to interface the supervised learning capabilities of the random forest model with regularized probabilistic segmentation using the recently developed ANTsR package--a comprehensive statistical and visualization interface between the popular Advanced Normalization Tools (ANTs) and the R statistical project. The reported algorithmic framework was the top-performing entry in the MICCAI 2013 Multimodal Brain Tumor Segmentation challenge. The challenge data were widely varying consisting of both high-grade and low-grade glioma tumor four-modality MRI from five different institutions. Average Dice overlap measures for the final algorithmic assessment were 0.87, 0.78, and 0.74 for "complete", "core", and "enhanced" tumor components, respectively.

Patterns of Emphysema Heterogeneity

PubMed Central

Valipour, Arschang; Shah, Pallav L.; Gesierich, Wolfgang; Eberhardt, Ralf; Snell, Greg; Strange, Charlie; Barry, Robert; Gupta, Avina; Henne, Erik; Bandyopadhyay, Sourish; Raffy, Philippe; Yin, Youbing; Tschirren, Juerg; Herth, Felix J.F.

2016-01-01

Background Although lobar patterns of emphysema heterogeneity are indicative of optimal target sites for lung volume reduction (LVR) strategies, the presence of segmental, or sublobar, heterogeneity is often underappreciated. Objective The aim of this study was to understand lobar and segmental patterns of emphysema heterogeneity, which may more precisely indicate optimal target sites for LVR procedures. Methods Patterns of emphysema heterogeneity were evaluated in a representative cohort of 150 severe (GOLD stage III/IV) chronic obstructive pulmonary disease (COPD) patients from the COPDGene study. High-resolution computerized tomography analysis software was used to measure tissue destruction throughout the lungs to compute heterogeneity (≥ 15% difference in tissue destruction) between (inter-) and within (intra-) lobes for each patient. Emphysema tissue destruction was characterized segmentally to define patterns of heterogeneity. Results Segmental tissue destruction revealed interlobar heterogeneity in the left lung (57%) and right lung (52%). Intralobar heterogeneity was observed in at least one lobe of all patients. No patient presented true homogeneity at a segmental level. There was true homogeneity across both lungs in 3% of the cohort when defining heterogeneity as ≥ 30% difference in tissue destruction. Conclusion Many LVR technologies for treatment of emphysema have focused on interlobar heterogeneity and target an entire lobe per procedure. Our observations suggest that a high proportion of patients with emphysema are affected by interlobar as well as intralobar heterogeneity. These findings prompt the need for a segmental approach to LVR in the majority of patients to treat only the most diseased segments and preserve healthier ones. PMID:26430783

Optimization of coronagraph design for segmented aperture telescopes

NASA Astrophysics Data System (ADS)

Jewell, Jeffrey; Ruane, Garreth; Shaklan, Stuart; Mawet, Dimitri; Redding, Dave

2017-09-01

The goal of directly imaging Earth-like planets in the habitable zone of other stars has motivated the design of coronagraphs for use with large segmented aperture space telescopes. In order to achieve an optimal trade-off between planet light throughput and diffracted starlight suppression, we consider coronagraphs comprised of a stage of phase control implemented with deformable mirrors (or other optical elements), pupil plane apodization masks (gray scale or complex valued), and focal plane masks (either amplitude only or complex-valued, including phase only such as the vector vortex coronagraph). The optimization of these optical elements, with the goal of achieving 10 or more orders of magnitude in the suppression of on-axis (starlight) diffracted light, represents a challenging non-convex optimization problem with a nonlinear dependence on control degrees of freedom. We develop a new algorithmic approach to the design optimization problem, which we call the "Auxiliary Field Optimization" (AFO) algorithm. The central idea of the algorithm is to embed the original optimization problem, for either phase or amplitude (apodization) in various planes of the coronagraph, into a problem containing additional degrees of freedom, specifically fictitious "auxiliary" electric fields which serve as targets to inform the variation of our phase or amplitude parameters leading to good feasible designs. We present the algorithm, discuss details of its numerical implementation, and prove convergence to local minima of the objective function (here taken to be the intensity of the on-axis source in a "dark hole" region in the science focal plane). Finally, we present results showing application of the algorithm to both unobscured off-axis and obscured on-axis segmented telescope aperture designs. The application of the AFO algorithm to the coronagraph design problem has produced solutions which are capable of directly imaging planets in the habitable zone, provided end-to-end telescope system stability requirements can be met. Ongoing work includes advances of the AFO algorithm reported here to design in additional robustness to a resolved star, and other phase or amplitude aberrations to be encountered in a real segmented aperture space telescope.

A segmental analysis of current and future scanning and optimizing technology in the hardwood sawmill industry

Treesearch

S.A. Bowe; R.L. Smith; D. Earl Kline; Philip A. Araman

2002-01-01

A nationwide survey of advanced scanning and optimizing technology in the hardwood sawmill industry was conducted in the fall of 1999. Three specific hardwood sawmill technologies were examined that included current edger-optimizer systems, future edger-optimizer systems, and future automated grading systems. The objectives of the research were to determine differences...

Optimizing SGLT inhibitor treatment for diabetes with chronic kidney diseases.

PubMed

Layton, Anita T

2018-06-28

Diabetes induces glomerular hyperfiltration, affects kidney function, and may lead to chronic kidney diseases. A novel therapeutic treatment for diabetic patients targets the sodium-glucose cotransporter isoform 2 (SGLT2) in the kidney. SGLT2 inhibitors enhance urinary glucose, [Formula: see text] and fluid excretion and lower hyperglycemia in diabetes by inhibiting [Formula: see text] and glucose reabsorption along the proximal convoluted tubule. A goal of this study is to predict the effects of SGLT2 inhibitors in diabetic patients with and without chronic kidney diseases. To that end, we applied computational rat kidney models to assess how SGLT2 inhibition affects renal solute transport and metabolism when nephron population are normal or reduced (the latter simulates chronic kidney disease). The model predicts that SGLT2 inhibition induces glucosuria and natriuresis, with those effects enhanced in a remnant kidney. The model also predicts that the [Formula: see text] transport load and thus oxygen consumption of the S3 segment are increased under SGLT2 inhibition, a consequence that may increase the risk of hypoxia for that segment. To protect the vulnerable S3 segment, we explore dual SGLT2/SGLT1 inhibition and seek to determine the optimal combination that would yield sufficient urinary glucose excretion while limiting the metabolic load on the S3 segment. The model predicts that the optimal combination of SGLT2/SGLT1 inhibition lowers the oxygen requirements of key tubular segments, but decreases urine flow and [Formula: see text] excretion; the latter effect may limit the cardiovascular protection of the treatment.

Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides.

PubMed

Frembgen-Kesner, Tamara; Andrews, Casey T; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A; Jain, Aakash; Olayiwola, Oluwatoni J; Weishaar, Mitch R; Elcock, Adrian H

2015-05-12

Recently, we reported the parametrization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral, and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral, and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downward in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multidomain proteins connected by flexible linkers.

Large-scale measurement and modeling of backbone Internet traffic

NASA Astrophysics Data System (ADS)

Roughan, Matthew; Gottlieb, Joel

2002-07-01

There is a brewing controversy in the traffic modeling community concerning how to model backbone traffic. The fundamental work on self-similarity in data traffic appears to be contradicted by recent findings that suggest that backbone traffic is smooth. The traffic analysis work to date has focused on high-quality but limited-scope packet trace measurements; this limits its applicability to high-speed backbone traffic. This paper uses more than one year's worth of SNMP traffic data covering an entire Tier 1 ISP backbone to address the question of how backbone network traffic should be modeled. Although the limitations of SNMP measurements do not permit us to comment on the fine timescale behavior of the traffic, careful analysis of the data suggests that irrespective of the variation at fine timescales, we can construct a simple traffic model that captures key features of the observed traffic. Furthermore, the model's parameters are measurable using existing network infrastructure, making this model practical in a present-day operational network. In addition to its practicality, the model verifies basic statistical multiplexing results, and thus sheds deep insight into how smooth backbone traffic really is.

Uncovering the essential links in online commercial networks

NASA Astrophysics Data System (ADS)

Zeng, Wei; Fang, Meiling; Shao, Junming; Shang, Mingsheng

2016-09-01

Recommender systems are designed to effectively support individuals' decision-making process on various web sites. It can be naturally represented by a user-object bipartite network, where a link indicates that a user has collected an object. Recently, research on the information backbone has attracted researchers' interests, which is a sub-network with fewer nodes and links but carrying most of the relevant information. With the backbone, a system can generate satisfactory recommenda- tions while saving much computing resource. In this paper, we propose an enhanced topology-aware method to extract the information backbone in the bipartite network mainly based on the information of neighboring users and objects. Our backbone extraction method enables the recommender systems achieve more than 90% of the accuracy of the top-L recommendation, however, consuming only 20% links. The experimental results show that our method outperforms the alternative backbone extraction methods. Moreover, the structure of the information backbone is studied in detail. Finally, we highlight that the information backbone is one of the most important properties of the bipartite network, with which one can significantly improve the efficiency of the recommender system.

Free-energy landscape of RNA hairpins constructed via dihedral angle principal component analysis.

PubMed

Riccardi, Laura; Nguyen, Phuong H; Stock, Gerhard

2009-12-31

To systematically construct a low-dimensional free-energy landscape of RNA systems from a classical molecular dynamics simulation, various versions of the principal component analysis (PCA) are compared: the cPCA using the Cartesian coordinates of all atoms, the dPCA using the sine/cosine-transformed six backbone dihedral angles as well as the glycosidic torsional angle chi and the pseudorotational angle P, the aPCA which ignores the circularity of the 6 + 2 dihedral angles of the RNA, and the dPCA(etatheta), which approximates the 6 backbone dihedral angles by 2 pseudotorsional angles eta and theta. As representative examples, a 10-nucleotide UUCG hairpin and the 36-nucleotide segment SL1 of the Psi site of HIV-1 are studied by classical molecular dynamics simulation, using the Amber all-atom force field and explicit solvent. It is shown that the conformational heterogeneity of the RNA hairpins can only be resolved by an angular PCA such as the dPCA but not by the cPCA using Cartesian coordinates. Apart from possible artifacts due to the coupling of overall and internal motion, this is because the details of hydrogen bonding and stacking interactions but also of global structural rearrangements of the RNA are better discriminated by dihedral angles. In line with recent experiments, it is found that the free energy landscape of RNA hairpins is quite rugged and contains various metastable conformational states which may serve as an intermediate for unfolding.

Effects of the Chemical Structures of Oligoarginines Conjugated to Biocompatible Polymers as a Mucosal Adjuvant on Antibody Induction in Nasal Cavities.

PubMed

Mohri, Kohta; Miyata, Kohei; Egawa, Tomomi; Tanishita, Sohei; Endo, Rikito; Yagi, Haruya; Ukawa, Masami; Ochiai, Kyohei; Hiwatari, Ken-Ichiro; Tsubaki, Kazufumi; Shigeno, Koichi; Tobita, Etsuo; Uto, Tomofumi; Baba, Masanori; Sakuma, Shinji

2018-01-01

We have been investigating the potential of oligoarginine-linked polymers as an adjuvant for mucosal vaccination that induces immunoglobulin G (IgG) in systemic circulation and immunoglobulin A (IgA) secreted on the mucosa. Our latest infection experiments demonstrated that mice immunized nasally with a mixture of inactivated influenza viruses and poly(N-vinylacetamide-co-acrylic acid) (PNVA-co-AA) modified with D-octaarginine were perfectly protected from homologous virus infection. On the contrary, virus infection was observed in mice immunized with the antigen alone. This difference was presumably due to insignificant induction of secreted IgA on the nasal mucosa in the latter mice. Since it was unclear whether the current induction level was sufficient for heterologous virus infection, we evaluated the effects of the chemical structures of oligoarginines conjugated to PNVA-co-AA on induction of intranasal IgA. The number and optical activity of the arginine residues and the degree of modification with oligoarginines in the polymer backbone were listed as a factor that would influence IgA induction. Mouse experiments revealed that maximization of the modification resulted in an increase in adjuvant activities of oligoarginine-linked polymers most effectively. Glycine segments inserted between oligoarginines and the polymer backbone were a prerequisite for the maximization. The highest IgA level was observed when antigens were coadministered with diglycine-D-octaarginine-linked PNVA-co-AA.

A pH and redox dual stimuli-responsive poly(amino acid) derivative for controlled drug release.

PubMed

Gong, Chu; Shan, Meng; Li, Bingqiang; Wu, Guolin

2016-10-01

A pH and redox dual stimuli-responsive poly(aspartic acid) derivative for controlled drug release was successfully developed through progressive ring-opening reactions of polysuccinimide (PSI). Polyethylene glycol (PEG) chains were grafted onto the polyaspartamide backbone via redox-responsive disulfide linkages, providing a sheddable shell for the polymeric micelles in a reductive environment. Phenyl groups were introduced into the polyaspartamide backbone via the aminolysis reaction of PSI to serve as the hydrophobic segment of micelles. The polyaspartamide scaffold was also functionalized with N-(3-aminopropyl)-imidazole to obtain the pH-responsiveness manifesting as a swelling of the core of micelles at a low pH. The polymeric micelles with a core-shell nanostructure forming in neutral media exhibited both pH and redox responsive characteristics. Doxorubicin (DOX) as a model drug was encapsulated into the core of micelles through both hydrophobic and π-π interactions between aromatic rings and the DOX-loaded polymeric micelles exhibited accelerated drug release behaviors in an acidic and reductive environment due to the swelling of hydrophobic cores and the shedding of PEG shells. Furthermore, the cytocompability of the polymer and the cytotoxicity of DOX-loaded micelles towards Hela cells under corresponding conditions were evaluated, and the endocytosis of DOX-loaded polymeric micelles and the intracellular drug release from micelles were observed. All obtained data indicated that the micelle was a promising candidate for controlled drug release. Copyright © 2016 Elsevier B.V. All rights reserved.

Designing a Novel Polymer Electrolyte for Improving the Electrode/Electrolyte Interface in Flexible All-Solid-State Electrical Double-Layer Capacitors.

PubMed

Wang, Jeng-An; Lu, Yi-Ting; Lin, Sheng-Chi; Wang, Yu-Sheng; Ma, Chen-Chi M; Hu, Chi-Chang

2018-05-30

A novel copolymer, polyurethane-poly(acrylic acid) (PAA), is successfully synthesized from poly(acrylic acid) (PAA) backbone cross-linked with waterborne polyurethane (WPU). This sticky polymer, which is neutralized with 1 M KOH and then soaked in 1 M KOH (denoted as WPU-PAAK-K), provides an ionic conductivity greater than 10 -2 S cm -1 and acts as a gel electrolyte perfectly improving the electrode/electrolyte interfaces in a flexible all-solid-state electrical double-layer capacitor (EDLC). The PAA backbone chains in the copolymer increase the amount of carboxyl groups and promote the segmental motion. The carboxyl groups enhance the water-uptake capacity, which facilitates the ion transport and promotes the ionic conductivity. The cross-linked agent, WPU chains, effectively maintains the rich water content and provides mechanical stickiness to bind two electrodes together. An acid-treated carbon paper (denoted as ACP) combining with such a gel polymer electrolyte demonstrates excellent capacitive behavior with a high areal capacitance of 211.6 mF cm -2 at 10 mV s -1 . A full cell consisting of ACP/WPU-PAAK-K/ACP displays a low equivalent series resistance of 0.44 Ω from the electrochemical impedance spectroscopic results. An all-solid-state ACP/WPU-PAAK-K/ACP EDLC provides an areal specific capacitance of 94.6 mF cm -2 at 1 mA cm -2 . This device under 180° bending shows a capacitance retention over 90%, revealing its remarkable flexibility.

Efficient 3D multi-region prostate MRI segmentation using dual optimization.

PubMed

Qiu, Wu; Yuan, Jing; Ukwatta, Eranga; Sun, Yue; Rajchl, Martin; Fenster, Aaron

2013-01-01

Efficient and accurate extraction of the prostate, in particular its clinically meaningful sub-regions from 3D MR images, is of great interest in image-guided prostate interventions and diagnosis of prostate cancer. In this work, we propose a novel multi-region segmentation approach to simultaneously locating the boundaries of the prostate and its two major sub-regions: the central gland and the peripheral zone. The proposed method utilizes the prior knowledge of the spatial region consistency and employs a customized prostate appearance model to simultaneously segment multiple clinically meaningful regions. We solve the resulted challenging combinatorial optimization problem by means of convex relaxation, for which we introduce a novel spatially continuous flow-maximization model and demonstrate its duality to the investigated convex relaxed optimization problem with the region consistency constraint. Moreover, the proposed continuous max-flow model naturally leads to a new and efficient continuous max-flow based algorithm, which enjoys great advantages in numerics and can be readily implemented on GPUs. Experiments using 15 T2-weighted 3D prostate MR images, by inter- and intra-operator variability, demonstrate the promising performance of the proposed approach.

SU-C-207B-05: Tissue Segmentation of Computed Tomography Images Using a Random Forest Algorithm: A Feasibility Study

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

Polan, D; Brady, S; Kaufman, R

2016-06-15

Purpose: Develop an automated Random Forest algorithm for tissue segmentation of CT examinations. Methods: Seven materials were classified for segmentation: background, lung/internal gas, fat, muscle, solid organ parenchyma, blood/contrast, and bone using Matlab and the Trainable Weka Segmentation (TWS) plugin of FIJI. The following classifier feature filters of TWS were investigated: minimum, maximum, mean, and variance each evaluated over a pixel radius of 2n, (n = 0–4). Also noise reduction and edge preserving filters, Gaussian, bilateral, Kuwahara, and anisotropic diffusion, were evaluated. The algorithm used 200 trees with 2 features per node. A training data set was established using anmore » anonymized patient’s (male, 20 yr, 72 kg) chest-abdomen-pelvis CT examination. To establish segmentation ground truth, the training data were manually segmented using Eclipse planning software, and an intra-observer reproducibility test was conducted. Six additional patient data sets were segmented based on classifier data generated from the training data. Accuracy of segmentation was determined by calculating the Dice similarity coefficient (DSC) between manual and auto segmented images. Results: The optimized autosegmentation algorithm resulted in 16 features calculated using maximum, mean, variance, and Gaussian blur filters with kernel radii of 1, 2, and 4 pixels, in addition to the original CT number, and Kuwahara filter (linear kernel of 19 pixels). Ground truth had a DSC of 0.94 (range: 0.90–0.99) for adult and 0.92 (range: 0.85–0.99) for pediatric data sets across all seven segmentation classes. The automated algorithm produced segmentation with an average DSC of 0.85 ± 0.04 (range: 0.81–1.00) for the adult patients, and 0.86 ± 0.03 (range: 0.80–0.99) for the pediatric patients. Conclusion: The TWS Random Forest auto-segmentation algorithm was optimized for CT environment, and able to segment seven material classes over a range of body habitus and CT protocol parameters with an average DSC of 0.86 ± 0.04 (range: 0.80–0.99).« less

Short-term vs. long-term heart rate variability in ischemic cardiomyopathy risk stratification.

