Three-dimensional reconstruction of clustered microcalcifications from two digitized mammograms

Science.gov (United States)

Stotzka, Rainer; Mueller, Tim O.; Epper, Wolfgang; Gemmeke, Hartmut

1998-06-01

X-ray mammography is one of the most significant diagnosis methods in early detection of breast cancer. Usually two X- ray images from different angles are taken from each mamma to make even overlapping structures visible. X-ray mammography has a very high spatial resolution and can show microcalcifications of 50 - 200 micron in size. Clusters of microcalcifications are one of the most important and often the only indicator for malignant tumors. These calcifications are in some cases extremely difficult to detect. Computer assisted diagnosis of digitized mammograms may improve detection and interpretation of microcalcifications and cause more reliable diagnostic findings. We build a low-cost mammography workstation to detect and classify clusters of microcalcifications and tissue densities automatically. New in this approach is the estimation of the 3D formation of segmented microcalcifications and its visualization which will put additional diagnostic information at the radiologists disposal. The real problem using only two or three projections for reconstruction is the big loss of volume information. Therefore the arrangement of a cluster is estimated using only the positions of segmented microcalcifications. The arrangement of microcalcifications is visualized to the physician by rotating.

Electron and photon reconstruction and performance in ATLAS using a dynamical, topological cell clustering-based approach

CERN Document Server

The ATLAS collaboration

2017-01-01

The electron and photon reconstruction in ATLAS has moved towards the use of a dynamical, topo- logical cell-based approach for cluster building, owing to advancements in the calibration procedure which allow for such a method to be applied. The move to this new technique allows for improved measurements of electron and photon energies, particularly in situations where an electron radiates a bremsstrahlung photon, or a photon converts to an electron-poistron pair. This note details the changes to the ATLAS electron and photon reconstruction software, and assesses its performance under current LHC luminosity conditions using simulated data. Changes to the converted photon reconstruction are also detailed, which improve the reconstruction efficiency of double-track converted photons, as well as reducing the reconstruction of spurious one-track converted photons. The performance of the new reconstruction algorithm is also presented in a number of important topologies relevant to precision Standard Model physics,...

Four-dimensional reconstruction of cultural heritage sites based on photogrammetry and clustering

Science.gov (United States)

Voulodimos, Athanasios; Doulamis, Nikolaos; Fritsch, Dieter; Makantasis, Konstantinos; Doulamis, Anastasios; Klein, Michael

2017-01-01

A system designed and developed for the three-dimensional (3-D) reconstruction of cultural heritage (CH) assets is presented. Two basic approaches are presented. The first one, resulting in an "approximate" 3-D model, uses images retrieved in online multimedia collections; it employs a clustering-based technique to perform content-based filtering and eliminate outliers that significantly reduce the performance of 3-D reconstruction frameworks. The second one is based on input image data acquired through terrestrial laser scanning, as well as close range and airborne photogrammetry; it follows a sophisticated multistep strategy, which leads to a "precise" 3-D model. Furthermore, the concept of change history maps is proposed to address the computational limitations involved in four-dimensional (4-D) modeling, i.e., capturing 3-D models of a CH landmark or site at different time instances. The system also comprises a presentation viewer, which manages the display of the multifaceted CH content collected and created. The described methods have been successfully applied and evaluated in challenging real-world scenarios, including the 4-D reconstruction of the historic Market Square of the German city of Calw in the context of the 4-D-CH-World EU project.

GALAXY HALO TRUNCATION AND GIANT ARC SURFACE BRIGHTNESS RECONSTRUCTION IN THE CLUSTER MACSJ1206.2-0847

Energy Technology Data Exchange (ETDEWEB)

Eichner, Thomas; Seitz, Stella; Monna, Anna [Universitaets-Sternwarte Muenchen, Scheinerstr. 1, D-81679 Muenchen (Germany); Suyu, Sherry H. [Department of Physics, University of California, Santa Barbara, CA 93106 (United States); Halkola, Aleksi [Institute of Medical Engineering, University of Luebeck, Ratzeburger Allee 160 23562 Luebeck (Germany); Umetsu, Keiichi [Institute of Astronomy and Astrophysics, Academia Sinica, P.O. Box 23-141, Taipei 10617, Taiwan (China); Zitrin, Adi [Institut fuer Theoretische Astrophysik, ZAH, Albert-Ueberle-Strasse 2, D-69120 Heidelberg (Germany); Coe, Dan; Postman, Marc; Koekemoer, Anton; Bradley, Larry [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21208 (United States); Rosati, Piero [ESO-European Southern Observatory, D-85748 Garching bei Muenchen (Germany); Grillo, Claudio; Host, Ole [Dark Cosmology Centre, Niels Bohr Institute, University of Copenhagen, Juliane Maries Vej 30, DK-2100 Copenhagen (Denmark); Balestra, Italo [Max-Planck-Institut fuer Extraterrestrische Physik, Giessenbachstrasse, D-85748 Garching (Germany); Zheng, Wei; Lemze, Doron [Department of Physics and Astronomy, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218 (United States); Broadhurst, Tom [Department of Theoretical Physics, University of the Basque Country, P.O. Box 644, E-48080 Bilbao (Spain); Moustakas, Leonidas [Jet Propulsion Laboratory, California Institute of Technology, MS 169-327, Pasadena, CA 91109 (United States); Molino, Alberto [Instituto de Astrofisica de Andalucia (CSIC), C/Camino Bajo de Huetor 24, Granada E-18008 (Spain); and others

2013-09-10

In this work, we analyze the mass distribution of MACSJ1206.2-0847, particularly focusing on the halo properties of its cluster members. The cluster appears relaxed in its X-ray emission, but has a significant amount of intracluster light that is not centrally concentrated, suggesting that galaxy-scale interactions are still ongoing despite the overall relaxed state. The cluster lenses 12 background galaxies into multiple images and one galaxy at z = 1.033 into a giant arc and its counterimage. The multiple image positions and the surface brightness (SFB) distribution of the arc, which is bent around several cluster members, are sensitive to the cluster galaxy halo properties. We model the cluster mass distribution with a Navarro-Frenk-White profile and the galaxy halos with two parameters for the mass normalization and the extent of a reference halo assuming scalings with their observed near-infrared light. We match the multiple image positions at an rms level of 0.''85 and can reconstruct the SFB distribution of the arc in several filters to a remarkable accuracy based on this cluster model. The length scale where the enclosed galaxy halo mass is best constrained is about 5 effective radii-a scale in between those accessible to dynamical and field strong-lensing mass estimates on the one hand and galaxy-galaxy weak-lensing results on the other hand. The velocity dispersion and halo size of a galaxy with m{sub 160W,AB} = 19.2 and M{sub B,Vega} = -20.7 are {sigma} = 150 km s{sup -1} and r Almost-Equal-To 26 {+-} 6 kpc, respectively, indicating that the halos of the cluster galaxies are tidally stripped. We also reconstruct the unlensed source, which is smaller by a factor of {approx}5.8 in area, demonstrating the increase in morphological information due to lensing. We conclude that this galaxy likely has star-forming spiral arms with a red (older) central component.

GALAXY HALO TRUNCATION AND GIANT ARC SURFACE BRIGHTNESS RECONSTRUCTION IN THE CLUSTER MACSJ1206.2-0847

International Nuclear Information System (INIS)

Eichner, Thomas; Seitz, Stella; Monna, Anna; Suyu, Sherry H.; Halkola, Aleksi; Umetsu, Keiichi; Zitrin, Adi; Coe, Dan; Postman, Marc; Koekemoer, Anton; Bradley, Larry; Rosati, Piero; Grillo, Claudio; Høst, Ole; Balestra, Italo; Zheng, Wei; Lemze, Doron; Broadhurst, Tom; Moustakas, Leonidas; Molino, Alberto

2013-01-01

In this work, we analyze the mass distribution of MACSJ1206.2-0847, particularly focusing on the halo properties of its cluster members. The cluster appears relaxed in its X-ray emission, but has a significant amount of intracluster light that is not centrally concentrated, suggesting that galaxy-scale interactions are still ongoing despite the overall relaxed state. The cluster lenses 12 background galaxies into multiple images and one galaxy at z = 1.033 into a giant arc and its counterimage. The multiple image positions and the surface brightness (SFB) distribution of the arc, which is bent around several cluster members, are sensitive to the cluster galaxy halo properties. We model the cluster mass distribution with a Navarro-Frenk-White profile and the galaxy halos with two parameters for the mass normalization and the extent of a reference halo assuming scalings with their observed near-infrared light. We match the multiple image positions at an rms level of 0.''85 and can reconstruct the SFB distribution of the arc in several filters to a remarkable accuracy based on this cluster model. The length scale where the enclosed galaxy halo mass is best constrained is about 5 effective radii—a scale in between those accessible to dynamical and field strong-lensing mass estimates on the one hand and galaxy-galaxy weak-lensing results on the other hand. The velocity dispersion and halo size of a galaxy with m 160W,AB = 19.2 and M B,Vega = –20.7 are σ = 150 km s –1 and r ≈ 26 ± 6 kpc, respectively, indicating that the halos of the cluster galaxies are tidally stripped. We also reconstruct the unlensed source, which is smaller by a factor of ∼5.8 in area, demonstrating the increase in morphological information due to lensing. We conclude that this galaxy likely has star-forming spiral arms with a red (older) central component

A Linux cluster for between-pulse magnetic equilibrium reconstructions and other processor bound analyses

International Nuclear Information System (INIS)

Peng, Q.; Groebner, R. J.; Lao, L. L.; Schachter, J.; Schissel, D. P.; Wade, M. R.

2001-01-01

A 12-processor Linux PC cluster has been installed to perform between-pulse magnetic equilibrium reconstructions during tokamak operations using the EFIT code written in FORTRAN. The MPICH package implementing message passing interface is employed by EFIT for data distribution and communication. The new system calculates equilibria eight times faster than the previous system yielding a complete equilibrium time history on a 25 ms time scale 4 min after the pulse ends. A graphical interface is provided for users to control the time resolution and the type of EFITs. The next analysis to benefit from the cluster is CERQUICK written in IDL for ion temperature profile analysis. The plan is to expand the cluster so that a full profile analysis (Te, Ti, ne, Vr, Zeff) can be made available between pulses, which lays the ground work for Kinetic EFIT and/or ONETWO power balance analyses

Cluster analysis of the biochemical composition in 53 Sichuan EGCG3"Me tea resources

Science.gov (United States)

Li, J. H.; Chen, S. X.; Zhu, M. Z.; Meng, X. L.

2017-09-01

The EGCG3"Me contents in the young tea leaves of 102 tea resources in sichuan were analyzed accurately using HPLC-DAD. The results revealed that there was a wide variation in EGCG3"Me levels among different tea resources. The EGCG3"Me content in different tea resources was in a range from 0 to 11.04 mg/g, mean was 2.33 mg/g.53 tea resources contained EGCG3"Me, accounting for 51.96% of the total number of resources survey. Shucha5, Jinguanyin, Chengxi11, Fenghuang-dancong, Chongpi 71-1 were found to contain higher EGCG3"Me content (>10mg/g).Cluster analysis showed that: 53 Sichuan EGCG3"Me tea resources were divided into six groups and the difference was obvious between their biochemical composition; tea resources rich in EGCG3"Me were mainly distributed in Sichuan, Chongqing and Fujian Province, mostly were shrub and mid-leaf, mainly existed in tea resources which were suitable to make green tea, oolong tea. The morphological and biochemical distribution provided a good theoretical basis for selecting and utilizing higher EGCG3"Me resources.

Jets from jets: re-clustering as a tool for large radius jet reconstruction and grooming at the LHC

Energy Technology Data Exchange (ETDEWEB)

Nachman, Benjamin; Nef, Pascal; Schwartzman, Ariel; Swiatlowski, Maximilian [SLAC National Accelerator Laboratory, Stanford University,2575 Sand Hill Rd, Menlo Park, CA 94025 (United States); Wanotayaroj, Chaowaroj [Center for High Energy Physics, University of Oregon,1371 E. 13th Ave, Eugene, OR 97403 (United States)

2015-02-12

Jets with a large radius R≳1 and grooming algorithms are widely used to fully capture the decay products of boosted heavy particles at the Large Hadron Collider (LHC). Unlike most discriminating variables used in such studies, the jet radius is usually not optimized for specific physics scenarios. This is because every jet configuration must be calibrated, insitu, to account for detector response and other experimental effects. One solution to enhance the availability of large-R jet configurations used by the LHC experiments is jet re-clustering. Jet re-clustering introduces an intermediate scale rreconstruct large radius jets. In this paper we systematically study and propose new jet re-clustering configurations and show that re-clustered large radius jets have essentially the same jet mass performance as large radius groomed jets. Jet re-clustering has the benefit that no additional large-R calibration is necessary, allowing the re-clustered large radius parameter to be optimized in the context of specific precision measurements or searches for new physics.

Jets from jets: re-clustering as a tool for large radius jet reconstruction and grooming at the LHC

International Nuclear Information System (INIS)

Nachman, Benjamin; Nef, Pascal; Schwartzman, Ariel; Swiatlowski, Maximilian; Wanotayaroj, Chaowaroj

2015-01-01

Jets with a large radius R≳1 and grooming algorithms are widely used to fully capture the decay products of boosted heavy particles at the Large Hadron Collider (LHC). Unlike most discriminating variables used in such studies, the jet radius is usually not optimized for specific physics scenarios. This is because every jet configuration must be calibrated, insitu, to account for detector response and other experimental effects. One solution to enhance the availability of large-R jet configurations used by the LHC experiments is jet re-clustering. Jet re-clustering introduces an intermediate scale rreconstruct large radius jets. In this paper we systematically study and propose new jet re-clustering configurations and show that re-clustered large radius jets have essentially the same jet mass performance as large radius groomed jets. Jet re-clustering has the benefit that no additional large-R calibration is necessary, allowing the re-clustered large radius parameter to be optimized in the context of specific precision measurements or searches for new physics.

Electron Reconstruction in the CMS Electromagnetic Calorimeter

CERN Document Server

Meschi, Emilio; Seez, Christopher; Vikas, Pratibha

2001-01-01

This note describes the reconstruction of electrons using the electromagnetic calorimeter (ECAL) alone. This represents the first step in the High Level Trigger reconstruction and selection chain. By making "super-clusters" (i.e. clusters of clusters) much of the energy radiated by bremsstrahlung in the tracker material can be recovered. Representative performance figures for energy and position resolution in the barrel are given.

Haplotyping Problem, A Clustering Approach

International Nuclear Information System (INIS)

Eslahchi, Changiz; Sadeghi, Mehdi; Pezeshk, Hamid; Kargar, Mehdi; Poormohammadi, Hadi

2007-01-01

Construction of two haplotypes from a set of Single Nucleotide Polymorphism (SNP) fragments is called haplotype reconstruction problem. One of the most popular computational model for this problem is Minimum Error Correction (MEC). Since MEC is an NP-hard problem, here we propose a novel heuristic algorithm based on clustering analysis in data mining for haplotype reconstruction problem. Based on hamming distance and similarity between two fragments, our iterative algorithm produces two clusters of fragments; then, in each iteration, the algorithm assigns a fragment to one of the clusters. Our results suggest that the algorithm has less reconstruction error rate in comparison with other algorithms

Reconstructing galaxy histories from globular clusters.

Science.gov (United States)

West, Michael J; Côté, Patrick; Marzke, Ronald O; Jordán, Andrés

2004-01-01

Nearly a century after the true nature of galaxies as distant 'island universes' was established, their origin and evolution remain great unsolved problems of modern astrophysics. One of the most promising ways to investigate galaxy formation is to study the ubiquitous globular star clusters that surround most galaxies. Globular clusters are compact groups of up to a few million stars. They generally formed early in the history of the Universe, but have survived the interactions and mergers that alter substantially their parent galaxies. Recent advances in our understanding of the globular cluster systems of the Milky Way and other galaxies point to a complex picture of galaxy genesis driven by cannibalism, collisions, bursts of star formation and other tumultuous events.

Palladium clusters deposited on the heterogeneous substrates

Energy Technology Data Exchange (ETDEWEB)

Wang, Kun, E-mail: cqdxwk@126.com [College of Power Engineering, Chongqing University, Chongqing 400044 (China); Key Laboratory of Low-grade Energy Utilization Technologies and Systems, Ministry of Education of PRC, Chongqing 400044 (China); Liu, Juanfang, E-mail: juanfang@cqu.edu.cn [College of Power Engineering, Chongqing University, Chongqing 400044 (China); Key Laboratory of Low-grade Energy Utilization Technologies and Systems, Ministry of Education of PRC, Chongqing 400044 (China); Chen, Qinghua, E-mail: qhchen@cqu.edu.cn [College of Power Engineering, Chongqing University, Chongqing 400044 (China); Key Laboratory of Low-grade Energy Utilization Technologies and Systems, Ministry of Education of PRC, Chongqing 400044 (China)

2016-07-15

Graphical abstract: The site-exchange between the substrate and cluster atoms can result in the formation of the surface alloys and the reconstruction of the cluster structure before the collision system approaching the thermal equilibrium. The deposited cluster adjusted the atom arrangement as possibly as to match the substrate lattice arrangement from bottom to up. The structural reconstruction is accompanied by the system potential energy minimization. - Highlights: • The deposition process can divide explicitly into three stages: adsorption, collision, relaxation. • The local melt does not emerge inside the substrate during the deposition process. • Surface alloys are formed by the site-exchange between the cluster and substrate atoms. • The cluster reconstructs the atom arrangement following as the substrate lattice arrangement from bottom to up. • The structural reconstruction ability and scope depend on the cluster size and incident energy. - Abstract: To improve the performance of the Pd composite membrane prepared by the cold spraying technology, it is extremely essential to give insights into the deposition process of the cluster and the heterogeneous deposition of the big Pd cluster at the different incident velocities on the atomic level. The deposition behavior, morphologies, energetic and interfacial configuration were examined by the molecular dynamic simulation and characterized by the cluster flattening ratio, the substrate maximum local temperature, the atom-embedded layer number and the surface-alloy formation. According to the morphology evolution, three deposition stages and the corresponding structural and energy evolution were clearly identified. The cluster deformation and penetrating depth increased with the enhancement of the incident velocity, but the increase degree also depended on the substrate hardness. The interfacial interaction between the cluster and the substrate can be improved by the higher substrate local temperature

Pheochromocytoma-paraganglioma: Biochemical and genetic diagnosis.

Science.gov (United States)

Cano Megías, Marta; Rodriguez Puyol, Diego; Fernández Rodríguez, Loreto; Sención Martinez, Gloria Lisette; Martínez Miguel, Patricia

Pheochromocytomas and paragangliomas are tumours derived from neural crest cells, which can be diagnosed by biochemical measurement of metanephrine and methoxytyramine. Advances in genetic research have identified many genes involved in the pathogenesis of these tumours, suggesting that up to 35-45% may have an underlying germline mutation. These genes have a singular transcriptional signature and can be grouped into 2 clusters (or groups): cluster 1 (VHL and SHDx), involved in angiogenesis and hypoxia pathways; and cluster 2 (MEN2 and NF1), linked to the kinase signalling pathway. In turn, these genes are associated with a characteristic biochemical phenotype (noradrenergic and adrenergic), and clinical features (location, biological behaviour, age of presentation, etc.) in a large number of cases. Early diagnosis of these tumours, accompanied by a correct genetic diagnosis, should eventually become a priority to enable better treatment, early detection of complications, proper screening of family members and related tumours, as well as an improvement in the overall prognosis of these patients. Copyright © 2016 Sociedad Española de Nefrología. Published by Elsevier España, S.L.U. All rights reserved.

BES-II fast data reconstruction

International Nuclear Information System (INIS)

Rong Gang; Zhang Jiawen; Guo Yiqing; Zhang Shaoqiang; Zhao Dixin

2002-01-01

The BES-II fast data reconstruction is reported. Based on PC FARM and/or a 'Distributed Clustered Linux PC System', BES-II fast data reconstruction system is set up. With this system the BES-II data can be fully reconstructed in about 20 minutes after data collection. It takes only 12 minutes to fully reconstruct 30000 events, collected with BES-II detector at BEPC Collider, with a P III-800 PC. The detector performance can be examined based on fully reconstructed data in about 20 minutes after data taking in the BES-II experiment

Biochemical markers of cartilage metabolism are associated with walking biomechanics 6-months following anterior cruciate ligament reconstruction.

Science.gov (United States)

Pietrosimone, Brian; Loeser, Richard F; Blackburn, J Troy; Padua, Darin A; Harkey, Matthew S; Stanley, Laura E; Luc-Harkey, Brittney A; Ulici, Veronica; Marshall, Stephen W; Jordan, Joanne M; Spang, Jeffery T

2017-10-01

The purpose of our study was to determine the association between biomechanical outcomes of walking gait (peak vertical ground reaction force [vGRF], vGRF loading rate [vGRF-LR], and knee adduction moment [KAM]) 6 months following anterior cruciate ligament reconstruction (ACLR) and biochemical markers of serum type-II collagen turnover (collagen type-II cleavage product to collagen type-II C-propeptide [C2C:CPII]), plasma degenerative enzymes (matrix metalloproteinase-3 [MMP-3]), and a pro-inflammatory cytokine (interleukin-6 [IL-6]). Biochemical markers were evaluated within the first 2 weeks (6.5 ± 3.8 days) following ACL injury and again 6 months following ACLR in eighteen participants. All peak biomechanical outcomes were extracted from the first 50% of the stance phase of walking gait during a 6-month follow-up exam. Limb symmetry indices (LSI) were used to normalize the biomechanical outcomes in the ACLR limb to that of the contralateral limb (ACLR/contralateral). Bivariate correlations were used to assess associations between biomechanical and biochemical outcomes. Greater plasma MMP-3 concentrations after ACL injury and at the 6-month follow-up exam were associated with lesser KAM LSI. Lesser KAM was associated with greater plasma IL-6 at the 6-month follow-up exam. Similarly, lesser vGRF-LR LSI was associated with greater plasma MMP-3 concentrations at the 6-month follow-up exam. Lesser peak vGRF LSI was associated with higher C2C:CPII after ACL injury, yet this association was not significant after accounting for walking speed. Therefore, lesser biomechanical loading in the ACLR limb, compared to the contralateral limb, 6 months following ACLR may be related to deleterious joint tissue metabolism that could influence future cartilage breakdown. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:2288-2297, 2017. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

Defining clusters in APT reconstructions of ODS steels.

Science.gov (United States)

Williams, Ceri A; Haley, Daniel; Marquis, Emmanuelle A; Smith, George D W; Moody, Michael P

2013-09-01

Oxide nanoclusters in a consolidated Fe-14Cr-2W-0.3Ti-0.3Y₂O₃ ODS steel and in the alloy powder after mechanical alloying (but before consolidation) are investigated by atom probe tomography (APT). The maximum separation method is a standard method to define and characterise clusters from within APT data, but this work shows that the extent of clustering between the two materials is sufficiently different that the nanoclusters in the mechanically alloyed powder and in the consolidated material cannot be compared directly using the same cluster selection parameters. As the cluster selection parameters influence the size and composition of the clusters significantly, a procedure to optimise the input parameters for the maximum separation method is proposed by sweeping the d(max) and N(min) parameter space. By applying this method of cluster parameter selection combined with a 'matrix correction' to account for trajectory aberrations, differences in the oxide nanoclusters can then be reliably quantified. Copyright © 2012 Elsevier B.V. All rights reserved.

Classification Scheme for Centuries of Reconstructed Streamflow Droughts in Water Resources Planning

Science.gov (United States)

Stagge, J.; Rosenberg, D. E.

2017-12-01

New advances in reconstructing streamflow from tree rings have permitted the reconstruction of flows back to the 1400s or earlier at a monthly, rather than annual, time scale. This is a critical step for incorporating centuries of streamflow reconstructions into water resources planning. Expanding the historical record is particularly important where the observed record contains few of these rare, but potentially disastrous extreme events. We present how a paleo-drought clustering approach was incorporated alongside more traditional water management planning in the Weber River basin, northern Utah. This study used newly developed monthly reconstructions of flow since 1430 CE and defined drought events as flow less than the 50th percentile during at least three contiguous months. Characteristics for each drought event included measures of drought duration, severity, cumulative loss, onset, seasonality, recession rate, and recovery rate. Reconstructed drought events were then clustered by hierarchical clustering to determine distinct drought "types" and the historical event that best represents the centroid of each cluster. The resulting 144 reconstructed drought events in the Weber basin clustered into nine distinct types, of which four were severe enough to potentially require drought management. Using the characteristic drought event for each of the severe drought clusters, water managers were able to estimate system reliability and the historical return frequency for each drought type. Plotting drought duration and severity from centuries of historical reconstructed events alongside observed events and climate change projections further placed recent events into a historical context. For example, the drought of record for the Weber River remains the most severe event in the record with regard to minimum flow percentile (1930, 7 years), but is far from the longest event in the longer historical record, where events beginning in 1658 and 1705 both lasted longer

Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network

Directory of Open Access Journals (Sweden)

Heavner Benjamin D

2012-06-01

Full Text Available Abstract Background Efforts to improve the computational reconstruction of the Saccharomyces cerevisiae biochemical reaction network and to refine the stoichiometrically constrained metabolic models that can be derived from such a reconstruction have continued since the first stoichiometrically constrained yeast genome scale metabolic model was published in 2003. Continuing this ongoing process, we have constructed an update to the Yeast Consensus Reconstruction, Yeast 5. The Yeast Consensus Reconstruction is a product of efforts to forge a community-based reconstruction emphasizing standards compliance and biochemical accuracy via evidence-based selection of reactions. It draws upon models published by a variety of independent research groups as well as information obtained from biochemical databases and primary literature. Results Yeast 5 refines the biochemical reactions included in the reconstruction, particularly reactions involved in sphingolipid metabolism; updates gene-reaction annotations; and emphasizes the distinction between reconstruction and stoichiometrically constrained model. Although it was not a primary goal, this update also improves the accuracy of model prediction of viability and auxotrophy phenotypes and increases the number of epistatic interactions. This update maintains an emphasis on standards compliance, unambiguous metabolite naming, and computer-readable annotations available through a structured document format. Additionally, we have developed MATLAB scripts to evaluate the model’s predictive accuracy and to demonstrate basic model applications such as simulating aerobic and anaerobic growth. These scripts, which provide an independent tool for evaluating the performance of various stoichiometrically constrained yeast metabolic models using flux balance analysis, are included as Additional files 1, 2 and 3. Additional file 1 Function testYeastModel.m.m. Click here for file Additional file 2 Function modelToReconstruction

Org.Lcsim: Event Reconstruction in Java

International Nuclear Information System (INIS)

Graf, Norman

2011-01-01

Maximizing the physics performance of detectors being designed for the International Linear Collider, while remaining sensitive to cost constraints, requires a powerful, efficient, and flexible simulation, reconstruction and analysis environment to study the capabilities of a large number of different detector designs. The preparation of Letters Of Intent for the International Linear Collider involved the detailed study of dozens of detector options, layouts and readout technologies; the final physics benchmarking studies required the reconstruction and analysis of hundreds of millions of events. We describe the Java-based software toolkit (org.lcsim) which was used for full event reconstruction and analysis. The components are fully modular and are available for tasks from digitization of tracking detector signals through to cluster finding, pattern recognition, track-fitting, calorimeter clustering, individual particle reconstruction, jet-finding, and analysis. The detector is defined by the same xml input files used for the detector response simulation, ensuring the simulation and reconstruction geometries are always commensurate by construction. We discuss the architecture as well as the performance.