PubMed

Voss, Andreas; Schroeder, Rico; Vallverdú, Montserrat; Schulz, Steffen; Cygankiewicz, Iwona; Vázquez, Rafael; Bayés de Luna, Antoni; Caminal, Pere

2013-01-01

In industrialized countries with aging populations, heart failure affects 0.3-2% of the general population. The investigation of 24 h-ECG recordings revealed the potential of nonlinear indices of heart rate variability (HRV) for enhanced risk stratification in patients with ischemic heart failure (IHF). However, long-term analyses are time-consuming, expensive, and delay the initial diagnosis. The objective of this study was to investigate whether 30 min short-term HRV analysis is sufficient for comparable risk stratification in IHF in comparison to 24 h-HRV analysis. From 256 IHF patients [221 at low risk (IHFLR) and 35 at high risk (IHFHR)] (a) 24 h beat-to-beat time series (b) the first 30 min segment (c) the 30 min most stationary day segment and (d) the 30 min most stationary night segment were investigated. We calculated linear (time and frequency domain) and nonlinear HRV analysis indices. Optimal parameter sets for risk stratification in IHF were determined for 24 h and for each 30 min segment by applying discriminant analysis on significant clinical and non-clinical indices. Long- and short-term HRV indices from frequency domain and particularly from nonlinear dynamics revealed high univariate significances (p < 0.01) discriminating between IHFLR and IHFHR. For multivariate risk stratification, optimal mixed parameter sets consisting of 5 indices (clinical and nonlinear) achieved 80.4% AUC (area under the curve of receiver operating characteristics) from 24 h HRV analysis, 84.3% AUC from first 30 min, 82.2 % AUC from daytime 30 min and 81.7% AUC from nighttime 30 min. The optimal parameter set obtained from the first 30 min showed nearly the same classification power when compared to the optimal 24 h-parameter set. As results from stationary daytime and nighttime, 30 min segments indicate that short-term analyses of 30 min may provide at least a comparable risk stratification power in IHF in comparison to a 24 h analysis period.

Fast globally optimal segmentation of cells in fluorescence microscopy images.

PubMed

Bergeest, Jan-Philip; Rohr, Karl

2011-01-01

Accurate and efficient segmentation of cells in fluorescence microscopy images is of central importance for the quantification of protein expression in high-throughput screening applications. We propose a new approach for segmenting cell nuclei which is based on active contours and convex energy functionals. Compared to previous work, our approach determines the global solution. Thus, the approach does not suffer from local minima and the segmentation result does not depend on the initialization. We also suggest a numeric approach for efficiently computing the solution. The performance of our approach has been evaluated using fluorescence microscopy images of different cell types. We have also performed a quantitative comparison with previous segmentation approaches.

Topology optimization of reduced rare-earth permanent magnet arrays with finite coercivity

NASA Astrophysics Data System (ADS)

Teyber, R.; Trevizoli, P. V.; Christiaanse, T. V.; Govindappa, P.; Rowe, A.

2018-05-01

The supply chain risk of rare-earth permanent magnets has yielded research efforts to improve both materials and magnetic circuits. While a number of magnet optimization techniques exist, literature has not incorporated the permanent magnet failure process stemming from finite coercivity. To address this, a mixed-integer topology optimization is formulated to maximize the flux density of a segmented Halbach cylinder while avoiding permanent demagnetization. The numerical framework is used to assess the efficacy of low-cost (rare-earth-free ferrite C9), medium-cost (rare-earth-free MnBi), and higher-cost (Dy-free NdFeB) permanent magnet materials. Novel magnet designs are generated that produce flux densities 70% greater than the segmented Halbach array, albeit with increased magnet mass. Three optimization formulations are then explored using ferrite C9 that demonstrates the trade-off between manufacturability and design sophistication, generating flux densities in the range of 0.366-0.483 T.

Optimal Design of Grid-Stiffened Panels and Shells With Variable Curvature

NASA Technical Reports Server (NTRS)

Ambur, Damodar R.; Jaunky, Navin

2001-01-01

A design strategy for optimal design of composite grid-stiffened structures with variable curvature subjected to global and local buckling constraints is developed using a discrete optimizer. An improved smeared stiffener theory is used for the global buckling analysis. Local buckling of skin segments is assessed using a Rayleigh-Ritz method that accounts for material anisotropy and transverse shear flexibility. The local buckling of stiffener segments is also assessed. Design variables are the axial and transverse stiffener spacing, stiffener height and thickness, skin laminate, and stiffening configuration. Stiffening configuration is herein defined as a design variable that indicates the combination of axial, transverse and diagonal stiffeners in the stiffened panel. The design optimization process is adapted to identify the lightest-weight stiffening configuration and stiffener spacing for grid-stiffened composite panels given the overall panel dimensions. in-plane design loads, material properties. and boundary conditions of the grid-stiffened panel or shell.

An Introduction to System-Level, Steady-State and Transient Modeling and Optimization of High-Power-Density Thermoelectric Generator Devices Made of Segmented Thermoelectric Elements

NASA Astrophysics Data System (ADS)

Crane, D. T.

2011-05-01

High-power-density, segmented, thermoelectric (TE) elements have been intimately integrated into heat exchangers, eliminating many of the loss mechanisms of conventional TE assemblies, including the ceramic electrical isolation layer. Numerical models comprising simultaneously solved, nonlinear, energy balance equations have been created to simulate these novel architectures. Both steady-state and transient models have been created in a MATLAB/Simulink environment. The models predict data from experiments in various configurations and applications over a broad range of temperature, flow, and current conditions for power produced, efficiency, and a variety of other important outputs. Using the validated models, devices and systems are optimized using advanced multiparameter optimization techniques. Devices optimized for particular steady-state operating conditions can then be dynamically simulated in a transient operating model. The transient model can simulate a variety of operating conditions including automotive and truck drive cycles.

Motion generation of peristaltic mobile robot with particle swarm optimization algorithm

NASA Astrophysics Data System (ADS)

Homma, Takahiro; Kamamichi, Norihiro

2015-03-01

In developments of robots, bio-mimetics is attracting attention, which is a technology for the design of the structure and function inspired from biological system. There are a lot of examples of bio-mimetics in robotics such as legged robots, flapping robots, insect-type robots, fish-type robots. In this study, we focus on the motion of earthworm and aim to develop a peristaltic mobile robot. The earthworm is a slender animal moving in soil. It has a segmented body, and each segment can be shorted and lengthened by muscular actions. It can move forward by traveling expanding motions of each segment backward. By mimicking the structure and motion of the earthworm, we can construct a robot with high locomotive performance against an irregular ground or a narrow space. In this paper, to investigate the motion analytically, a dynamical model is introduced, which consist of a series-connected multi-mass model. Simple periodic patterns which mimic the motions of earthworms are applied in an open-loop fashion, and the moving patterns are verified through numerical simulations. Furthermore, to generate efficient motion of the robot, a particle swarm optimization algorithm, one of the meta-heuristic optimization, is applied. The optimized results are investigated by comparing to simple periodic patterns.

Competitive game theoretic optimal routing in optical networks

NASA Astrophysics Data System (ADS)

Yassine, Abdulsalam; Kabranov, Ognian; Makrakis, Dimitrios

2002-09-01

Optical transport service providers need control and optimization strategies for wavelength management, network provisioning, restoration and protection, allowing them to define and deploy new services and maintain competitiveness. In this paper, we investigate a game theory based model for wavelength and flow assignment in multi wavelength optical networks, consisting of several backbone long-haul optical network transport service providers (TSPs) who are offering their services -in terms of bandwidth- to Internet service providers (ISPs). The ISPs act as brokers or agents between the TSP and end user. The agent (ISP) buys services (bandwidth) from the TSP. The TSPs compete among themselves to sell their services and maintain profitability. We present a case study, demonstrating the impact of different bandwidth broker demands on the supplier's profit and the price paid by the network broker.

Radio Frequency Ablation Registration, Segmentation, and Fusion Tool

PubMed Central

McCreedy, Evan S.; Cheng, Ruida; Hemler, Paul F.; Viswanathan, Anand; Wood, Bradford J.; McAuliffe, Matthew J.

2008-01-01

The Radio Frequency Ablation Segmentation Tool (RFAST) is a software application developed using NIH's Medical Image Processing Analysis and Visualization (MIPAV) API for the specific purpose of assisting physicians in the planning of radio frequency ablation (RFA) procedures. The RFAST application sequentially leads the physician through the steps necessary to register, fuse, segment, visualize and plan the RFA treatment. Three-dimensional volume visualization of the CT dataset with segmented 3D surface models enables the physician to interactively position the ablation probe to simulate burns and to semi-manually simulate sphere packing in an attempt to optimize probe placement. PMID:16871716

Identification, Characterization, and Three-Dimensional Structure of the Novel Circular Bacteriocin, Enterocin NKR-5-3B, from Enterococcus faecium.

PubMed

Himeno, Kohei; Rosengren, K Johan; Inoue, Tomoko; Perez, Rodney H; Colgrave, Michelle L; Lee, Han Siean; Chan, Lai Y; Henriques, Sónia Troeira; Fujita, Koji; Ishibashi, Naoki; Zendo, Takeshi; Wilaipun, Pongtep; Nakayama, Jiro; Leelawatcharamas, Vichien; Jikuya, Hiroyuki; Craik, David J; Sonomoto, Kenji

2015-08-11

Enterocin NKR-5-3B, one of the multiple bacteriocins produced by Enterococcus faecium NKR-5-3, is a 64-amino acid novel circular bacteriocin that displays broad-spectrum antimicrobial activity. Here we report the identification, characterization, and three-dimensional nuclear magnetic resonance solution structure determination of enterocin NKR-5-3B. Enterocin NKR-5-3B is characterized by four helical segments that enclose a compact hydrophobic core, which together with its circular backbone impart high stability and structural integrity. We also report the corresponding structural gene, enkB, that encodes an 87-amino acid precursor peptide that undergoes a yet to be described enzymatic processing that involves adjacent cleavage and ligation of Leu(24) and Trp(87) to yield the mature (circular) enterocin NKR-5-3B.

Methods for removing contaminant matter from a porous material

DOEpatents

Fox, Robert V [Idaho Falls, ID; Avci, Recep [Bozeman, MT; Groenewold, Gary S [Idaho Falls, ID

2010-11-16

Methods of removing contaminant matter from porous materials include applying a polymer material to a contaminated surface, irradiating the contaminated surface to cause redistribution of contaminant matter, and removing at least a portion of the polymer material from the surface. Systems for decontaminating a contaminated structure comprising porous material include a radiation device configured to emit electromagnetic radiation toward a surface of a structure, and at least one spray device configured to apply a capture material onto the surface of the structure. Polymer materials that can be used in such methods and systems include polyphosphazine-based polymer materials having polyphosphazine backbone segments and side chain groups that include selected functional groups. The selected functional groups may include iminos, oximes, carboxylates, sulfonates, .beta.-diketones, phosphine sulfides, phosphates, phosphites, phosphonates, phosphinates, phosphine oxides, monothio phosphinic acids, and dithio phosphinic acids.

Systems and strippable coatings for decontaminating structures that include porous material

DOEpatents

Fox, Robert V [Idaho Falls, ID; Avci, Recep [Bozeman, MT; Groenewold, Gary S [Idaho Falls, ID

2011-12-06

Methods of removing contaminant matter from porous materials include applying a polymer material to a contaminated surface, irradiating the contaminated surface to cause redistribution of contaminant matter, and removing at least a portion of the polymer material from the surface. Systems for decontaminating a contaminated structure comprising porous material include a radiation device configured to emit electromagnetic radiation toward a surface of a structure, and at least one spray device configured to apply a capture material onto the surface of the structure. Polymer materials that can be used in such methods and systems include polyphosphazine-based polymer materials having polyphosphazine backbone segments and side chain groups that include selected functional groups. The selected functional groups may include iminos, oximes, carboxylates, sulfonates, .beta.-diketones, phosphine sulfides, phosphates, phosphites, phosphonates, phosphinates, phosphine oxides, monothio phosphinic acids, and dithio phosphinic acids.

In-situ spectroscopic investigations of the redox behavior of poly(indole-5-carboxylic-acid) modified electrodes in acidic aqueous solutions.

PubMed

Talbi, H; Billaud, D; Louarn, G; Pron, A

2001-03-01

The oxidation of electrochemically grown poly(indole-5-carboxylic-acid) (P5CO2H) and its spectroscopic properties have been studied by in-situ spectroelectrochemical techniques. The purpose of this paper is to characterize the different modifications on the P5CO2H backbone, induced by the electrochemical oxidation in aqueous acidic solution. We have identified, on the basis of Raman spectra, the vibrational modes associated with neutral and oxidized segments of polymer. It was shown that at least three chemically and optically different species (perhaps other products too) are produced in different potential regimes upon oxidation of this polymer. The results obtained also indicate that the molecular properties of this conducting polymer are better revealed by in-situ resonant spectra than by ex-situ infrared and Raman studies.

Distribution path robust optimization of electric vehicle with multiple distribution centers

PubMed Central

Hao, Wei; He, Ruichun; Jia, Xiaoyan; Pan, Fuquan; Fan, Jing; Xiong, Ruiqi

2018-01-01

To identify electrical vehicle (EV) distribution paths with high robustness, insensitivity to uncertainty factors, and detailed road-by-road schemes, optimization of the distribution path problem of EV with multiple distribution centers and considering the charging facilities is necessary. With the minimum transport time as the goal, a robust optimization model of EV distribution path with adjustable robustness is established based on Bertsimas’ theory of robust discrete optimization. An enhanced three-segment genetic algorithm is also developed to solve the model, such that the optimal distribution scheme initially contains all road-by-road path data using the three-segment mixed coding and decoding method. During genetic manipulation, different interlacing and mutation operations are carried out on different chromosomes, while, during population evolution, the infeasible solution is naturally avoided. A part of the road network of Xifeng District in Qingyang City is taken as an example to test the model and the algorithm in this study, and the concrete transportation paths are utilized in the final distribution scheme. Therefore, more robust EV distribution paths with multiple distribution centers can be obtained using the robust optimization model. PMID:29518169

Three-dimensional data-tracking dynamic optimization simulations of human locomotion generated by direct collocation.

PubMed

Lin, Yi-Chung; Pandy, Marcus G

2017-07-05

The aim of this study was to perform full-body three-dimensional (3D) dynamic optimization simulations of human locomotion by driving a neuromusculoskeletal model toward in vivo measurements of body-segmental kinematics and ground reaction forces. Gait data were recorded from 5 healthy participants who walked at their preferred speeds and ran at 2m/s. Participant-specific data-tracking dynamic optimization solutions were generated for one stride cycle using direct collocation in tandem with an OpenSim-MATLAB interface. The body was represented as a 12-segment, 21-degree-of-freedom skeleton actuated by 66 muscle-tendon units. Foot-ground interaction was simulated using six contact spheres under each foot. The dynamic optimization problem was to find the set of muscle excitations needed to reproduce 3D measurements of body-segmental motions and ground reaction forces while minimizing the time integral of muscle activations squared. Direct collocation took on average 2.7±1.0h and 2.2±1.6h of CPU time, respectively, to solve the optimization problems for walking and running. Model-computed kinematics and foot-ground forces were in good agreement with corresponding experimental data while the calculated muscle excitation patterns were consistent with measured EMG activity. The results demonstrate the feasibility of implementing direct collocation on a detailed neuromusculoskeletal model with foot-ground contact to accurately and efficiently generate 3D data-tracking dynamic optimization simulations of human locomotion. The proposed method offers a viable tool for creating feasible initial guesses needed to perform predictive simulations of movement using dynamic optimization theory. The source code for implementing the model and computational algorithm may be downloaded at http://simtk.org/home/datatracking. Copyright © 2017 Elsevier Ltd. All rights reserved.

Rate-distortion optimized tree-structured compression algorithms for piecewise polynomial images.

PubMed

Shukla, Rahul; Dragotti, Pier Luigi; Do, Minh N; Vetterli, Martin

2005-03-01

This paper presents novel coding algorithms based on tree-structured segmentation, which achieve the correct asymptotic rate-distortion (R-D) behavior for a simple class of signals, known as piecewise polynomials, by using an R-D based prune and join scheme. For the one-dimensional case, our scheme is based on binary-tree segmentation of the signal. This scheme approximates the signal segments using polynomial models and utilizes an R-D optimal bit allocation strategy among the different signal segments. The scheme further encodes similar neighbors jointly to achieve the correct exponentially decaying R-D behavior (D(R) - c(o)2(-c1R)), thus improving over classic wavelet schemes. We also prove that the computational complexity of the scheme is of O(N log N). We then show the extension of this scheme to the two-dimensional case using a quadtree. This quadtree-coding scheme also achieves an exponentially decaying R-D behavior, for the polygonal image model composed of a white polygon-shaped object against a uniform black background, with low computational cost of O(N log N). Again, the key is an R-D optimized prune and join strategy. Finally, we conclude with numerical results, which show that the proposed quadtree-coding scheme outperforms JPEG2000 by about 1 dB for real images, like cameraman, at low rates of around 0.15 bpp.

A fuzzy optimal threshold technique for medical images

NASA Astrophysics Data System (ADS)

Thirupathi Kannan, Balaji; Krishnasamy, Krishnaveni; Pradeep Kumar Kenny, S.

2012-01-01

A new fuzzy based thresholding method for medical images especially cervical cytology images having blob and mosaic structures is proposed in this paper. Many existing thresholding algorithms may segment either blob or mosaic images but there aren't any single algorithm that can do both. In this paper, an input cervical cytology image is binarized, preprocessed and the pixel value with minimum Fuzzy Gaussian Index is identified as an optimal threshold value and used for segmentation. The proposed technique is tested on various cervical cytology images having blob or mosaic structures, compared with various existing algorithms and proved better than the existing algorithms.

An exhaustive survey of regular peptide conformations using a new metric for backbone handedness (h)

PubMed Central

2017-01-01

The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom—the backbone dihedral angles φ and ψ (Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial tool to characterize protein backbone features. However, the conformation or twist of a backbone as a function of φ and ψ has not been completely described for both cis and trans backbones. Additionally, little intuitive understanding is available about a peptide’s conformation simply from knowing the φ and ψ values of a peptide (e.g., is the regular peptide defined by φ = ψ =  − 100°  left-handed or right-handed?). This report provides a new metric for backbone handedness (h) based on interpreting a peptide backbone as a helix with axial displacement d and angular displacement θ, both of which are derived from a peptide backbone’s internal coordinates, especially dihedral angles φ, ψ and ω. In particular, h equals sin(θ)d∕|d|, with range [−1, 1] and negative (or positive) values indicating left(or right)-handedness. The metric h is used to characterize the handedness of every region of the Ramachandran plot for both cis (ω = 0°) and trans (ω = 180°) backbones, which provides the first exhaustive survey of twist handedness in Ramachandran (φ, ψ) space. These maps fill in the ‘dead space’ within the Ramachandran plot, which are regions that are not commonly accessed by structured proteins, but which may be accessible to intrinsically disordered proteins, short peptide fragments, and protein mimics such as peptoids. Finally, building on the work of (Zacharias & Knapp, 2013), this report presents a new plot based on d and θ that serves as a universal and intuitive alternative to the Ramachandran plot. The universality arises from the fact that the co-inhabitants of such a plot include every possible peptide backbone including cis and trans backbones. The intuitiveness arises from the fact that d and θ provide, at a glance, numerous aspects of the backbone including compactness, handedness, and planarity. PMID:28533975

Automated MRI Segmentation for Individualized Modeling of Current Flow in the Human Head

PubMed Central

Huang, Yu; Dmochowski, Jacek P.; Su, Yuzhuo; Datta, Abhishek; Rorden, Christopher; Parra, Lucas C.