Plasmon enhanced silver quantum cluster fluorescence for biochemical applications

DEFF Research Database (Denmark)

Bernard, S.; Kutter, J.P.; Mogensen, Klaus Bo

2014-01-01

Fluorescence microscopy of individual silver quantum clusters on the surface of silver nanoparticles reveals strong photoactivated emission under blue light excitation [1-4]. In this work, silver nanoparticles are produced by annealing silver thin films deposited on a glass substrate and silver q...... purposes. It was found, that in presence of a strong nucleophile (such as CN-), silver quantum clusters are dissolved into non-fluorescing AgCN complexes, resulting in a fast and observable decrease of the fluorescent signal....

Reconstruction of the central carbon metabolism of Aspergillus niger

DEFF Research Database (Denmark)

David, Helga; Åkesson, Mats Fredrik; Nielsen, Jens

2003-01-01

The topology of central carbon metabolism of Aspergillus niger was identified and the metabolic network reconstructed, by integrating genomic, biochemical and physiological information available for this microorganism and other related fungi. The reconstructed network may serve as a valuable...... of metabolic fluxes using metabolite balancing. This framework was employed to perform an in silico characterisation of the phenotypic behaviour of A. niger grown on different carbon sources. The effects on growth of single reaction deletions were assessed and essential biochemical reactions were identified...... for different carbon sources. Furthermore, application of the stoichiometric model for assessing the metabolic capabilities of A. niger to produce metabolites was evaluated by using succinate production as a case study....

THE GRISM LENS-AMPLIFIED SURVEY FROM SPACE (GLASS). IV. MASS RECONSTRUCTION OF THE LENSING CLUSTER ABELL 2744 FROM FRONTIER FIELD IMAGING AND GLASS SPECTROSCOPY

Energy Technology Data Exchange (ETDEWEB)

Wang, X.; Schmidt, K. B.; Jones, T. A. [Department of Physics, University of California, Santa Barbara, CA 93106-9530 (United States); Hoag, A.; Huang, K.-H.; Bradac, M. [Department of Physics, University of California, Davis, CA 95616 (United States); Treu, T. [Department of Physics and Astronomy, UCLA, Los Angeles, CA 90095-1547 (United States); Brammer, G. B.; Ryan, R. E. Jr. [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD, 21218 (United States); Vulcani, B. [Kavli Institute for the Physics and Mathematics of the Universe (WPI), The University of Tokyo Institutes for Advanced Study (UTIAS), the University of Tokyo, Kashiwa, 277-8582 (Japan); Amorín, R.; Castellano, M.; Fontana, A.; Merlin, E. [INAF—Osservatorio Astronomico di Roma Via Frascati 33, I-00040 Monte Porzio Catone (Italy); Trenti, M., E-mail: xinwang@physics.ucsb.edu [School of Physics, The University of Melbourne, VIC 3010 (Australia)

2015-09-20

We present a strong and weak lensing reconstruction of the massive cluster Abell 2744, the first cluster for which deep Hubble Frontier Fields (HFF) images and spectroscopy from the Grism Lens-Amplified Survey from Space (GLASS) are available. By performing a targeted search for emission lines in multiply imaged sources using the GLASS spectra, we obtain five high-confidence spectroscopic redshifts and two tentative ones. We confirm one strongly lensed system by detecting the same emission lines in all three multiple images. We also search for additional line emitters blindly and use the full GLASS spectroscopic catalog to test reliability of photometric redshifts for faint line emitters. We see a reasonable agreement between our photometric and spectroscopic redshift measurements, when including nebular emission in photometric redshift estimations. We introduce a stringent procedure to identify only secure multiple image sets based on colors, morphology, and spectroscopy. By combining 7 multiple image systems with secure spectroscopic redshifts (at 5 distinct redshift planes) with 18 multiple image systems with secure photometric redshifts, we reconstruct the gravitational potential of the cluster pixellated on an adaptive grid, using a total of 72 images. The resulting mass map is compared with a stellar mass map obtained from the deep Spitzer Frontier Fields data to study the relative distribution of stars and dark matter in the cluster. We find that the stellar to total mass ratio varies substantially across the cluster field, suggesting that stars do not trace exactly the total mass in this interacting system. The maps of convergence, shear, and magnification are made available in the standard HFF format.

The Grism Lens-amplified Survey from Space (GLASS). IV. Mass Reconstruction of the Lensing Cluster Abell 2744 from Frontier Field Imaging and GLASS Spectroscopy

Science.gov (United States)

Wang, X.; Hoag, A.; Huang, K.-H.; Treu, T.; Bradač, M.; Schmidt, K. B.; Brammer, G. B.; Vulcani, B.; Jones, T. A.; Ryan, R. E., Jr.; Amorín, R.; Castellano, M.; Fontana, A.; Merlin, E.; Trenti, M.

2015-09-01

We present a strong and weak lensing reconstruction of the massive cluster Abell 2744, the first cluster for which deep Hubble Frontier Fields (HFF) images and spectroscopy from the Grism Lens-Amplified Survey from Space (GLASS) are available. By performing a targeted search for emission lines in multiply imaged sources using the GLASS spectra, we obtain five high-confidence spectroscopic redshifts and two tentative ones. We confirm one strongly lensed system by detecting the same emission lines in all three multiple images. We also search for additional line emitters blindly and use the full GLASS spectroscopic catalog to test reliability of photometric redshifts for faint line emitters. We see a reasonable agreement between our photometric and spectroscopic redshift measurements, when including nebular emission in photometric redshift estimations. We introduce a stringent procedure to identify only secure multiple image sets based on colors, morphology, and spectroscopy. By combining 7 multiple image systems with secure spectroscopic redshifts (at 5 distinct redshift planes) with 18 multiple image systems with secure photometric redshifts, we reconstruct the gravitational potential of the cluster pixellated on an adaptive grid, using a total of 72 images. The resulting mass map is compared with a stellar mass map obtained from the deep Spitzer Frontier Fields data to study the relative distribution of stars and dark matter in the cluster. We find that the stellar to total mass ratio varies substantially across the cluster field, suggesting that stars do not trace exactly the total mass in this interacting system. The maps of convergence, shear, and magnification are made available in the standard HFF format.

Hierarchical thinking in network biology: the unbiased modularization of biochemical networks.

Science.gov (United States)

Papin, Jason A; Reed, Jennifer L; Palsson, Bernhard O

2004-12-01

As reconstructed biochemical reaction networks continue to grow in size and scope, there is a growing need to describe the functional modules within them. Such modules facilitate the study of biological processes by deconstructing complex biological networks into conceptually simple entities. The definition of network modules is often based on intuitive reasoning. As an alternative, methods are being developed for defining biochemical network modules in an unbiased fashion. These unbiased network modules are mathematically derived from the structure of the whole network under consideration.

Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network

DEFF Research Database (Denmark)

Förster, Jochen; Famili, I.; Fu, P.

2003-01-01

The metabolic network in the yeast Saccharomyces cerevisiae was reconstructed using currently available genomic, biochemical, and physiological information. The metabolic reactions were compartmentalized between the cytosol and the mitochondria, and transport steps between the compartments...

ON THE ACCURACY OF WEAK-LENSING CLUSTER MASS RECONSTRUCTIONS

International Nuclear Information System (INIS)

Becker, Matthew R.; Kravtsov, Andrey V.

2011-01-01

We study the bias and scatter in mass measurements of galaxy clusters resulting from fitting a spherically symmetric Navarro, Frenk, and White model to the reduced tangential shear profile measured in weak-lensing (WL) observations. The reduced shear profiles are generated for ∼10 4 cluster-sized halos formed in a ΛCDM cosmological N-body simulation of a 1 h -1 Gpc box. In agreement with previous studies, we find that the scatter in the WL masses derived using this fitting method has irreducible contributions from the triaxial shapes of cluster-sized halos and uncorrelated large-scale matter projections along the line of sight. Additionally, we find that correlated large-scale structure within several virial radii of clusters contributes a smaller, but nevertheless significant, amount to the scatter. The intrinsic scatter due to these physical sources is ∼20% for massive clusters and can be as high as ∼30% for group-sized systems. For current, ground-based observations, however, the total scatter should be dominated by shape noise from the background galaxies used to measure the shear. Importantly, we find that WL mass measurements can have a small, ∼5%-10%, but non-negligible amount of bias. Given that WL measurements of cluster masses are a powerful way to calibrate cluster mass-observable relations for precision cosmological constraints, we strongly emphasize that a robust calibration of the bias requires detailed simulations that include more observational effects than we consider here. Such a calibration exercise needs to be carried out for each specific WL mass estimation method, as the details of the method determine in part the expected scatter and bias. We present an iterative method for estimating mass M 500c that can eliminate the bias for analyses of ground-based data.

Honey bee-inspired algorithms for SNP haplotype reconstruction problem

Science.gov (United States)

PourkamaliAnaraki, Maryam; Sadeghi, Mehdi

2016-03-01

Reconstructing haplotypes from SNP fragments is an important problem in computational biology. There have been a lot of interests in this field because haplotypes have been shown to contain promising data for disease association research. It is proved that haplotype reconstruction in Minimum Error Correction model is an NP-hard problem. Therefore, several methods such as clustering techniques, evolutionary algorithms, neural networks and swarm intelligence approaches have been proposed in order to solve this problem in appropriate time. In this paper, we have focused on various evolutionary clustering techniques and try to find an efficient technique for solving haplotype reconstruction problem. It can be referred from our experiments that the clustering methods relying on the behaviour of honey bee colony in nature, specifically bees algorithm and artificial bee colony methods, are expected to result in more efficient solutions. An application program of the methods is available at the following link. http://www.bioinf.cs.ipm.ir/software/haprs/

Super resolution reconstruction of infrared images based on classified dictionary learning

Science.gov (United States)

Liu, Fei; Han, Pingli; Wang, Yi; Li, Xuan; Bai, Lu; Shao, Xiaopeng

2018-05-01

Infrared images always suffer from low-resolution problems resulting from limitations of imaging devices. An economical approach to combat this problem involves reconstructing high-resolution images by reasonable methods without updating devices. Inspired by compressed sensing theory, this study presents and demonstrates a Classified Dictionary Learning method to reconstruct high-resolution infrared images. It classifies features of the samples into several reasonable clusters and trained a dictionary pair for each cluster. The optimal pair of dictionaries is chosen for each image reconstruction and therefore, more satisfactory results is achieved without the increase in computational complexity and time cost. Experiments and results demonstrated that it is a viable method for infrared images reconstruction since it improves image resolution and recovers detailed information of targets.

A multi-instrument non-parametric reconstruction of the electron pressure profile in the galaxy cluster CLJ1226.9+3332

Science.gov (United States)

Romero, C.; McWilliam, M.; Macías-Pérez, J.-F.; Adam, R.; Ade, P.; André, P.; Aussel, H.; Beelen, A.; Benoît, A.; Bideaud, A.; Billot, N.; Bourrion, O.; Calvo, M.; Catalano, A.; Coiffard, G.; Comis, B.; de Petris, M.; Désert, F.-X.; Doyle, S.; Goupy, J.; Kramer, C.; Lagache, G.; Leclercq, S.; Lestrade, J.-F.; Mauskopf, P.; Mayet, F.; Monfardini, A.; Pascale, E.; Perotto, L.; Pisano, G.; Ponthieu, N.; Revéret, V.; Ritacco, A.; Roussel, H.; Ruppin, F.; Schuster, K.; Sievers, A.; Triqueneaux, S.; Tucker, C.; Zylka, R.

2018-04-01

Context. In the past decade, sensitive, resolved Sunyaev-Zel'dovich (SZ) studies of galaxy clusters have become common. Whereas many previous SZ studies have parameterized the pressure profiles of galaxy clusters, non-parametric reconstructions will provide insights into the thermodynamic state of the intracluster medium. Aim. We seek to recover the non-parametric pressure profiles of the high redshift (z = 0.89) galaxy cluster CLJ 1226.9+3332 as inferred from SZ data from the MUSTANG, NIKA, Bolocam, and Planck instruments, which all probe different angular scales. Methods: Our non-parametric algorithm makes use of logarithmic interpolation, which under the assumption of ellipsoidal symmetry is analytically integrable. For MUSTANG, NIKA, and Bolocam we derive a non-parametric pressure profile independently and find good agreement among the instruments. In particular, we find that the non-parametric profiles are consistent with a fitted generalized Navaro-Frenk-White (gNFW) profile. Given the ability of Planck to constrain the total signal, we include a prior on the integrated Compton Y parameter as determined by Planck. Results: For a given instrument, constraints on the pressure profile diminish rapidly beyond the field of view. The overlap in spatial scales probed by these four datasets is therefore critical in checking for consistency between instruments. By using multiple instruments, our analysis of CLJ 1226.9+3332 covers a large radial range, from the central regions to the cluster outskirts: 0.05 R500 generation of SZ instruments such as NIKA2 and MUSTANG2.

Modularization of biochemical networks based on classification of Petri net t-invariants.

Science.gov (United States)

Grafahrend-Belau, Eva; Schreiber, Falk; Heiner, Monika; Sackmann, Andrea; Junker, Björn H; Grunwald, Stefanie; Speer, Astrid; Winder, Katja; Koch, Ina

2008-02-08

Structural analysis of biochemical networks is a growing field in bioinformatics and systems biology. The availability of an increasing amount of biological data from molecular biological networks promises a deeper understanding but confronts researchers with the problem of combinatorial explosion. The amount of qualitative network data is growing much faster than the amount of quantitative data, such as enzyme kinetics. In many cases it is even impossible to measure quantitative data because of limitations of experimental methods, or for ethical reasons. Thus, a huge amount of qualitative data, such as interaction data, is available, but it was not sufficiently used for modeling purposes, until now. New approaches have been developed, but the complexity of data often limits the application of many of the methods. Biochemical Petri nets make it possible to explore static and dynamic qualitative system properties. One Petri net approach is model validation based on the computation of the system's invariant properties, focusing on t-invariants. T-invariants correspond to subnetworks, which describe the basic system behavior.With increasing system complexity, the basic behavior can only be expressed by a huge number of t-invariants. According to our validation criteria for biochemical Petri nets, the necessary verification of the biological meaning, by interpreting each subnetwork (t-invariant) manually, is not possible anymore. Thus, an automated, biologically meaningful classification would be helpful in analyzing t-invariants, and supporting the understanding of the basic behavior of the considered biological system. Here, we introduce a new approach to automatically classify t-invariants to cope with network complexity. We apply clustering techniques such as UPGMA, Complete Linkage, Single Linkage, and Neighbor Joining in combination with different distance measures to get biologically meaningful clusters (t-clusters), which can be interpreted as modules. To find

Modularization of biochemical networks based on classification of Petri net t-invariants

Directory of Open Access Journals (Sweden)

Grunwald Stefanie

2008-02-01

Full Text Available Abstract Background Structural analysis of biochemical networks is a growing field in bioinformatics and systems biology. The availability of an increasing amount of biological data from molecular biological networks promises a deeper understanding but confronts researchers with the problem of combinatorial explosion. The amount of qualitative network data is growing much faster than the amount of quantitative data, such as enzyme kinetics. In many cases it is even impossible to measure quantitative data because of limitations of experimental methods, or for ethical reasons. Thus, a huge amount of qualitative data, such as interaction data, is available, but it was not sufficiently used for modeling purposes, until now. New approaches have been developed, but the complexity of data often limits the application of many of the methods. Biochemical Petri nets make it possible to explore static and dynamic qualitative system properties. One Petri net approach is model validation based on the computation of the system's invariant properties, focusing on t-invariants. T-invariants correspond to subnetworks, which describe the basic system behavior. With increasing system complexity, the basic behavior can only be expressed by a huge number of t-invariants. According to our validation criteria for biochemical Petri nets, the necessary verification of the biological meaning, by interpreting each subnetwork (t-invariant manually, is not possible anymore. Thus, an automated, biologically meaningful classification would be helpful in analyzing t-invariants, and supporting the understanding of the basic behavior of the considered biological system. Methods Here, we introduce a new approach to automatically classify t-invariants to cope with network complexity. We apply clustering techniques such as UPGMA, Complete Linkage, Single Linkage, and Neighbor Joining in combination with different distance measures to get biologically meaningful clusters (t-clusters

Beyond Low-Rank Representations: Orthogonal clustering basis reconstruction with optimized graph structure for multi-view spectral clustering.

Science.gov (United States)

Wang, Yang; Wu, Lin

2018-07-01

Low-Rank Representation (LRR) is arguably one of the most powerful paradigms for Multi-view spectral clustering, which elegantly encodes the multi-view local graph/manifold structures into an intrinsic low-rank self-expressive data similarity embedded in high-dimensional space, to yield a better graph partition than their single-view counterparts. In this paper we revisit it with a fundamentally different perspective by discovering LRR as essentially a latent clustered orthogonal projection based representation winged with an optimized local graph structure for spectral clustering; each column of the representation is fundamentally a cluster basis orthogonal to others to indicate its members, which intuitively projects the view-specific feature representation to be the one spanned by all orthogonal basis to characterize the cluster structures. Upon this finding, we propose our technique with the following: (1) We decompose LRR into latent clustered orthogonal representation via low-rank matrix factorization, to encode the more flexible cluster structures than LRR over primal data objects; (2) We convert the problem of LRR into that of simultaneously learning orthogonal clustered representation and optimized local graph structure for each view; (3) The learned orthogonal clustered representations and local graph structures enjoy the same magnitude for multi-view, so that the ideal multi-view consensus can be readily achieved. The experiments over multi-view datasets validate its superiority, especially over recent state-of-the-art LRR models. Copyright © 2018 Elsevier Ltd. All rights reserved.

Reconstruction of the central carbon metabolism of Aspergillus niger

DEFF Research Database (Denmark)

David, Helga; Åkesson, Mats Fredrik; Nielsen, Jens

2003-01-01

database for annotation of genes identified in future genome sequencing projects on aspergilli. Based on the metabolic reconstruction, a stoichiometric model was set up that includes 284 metabolites and 335 reactions, of which 268 represent biochemical conversions and 67 represent transport processes...

Assessment of phylogenetic sensitivity for reconstructing HIV-1 epidemiological relationships.

Science.gov (United States)

Beloukas, Apostolos; Magiorkinis, Emmanouil; Magiorkinis, Gkikas; Zavitsanou, Asimina; Karamitros, Timokratis; Hatzakis, Angelos; Paraskevis, Dimitrios

2012-06-01

Phylogenetic analysis has been extensively used as a tool for the reconstruction of epidemiological relations for research or for forensic purposes. It was our objective to assess the sensitivity of different phylogenetic methods and various phylogenetic programs to reconstruct epidemiological links among HIV-1 infected patients that is the probability to reveal a true transmission relationship. Multiple datasets (90) were prepared consisting of HIV-1 sequences in protease (PR) and partial reverse transcriptase (RT) sampled from patients with documented epidemiological relationship (target population), and from unrelated individuals (control population) belonging to the same HIV-1 subtype as the target population. Each dataset varied regarding the number, the geographic origin and the transmission risk groups of the sequences among the control population. Phylogenetic trees were inferred by neighbor-joining (NJ), maximum likelihood heuristics (hML) and Bayesian methods. All clusters of sequences belonging to the target population were correctly reconstructed by NJ and Bayesian methods receiving high bootstrap and posterior probability (PP) support, respectively. On the other hand, TreePuzzle failed to reconstruct or provide significant support for several clusters; high puzzling step support was associated with the inclusion of control sequences from the same geographic area as the target population. In contrary, all clusters were correctly reconstructed by hML as implemented in PhyML 3.0 receiving high bootstrap support. We report that under the conditions of our study, hML using PhyML, NJ and Bayesian methods were the most sensitive for the reconstruction of epidemiological links mostly from sexually infected individuals. Copyright © 2012 Elsevier B.V. All rights reserved.

A protocol for generating a high-quality genome-scale metabolic reconstruction.

Science.gov (United States)

Thiele, Ines; Palsson, Bernhard Ø

2010-01-01

Network reconstructions are a common denominator in systems biology. Bottom-up metabolic network reconstructions have been developed over the last 10 years. These reconstructions represent structured knowledge bases that abstract pertinent information on the biochemical transformations taking place within specific target organisms. The conversion of a reconstruction into a mathematical format facilitates a myriad of computational biological studies, including evaluation of network content, hypothesis testing and generation, analysis of phenotypic characteristics and metabolic engineering. To date, genome-scale metabolic reconstructions for more than 30 organisms have been published and this number is expected to increase rapidly. However, these reconstructions differ in quality and coverage that may minimize their predictive potential and use as knowledge bases. Here we present a comprehensive protocol describing each step necessary to build a high-quality genome-scale metabolic reconstruction, as well as the common trials and tribulations. Therefore, this protocol provides a helpful manual for all stages of the reconstruction process.

Universal Spatial Correlation Functions for Describing and Reconstructing Soil Microstructure

Science.gov (United States)

Skvortsova, Elena B.; Mallants, Dirk

2015-01-01

Structural features of porous materials such as soil define the majority of its physical properties, including water infiltration and redistribution, multi-phase flow (e.g. simultaneous water/air flow, or gas exchange between biologically active soil root zone and atmosphere) and solute transport. To characterize soil microstructure, conventional soil science uses such metrics as pore size and pore-size distributions and thin section-derived morphological indicators. However, these descriptors provide only limited amount of information about the complex arrangement of soil structure and have limited capability to reconstruct structural features or predict physical properties. We introduce three different spatial correlation functions as a comprehensive tool to characterize soil microstructure: 1) two-point probability functions, 2) linear functions, and 3) two-point cluster functions. This novel approach was tested on thin-sections (2.21×2.21 cm2) representing eight soils with different pore space configurations. The two-point probability and linear correlation functions were subsequently used as a part of simulated annealing optimization procedures to reconstruct soil structure. Comparison of original and reconstructed images was based on morphological characteristics, cluster correlation functions, total number of pores and pore-size distribution. Results showed excellent agreement for soils with isolated pores, but relatively poor correspondence for soils exhibiting dual-porosity features (i.e. superposition of pores and micro-cracks). Insufficient information content in the correlation function sets used for reconstruction may have contributed to the observed discrepancies. Improved reconstructions may be obtained by adding cluster and other correlation functions into reconstruction sets. Correlation functions and the associated stochastic reconstruction algorithms introduced here are universally applicable in soil science, such as for soil classification

Reconstruction of Cluster Positions in the LHCb Velo

CERN Document Server

Parkes, C; Szumlak, T

2007-01-01

This note describes the `Velo Cluster Position Tool'. This software is used in the GAUDI framework to estimate the hit position of a particle traversing the silicon sensors of the LHCb VELO and to estimate the uncertainty on this position. This estimate and its uncertainty are used in the LHCb track fit. The definition of the cluster centre is given and the baseline linear approximation method presented. The position error is strongly dependent on the angle of incidence of the particle on the silicon sensors measured perpendicularly to the strips -- known as the projected angle -- and on the silicon sensor pitch at the point of incidence, and is parametrised in terms of these variables. Pull plots are presented to show the quality of the current tuning implemented for simulation events.

Structural and biochemical analysis of nuclease domain of clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 3 (Cas3).

Science.gov (United States)

Mulepati, Sabin; Bailey, Scott

2011-09-09

RNA transcribed from clustered regularly interspaced short palindromic repeats (CRISPRs) protects many prokaryotes from invasion by foreign DNA such as viruses, conjugative plasmids, and transposable elements. Cas3 (CRISPR-associated protein 3) is essential for this CRISPR protection and is thought to mediate cleavage of the foreign DNA through its N-terminal histidine-aspartate (HD) domain. We report here the 1.8 Å crystal structure of the HD domain of Cas3 from Thermus thermophilus HB8. Structural and biochemical studies predict that this enzyme binds two metal ions at its active site. We also demonstrate that the single-stranded DNA endonuclease activity of this T. thermophilus domain is activated not by magnesium but by transition metal ions such as manganese and nickel. Structure-guided mutagenesis confirms the importance of the metal-binding residues for the nuclease activity and identifies other active site residues. Overall, these results provide a framework for understanding the role of Cas3 in the CRISPR system.