2013-01-01

Objective High-definition transcranial direct current stimulation (HD-tDCS) and high-density electroencephalography (HD-EEG) require accurate models of current flow for precise targeting and current source reconstruction. At a minimum, such modeling must capture the idiosyncratic anatomy of brain, cerebrospinal fluid (CSF) and skull for each individual subject. Currently, the process to build such high-resolution individualized models from structural magnetic resonance images (MRI) requires labor-intensive manual segmentation, even when leveraging available automated segmentation tools. Also, accurate placement of many high-density electrodes on individual scalp is a tedious procedure. The goal was to develop fully automated techniques to reduce the manual effort in such a modeling process. Approach A fully automated segmentation technique based on Statical Parametric Mapping 8 (SPM8), including an improved tissue probability map (TPM) and an automated correction routine for segmentation errors, was developed, along with an automated electrode placement tool for high-density arrays. The performance of these automated routines was evaluated against results from manual segmentation on 4 healthy subjects and 7 stroke patients. The criteria include segmentation accuracy, the difference of current flow distributions in resulting HD-tDCS models and the optimized current flow intensities on cortical targets. Main results The segmentation tool can segment out not just the brain but also provide accurate results for CSF, skull and other soft tissues with a field of view (FOV) extending to the neck. Compared to manual results, automated segmentation deviates by only 7% and 18% for normal and stroke subjects, respectively. The predicted electric fields in the brain deviate by 12% and 29% respectively, which is well within the variability observed for various modeling choices. Finally, optimized current flow intensities on cortical targets do not differ significantly. Significance Fully automated individualized modeling may now be feasible for large-sample EEG research studies and tDCS clinical trials. PMID:24099977

Automated MRI segmentation for individualized modeling of current flow in the human head

NASA Astrophysics Data System (ADS)

Huang, Yu; Dmochowski, Jacek P.; Su, Yuzhuo; Datta, Abhishek; Rorden, Christopher; Parra, Lucas C.

2013-12-01

Objective. High-definition transcranial direct current stimulation (HD-tDCS) and high-density electroencephalography require accurate models of current flow for precise targeting and current source reconstruction. At a minimum, such modeling must capture the idiosyncratic anatomy of the brain, cerebrospinal fluid (CSF) and skull for each individual subject. Currently, the process to build such high-resolution individualized models from structural magnetic resonance images requires labor-intensive manual segmentation, even when utilizing available automated segmentation tools. Also, accurate placement of many high-density electrodes on an individual scalp is a tedious procedure. The goal was to develop fully automated techniques to reduce the manual effort in such a modeling process. Approach. A fully automated segmentation technique based on Statical Parametric Mapping 8, including an improved tissue probability map and an automated correction routine for segmentation errors, was developed, along with an automated electrode placement tool for high-density arrays. The performance of these automated routines was evaluated against results from manual segmentation on four healthy subjects and seven stroke patients. The criteria include segmentation accuracy, the difference of current flow distributions in resulting HD-tDCS models and the optimized current flow intensities on cortical targets.Main results. The segmentation tool can segment out not just the brain but also provide accurate results for CSF, skull and other soft tissues with a field of view extending to the neck. Compared to manual results, automated segmentation deviates by only 7% and 18% for normal and stroke subjects, respectively. The predicted electric fields in the brain deviate by 12% and 29% respectively, which is well within the variability observed for various modeling choices. Finally, optimized current flow intensities on cortical targets do not differ significantly.Significance. Fully automated individualized modeling may now be feasible for large-sample EEG research studies and tDCS clinical trials.

Do 3D Printing Models Improve Anatomical Teaching About Hepatic Segments to Medical Students? A Randomized Controlled Study.

PubMed

Kong, Xiangxue; Nie, Lanying; Zhang, Huijian; Wang, Zhanglin; Ye, Qiang; Tang, Lei; Huang, Wenhua; Li, Jianyi

2016-08-01

It is a difficult and frustrating task for young surgeons and medical students to understand the anatomy of hepatic segments. We tried to develop an optimal 3D printing model of hepatic segments as a teaching aid to improve the teaching of hepatic segments. A fresh human cadaveric liver without hepatic disease was CT scanned. After 3D reconstruction, three types of 3D computer models of hepatic structures were designed and 3D printed as models of hepatic segments without parenchyma (type 1) and with transparent parenchyma (type 2), and hepatic ducts with segmental partitions (type 3). These models were evaluated by six experts using a five-point Likert scale. Ninety two medical freshmen were randomized into four groups to learn hepatic segments with the aid of the three types of models and traditional anatomic atlas (TAA). Their results of two quizzes were compared to evaluate the teaching effects of the four methods. Three types of models were successful produced which displayed the structures of hepatic segments. By experts' evaluation, type 3 model was better than type 1 and 2 models in anatomical condition, type 2 and 3 models were better than type 1 model in tactility, and type 3 model was better than type 1 model in overall satisfaction (P < 0.05). The first quiz revealed that type 1 model was better than type 2 model and TAA, while type 3 model was better than type 2 and TAA in teaching effects (P < 0.05). The second quiz found that type 1 model was better than TAA, while type 3 model was better than type 2 model and TAA regarding teaching effects (P < 0.05). Only TAA group had significant declines between two quizzes (P < 0.05). The model with segmental partitions proves to be optimal, because it can best improve anatomical teaching about hepatic segments.

An Interactive Image Segmentation Method in Hand Gesture Recognition

PubMed Central

Chen, Disi; Li, Gongfa; Sun, Ying; Kong, Jianyi; Jiang, Guozhang; Tang, Heng; Ju, Zhaojie; Yu, Hui; Liu, Honghai

2017-01-01

In order to improve the recognition rate of hand gestures a new interactive image segmentation method for hand gesture recognition is presented, and popular methods, e.g., Graph cut, Random walker, Interactive image segmentation using geodesic star convexity, are studied in this article. The Gaussian Mixture Model was employed for image modelling and the iteration of Expectation Maximum algorithm learns the parameters of Gaussian Mixture Model. We apply a Gibbs random field to the image segmentation and minimize the Gibbs Energy using Min-cut theorem to find the optimal segmentation. The segmentation result of our method is tested on an image dataset and compared with other methods by estimating the region accuracy and boundary accuracy. Finally five kinds of hand gestures in different backgrounds are tested on our experimental platform, and the sparse representation algorithm is used, proving that the segmentation of hand gesture images helps to improve the recognition accuracy. PMID:28134818

Missing observations in multiyear rotation sampling designs

NASA Technical Reports Server (NTRS)

Gbur, E. E.; Sielken, R. L., Jr. (Principal Investigator)

1982-01-01

Because Multiyear estimation of at-harvest stratum crop proportions is more efficient than single year estimation, the behavior of multiyear estimators in the presence of missing acquisitions was studied. Only the (worst) case when a segment proportion cannot be estimated for the entire year is considered. The effect of these missing segments on the variance of the at-harvest stratum crop proportion estimator is considered when missing segments are not replaced, and when missing segments are replaced by segments not sampled in previous years. The principle recommendations are to replace missing segments according to some specified strategy, and to use a sequential procedure for selecting a sampling design; i.e., choose an optimal two year design and then, based on the observed two year design after segment losses have been taken into account, choose the best possible three year design having the observed two year parent design.

Aberration correction in wide-field fluorescence microscopy by segmented-pupil image interferometry.

PubMed

Scrimgeour, Jan; Curtis, Jennifer E

2012-06-18

We present a new technique for the correction of optical aberrations in wide-field fluorescence microscopy. Segmented-Pupil Image Interferometry (SPII) uses a liquid crystal spatial light modulator placed in the microscope's pupil plane to split the wavefront originating from a fluorescent object into an array of individual beams. Distortion of the wavefront arising from either system or sample aberrations results in displacement of the images formed from the individual pupil segments. Analysis of image registration allows for the local tilt in the wavefront at each segment to be corrected with respect to a central reference. A second correction step optimizes the image intensity by adjusting the relative phase of each pupil segment through image interferometry. This ensures that constructive interference between all segments is achieved at the image plane. Improvements in image quality are observed when Segmented-Pupil Image Interferometry is applied to correct aberrations arising from the microscope's optical path.

Bokeh mirror alignment for Cherenkov telescopes

NASA Astrophysics Data System (ADS)

Ahnen, M. L.; Baack, D.; Balbo, M.; Bergmann, M.; Biland, A.; Blank, M.; Bretz, T.; Bruegge, K. A.; Buss, J.; Domke, M.; Dorner, D.; Einecke, S.; Hempfling, C.; Hildebrand, D.; Hughes, G.; Lustermann, W.; Mannheim, K.; Mueller, S. A.; Neise, D.; Neronov, A.; Noethe, M.; Overkemping, A.-K.; Paravac, A.; Pauss, F.; Rhode, W.; Shukla, A.; Temme, F.; Thaele, J.; Toscano, S.; Vogler, P.; Walter, R.; Wilbert, A.

2016-09-01

Imaging Atmospheric Cherenkov Telescopes (IACTs) need imaging optics with large apertures and high image intensities to map the faint Cherenkov light emitted from cosmic ray air showers onto their image sensors. Segmented reflectors fulfill these needs, and composed from mass production mirror facets they are inexpensive and lightweight. However, as the overall image is a superposition of the individual facet images, alignment remains a challenge. Here we present a simple, yet extendable method, to align a segmented reflector using its Bokeh. Bokeh alig nment does not need a star or good weather nights but can be done even during daytime. Bokeh alignment optimizes the facet orientations by comparing the segmented reflectors Bokeh to a predefined template. The optimal Bokeh template is highly constricted by the reflector's aperture and is easy accessible. The Bokeh is observed using the out of focus image of a near by point like light source in a distance of about 10 focal lengths. We introduce Bokeh alignment on segmented reflectors and demonstrate it on the First Geiger-mode Avalanche Cherenkov Telescope (FACT) on La Palma, Spain.

Cost-effectiveness analysis of dolutegravir plus backbone compared with raltegravir plus backbone, darunavir+ritonavir plus backbone and efavirenz/tenofovir/emtricitabine in treatment naïve and experienced HIV-positive patients

PubMed Central

Restelli, Umberto; Rizzardini, Giuliano; Antinori, Andrea; Lazzarin, Adriano; Bonfanti, Marzia; Bonfanti, Paolo; Croce, Davide

2017-01-01

Background In January 2014, the European Medicines Agency issued a marketing authorization for dolutegravir (DTG), a second-generation integrase strand transfer inhibitor for HIV treatment. The study aimed at determining the incremental cost-effectiveness ratio (ICER) of the use of DTG+backbone compared with raltegravir (RAL)+backbone, darunavir (DRV)+ritonavir(r)+backbone and efavirenz/tenofovir/emtricitabine (EFV/TDF/FTC) in HIV-positive treatment-naïve patients and compared with RAL+backbone in treatment-experienced patients, from the Italian National Health Service’s point of view. Materials and methods A published Monte Carlo Individual Simulation Model (ARAMIS-DTG model) was used to perform the analysis. Patients pass through mutually exclusive health states (defined in terms of diagnosis of HIV with or without opportunistic infections [OIs] and cardiovascular disease [CVD]) and successive lines of therapy. The model considers costs (2014) and quality of life per monthly cycle in a lifetime horizon. Costs and quality-adjusted life years (QALYs) are dependent on OI, CVD, AIDS events, adverse events and antiretroviral therapies. Results In treatment-naïve patients, DTG dominates RAL; compared with DRV/r, the ICER obtained is of 38,586 €/QALY (6,170 €/QALY in patients with high viral load) and over EFV/TDF/FTC, DTG generates an ICER of 33,664 €/QALY. In treatment-experienced patients, DTG compared to RAL leads to an ICER of 12,074 €/QALY. Conclusion The use of DTG+backbone may be cost effective in treatment-naïve and treatment-experienced patients compared with RAL+backbone and in treatment-naïve patients compared with DRV/r+backbone and EFV/TDF/FTC considering a threshold of 40,000 €/QALY. PMID:28721059

Design and synthesis of an amphiphilic graft hydrogel having a hydrophobic domain formed by multiple interactions.

PubMed

Nitta, Kyohei; Kimoto, Atsushi; Watanabe, Junji

2016-11-01

A novel hydrogel having hydrophobic oligo segments and hydrophilic poly(acrylamidoglycolic acid) (PAGA) as pH responsive polymer segments was designed and synthesized to be used as a soft biomaterial. Poly(trimethylene carbonate) (PTMC) as the side chain, for which the degrees of polymerization were 9, 19, and 49, and the composition ratios were 1, 5, and 10mol%, was used as the oligo segment in the hydrogel. The swelling ratio of the hydrogel was investigated under various changes in conditions such as pH, temperature, and hydrogen bonding upon urea addition. Under pH2-11 conditions, the graft gel reversibly swelled and shrank due to the effect of PAGA main chain. The interior morphology and skin layer of the hydrogel was observed by a scanning electron microscope. The hydrogel composed of PAGA as the hydrophilic polymer backbone had a sponge-like structure, with a pore size of approximately 100μm. On the other hand, upon increasing the ratio of trimethylene carbonate (TMC) units in the hydrogel, the pores became smaller or disappeared. Moreover, thickness of the skin layer significantly increased with the swelling ratio depended on the incorporation ratios of the PTMC macromonomer. Molecular incorporation in the hydrogel was evaluated using a dye as a model drug molecule. These features would play an important role in drug loading. Increasing the ratio of TMC units favored the adsorption of the dye and activation of the incorporation behavior. Copyright © 2016 Elsevier B.V. All rights reserved.

Computational study of the fibril organization of polyglutamine repeats reveals a common motif identified in beta-helices.

PubMed

Zanuy, David; Gunasekaran, Kannan; Lesk, Arthur M; Nussinov, Ruth

2006-04-21

The formation of fibril aggregates by long polyglutamine sequences is assumed to play a major role in neurodegenerative diseases such as Huntington. Here, we model peptides rich in glutamine, through a series of molecular dynamics simulations. Starting from a rigid nanotube-like conformation, we have obtained a new conformational template that shares structural features of a tubular helix and of a beta-helix conformational organization. Our new model can be described as a super-helical arrangement of flat beta-sheet segments linked by planar turns or bends. Interestingly, our comprehensive analysis of the Protein Data Bank reveals that this is a common motif in beta-helices (termed beta-bend), although it has not been identified so far. The motif is based on the alternation of beta-sheet and helical conformation as the protein sequence is followed from the N to the C termini (beta-alpha(R)-beta-polyPro-beta). We further identify this motif in the ssNMR structure of the protofibril of the amyloidogenic peptide Abeta(1-40). The recurrence of the beta-bend suggests a general mode of connecting long parallel beta-sheet segments that would allow the growth of partially ordered fibril structures. The design allows the peptide backbone to change direction with a minimal loss of main chain hydrogen bonds. The identification of a coherent organization beyond that of the beta-sheet segments in different folds rich in parallel beta-sheets suggests a higher degree of ordered structure in protein fibrils, in agreement with their low solubility and dense molecular packing.

Designing area optimized application-specific network-on-chip architectures while providing hard QoS guarantees.

PubMed

Khawaja, Sajid Gul; Mushtaq, Mian Hamza; Khan, Shoab A; Akram, M Usman; Jamal, Habib Ullah

2015-01-01

With the increase of transistors' density, popularity of System on Chip (SoC) has increased exponentially. As a communication module for SoC, Network on Chip (NoC) framework has been adapted as its backbone. In this paper, we propose a methodology for designing area-optimized application specific NoC while providing hard Quality of Service (QoS) guarantees for real time flows. The novelty of the proposed system lies in derivation of a Mixed Integer Linear Programming model which is then used to generate a resource optimal Network on Chip (NoC) topology and architecture while considering traffic and QoS requirements. We also present the micro-architectural design features used for enabling traffic and latency guarantees and discuss how the solution adapts for dynamic variations in the application traffic. The paper highlights the effectiveness of proposed method by generating resource efficient NoC solutions for both industrial and benchmark applications. The area-optimized results are generated in few seconds by proposed technique, without resorting to heuristics, even for an application with 48 traffic flows.

Designing Area Optimized Application-Specific Network-On-Chip Architectures while Providing Hard QoS Guarantees

PubMed Central

Khawaja, Sajid Gul; Mushtaq, Mian Hamza; Khan, Shoab A.; Akram, M. Usman; Jamal, Habib ullah

2015-01-01

With the increase of transistors' density, popularity of System on Chip (SoC) has increased exponentially. As a communication module for SoC, Network on Chip (NoC) framework has been adapted as its backbone. In this paper, we propose a methodology for designing area-optimized application specific NoC while providing hard Quality of Service (QoS) guarantees for real time flows. The novelty of the proposed system lies in derivation of a Mixed Integer Linear Programming model which is then used to generate a resource optimal Network on Chip (NoC) topology and architecture while considering traffic and QoS requirements. We also present the micro-architectural design features used for enabling traffic and latency guarantees and discuss how the solution adapts for dynamic variations in the application traffic. The paper highlights the effectiveness of proposed method by generating resource efficient NoC solutions for both industrial and benchmark applications. The area-optimized results are generated in few seconds by proposed technique, without resorting to heuristics, even for an application with 48 traffic flows. PMID:25898016

Optical burst switching based satellite backbone network

NASA Astrophysics Data System (ADS)

Li, Tingting; Guo, Hongxiang; Wang, Cen; Wu, Jian

2018-02-01

We propose a novel time slot based optical burst switching (OBS) architecture for GEO/LEO based satellite backbone network. This architecture can provide high speed data transmission rate and high switching capacity . Furthermore, we design the control plane of this optical satellite backbone network. The software defined network (SDN) and network slice (NS) technologies are introduced. Under the properly designed control mechanism, this backbone network is flexible to support various services with diverse transmission requirements. Additionally, the LEO access and handoff management in this network is also discussed.

Comparing blends and blocks: Synthesis of partially fluorinated diblock polythiophene copolymers to investigate the thermal stability of optical and morphological properties

PubMed Central

Boufflet, Pierre; Wood, Sebastian; Wade, Jessica; Fei, Zhuping; Kim, Ji-Seon

2016-01-01

Summary The microstructure of the active blend layer has been shown to be a critically important factor in the performance of organic solar devices. Block copolymers provide a potentially interesting avenue for controlling this active layer microstructure in solar cell blends. Here we explore the impact of backbone fluorination in block copolymers of poly(3-octyl-4-fluorothiophene)s and poly(3-octylthiophene) (F-P3OT-b-P3OT). Two block co-polymers with varying block lengths were prepared via sequential monomer addition under Kumada catalyst transfer polymerisation (KCTP) conditions. We compare the behavior of the block copolymer to that of the corresponding homopolymer blends. In both types of system, we find the fluorinated segments tend to dominate the UV–visible absorption and molecular vibrational spectral features, as well as the thermal behavior. In the block copolymer case, non-fluorinated segments appear to slightly frustrate the aggregation of the more fluorinated block. However, in situ temperature dependent Raman spectroscopy shows that the intramolecular order is more thermally stable in the block copolymer than in the corresponding blend, suggesting that such materials may be interesting for enhanced thermal stability of organic photovoltaic active layers based on similar systems. PMID:27829922

Nuclear magnetic resonance investigation of dynamics in poly(ethylene oxide)-based lithium polyether-ester-sulfonate ionomers

DOE PAGES

Roach, David J.; Dou, Shichen; Colby, Ralph H.; ...

2012-01-06

Nuclear magnetic resonance (NMR) spectroscopy has been utilized to investigate the dynamics of poly(ethylene oxide)-based lithium sulfonate ionomer samples that have low glass transition temperatures. 1H and 7Li spin-lattice relaxation times (T 1) of the bulk polymer and lithium ions, respectively, were measured and analyzed in samples with a range of ion contents. The temperature dependence of T 1 values along with the presence of minima in T 1 as a function of temperature enabled correlation times and activation energies to be obtained for both the segmental motion of the polymer backbone and the hopping motion of lithium cations. Similarmore » activation energies for motion of both the polymer and lithium ions in the samples with lower ion content indicate that the polymer segmental motion and lithium ion hopping motion are correlated in these samples, even though their respective correlation times differ significantly. A divergent trend is observed for correlation times and activation energies of the highest ion content sample with 100% lithium sulfonation due to the presence of ionic aggregation. Details of the polymer and cation dynamics on the nanosecond timescale are discussed and complement the findings of X-ray scattering and Quasi Elastic Neutron Scattering experiments.« less

Rapid search for tertiary fragments reveals protein sequence–structure relationships

PubMed Central

Zhou, Jianfu; Grigoryan, Gevorg

2015-01-01

Finding backbone substructures from the Protein Data Bank that match an arbitrary query structural motif, composed of multiple disjoint segments, is a problem of growing relevance in structure prediction and protein design. Although numerous protein structure search approaches have been proposed, methods that address this specific task without additional restrictions and on practical time scales are generally lacking. Here, we propose a solution, dubbed MASTER, that is both rapid, enabling searches over the Protein Data Bank in a matter of seconds, and provably correct, finding all matches below a user-specified root-mean-square deviation cutoff. We show that despite the potentially exponential time complexity of the problem, running times in practice are modest even for queries with many segments. The ability to explore naturally plausible structural and sequence variations around a given motif has the potential to synthesize its design principles in an automated manner; so we go on to illustrate the utility of MASTER to protein structural biology. We demonstrate its capacity to rapidly establish structure–sequence relationships, uncover the native designability landscapes of tertiary structural motifs, identify structural signatures of binding, and automatically rewire protein topologies. Given the broad utility of protein tertiary fragment searches, we hope that providing MASTER in an open-source format will enable novel advances in understanding, predicting, and designing protein structure. PMID:25420575

Hippocampal unified multi-atlas network (HUMAN): protocol and scale validation of a novel segmentation tool.

PubMed

Amoroso, N; Errico, R; Bruno, S; Chincarini, A; Garuccio, E; Sensi, F; Tangaro, S; Tateo, A; Bellotti, R

2015-11-21

In this study we present a novel fully automated Hippocampal Unified Multi-Atlas-Networks (HUMAN) algorithm for the segmentation of the hippocampus in structural magnetic resonance imaging. In multi-atlas approaches atlas selection is of crucial importance for the accuracy of the segmentation. Here we present an optimized method based on the definition of a small peri-hippocampal region to target the atlas learning with linear and non-linear embedded manifolds. All atlases were co-registered to a data driven template resulting in a computationally efficient method that requires only one test registration. The optimal atlases identified were used to train dedicated artificial neural networks whose labels were then propagated and fused to obtain the final segmentation. To quantify data heterogeneity and protocol inherent effects, HUMAN was tested on two independent data sets provided by the Alzheimer's Disease Neuroimaging Initiative and the Open Access Series of Imaging Studies. HUMAN is accurate and achieves state-of-the-art performance (Dice[Formula: see text] and Dice[Formula: see text]). It is also a robust method that remains stable when applied to the whole hippocampus or to sub-regions (patches). HUMAN also compares favorably with a basic multi-atlas approach and a benchmark segmentation tool such as FreeSurfer.

Recursive Hierarchical Image Segmentation by Region Growing and Constrained Spectral Clustering

NASA Technical Reports Server (NTRS)

Tilton, James C.

2002-01-01

This paper describes an algorithm for hierarchical image segmentation (referred to as HSEG) and its recursive formulation (referred to as RHSEG). The HSEG algorithm is a hybrid of region growing and constrained spectral clustering that produces a hierarchical set of image segmentations based on detected convergence points. In the main, HSEG employs the hierarchical stepwise optimization (HS WO) approach to region growing, which seeks to produce segmentations that are more optimized than those produced by more classic approaches to region growing. In addition, HSEG optionally interjects between HSWO region growing iterations merges between spatially non-adjacent regions (i.e., spectrally based merging or clustering) constrained by a threshold derived from the previous HSWO region growing iteration. While the addition of constrained spectral clustering improves the segmentation results, especially for larger images, it also significantly increases HSEG's computational requirements. To counteract this, a computationally efficient recursive, divide-and-conquer, implementation of HSEG (RHSEG) has been devised and is described herein. Included in this description is special code that is required to avoid processing artifacts caused by RHSEG s recursive subdivision of the image data. Implementations for single processor and for multiple processor computer systems are described. Results with Landsat TM data are included comparing HSEG with classic region growing. Finally, an application to image information mining and knowledge discovery is discussed.

Adhesion promotion at a homopolymer-solid interface using random heteropolymers

NASA Astrophysics Data System (ADS)

Simmons, Edward Read; Chakraborty, Arup K.

1998-11-01

We investigate the potential uses for random heteropolymers (RHPs) as adhesion promoters between a homopolymer melt and a solid surface. We consider homopolymers of monomer (segment) type A which are naturally repelled from a solid surface. To this system we add RHPs with both A and B (attractive to the surface) type monomers to promote adhesion between the two incompatible substrates. We employ Monte Carlo simulations to investigate the effects of variations in the sequence statistics of the RHPs, amount of promoter added, and strength of the segment-segment and segment-surface interaction parameters. Clearly, the parameter space in such a system is quite large, but we are able to describe, in a qualitative manner, the optimal parameters for adhesion promotion. The optimal set of parameters yield interfacial conformational statistics for the RHPs which have a relatively high adsorbed fraction and also long loops extending away from the surface that promote entanglements with the bulk homopolymer melt. In addition, we present qualitative evidence that the concentration of RHP segments per surface site plays an important role in determining the mechanism of failure (cohesive versus adhesive) at such an interface. Our results also provide the necessary input for future simulations in which the system may be strained to the limit of fracture.

A diabetic retinopathy detection method using an improved pillar K-means algorithm.

PubMed

Gogula, Susmitha Valli; Divakar, Ch; Satyanarayana, Ch; Rao, Allam Appa

2014-01-01

The paper presents a new approach for medical image segmentation. Exudates are a visible sign of diabetic retinopathy that is the major reason of vision loss in patients with diabetes. If the exudates extend into the macular area, blindness may occur. Automated detection of exudates will assist ophthalmologists in early diagnosis. This segmentation process includes a new mechanism for clustering the elements of high-resolution images in order to improve precision and reduce computation time. The system applies K-means clustering to the image segmentation after getting optimized by Pillar algorithm; pillars are constructed in such a way that they can withstand the pressure. Improved pillar algorithm can optimize the K-means clustering for image segmentation in aspects of precision and computation time. This evaluates the proposed approach for image segmentation by comparing with Kmeans and Fuzzy C-means in a medical image. Using this method, identification of dark spot in the retina becomes easier and the proposed algorithm is applied on diabetic retinal images of all stages to identify hard and soft exudates, where the existing pillar K-means is more appropriate for brain MRI images. This proposed system help the doctors to identify the problem in the early stage and can suggest a better drug for preventing further retinal damage.

Hippocampal unified multi-atlas network (HUMAN): protocol and scale validation of a novel segmentation tool

NASA Astrophysics Data System (ADS)

Amoroso, N.; Errico, R.; Bruno, S.; Chincarini, A.; Garuccio, E.; Sensi, F.; Tangaro, S.; Tateo, A.; Bellotti, R.; Alzheimers Disease Neuroimaging Initiative,the

2015-11-01

In this study we present a novel fully automated Hippocampal Unified Multi-Atlas-Networks (HUMAN) algorithm for the segmentation of the hippocampus in structural magnetic resonance imaging. In multi-atlas approaches atlas selection is of crucial importance for the accuracy of the segmentation. Here we present an optimized method based on the definition of a small peri-hippocampal region to target the atlas learning with linear and non-linear embedded manifolds. All atlases were co-registered to a data driven template resulting in a computationally efficient method that requires only one test registration. The optimal atlases identified were used to train dedicated artificial neural networks whose labels were then propagated and fused to obtain the final segmentation. To quantify data heterogeneity and protocol inherent effects, HUMAN was tested on two independent data sets provided by the Alzheimer’s Disease Neuroimaging Initiative and the Open Access Series of Imaging Studies. HUMAN is accurate and achieves state-of-the-art performance (Dice{{}\\text{ADNI}} =0.929+/- 0.003 and Dice{{}\\text{OASIS}} =0.869+/- 0.002 ). It is also a robust method that remains stable when applied to the whole hippocampus or to sub-regions (patches). HUMAN also compares favorably with a basic multi-atlas approach and a benchmark segmentation tool such as FreeSurfer.

Optimal Multiple Surface Segmentation With Shape and Context Priors

PubMed Central

Bai, Junjie; Garvin, Mona K.; Sonka, Milan; Buatti, John M.; Wu, Xiaodong

2014-01-01

Segmentation of multiple surfaces in medical images is a challenging problem, further complicated by the frequent presence of weak boundary evidence, large object deformations, and mutual influence between adjacent objects. This paper reports a novel approach to multi-object segmentation that incorporates both shape and context prior knowledge in a 3-D graph-theoretic framework to help overcome the stated challenges. We employ an arc-based graph representation to incorporate a wide spectrum of prior information through pair-wise energy terms. In particular, a shape-prior term is used to penalize local shape changes and a context-prior term is used to penalize local surface-distance changes from a model of the expected shape and surface distances, respectively. The globally optimal solution for multiple surfaces is obtained by computing a maximum flow in a low-order polynomial time. The proposed method was validated on intraretinal layer segmentation of optical coherence tomography images and demonstrated statistically significant improvement of segmentation accuracy compared to our earlier graph-search method that was not utilizing shape and context priors. The mean unsigned surface positioning errors obtained by the conventional graph-search approach (6.30 ± 1.58 μm) was improved to 5.14 ± 0.99 μm when employing our new method with shape and context priors. PMID:23193309

[A graph cuts-based interactive method for segmentation of magnetic resonance images of meningioma].

PubMed

Li, Shuan-qiang; Feng, Qian-jin; Chen, Wu-fan; Lin, Ya-zhong

2011-06-01

For accurate segmentation of the magnetic resonance (MR) images of meningioma, we propose a novel interactive segmentation method based on graph cuts. The high dimensional image features was extracted, and for each pixel, the probabilities of its origin, either the tumor or the background regions, were estimated by exploiting the weighted K-nearest neighborhood classifier. Based on these probabilities, a new energy function was proposed. Finally, a graph cut optimal framework was used for the solution of the energy function. The proposed method was evaluated by application in the segmentation of MR images of meningioma, and the results showed that the method significantly improved the segmentation accuracy compared with the gray level information-based graph cut method.

[Tumor segmentation of brain MRI with adaptive bandwidth mean shift].

PubMed

Hou, Xiaowen; Liu, Qi

2014-10-01

In order to get the adaptive bandwidth of mean shift to make the tumor segmentation of brain magnetic resonance imaging (MRI) to be more accurate, we in this paper present an advanced mean shift method. Firstly, we made use of the space characteristics of brain image to eliminate the impact on segmentation of skull; and then, based on the characteristics of spatial agglomeration of different tissues of brain (includes tumor), we applied edge points to get the optimal initial mean value and the respectively adaptive bandwidth, in order to improve the accuracy of tumor segmentation. The results of experiment showed that, contrast to the fixed bandwidth mean shift method, the method in this paper could segment the tumor more accurately.

Use of C-Arm Cone Beam CT During Hepatic Radioembolization: Protocol Optimization for Extrahepatic Shunting and Parenchymal Enhancement

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

Hoven, Andor F. van den, E-mail: a.f.vandenhoven@umcutrecht.nl; Prince, Jip F.; Keizer, Bart de

PurposeTo optimize a C-arm computed tomography (CT) protocol for radioembolization (RE), specifically for extrahepatic shunting and parenchymal enhancement.Materials and MethodsA prospective development study was performed per IDEAL recommendations. A literature-based protocol was applied in patients with unresectable and chemorefractory liver malignancies undergoing an angiography before radioembolization. Contrast and scan settings were adjusted stepwise and repeatedly reviewed in a consensus meeting. Afterwards, two independent raters analyzed all scans. A third rater evaluated the SPECT/CT scans as a reference standard for extrahepatic shunting and lack of target segment perfusion.ResultsFifty scans were obtained in 29 procedures. The first protocol, using a 6 s delaymore » and 10 s scan, showed insufficient parenchymal enhancement. In the second protocol, the delay was determined by timing parenchymal enhancement on DSA power injection (median 8 s, range 4–10 s): enhancement improved, but breathing artifacts increased (from 0 to 27 %). Since the third protocol with a 5 s scan decremented subjective image quality, the second protocol was deemed optimal. Median CNR (range) was 1.7 (0.6–3.2), 2.2 (−1.4–4.0), and 2.1 (−0.3–3.0) for protocol 1, 2, and 3 (p = 0.80). Delineation of perfused segments was possible in 57, 73, and 44 % of scans (p = 0.13). In all C-arm CTs combined, the negative predictive value was 95 % for extrahepatic shunting and 83 % for lack of target segment perfusion.ConclusionAn optimized C-arm CT protocol was developed that can be used to detect extrahepatic shunts and non-perfusion of target segments during RE.« less

Motional timescale predictions by molecular dynamics simulations: case study using proline and hydroxyproline sidechain dynamics.

PubMed

Aliev, Abil E; Kulke, Martin; Khaneja, Harmeet S; Chudasama, Vijay; Sheppard, Tom D; Lanigan, Rachel M

2014-02-01

We propose a new approach for force field optimizations which aims at reproducing dynamics characteristics using biomolecular MD simulations, in addition to improved prediction of motionally averaged structural properties available from experiment. As the source of experimental data for dynamics fittings, we use (13) C NMR spin-lattice relaxation times T1 of backbone and sidechain carbons, which allow to determine correlation times of both overall molecular and intramolecular motions. For structural fittings, we use motionally averaged experimental values of NMR J couplings. The proline residue and its derivative 4-hydroxyproline with relatively simple cyclic structure and sidechain dynamics were chosen for the assessment of the new approach in this work. Initially, grid search and simplexed MD simulations identified large number of parameter sets which fit equally well experimental J couplings. Using the Arrhenius-type relationship between the force constant and the correlation time, the available MD data for a series of parameter sets were analyzed to predict the value of the force constant that best reproduces experimental timescale of the sidechain dynamics. Verification of the new force-field (termed as AMBER99SB-ILDNP) against NMR J couplings and correlation times showed consistent and significant improvements compared to the original force field in reproducing both structural and dynamics properties. The results suggest that matching experimental timescales of motions together with motionally averaged characteristics is the valid approach for force field parameter optimization. Such a comprehensive approach is not restricted to cyclic residues and can be extended to other amino acid residues, as well as to the backbone. Copyright © 2013 Wiley Periodicals, Inc.

Analysis of a Segmented Annular Coplanar Capacitive Tilt Sensor with Increased Sensitivity.

PubMed

Guo, Jiahao; Hu, Pengcheng; Tan, Jiubin

2016-01-21

An investigation of a segmented annular coplanar capacitor is presented. We focus on its theoretical model, and a mathematical expression of the capacitance value is derived by solving a Laplace equation with Hankel transform. The finite element method is employed to verify the analytical result. Different control parameters are discussed, and each contribution to the capacitance value of the capacitor is obtained. On this basis, we analyze and optimize the structure parameters of a segmented coplanar capacitive tilt sensor, and three models with different positions of the electrode gap are fabricated and tested. The experimental result shows that the model (whose electrode-gap position is 10 mm from the electrode center) realizes a high sensitivity: 0.129 pF/° with a non-linearity of <0.4% FS (full scale of ± 40°). This finding offers plenty of opportunities for various measurement requirements in addition to achieving an optimized structure in practical design.

pi-Turns: types, systematics and the context of their occurrence in protein structures

PubMed Central

Dasgupta, Bhaskar; Chakrabarti, Pinak

2008-01-01

Background For a proper understanding of protein structure and folding it is important to know if a polypeptide segment adopts a conformation inherent in the sequence or it depends on the context of its flanking secondary structures. Turns of various lengths have been studied and characterized starting from three-residue γ-turn to six-residue π-turn. The Schellman motif occurring at the C-terminal end of α-helices is a classical example of hydrogen bonded π-turn involving residues at (i) and (i+5) positions. Hydrogen bonded and non-hydrogen bonded β- and α-turns have been identified previously; likewise, a systematic characterization of π-turns would provide valuable insight into turn structures. Results An analysis of protein structures indicates that at least 20% of π-turns occur independent of the Schellman motif. The two categories of π-turns, designated as π-HB and SCH, have been further classified on the basis of backbone conformation and both have AAAa as the major class. They differ in the residue usage at position (i+1), the former having a large preference for Pro that is absent in the latter. As in the case of shorter length β- and α-turns, π-turns have also been identified not only on the basis of the existence of hydrogen bond, but also using the distance between terminal Cα-atoms, and this resulted in a comparable number of non-hydrogen-bonded π-turns (π-NHB). The presence of shorter β- and α-turns within all categories of π-turns, the subtle variations in backbone torsion angles along the turn residues, the location of the turns in the context of tertiary structures have been studied. Conclusion π-turns have been characterized, first using hydrogen bond and the distance between Cα atoms of the terminal residues, and then using backbone torsion angles. While the Schellman motif has a structural role in helix termination, many of the π-HB turns, being located on surface cavities, have functional role and there is also sequence conservation. PMID:18808671

pi-Turns: types, systematics and the context of their occurrence in protein structures.