Topological cell clustering in the ATLAS calorimeters and its performance in LHC Run 1

Energy Technology Data Exchange (ETDEWEB)

Aad, G. [CPPM, Aix-Marseille Univ. et CNRS/IN2P3, Marseille (France); Abbott, B. [Oklahoma Univ., Norman, OK (United States). Homer L. Dodge Dept. of Physics and Astronomy; Abdallah, J. [Academia Sinica, Taipei (China). Inst. of Physics; Collaboration: ATLAS Collaboration; and others

2017-07-15

The reconstruction of the signal from hadrons and jets emerging from the proton-proton collisions at the Large Hadron Collider (LHC) and entering the ATLAS calorimeters is based on a three-dimensional topological clustering of individual calorimeter cell signals. The cluster formation follows cell signal-significance patterns generated by electromagnetic and hadronic showers. In this, the clustering algorithm implicitly performs a topological noise suppression by removing cells with insignificant signals which are not in close proximity to cells with significant signals. The resulting topological cell clusters have shape and location information, which is exploited to apply a local energy calibration and corrections depending on the nature of the cluster. Topological cell clustering is established as a well-performing calorimeter signal definition for jet and missing transverse momentum reconstruction in ATLAS. (orig.)

Fully 3-D list-mode positron emission tomography image reconstruction on a multi-GPU cluster

Energy Technology Data Exchange (ETDEWEB)

Cui, Jingyu [Stanford Univ., CA (United States). Dept. of Electrical Engineering; Prevrhal, Sven; Shao, Lingxiong [Philips Healthcare, San Jose, CA (United States); Pratx, Guillem [Stanford Univ., CA (United States). Dept. of Radiation Oncology; Levin, Craig S. [Stanford Univ., CA (United States). Dept. of Radiology, Electrical Engineering, and Physics; Stanford Univ., CA (United States). Molecular Imaging Program at Stanford (MIPS); Stanford Univ., CA (United States). School of Medicine

2011-07-01

List-mode processing is an efficient way of dealing with the sparse nature of PET data sets, and is the processing method of choice for time-of-flight (ToF) PET. We present a novel method of computing line projection operations required for list-mode ordered subsets expectation maximization (OSEM) for fully 3-D PET image reconstruction on a graphics processing unit (GPU) using the compute unified device architecture (CUDA) framework. Our method overcomes challenges such as compute thread divergence, and exploits GPU capabilities such as shared memory and atomic operations. When applied to line projection operations for list-mode time-of-flight PET, this new GPU-CUDA reformulation is 188X faster than a single-threaded reference CPU implementation. When embedded in a multi-process environment on a GPU-equipped small cluster, a speedup of 4X was observed over the same configuration but without GPU support. Image quality is preserved with root mean squared (RMS) deviation of 0.05% between CPU and GPU-generated images, which has negligible effect in typical clinical applications. (orig.)

Identifying specific profiles in patients with different degrees of painful knee osteoarthritis based on serological biochemical and mechanistic pain biomarkers: a diagnostic approach based on cluster analysis.

Science.gov (United States)

Egsgaard, Line Lindhardt; Eskehave, Thomas Navndrup; Bay-Jensen, Anne C; Hoeck, Hans Christian; Arendt-Nielsen, Lars

2015-01-01

Biochemical and pain biomarkers can be applied to patients with painful osteoarthritis profiles and may provide more details compared with conventional clinical tools. The aim of this study was to identify an optimal combination of biochemical and pain biomarkers for classification of patients with different degrees of knee pain and joint damage. Such profiling may provide new diagnostic and therapeutic options. A total of 216 patients with different degrees of knee pain (maximal pain during the last 24 hours rated on a visual analog scale [VAS]) (VAS 0-100) and 64 controls (VAS 0-9) were recruited. Patients were separated into 3 groups: VAS 10 to 39 (N = 81), VAS 40 to 69 (N = 70), and VAS 70 to 100 (N = 65). Pressure pain thresholds, temporal summation to pressure stimuli, and conditioning pain modulation were measured from the peripatellar and extrasegmental sites. Biochemical markers indicative for autoinflammation and immunity (VICM, CRP, and CRPM), synovial inflammation (CIIIM), cartilage loss (CIIM), and bone degradation (CIM) were analyzed. WOMAC, Lequesne, and pain catastrophizing scores were collected. Principal component analysis was applied to select the optimal variable subset, and cluster analysis was applied to this subset to create distinctly different knee pain profiles. Four distinct knee pain profiles were identified: profile A (N = 27), profile B (N = 59), profile C (N = 85), and profile D (N = 41). Each knee pain profile had a unique combination of biochemical markers, pain biomarkers, physical impairments, and psychological factors that may provide the basis for mechanism-based diagnosis, individualized treatment, and selection of patients for clinical trials evaluating analgesic compounds. These results introduce a new profiling for knee OA and should be regarded as preliminary.

High spatial resolution CT image reconstruction using parallel computing

International Nuclear Information System (INIS)

Yin Yin; Liu Li; Sun Gongxing

2003-01-01

Using the PC cluster system with 16 dual CPU nodes, we accelerate the FBP and OR-OSEM reconstruction of high spatial resolution image (2048 x 2048). Based on the number of projections, we rewrite the reconstruction algorithms into parallel format and dispatch the tasks to each CPU. By parallel computing, the speedup factor is roughly equal to the number of CPUs, which can be up to about 25 times when 25 CPUs used. This technique is very suitable for real-time high spatial resolution CT image reconstruction. (authors)

A Denoising Scheme for Randomly Clustered Noise Removal in ICCD Sensing Image

Directory of Open Access Journals (Sweden)

Fei Wang

2017-01-01

Full Text Available An Intensified Charge-Coupled Device (ICCD image is captured by the ICCD image sensor in extremely low-light conditions. Its noise has two distinctive characteristics. (a Different from the independent identically distributed (i.i.d. noise in natural image, the noise in the ICCD sensing image is spatially clustered, which induces unexpected structure information; (b The pattern of the clustered noise is formed randomly. In this paper, we propose a denoising scheme to remove the randomly clustered noise in the ICCD sensing image. First, we decompose the image into non-overlapped patches and classify them into flat patches and structure patches according to if real structure information is included. Then, two denoising algorithms are designed for them, respectively. For each flat patch, we simulate multiple similar patches for it in pseudo-time domain and remove its noise by averaging all the simulated patches, considering that the structure information induced by the noise varies randomly over time. For each structure patch, we design a structure-preserved sparse coding algorithm to reconstruct the real structure information. It reconstructs each patch by describing it as a weighted summation of its neighboring patches and incorporating the weights into the sparse representation of the current patch. Based on all the reconstructed patches, we generate a reconstructed image. After that, we repeat the whole process by changing relevant parameters, considering that blocking artifacts exist in a single reconstructed image. Finally, we obtain the reconstructed image by merging all the generated images into one. Experiments are conducted on an ICCD sensing image dataset, which verifies its subjective performance in removing the randomly clustered noise and preserving the real structure information in the ICCD sensing image.

Impact of Alternative Inputs and Grooming Methods on Large-R Jet Reconstruction in ATLAS

CERN Document Server

The ATLAS collaboration

2017-01-01

During Run 1 of the LHC, the optimal reconstruction algorithm for large-$R$ jets in ATLAS, characterized in terms of the ability to discriminate signal from background and robust reconstruction in the presence of pileup, was found to be anti-$k_{t}$ jets with a radius parameter of 1.0, formed from locally calibrated topological calorimeter cell clusters and groomed with the trimming algorithm to remove contributions from pileup and underlying event. Since that time, much theoretical, phenomenological, and experimental work has been performed to improve both the reconstruction of the jet inputs as well as the grooming techniques applied to reconstructed jets. In this work, an inclusive survey of both pileup mitigation algorithms applied to calorimeter cell clusters and grooming algorithms is done to study their pileup stability and ability to identify hadronically decaying W bosons within the ATLAS experiment. It is found that compared to the conventional reconstruction algorithm of large-$R$ trimmed jets form...

Distributed MRI reconstruction using Gadgetron-based cloud computing.

Science.gov (United States)

Xue, Hui; Inati, Souheil; Sørensen, Thomas Sangild; Kellman, Peter; Hansen, Michael S

2015-03-01

To expand the open source Gadgetron reconstruction framework to support distributed computing and to demonstrate that a multinode version of the Gadgetron can be used to provide nonlinear reconstruction with clinically acceptable latency. The Gadgetron framework was extended with new software components that enable an arbitrary number of Gadgetron instances to collaborate on a reconstruction task. This cloud-enabled version of the Gadgetron was deployed on three different distributed computing platforms ranging from a heterogeneous collection of commodity computers to the commercial Amazon Elastic Compute Cloud. The Gadgetron cloud was used to provide nonlinear, compressed sensing reconstruction on a clinical scanner with low reconstruction latency (eg, cardiac and neuroimaging applications). The proposed setup was able to handle acquisition and 11 -SPIRiT reconstruction of nine high temporal resolution real-time, cardiac short axis cine acquisitions, covering the ventricles for functional evaluation, in under 1 min. A three-dimensional high-resolution brain acquisition with 1 mm(3) isotropic pixel size was acquired and reconstructed with nonlinear reconstruction in less than 5 min. A distributed computing enabled Gadgetron provides a scalable way to improve reconstruction performance using commodity cluster computing. Nonlinear, compressed sensing reconstruction can be deployed clinically with low image reconstruction latency. © 2014 Wiley Periodicals, Inc.

The complete coenzyme B12 biosynthesis gene cluster of Lactobacillus reuteri CRL 1098

NARCIS (Netherlands)

Santos, dos F.; Vera, J.L.; Heijden, van der R.; Valdez, G.F.; Vos, de W.M.; Sesma, F.; Hugenholtz, J.

2008-01-01

The coenzyme B12 production pathway in Lactobacillus reuteri has been deduced using a combination of genetic, biochemical and bioinformatics approaches. The coenzyme B12 gene cluster of Lb. reuteri CRL1098 has the unique feature of clustering together the cbi, cob and hem genes. It consists of 29

Time-based Reconstruction of Free-streaming Data in CBM

Science.gov (United States)

Akishina, Valentina; Kisel, Ivan; Vassiliev, Iouri; Zyzak, Maksym

2018-02-01

Traditional latency-limited trigger architectures typical for conventional experiments are inapplicable for the CBM experiment. Instead, CBM will ship and collect time-stamped data into a readout buffer in a form of a time-slice of a certain length and deliver it to a large computer farm, where online event reconstruction and selection will be performed. Grouping measurements into physical collisions must be performed in software and requires reconstruction not only in space, but also in time, the so-called 4-dimensional track reconstruction and event building. The tracks, reconstructed with 4D Cellular Automaton track finder, are combined into event-corresponding clusters according to the estimated time in the target position and the errors, obtained with the Kalman Filter method. The reconstructed events are given as inputs to the KF Particle Finder package for short-lived particle reconstruction. The results of time-based reconstruction of simulated collisions in CBM are presented and discussed in details.

New Developments for Jet Substructure Reconstruction in CMS

CERN Document Server

CMS Collaboration

2017-01-01

We present Monte Carlo based studies showcasing several developments for jet substructure reconstruction in CMS. This include Quark/Gluon tagging algorithms using Boosted Decision Trees and Deep Neural Networks, the XCone jet clustering algorithm and the Boosted Event Shape Tagger (BEST).

Environment-based pin-power reconstruction method for homogeneous core calculations

International Nuclear Information System (INIS)

Leroyer, H.; Brosselard, C.; Girardi, E.

2012-01-01

Core calculation schemes are usually based on a classical two-step approach associated with assembly and core calculations. During the first step, infinite lattice assemblies calculations relying on a fundamental mode approach are used to generate cross-sections libraries for PWRs core calculations. This fundamental mode hypothesis may be questioned when dealing with loading patterns involving several types of assemblies (UOX, MOX), burnable poisons, control rods and burn-up gradients. This paper proposes a calculation method able to take into account the heterogeneous environment of the assemblies when using homogeneous core calculations and an appropriate pin-power reconstruction. This methodology is applied to MOX assemblies, computed within an environment of UOX assemblies. The new environment-based pin-power reconstruction is then used on various clusters of 3x3 assemblies showing burn-up gradients and UOX/MOX interfaces, and compared to reference calculations performed with APOLLO-2. The results show that UOX/MOX interfaces are much better calculated with the environment-based calculation scheme when compared to the usual pin-power reconstruction method. The power peak is always better located and calculated with the environment-based pin-power reconstruction method on every cluster configuration studied. This study shows that taking into account the environment in transport calculations can significantly improve the pin-power reconstruction so far as it is consistent with the core loading pattern. (authors)

Splitting Strip Detector Clusters in Dense Environments

CERN Document Server

Nachman, Benjamin Philip; The ATLAS collaboration

2018-01-01

Tracking in high density environments, particularly in high energy jets, plays an important role in many physics analyses at the LHC. In such environments, there is significant degradation of track reconstruction performance. Between runs 1 and 2, ATLAS implemented an algorithm that splits pixel clusters originating from multiple charged particles, using charge information, resulting in the recovery of much of the lost efficiency. However, no attempt was made in prior work to split merged clusters in the Semi Conductor Tracker (SCT), which does not measure charge information. In spite of the lack of charge information in SCT, a cluster-splitting algorithm has been developed in this work. It is based primarily on the difference between the observed cluster width and the expected cluster width, which is derived from track incidence angle. The performance of this algorithm is found to be competitive with the existing pixel cluster splitting based on track information.

Large R jet reconstruction and calibration at 13 TeV with the ATLAS detector

CERN Document Server

Taenzer, Joe; The ATLAS collaboration

2017-01-01

Large-R jets are used by many ATLAS analyses working in boosted regimes. ATLAS Large-R jets are reconstructed from locally callibrated calorimeter topoclusters with the Anti-k_{t} algorithm with radius parameter R=1.0, and then groomed to remove pile-up with the trimming algorithm with f_{cut} 0.05 and subjet radius R=0.2. Monte Carlo based energy and mass calibrations correct the reconstructed jet energy and mass to truth, followed by in-situ calibrations using a number of different techniques. Large-R jets can also be reconstructed using small-R jets as constituents, instead of topoclusters, a technique called jet reclustering, or from track calo clusters (TCCs), which are constituents constructed using both tracking and calorimeter information. An overview of large-R jet reconstruction will be presented here, along with selected results from the jet mass calibrations, both Monte Carlo based an insitu, from jet reclustering, and from track calo clusters.

Classification and fingerprinting of different berries based on biochemical profiling and antioxidant capacity

Directory of Open Access Journals (Sweden)

Jasminka Milivojević

2013-09-01

Full Text Available The objective of this work was to evaluate the biochemical composition of six berry types belonging to Fragaria, Rubus, Vaccinium and Ribes genus. Fruit samples were collected in triplicate (50 fruit each from 18 different species or cultivars of the mentioned genera, during three years (2008 to 2010. Content of individual sugars, organic acids, flavonols, and phenolic acids were determined by high performance liquid chromatography (HPLC analysis, while total phenolics (TPC and total antioxidant capacity (TAC, by using spectrophotometry. Principal component analysis (PCA and hierarchical cluster analysis (CA were performed to evaluate the differences in fruit biochemical profile. The highest contents of bioactive components were found in Ribes nigrum and in Fragaria vesca, Rubus plicatus, and Vaccinium myrtillus. PCA and CA were able to partially discriminate between berries on the basis of their biochemical composition. Individual and total sugars, myricetin, ellagic acid, TPC and TAC showed the highest impact on biochemical composition of the berry fruits. CA separated blackberry, raspberry, and blueberry as isolate groups, while classification of strawberry, black and red currant in a specific group has not occurred. There is a large variability both between and within the different types of berries. Metabolite fingerprinting of the evaluated berries showed unique biochemical profiles and specific combination of bioactive compound contents.

BlastNeuron for Automated Comparison, Retrieval and Clustering of 3D Neuron Morphologies.

Science.gov (United States)

Wan, Yinan; Long, Fuhui; Qu, Lei; Xiao, Hang; Hawrylycz, Michael; Myers, Eugene W; Peng, Hanchuan

2015-10-01

Characterizing the identity and types of neurons in the brain, as well as their associated function, requires a means of quantifying and comparing 3D neuron morphology. Presently, neuron comparison methods are based on statistics from neuronal morphology such as size and number of branches, which are not fully suitable for detecting local similarities and differences in the detailed structure. We developed BlastNeuron to compare neurons in terms of their global appearance, detailed arborization patterns, and topological similarity. BlastNeuron first compares and clusters 3D neuron reconstructions based on global morphology features and moment invariants, independent of their orientations, sizes, level of reconstruction and other variations. Subsequently, BlastNeuron performs local alignment between any pair of retrieved neurons via a tree-topology driven dynamic programming method. A 3D correspondence map can thus be generated at the resolution of single reconstruction nodes. We applied BlastNeuron to three datasets: (1) 10,000+ neuron reconstructions from a public morphology database, (2) 681 newly and manually reconstructed neurons, and (3) neurons reconstructions produced using several independent reconstruction methods. Our approach was able to accurately and efficiently retrieve morphologically and functionally similar neuron structures from large morphology database, identify the local common structures, and find clusters of neurons that share similarities in both morphology and molecular profiles.

Cluster Correlation in Mixed Models

Science.gov (United States)

Gardini, A.; Bonometto, S. A.; Murante, G.; Yepes, G.

2000-10-01

We evaluate the dependence of the cluster correlation length, rc, on the mean intercluster separation, Dc, for three models with critical matter density, vanishing vacuum energy (Λ=0), and COBE normalization: a tilted cold dark matter (tCDM) model (n=0.8) and two blue mixed models with two light massive neutrinos, yielding Ωh=0.26 and 0.14 (MDM1 and MDM2, respectively). All models approach the observational value of σ8 (and hence the observed cluster abundance) and are consistent with the observed abundance of damped Lyα systems. Mixed models have a motivation in recent results of neutrino physics; they also agree with the observed value of the ratio σ8/σ25, yielding the spectral slope parameter Γ, and nicely fit Las Campanas Redshift Survey (LCRS) reconstructed spectra. We use parallel AP3M simulations, performed in a wide box (of side 360 h-1 Mpc) and with high mass and distance resolution, enabling us to build artificial samples of clusters, whose total number and mass range allow us to cover the same Dc interval inspected through Automatic Plate Measuring Facility (APM) and Abell cluster clustering data. We find that the tCDM model performs substantially better than n=1 critical density CDM models. Our main finding, however, is that mixed models provide a surprisingly good fit to cluster clustering data.

Symptom clusters and related factors in bladder cancer patients three months after radical cystectomy.

Science.gov (United States)

Ren, Hongyan; Tang, Ping; Zhao, Qinghua; Ren, Guosheng

2017-08-23

To identify symptom distress and clusters in patients 3 months after radical cystectomy and to explore their potential predictors. A cross-sectional design was used to investigate 99 bladder cancer patients 3 months after radical cystectomy. Data were collected by demographic and disease characteristic questionnaires, the symptom experience scale of the M.D. Anderson symptom inventory, two additional symptoms specific to radical cystectomy, and the functional assessment of cancer therapy questionnaire. A factor analysis, stepwise regression, and correlation analysis were applied. Three symptom clusters were identified: fatigue-malaise, gastrointestinal, and psycho-urinary. Age, complication severity, albumin post-surgery (negative), orthotropic neobladder reconstruction, adjuvant chemotherapy and American Society of Anesthesiologists (ASA) scores were significant predictors of fatigue-malaise. Adjuvant chemotherapy, orthotropic neobladder reconstruction, female gender, ASA scores and albumin (negative) were significant predictors of gastrointestinal symptoms. Being unmarried, having a higher educational level and complication severity were significant predictors of psycho-urinary symptoms. The correlations between clusters and for each cluster with quality of life were significant, with the highest correlation observed between the psycho-urinary cluster and quality of life. Bladder cancer patients experience concurrent symptoms that appear to cluster and are significantly correlated with quality of life. Moreover, symptom clusters may be predicted by certain demographic and clinical characteristics.

Liquid argon TPC signal formation, signal processing and reconstruction techniques

Science.gov (United States)

Baller, B.

2017-07-01

This document describes a reconstruction chain that was developed for the ArgoNeuT and MicroBooNE experiments at Fermilab. These experiments study accelerator neutrino interactions that occur in a Liquid Argon Time Projection Chamber. Reconstructing the properties of particles produced in these interactions benefits from the knowledge of the micro-physics processes that affect the creation and transport of ionization electrons to the readout system. A wire signal deconvolution technique was developed to convert wire signals to a standard form for hit reconstruction, to remove artifacts in the electronics chain and to remove coherent noise. A unique clustering algorithm reconstructs line-like trajectories and vertices in two dimensions which are then matched to create of 3D objects. These techniques and algorithms are available to all experiments that use the LArSoft suite of software.

Progeny Clustering: A Method to Identify Biological Phenotypes

Science.gov (United States)

Hu, Chenyue W.; Kornblau, Steven M.; Slater, John H.; Qutub, Amina A.

2015-01-01

Estimating the optimal number of clusters is a major challenge in applying cluster analysis to any type of dataset, especially to biomedical datasets, which are high-dimensional and complex. Here, we introduce an improved method, Progeny Clustering, which is stability-based and exceptionally efficient in computing, to find the ideal number of clusters. The algorithm employs a novel Progeny Sampling method to reconstruct cluster identity, a co-occurrence probability matrix to assess the clustering stability, and a set of reference datasets to overcome inherent biases in the algorithm and data space. Our method was shown successful and robust when applied to two synthetic datasets (datasets of two-dimensions and ten-dimensions containing eight dimensions of pure noise), two standard biological datasets (the Iris dataset and Rat CNS dataset) and two biological datasets (a cell phenotype dataset and an acute myeloid leukemia (AML) reverse phase protein array (RPPA) dataset). Progeny Clustering outperformed some popular clustering evaluation methods in the ten-dimensional synthetic dataset as well as in the cell phenotype dataset, and it was the only method that successfully discovered clinically meaningful patient groupings in the AML RPPA dataset. PMID:26267476

Percolation Analysis of a Wiener Reconstruction of the IRAS 1.2 Jy Redshift Catalog

Science.gov (United States)

Yess, Capp; Shandarin, Sergei F.; Fisher, Karl B.

1997-01-01

We present percolation analyses of Wiener reconstructions of the IRAS 1.2 Jy redshift survey. There are 10 reconstructions of galaxy density fields in real space spanning the range β = 0.1-1.0, where β = Ω0.6/b, Ω is the present dimensionless density, and b is the bias factor. Our method uses the growth of the largest cluster statistic to characterize the topology of a density field, where Gaussian randomized versions of the reconstructions are used as standards for analysis. For the reconstruction volume of radius R ~ 100 h-1 Mpc, percolation analysis reveals a slight ``meatball'' topology for the real space, galaxy distribution of the IRAS survey.

Surface EMG decomposition based on K-means clustering and convolution kernel compensation.

Science.gov (United States)

Ning, Yong; Zhu, Xiangjun; Zhu, Shanan; Zhang, Yingchun

2015-03-01

A new approach has been developed by combining the K-mean clustering (KMC) method and a modified convolution kernel compensation (CKC) method for multichannel surface electromyogram (EMG) decomposition. The KMC method was first utilized to cluster vectors of observations at different time instants and then estimate the initial innervation pulse train (IPT). The CKC method, modified with a novel multistep iterative process, was conducted to update the estimated IPT. The performance of the proposed K-means clustering-Modified CKC (KmCKC) approach was evaluated by reconstructing IPTs from both simulated and experimental surface EMG signals. The KmCKC approach successfully reconstructed all 10 IPTs from the simulated surface EMG signals with true positive rates (TPR) of over 90% with a low signal-to-noise ratio (SNR) of -10 dB. More than 10 motor units were also successfully extracted from the 64-channel experimental surface EMG signals of the first dorsal interosseous (FDI) muscles when a contraction force was held at 8 N by using the KmCKC approach. A "two-source" test was further conducted with 64-channel surface EMG signals. The high percentage of common MUs and common pulses (over 92% at all force levels) between the IPTs reconstructed from the two independent groups of surface EMG signals demonstrates the reliability and capability of the proposed KmCKC approach in multichannel surface EMG decomposition. Results from both simulated and experimental data are consistent and confirm that the proposed KmCKC approach can successfully reconstruct IPTs with high accuracy at different levels of contraction.

Chromium (VI Induced Biochemical Changes and Gum Content in Cluster Bean (Cyamopsis tetragonoloba L. at Different Developmental Stages

Directory of Open Access Journals (Sweden)

Punesh Sangwan

2013-01-01

Full Text Available Chromium (Cr contamination by various industries and other activities is known to inhibit plants growth and development. The present study was conducted using pot experiments in a net house to determine the effect of Cr (VI on biochemical parameters such as photosynthetic pigments, reducing sugars, and important minerals at different stages of growth in leaves, stem, and roots of clusterbean, a multipurpose fodder crop including a source of guar gum. Guar gum content was estimated in seeds at maturity. All biochemical contents showed a great variation with respect to increase in Cr concentration at different stages of growth. The levels of K, Fe, and Zn decreased, while Cr and Na content increased with increase in Cr concentration. Cr induced toxicity in clusterbean appears at 0.5 mg Cr (VI Kg−1 soil with maximum inhibitory effect at 2 mg Cr (VI Kg−1 soil, where impaired sugar supply resulted in decreased guar gum synthesis and altered micronutrient content. The study reveals the possible role of these biochemical parameters in decreasing plant growth and development under heavy metal stress.

Probability Density Function Method for Observing Reconstructed Attractor Structure

Institute of Scientific and Technical Information of China (English)

陆宏伟; 陈亚珠; 卫青

2004-01-01

Probability density function (PDF) method is proposed for analysing the structure of the reconstructed attractor in computing the correlation dimensions of RR intervals of ten normal old men. PDF contains important information about the spatial distribution of the phase points in the reconstructed attractor. To the best of our knowledge, it is the first time that the PDF method is put forward for the analysis of the reconstructed attractor structure. Numerical simulations demonstrate that the cardiac systems of healthy old men are about 6 - 6.5 dimensional complex dynamical systems. It is found that PDF is not symmetrically distributed when time delay is small, while PDF satisfies Gaussian distribution when time delay is big enough. A cluster effect mechanism is presented to explain this phenomenon. By studying the shape of PDFs, that the roles played by time delay are more important than embedding dimension in the reconstruction is clearly indicated. Results have demonstrated that the PDF method represents a promising numerical approach for the observation of the reconstructed attractor structure and may provide more information and new diagnostic potential of the analyzed cardiac system.

Hierarchical Cluster Analysis of Three-Dimensional Reconstructions of Unbiased Sampled Microglia Shows not Continuous Morphological Changes from Stage 1 to 2 after Multiple Dengue Infections in Callithrix penicillata

Science.gov (United States)

Diniz, Daniel G.; Silva, Geane O.; Naves, Thaís B.; Fernandes, Taiany N.; Araújo, Sanderson C.; Diniz, José A. P.; de Farias, Luis H. S.; Sosthenes, Marcia C. K.; Diniz, Cristovam G.; Anthony, Daniel C.; da Costa Vasconcelos, Pedro F.; Picanço Diniz, Cristovam W.

2016-01-01

It is known that microglial morphology and function are related, but few studies have explored the subtleties of microglial morphological changes in response to specific pathogens. In the present report we quantitated microglia morphological changes in a monkey model of dengue disease with virus CNS invasion. To mimic multiple infections that usually occur in endemic areas, where higher dengue infection incidence and abundant mosquito vectors carrying different serotypes coexist, subjects received once a week subcutaneous injections of DENV3 (genotype III)-infected culture supernatant followed 24 h later by an injection of anti-DENV2 antibody. Control animals received either weekly anti-DENV2 antibodies, or no injections. Brain sections were immunolabeled for DENV3 antigens and IBA-1. Random and systematic microglial samples were taken from the polymorphic layer of dentate gyrus for 3-D reconstructions, where we found intense immunostaining for TNFα and DENV3 virus antigens. We submitted all bi- or multimodal morphological parameters of microglia to hierarchical cluster analysis and found two major morphological phenotypes designated types I and II. Compared to type I (stage 1), type II microglia were more complex; displaying higher number of nodes, processes and trees and larger surface area and volumes (stage 2). Type II microglia were found only in infected monkeys, whereas type I microglia was found in both control and infected subjects. Hierarchical cluster analysis of morphological parameters of 3-D reconstructions of random and systematic selected samples in control and ADE dengue infected monkeys suggests that microglia morphological changes from stage 1 to stage 2 may not be continuous. PMID:27047345

Evaluation of biochemical and molecular methods for Lactobacillus reuteri strains differentiation.

Science.gov (United States)

Andrea, Bilková; Hana, Kiňová Sepová; Martina, Dubničková; Hyacinta, Májeková; František, Bilka

2015-03-01

Several biochemical and molecular methods were used for discrimination of four Lactobacillus reuteri strains isolated from goatling and lamb stomach mucosa. Internal transcribed spacer (ITS)-PCR method and protein analysis by SDS-PAGE and MALDI-TOF showed to be suitable for strain discrimination whereas ITS-PCR/RFLP and enterobacterial repetitive intergenic consensus (ERIC)-PCR were not strain specific. The used methods differentiated tested strains into distinct groups; however, the location of strains in groups varied. Consistency in results was observed in the case of L. reuteri E and L. reuteri KO4m that were clustered into the same groups using all techniques, except of MALDI-TOF MS. The last one grouped goatling strains and lamb isolate into separate clusters. All investigated methods, except of ITS-PCR/RFLP and ERIC-PCR, were assessed as appropriate for distinguishing of L. reuteri strains.

Fast half-sibling population reconstruction: theory and algorithms.

Science.gov (United States)

Dexter, Daniel; Brown, Daniel G

2013-07-12

Kinship inference is the task of identifying genealogically related individuals. Kinship information is important for determining mating structures, notably in endangered populations. Although many solutions exist for reconstructing full sibling relationships, few exist for half-siblings. We consider the problem of determining whether a proposed half-sibling population reconstruction is valid under Mendelian inheritance assumptions. We show that this problem is NP-complete and provide a 0/1 integer program that identifies the minimum number of individuals that must be removed from a population in order for the reconstruction to become valid. We also present SibJoin, a heuristic-based clustering approach based on Mendelian genetics, which is strikingly fast. The software is available at http://github.com/ddexter/SibJoin.git+. Our SibJoin algorithm is reasonably accurate and thousands of times faster than existing algorithms. The heuristic is used to infer a half-sibling structure for a population which was, until recently, too large to evaluate.

Automatic Texture Optimization for 3D Urban Reconstruction

Directory of Open Access Journals (Sweden)

LI Ming

2017-03-01

Full Text Available In order to solve the problem of texture optimization in 3D city reconstruction by using multi-lens oblique images, the paper presents a method of seamless texture model reconstruction. At first, it corrects the radiation information of images by camera response functions and image dark channel. Then, according to the corresponding relevance between terrain triangular mesh surface model to image, implements occlusion detection by sparse triangulation method, and establishes the triangles' texture list of visible. Finally, combines with triangles' topology relationship in 3D triangular mesh surface model and means and variances of image, constructs a graph-cuts-based texture optimization algorithm under the framework of MRF(Markov random filed, to solve the discrete label problem of texture optimization selection and clustering, ensures the consistency of the adjacent triangles in texture mapping, achieves the seamless texture reconstruction of city. The experimental results verify the validity and superiority of our proposed method.

Observations of sensor bias dependent cluster centroid shifts in a prototype sensor for the LHCb Vertex Locator detector

CERN Document Server

Papadelis, Aras

2006-01-01

We present results from a recent beam test of a prototype sensor for the LHCb Vertex Locator detector, read out with the Beetle 1.3 front-end chip. We have studied the effect of the sensor bias voltage on the reconstructed cluster positions in a sensor placed in a 120GeV pion beam at a 10° incidence angle. We find an unexplained sysematic shift in the reconstructed cluster centroid when increasing the bias voltage on an already overdepleted sensor. The shift is independent of strip pitch and sensor thickness.

Network reconstruction via graph blending

Science.gov (United States)

Estrada, Rolando

2016-05-01

Graphs estimated from empirical data are often noisy and incomplete due to the difficulty of faithfully observing all the components (nodes and edges) of the true graph. This problem is particularly acute for large networks where the number of components may far exceed available surveillance capabilities. Errors in the observed graph can render subsequent analyses invalid, so it is vital to develop robust methods that can minimize these observational errors. Errors in the observed graph may include missing and spurious components, as well fused (multiple nodes are merged into one) and split (a single node is misinterpreted as many) nodes. Traditional graph reconstruction methods are only able to identify missing or spurious components (primarily edges, and to a lesser degree nodes), so we developed a novel graph blending framework that allows us to cast the full estimation problem as a simple edge addition/deletion problem. Armed with this framework, we systematically investigate the viability of various topological graph features, such as the degree distribution or the clustering coefficients, and existing graph reconstruction methods for tackling the full estimation problem. Our experimental results suggest that incorporating any topological feature as a source of information actually hinders reconstruction accuracy. We provide a theoretical analysis of this phenomenon and suggest several avenues for improving this estimation problem.

Limited-angle multi-energy CT using joint clustering prior and sparsity regularization

Science.gov (United States)

Zhang, Huayu; Xing, Yuxiang

2016-03-01

In this article, we present an easy-to-implement Multi-energy CT scanning strategy and a corresponding reconstruction method, which facilitate spectral CT imaging by improving the data efficiency the number-of-energy- channel fold without introducing visible limited-angle artifacts caused by reducing projection views. Leveraging the structure coherence at different energies, we first pre-reconstruct a prior structure information image using projection data from all energy channels. Then, we perform a k-means clustering on the prior image to generate a sparse dictionary representation for the image, which severs as a structure information constraint. We com- bine this constraint with conventional compressed sensing method and proposed a new model which we referred as Joint Clustering Prior and Sparsity Regularization (CPSR). CPSR is a convex problem and we solve it by Alternating Direction Method of Multipliers (ADMM). We verify our CPSR reconstruction method with a numerical simulation experiment. A dental phantom with complicate structures of teeth and soft tissues is used. X-ray beams from three spectra of different peak energies (120kVp, 90kVp, 60kVp) irradiate the phantom to form tri-energy projections. Projection data covering only 75◦ from each energy spectrum are collected for reconstruction. Independent reconstruction for each energy will cause severe limited-angle artifacts even with the help of compressed sensing approaches. Our CPSR provides us with images free of the limited-angle artifact. All edge details are well preserved in our experimental study.

The simulation of 3D microcalcification clusters in 2D digital mammography and breast tomosynthesis

International Nuclear Information System (INIS)

Shaheen, Eman; Van Ongeval, Chantal; Zanca, Federica; Cockmartin, Lesley; Marshall, Nicholas; Jacobs, Jurgen; Young, Kenneth C.; Dance, David R.; Bosmans, Hilde

2011-01-01

Purpose: This work proposes a new method of building 3D models of microcalcification clusters and describes the validation of their realistic appearance when simulated into 2D digital mammograms and into breast tomosynthesis images. Methods: A micro-CT unit was used to scan 23 breast biopsy specimens of microcalcification clusters with malignant and benign characteristics and their 3D reconstructed datasets were segmented to obtain 3D models of microcalcification clusters. These models were then adjusted for the x-ray spectrum used and for the system resolution and simulated into 2D projection images to obtain mammograms after image processing and into tomographic sequences of projection images, which were then reconstructed to form 3D tomosynthesis datasets. Six radiologists were asked to distinguish between 40 real and 40 simulated clusters of microcalcifications in two separate studies on 2D mammography and tomosynthesis datasets. Receiver operating characteristic (ROC) analysis was used to test the ability of each observer to distinguish between simulated and real microcalcification clusters. The kappa statistic was applied to assess how often the individual simulated and real microcalcification clusters had received similar scores (''agreement'') on their realistic appearance in both modalities. This analysis was performed for all readers and for the real and the simulated group of microcalcification clusters separately. ''Poor'' agreement would reflect radiologists' confusion between simulated and real clusters, i.e., lesions not systematically evaluated in both modalities as either simulated or real, and would therefore be interpreted as a success of the present models. Results: The area under the ROC curve, averaged over the observers, was 0.55 (95% confidence interval [0.44, 0.66]) for the 2D study, and 0.46 (95% confidence interval [0.29, 0.64]) for the tomosynthesis study, indicating no statistically significant difference between real and simulated

Gaussian mixture models and semantic gating improve reconstructions from human brain activity

Directory of Open Access Journals (Sweden)

Sanne eSchoenmakers

2015-01-01

Full Text Available Better acquisition protocols and analysis techniques are making it possible to use fMRI to obtain highly detailed visualizations of brain processes. In particular we focus on the reconstruction of natural images from BOLD responses in visual cortex. We expand our linear Gaussian framework for percept decoding with Gaussian mixture models to better represent the prior distribution of natural images. Reconstruction of such images then boils down to probabilistic inference in a hybrid Bayesian network. In our set-up, different mixture components correspond to different character categories. Our framework can automatically infer higher-order semantic categories from lower-level brain areas. Furthermore the framework can gate semantic information from higher-order brain areas to enforce the correct category during reconstruction. When categorical information is not available, we show that automatically learned clusters in the data give a similar improvement in reconstruction. The hybrid Bayesian network leads to highly accurate reconstructions in both supervised and unsupervised settings.

Strain-activated edge reconstruction of graphene nanoribbons

KAUST Repository

Cheng, Yingchun

2012-02-17

The edge structure and width of graphene nanoribbons (GNRs) are crucial factors for the electronic properties. A combination of experiment and first-principles calculations allows us to determine the mechanism of the hexagon-hexagon to pentagon-heptagon transformation. GNRs thinner than 2 nm have been fabricated by bombardment of graphene with high-energetic Au clusters. The edges of the GNRs are modified in situ by electron irradiation. Tensile strain along the edge decreases the transformation energy barrier. Antiferromagnetism and a direct band gap are found for a zigzag GNR, while a fully reconstructed GNR shows an indirect band gap. A GNR reconstructed on only one edge exhibits ferromagnetism. We propose that strain is an effective method to tune the edge and, therefore, the electronic structure of thin GNRs for graphene-based electronics.

Strain-activated edge reconstruction of graphene nanoribbons

KAUST Repository

Cheng, Yingchun; Han, Yu; Schwingenschlö gl, Udo; Wang, H. T.; Zhang, Xixiang; Zhu, Y. H.; Zhu, Zhiyong

2012-01-01

The edge structure and width of graphene nanoribbons (GNRs) are crucial factors for the electronic properties. A combination of experiment and first-principles calculations allows us to determine the mechanism of the hexagon-hexagon to pentagon-heptagon transformation. GNRs thinner than 2 nm have been fabricated by bombardment of graphene with high-energetic Au clusters. The edges of the GNRs are modified in situ by electron irradiation. Tensile strain along the edge decreases the transformation energy barrier. Antiferromagnetism and a direct band gap are found for a zigzag GNR, while a fully reconstructed GNR shows an indirect band gap. A GNR reconstructed on only one edge exhibits ferromagnetism. We propose that strain is an effective method to tune the edge and, therefore, the electronic structure of thin GNRs for graphene-based electronics.

Personality traits and clinical/biochemical course in the first year after kidney transplant.

Science.gov (United States)

Thomas, Caroline Venzon; de Castro, Elisa Kern; Antonello, Ivan Carlos Ferreira

2016-10-01

The relationship between personality and health is frequently studied in scientific research. This study investigated the clinical/biochemical course of kidney transplant patients based on personality traits. A longitudinal study assessed 114 kidney transplant patients (men = 68 and women = 46) with an average age of 47.72 years (SD = 11.4). Personality was evaluated using the Brazilian Factorial Personality Inventory (BFP/Big Five Model). Clinical variables were analyzed based on patient charts (estimated glomerular filtration rate (eGFR), hypertension, acute rejection, infection, graft loss, and death). Personality types were assessed by hierarchical cluster analysis. Two groups with personality types were differentiated by psychological characteristics: Cluster 1 - average neuroticism, high surgency, agreeableness and conscientiousness, and low openness; Cluster 2 - high neuroticism, average surgency and agreeableness, average conscientiousness, and low openness. There was no statistically significant difference between the clusters in terms of hypertension, acute infection, graft loss, death, and Human Leukocyte Antigen (HLA) I and II panel reactive antibodies. eGFR was associated with the personality types. Cluster 2 was associated with a better renal function in the 9-month follow-up period after kidney transplantation. In this study, patients from Cluster 2 exhibited higher eGFR 9 months after the transplant procedure compared to those from Cluster 1. Monitoring these patients over a longer period may provide a better understanding of the relationship between personality traits and clinical course during the post-transplant period.

Robustness of the ATLAS pixel clustering neural network algorithm

CERN Document Server

AUTHOR|(INSPIRE)INSPIRE-00407780; The ATLAS collaboration

2016-01-01

Proton-proton collisions at the energy frontier puts strong constraints on track reconstruction algorithms. In the ATLAS track reconstruction algorithm, an artificial neural network is utilised to identify and split clusters of neighbouring read-out elements in the ATLAS pixel detector created by multiple charged particles. The robustness of the neural network algorithm is presented, probing its sensitivity to uncertainties in the detector conditions. The robustness is studied by evaluating the stability of the algorithm's performance under a range of variations in the inputs to the neural networks. Within reasonable variation magnitudes, the neural networks prove to be robust to most variation types.

Direct reconstruction of pharmacokinetic parameters in dynamic fluorescence molecular tomography by the augmented Lagrangian method

Science.gov (United States)

Zhu, Dianwen; Zhang, Wei; Zhao, Yue; Li, Changqing

2016-03-01

Dynamic fluorescence molecular tomography (FMT) has the potential to quantify physiological or biochemical information, known as pharmacokinetic parameters, which are important for cancer detection, drug development and delivery etc. To image those parameters, there are indirect methods, which are easier to implement but tend to provide images with low signal-to-noise ratio, and direct methods, which model all the measurement noises together and are statistically more efficient. The direct reconstruction methods in dynamic FMT have attracted a lot of attention recently. However, the coupling of tomographic image reconstruction and nonlinearity of kinetic parameter estimation due to the compartment modeling has imposed a huge computational burden to the direct reconstruction of the kinetic parameters. In this paper, we propose to take advantage of both the direct and indirect reconstruction ideas through a variable splitting strategy under the augmented Lagrangian framework. Each iteration of the direct reconstruction is split into two steps: the dynamic FMT image reconstruction and the node-wise nonlinear least squares fitting of the pharmacokinetic parameter images. Through numerical simulation studies, we have found that the proposed algorithm can achieve good reconstruction results within a small amount of time. This will be the first step for a combined dynamic PET and FMT imaging in the future.

FPGA cluster for high-performance AO real-time control system

Science.gov (United States)

Geng, Deli; Goodsell, Stephen J.; Basden, Alastair G.; Dipper, Nigel A.; Myers, Richard M.; Saunter, Chris D.

2006-06-01

Whilst the high throughput and low latency requirements for the next generation AO real-time control systems have posed a significant challenge to von Neumann architecture processor systems, the Field Programmable Gate Array (FPGA) has emerged as a long term solution with high performance on throughput and excellent predictability on latency. Moreover, FPGA devices have highly capable programmable interfacing, which lead to more highly integrated system. Nevertheless, a single FPGA is still not enough: multiple FPGA devices need to be clustered to perform the required subaperture processing and the reconstruction computation. In an AO real-time control system, the memory bandwidth is often the bottleneck of the system, simply because a vast amount of supporting data, e.g. pixel calibration maps and the reconstruction matrix, need to be accessed within a short period. The cluster, as a general computing architecture, has excellent scalability in processing throughput, memory bandwidth, memory capacity, and communication bandwidth. Problems, such as task distribution, node communication, system verification, are discussed.

Reconstruction of Daily Sea Surface Temperature Based on Radial Basis Function Networks

Directory of Open Access Journals (Sweden)

Zhihong Liao

2017-11-01

Full Text Available A radial basis function network (RBFN method is proposed to reconstruct daily Sea surface temperatures (SSTs with limited SST samples. For the purpose of evaluating the SSTs using this method, non-biased SST samples in the Pacific Ocean (10°N–30°N, 115°E–135°E are selected when the tropical storm Hagibis arrived in June 2014, and these SST samples are obtained from the Reynolds optimum interpolation (OI v2 daily 0.25° SST (OISST products according to the distribution of AVHRR L2p SST and in-situ SST data. Furthermore, an improved nearest neighbor cluster (INNC algorithm is designed to search for the optimal hidden knots for RBFNs from both the SST samples and the background fields. Then, the reconstructed SSTs from the RBFN method are compared with the results from the OI method. The statistical results show that the RBFN method has a better performance of reconstructing SST than the OI method in the study, and that the average RMSE is 0.48 °C for the RBFN method, which is quite smaller than the value of 0.69 °C for the OI method. Additionally, the RBFN methods with different basis functions and clustering algorithms are tested, and we discover that the INNC algorithm with multi-quadric function is quite suitable for the RBFN method to reconstruct SSTs when the SST samples are sparsely distributed.

Biochemical and molecular genetic studies on some cyanobacterial isolates

International Nuclear Information System (INIS)

Kamal, E.A.R.; Ebrahim, S.A.A.

2011-01-01

In the present study, the isolation and purification of a set of Cyanobacteria strains belonging to genus Oscillatoria was undertaken, followed by the analyses of phylogenetic relationships using different biochemical and molecular genetic techniques (SOS-PAGE and RAPO-PCR). A total of 45 protein bands were observed within the studied Osci/latoria isolates by SOS-PAGE (only three unique bands, eight monomorphic bands and 37 polymorphic bands). On the other hand, extracted ONA from isolates was used to identify the molecular fingerprints. A sum of 94 polymorphic bands was generated by these primers in the Ocsi/laloria genotypes under study. A total of 20 unique bands were identified out of the polymorphic ones. These unique bands were used to discriminate among the studied Ocsi/latoria isolates. Most isolates of Ocsi/latoria genotypes were discriminated by one or more unique bands. Numerical taxonomic using 45 protein attributes of 19 isolates and RAPO markers on five isolates. Two methods -Clustering (UPGMA) and Principal Component Analysis (PCA) were used for these analyses. The similarities and clusters produced between the studied isolates were discussed.

Biochemical and molecular genetic studies on some cyanobacterial isolates

Energy Technology Data Exchange (ETDEWEB)

Kamal, E A.R. [Umm Al-Qura University, Makkah (Saudi Arabia). Dept. of Biology; Ebrahim, S A.A. [Ain Sham University, Cairo (Egypt). Dept. of Cytogenetic

2011-11-15

In the present study, the isolation and purification of a set of Cyanobacteria strains belonging to genus Oscillatoria was undertaken, followed by the analyses of phylogenetic relationships using different biochemical and molecular genetic techniques (SOS-PAGE and RAPO-PCR). A total of 45 protein bands were observed within the studied Osci/latoria isolates by SOS-PAGE (only three unique bands, eight monomorphic bands and 37 polymorphic bands). On the other hand, extracted ONA from isolates was used to identify the molecular fingerprints. A sum of 94 polymorphic bands was generated by these primers in the Ocsi/laloria genotypes under study. A total of 20 unique bands were identified out of the polymorphic ones. These unique bands were used to discriminate among the studied Ocsi/latoria isolates. Most isolates of Ocsi/latoria genotypes were discriminated by one or more unique bands. Numerical taxonomic using 45 protein attributes of 19 isolates and RAPO markers on five isolates. Two methods -Clustering (UPGMA) and Principal Component Analysis (PCA) were used for these analyses. The similarities and clusters produced between the studied isolates were discussed.

Hierarchical modularization of biochemical pathways using fuzzy-c means clustering.

Science.gov (United States)

de Luis Balaguer, Maria A; Williams, Cranos M

2014-08-01

Biological systems that are representative of regulatory, metabolic, or signaling pathways can be highly complex. Mathematical models that describe such systems inherit this complexity. As a result, these models can often fail to provide a path toward the intuitive comprehension of these systems. More coarse information that allows a perceptive insight of the system is sometimes needed in combination with the model to understand control hierarchies or lower level functional relationships. In this paper, we present a method to identify relationships between components of dynamic models of biochemical pathways that reside in different functional groups. We find primary relationships and secondary relationships. The secondary relationships reveal connections that are present in the system, which current techniques that only identify primary relationships are unable to show. We also identify how relationships between components dynamically change over time. This results in a method that provides the hierarchy of the relationships among components, which can help us to understand the low level functional structure of the system and to elucidate potential hierarchical control. As a proof of concept, we apply the algorithm to the epidermal growth factor signal transduction pathway, and to the C3 photosynthesis pathway. We identify primary relationships among components that are in agreement with previous computational decomposition studies, and identify secondary relationships that uncover connections among components that current computational approaches were unable to reveal.

Automatic reconstruction of fault networks from seismicity catalogs including location uncertainty

International Nuclear Information System (INIS)

Wang, Y.

2013-01-01

Within the framework of plate tectonics, the deformation that arises from the relative movement of two plates occurs across discontinuities in the earth's crust, known as fault zones. Active fault zones are the causal locations of most earthquakes, which suddenly release tectonic stresses within a very short time. In return, fault zones slowly grow by accumulating slip due to such earthquakes by cumulated damage at their tips, and by branching or linking between pre-existing faults of various sizes. Over the last decades, a large amount of knowledge has been acquired concerning the overall phenomenology and mechanics of individual faults and earthquakes: A deep physical and mechanical understanding of the links and interactions between and among them is still missing, however. One of the main issues lies in our failure to always succeed in assigning an earthquake to its causative fault. Using approaches based in pattern-recognition theory, more insight into the relationship between earthquakes and fault structure can be gained by developing an automatic fault network reconstruction approach using high resolution earthquake data sets at largely different scales and by considering individual event uncertainties. This thesis introduces the Anisotropic Clustering of Location Uncertainty Distributions (ACLUD) method to reconstruct active fault networks on the basis of both earthquake locations and their estimated individual uncertainties. This method consists in fitting a given set of hypocenters with an increasing amount of finite planes until the residuals of the fit compare with location uncertainties. After a massive search through the large solution space of possible reconstructed fault networks, six different validation procedures are applied in order to select the corresponding best fault network. Two of the validation steps (cross-validation and Bayesian Information Criterion (BIC)) process the fit residuals, while the four others look for solutions that

Automatic reconstruction of fault networks from seismicity catalogs including location uncertainty

Energy Technology Data Exchange (ETDEWEB)

Wang, Y.