PubMed

Dasgupta, Bhaskar; Chakrabarti, Pinak

2008-09-22

For a proper understanding of protein structure and folding it is important to know if a polypeptide segment adopts a conformation inherent in the sequence or it depends on the context of its flanking secondary structures. Turns of various lengths have been studied and characterized starting from three-residue gamma-turn to six-residue pi-turn. The Schellman motif occurring at the C-terminal end of alpha-helices is a classical example of hydrogen bonded pi-turn involving residues at (i) and (i+5) positions. Hydrogen bonded and non-hydrogen bonded beta- and alpha-turns have been identified previously; likewise, a systematic characterization of pi-turns would provide valuable insight into turn structures. An analysis of protein structures indicates that at least 20% of pi-turns occur independent of the Schellman motif. The two categories of pi-turns, designated as pi-HB and SCH, have been further classified on the basis of backbone conformation and both have AAAa as the major class. They differ in the residue usage at position (i+1), the former having a large preference for Pro that is absent in the latter. As in the case of shorter length beta- and alpha-turns, pi-turns have also been identified not only on the basis of the existence of hydrogen bond, but also using the distance between terminal C alpha-atoms, and this resulted in a comparable number of non-hydrogen-bonded pi-turns (pi-NHB). The presence of shorter beta- and alpha-turns within all categories of pi-turns, the subtle variations in backbone torsion angles along the turn residues, the location of the turns in the context of tertiary structures have been studied. pi-turns have been characterized, first using hydrogen bond and the distance between C alpha atoms of the terminal residues, and then using backbone torsion angles. While the Schellman motif has a structural role in helix termination, many of the pi-HB turns, being located on surface cavities, have functional role and there is also sequence conservation.

Multiscale 3-D shape representation and segmentation using spherical wavelets.

PubMed

Nain, Delphine; Haker, Steven; Bobick, Aaron; Tannenbaum, Allen

2007-04-01

This paper presents a novel multiscale shape representation and segmentation algorithm based on the spherical wavelet transform. This work is motivated by the need to compactly and accurately encode variations at multiple scales in the shape representation in order to drive the segmentation and shape analysis of deep brain structures, such as the caudate nucleus or the hippocampus. Our proposed shape representation can be optimized to compactly encode shape variations in a population at the needed scale and spatial locations, enabling the construction of more descriptive, nonglobal, nonuniform shape probability priors to be included in the segmentation and shape analysis framework. In particular, this representation addresses the shortcomings of techniques that learn a global shape prior at a single scale of analysis and cannot represent fine, local variations in a population of shapes in the presence of a limited dataset. Specifically, our technique defines a multiscale parametric model of surfaces belonging to the same population using a compact set of spherical wavelets targeted to that population. We further refine the shape representation by separating into groups wavelet coefficients that describe independent global and/or local biological variations in the population, using spectral graph partitioning. We then learn a prior probability distribution induced over each group to explicitly encode these variations at different scales and spatial locations. Based on this representation, we derive a parametric active surface evolution using the multiscale prior coefficients as parameters for our optimization procedure to naturally include the prior for segmentation. Additionally, the optimization method can be applied in a coarse-to-fine manner. We apply our algorithm to two different brain structures, the caudate nucleus and the hippocampus, of interest in the study of schizophrenia. We show: 1) a reconstruction task of a test set to validate the expressiveness of our multiscale prior and 2) a segmentation task. In the reconstruction task, our results show that for a given training set size, our algorithm significantly improves the approximation of shapes in a testing set over the Point Distribution Model, which tends to oversmooth data. In the segmentation task, our validation shows our algorithm is computationally efficient and outperforms the Active Shape Model algorithm, by capturing finer shape details.

Multiscale 3-D Shape Representation and Segmentation Using Spherical Wavelets

PubMed Central

Nain, Delphine; Haker, Steven; Bobick, Aaron

2013-01-01

This paper presents a novel multiscale shape representation and segmentation algorithm based on the spherical wavelet transform. This work is motivated by the need to compactly and accurately encode variations at multiple scales in the shape representation in order to drive the segmentation and shape analysis of deep brain structures, such as the caudate nucleus or the hippocampus. Our proposed shape representation can be optimized to compactly encode shape variations in a population at the needed scale and spatial locations, enabling the construction of more descriptive, nonglobal, nonuniform shape probability priors to be included in the segmentation and shape analysis framework. In particular, this representation addresses the shortcomings of techniques that learn a global shape prior at a single scale of analysis and cannot represent fine, local variations in a population of shapes in the presence of a limited dataset. Specifically, our technique defines a multiscale parametric model of surfaces belonging to the same population using a compact set of spherical wavelets targeted to that population. We further refine the shape representation by separating into groups wavelet coefficients that describe independent global and/or local biological variations in the population, using spectral graph partitioning. We then learn a prior probability distribution induced over each group to explicitly encode these variations at different scales and spatial locations. Based on this representation, we derive a parametric active surface evolution using the multiscale prior coefficients as parameters for our optimization procedure to naturally include the prior for segmentation. Additionally, the optimization method can be applied in a coarse-to-fine manner. We apply our algorithm to two different brain structures, the caudate nucleus and the hippocampus, of interest in the study of schizophrenia. We show: 1) a reconstruction task of a test set to validate the expressiveness of our multiscale prior and 2) a segmentation task. In the reconstruction task, our results show that for a given training set size, our algorithm significantly improves the approximation of shapes in a testing set over the Point Distribution Model, which tends to oversmooth data. In the segmentation task, our validation shows our algorithm is computationally efficient and outperforms the Active Shape Model algorithm, by capturing finer shape details. PMID:17427745

Generation of a mixture model ground-motion prediction equation for Northern Chile

NASA Astrophysics Data System (ADS)

Haendel, A.; Kuehn, N. M.; Scherbaum, F.

2012-12-01

In probabilistic seismic hazard analysis (PSHA) empirically derived ground motion prediction equations (GMPEs) are usually applied to estimate the ground motion at a site of interest as a function of source, path and site related predictor variables. Because GMPEs are derived from limited datasets they are not expected to give entirely accurate estimates or to reflect the whole range of possible future ground motion, thus giving rise to epistemic uncertainty in the hazard estimates. This is especially true for regions without an indigenous GMPE where foreign models have to be applied. The choice of appropriate GMPEs can then dominate the overall uncertainty in hazard assessments. In order to quantify this uncertainty, the set of ground motion models used in a modern PSHA has to capture (in SSHAC language) the center, body, and range of the possible ground motion at the site of interest. This was traditionally done within a logic tree framework in which existing (or only slightly modified) GMPEs occupy the branches of the tree and the branch weights describe the degree-of-belief of the analyst in their applicability. This approach invites the problem to combine GMPEs of very different quality and hence to potentially overestimate epistemic uncertainty. Some recent hazard analysis have therefore resorted to using a small number of high quality GMPEs as backbone models from which the full distribution of GMPEs for the logic tree (to capture the full range of possible ground motion uncertainty) where subsequently generated by scaling (in a general sense). In the present study, a new approach is proposed to determine an optimized backbone model as weighted components of a mixture model. In doing so, each GMPE is assumed to reflect the generation mechanism (e. g. in terms of stress drop, propagation properties, etc.) for at least a fraction of possible ground motions in the area of interest. The combination of different models into a mixture model (which is learned from observed ground motion data in the region of interest) is then transferring information from other regions to the region where the observations have been produced in a data driven way. The backbone model is learned by comparing the model predictions to observations of the target region. For each observation and each model, the likelihood of an observation given a certain GMPE is calculated. Mixture weights can then be assigned using the expectation maximization (EM) algorithm or Bayesian inference. The new method is used to generate a backbone reference model for Northern Chile, an area for which no dedicated GMPE exists. Strong motion recordings from the target area are used to learn the backbone model from a set of 10 GMPEs developed for different subduction zones of the world. The formation of mixture models is done individually for interface and intraslab type events. The ability of the resulting backbone models to describe ground motions in Northern Chile is then compared to the predictive performance of their constituent models.

Denoising and segmentation of retinal layers in optical coherence tomography images

NASA Astrophysics Data System (ADS)

Dash, Puspita; Sigappi, A. N.

2018-04-01

Optical Coherence Tomography (OCT) is an imaging technique used to localize the intra-retinal boundaries for the diagnostics of macular diseases. Due to speckle noise, low image contrast and accurate segmentation of individual retinal layers is difficult. Due to this, a method for retinal layer segmentation from OCT images is presented. This paper proposes a pre-processing filtering approach for denoising and segmentation methods for segmenting retinal layers OCT images using graph based segmentation technique. These techniques are used for segmentation of retinal layers for normal as well as patients with Diabetic Macular Edema. The algorithm based on gradient information and shortest path search is applied to optimize the edge selection. In this paper the four main layers of the retina are segmented namely Internal limiting membrane (ILM), Retinal pigment epithelium (RPE), Inner nuclear layer (INL) and Outer nuclear layer (ONL). The proposed method is applied on a database of OCT images of both ten normal and twenty DME affected patients and the results are found to be promising.

Using multimodal information for the segmentation of fluorescent micrographs with application to virology and microbiology.

PubMed

Held, Christian; Wenzel, Jens; Webel, Rike; Marschall, Manfred; Lang, Roland; Palmisano, Ralf; Wittenberg, Thomas

2011-01-01

In order to improve reproducibility and objectivity of fluorescence microscopy based experiments and to enable the evaluation of large datasets, flexible segmentation methods are required which are able to adapt to different stainings and cell types. This adaption is usually achieved by the manual adjustment of the segmentation methods parameters, which is time consuming and challenging for biologists with no knowledge on image processing. To avoid this, parameters of the presented methods automatically adapt to user generated ground truth to determine the best method and the optimal parameter setup. These settings can then be used for segmentation of the remaining images. As robust segmentation methods form the core of such a system, the currently used watershed transform based segmentation routine is replaced by a fast marching level set based segmentation routine which incorporates knowledge on the cell nuclei. Our evaluations reveal that incorporation of multimodal information improves segmentation quality for the presented fluorescent datasets.

Paroxysmal atrial fibrillation prediction method with shorter HRV sequences.

PubMed

Boon, K H; Khalil-Hani, M; Malarvili, M B; Sia, C W

2016-10-01

This paper proposes a method that predicts the onset of paroxysmal atrial fibrillation (PAF), using heart rate variability (HRV) segments that are shorter than those applied in existing methods, while maintaining good prediction accuracy. PAF is a common cardiac arrhythmia that increases the health risk of a patient, and the development of an accurate predictor of the onset of PAF is clinical important because it increases the possibility to stabilize (electrically) and prevent the onset of atrial arrhythmias with different pacing techniques. We investigate the effect of HRV features extracted from different lengths of HRV segments prior to PAF onset with the proposed PAF prediction method. The pre-processing stage of the predictor includes QRS detection, HRV quantification and ectopic beat correction. Time-domain, frequency-domain, non-linear and bispectrum features are then extracted from the quantified HRV. In the feature selection, the HRV feature set and classifier parameters are optimized simultaneously using an optimization procedure based on genetic algorithm (GA). Both full feature set and statistically significant feature subset are optimized by GA respectively. For the statistically significant feature subset, Mann-Whitney U test is used to filter non-statistical significance features that cannot pass the statistical test at 20% significant level. The final stage of our predictor is the classifier that is based on support vector machine (SVM). A 10-fold cross-validation is applied in performance evaluation, and the proposed method achieves 79.3% prediction accuracy using 15-minutes HRV segment. This accuracy is comparable to that achieved by existing methods that use 30-minutes HRV segments, most of which achieves accuracy of around 80%. More importantly, our method significantly outperforms those that applied segments shorter than 30 minutes. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Need for denser geodetic network to get real constrain on the fault behavior along the Main Marmara Sea segments of the NAF, toward an optimized GPS network.

NASA Astrophysics Data System (ADS)

Klein, E.; Masson, F.; Duputel, Z.; Yavasoglu, H.; Agram, P. S.

2016-12-01

Over the last two decades, the densification of GPS networks and the development of new radar satellites offered an unprecedented opportunity to study crustal deformation due to faulting. Yet, submarine strike slip fault segments remain a major issue, especially when the landscape appears unfavorable to the use of SAR measurements. It is the case of the North Anatolian fault segments located in the Main Marmara Sea, that remain unbroken ever since the Mw7.4 earthquake of Izmit in 1999, which ended a eastward migrating seismic sequence of Mw > 7 earthquakes. Located directly offshore Istanbul, evaluation of seismic hazard appears capital. But a strong controversy remains over whether these segments are accumulating strain and are likely to experience a major earthquake, or are creeping, resulting both from the simplicity of current geodetic models and the scarcity of geodetic data. We indeed show that 2D infinite fault models cannot account for the complexity of the Marmara fault segments. But current geodetic data in the western region of Istanbul are also insufficient to invert for the coupling using a 3D geometry of the fault. Therefore, we implement a global optimization procedure aiming at identifying the most favorable distribution of GPS stations to explore the strain accumulation. We present here the results of this procedure that allows to determine both the optimal number and location of the new stations. We show that a denser terrestrial survey network can indeed locally improve the resolution on the shallower part of the fault, even more efficiently with permanent stations. But data closer from the fault, only possible by submarine measurements, remain necessary to properly constrain the fault behavior and its potential along strike coupling variations.

Segmentation of discrete vector fields.

PubMed

Li, Hongyu; Chen, Wenbin; Shen, I-Fan

2006-01-01

In this paper, we propose an approach for 2D discrete vector field segmentation based on the Green function and normalized cut. The method is inspired by discrete Hodge Decomposition such that a discrete vector field can be broken down into three simpler components, namely, curl-free, divergence-free, and harmonic components. We show that the Green Function Method (GFM) can be used to approximate the curl-free and the divergence-free components to achieve our goal of the vector field segmentation. The final segmentation curves that represent the boundaries of the influence region of singularities are obtained from the optimal vector field segmentations. These curves are composed of piecewise smooth contours or streamlines. Our method is applicable to both linear and nonlinear discrete vector fields. Experiments show that the segmentations obtained using our approach essentially agree with human perceptual judgement.

Temporally consistent segmentation of point clouds

NASA Astrophysics Data System (ADS)

Owens, Jason L.; Osteen, Philip R.; Daniilidis, Kostas

2014-06-01

We consider the problem of generating temporally consistent point cloud segmentations from streaming RGB-D data, where every incoming frame extends existing labels to new points or contributes new labels while maintaining the labels for pre-existing segments. Our approach generates an over-segmentation based on voxel cloud connectivity, where a modified k-means algorithm selects supervoxel seeds and associates similar neighboring voxels to form segments. Given the data stream from a potentially mobile sensor, we solve for the camera transformation between consecutive frames using a joint optimization over point correspondences and image appearance. The aligned point cloud may then be integrated into a consistent model coordinate frame. Previously labeled points are used to mask incoming points from the new frame, while new and previous boundary points extend the existing segmentation. We evaluate the algorithm on newly-generated RGB-D datasets.

Marked Consequences of Systematic Oligothiophene Catenation in Thieno[3,4-c]pyrrole-4,6-dione and Bithiopheneimide Photovoltaic Copolymers

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

Zhou, Nanjia; Guo, Xugang; Ponce Ortiz, Rocio

As effective building blocks for high-mobility transistor polymers, oligothiophenes are receiving attention for polymer solar cells (PSCs) because the resulting polymers can effectively suppress charge recombination. Here we investigate two series of in-chain donor-acceptor copolymers, PTPDnT and PBTInT, based on thieno[3,4-c]pyrrole-4,6-dione (TPD) or bithiopheneimide (BTI) as electron acceptor units, respectively, and oligothiophenes (nTs) as donor counits, for high-performance PSCs. Intramolecular S···O interaction leads to more planar TPD polymer backbones, however backbone torsion yields greater open-circuit voltages for BTI polymers. Thiophene addition progressively raises polymer HOMOs but marginally affects their band gaps. FT-Raman spectra indicate that PTPDnT and PBTInT conjugation lengthsmore » scale with nT catenation up to n = 3 and then saturate for longer oligomer. Furthermore, the effects of oligothiophene alkylation position are explored, revealing that the alkylation pattern greatly affects film morphology and PSC performance. The 3T with “outward” alkylation in PTPD3T and PBTI3T affords optimal π-conjugation, close stacking, long-range order, and high hole mobilities (0.1 cm 2/(V s)). These characteristics contribute to the exceptional ~80% fill factors for PTPD3T-based PSCs with PCE = 7.7%. The results demonstrate that 3T is the optimal donor unit among nTs (n = 1-4) for photovoltaic polymers. Grazing incidence wide-angle X-ray scattering, transmission electron microscopy, and time-resolved microwave conductivity measurements reveal that the terthiophene-based PTPD3T blend maintains high crystallinity with appreciable local mobility and long charge carrier lifetime. These results provide fundamental materials structure-device performance correlations and suggest guidelines for designing oligothiophene-based polymers with optimal thiophene catenation and appropriate alkylation pattern to maximize PSC performance.« less

Partitioned-Interval Quantum Optical Communications Receiver

NASA Technical Reports Server (NTRS)

Vilnrotter, Victor A.

2013-01-01

The proposed quantum receiver in this innovation partitions each binary signal interval into two unequal segments: a short "pre-measurement" segment in the beginning of the symbol interval used to make an initial guess with better probability than 50/50 guessing, and a much longer segment used to make the high-sensitivity signal detection via field-cancellation and photon-counting detection. It was found that by assigning as little as 10% of the total signal energy to the pre-measurement segment, the initial 50/50 guess can be improved to about 70/30, using the best available measurements such as classical coherent or "optimized Kennedy" detection.

Integration of safety engineering into a cost optimized development program.

NASA Technical Reports Server (NTRS)

Ball, L. W.

1972-01-01

A six-segment management model is presented, each segment of which represents a major area in a new product development program. The first segment of the model covers integration of specialist engineers into 'systems requirement definition' or the system engineering documentation process. The second covers preparation of five basic types of 'development program plans.' The third segment covers integration of system requirements, scheduling, and funding of specialist engineering activities into 'work breakdown structures,' 'cost accounts,' and 'work packages.' The fourth covers 'requirement communication' by line organizations. The fifth covers 'performance measurement' based on work package data. The sixth covers 'baseline requirements achievement tracking.'

End-to-End Assessment of a Large Aperture Segmented Ultraviolet Optical Infrared (UVOIR) Telescope Architecture

NASA Technical Reports Server (NTRS)

Feinberg, Lee; Bolcar, Matt; Liu, Alice; Guyon, Olivier; Stark,Chris; Arenberg, Jon

2016-01-01

Key challenges of a future large aperture, segmented Ultraviolet Optical Infrared (UVOIR) Telescope capable of performing a spectroscopic survey of hundreds of Exoplanets will be sufficient stability to achieve 10-10 contrast measurements and sufficient throughput and sensitivity for high yield Exo-Earth spectroscopic detection. Our team has collectively assessed an optimized end to end architecture including a high throughput coronagraph capable of working with a segmented telescope, a cost-effective and heritage based stable segmented telescope, a control architecture that minimizes the amount of new technologies, and an Exo-Earth yield assessment to evaluate potential performance.