2013-07-01

Within the framework of plate tectonics, the deformation that arises from the relative movement of two plates occurs across discontinuities in the earth's crust, known as fault zones. Active fault zones are the causal locations of most earthquakes, which suddenly release tectonic stresses within a very short time. In return, fault zones slowly grow by accumulating slip due to such earthquakes by cumulated damage at their tips, and by branching or linking between pre-existing faults of various sizes. Over the last decades, a large amount of knowledge has been acquired concerning the overall phenomenology and mechanics of individual faults and earthquakes: A deep physical and mechanical understanding of the links and interactions between and among them is still missing, however. One of the main issues lies in our failure to always succeed in assigning an earthquake to its causative fault. Using approaches based in pattern-recognition theory, more insight into the relationship between earthquakes and fault structure can be gained by developing an automatic fault network reconstruction approach using high resolution earthquake data sets at largely different scales and by considering individual event uncertainties. This thesis introduces the Anisotropic Clustering of Location Uncertainty Distributions (ACLUD) method to reconstruct active fault networks on the basis of both earthquake locations and their estimated individual uncertainties. This method consists in fitting a given set of hypocenters with an increasing amount of finite planes until the residuals of the fit compare with location uncertainties. After a massive search through the large solution space of possible reconstructed fault networks, six different validation procedures are applied in order to select the corresponding best fault network. Two of the validation steps (cross-validation and Bayesian Information Criterion (BIC)) process the fit residuals, while the four others look for solutions that

A high performance image processing platform based on CPU-GPU heterogeneous cluster with parallel image reconstroctions for micro-CT

International Nuclear Information System (INIS)

Ding Yu; Qi Yujin; Zhang Xuezhu; Zhao Cuilan

2011-01-01

In this paper, we report the development of a high-performance image processing platform, which is based on CPU-GPU heterogeneous cluster. Currently, it consists of a Dell Precision T7500 and HP XW8600 workstations with parallel programming and runtime environment, using the message-passing interface (MPI) and CUDA (Compute Unified Device Architecture). We succeeded in developing parallel image processing techniques for 3D image reconstruction of X-ray micro-CT imaging. The results show that a GPU provides a computing efficiency of about 194 times faster than a single CPU, and the CPU-GPU clusters provides a computing efficiency of about 46 times faster than the CPU clusters. These meet the requirements of rapid 3D image reconstruction and real time image display. In conclusion, the use of CPU-GPU heterogeneous cluster is an effective way to build high-performance image processing platform. (authors)

Spin magnetic moments from single atoms to small Cr clusters

Energy Technology Data Exchange (ETDEWEB)

Boeglin, C.; Decker, R.; Bulou, H.; Scheurer, F.; Chado, I. [IPCMS-GSI - UMR 7504, 67037 Strasbourg Cedex (France); Ohresser, P. [LURE, 91405 Orsay (France); Dhesi, S.S. [ESRF, BP 220, 38043 Grenoble Cedex (France); Present permanent address: Diamond Light Source, Chilton, Didcot OX11 0QX (United Kingdom); Gaudry, E. [LMCP, 4, place Jussieu, 75252 Paris (France); Lazarovits, B. [CCMS, T.U. Vienna, Gumpendorfstr. 1a, 1060 Wien (Austria)

2005-07-01

Morphology studies at the first stages of the growth of Cr/Au(111) are reported and compared to the magnetic properties of the nanostructures. We analyze by Scanning Tunneling Microscopy and Low Energy Electron Diffraction the Cr clusters growth between 200 K and 300 K. In the early stages of the growth the morphology of the clusters shows monoatomic high islands located at the kinks of the herringbone reconstructed Au(111) surface. By X-ray Magnetic Circular Dichroism performed on the Cr L{sub 2,3} edges it is shown that the temperature dependent morphology strongly influences the magnetic properties of the Cr clusters. We show that in the sub-monolayer regime Cr clusters are antiferromagnetic and paramagnetic when the size reaches the atomic limit. (copyright 2005 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

Optical Materials with a Genome: Nanophotonics with DNA-Stabilized Silver Clusters

Science.gov (United States)

Copp, Stacy M.

Fluorescent silver clusters with unique rod-like geometries are stabilized by DNA. The sizes and colors of these clusters, or AgN-DNA, are selected by DNA base sequence, which can tune peak emission from blue-green into the near-infrared. Combined with DNA nanostructures, AgN-DNA promise exciting applications in nanophotonics and sensing. Until recently, however, a lack of understanding of the mechanisms controlling AgN-DNA fluorescence has challenged such applications. This dissertation discusses progress toward understanding the role of DNA as a "genome" for silver clusters and toward using DNA to achieve atomic-scale precision of silver cluster size and nanometer-scale precision of silver cluster position on a DNA breadboard. We also investigate sensitivity of AgN-DNA to local solvent environment, with an eye toward applications in chemical and biochemical sensing. Using robotic techniques to generate large data sets, we show that fluorescent silver clusters are templated by certain DNA base motifs that select "magic-sized" cluster cores of enhanced stabilities. The linear arrangement of bases on the phosphate backbone imposes a unique rod-like geometry on the clusters. Harnessing machine learning and bioinformatics techniques, we also demonstrate that sequences of DNA templates can be selected to stabilize silver clusters with desired optical properties, including high fluorescence intensity and specific fluorescence wavelengths, with much higher rates of success as compared to current strategies. The discovered base motifs can be also used to design modular DNA host strands that enable individual silver clusters with atomically precise sizes to bind at specific programmed locations on a DNA nanostructure. We show that DNA-mediated nanoscale arrangement enables near-field coupling of distinct clusters, demonstrated by dual-color cluster assemblies exhibiting resonant energy transfer. These results demonstrate a new degree of control over the optical properties

Weak lensing study of dark matter filaments and application to the binary cluster A 222 and A 223

NARCIS (Netherlands)

Dietrich, JP; Schneider, P; Clowe, D; Romano-Diaz, E; Kerp, J

We present a weak lensing analysis of the double cluster system Abell 222 and Abell 223. The lensing reconstruction shows evidence for a possible dark matter filament connecting both clusters. The case for a filamentary connection between A 222/223 is supported by an analysis of the galaxy density

Towards an inline reconstruction architecture for micro-CT systems

International Nuclear Information System (INIS)

Brasse, David; Humbert, Bernard; Mathelin, Carole; Rio, Marie-Christine; Guyonnet, Jean-Louis

2005-01-01

Recent developments in micro-CT have revolutionized the ability to examine in vivo living experimental animal models such as mouse with a spatial resolution less than 50 μm. The main requirements of in vivo imaging for biological researchers are a good spatial resolution, a low dose induced to the animal during the full examination and a reduced acquisition and reconstruction time for screening purposes. We introduce inline acquisition and reconstruction architecture to obtain in real time the 3D attenuation map of the animal fulfilling the three previous requirements. The micro-CT system is based on commercially available x-ray detector and micro-focus x-ray source. The reconstruction architecture is based on a cluster of PCs where a dedicated communication scheme combining serial and parallel treatments is implemented. In order to obtain high performance transmission rate between the detector and the reconstruction architecture, a dedicated data acquisition system is also developed. With the proposed solution, the time required to filter and backproject a projection of 2048 x 2048 pixels inside a volume of 140 mega voxels using the Feldkamp algorithm is similar to 500 ms, the time needed to acquire the same projection

3D reconstruction by serial sections and gas transport in a porous medium. Application to the study of a clay-loamy soil

International Nuclear Information System (INIS)

Cousin, Isabelle

1996-01-01

The transport properties of porous media like soil are clearly related to the geometrical characteristics of their porous network. The study of these geometrical properties can be divided in two parts: a morphological study (like form and size of the pores) and a topological part (pore space distribution and connectivity). The properties of gaseous diffusion in a clay-loamy soil have been studied by experiments of marked molecules ( 85 Kr) self-diffusion. The tortuosity measured in this soil core is 2.3 with a free-air porosity of 11.3 %. This soil core was then impregnated with polyester resin and ground as serial sections, 100 micrometers apart. The superimposition of the images made from these sections were characterised by stereo-logical functions (chord distributions functions and correlation functions) and by connected and percolating clusters. We showed that a 2D image, with a porosity close to the 3D reconstruction, exhibits chord distributions similar to the chord distribution of the 3D reconstruction. On the contrary, the distribution of connected clusters calculated on a 2D image and on the 3D reconstruction are different, due to the fact that the determination of connected clusters has no real stereo-logical properties. The determination of the connected clusters within the 3D reconstructed sample showed that 87.6 % of the porous network (studied at this scale) and corresponding to 17.7 % as porosity, is made of a single percolating cluster. The numerical simulation of self-diffusion propagator in the percolating system gives the tortuosity of the reconstructed system. This calculated tortuosity is equal to 1.75 and is close to the experimental tortuosity measured on the real soil sample. This low difference between the calculated and the numerical tortuosity is due to the resolution of the serial sections. This work gives also perspectives for the study of hierarchical porous media at different scales. (author) [fr

Stochastic microstructure characterization and reconstruction via supervised learning

International Nuclear Information System (INIS)

Bostanabad, Ramin; Bui, Anh Tuan; Xie, Wei; Apley, Daniel W.; Chen, Wei

2016-01-01

Microstructure characterization and reconstruction have become indispensable parts of computational materials science. The main contribution of this paper is to introduce a general methodology for practical and efficient characterization and reconstruction of stochastic microstructures based on supervised learning. The methodology is general in that it can be applied to a broad range of microstructures (clustered, porous, and anisotropic). By treating the digitized microstructure image as a set of training data, we generically learn the stochastic nature of the microstructure via fitting a supervised learning model to it (we focus on classification trees). The fitted supervised learning model provides an implicit characterization of the joint distribution of the collection of pixel phases in the image. Based on this characterization, we propose two different approaches to efficiently reconstruct any number of statistically equivalent microstructure samples. We test the approach on five examples and show that the spatial dependencies within the microstructures are well preserved, as evaluated via correlation and lineal-path functions. The main advantages of our approach stem from having a compact empirically-learned model that characterizes the stochastic nature of the microstructure, which not only makes reconstruction more computationally efficient than existing methods, but also provides insight into morphological complexity.

Atomic characterization of Au clusters in vapor-liquid-solid grown silicon nanowires

International Nuclear Information System (INIS)

Chen, Wanghua; Roca i Cabarrocas, Pere; Pareige, Philippe; Castro, Celia; Xu, Tao; Grandidier, Bruno; Stiévenard, Didier

2015-01-01

By correlating atom probe tomography with other conventional microscope techniques (scanning electron microscope, scanning transmission electron microscope, and scanning tunneling microscopy), the distribution and composition of Au clusters in individual vapor-liquid-solid grown Si nanowires is investigated. Taking advantage of the characteristics of atom probe tomography, we have developed a sample preparation method by inclining the sample at certain angle to characterize the nanowire sidewall without using focused ion beam. With three-dimensional atomic scale reconstruction, we provide direct evidence of Au clusters tending to remain on the nanowire sidewall rather than being incorporated into the Si nanowires. Based on the composition measurement of Au clusters (28% ± 1%), we have demonstrated the supersaturation of Si atoms in Au clusters, which supports the hypothesis that Au clusters are formed simultaneously during nanowire growth rather than during the cooling process

Atomic characterization of Au clusters in vapor-liquid-solid grown silicon nanowires

Energy Technology Data Exchange (ETDEWEB)

Chen, Wanghua; Roca i Cabarrocas, Pere [Laboratoire de Physique des Interfaces et Couches Minces (LPICM), UMR 7647, CNRS, Ecole Polytechnique, 91128 Palaiseau (France); Pareige, Philippe; Castro, Celia [Groupe de Physique des Matériaux (GPM), Université et INSA de Rouen, UMR 6634, CNRS, Av. de l' Université, BP 12, 76801 Saint Etienne du Rouvray (France); Xu, Tao; Grandidier, Bruno; Stiévenard, Didier [Institut d' Electronique et de Microélectronique et de Nanotechnologies (IEMN), UMR 8520, CNRS, Département ISEN, 41 bd Vauban, 59046 Lille Cedex (France)

2015-09-14

By correlating atom probe tomography with other conventional microscope techniques (scanning electron microscope, scanning transmission electron microscope, and scanning tunneling microscopy), the distribution and composition of Au clusters in individual vapor-liquid-solid grown Si nanowires is investigated. Taking advantage of the characteristics of atom probe tomography, we have developed a sample preparation method by inclining the sample at certain angle to characterize the nanowire sidewall without using focused ion beam. With three-dimensional atomic scale reconstruction, we provide direct evidence of Au clusters tending to remain on the nanowire sidewall rather than being incorporated into the Si nanowires. Based on the composition measurement of Au clusters (28% ± 1%), we have demonstrated the supersaturation of Si atoms in Au clusters, which supports the hypothesis that Au clusters are formed simultaneously during nanowire growth rather than during the cooling process.

Three-Dimensional Computer-Aided Detection of Microcalcification Clusters in Digital Breast Tomosynthesis

Directory of Open Access Journals (Sweden)

Ji-wook Jeong

2016-01-01

Full Text Available We propose computer-aided detection (CADe algorithm for microcalcification (MC clusters in reconstructed digital breast tomosynthesis (DBT images. The algorithm consists of prescreening, MC detection, clustering, and false-positive (FP reduction steps. The DBT images containing the MC-like objects were enhanced by a multiscale Hessian-based three-dimensional (3D objectness response function and a connected-component segmentation method was applied to extract the cluster seed objects as potential clustering centers of MCs. Secondly, a signal-to-noise ratio (SNR enhanced image was also generated to detect the individual MC candidates and prescreen the MC-like objects. Each cluster seed candidate was prescreened by counting neighboring individual MC candidates nearby the cluster seed object according to several microcalcification clustering criteria. As a second step, we introduced bounding boxes for the accepted seed candidate, clustered all the overlapping cubes, and examined. After the FP reduction step, the average number of FPs per case was estimated to be 2.47 per DBT volume with a sensitivity of 83.3%.

Sparse regularization for EIT reconstruction incorporating structural information derived from medical imaging.

Science.gov (United States)

Gong, Bo; Schullcke, Benjamin; Krueger-Ziolek, Sabine; Mueller-Lisse, Ullrich; Moeller, Knut

2016-06-01

Electrical impedance tomography (EIT) reconstructs the conductivity distribution of a domain using electrical data on its boundary. This is an ill-posed inverse problem usually solved on a finite element mesh. For this article, a special regularization method incorporating structural information of the targeted domain is proposed and evaluated. Structural information was obtained either from computed tomography images or from preliminary EIT reconstructions by a modified k-means clustering. The proposed regularization method integrates this structural information into the reconstruction as a soft constraint preferring sparsity in group level. A first evaluation with Monte Carlo simulations indicated that the proposed solver is more robust to noise and the resulting images show fewer artifacts. This finding is supported by real data analysis. The structure based regularization has the potential to balance structural a priori information with data driven reconstruction. It is robust to noise, reduces artifacts and produces images that reflect anatomy and are thus easier to interpret for physicians.

Fuzzy clustering-based segmented attenuation correction in whole-body PET

CERN Document Server

Zaidi, H; Boudraa, A; Slosman, DO

2001-01-01

Segmented-based attenuation correction is now a widely accepted technique to reduce noise contribution of measured attenuation correction. In this paper, we present a new method for segmenting transmission images in positron emission tomography. This reduces the noise on the correction maps while still correcting for differing attenuation coefficients of specific tissues. Based on the Fuzzy C-Means (FCM) algorithm, the method segments the PET transmission images into a given number of clusters to extract specific areas of differing attenuation such as air, the lungs and soft tissue, preceded by a median filtering procedure. The reconstructed transmission image voxels are therefore segmented into populations of uniform attenuation based on the human anatomy. The clustering procedure starts with an over-specified number of clusters followed by a merging process to group clusters with similar properties and remove some undesired substructures using anatomical knowledge. The method is unsupervised, adaptive and a...

Health insurance coverage and racial disparities in breast reconstruction after mastectomy.

Science.gov (United States)

Shippee, Tetyana P; Kozhimannil, Katy B; Rowan, Kathleen; Virnig, Beth A

2014-01-01

Breast reconstruction after mastectomy offers clinical, cosmetic, and psychological benefits compared with mastectomy alone. Although reconstruction rates have increased, racial/ethnic disparities in breast reconstruction persist. Insurance coverage facilitates access to care, but few studies have examined whether health insurance ameliorates disparities. We used the Nationwide Inpatient Sample for 2002 through 2006 to examine the relationships between health insurance coverage, race/ethnicity, and breast reconstruction rates among women who underwent mastectomy for breast cancer. We examined reconstruction rates as a function of the interaction of race and the primary payer (self-pay, private health insurance, government) while controlling for patient comorbidity, and we used generalized estimating equations to account for clustering and hospital characteristics. Minority women had lower breast reconstruction rates than White women (adjusted odds ratio [AOR], 0.57 for African American; AOR, 0.70 for Hispanic; AOR, 0.45 for Asian; p women (AOR, 0.33) and those with public coverage were less likely to undergo reconstruction (AOR, 0.35; p women. Racial/ethnic disparities were less prominent within insurance types. Minority women, whether privately or publicly insured, had lower odds of undergoing reconstruction than White women. Among those without insurance, reconstruction rates did not differ by race/ethnicity. Insurance facilitates access to care, but does not eliminate racial/ethnic disparities in reconstruction rates. Our findings-which reveal persistent health care disparities not explained by patient health status-should prompt efforts to promote both access to and use of beneficial covered services for women with breast cancer. Copyright © 2014 Jacobs Institute of Women's Health. Published by Elsevier Inc. All rights reserved.

Unsupervised Cryo-EM Data Clustering through Adaptively Constrained K-Means Algorithm.

Science.gov (United States)

Xu, Yaofang; Wu, Jiayi; Yin, Chang-Cheng; Mao, Youdong

2016-01-01

In single-particle cryo-electron microscopy (cryo-EM), K-means clustering algorithm is widely used in unsupervised 2D classification of projection images of biological macromolecules. 3D ab initio reconstruction requires accurate unsupervised classification in order to separate molecular projections of distinct orientations. Due to background noise in single-particle images and uncertainty of molecular orientations, traditional K-means clustering algorithm may classify images into wrong classes and produce classes with a large variation in membership. Overcoming these limitations requires further development on clustering algorithms for cryo-EM data analysis. We propose a novel unsupervised data clustering method building upon the traditional K-means algorithm. By introducing an adaptive constraint term in the objective function, our algorithm not only avoids a large variation in class sizes but also produces more accurate data clustering. Applications of this approach to both simulated and experimental cryo-EM data demonstrate that our algorithm is a significantly improved alterative to the traditional K-means algorithm in single-particle cryo-EM analysis.

Neural network based cluster creation in the ATLAS silicon pixel detector

CERN Document Server

Selbach, K E; The ATLAS collaboration

2012-01-01

The read-out from individual pixels on planar semi-conductor sensors are grouped into clusters to reconstruct the location where a charged particle passed through the sensor. The resolution given by individual pixel sizes is significantly improved by using the information from the charge sharing between pixels. Such analog cluster creation techniques have been used by the ATLAS experiment for many years to obtain an excellent performance. However, in dense environments, such as those inside high-energy jets, clusters have an increased probability of merging the charge deposited by multiple particles. Recently, a neural network based algorithm which estimates both the cluster position and whether a cluster should be split has been developed for the ATLAS pixel detector. The algorithm significantly reduces ambiguities in the assignment of pixel detector measurement to tracks within jets and improves the position accuracy with respect to standard interpolation techniques by taking into account the 2-dimensional ...

Neural network based cluster creation in the ATLAS silicon Pixel Detector

CERN Document Server

Andreazza, A; The ATLAS collaboration

2013-01-01

The read-out from individual pixels on planar semi-conductor sensors are grouped into clusters to reconstruct the location where a charged particle passed through the sensor. The resolution given by individual pixel sizes is significantly improved by using the information from the charge sharing between pixels. Such analog cluster creation techniques have been used by the ATLAS experiment for many years to obtain an excellent performance. However, in dense environments, such as those inside high-energy jets, clusters have an increased probability of merging the charge deposited by multiple particles. Recently, a neural network based algorithm which estimates both the cluster position and whether a cluster should be split has been developed for the ATLAS Pixel Detector. The algorithm significantly reduces ambiguities in the assignment of pixel detector measurement to tracks within jets and improves the position accuracy with respect to standard interpolation techniques by taking into account the 2-dimensional ...

Phylogenetic reconstruction of transmission events from individuals with acute HIV infection: toward more-rigorous epidemiological definitions

NARCIS (Netherlands)

Brown, Alison E.; Gifford, Robert J.; Clewley, Jonathan P.; Kucherer, Claudia; Masquelier, Bernard; Porter, Kholoud; Balotta, Claudia; Back, Nicole K. T.; Jorgensen, Louise Bruun; de Mendoza, Carmen; Bhaskaran, Krishnan; Gill, O. Noel; Johnson, Anne M.; Pillay, Deenan; del Amo, Julia; Meyer, Laurence; Bucher, Heiner; Chene, Genevieve; Prins, Maria; Rosinska, Magda; Sabin, Caroline; Touloumi, Giota; Lodi, Sara; Walker, Sarah; Babiker, Abdel; Darbyshire, Janet; de Luca, Andrea; Fisher, Martin; Muga, Roberto; Kaldor, John; Kelleher, Tony; Ramacciotti, Tim; Gelgor, Linda; Cooper, David; Smith, Don; Gill, John; Nielsen, Claus; Pedersen, Court; Lutsar, Irja; Dabis, Francois; Thiebaut, Rodolphe; Costagliola, Dominique; Guiguet, Marguerite; Vanhems, Philippe; Boufassa, Faroudy; Hamouda, Osamah; Pantazis, Nikos; Hatzakis, Angelos; Geskus, Ronald; Coutinho, Roel

2009-01-01

Phylogenetic reconstructions of transmission events from individuals with acute human immunodeficiency virus (HIV) infection are conducted to illustrate this group's heightened infectivity. Varied definitions of acute infection and assumptions about observed phylogenetic clusters may produce

Clustering of near clusters versus cluster compactness

International Nuclear Information System (INIS)

Yu Gao; Yipeng Jing

1989-01-01

The clustering properties of near Zwicky clusters are studied by using the two-point angular correlation function. The angular correlation functions for compact and medium compact clusters, for open clusters, and for all near Zwicky clusters are estimated. The results show much stronger clustering for compact and medium compact clusters than for open clusters, and that open clusters have nearly the same clustering strength as galaxies. A detailed study of the compactness-dependence of correlation function strength is worth investigating. (author)

Dark matter phenomenology of high-speed galaxy cluster collisions

International Nuclear Information System (INIS)

Mishchenko, Yuriy; Ji, Chueng-Ryong

2017-01-01

We perform a general computational analysis of possible post-collision mass distributions in high-speed galaxy cluster collisions in the presence of self-interacting dark matter. Using this analysis, we show that astrophysically weakly self-interacting dark matter can impart subtle yet measurable features in the mass distributions of colliding galaxy clusters even without significant disruptions to the dark matter halos of the colliding galaxy clusters themselves. Most profound such evidence is found to reside in the tails of dark matter halos' distributions, in the space between the colliding galaxy clusters. Such features appear in our simulations as shells of scattered dark matter expanding in alignment with the outgoing original galaxy clusters, contributing significant densities to projected mass distributions at large distances from collision centers and large scattering angles of up to 90 "c"i"r"c"l"e. Our simulations indicate that as much as 20% of the total collision's mass may be deposited into such structures without noticeable disruptions to the main galaxy clusters. Such structures at large scattering angles are forbidden in purely gravitational high-speed galaxy cluster collisions. Convincing identification of such structures in real colliding galaxy clusters would be a clear indication of the self-interacting nature of dark matter. Our findings may offer an explanation for the ring-like dark matter feature recently identified in the long-range reconstructions of the mass distribution of the colliding galaxy cluster CL0024+017. (orig.)

Dark matter phenomenology of high-speed galaxy cluster collisions

Energy Technology Data Exchange (ETDEWEB)

Mishchenko, Yuriy [Izmir University of Economics, Faculty of Engineering, Izmir (Turkey); Ji, Chueng-Ryong [North Carolina State University, Department of Physics, Raleigh, NC (United States)

2017-08-15

We perform a general computational analysis of possible post-collision mass distributions in high-speed galaxy cluster collisions in the presence of self-interacting dark matter. Using this analysis, we show that astrophysically weakly self-interacting dark matter can impart subtle yet measurable features in the mass distributions of colliding galaxy clusters even without significant disruptions to the dark matter halos of the colliding galaxy clusters themselves. Most profound such evidence is found to reside in the tails of dark matter halos' distributions, in the space between the colliding galaxy clusters. Such features appear in our simulations as shells of scattered dark matter expanding in alignment with the outgoing original galaxy clusters, contributing significant densities to projected mass distributions at large distances from collision centers and large scattering angles of up to 90 {sup circle}. Our simulations indicate that as much as 20% of the total collision's mass may be deposited into such structures without noticeable disruptions to the main galaxy clusters. Such structures at large scattering angles are forbidden in purely gravitational high-speed galaxy cluster collisions. Convincing identification of such structures in real colliding galaxy clusters would be a clear indication of the self-interacting nature of dark matter. Our findings may offer an explanation for the ring-like dark matter feature recently identified in the long-range reconstructions of the mass distribution of the colliding galaxy cluster CL0024+017. (orig.)

Cluster-cluster clustering

International Nuclear Information System (INIS)

Barnes, J.; Dekel, A.; Efstathiou, G.; Frenk, C.S.; Yale Univ., New Haven, CT; California Univ., Santa Barbara; Cambridge Univ., England; Sussex Univ., Brighton, England)

1985-01-01

The cluster correlation function xi sub c(r) is compared with the particle correlation function, xi(r) in cosmological N-body simulations with a wide range of initial conditions. The experiments include scale-free initial conditions, pancake models with a coherence length in the initial density field, and hybrid models. Three N-body techniques and two cluster-finding algorithms are used. In scale-free models with white noise initial conditions, xi sub c and xi are essentially identical. In scale-free models with more power on large scales, it is found that the amplitude of xi sub c increases with cluster richness; in this case the clusters give a biased estimate of the particle correlations. In the pancake and hybrid models (with n = 0 or 1), xi sub c is steeper than xi, but the cluster correlation length exceeds that of the points by less than a factor of 2, independent of cluster richness. Thus the high amplitude of xi sub c found in studies of rich clusters of galaxies is inconsistent with white noise and pancake models and may indicate a primordial fluctuation spectrum with substantial power on large scales. 30 references

Reconstruction of phylogenetic trees of prokaryotes using maximal common intervals.

Science.gov (United States)

Heydari, Mahdi; Marashi, Sayed-Amir; Tusserkani, Ruzbeh; Sadeghi, Mehdi

2014-10-01

One of the fundamental problems in bioinformatics is phylogenetic tree reconstruction, which can be used for classifying living organisms into different taxonomic clades. The classical approach to this problem is based on a marker such as 16S ribosomal RNA. Since evolutionary events like genomic rearrangements are not included in reconstructions of phylogenetic trees based on single genes, much effort has been made to find other characteristics for phylogenetic reconstruction in recent years. With the increasing availability of completely sequenced genomes, gene order can be considered as a new solution for this problem. In the present work, we applied maximal common intervals (MCIs) in two or more genomes to infer their distance and to reconstruct their evolutionary relationship. Additionally, measures based on uncommon segments (UCS's), i.e., those genomic segments which are not detected as part of any of the MCIs, are also used for phylogenetic tree reconstruction. We applied these two types of measures for reconstructing the phylogenetic tree of 63 prokaryotes with known COG (clusters of orthologous groups) families. Similarity between the MCI-based (resp. UCS-based) reconstructed phylogenetic trees and the phylogenetic tree obtained from NCBI taxonomy browser is as high as 93.1% (resp. 94.9%). We show that in the case of this diverse dataset of prokaryotes, tree reconstruction based on MCI and UCS outperforms most of the currently available methods based on gene orders, including breakpoint distance and DCJ. We additionally tested our new measures on a dataset of 13 closely-related bacteria from the genus Prochlorococcus. In this case, distances like rearrangement distance, breakpoint distance and DCJ proved to be useful, while our new measures are still appropriate for phylogenetic reconstruction. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Cluster emergence and network evolution A longitudinal analysis of the inventor network in Sophia-Antipolis

OpenAIRE

Anne L. J. ter Wal

2008-01-01

Abstract It is increasingly acknowledged that clusters do not necessarily exhibit networks of local collective learning. This paper addresses the question under which conditions this is the case. Through a longitudinal case study of the business park Sophia-Antipolis it investigates how networks of collective learning emerged throughout the growth of the cluster. Network reconstruction with patent data shows that an innovation network emerged only in Information Technology, in whic...

[Post-gastrectomy reconstruction versus enteral alimentation--a one year follow-up study].

Science.gov (United States)

Kostov, D; Balabanova, G; Vasilev, B; Plachkov, I; Ignatov, G

2000-01-01

This is a report on various post-gastrectomy reconstructive procedures, proceeding from personal experience had with 14 patients undergoing gastrectomy for carcinoma of the stomach and five patients with operations of esophagus and stomach for various pathological conditions. An assessment is done of the reconstructive methods used on the ground of objective indicators. All patients are subjected to enteral alimentation through nutritive jejunostomy. In the pre- and postoperatived periods, the trophic state of patients is evaluated on basis of biochemical, anthropometric and immunologic study data. Postoperatively, in those with small-intestinal reservoir a lower degree negative symptomatology is established, along with life style improvement. Post-gastrectomy patients presenting I-II (UICC) stage of the oncological disease are indicated for small-intestinal reservoir formation. In the overall therapeutic approach to post-gastrectomy patients adequate clinical therapeutic feeding proves absolutely indispensable.

A fast 4D cone beam CT reconstruction method based on the OSC-TV algorithm.

Science.gov (United States)

Mascolo-Fortin, Julia; Matenine, Dmitri; Archambault, Louis; Després, Philippe

2018-01-01

Four-dimensional cone beam computed tomography allows for temporally resolved imaging with useful applications in radiotherapy, but raises particular challenges in terms of image quality and computation time. The purpose of this work is to develop a fast and accurate 4D algorithm by adapting a GPU-accelerated ordered subsets convex algorithm (OSC), combined with the total variation minimization regularization technique (TV). Different initialization schemes were studied to adapt the OSC-TV algorithm to 4D reconstruction: each respiratory phase was initialized either with a 3D reconstruction or a blank image. Reconstruction algorithms were tested on a dynamic numerical phantom and on a clinical dataset. 4D iterations were implemented for a cluster of 8 GPUs. All developed methods allowed for an adequate visualization of the respiratory movement and compared favorably to the McKinnon-Bates and adaptive steepest descent projection onto convex sets algorithms, while the 4D reconstructions initialized from a prior 3D reconstruction led to better overall image quality. The most suitable adaptation of OSC-TV to 4D CBCT was found to be a combination of a prior FDK reconstruction and a 4D OSC-TV reconstruction with a reconstruction time of 4.5 minutes. This relatively short reconstruction time could facilitate a clinical use.

Rack Aware Data Placement for Network Consumption in Erasure-Coded Clustered Storage Systems

Directory of Open Access Journals (Sweden)

Bilin Shao

2018-06-01

Full Text Available The amount of encoded data replication in an erasure-coded clustered storage system has a great impact on the bandwidth consumption and network latency, mostly during data reconstruction. Aimed at the reasons that lead to the excess data transmission between racks, a rack aware data block placement method is proposed. In order to ensure rack-level fault tolerance and reduce the frequency and amount of the cross-rack data transmission during data reconstruction, the method deploys partial data block concentration to store the data blocks of a file in fewer racks. Theoretical analysis and simulation results show that our proposed strategy greatly reduces the frequency and data volume of the cross-rack transmission during data reconstruction. At the same time, it has better performance than the typical random distribution method in terms of network usage and data reconstruction efficiency.

Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach.

Directory of Open Access Journals (Sweden)

Christian L Barrett

2006-05-01

Full Text Available The number of complete, publicly available genome sequences is now greater than 200, and this number is expected to rapidly grow in the near future as metagenomic and environmental sequencing efforts escalate and the cost of sequencing drops. In order to make use of this data for understanding particular organisms and for discerning general principles about how organisms function, it will be necessary to reconstruct their various biochemical reaction networks. Principal among these will be transcriptional regulatory networks. Given the physical and logical complexity of these networks, the various sources of (often noisy data that can be utilized for their elucidation, the monetary costs involved, and the huge number of potential experiments approximately 10(12 that can be performed, experiment design algorithms will be necessary for synthesizing the various computational and experimental data to maximize the efficiency of regulatory network reconstruction. This paper presents an algorithm for experimental design to systematically and efficiently reconstruct transcriptional regulatory networks. It is meant to be applied iteratively in conjunction with an experimental laboratory component. The algorithm is presented here in the context of reconstructing transcriptional regulation for metabolism in Escherichia coli, and, through a retrospective analysis with previously performed experiments, we show that the produced experiment designs conform to how a human would design experiments. The algorithm is able to utilize probability estimates based on a wide range of computational and experimental sources to suggest experiments with the highest potential of discovering the greatest amount of new regulatory knowledge.

Performance of the ATLAS track reconstruction algorithms in dense environments in LHC Run 2.

Science.gov (United States)

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Scannicchio, D A; Scarcella, M; Scarfone, V; Schaarschmidt, J; Schacht, P; Schachtner, B M; Schaefer, D; Schaefer, L; Schaefer, R; Schaeffer, J; Schaepe, S; Schaetzel, S; Schäfer, U; Schaffer, A C; Schaile, D; Schamberger, R D; Scharf, V; Schegelsky, V A; Scheirich, D; Schernau, M; Schiavi, C; Schier, S; Schildgen, L K; Schillo, C; Schioppa, M; Schlenker, S; Schmidt-Sommerfeld, K R; Schmieden, K; Schmitt, C; Schmitt, S; Schmitz, S; Schnoor, U; Schoeffel, L; Schoening, A; Schoenrock, B D; Schopf, E; Schott, M; Schouwenberg, J F P; Schovancova, J; Schramm, S; Schuh, N; Schulte, A; Schultens, M J; Schultz-Coulon, H-C; Schulz, H; Schumacher, M; Schumm, B A; Schune, Ph; Schwartzman, A; Schwarz, T A; Schweiger, H; Schwemling, Ph; Schwienhorst, R; Schwindling, J; Sciandra, A; Sciolla, G; Scuri, F; Scutti, F; Searcy, J; Seema, P; Seidel, S C; Seiden, A; Seixas, J M; Sekhniaidze, G; Sekhon, K; Sekula, S J; Semprini-Cesari, N; Senkin, S; Serfon, C; Serin, L; Serkin, L; Sessa, M; Seuster, R; Severini, H; Sfiligoj, T; Sforza, F; Sfyrla, A; Shabalina, E; Shaikh, N W; Shan, L Y; Shang, R; Shank, J T; Shapiro, M; Shatalov, P B; Shaw, K; Shaw, S M; Shcherbakova, A; Shehu, C Y; Shen, Y; Sherafati, N; Sherwood, P; Shi, L; Shimizu, S; Shimmin, C O; Shimojima, M; Shipsey, I P J; Shirabe, S; Shiyakova, M; Shlomi, J; Shmeleva, A; Shoaleh Saadi, D; Shochet, M J; Shojaii, S; Shope, D R; Shrestha, S; Shulga, E; Shupe, M A; Sicho, P; Sickles, A M; Sidebo, P E; Sideras Haddad, E; Sidiropoulou, O; Sidoti, A; Siegert, F; Sijacki, Dj; Silva, J; Silverstein, S B; Simak, V; Simic, Lj; Simion, S; Simioni, E; Simmons, B; Simon, M; Sinervo, P; Sinev, N B; Sioli, M; Siragusa, G; Siral, I; Sivoklokov, S Yu; Sjölin, J; Skinner, M B; Skubic, P; Slater, M; Slavicek, T; Slawinska, M; Sliwa, K; Slovak, R; Smakhtin, V; Smart, B H; Smiesko, J; Smirnov, N; Smirnov, S Yu; Smirnov, Y; Smirnova, L N; Smirnova, O; Smith, J W; Smith, M N K; Smith, R W; Smizanska, M; Smolek, K; Snesarev, A A; Snyder, I M; Snyder, S; Sobie, R; Socher, F; Soffer, A; Søgaard, A; Soh, D A; Sokhrannyi, G; Solans Sanchez, C A; Solar, M; Soldatov, E Yu; Soldevila, U; Solodkov, A A; Soloshenko, A; Solovyanov, O V; Solovyev, V; Sommer, P; Son, H; Sopczak, A; Sosa, D; Sotiropoulou, C L; Soualah, R; Soukharev, A M; South, D; Sowden, B C; Spagnolo, S; Spalla, M; Spangenberg, M; Spanò, F; Sperlich, D; Spettel, F; Spieker, T M; Spighi, R; Spigo, G; Spiller, L A; Spousta, M; St Denis, R D; Stabile, A; Stamen, R; Stamm, S; Stanecka, E; Stanek, R W; Stanescu, C; Stanitzki, M M; Stapf, B S; Stapnes, S; Starchenko, E A; Stark, G H; Stark, J; Stark, S H; Staroba, P; Starovoitov, P; Stärz, S; Staszewski, R; Steinberg, P; Stelzer, B; Stelzer, H J; Stelzer-Chilton, O; Stenzel, H; Stewart, G A; Stockton, M C; Stoebe, M; Stoicea, G; Stolte, P; Stonjek, S; Stradling, A R; Straessner, A; Stramaglia, M E; Strandberg, J; Strandberg, S; Strauss, M; Strizenec, P; Ströhmer, R; Strom, D M; Stroynowski, R; Strubig, A; Stucci, S A; Stugu, B; Styles, N A; Su, D; Su, J; Suchek, S; Sugaya, Y; Suk, M; Sulin, V V; Sultan, Dms; Sultansoy, S; Sumida, T; Sun, S; Sun, X; Suruliz, K; Suster, C J E; Sutton, M R; Suzuki, S; Svatos, M; Swiatlowski, M; Swift, S P; Sykora, I; Sykora, T; Ta, D; Tackmann, K; Taenzer, J; Taffard, A; Tafirout, R; Tahirovic, E; Taiblum, N; Takai, H; Takashima, R; Takasugi, E H; Takeshita, T; Takubo, Y; Talby, M; Talyshev, A A; Tanaka, J; Tanaka, M; Tanaka, R; Tanaka, S; Tanioka, R; Tannenwald, B B; Tapia Araya, S; Tapprogge, S; Tarem, S; Tartarelli, G F; Tas, P; Tasevsky, M; Tashiro, T; Tassi, E; Tavares Delgado, A; Tayalati, Y; Taylor, A C; Taylor, G N; Taylor, P T E; Taylor, W; Teixeira-Dias, P; Temple, D; Ten Kate, H; Teng, P K; Teoh, J J; Tepel, F; Terada, S; Terashi, K; Terron, J; Terzo, S; Testa, M; Teuscher, R J; Theveneaux-Pelzer, T; Thomas, J P; Thomas-Wilsker, J; Thompson, P D; Thompson, A S; Thomsen, L A; Thomson, E; Tibbetts, M J; Ticse Torres, R E; Tikhomirov, V O; Tikhonov, Yu A; Timoshenko, S; Tipton, P; Tisserant, S; Todome, K; Todorova-Nova, S; Tojo, J; Tokár, S; Tokushuku, K; Tolley, E; Tomlinson, L; Tomoto, M; Tompkins, L; Toms, K; Tong, B; Tornambe, P; Torrence, E; Torres, H; Torró Pastor, E; Toth, J; Touchard, F; Tovey, D R; Treado, C J; Trefzger, T; Tresoldi, F; Tricoli, A; Trigger, I M; Trincaz-Duvoid, S; Tripiana, M F; Trischuk, W; Trocmé, B; Trofymov, A; Troncon, C; Trottier-McDonald, M; Trovatelli, M; Truong, L; Trzebinski, M; Trzupek, A; Tsang, K W; Tseng, J C-L; Tsiareshka, P V; Tsipolitis, G; Tsirintanis, N; Tsiskaridze, S; Tsiskaridze, V; Tskhadadze, E G; Tsui, K M; Tsukerman, I I; Tsulaia, V; Tsuno, S; Tsybychev, D; Tu, Y; Tudorache, A; Tudorache, V; Tulbure, T T; Tuna, A N; Tupputi, S A; Turchikhin, S; Turgeman, D; Turk Cakir, I; Turra, R; Tuts, P M; Ucchielli, G; Ueda, I; Ughetto, M; Ukegawa, F; Unal, G; Undrus, A; Unel, G; Ungaro, F C; Unno, Y; Unverdorben, C; Urban, J; Urquijo, P; Urrejola, P; Usai, G; Usui, J; Vacavant, L; Vacek, V; Vachon, B; Vadla, K O H; Vaidya, A; Valderanis, C; Valdes Santurio, E; Valente, M; Valentinetti, S; Valero, A; Valéry, L; Valkar, S; Vallier, A; Valls Ferrer, J A; Van Den Wollenberg, W; van der Graaf, H; van Gemmeren, P; Van Nieuwkoop, J; van Vulpen, I; van Woerden, M C; Vanadia, M; Vandelli, W; Vaniachine, A; Vankov, P; Vardanyan, G; Vari, R; Varnes, E W; Varni, C; Varol, T; Varouchas, D; Vartapetian, A; Varvell, K E; Vasquez, J G; Vasquez, G A; Vazeille, F; Vazquez Schroeder, T; Veatch, J; Veeraraghavan, V; Veloce, L M; Veloso, F; Veneziano, S; Ventura, A; Venturi, M; Venturi, N; Venturini, A; Vercesi, V; Verducci, M; Verkerke, W; Vermeulen, A T; Vermeulen, J C; Vetterli, M C; Viaux Maira, N; Viazlo, O; Vichou, I; Vickey, T; Vickey Boeriu, O E; Viehhauser, G H A; Viel, S; Vigani, L; Villa, M; Villaplana Perez, M; Vilucchi, E; Vincter, M G; Vinogradov, V B; Vishwakarma, A; Vittori, C; Vivarelli, I; Vlachos, S; Vlasak, M; Vogel, M; Vokac, P; Volpi, G; von der Schmitt, H; von Toerne, E; Vorobel, V; Vorobev, K; Vos, M; Voss, R; Vossebeld, J H; Vranjes, N; Vranjes Milosavljevic, M; Vrba, V; Vreeswijk, M; Vuillermet, R; Vukotic, I; Wagner, P; Wagner, W; Wagner-Kuhr, J; Wahlberg, H; Wahrmund, S; Wakabayashi, J; Walder, J; Walker, R; Walkowiak, W; Wallangen, V; Wang, C; Wang, C; Wang, F; Wang, H; Wang, H; Wang, J; Wang, J; Wang, Q; Wang, R; Wang, S M; Wang, T; Wang, W; Wang, W; Wang, Z; Wanotayaroj, C; Warburton, A; Ward, C P; Wardrope, D R; Washbrook, A; Watkins, P M; Watson, A T; Watson, M F; Watts, G; Watts, S; Waugh, B M; Webb, A F; Webb, S; Weber, M S; Weber, S W; Weber, S A; Webster, J S; Weidberg, A R; Weinert, B; Weingarten, J; Weirich, M; Weiser, C; Weits, H; Wells, P S; Wenaus, T; Wengler, T; Wenig, S; Wermes, N; Werner, M D; Werner, P; Wessels, M; Weston, T D; Whalen, K; Whallon, N L; Wharton, A M; White, A S; White, A; White, M J; White, R; Whiteson, D; Whitmore, B W; Wickens, F J; Wiedenmann, W; Wielers, M; Wiglesworth, C; Wiik-Fuchs, L A M; Wildauer, A; Wilk, F; Wilkens, H G; Williams, H H; Williams, S; Willis, C; Willocq, S; Wilson, J A; Wingerter-Seez, I; Winkels, E; Winklmeier, F; Winston, O J; Winter, B T; Wittgen, M; Wobisch, M; Wolf, T M H; Wolff, R; Wolter, M W; Wolters, H; Wong, V W S; Worm, S D; Wosiek, B K; Wotschack, J; Wozniak, K W; Wu, M; Wu, S L; Wu, X; Wu, Y; Wyatt, T R; Wynne, B M; Xella, S; Xi, Z; Xia, L; Xu, D; Xu, L; Yabsley, B; Yacoob, S; Yamaguchi, D; Yamaguchi, Y; Yamamoto, A; Yamamoto, S; Yamanaka, T; Yamatani, M; Yamauchi, K; Yamazaki, Y; Yan, Z; Yang, H; Yang, H; Yang, Y; Yang, Z; Yao, W-M; Yap, Y C; Yasu, Y; Yatsenko, E; Yau Wong, K H; Ye, J; Ye, S; Yeletskikh, I; Yigitbasi, E; Yildirim, E; Yorita, K; Yoshihara, K; Young, C; Young, C J S; Yu, J; Yu, J; Yuen, S P Y; Yusuff, I; Zabinski, B; Zacharis, G; Zaidan, R; Zaitsev, A M; Zakharchuk, N; Zalieckas, J; Zaman, A; Zambito, S; Zanzi, D; Zeitnitz, C; Zemaityte, G; Zemla, A; Zeng, J C; Zeng, Q; Zenin, O; Ženiš, T; Zerwas, D; Zhang, D; Zhang, F; Zhang, G; Zhang, H; Zhang, J; Zhang, L; Zhang, L; Zhang, M; Zhang, P; Zhang, R; Zhang, R; Zhang, X; Zhang, Y; Zhang, Z; Zhao, X; Zhao, Y; Zhao, Z; Zhemchugov, A; Zhou, B; Zhou, C; Zhou, L; Zhou, M; Zhou, M; Zhou, N; Zhu, C G; Zhu, H; Zhu, J; Zhu, Y; Zhuang, X; Zhukov, K; Zibell, A; Zieminska, D; Zimine, N I; Zimmermann, C; Zimmermann, S; Zinonos, Z; Zinser, M; Ziolkowski, M; Živković, L; Zobernig, G; Zoccoli, A; Zou, R; Zur Nedden, M; Zwalinski, L

2017-01-01

With the increase in energy of the Large Hadron Collider to a centre-of-mass energy of 13 [Formula: see text] for Run 2, events with dense environments, such as in the cores of high-energy jets, became a focus for new physics searches as well as measurements of the Standard Model. These environments are characterized by charged-particle separations of the order of the tracking detectors sensor granularity. Basic track quantities are compared between 3.2 fb[Formula: see text] of data collected by the ATLAS experiment and simulation of proton-proton collisions producing high-transverse-momentum jets at a centre-of-mass energy of 13 [Formula: see text]. The impact of charged-particle separations and multiplicities on the track reconstruction performance is discussed. The track reconstruction efficiency in the cores of jets with transverse momenta between 200 and 1600 [Formula: see text] is quantified using a novel, data-driven, method. The method uses the energy loss, [Formula: see text], to identify pixel clusters originating from two charged particles. Of the charged particles creating these clusters, the measured fraction that fail to be reconstructed is [Formula: see text] and [Formula: see text] for jet transverse momenta of 200-400 [Formula: see text] and 1400-1600 [Formula: see text], respectively.

Fe-S Cluster Biogenesis in Isolated Mammalian Mitochondria

Science.gov (United States)

Pandey, Alok; Pain, Jayashree; Ghosh, Arnab K.; Dancis, Andrew; Pain, Debkumar

2015-01-01

Iron-sulfur (Fe-S) clusters are essential cofactors, and mitochondria contain several Fe-S proteins, including the [4Fe-4S] protein aconitase and the [2Fe-2S] protein ferredoxin. Fe-S cluster assembly of these proteins occurs within mitochondria. Although considerable data exist for yeast mitochondria, this biosynthetic process has never been directly demonstrated in mammalian mitochondria. Using [35S]cysteine as the source of sulfur, here we show that mitochondria isolated from Cath.A-derived cells, a murine neuronal cell line, can synthesize and insert new Fe-35S clusters into aconitase and ferredoxins. The process requires GTP, NADH, ATP, and iron, and hydrolysis of both GTP and ATP is necessary. Importantly, we have identified the 35S-labeled persulfide on the NFS1 cysteine desulfurase as a genuine intermediate en route to Fe-S cluster synthesis. In physiological settings, the persulfide sulfur is released from NFS1 and transferred to a scaffold protein, where it combines with iron to form an Fe-S cluster intermediate. We found that the release of persulfide sulfur from NFS1 requires iron, showing that the use of iron and sulfur for the synthesis of Fe-S cluster intermediates is a highly coordinated process. The release of persulfide sulfur also requires GTP and NADH, probably mediated by a GTPase and a reductase, respectively. ATP, a cofactor for a multifunctional Hsp70 chaperone, is not required at this step. The experimental system described here may help to define the biochemical basis of diseases that are associated with impaired Fe-S cluster biogenesis in mitochondria, such as Friedreich ataxia. PMID:25398879

Source Plane Reconstruction of the Bright Lensed Galaxy RCSGA 032727-132609

Science.gov (United States)

Sharon, Keren; Gladders, Michael D.; Rigby, Jane R.; Wuyts, Eva; Koester, Benjamin P.; Bayliss, Matthew B.; Barrientos, L. Felipe

2011-01-01

We present new HST/WFC3 imaging data of RCS2 032727-132609, a bright lensed galaxy at z=1.7 that is magnified and stretched by the lensing cluster RCS2 032727-132623. Using this new high-resolution imaging, we modify our previous lens model (which was based on ground-based data) to fully understand the lensing geometry, and use it to reconstruct the lensed galaxy in the source plane. This giant arc represents a unique opportunity to peer into 100-pc scale structures in a high redshift galaxy. This new source reconstruction will be crucial for a future analysis of the spatially-resolved rest-UV and rest-optical spectra of the brightest parts of the arc.

BISEN: Biochemical simulation environment

NARCIS (Netherlands)

Vanlier, J.; Wu, F.; Qi, F.; Vinnakota, K.C.; Han, Y.; Dash, R.K.; Yang, F.; Beard, D.A.

2009-01-01

The Biochemical Simulation Environment (BISEN) is a suite of tools for generating equations and associated computer programs for simulating biochemical systems in the MATLAB® computing environment. This is the first package that can generate appropriate systems of differential equations for

Online Event Reconstruction in the CBM Experiment at FAIR

Science.gov (United States)

Akishina, Valentina; Kisel, Ivan

2018-02-01

Targeting for rare observables, the CBM experiment will operate at high interaction rates of up to 10 MHz, which is unprecedented in heavy-ion experiments so far. It requires a novel free-streaming readout system and a new concept of data processing. The huge data rates of the CBM experiment will be reduced online to the recordable rate before saving the data to the mass storage. Full collision reconstruction and selection will be performed online in a dedicated processor farm. In order to make an efficient event selection online a clean sample of particles has to be provided by the reconstruction package called First Level Event Selection (FLES). The FLES reconstruction and selection package consists of several modules: track finding, track fitting, event building, short-lived particles finding, and event selection. Since detector measurements contain also time information, the event building is done at all stages of the reconstruction process. The input data are distributed within the FLES farm in a form of time-slices. A time-slice is reconstructed in parallel between processor cores. After all tracks of the whole time-slice are found and fitted, they are collected into clusters of tracks originated from common primary vertices, which then are fitted, thus identifying the interaction points. Secondary tracks are associated with primary vertices according to their estimated production time. After that short-lived particles are found and the full event building process is finished. The last stage of the FLES package is a selection of events according to the requested trigger signatures. The event reconstruction procedure and the results of its application to simulated collisions in the CBM detector setup are presented and discussed in detail.

Three-dimensional Reconstruction and Homogenization of Heterogeneous Materials Using Statistical Correlation Functions and FEM

Energy Technology Data Exchange (ETDEWEB)

Baniassadi, Majid; Mortazavi, Behzad; Hamedani, Amani; Garmestani, Hamid; Ahzi, Said; Fathi-Torbaghan, Madjid; Ruch, David; Khaleel, Mohammad A.

2012-01-31

In this study, a previously developed reconstruction methodology is extended to three-dimensional reconstruction of a three-phase microstructure, based on two-point correlation functions and two-point cluster functions. The reconstruction process has been implemented based on hybrid stochastic methodology for simulating the virtual microstructure. While different phases of the heterogeneous medium are represented by different cells, growth of these cells is controlled by optimizing parameters such as rotation, shrinkage, translation, distribution and growth rates of the cells. Based on the reconstructed microstructure, finite element method (FEM) was used to compute the effective elastic modulus and effective thermal conductivity. A statistical approach, based on two-point correlation functions, was also used to directly estimate the effective properties of the developed microstructures. Good agreement between the predicted results from FEM analysis and statistical methods was found confirming the efficiency of the statistical methods for prediction of thermo-mechanical properties of three-phase composites.