Inverse-optimized 3D conformal planning: Minimizing complexity while achieving equivalence with beamlet IMRT in multiple clinical sites

PubMed Central

Fraass, Benedick A.; Steers, Jennifer M.; Matuszak, Martha M.; McShan, Daniel L.

2012-01-01

Purpose: Inverse planned intensity modulated radiation therapy (IMRT) has helped many centers implement highly conformal treatment planning with beamlet-based techniques. The many comparisons between IMRT and 3D conformal (3DCRT) plans, however, have been limited because most 3DCRT plans are forward-planned while IMRT plans utilize inverse planning, meaning both optimization and delivery techniques are different. This work avoids that problem by comparing 3D plans generated with a unique inverse planning method for 3DCRT called inverse-optimized 3D (IO-3D) conformal planning. Since IO-3D and the beamlet IMRT to which it is compared use the same optimization techniques, cost functions, and plan evaluation tools, direct comparisons between IMRT and simple, optimized IO-3D plans are possible. Though IO-3D has some similarity to direct aperture optimization (DAO), since it directly optimizes the apertures used, IO-3D is specifically designed for 3DCRT fields (i.e., 1–2 apertures per beam) rather than starting with IMRT-like modulation and then optimizing aperture shapes. The two algorithms are very different in design, implementation, and use. The goals of this work include using IO-3D to evaluate how close simple but optimized IO-3D plans come to nonconstrained beamlet IMRT, showing that optimization, rather than modulation, may be the most important aspect of IMRT (for some sites). Methods: The IO-3D dose calculation and optimization functionality is integrated in the in-house 3D planning/optimization system. New features include random point dose calculation distributions, costlet and cost function capabilities, fast dose volume histogram (DVH) and plan evaluation tools, optimization search strategies designed for IO-3D, and an improved, reimplemented edge/octree calculation algorithm. The IO-3D optimization, in distinction to DAO, is designed to optimize 3D conformal plans (one to two segments per beam) and optimizes MLC segment shapes and weights with various user-controllable search strategies which optimize plans without beamlet or pencil beam approximations. IO-3D allows comparisons of beamlet, multisegment, and conformal plans optimized using the same cost functions, dose points, and plan evaluation metrics, so quantitative comparisons are straightforward. Here, comparisons of IO-3D and beamlet IMRT techniques are presented for breast, brain, liver, and lung plans. Results: IO-3D achieves high quality results comparable to beamlet IMRT, for many situations. Though the IO-3D plans have many fewer degrees of freedom for the optimization, this work finds that IO-3D plans with only one to two segments per beam are dosimetrically equivalent (or nearly so) to the beamlet IMRT plans, for several sites. IO-3D also reduces plan complexity significantly. Here, monitor units per fraction (MU/Fx) for IO-3D plans were 22%–68% less than that for the 1 cm × 1 cm beamlet IMRT plans and 72%–84% than the 0.5 cm × 0.5 cm beamlet IMRT plans. Conclusions: The unique IO-3D algorithm illustrates that inverse planning can achieve high quality 3D conformal plans equivalent (or nearly so) to unconstrained beamlet IMRT plans, for many sites. IO-3D thus provides the potential to optimize flat or few-segment 3DCRT plans, creating less complex optimized plans which are efficient and simple to deliver. The less complex IO-3D plans have operational advantages for scenarios including adaptive replanning, cases with interfraction and intrafraction motion, and pediatric patients. PMID:22755717

An Optimal CDS Construction Algorithm with Activity Scheduling in Ad Hoc Networks

PubMed Central

Penumalli, Chakradhar; Palanichamy, Yogesh

2015-01-01

A new energy efficient optimal Connected Dominating Set (CDS) algorithm with activity scheduling for mobile ad hoc networks (MANETs) is proposed. This algorithm achieves energy efficiency by minimizing the Broadcast Storm Problem [BSP] and at the same time considering the node's remaining energy. The Connected Dominating Set is widely used as a virtual backbone or spine in mobile ad hoc networks [MANETs] or Wireless Sensor Networks [WSN]. The CDS of a graph representing a network has a significant impact on an efficient design of routing protocol in wireless networks. Here the CDS is a distributed algorithm with activity scheduling based on unit disk graph [UDG]. The node's mobility and residual energy (RE) are considered as parameters in the construction of stable optimal energy efficient CDS. The performance is evaluated at various node densities, various transmission ranges, and mobility rates. The theoretical analysis and simulation results of this algorithm are also presented which yield better results. PMID:26221627

Optimizing the 3D-reconstruction technique for serial block-face scanning electron microscopy.

PubMed

Wernitznig, Stefan; Sele, Mariella; Urschler, Martin; Zankel, Armin; Pölt, Peter; Rind, F Claire; Leitinger, Gerd

2016-05-01

Elucidating the anatomy of neuronal circuits and localizing the synaptic connections between neurons, can give us important insights in how the neuronal circuits work. We are using serial block-face scanning electron microscopy (SBEM) to investigate the anatomy of a collision detection circuit including the Lobula Giant Movement Detector (LGMD) neuron in the locust, Locusta migratoria. For this, thousands of serial electron micrographs are produced that allow us to trace the neuronal branching pattern. The reconstruction of neurons was previously done manually by drawing cell outlines of each cell in each image separately. This approach was very time consuming and troublesome. To make the process more efficient a new interactive software was developed. It uses the contrast between the neuron under investigation and its surrounding for semi-automatic segmentation. For segmentation the user sets starting regions manually and the algorithm automatically selects a volume within the neuron until the edges corresponding to the neuronal outline are reached. Internally the algorithm optimizes a 3D active contour segmentation model formulated as a cost function taking the SEM image edges into account. This reduced the reconstruction time, while staying close to the manual reference segmentation result. Our algorithm is easy to use for a fast segmentation process, unlike previous methods it does not require image training nor an extended computing capacity. Our semi-automatic segmentation algorithm led to a dramatic reduction in processing time for the 3D-reconstruction of identified neurons. Copyright © 2016 Elsevier B.V. All rights reserved.

An Efficient, Hierarchical Viewpoint Planning Strategy for Terrestrial Laser Scanner Networks

NASA Astrophysics Data System (ADS)

Jia, F.; Lichti, D. D.

2018-05-01

Terrestrial laser scanner (TLS) techniques have been widely adopted in a variety of applications. However, unlike in geodesy or photogrammetry, insufficient attention has been paid to the optimal TLS network design. It is valuable to develop a complete design system that can automatically provide an optimal plan, especially for high-accuracy, large-volume scanning networks. To achieve this goal, one should look at the "optimality" of the solution as well as the computational complexity in reaching it. In this paper, a hierarchical TLS viewpoint planning strategy is developed to solve the optimal scanner placement problems. If one targeted object to be scanned is simplified as discretized wall segments, any possible viewpoint can be evaluated by a score table representing its visible segments under certain scanning geometry constraints. Thus, the design goal is to find a minimum number of viewpoints that achieves complete coverage of all wall segments. The efficiency is improved by densifying viewpoints hierarchically, instead of a "brute force" search within the entire workspace. The experiment environments in this paper were simulated from two buildings located on University of Calgary campus. Compared with the "brute force" strategy in terms of the quality of the solutions and the runtime, it is shown that the proposed strategy can provide a scanning network with a compatible quality but with more than a 70 % time saving.

RFA-cut: Semi-automatic segmentation of radiofrequency ablation zones with and without needles via optimal s-t-cuts.

PubMed

Egger, Jan; Busse, Harald; Brandmaier, Philipp; Seider, Daniel; Gawlitza, Matthias; Strocka, Steffen; Voglreiter, Philip; Dokter, Mark; Hofmann, Michael; Kainz, Bernhard; Chen, Xiaojun; Hann, Alexander; Boechat, Pedro; Yu, Wei; Freisleben, Bernd; Alhonnoro, Tuomas; Pollari, Mika; Moche, Michael; Schmalstieg, Dieter

2015-01-01

In this contribution, we present a semi-automatic segmentation algorithm for radiofrequency ablation (RFA) zones via optimal s-t-cuts. Our interactive graph-based approach builds upon a polyhedron to construct the graph and was specifically designed for computed tomography (CT) acquisitions from patients that had RFA treatments of Hepatocellular Carcinomas (HCC). For evaluation, we used twelve post-interventional CT datasets from the clinical routine and as evaluation metric we utilized the Dice Similarity Coefficient (DSC), which is commonly accepted for judging computer aided medical segmentation tasks. Compared with pure manual slice-by-slice expert segmentations from interventional radiologists, we were able to achieve a DSC of about eighty percent, which is sufficient for our clinical needs. Moreover, our approach was able to handle images containing (DSC=75.9%) and not containing (78.1%) the RFA needles still in place. Additionally, we found no statistically significant difference (p<;0.423) between the segmentation results of the subgroups for a Mann-Whitney test. Finally, to the best of our knowledge, this is the first time a segmentation approach for CT scans including the RFA needles is reported and we show why another state-of-the-art segmentation method fails for these cases. Intraoperative scans including an RFA probe are very critical in the clinical practice and need a very careful segmentation and inspection to avoid under-treatment, which may result in tumor recurrence (up to 40%). If the decision can be made during the intervention, an additional ablation can be performed without removing the entire needle. This decreases the patient stress and associated risks and costs of a separate intervention at a later date. Ultimately, the segmented ablation zone containing the RFA needle can be used for a precise ablation simulation as the real needle position is known.

Robustness analysis of superpixel algorithms to image blur, additive Gaussian noise, and impulse noise

NASA Astrophysics Data System (ADS)

Brekhna, Brekhna; Mahmood, Arif; Zhou, Yuanfeng; Zhang, Caiming

2017-11-01

Superpixels have gradually become popular in computer vision and image processing applications. However, no comprehensive study has been performed to evaluate the robustness of superpixel algorithms in regard to common forms of noise in natural images. We evaluated the robustness of 11 recently proposed algorithms to different types of noise. The images were corrupted with various degrees of Gaussian blur, additive white Gaussian noise, and impulse noise that either made the object boundaries weak or added extra information to it. We performed a robustness analysis of simple linear iterative clustering (SLIC), Voronoi Cells (VCells), flooding-based superpixel generation (FCCS), bilateral geodesic distance (Bilateral-G), superpixel via geodesic distance (SSS-G), manifold SLIC (M-SLIC), Turbopixels, superpixels extracted via energy-driven sampling (SEEDS), lazy random walk (LRW), real-time superpixel segmentation by DBSCAN clustering, and video supervoxels using partially absorbing random walks (PARW) algorithms. The evaluation process was carried out both qualitatively and quantitatively. For quantitative performance comparison, we used achievable segmentation accuracy (ASA), compactness, under-segmentation error (USE), and boundary recall (BR) on the Berkeley image database. The results demonstrated that all algorithms suffered performance degradation due to noise. For Gaussian blur, Bilateral-G exhibited optimal results for ASA and USE measures, SLIC yielded optimal compactness, whereas FCCS and DBSCAN remained optimal for BR. For the case of additive Gaussian and impulse noises, FCCS exhibited optimal results for ASA, USE, and BR, whereas Bilateral-G remained a close competitor in ASA and USE for Gaussian noise only. Additionally, Turbopixel demonstrated optimal performance for compactness for both types of noise. Thus, no single algorithm was able to yield optimal results for all three types of noise across all performance measures. Conclusively, to solve real-world problems effectively, more robust superpixel algorithms must be developed.

High Quality Facade Segmentation Based on Structured Random Forest, Region Proposal Network and Rectangular Fitting

NASA Astrophysics Data System (ADS)

Rahmani, K.; Mayer, H.

2018-05-01

In this paper we present a pipeline for high quality semantic segmentation of building facades using Structured Random Forest (SRF), Region Proposal Network (RPN) based on a Convolutional Neural Network (CNN) as well as rectangular fitting optimization. Our main contribution is that we employ features created by the RPN as channels in the SRF.We empirically show that this is very effective especially for doors and windows. Our pipeline is evaluated on two datasets where we outperform current state-of-the-art methods. Additionally, we quantify the contribution of the RPN and the rectangular fitting optimization on the accuracy of the result.

Segmentation quality evaluation using region-based precision and recall measures for remote sensing images

NASA Astrophysics Data System (ADS)

Zhang, Xueliang; Feng, Xuezhi; Xiao, Pengfeng; He, Guangjun; Zhu, Liujun

2015-04-01

Segmentation of remote sensing images is a critical step in geographic object-based image analysis. Evaluating the performance of segmentation algorithms is essential to identify effective segmentation methods and optimize their parameters. In this study, we propose region-based precision and recall measures and use them to compare two image partitions for the purpose of evaluating segmentation quality. The two measures are calculated based on region overlapping and presented as a point or a curve in a precision-recall space, which can indicate segmentation quality in both geometric and arithmetic respects. Furthermore, the precision and recall measures are combined by using four different methods. We examine and compare the effectiveness of the combined indicators through geometric illustration, in an effort to reveal segmentation quality clearly and capture the trade-off between the two measures. In the experiments, we adopted the multiresolution segmentation (MRS) method for evaluation. The proposed measures are compared with four existing discrepancy measures to further confirm their capabilities. Finally, we suggest using a combination of the region-based precision-recall curve and the F-measure for supervised segmentation evaluation.

Progressive Label Fusion Framework for Multi-atlas Segmentation by Dictionary Evolution

PubMed Central

Song, Yantao; Wu, Guorong; Sun, Quansen; Bahrami, Khosro; Li, Chunming; Shen, Dinggang

2015-01-01

Accurate segmentation of anatomical structures in medical images is very important in neuroscience studies. Recently, multi-atlas patch-based label fusion methods have achieved many successes, which generally represent each target patch from an atlas patch dictionary in the image domain and then predict the latent label by directly applying the estimated representation coefficients in the label domain. However, due to the large gap between these two domains, the estimated representation coefficients in the image domain may not stay optimal for the label fusion. To overcome this dilemma, we propose a novel label fusion framework to make the weighting coefficients eventually to be optimal for the label fusion by progressively constructing a dynamic dictionary in a layer-by-layer manner, where a sequence of intermediate patch dictionaries gradually encode the transition from the patch representation coefficients in image domain to the optimal weights for label fusion. Our proposed framework is general to augment the label fusion performance of the current state-of-the-art methods. In our experiments, we apply our proposed method to hippocampus segmentation on ADNI dataset and achieve more accurate labeling results, compared to the counterpart methods with single-layer dictionary. PMID:26942233

Progressive Label Fusion Framework for Multi-atlas Segmentation by Dictionary Evolution.

PubMed

Song, Yantao; Wu, Guorong; Sun, Quansen; Bahrami, Khosro; Li, Chunming; Shen, Dinggang

2015-10-01

Accurate segmentation of anatomical structures in medical images is very important in neuroscience studies. Recently, multi-atlas patch-based label fusion methods have achieved many successes, which generally represent each target patch from an atlas patch dictionary in the image domain and then predict the latent label by directly applying the estimated representation coefficients in the label domain. However, due to the large gap between these two domains, the estimated representation coefficients in the image domain may not stay optimal for the label fusion. To overcome this dilemma, we propose a novel label fusion framework to make the weighting coefficients eventually to be optimal for the label fusion by progressively constructing a dynamic dictionary in a layer-by-layer manner, where a sequence of intermediate patch dictionaries gradually encode the transition from the patch representation coefficients in image domain to the optimal weights for label fusion. Our proposed framework is general to augment the label fusion performance of the current state-of-the-art methods. In our experiments, we apply our proposed method to hippocampus segmentation on ADNI dataset and achieve more accurate labeling results, compared to the counterpart methods with single-layer dictionary.

Optimized doppler optical coherence tomography for choroidal capillary vasculature imaging

NASA Astrophysics Data System (ADS)

Liu, Gangjun; Qi, Wenjuan; Yu, Lingfeng; Chen, Zhongping

2011-03-01

In this paper, we analyzed the retinal and choroidal blood vasculature in the posterior segment of the human eye with optimized color Doppler and Doppler variance optical coherence tomography. Depth-resolved structure, color Doppler and Doppler variance images were compared. Blood vessels down to capillary level were able to be obtained with the optimized optical coherence color Doppler and Doppler variance method. For in-vivo imaging of human eyes, bulkmotion induced bulk phase must be identified and removed before using color Doppler method. It was found that the Doppler variance method is not sensitive to bulk motion and the method can be used without removing the bulk phase. A novel, simple and fast segmentation algorithm to indentify retinal pigment epithelium (RPE) was proposed and used to segment the retinal and choroidal layer. The algorithm was based on the detected OCT signal intensity difference between different layers. A spectrometer-based Fourier domain OCT system with a central wavelength of 890 nm and bandwidth of 150nm was used in this study. The 3-dimensional imaging volume contained 120 sequential two dimensional images with 2048 A-lines per image. The total imaging time was 12 seconds and the imaging area was 5x5 mm2.

SU-C-9A-01: Parameter Optimization in Adaptive Region-Growing for Tumor Segmentation in PET

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

Tan, S; Huazhong University of Science and Technology, Wuhan, Hubei; Xue, M

Purpose: To design a reliable method to determine the optimal parameter in the adaptive region-growing (ARG) algorithm for tumor segmentation in PET. Methods: The ARG uses an adaptive similarity criterion m - fσ ≤ I-PET ≤ m + fσ, so that a neighboring voxel is appended to the region based on its similarity to the current region. When increasing the relaxing factor f (f ≥ 0), the resulting volumes monotonically increased with a sharp increase when the region just grew into the background. The optimal f that separates the tumor from the background is defined as the first point withmore » the local maximum curvature on an Error function fitted to the f-volume curve. The ARG was tested on a tumor segmentation Benchmark that includes ten lung cancer patients with 3D pathologic tumor volume as ground truth. For comparison, the widely used 42% and 50% SUVmax thresholding, Otsu optimal thresholding, Active Contours (AC), Geodesic Active Contours (GAC), and Graph Cuts (GC) methods were tested. The dice similarity index (DSI), volume error (VE), and maximum axis length error (MALE) were calculated to evaluate the segmentation accuracy. Results: The ARG provided the highest accuracy among all tested methods. Specifically, the ARG has an average DSI, VE, and MALE of 0.71, 0.29, and 0.16, respectively, better than the absolute 42% thresholding (DSI=0.67, VE= 0.57, and MALE=0.23), the relative 42% thresholding (DSI=0.62, VE= 0.41, and MALE=0.23), the absolute 50% thresholding (DSI=0.62, VE=0.48, and MALE=0.21), the relative 50% thresholding (DSI=0.48, VE=0.54, and MALE=0.26), OTSU (DSI=0.44, VE=0.63, and MALE=0.30), AC (DSI=0.46, VE= 0.85, and MALE=0.47), GAC (DSI=0.40, VE= 0.85, and MALE=0.46) and GC (DSI=0.66, VE= 0.54, and MALE=0.21) methods. Conclusions: The results suggest that the proposed method reliably identified the optimal relaxing factor in ARG for tumor segmentation in PET. This work was supported in part by National Cancer Institute Grant R01 CA172638; The dataset is provided by AAPM TG211.« less

[Application of an Adaptive Inertia Weight Particle Swarm Algorithm in the Magnetic Resonance Bias Field Correction].