A Deep Learning Prediction Model Based on Extreme-Point Symmetric Mode Decomposition and Cluster Analysis

OpenAIRE

Li, Guohui; Zhang, Songling; Yang, Hong

2017-01-01

Aiming at the irregularity of nonlinear signal and its predicting difficulty, a deep learning prediction model based on extreme-point symmetric mode decomposition (ESMD) and clustering analysis is proposed. Firstly, the original data is decomposed by ESMD to obtain the finite number of intrinsic mode functions (IMFs) and residuals. Secondly, the fuzzy c-means is used to cluster the decomposed components, and then the deep belief network (DBN) is used to predict it. Finally, the reconstructed ...

ALICE HLT Cluster operation during ALICE Run 2

Science.gov (United States)

Lehrbach, J.; Krzewicki, M.; Rohr, D.; Engel, H.; Gomez Ramirez, A.; Lindenstruth, V.; Berzano, D.; ALICE Collaboration

2017-10-01

ALICE (A Large Ion Collider Experiment) is one of the four major detectors located at the LHC at CERN, focusing on the study of heavy-ion collisions. The ALICE High Level Trigger (HLT) is a compute cluster which reconstructs the events and compresses the data in real-time. The data compression by the HLT is a vital part of data taking especially during the heavy-ion runs in order to be able to store the data which implies that reliability of the whole cluster is an important matter. To guarantee a consistent state among all compute nodes of the HLT cluster we have automatized the operation as much as possible. For automatic deployment of the nodes we use Foreman with locally mirrored repositories and for configuration management of the nodes we use Puppet. Important parameters like temperatures, network traffic, CPU load etc. of the nodes are monitored with Zabbix. During periods without beam the HLT cluster is used for tests and as one of the WLCG Grid sites to compute offline jobs in order to maximize the usage of our cluster. To prevent interference with normal HLT operations we separate the virtual machines running the Grid jobs from the normal HLT operation via virtual networks (VLANs). In this paper we give an overview of the ALICE HLT operation in 2016.

Reconstruction of composite in-line electron holograms using a small emission cone

International Nuclear Information System (INIS)

Holenstein, Roman; Rothwell, Timothy A.; Shegelski, Mark R.A.

2003-01-01

We report a new method that gives atomic resolution in the reconstruction of simulated holograms in theoretical low energy electron point source (LEEPS) microscopy, and that uses a screen size that is commensurate with screen sizes used in experimental LEEPS. The method exploits the spherical symmetry in the electron waves emerging from the source. We compare holograms obtained by rotating the screen about an axis passing through the point source as opposed to rotating the atomic cluster in the opposite sense about the same axis. We show that, by generating and combining simulated holograms obtained by rotating the cluster, with the screen held fixed, a composite hologram, comprised of the individual holograms, captures enough information that atomic resolution in the reconstructions is obtained. A key feature is to choose the rotations to optimize the collective interference pattern on the composite hologram. This results in sharper resolution while using a considerably smaller screen size; results are reported for a screen size about ten times smaller than screen sizes typically used in theoretical LEEPS. The method used gives commensurate or better resolution on comparison to results obtained using the larger screen size. Possible implications for experimental LEEPS are briefly discussed

Deep linear autoencoder and patch clustering-based unified one-dimensional coding of image and video

Science.gov (United States)

Li, Honggui

2017-09-01

This paper proposes a unified one-dimensional (1-D) coding framework of image and video, which depends on deep learning neural network and image patch clustering. First, an improved K-means clustering algorithm for image patches is employed to obtain the compact inputs of deep artificial neural network. Second, for the purpose of best reconstructing original image patches, deep linear autoencoder (DLA), a linear version of the classical deep nonlinear autoencoder, is introduced to achieve the 1-D representation of image blocks. Under the circumstances of 1-D representation, DLA is capable of attaining zero reconstruction error, which is impossible for the classical nonlinear dimensionality reduction methods. Third, a unified 1-D coding infrastructure for image, intraframe, interframe, multiview video, three-dimensional (3-D) video, and multiview 3-D video is built by incorporating different categories of videos into the inputs of patch clustering algorithm. Finally, it is shown in the results of simulation experiments that the proposed methods can simultaneously gain higher compression ratio and peak signal-to-noise ratio than those of the state-of-the-art methods in the situation of low bitrate transmission.

Performance of the ATLAS track reconstruction algorithms in dense environments in LHC Run 2

Energy Technology Data Exchange (ETDEWEB)

Aaboud, M. [Univ. Mohamed Premier et LPTPM, Oujda (Morocco). Faculte des Sciences; Aad, G. [CPPM, Aix-Marseille Univ. et CNRS/IN2P3, Marseille (France); Abbott, B. [Oklahoma Univ., Norman, OK (United States). Homer L. Dodge Dept. of Physics and Astronomy; Collaboration: ATLAS Collaboration; and others

2017-10-15

With the increase in energy of the Large Hadron Collider to a centre-of-mass energy of 13 TeV for Run 2, events with dense environments, such as in the cores of high-energy jets, became a focus for new physics searches as well as measurements of the Standard Model. These environments are characterized by charged-particle separations of the order of the tracking detectors sensor granularity. Basic track quantities are compared between 3.2 fb{sup -1} of data collected by the ATLAS experiment and simulation of proton-proton collisions producing high-transverse-momentum jets at a centre-of-mass energy of 13 TeV. The impact of charged-particle separations and multiplicities on the track reconstruction performance is discussed. The track reconstruction efficiency in the cores of jets with transverse momenta between 200 and 1600 GeV is quantified using a novel, data-driven, method. The method uses the energy loss, dE/dx, to identify pixel clusters originating from two charged particles. Of the charged particles creating these clusters, the measured fraction that fail to be reconstructed is 0.061 ± 0.006(stat.) ± 0.014(syst.) and 0.093 ± 0.017(stat.) ± 0.021(syst.) for jet transverse momenta of 200-400 GeV and 1400-1600 GeV, respectively. (orig.)

Study of a reconstruction algorithm for electrons in the ATLAS experiment in LHC

International Nuclear Information System (INIS)

Kerschen, N.

2006-09-01

The ATLAS experiment is a general purpose particle physics experiment mainly aimed at the discovery of the origin of mass through the research of the Higgs boson. In order to achieve this, the Large Hadron Collider at CERN will accelerate two proton beams and make them collide at the centre of the experiment. ATLAS will discover new particles through the measurement of their decay products. Electrons are such decay products: they produce an electromagnetic shower in the calorimeter by which they lose all their energy. The calorimeter is divided into cells and the deposited energy is reconstructed using an algorithm to assemble the cells into clusters. The purpose of this thesis is to study a new kind of algorithm adapting the cluster to the shower topology. In order to reconstruct the energy of the initially created electron, the cluster has to be calibrated by taking into account the energy lost in the dead material in front of the calorimeter. Therefore. a Monte-Carlo simulation of the ATLAS detector has been used to correct for effects of response modulation in position and in energy and to optimise the energy resolution as well as the linearity. An analysis of test beam data has been performed to study the behaviour of the algorithm in a more realistic environment. We show that the requirements of the experiment can be met for the linearity and resolution. The improvement of this new algorithm, compared to a fixed sized cluster. is the better recovery of Bremsstrahlung photons emitted by the electron in the material in front of the calorimeter. A Monte-Carlo analysis of the Higgs boson decay in four electrons confirms this result. (author)

Dynamic parallel ROOT facility clusters on the Alice Environment

International Nuclear Information System (INIS)

Luzzi, C; Betev, L; Carminati, F; Grigoras, C; Saiz, P; Manafov, A

2012-01-01

The ALICE collaboration has developed a production environment (AliEn) that implements the full set of the Grid tools enabling the full offline computational work-flow of the experiment, simulation, reconstruction and data analysis, in a distributed and heterogeneous computing environment. In addition to the analysis on the Grid, ALICE uses a set of local interactive analysis facilities installed with the Parallel ROOT Facility (PROOF). PROOF enables physicists to analyze medium-sized (order of 200-300 TB) data sets on a short time scale. The default installation of PROOF is on a static dedicated cluster, typically 200-300 cores. This well-proven approach, has its limitations, more specifically for analysis of larger datasets or when the installation of a dedicated cluster is not possible. Using a new framework called PoD (Proof on Demand), PROOF can be used directly on Grid-enabled clusters, by dynamically assigning interactive nodes on user request. The integration of Proof on Demand in the AliEn framework provides private dynamic PROOF clusters as a Grid service. This functionality is transparent to the user who will submit interactive jobs to the AliEn system.

Combinations of elevated tissue miRNA-17-92 cluster expression and serum prostate-specific antigen as potential diagnostic biomarkers for prostate cancer.

Science.gov (United States)

Feng, Sujuan; Qian, Xiaosong; Li, Han; Zhang, Xiaodong

2017-12-01

The aim of the present study was to investigate the effectiveness of the miR-17-92 cluster as a disease progression marker in prostate cancer (PCa). Reverse transcription-quantitative polymerase chain reaction analysis was used to detect the microRNA (miR)-17-92 cluster expression levels in tissues from patients with PCa or benign prostatic hyperplasia (BPH), in addition to in PCa and BPH cell lines. Spearman correlation was used for comparison and estimation of correlations between miRNA expression levels and clinicopathological characteristics such as the Gleason score and prostate-specific antigen (PSA). Receiver operating curve (ROC) analysis was performed for evaluation of specificity and sensitivity of miR-17-92 cluster expression levels for discriminating patients with PCa from patients with BPH. Kaplan-Meier analysis was plotted to investigate the predictive potential of miR-17-92 cluster for PCa biochemical recurrence. Expression of the majority of miRNAs in the miR-17-92 cluster was identified to be significantly increased in PCa tissues and cell lines. Bivariate correlation analysis indicated that the high expression of unregulated miRNAs was positively correlated with Gleason grade, but had no significant association with PSA. ROC curves demonstrated that high expression of miR-17-92 cluster predicted a higher diagnostic accuracy compared with PSA. Improved discriminating quotients were observed when combinations of unregulated miRNAs with PSA were used. Survival analysis confirmed a high combined miRNA score of miR-17-92 cluster was associated with shorter biochemical recurrence interval. miR-17-92 cluster could be a potential diagnostic and prognostic biomarker for PCa, and the combination of the miR-17-92 cluster and serum PSA may enhance the accuracy for diagnosis of PCa.

Correlations and clustering in wholesale electricity markets

Science.gov (United States)

Cui, Tianyu; Caravelli, Francesco; Ududec, Cozmin

2018-02-01

We study the structure of locational marginal prices in day-ahead and real-time wholesale electricity markets. In particular, we consider the case of two North American markets and show that the price correlations contain information on the locational structure of the grid. We study various clustering methods and introduce a type of correlation function based on event synchronization for spiky time series, and another based on string correlations of location names provided by the markets. This allows us to reconstruct aspects of the locational structure of the grid.

Correlations and clustering in wholesale electricity markets

International Nuclear Information System (INIS)

Cui, Tianyu; Caravelli, Francesco; Ududec, Cozmin

2017-01-01

We study the structure of locational marginal prices in day-ahead and real-time wholesale electricity markets. In particular, we consider the case of two North American markets and show that the price correlations contain information on the locational structure of the grid. We study various clustering methods and introduce a type of correlation function based on event synchronization for spiky time series, and another based on string correlations of location names provided by the markets. As a result, this allows us to reconstruct aspects of the locational structure of the grid.

Reconstruction of the energy flux and search for squarks and gluinos in D0 experiment; Reconstruction du flux d'energie et recherche de squarks et gluinos dans l'experience D0

Energy Technology Data Exchange (ETDEWEB)

Ridel, M

2002-04-01

The D{phi} experiment is located at the Fermi National Accelerator Laboratory on the TeVatron proton-antiproton collider. The Run II has started in march 2001 after 5 years of shutdown and will allow D{phi} extend its reach in squarks and gluinos searches, particles predicted by supersymmetry. In this work, I focussed on their decays that lead to signature with jets and missing transverse energy. But before the data taking started, I studied both software and hardware ways to improve the energy measurement which is crucial for jets and for missing transverse energy. Energy deposits in the calorimeter has been clustered with cellNN, at the cell level instead of the tower level. Efforts have been made to take advantage of the calorimeter granularity to aim at individual particles showers reconstruction. CellNN starts from the third floor which has a quadruple granularity compared to the other floors. The longitudinal information has been used to detect electromagnetic and hadronic showers overlaps. Then, clusters and reconstructed tracks from the central detectors are combined and their energies compared. The better measurement is kept. Using this procedure allows to improve the reconstruction of each event energy flow. The efficiency of the current calorimeter triggers has been determined. They has been used to perform a Monte Carlo search analysis of squarks and gluinos in the mSUGRA framework. The lower bound that Ddiameter will be able to put on squarks and gluinos masses with a 100 pb{sup -1} integrated luminosity has been predicted. The use of the energy flow instead of standard reconstruction tools will be able to improve this lower limit. (author)

Mastectomy Skin Necrosis After Breast Reconstruction: A Comparative Analysis Between Autologous Reconstruction and Implant-Based Reconstruction.

Science.gov (United States)

Sue, Gloria R; Lee, Gordon K

2018-05-01

Mastectomy skin necrosis is a significant problem after breast reconstruction. We sought to perform a comparative analysis on this complication between patients undergoing autologous breast reconstruction and patients undergoing 2-stage expander implant breast reconstruction. A retrospective review was performed on consecutive patients undergoing autologous breast reconstruction or 2-stage expander implant breast reconstruction by the senior author from 2006 through 2015. Patient demographic factors including age, body mass index, history of diabetes, history of smoking, and history of radiation to the breast were collected. Our primary outcome measure was mastectomy skin necrosis. Fisher exact test was used for statistical analysis between the 2 patient cohorts. The treatment patterns of mastectomy skin necrosis were then analyzed. We identified 204 patients who underwent autologous breast reconstruction and 293 patients who underwent 2-stage expander implant breast reconstruction. Patients undergoing autologous breast reconstruction were older, heavier, more likely to have diabetes, and more likely to have had prior radiation to the breast compared with patients undergoing implant-based reconstruction. The incidence of mastectomy skin necrosis was 30.4% of patients in the autologous group compared with only 10.6% of patients in the tissue expander group (P care in the autologous group, only 3.2% were treated with local wound care in the tissue expander group (P skin necrosis is significantly more likely to occur after autologous breast reconstruction compared with 2-stage expander implant-based breast reconstruction. Patients with autologous reconstructions are more readily treated with local wound care compared with patients with tissue expanders, who tended to require operative treatment of this complication. Patients considering breast reconstruction should be counseled appropriately regarding the differences in incidence and management of mastectomy skin

CT coronary angiography: Influence of different cardiac reconstruction intervals on image quality and diagnostic accuracy

Energy Technology Data Exchange (ETDEWEB)

Dewey, Marc [Department of Radiology, Charite Medical School, Humboldt-Universitaet zu Berlin (Germany)], E-mail: marc.dewey@charite.de; Teige, Florian [Department of Radiology, Charite Medical School, Humboldt-Universitaet zu Berlin (Germany); Rutsch, Wolfgang [Department of Cardiology, Charite Medical School, Humboldt-Universitaet zu Berlin (Germany)], E-mail: wolfgang.rutsch@charite.de; Schink, Tania [Department of Medical Biometry, Charite Medical School, Humboldt-Universitaet zu Berlin (Germany)], E-mail: peter.martus@charite.de; Hamm, Bernd [Department of Radiology, Charite Medical School, Humboldt-Universitaet zu Berlin (Germany)

2008-07-15

Purpose: To prospectively analyze image quality and diagnostic accuracy of different reconstruction intervals of coronary angiography using multislice computed tomography (MSCT). Materials and methods: For each of 47 patients, 10 ECG-gated MSCT reconstructions were generated throughout the RR interval from 0 to 90%, resulting in altogether 470 datasets. These datasets were randomly analyzed for image quality and accuracy and compared with conventional angiography. Statistical comparison of intervals was performed using nonparametric analysis for repeated measurements to account for clustering of arteries within patients. Results: Image reconstruction intervals centered at 80, 70, and 40% of the RR interval resulted (in that order) in the best overall image quality for all four main coronary vessels. Eighty percent reconstructions also yielded the highest diagnostic accuracy of all intervals. The combination of the three best intervals (80, 70, and 40%) significantly reduced the nondiagnostic rate as compared with 80% alone (p = 0.005). However, the optimal reconstruction interval combination achieved significantly improved specificities and nondiagnostic rates (p < 0.05). The optimal combination consisted of 1.7 {+-} 0.9 reconstruction intervals on average. In approximately half of the patients (49%, 23/47) a single reconstruction was optimal. In 18 (38%), 3 (6%), and 3 (6%) patients one, two, and three additional reconstruction intervals were required, respectively, to achieve optimal quality. In 28% of the patients the optimal combination consisted of reconstructions other than the three best intervals (80, 70, and 40%). Conclusion: Multiple image reconstruction intervals are essential to ensure high image quality and accuracy of CT coronary angiography.

Studies of the charge instabilities in the complex nano-objects: clusters and bio-molecular systems

International Nuclear Information System (INIS)

Manil, B.

2007-11-01

For the last 6 years, my main research works focused on i) the Coulomb instabilities and the fragmentation processes of fullerenes and clusters of fullerenes ii) the stability and the reactivity of complex bio-molecular systems. Concerning the clusters of fullerenes, which are van der Waals type clusters, we have shown that the multiply charged species, obtained in collisions with slow highly charged ions, keep their structural properties but become very good electric conductor. In another hand, with the aim to understand the role of the biologic environment at the molecular scale in the irradiation damage of complex biomolecules, we have studied the charge stabilities of clusters of small biomolecules and the dissociation processes of larger nano-hydrated biomolecules. Theses studies have shown that first, specific molecular recognition mechanisms continue to exist in gas phase and secondly, a small and very simple biochemical environment is enough to change the dynamics of instabilities. (author)

Scale-dependent bias from the reconstruction of non-Gaussian distributions

International Nuclear Information System (INIS)

Chongchitnan, Sirichai; Silk, Joseph

2011-01-01

Primordial non-Gaussianity introduces a scale-dependent variation in the clustering of density peaks corresponding to rare objects. This variation, parametrized by the bias, is investigated on scales where a linear perturbation theory is sufficiently accurate. The bias is obtained directly in real space by comparing the one- and two-point probability distributions of density fluctuations. We show that these distributions can be reconstructed using a bivariate Edgeworth series, presented here up to an arbitrarily high order. The Edgeworth formalism is shown to be well-suited for ''local'' cubic-order non-Gaussianity parametrized by g NL . We show that a strong scale dependence in the bias can be produced by g NL of order 10 5 , consistent with cosmic microwave background constraints. On a separation length of ∼100 Mpc, current constraints on g NL still allow the bias for the most massive clusters to be enhanced by 20-30% of the Gaussian value. We further examine the bias as a function of mass scale, and also explore the relationship between the clustering and the abundance of massive clusters in the presence of g NL . We explain why the Edgeworth formalism, though technically challenging, is a very powerful technique for constraining high-order non-Gaussianity with large-scale structures.

Dark Matter in Galaxy Clusters: Shape, Projection, and Environment

Science.gov (United States)

Groener, Austen M.

We explore the intrinsic distribution of dark matter within galaxy clusters, by combining insights from the largest N-body simulations as well as the largest observational dataset of its kind. Firstly, we study the intrinsic shape and alignment of isodensities of galaxy cluster halos extracted from the MultiDark MDR1 cosmological simulation. We find that the simulated halos are extremely prolate on small scales and increasingly spherical on larger ones. Due to this trend, analytical projection along the line of sight produces an overestimate of the concentration index as a decreasing function of radius, which we quantify by using both the intrinsic distribution of 3D concentrations (c200) and isodensity shape on weak and strong lensing scales. We find this difference to be ˜ 18% (˜ 9%) for low (medium) mass cluster halos with intrinsically low concentrations (c200=1- 3), while we find virtually no difference for halos with intrinsically high concentrations. Isodensities are found to be fairly well-aligned throughout the entirety of the radial scale of each halo population. However, major axes of individual halos have been found to deviate by as much as ˜ 30°. We also present a value-added catalog of our analysis results, which we have made publicly available to download. Following that, we then turn to observational measurements galaxy clusters. Scaling relations of clusters have made them particularly important cosmological probes of structure formation. In this work, we present a comprehensive study of the relation between two profile observables, concentration (cvir ) and mass (Mvir). We have collected the largest known sample of measurements from the literature which make use of one or more of the following reconstruction techniques: Weak gravitational lensing (WL), strong gravitational lensing (SL), Weak+Strong Lensing (WL+SL), the Caustic Method (CM), Line-of-sight Velocity Dispersion (LOSVD), and X-ray. We find that the concentration-mass (c-M) relation

Contribution of G.A. Ilizarov to bone reconstruction: historical achievements and state of the art

Directory of Open Access Journals (Sweden)

Alexander V. Gubin

2016-07-01

Full Text Available Abstract Methodological solutions of Prof. G.A. Ilizarov are the core stone of the contemporary bone lengthening and reconstruction surgery. They have been acknowledged in the orthopaedic world as one of the greatest contributions to treating bone pathologies. The Ilizarov method of transosseous compression–distraction osteosynthesis has been widely used for managing bone non-union and defects, bone infection, congenital and posttraumatic limb length discrepancies, hand and foot disorders. The optimal conditions for implementing distraction and compression osteogenesis were proven by numerous experimental studies that Prof. G.A. Ilizarov organized and supervised at a large orthopaedic research institute in Kurgan. The tension stress effect on regeneration and growth of tissues was thoroughly investigated with radiographic, histological and biochemical methods. The impact of the Ilizarov method on the progress of bone lengthening and reconstruction surgery could be called revolutionary.

A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism

KAUST Repository

Hefzi, Hooman

2016-11-23

Chinese hamster ovary (CHO) cells dominate biotherapeutic protein production and are widely used in mammalian cell line engineering research. To elucidate metabolic bottlenecks in protein production and to guide cell engineering and bioprocess optimization, we reconstructed the metabolic pathways in CHO and associated them with >1,700 genes in the Cricetulus griseus genome. The genome-scale metabolic model based on this reconstruction, iCHO1766, and cell-line-specific models for CHO-K1, CHO-S, and CHO-DG44 cells provide the biochemical basis of growth and recombinant protein production. The models accurately predict growth phenotypes and known auxotrophies in CHO cells. With the models, we quantify the protein synthesis capacity of CHO cells and demonstrate that common bioprocess treatments, such as histone deacetylase inhibitors, inefficiently increase product yield. However, our simulations show that the metabolic resources in CHO are more than three times more efficiently utilized for growth or recombinant protein synthesis following targeted efforts to engineer the CHO secretory pathway. This model will further accelerate CHO cell engineering and help optimize bioprocesses.

Non-random intrachromosomal distribution of radiation-induced chromatid aberrations in Vicia faba. [Aberration clustering

Energy Technology Data Exchange (ETDEWEB)

Schubert, I; Rieger, R [Akademie der Wissenschaften der DDR, Gatersleben. Zentralinst. fuer Genetik und Kulturpflanzenforschung

1976-04-01

A reconstructed karyotype of Vicia faba, with all chromosomes individually distinguishable, was treated with X-rays, fast neutrons, (/sup 3/H) uridine (/sup 3/HU). The distribution within metaphase chromosomes of induced chromatid aberrations was non-random for all agents used. Aberration clustering, in part agent specific, occurred in chromosome segments containing heterochromatin as defined by the presence of G bands. The pattern of aberration clustering found after treatment with /sup 3/HU did not allow the recognition of chromosome regions active in transcription during treatment. Furthermore, it was impossible to obtain unambiguous indications of the presence of AT- and GC-base clusters from the patterns of /sup 3/HT- and /sup 3/HC-induced chromatid aberrations, respectively. Possible reasons underlying these observations are discussed.

Jets from jets: re-clustering as a tool for large radius jet reconstruction and grooming at the LHC

Science.gov (United States)

Nachman, Benjamin; Nef, Pascal; Schwartzman, Ariel; Swiatlowski, Maximilian; Wanotayaroj, Chaowaroj

2015-02-01

Jets with a large radius R ≳ 1 and grooming algorithms are widely used to fully capture the decay products of boosted heavy particles at the Large Hadron Collider (LHC). Unlike most discriminating variables used in such studies, the jet radius is usually not optimized for specific physics scenarios. This is because every jet configuration must be calibrated, insitu, to account for detector response and other experimental effects. One solution to enhance the availability of large- R jet configurations used by the LHC experiments is jet re-clustering. Jet re-clustering introduces an intermediate scale r groomed jets. Jet re-clustering has the benefit that no additional large-R calibration is necessary, allowing the re-clustered large radius parameter to be optimized in the context of specific precision measurements or searches for new physics.

Application of Delaunay tessellation for the characterization of solute-rich clusters in atom probe tomography

International Nuclear Information System (INIS)

Lefebvre, W.; Philippe, T.; Vurpillot, F.

2011-01-01

This work presents an original method for cluster selection in Atom Probe Tomography designed to be applied to large datasets. It is based on the calculation of the Delaunay tessellation generated by the distribution of atoms of a selected element. It requires a single input parameter from the user. Furthermore, no prior knowledge of the material is needed. The sensitivity of the proposed Delaunay cluster selection is demonstrated by its application on simulated APT datasets. A strong advantage of the proposed methodology is that it is reinforced by the availability of an analytical model for the distribution of Delaunay cells circumspheres, which is used to control the accuracy of the cluster selection procedure. Another advantage of the Delaunay cluster selection is the direct calculation of a sharp envelope for each identified cluster or precipitate, which leads to the more appropriate morphology of the objects as they are reconstructed in the APT dataset. -- Research Highligthts: →Original method for cluster selection in Atom Probe Tomography. →Delaunay tessellation generated by the distribution of solute atoms. →Direct calculation of a sharp envelope for each identified cluster or precipitate. →Delaunay cluster selection demonstrated by its application on simulated APT datasets.