PubMed

Wang, Chang; Qin, Xin; Liu, Yan; Zhang, Wenchao

2016-06-01

An adaptive inertia weight particle swarm algorithm is proposed in this study to solve the local optimal problem with the method of traditional particle swarm optimization in the process of estimating magnetic resonance(MR)image bias field.An indicator measuring the degree of premature convergence was designed for the defect of traditional particle swarm optimization algorithm.The inertia weight was adjusted adaptively based on this indicator to ensure particle swarm to be optimized globally and to avoid it from falling into local optimum.The Legendre polynomial was used to fit bias field,the polynomial parameters were optimized globally,and finally the bias field was estimated and corrected.Compared to those with the improved entropy minimum algorithm,the entropy of corrected image was smaller and the estimated bias field was more accurate in this study.Then the corrected image was segmented and the segmentation accuracy obtained in this research was 10% higher than that with improved entropy minimum algorithm.This algorithm can be applied to the correction of MR image bias field.

Morphing Wing Weight Predictors and Their Application in a Template-Based Morphing Aircraft Sizing Environment II. Part 2; Morphing Aircraft Sizing via Multi-level Optimization

NASA Technical Reports Server (NTRS)

Skillen, Michael D.; Crossley, William A.

2008-01-01

This report presents an approach for sizing of a morphing aircraft based upon a multi-level design optimization approach. For this effort, a morphing wing is one whose planform can make significant shape changes in flight - increasing wing area by 50% or more from the lowest possible area, changing sweep 30 or more, and/or increasing aspect ratio by as much as 200% from the lowest possible value. The top-level optimization problem seeks to minimize the gross weight of the aircraft by determining a set of "baseline" variables - these are common aircraft sizing variables, along with a set of "morphing limit" variables - these describe the maximum shape change for a particular morphing strategy. The sub-level optimization problems represent each segment in the morphing aircraft's design mission; here, each sub-level optimizer minimizes fuel consumed during each mission segment by changing the wing planform within the bounds set by the baseline and morphing limit variables from the top-level problem.

Analysis of Intergrade Variables In The Fuzzy C-Means And Improved Algorithm Cat Swarm Optimization(FCM-ISO) In Search Segmentation

NASA Astrophysics Data System (ADS)

Saragih, Jepronel; Salim Sitompul, Opim; Situmorang, Zakaria

2017-12-01

One of the techniques known in Data Mining namely clustering. Image segmentation process does not always represent the actual image which is caused by a combination of algorithms as long as it has not been able to obtain optimal cluster centers. In this research will search for the smallest error with the counting result of a Fuzzy C Means process optimized with Cat swam Algorithm Optimization that has been developed by adding the weight of the energy in the process of Tracing Mode.So with the parameter can be determined the most optimal cluster centers and most closely with the data will be made the cluster. Weigh inertia in this research, namely: (0.1), (0.2), (0.3), (0.4), (0.5), (0.6), (0.7), (0.8) and (0.9). Then compare the results of each variable values inersia (W) which is different and taken the smallest results. Of this weighting analysis process can acquire the right produce inertia variable cost function the smallest.

Determination of Equine Cytochrome c Backbone Amide Hydrogen/Deuterium Exchange Rates by Mass Spectrometry Using a Wider Time Window and Isotope Envelope.

PubMed

Hamuro, Yoshitomo

2017-03-01

A new strategy to analyze amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) data is proposed, utilizing a wider time window and isotope envelope analysis of each peptide. While most current scientific reports present HDX-MS data as a set of time-dependent deuteration levels of peptides, the ideal HDX-MS data presentation is a complete set of backbone amide hydrogen exchange rates. The ideal data set can provide single amide resolution, coverage of all exchange events, and the open/close ratio of each amide hydrogen in EX2 mechanism. Toward this goal, a typical HDX-MS protocol was modified in two aspects: measurement of a wider time window in HDX-MS experiments and deconvolution of isotope envelope of each peptide. Measurement of a wider time window enabled the observation of deuterium incorporation of most backbone amide hydrogens. Analysis of the isotope envelope instead of centroid value provides the deuterium distribution instead of the sum of deuteration levels in each peptide. A one-step, global-fitting algorithm optimized exchange rate and deuterium retention during the analysis of each amide hydrogen by fitting the deuterated isotope envelopes at all time points of all peptides in a region. Application of this strategy to cytochrome c yielded 97 out of 100 amide hydrogen exchange rates. A set of exchange rates determined by this approach is more appropriate for a patent or regulatory filing of a biopharmaceutical than a set of peptide deuteration levels obtained by a typical protocol. A wider time window of this method also eliminates false negatives in protein-ligand binding site identification. Graphical Abstract ᅟ.

Determination of Equine Cytochrome c Backbone Amide Hydrogen/Deuterium Exchange Rates by Mass Spectrometry Using a Wider Time Window and Isotope Envelope

NASA Astrophysics Data System (ADS)

Hamuro, Yoshitomo

2017-03-01

A new strategy to analyze amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) data is proposed, utilizing a wider time window and isotope envelope analysis of each peptide. While most current scientific reports present HDX-MS data as a set of time-dependent deuteration levels of peptides, the ideal HDX-MS data presentation is a complete set of backbone amide hydrogen exchange rates. The ideal data set can provide single amide resolution, coverage of all exchange events, and the open/close ratio of each amide hydrogen in EX2 mechanism. Toward this goal, a typical HDX-MS protocol was modified in two aspects: measurement of a wider time window in HDX-MS experiments and deconvolution of isotope envelope of each peptide. Measurement of a wider time window enabled the observation of deuterium incorporation of most backbone amide hydrogens. Analysis of the isotope envelope instead of centroid value provides the deuterium distribution instead of the sum of deuteration levels in each peptide. A one-step, global-fitting algorithm optimized exchange rate and deuterium retention during the analysis of each amide hydrogen by fitting the deuterated isotope envelopes at all time points of all peptides in a region. Application of this strategy to cytochrome c yielded 97 out of 100 amide hydrogen exchange rates. A set of exchange rates determined by this approach is more appropriate for a patent or regulatory filing of a biopharmaceutical than a set of peptide deuteration levels obtained by a typical protocol. A wider time window of this method also eliminates false negatives in protein-ligand binding site identification.

Parameterization of backbone flexibility in a coarse-grained force field for proteins (COFFDROP) derived from all-atom explicit-solvent molecular dynamics simulations of all possible two-residue peptides

PubMed Central

Frembgen-Kesner, Tamara; Andrews, Casey T.; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A.; Jain, Aakash; Olayiwola, Oluwatoni; Weishaar, Mitch R.; Elcock, Adrian H.

2015-01-01

Recently, we reported the parameterization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs, and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downwards in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multi-domain proteins connected by flexible linkers. PMID:26574429

Ultra-sensitive EUV resists based on acid-catalyzed polymer backbone breaking

NASA Astrophysics Data System (ADS)

Manouras, Theodoros; Kazazis, Dimitrios; Koufakis, Eleftherios; Ekinci, Yasin; Vamvakaki, Maria; Argitis, Panagiotis

2018-03-01

The main target of the current work was to develop new sensitive polymeric materials for lithographic applications, focusing in particular to EUV lithography, the main chain of which is cleaved under the influence of photogenerated acid. Resist materials based on the cleavage of polymer main chain are in principle capable to create very small structures, to the dimensions of the monomers that they consist of. Nevertheless, in the case of the commonly used nonchemically amplified materials of this type issues like sensitivity and poor etch resistance limit their areas of application, whereas inadequate etch resistance and non- satisfactory process reliability are the usual problems encountered in acid catalysed materials based on main chain scission. In our material design the acid catalyzed chain cleavable polymers contain very sensitive moieties in their backbone while they remain intact in alkaline ambient. These newly synthesized polymers bear in addition suitable functional groups for the achievement of desirable lithographic characteristics (thermal stability, acceptable glass transition temperature, etch resistance, proper dissolution behavior, adhesion to the substrate). Our approach for achieving acceptable etch resistance, a main drawback in other main chain cleavable resists, is based on the introduction of polyaromatic hydrocarbons in the polymeric backbone, whereas the incorporation of an inorganic component further enhances the etch resistance. Single component systems can also be designed following the proposed approach by the incorporation of suitable PAGs and base quencher molecules in the main chain. Resist formulations based on a random copolymer designed according to the described rules evaluated in EUV exhibit ultrahigh sensitivity, capability for high resolution patterning and overall processing characteristics that make them strong candidates for industrial use upon further optimization.

Mechanics of collective unfolding

NASA Astrophysics Data System (ADS)

Caruel, M.; Allain, J.-M.; Truskinovsky, L.

2015-03-01

Mechanically induced unfolding of passive crosslinkers is a fundamental biological phenomenon encountered across the scales from individual macro-molecules to cytoskeletal actin networks. In this paper we study a conceptual model of athermal load-induced unfolding and use a minimalistic setting allowing one to emphasize the role of long-range interactions while maintaining full analytical transparency. Our model can be viewed as a description of a parallel bundle of N bistable units confined between two shared rigid backbones that are loaded through a series spring. We show that the ground states in this model correspond to synchronized, single phase configurations where all individual units are either folded or unfolded. We then study the fine structure of the wiggly energy landscape along the reaction coordinate linking the two coherent states and describing the optimal mechanism of cooperative unfolding. Quite remarkably, our study shows the fundamental difference in the size and the structure of the folding-unfolding energy barriers in the hard (fixed displacements) and soft (fixed forces) loading devices which persists in the continuum limit. We argue that both, the synchronization and the non-equivalence of the mechanical responses in hard and soft devices, have their origin in the dominance of long-range interactions. We then apply our minimal model to skeletal muscles where the power-stroke in acto-myosin crossbridges can be interpreted as passive folding. A quantitative analysis of the muscle model shows that the relative rigidity of myosin backbone provides the long-range interaction mechanism allowing the system to effectively synchronize the power-stroke in individual crossbridges even in the presence of thermal fluctuations. In view of the prototypical nature of the proposed model, our general conclusions pertain to a variety of other biological systems where elastic interactions are mediated by effective backbones.

A novel fully automatic multilevel thresholding technique based on optimized intuitionistic fuzzy sets and tsallis entropy for MR brain tumor image segmentation.

PubMed

Kaur, Taranjit; Saini, Barjinder Singh; Gupta, Savita

2018-03-01

In the present paper, a hybrid multilevel thresholding technique that combines intuitionistic fuzzy sets and tsallis entropy has been proposed for the automatic delineation of the tumor from magnetic resonance images having vague boundaries and poor contrast. This novel technique takes into account both the image histogram and the uncertainty information for the computation of multiple thresholds. The benefit of the methodology is that it provides fast and improved segmentation for the complex tumorous images with imprecise gray levels. To further boost the computational speed, the mutation based particle swarm optimization is used that selects the most optimal threshold combination. The accuracy of the proposed segmentation approach has been validated on simulated, real low-grade glioma tumor volumes taken from MICCAI brain tumor segmentation (BRATS) challenge 2012 dataset and the clinical tumor images, so as to corroborate its generality and novelty. The designed technique achieves an average Dice overlap equal to 0.82010, 0.78610 and 0.94170 for three datasets. Further, a comparative analysis has also been made between the eight existing multilevel thresholding implementations so as to show the superiority of the designed technique. In comparison, the results indicate a mean improvement in Dice by an amount equal to 4.00% (p < 0.005), 9.60% (p < 0.005) and 3.58% (p < 0.005), respectively in contrast to the fuzzy tsallis approach.

Coronary artery segmentation in X-ray angiograms using gabor filters and differential evolution.

PubMed

Cervantes-Sanchez, Fernando; Cruz-Aceves, Ivan; Hernandez-Aguirre, Arturo; Solorio-Meza, Sergio; Cordova-Fraga, Teodoro; Aviña-Cervantes, Juan Gabriel

2018-08-01

Segmentation of coronary arteries in X-ray angiograms represents an essential task for computer-aided diagnosis, since it can help cardiologists in diagnosing and monitoring vascular abnormalities. Due to the main disadvantages of the X-ray angiograms are the nonuniform illumination, and the weak contrast between blood vessels and image background, different vessel enhancement methods have been introduced. In this paper, a novel method for blood vessel enhancement based on Gabor filters tuned using the optimization strategy of Differential evolution (DE) is proposed. Because the Gabor filters are governed by three different parameters, the optimal selection of those parameters is highly desirable in order to maximize the vessel detection rate while reducing the computational cost of the training stage. To obtain the optimal set of parameters for the Gabor filters, the area (Az) under the receiver operating characteristics curve is used as objective function. In the experimental results, the proposed method achieves an A z =0.9388 in a training set of 40 images, and for a test set of 40 images it obtains the highest performance with an A z =0.9538 compared with six state-of-the-art vessel detection methods. Finally, the proposed method achieves an accuracy of 0.9423 for vessel segmentation using the test set. In addition, the experimental results have also shown that the proposed method can be highly suitable for clinical decision support in terms of computational time and vessel segmentation performance. Copyright © 2017 Elsevier Ltd. All rights reserved.

JWST Wavefront Control Toolbox

NASA Technical Reports Server (NTRS)

Shin, Shahram Ron; Aronstein, David L.

2011-01-01

A Matlab-based toolbox has been developed for the wavefront control and optimization of segmented optical surfaces to correct for possible misalignments of James Webb Space Telescope (JWST) using influence functions. The toolbox employs both iterative and non-iterative methods to converge to an optimal solution by minimizing the cost function. The toolbox could be used in either of constrained and unconstrained optimizations. The control process involves 1 to 7 degrees-of-freedom perturbations per segment of primary mirror in addition to the 5 degrees of freedom of secondary mirror. The toolbox consists of a series of Matlab/Simulink functions and modules, developed based on a "wrapper" approach, that handles the interface and data flow between existing commercial optical modeling software packages such as Zemax and Code V. The limitations of the algorithm are dictated by the constraints of the moving parts in the mirrors.

Biosynthesis and NMR-studies of a double transmembrane domain from the Y4 receptor, a human GPCR.

PubMed

Zou, Chao; Naider, Fred; Zerbe, Oliver

2008-12-01

The human Y4 receptor, a class A G-protein coupled receptor (GPCR) primarily targeted by the pancreatic polypeptide (PP), is involved in a large number of physiologically important functions. This paper investigates a Y4 receptor fragment (N-TM1-TM2) comprising the N-terminal domain, the first two transmembrane (TM) helices and the first extracellular loop followed by a (His)(6) tag, and addresses synthetic problems encountered when recombinantly producing such fragments from GPCRs in Escherichia coli. Rigorous purification and usage of the optimized detergent mixture 28 mM dodecylphosphocholine (DPC)/118 mM% 1-palmitoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)] (LPPG) resulted in high quality TROSY spectra indicating protein conformational homogeneity. Almost complete assignment of the backbone, including all TM residue resonances was obtained. Data on internal backbone dynamics revealed a high secondary structure content for N-TM1-TM2. Secondary chemical shifts and sequential amide proton nuclear Overhauser effects defined the TM helices. Interestingly, the properties of the N-terminal domain of this large fragment are highly similar to those determined on the isolated N-terminal domain in the presence of DPC micelles.

Relative stability of major types of beta-turns as a function of amino acid composition: a study based on Ab initio energetic and natural abundance data.

PubMed

Perczel, András; Jákli, Imre; McAllister, Michael A; Csizmadia, Imre G

2003-06-06

Folding properties of small globular proteins are determined by their amino acid sequence (primary structure). This holds both for local (secondary structure) and for global conformational features of linear polypeptides and proteins composed from natural amino acid derivatives. It thus provides the rational basis of structure prediction algorithms. The shortest secondary structure element, the beta-turn, most typically adopts either a type I or a type II form, depending on the amino acid composition. Herein we investigate the sequence-dependent folding stability of both major types of beta-turns using simple dipeptide models (-Xxx-Yyy-). Gas-phase ab initio properties of 16 carefully selected and suitably protected dipeptide models (for example Val-Ser, Ala-Gly, Ser-Ser) were studied. For each backbone fold most probable side-chain conformers were considered. Fully optimized 321G RHF molecular structures were employed in medium level [B3LYP/6-311++G(d,p)//RHF/3-21G] energy calculations to estimate relative populations of the different backbone conformers. Our results show that the preference for beta-turn forms as calculated by quantum mechanics and observed in Xray determined proteins correlates significantly.

Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides.

PubMed

Luis, Ana S; Briggs, Jonathon; Zhang, Xiaoyang; Farnell, Benjamin; Ndeh, Didier; Labourel, Aurore; Baslé, Arnaud; Cartmell, Alan; Terrapon, Nicolas; Stott, Katherine; Lowe, Elisabeth C; McLean, Richard; Shearer, Kaitlyn; Schückel, Julia; Venditto, Immacolata; Ralet, Marie-Christine; Henrissat, Bernard; Martens, Eric C; Mosimann, Steven C; Abbott, D Wade; Gilbert, Harry J

2018-02-01

The major nutrients available to human colonic Bacteroides species are glycans, exemplified by pectins, a network of covalently linked plant cell wall polysaccharides containing galacturonic acid (GalA). Metabolism of complex carbohydrates by the Bacteroides genus is orchestrated by polysaccharide utilization loci (PULs). In Bacteroides thetaiotaomicron, a human colonic bacterium, the PULs activated by different pectin domains have been identified; however, the mechanism by which these loci contribute to the degradation of these GalA-containing polysaccharides is poorly understood. Here we show that each PUL orchestrates the metabolism of specific pectin molecules, recruiting enzymes from two previously unknown glycoside hydrolase families. The apparatus that depolymerizes the backbone of rhamnogalacturonan-I is particularly complex. This system contains several glycoside hydrolases that trim the remnants of other pectin domains attached to rhamnogalacturonan-I, and nine enzymes that contribute to the degradation of the backbone that makes up a rhamnose-GalA repeating unit. The catalytic properties of the pectin-degrading enzymes are optimized to protect the glycan cues that activate the specific PULs ensuring a continuous supply of inducing molecules throughout growth. The contribution of Bacteroides spp. to metabolism of the pectic network is illustrated by cross-feeding between organisms.

Amphiphilic semiconducting polymer as multifunctional nanocarrier for fluorescence/photoacoustic imaging guided chemo-photothermal therapy.

PubMed

Jiang, Yuyan; Cui, Dong; Fang, Yuan; Zhen, Xu; Upputuri, Paul Kumar; Pramanik, Manojit; Ding, Dan; Pu, Kanyi

2017-11-01

Chemo-photothermal nanotheranostics has the advantage of synergistic therapeutic effect, providing opportunities for optimized cancer therapy. However, current chemo-photothermal nanotheranostic systems generally comprise more than three components, encountering the potential issues of unstable nanostructures and unexpected conflicts in optical and biophysical properties among different components. We herein synthesize an amphiphilic semiconducting polymer (PEG-PCB) and utilize it as a multifunctional nanocarrier to simplify chemo-photothermal nanotheranostics. PEG-PCB has a semiconducting backbone that not only serves as the diagnostic component for near-infrared (NIR) fluorescence and photoacoustic (PA) imaging, but also acts as the therapeutic agent for photothermal therapy. In addition, the hydrophobic backbone of PEG-PCB provides strong hydrophobic and π-π interactions with the aromatic anticancer drug such as doxorubicin for drug encapsulation and delivery. Such a trifunctionality of PEG-PCB eventually results in a greatly simplified nanotheranostic system with only two components but multimodal imaging and therapeutic capacities, permitting effective NIR fluorescence/PA imaging guided chemo-photothermal therapy of cancer in living mice. Our study thus provides a molecular engineering approach to integrate essential properties into one polymer for multimodal nanotheranostics. Copyright © 2017 Elsevier Ltd. All rights reserved.

Electroactive polyurethane/siloxane derived from castor oil as a versatile cardiac patch, part I: Synthesis, characterization, and myoblast proliferation and differentiation.

PubMed

Baheiraei, Nafiseh; Gharibi, Reza; Yeganeh, Hamid; Miragoli, Michele; Salvarani, Nicolò; Di Pasquale, Elisa; Condorelli, Gianluigi

2016-03-01

Tissue-engineered cardiac patch aims at regenerating an infarcted heart by improving cardiac function and providing mechanical support to the diseased myocardium. In order to take advantages of electroactivity, a new synthetic method was developed for the introduction of an electroactive oligoaniline into the backbone of prepared patches. For this purpose, a series of electroactive polyurethane/siloxane films containing aniline tetramer (AT) was prepared through sol-gel reaction of trimethoxysilane functional intermediate polyurethane prepolymers made from castor oil and poly(ethylene glycol). Physicochemical, mechanical, and electrical conductivity of samples were evaluated and the recorded results were correlated to their structural characteristics. The optimized films were proved to be biodegradable and have tensile properties suitable for cardiac patch application. The embedded AT moieties in the backbone of the prepared samples preserved their electroactivity with the electrical conductivity in the range of 10 -4 S/cm. The prepared films were compatible with proliferation of C2C12 and had potential for enhancing myotube formation even without external electrical stimulation. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 775-787, 2016. © 2015 Wiley Periodicals, Inc.

Macromolecular scaffolding: the relationship between nanoscale architecture and function in multichromophoric arrays for organic electronics.

PubMed

Palermo, Vincenzo; Schwartz, Erik; Finlayson, Chris E; Liscio, Andrea; Otten, Matthijs B J; Trapani, Sara; Müllen, Klaus; Beljonne, David; Friend, Richard H; Nolte, Roeland J M; Rowan, Alan E; Samorì, Paolo

2010-02-23

The optimization of the electronic properties of molecular materials based on optically or electrically active organic building blocks requires a fine-tuning of their self-assembly properties at surfaces. Such a fine-tuning can be obtained on a scale up to 10 nm by mastering principles of supramolecular chemistry, i.e., by using suitably designed molecules interacting via pre-programmed noncovalent forces. The control and fine-tuning on a greater length scale is more difficult and challenging. This Research News highlights recent results we obtained on a new class of macromolecules that possess a very rigid backbone and side chains that point away from this backbone. Each side chain contains an organic semiconducting moiety, whose position and electronic interaction with neighboring moieties are dictated by the central macromolecular scaffold. A combined experimental and theoretical approach has made it possible to unravel the physical and chemical properties of this system across multiple length scales. The (opto)electronic properties of the new functional architectures have been explored by constructing prototypes of field-effect transistors and solar cells, thereby providing direct insight into the relationship between architecture and function.

Whole-genome analyses of DS-1-like human G2P[4] and G8P[4] rotavirus strains from Eastern, Western and Southern Africa

PubMed Central

Nyaga, Martin M.; Stucker, Karla M.; Esona, Mathew D.; Jere, Khuzwayo C.; Mwinyi, Bakari; Shonhai, Annie; Tsolenyanu, Enyonam; Mulindwa, Augustine; Chibumbya, Julia N.; Adolfine, Hokororo; Halpin, Rebecca A.; Roy, Sunando; Stockwell, Timothy B.; Berejena, Chipo; Seheri, Mapaseka L.; Mwenda, Jason M.; Steele, A. Duncan; Wentworth, David E.

2018-01-01

Group A rotaviruses (RVAs) with distinct G and P genotype combinations have been reported globally. We report the genome composition and possible origin of seven G8P[4] and five G2P[4] human RVA strains based on the genetic evolution of all 11 genome segments at the nucleotide level. Twelve RVA ELISA positive stool samples collected in the representative countries of Eastern, Southern and West Africa during the 2007–2012 surveillance seasons were subjected to sequencing using the Ion Torrent PGM and Illumina MiSeq platforms. A reference-based assembly was performed using CLC Bio’s clc_ref_assemble_long program, and full-genome consensus sequences were obtained. With the exception of the neutralising antigen, VP7, all study strains exhibited the DS-1-like genome constellation (P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2) and clustered phylogenetically with reference strains having a DS-1-like genetic backbone. Comparison of the nucleotide and amino acid sequences with selected global cognate genome segments revealed nucleotide and amino acid sequence identities of 81.7–100 % and 90.6–100 %, respectively, with NSP4 gene segment showing the most diversity among the strains. Bayesian analyses of all gene sequences to estimate the time of divergence of the lineage indicated that divergence times ranged from 16 to 44 years, except for the NSP4 gene where the lineage seemed to arise in the more distant past at an estimated 203 years ago. However, the long-term effects of changes found within the NSP4 genome segment should be further explored, and thus we recommend continued whole-genome analyses from larger sample sets to determine the evolutionary mechanisms of the DS-1-like strains collected in Africa. PMID:24952422

Remote Enantioselection Transmitted by an Achiral Peptide Nucleic Acid Backbone

NASA Technical Reports Server (NTRS)

Kozlov, Igor A.; Orgel, Leslie E.; Nielsen, Peter E.

2000-01-01

short homochiral segment of DNA into a PNA helix could have guaranteed that the next short segment of DNA to be incorporated would have the same handedness as the first. Once two segments of the same handedness were present, the probability that a third segment would have the same handedness would increase, and so on. Evolution could then slowly dilute out the PNA part. This scenario would ultimately allow the formation of a chiral oligonucleotide by processes that are largely resistant to enantiomeric crossinhibition. It is important to note that the ligation of homochiral dinucleotides on a nucleic acid template would probably be at least as enantiospecific as the reaction that we have studied. The disadvantage of using chiral monomers as components of a replicating system arises from the difficulty of generating a first long homochiral template from a racemic mixture of monomers, although results of experiments designed to overcome this difficulty by employing homochiral tetramers have been reported.l l The probability of obtaining a homochiral n-mer from achiral substrates is approximately 1P-I if the nontemplate-directed extension of the primer is not enantioselective. Hence, it would be very hard to get started with a homochiral 40-mer, for example. No such difficulty exists in a scenario that originates with an achiral genetic material and in which the incorporation of very few chiral monomers in this achiral background gradually progresses towards homochirality. It seems possible that some PNA sequences could act as catalysts, analogous to ribozymes, even though PNA lacks clear metal binding sites. Although such catalysts could not be enantioselective, the incorporation of as few as two chiral nucleotides could then impose chiral specificity on the system. Furthermore, such patch chimeras could help to bridge the gap in catalytic potential between PNA and RNA, while guaranteeing enantioselectivity.

Improved Speech Coding Based on Open-Loop Parameter Estimation

NASA Technical Reports Server (NTRS)

Juang, Jer-Nan; Chen, Ya-Chin; Longman, Richard W.

2000-01-01

A nonlinear optimization algorithm for linear predictive speech coding was developed early that not only optimizes the linear model coefficients for the open loop predictor, but does the optimization including the effects of quantization of the transmitted residual. It also simultaneously optimizes the quantization levels used for each speech segment. In this paper, we present an improved method for initialization of this nonlinear algorithm, and demonstrate substantial improvements in performance. In addition, the new procedure produces monotonically improving speech quality with increasing numbers of bits used in the transmitted error residual. Examples of speech encoding and decoding are given for 8 speech segments and signal to noise levels as high as 47 dB are produced. As in typical linear predictive coding, the optimization is done on the open loop speech analysis model. Here we demonstrate that minimizing the error of the closed loop speech reconstruction, instead of the simpler open loop optimization, is likely to produce negligible improvement in speech quality. The examples suggest that the algorithm here is close to giving the best performance obtainable from a linear model, for the chosen order with the chosen number of bits for the codebook.

An exhaustive survey of regular peptide conformations using a new metric for backbone handedness ( h )

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

Mannige, Ranjan V.

The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom—the backbone dihedral anglesφandψ(Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial tool to characterize protein backbone features. However, the conformation or twist of a backbone as a function ofφandψhas not been completely described for bothcisandtransbackbones. Additionally, little intuitive understanding is available about a peptide’s conformation simply from knowing theφandψvalues of a peptide (e.g., is the regular peptide defined byφ = ψ =  - 100°  left-handed or right-handed?). This report provides a new metric for backbone handednessmore » (h) based on interpreting a peptide backbone as a helix with axial displacementdand angular displacementθ, both of which are derived from a peptide backbone’s internal coordinates, especially dihedral anglesφ,ψandω. In particular,hequals sin(θ)d/d|, with range [-1, 1] and negative (or positive) values indicating left(or right)-handedness. The metrichis used to characterize the handedness of every region of the Ramachandran plot for bothcis(ω = 0°) and trans (ω = 180°) backbones, which provides the first exhaustive survey of twist handedness in Ramachandran (φ,ψ) space. These maps fill in the ‘dead space’ within the Ramachandran plot, which are regions that are not commonly accessed by structured proteins, but which may be accessible to intrinsically disordered proteins, short peptide fragments, and protein mimics such as peptoids. Finally, building on the work of (Zacharias & Knapp, 2013), this report presents a new plot based ondandθthat serves as a universal and intuitive alternative to the Ramachandran plot. The universality arises from the fact that the co-inhabitants of such a plot include every possible peptide backbone includingcisandtransbackbones. The intuitiveness arises from the fact thatdandθprovide, at a glance, numerous aspects of the backbone including compactness, handedness, and planarity.« less

An exhaustive survey of regular peptide conformations using a new metric for backbone handedness ( h )

DOE PAGES

Mannige, Ranjan V.

2017-05-16

The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom—the backbone dihedral anglesφandψ(Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial tool to characterize protein backbone features. However, the conformation or twist of a backbone as a function ofφandψhas not been completely described for bothcisandtransbackbones. Additionally, little intuitive understanding is available about a peptide’s conformation simply from knowing theφandψvalues of a peptide (e.g., is the regular peptide defined byφ = ψ =  - 100°  left-handed or right-handed?). This report provides a new metric for backbone handednessmore » (h) based on interpreting a peptide backbone as a helix with axial displacementdand angular displacementθ, both of which are derived from a peptide backbone’s internal coordinates, especially dihedral anglesφ,ψandω. In particular,hequals sin(θ)d/d|, with range [-1, 1] and negative (or positive) values indicating left(or right)-handedness. The metrichis used to characterize the handedness of every region of the Ramachandran plot for bothcis(ω = 0°) and trans (ω = 180°) backbones, which provides the first exhaustive survey of twist handedness in Ramachandran (φ,ψ) space. These maps fill in the ‘dead space’ within the Ramachandran plot, which are regions that are not commonly accessed by structured proteins, but which may be accessible to intrinsically disordered proteins, short peptide fragments, and protein mimics such as peptoids. Finally, building on the work of (Zacharias & Knapp, 2013), this report presents a new plot based ondandθthat serves as a universal and intuitive alternative to the Ramachandran plot. The universality arises from the fact that the co-inhabitants of such a plot include every possible peptide backbone includingcisandtransbackbones. The intuitiveness arises from the fact thatdandθprovide, at a glance, numerous aspects of the backbone including compactness, handedness, and planarity.« less

Solid state nuclear magnetic resonance investigation of polymer backbone dynamics in poly(ethylene oxide) based lithium and sodium polyether-ester-sulfonate ionomers.

PubMed

Roach, David J; Dou, Shichen; Colby, Ralph H; Mueller, Karl T

2013-05-21

Polymer backbone dynamics of single ion conducting poly(ethylene oxide) (PEO)-based ionomer samples with low glass transition temperatures (T(g)) have been investigated using solid-state nuclear magnetic resonance. Experiments detecting (13)C with (1)H decoupling under magic angle spinning (MAS) conditions identified the different components of the polymer backbone (PEO spacer and isophthalate groups) and their relative mobilities for a suite of lithium- and sodium-containing ionomer samples with varying cation contents. Variable temperature (203-373 K) (1)H-(13)C cross-polarization MAS (CP-MAS) experiments also provided qualitative assessment of the differences in the motions of the polymer backbone components as a function of cation content and identity. Each of the main backbone components exhibit distinct motions, following the trends expected for motional characteristics based on earlier Quasi Elastic Neutron Scattering and (1)H spin-lattice relaxation rate measurements. Previous (1)H and (7)Li spin-lattice relaxation measurements focused on both the polymer backbone and cation motion on the nanosecond timescale. The studies presented here assess the slower timescale motion of the polymer backbone allowing for a more comprehensive understanding of the polymer dynamics. The temperature dependences of (13)C linewidths were used to both qualitatively and quantitatively examine the effects of cation content and identity on PEO spacer mobility. Variable contact time (1)H-(13)C CP-MAS experiments were used to further assess the motions of the polymer backbone on the microsecond timescale. The motion of the PEO spacer, reported via the rate of magnetization transfer from (1)H to (13)C nuclei, becomes similar for T≳1.1 T(g) in all ionic samples, indicating that at similar elevated reduced temperatures the motions of the polymer backbones on the microsecond timescale become insensitive to ion interactions. These results present an improved picture, beyond those of previous findings, for the dependence of backbone dynamics on cation density (and here, cation identity as well) in these amorphous PEO-based ionomer systems.

Revealing the Charge Transport Mechanism in Polymerized Ionic Liquids: Insight from High Pressure Conductivity Studies

DOE PAGES

Wojnarowska, Zaneta; Feng, Hongbo; Diaz, Mariana; ...

2017-09-05

Polymerized ionic liquids (polyILs), composed mostly of organic ions covalently bonded to the polymer backbone and free counterions, are considered as an ideal electrolytes for various electrochemical devices, including fuel cells, supercapacitors and batteries. Despite large structural diversity of these systems, all of them reveal a universal but poorly understood feature - a charge transport faster than the segmental dynamics. Here, to address this issue, we have studied three novel polymer electrolyte membrane for fuel cells as well as four single-ion conductors including highly conductive siloxane-based polyIL. Our ambient and high pressure studies revealed fundamental differences in the conducting propertiesmore » of the examined systems. Finally, we demonstrate that the proposed methodology is a powerful tool to identify the charge transport mechanism in polyILs in general and thereby contribute to unraveling the microscopic nature of the decoupling phenomenon in these materials.« less

Transportation Electrification Beyond Light Duty: Technology and Market Assessment

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

Tartaglia, Katie; Birky, Alicia; Laughlin, Michael

Commercial fleets form the backbone of the nation’s economy, getting people and the things they need to the places they need to go and performing services necessary to keep public and private physical infrastructure in working order. Commercial fleets include a wide range of vehicle and equipment types, typical uses, and sizes, and involve millions of on-road and offroad vehicles. This diversity means there is no single solution to the challenges these vehicles pose for reducing petroleum dependence, impact on air quality, and emission of greenhouse gases. This document focuses on electrification of government, commercial, and industrial fleets. These fleetsmore » have been divided into three market segments based on equipment use: service fleets, goods movement, and people movement. In particular, it addresses highway vehicles not used for personal transport; non-highway modes, including air, rail, and water; and non-road equipment used directly or in support of these uses.« less

Charge-transfer crystallites as molecular electrical dopants

PubMed Central

Méndez, Henry; Heimel, Georg; Winkler, Stefanie; Frisch, Johannes; Opitz, Andreas; Sauer, Katrein; Wegner, Berthold; Oehzelt, Martin; Röthel, Christian; Duhm, Steffen; Többens, Daniel; Koch, Norbert; Salzmann, Ingo

2015-01-01

Ground-state integer charge transfer is commonly regarded as the basic mechanism of molecular electrical doping in both, conjugated polymers and oligomers. Here, we demonstrate that fundamentally different processes can occur in the two types of organic semiconductors instead. Using complementary experimental techniques supported by theory, we contrast a polythiophene, where molecular p-doping leads to integer charge transfer reportedly localized to one quaterthiophene backbone segment, to the quaterthiophene oligomer itself. Despite a comparable relative increase in conductivity, we observe only partial charge transfer for the latter. In contrast to the parent polymer, pronounced intermolecular frontier-orbital hybridization of oligomer and dopant in 1:1 mixed-stack co-crystallites leads to the emergence of empty electronic states within the energy gap of the surrounding quaterthiophene matrix. It is their Fermi–Dirac occupation that yields mobile charge carriers and, therefore, the co-crystallites—rather than individual acceptor molecules—should be regarded as the dopants in such systems. PMID:26440403

Molecular characterization of different equine-like G3 rotavirus strains from Germany.

PubMed

Pietsch, Corinna; Liebert, Uwe G

2018-01-01

The genetic heterogeneity of rotaviruses constitutes a substantial burden to human and animal health. Occasional interspecies transmissions can generate novel virus strains in the human population. We detected equine-like G3P[8] strains in feces sampled from three children in Germany in 2015 and 2016, respectively. Thereof two showed a DS-1-like backbone. In one strain the NSP2 gene segment was of distinct genotype (G3-P[8]-I2-R2-C2-M2-A2-N1-T2-E2-H2). Phylogenetic analyses of the German strains showed a relation to other equine-like G3 rotaviruses circulating in different countries. The reconstruction of reassortment events in the evolution of novel equine-like G3 rotaviruses suggests an independent introduction of the three strains into the local human rotavirus population. Copyright © 2017 Elsevier B.V. All rights reserved.

Revealing the Charge Transport Mechanism in Polymerized Ionic Liquids: Insight from High Pressure Conductivity Studies

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

Wojnarowska, Zaneta; Feng, Hongbo; Diaz, Mariana

Polymerized ionic liquids (polyILs), composed mostly of organic ions covalently bonded to the polymer backbone and free counterions, are considered as an ideal electrolytes for various electrochemical devices, including fuel cells, supercapacitors and batteries. Despite large structural diversity of these systems, all of them reveal a universal but poorly understood feature - a charge transport faster than the segmental dynamics. Here, to address this issue, we have studied three novel polymer electrolyte membrane for fuel cells as well as four single-ion conductors including highly conductive siloxane-based polyIL. Our ambient and high pressure studies revealed fundamental differences in the conducting propertiesmore » of the examined systems. Finally, we demonstrate that the proposed methodology is a powerful tool to identify the charge transport mechanism in polyILs in general and thereby contribute to unraveling the microscopic nature of the decoupling phenomenon in these materials.« less