Reconstruction of the energy flux and search for squarks and gluinos in D0 experiment

International Nuclear Information System (INIS)

Ridel, M.

2002-04-01

The DΦ experiment is located at the Fermi National Accelerator Laboratory on the TeVatron proton-antiproton collider. The Run II has started in march 2001 after 5 years of shutdown and will allow DΦ extend its reach in squarks and gluinos searches, particles predicted by supersymmetry. In this work, I focussed on their decays that lead to signature with jets and missing transverse energy. But before the data taking started, I studied both software and hardware ways to improve the energy measurement which is crucial for jets and for missing transverse energy. Energy deposits in the calorimeter has been clustered with cellNN, at the cell level instead of the tower level. Efforts have been made to take advantage of the calorimeter granularity to aim at individual particles showers reconstruction. CellNN starts from the third floor which has a quadruple granularity compared to the other floors. The longitudinal information has been used to detect electromagnetic and hadronic showers overlaps. Then, clusters and reconstructed tracks from the central detectors are combined and their energies compared. The better measurement is kept. Using this procedure allows to improve the reconstruction of each event energy flow. The efficiency of the current calorimeter triggers has been determined. They has been used to perform a Monte Carlo search analysis of squarks and gluinos in the mSUGRA framework. The lower bound that Ddiameter will be able to put on squarks and gluinos masses with a 100 pb -1 integrated luminosity has been predicted. The use of the energy flow instead of standard reconstruction tools will be able to improve this lower limit. (author)

Improvements of the ALICE high level trigger for LHC Run 2 to facilitate online reconstruction, QA, and calibration

Energy Technology Data Exchange (ETDEWEB)

Rohr, David [Frankfurt Institute for Advanced Studies, Frankfurt (Germany); Collaboration: ALICE-Collaboration

2016-07-01

ALICE is one of the four major experiments at the Large Hadron Collider (LHC) at CERN. Its main goal is the study of matter under extreme pressure and temperature as produced in heavy ion collisions at LHC. The ALICE High Level Trigger (HLT) is an online compute farm of around 200 nodes that performs a real time event reconstruction of the data delivered by the ALICE detectors. The HLT employs a fast FPGA based cluster finder algorithm as well as a GPU based track reconstruction algorithm and it is designed to process the maximum data rate expected from the ALICE detectors in real time. We present new features of the HLT for LHC Run 2 that started in 2015. A new fast standalone track reconstruction algorithm for the Inner Tracking System (ITS) enables the HLT to compute and report to LHC the luminous region of the interactions in real time. We employ a new dynamically reconfigurable histogram component that allows the visualization of characteristics of the online reconstruction using the full set of events measured by the detectors. This improves our monitoring and QA capabilities. During Run 2, we plan to deploy online calibration, starting with the calibration of the TPC (Time Projection Chamber) detector's drift time. First proof of concept tests were successfully performed using data-replay on our development cluster and during the heavy ion period at the end of 2015.

A Comparison of Manual Neuronal Reconstruction from Biocytin Histology or 2-Photon Imaging: Morphometry and Computer Modeling

Directory of Open Access Journals (Sweden)

Arne Vladimir Blackman

2014-07-01

Full Text Available Accurate 3D reconstruction of neurons is vital for applications linking anatomy and physiology. Reconstructions are typically created using Neurolucida after biocytin histology (BH. An alternative inexpensive and fast method is to use freeware such as Neuromantic to reconstruct from fluorescence imaging (FI stacks acquired using 2-photon laser-scanning microscopy during physiological recording. We compare these two methods with respect to morphometry, cell classification, and multicompartmental modeling in the NEURON simulation environment. Quantitative morphological analysis of the same cells reconstructed using both methods reveals that whilst biocytin reconstructions facilitate tracing of more distal collaterals, both methods are comparable in representing the overall morphology: automated clustering of reconstructions from both methods successfully separates neocortical basket cells from pyramidal cells but not BH from FI reconstructions. BH reconstructions suffer more from tissue shrinkage and compression artifacts than FI reconstructions do. FI reconstructions, on the other hand, consistently have larger process diameters. Consequently, significant differences in NEURON modeling of excitatory post-synaptic potential (EPSP forward propagation are seen between the two methods, with FI reconstructions exhibiting smaller depolarizations. Simulated action potential backpropagation (bAP, however, is indistinguishable between reconstructions obtained with the two methods. In our hands, BH reconstructions are necessary for NEURON modeling and detailed morphological tracing, and thus remain state of the art, although they are more labor intensive, more expensive, and suffer from a higher failure rate. However, for a subset of anatomical applications such as cell type identification, FI reconstructions are superior, because of indistinguishable classification performance with greater ease of use, essentially 100% success rate, and lower cost.

Isotopic and molecular distributions of biochemicals from fresh and buried Rhizophora mangle leaves†

Science.gov (United States)

Smallwood, Barbara J; Wooller, Matthew J; Jacobson, Myrna E; Fogel, Marilyn L

2003-01-01

Rhizophora mangle L. (red mangrove) is the dominant species of mangrove in the Americas. At Twin Cays, Belize (BZ) red mangroves are present in a variety of stand structures (tall >5 m in height, transition ~2–4 m and dwarf ~1–1.5 m). These height differences are coupled with very different stable carbon and nitrogen isotopic values[1] (mean tall δ13C = -28.3‰, δ15N = 0‰; mean tall δ13C = -25.3‰, δ15N = -10‰). To determine the utility of using these distinct isotopic compositions as 'biomarkers' for paleoenvironmental reconstruction of mangrove ecosystems and nutrient availability, we investigated the distribution and isotopic (δ13C and δ15N) composition of different biochemical fractions (water soluble compounds, free lipids, acid hydrolysable compounds, individual amino acids, and the residual un-extractable compounds) in fresh and preserved red mangrove leaves from dwarf and tall trees. The distribution of biochemicals are similar in dwarf and tall red mangrove leaves, suggesting that, regardless of stand structure, red mangroves use nutrients for biosynthesis and metabolism in a similar manner. However, the δ13C and δ15N of the bulk leaf, the biochemical fractions, and seven amino acids can be used to distinguish dwarf and tall trees at Twin Cays, BZ. The data support the theory that the fractionation of carbon and nitrogen occurs prior to or during uptake in dwarf and tall red mangrove trees. Stable carbon and nitrogen isotopes could, therefore, be powerful tools for predicting levels of nutrient limitation at Twin Cays. The δ13C and δ15N of biochemical fractions within preserved leaves, reflect sedimentary cycling and nitrogen immobilization. The δ15N of the immobilized fraction reveals the overlying stand structure at the time of leaf deposition. The isotopic composition of preserved mangrove leaves could yield significant information about changes in ecosystem dynamics, nutrient limitation and past stand structure in mangrove

Isotopic and molecular distributions of biochemicals from fresh and buried Rhizophora mangle leaves†

Directory of Open Access Journals (Sweden)

Jacobson Myrna E

2003-12-01

Full Text Available Rhizophora mangle L. (red mangrove is the dominant species of mangrove in the Americas. At Twin Cays, Belize (BZ red mangroves are present in a variety of stand structures (tall >5 m in height, transition ~2–4 m and dwarf ~1–1.5 m. These height differences are coupled with very different stable carbon and nitrogen isotopic values1 (mean tall δ13C = -28.3‰, δ15N = 0‰; mean tall δ13C = -25.3‰, δ15N = -10‰. To determine the utility of using these distinct isotopic compositions as 'biomarkers' for paleoenvironmental reconstruction of mangrove ecosystems and nutrient availability, we investigated the distribution and isotopic (δ13C and δ15N composition of different biochemical fractions (water soluble compounds, free lipids, acid hydrolysable compounds, individual amino acids, and the residual un-extractable compounds in fresh and preserved red mangrove leaves from dwarf and tall trees. The distribution of biochemicals are similar in dwarf and tall red mangrove leaves, suggesting that, regardless of stand structure, red mangroves use nutrients for biosynthesis and metabolism in a similar manner. However, the δ13C and δ15N of the bulk leaf, the biochemical fractions, and seven amino acids can be used to distinguish dwarf and tall trees at Twin Cays, BZ. The data support the theory that the fractionation of carbon and nitrogen occurs prior to or during uptake in dwarf and tall red mangrove trees. Stable carbon and nitrogen isotopes could, therefore, be powerful tools for predicting levels of nutrient limitation at Twin Cays. The δ13C and δ15N of biochemical fractions within preserved leaves, reflect sedimentary cycling and nitrogen immobilization. The δ15N of the immobilized fraction reveals the overlying stand structure at the time of leaf deposition. The isotopic composition of preserved mangrove leaves could yield significant information about changes in ecosystem dynamics, nutrient limitation and past stand structure in

Adaptive Microwave Staring Correlated Imaging for Targets Appearing in Discrete Clusters.

Science.gov (United States)

Tian, Chao; Jiang, Zheng; Chen, Weidong; Wang, Dongjin

2017-10-21

Microwave staring correlated imaging (MSCI) can achieve ultra-high resolution in real aperture staring radar imaging using the correlated imaging process (CIP) under all-weather and all-day circumstances. The CIP must combine the received echo signal with the temporal-spatial stochastic radiation field. However, a precondition of the CIP is that the continuous imaging region must be discretized to a fine grid, and the measurement matrix should be accurately computed, which makes the imaging process highly complex when the MSCI system observes a wide area. This paper proposes an adaptive imaging approach for the targets in discrete clusters to reduce the complexity of the CIP. The approach is divided into two main stages. First, as discrete clustered targets are distributed in different range strips in the imaging region, the transmitters of the MSCI emit narrow-pulse waveforms to separate the echoes of the targets in different strips in the time domain; using spectral entropy, a modified method robust against noise is put forward to detect the echoes of the discrete clustered targets, based on which the strips with targets can be adaptively located. Second, in a strip with targets, the matched filter reconstruction algorithm is used to locate the regions with targets, and only the regions of interest are discretized to a fine grid; sparse recovery is used, and the band exclusion is used to maintain the non-correlation of the dictionary. Simulation results are presented to demonstrate that the proposed approach can accurately and adaptively locate the regions with targets and obtain high-quality reconstructed images.

EXTRACTION OF THE MEAN RADIAL MASS-DISTRIBUTION IN CLUSTERS OF GALAXIES BY OBSERVATIONS OF WEAK GRAVITATIONAL IMAGING

NARCIS (Netherlands)

BREIMER, TG

The gravitational fields of clusters of galaxies cause systematic distortions of the images of background galaxies. Recently, the lens inversion problem, reconstruction of the mean surface density distribution in the lens from the pattern of systematic distortions, has been the object of several

ADPROCLUS: a graphical user interface for fitting additive profile clustering models to object by variable data matrices.

Science.gov (United States)

Wilderjans, Tom F; Ceulemans, Eva; Van Mechelen, Iven; Depril, Dirk

2011-03-01

In many areas of psychology, one is interested in disclosing the underlying structural mechanisms that generated an object by variable data set. Often, based on theoretical or empirical arguments, it may be expected that these underlying mechanisms imply that the objects are grouped into clusters that are allowed to overlap (i.e., an object may belong to more than one cluster). In such cases, analyzing the data with Mirkin's additive profile clustering model may be appropriate. In this model: (1) each object may belong to no, one or several clusters, (2) there is a specific variable profile associated with each cluster, and (3) the scores of the objects on the variables can be reconstructed by adding the cluster-specific variable profiles of the clusters the object in question belongs to. Until now, however, no software program has been publicly available to perform an additive profile clustering analysis. For this purpose, in this article, the ADPROCLUS program, steered by a graphical user interface, is presented. We further illustrate its use by means of the analysis of a patient by symptom data matrix.

Investigation of ADAMO performance in the ZEUS calorimeter reconstruction program

International Nuclear Information System (INIS)

Kowalski, H.; Poser, T.; Stanco, L.; Tscheslog, E.

1989-01-01

The ADAMO package has been investigated for the reconstruction of jets simulated in the ZEUS calorimeter. The feasibility of ADAMO routines was tested under various aspects. The study was based on different versions of a cluster algorithm using ADAMO tools or direct BOS memory management tools. In particular, the amount of CPU time needed by each of the versions was determined. Results are quite promising and support an extensive use of the ADAMO package in the software development of high energy physics experiments. (orig.)

Biochemical Network Stochastic Simulator (BioNetS: software for stochastic modeling of biochemical networks

Directory of Open Access Journals (Sweden)

Elston Timothy C

2004-03-01

Full Text Available Abstract Background Intrinsic fluctuations due to the stochastic nature of biochemical reactions can have large effects on the response of biochemical networks. This is particularly true for pathways that involve transcriptional regulation, where generally there are two copies of each gene and the number of messenger RNA (mRNA molecules can be small. Therefore, there is a need for computational tools for developing and investigating stochastic models of biochemical networks. Results We have developed the software package Biochemical Network Stochastic Simulator (BioNetS for efficientlyand accurately simulating stochastic models of biochemical networks. BioNetS has a graphical user interface that allows models to be entered in a straightforward manner, and allows the user to specify the type of random variable (discrete or continuous for each chemical species in the network. The discrete variables are simulated using an efficient implementation of the Gillespie algorithm. For the continuous random variables, BioNetS constructs and numerically solvesthe appropriate chemical Langevin equations. The software package has been developed to scale efficiently with network size, thereby allowing large systems to be studied. BioNetS runs as a BioSpice agent and can be downloaded from http://www.biospice.org. BioNetS also can be run as a stand alone package. All the required files are accessible from http://x.amath.unc.edu/BioNetS. Conclusions We have developed BioNetS to be a reliable tool for studying the stochastic dynamics of large biochemical networks. Important features of BioNetS are its ability to handle hybrid models that consist of both continuous and discrete random variables and its ability to model cell growth and division. We have verified the accuracy and efficiency of the numerical methods by considering several test systems.

Reconstruction of a large-scale reconnection exhaust structure in the solar wind

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W.-L. Teh

2009-02-01

Full Text Available We recover two-dimensional (2-D magnetic field and flow field configurations from three spacecraft encounters with a single large-scale reconnection exhaust structure in the solar wind, using a new reconstruction method (Sonnerup and Teh, 2008 based on the ideal single-fluid MHD equations in a steady-state, 2-D geometry. The reconstruction is performed in the rest frame of the X-line, where the flow into, and the plasma jetting within, the exhaust region are clearly visible. The event was first identified by Phan et al. (2006 in the ACE, Cluster, and Wind data sets; they argued that quasi-steady reconnection persisted for over 2 h at a long (390 R_E X-line. The reconnection exhaust is sandwiched between two discontinuities, both of which contain elements of intermediate- and slow-mode behavior; these elements are co-located rather than being spatially separated. These composite discontinuities do not satisfy the coplanarity condition or the standard MHD jump conditions. For all three spacecraft, the Walén regression line slope was positive (negative for the leading (trailing discontinuity. Our MHD reconstruction shows that: (1 the X-line orientation was close to the bisector of the overall magnetic shear angle and exhibited a slow rotating motion toward the Sun-Earth line; (2 the X-line moved earthward, dawnward, and southward; (3 the reconnection electric field was small (~0.02 mV/m on average and gradually decreased from the first crossing (ACE to the last (Wind. The magnetic field and flow field configurations recovered from ACE and Cluster are similar while those recovered from Wind also include a magnetic island and an associated vortex. Reconnection persisted for at least 2.4 h involving inflow into the exhaust region from its two sides. Time-dependence in the reconnection electric fields seen by ACE and Wind indicates local temporal variations in the field configuration. In addition to the reconstruction results, we

Reconstruction of a large-scale reconnection exhaust structure in the solar wind

International Nuclear Information System (INIS)

Teh, W.L.; Sonnerup, B.U.Oe.; Hu, Q.; Farrugia, C.J.

2009-01-01

We recover two-dimensional (2-D) magnetic field and flow field configurations from three spacecraft encounters with a single large-scale reconnection exhaust structure in the solar wind, using a new reconstruction method (Sonnerup and Teh, 2008) based on the ideal single-fluid MHD equations in a steady-state, 2-D geometry. The reconstruction is performed in the rest frame of the X-line, where the flow into, and the plasma jetting within, the exhaust region are clearly visible. The event was first identified by Phan et al. (2006) in the ACE, Cluster, and Wind data sets; they argued that quasi-steady reconnection persisted for over 2 h at a long (390 R E ) X-line. The reconnection exhaust is sandwiched between two discontinuities, both of which contain elements of intermediate- and slow-mode behavior; these elements are co-located rather than being spatially separated. These composite discontinuities do not satisfy the coplanarity condition or the standard MHD jump conditions. For all three spacecraft, the Walen regression line slope was positive (negative) for the leading (trailing) discontinuity. Our MHD reconstruction shows that: (1) the X-line orientation was close to the bisector of the overall magnetic shear angle and exhibited a slow rotating motion toward the Sun-Earth line; (2) the X-line moved earthward, dawnward, and southward; (3) the reconnection electric field was small (∝0.02 mV/m on average) and gradually decreased from the first crossing (ACE) to the last (Wind). The magnetic field and flow field configurations recovered from ACE and Cluster are similar while those recovered from Wind also include a magnetic island and an associated vortex. Reconnection persisted for at least 2.4 h involving inflow into the exhaust region from its two sides. Time-dependence in the reconnection electric fields seen by ACE and Wind indicates local temporal variations in the field configuration. In addition to the reconstruction results, we provide a description and

Reconstruction of a large-scale reconnection exhaust structure in the solar wind

Directory of Open Access Journals (Sweden)

W.-L. Teh

2009-02-01

Full Text Available We recover two-dimensional (2-D magnetic field and flow field configurations from three spacecraft encounters with a single large-scale reconnection exhaust structure in the solar wind, using a new reconstruction method (Sonnerup and Teh, 2008 based on the ideal single-fluid MHD equations in a steady-state, 2-D geometry. The reconstruction is performed in the rest frame of the X-line, where the flow into, and the plasma jetting within, the exhaust region are clearly visible. The event was first identified by Phan et al. (2006 in the ACE, Cluster, and Wind data sets; they argued that quasi-steady reconnection persisted for over 2 h at a long (390 RE X-line. The reconnection exhaust is sandwiched between two discontinuities, both of which contain elements of intermediate- and slow-mode behavior; these elements are co-located rather than being spatially separated. These composite discontinuities do not satisfy the coplanarity condition or the standard MHD jump conditions. For all three spacecraft, the Walén regression line slope was positive (negative for the leading (trailing discontinuity. Our MHD reconstruction shows that: (1 the X-line orientation was close to the bisector of the overall magnetic shear angle and exhibited a slow rotating motion toward the Sun-Earth line; (2 the X-line moved earthward, dawnward, and southward; (3 the reconnection electric field was small (~0.02 mV/m on average and gradually decreased from the first crossing (ACE to the last (Wind. The magnetic field and flow field configurations recovered from ACE and Cluster are similar while those recovered from Wind also include a magnetic island and an associated vortex. Reconnection persisted for at least 2.4 h involving inflow into the exhaust region from its two sides. Time-dependence in the reconnection electric fields seen by ACE and Wind indicates local temporal variations in the field configuration. In addition to the reconstruction results, we provide a description

Nutrient-deprivation autophagy factor-1 (NAF-1: biochemical properties of a novel cellular target for anti-diabetic drugs.

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Sagi Tamir

Full Text Available Nutrient-deprivation autophagy factor-1 (NAF-1 (synonyms: Cisd2, Eris, Miner1, and Noxp70 is a [2Fe-2S] cluster protein immune-detected both in endoplasmic reticulum (ER and mitochondrial outer membrane. It was implicated in human pathology (Wolfram Syndrome 2 and in BCL-2 mediated antagonization of Beclin 1-dependent autophagy and depression of ER calcium stores. To gain insights about NAF-1 functions, we investigated the biochemical properties of its 2Fe-2S cluster and sensitivity of those properties to small molecules. The structure of the soluble domain of NAF-1 shows that it forms a homodimer with each protomer containing a [2Fe-2S] cluster bound by 3 Cys and one His. NAF-1 has shown the unusual abilities to transfer its 2Fe-2S cluster to an apo-acceptor protein (followed in vitro by spectrophotometry and by native PAGE electrophoresis and to transfer iron to intact mitochondria in cell models (monitored by fluorescence imaging with iron fluorescent sensors targeted to mitochondria. Importantly, the drug pioglitazone abrogates NAF-1's ability to transfer the cluster to acceptor proteins and iron to mitochondria. Similar effects were found for the anti-diabetes and longevity-promoting antioxidant resveratrol. These results reveal NAF-1 as a previously unidentified cell target of anti-diabetes thiazolidinedione drugs like pioglitazone and of the natural product resveratrol, both of which interact with the protein and stabilize its labile [2Fe-2S] cluster.

Three-dimensional seed reconstruction from an incomplete data set for prostate brachytherapy

International Nuclear Information System (INIS)

Narayanan, Sreeram; Cho, Paul S; MarksII, Robert J

2004-01-01

Intra-operative dosimetry in prostate brachytherapy requires 3D coordinates of the implanted, radioactive seeds. Since CT is not readily available during the implant operation, projection x-rays are commonly used for intra-operative seed localization. Three x-ray projections are usually used. The requirement of the current seed reconstruction algorithms is that the seeds must be identified on all three projections. However, in practice this is often difficult to accomplish due to the problem of heavily clustered and overlapping seeds. We have developed an algorithm that permits seed reconstruction from an incomplete data set. Instead of all three projections, the new algorithm requires only one of the three projections to be complete. Furthermore, even if all three projections are incomplete, it can reconstruct 100% of the implanted seeds depending on how the undetected seeds are distributed among the projections. The method utilizes the principles of epipolar imaging geometry and pseudo-matching of the undetected seeds. The algorithm was successfully applied to a large number of clinical cases where seeds imperceptibly overlap in some projections

Segmentation, Reconstruction, and Analysis of Blood Thrombus Formation in 3D 2-Photon Microscopy Images

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Xu Zhiliang

2010-01-01

Full Text Available We study the problem of segmenting, reconstructing, and analyzing the structure growth of thrombi (clots in blood vessels in vivo based on 2-photon microscopic image data. First, we develop an algorithm for segmenting clots in 3D microscopic images based on density-based clustering and methods for dealing with imaging artifacts. Next, we apply the union-of-balls (or alpha-shape algorithm to reconstruct the boundary of clots in 3D. Finally, we perform experimental studies and analysis on the reconstructed clots and obtain quantitative data of thrombus growth and structures. We conduct experiments on laser-induced injuries in vessels of two types of mice (the wild type and the type with low levels of coagulation factor VII and analyze and compare the developing clot structures based on their reconstructed clots from image data. The results we obtain are of biomedical significance. Our quantitative analysis of the clot composition leads to better understanding of the thrombus development, and is valuable to the modeling and verification of computational simulation of thrombogenesis.

Study of acute biochemical effects of thallium toxicity in mouse urine by NMR spectroscopy.

Science.gov (United States)

Tyagi, Ritu; Rana, Poonam; Khan, Ahmad Raza; Bhatnagar, Deepak; Devi, M Memita; Chaturvedi, Shubhra; Tripathi, Rajendra P; Khushu, Subash

2011-10-01

Thallium (Tl) is a toxic heavy metal and its exposure to the human body causes physiological and biochemical changes due to its interference with potassium-dependent biological reactions. A high-resolution (1)H NMR spectroscopy based metabonomic approach has been applied for investigating acute biochemical effects caused by thallium sulfate (Tl(2)SO(4)). Male strain A mice were divided in three groups and received three doses of Tl(2)SO(4) (5, 10 and 20 mg kg(-1) b.w., i.p.). Urine samples collected at 3, 24, 72 and 96 h post-dose time points were analyzed by (1)H NMR spectroscopy. NMR spectral data were processed and analyzed using principal components analysis to represent biochemical variations induced by Tl(2)SO(4). Results showed Tl-exposed mice urine to have distinct metabonomic phenotypes and revealed dose- and time-dependent clustering of treated groups. The metabolic signature of urine analysis from Tl(2)SO(4)-treated animals exhibited an increase in the levels of creatinine, taurine, hippurate and β-hydroxybutyrate along with a decrease in energy metabolites trimethylamine and choline. These findings revealed Tl-induced disturbed gut flora, membrane metabolite, energy and protein metabolism, representing physiological dysfunction of vital organs. The present study indicates the great potential of NMR-based metabonomics in mapping metabolic response for toxicology, which could ultimately lead to identification of potential markers for Tl toxicity. Copyright © 2011 John Wiley & Sons, Ltd.

3D Building Models Segmentation Based on K-Means++ Cluster Analysis

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Zhang, C.; Mao, B.

2016-10-01

3D mesh model segmentation is drawing increasing attentions from digital geometry processing field in recent years. The original 3D mesh model need to be divided into separate meaningful parts or surface patches based on certain standards to support reconstruction, compressing, texture mapping, model retrieval and etc. Therefore, segmentation is a key problem for 3D mesh model segmentation. In this paper, we propose a method to segment Collada (a type of mesh model) 3D building models into meaningful parts using cluster analysis. Common clustering methods segment 3D mesh models by K-means, whose performance heavily depends on randomized initial seed points (i.e., centroid) and different randomized centroid can get quite different results. Therefore, we improved the existing method and used K-means++ clustering algorithm to solve this problem. Our experiments show that K-means++ improves both the speed and the accuracy of K-means, and achieve good and meaningful results.

3D BUILDING MODELS SEGMENTATION BASED ON K-MEANS++ CLUSTER ANALYSIS

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C. Zhang

2016-10-01

Full Text Available 3D mesh model segmentation is drawing increasing attentions from digital geometry processing field in recent years. The original 3D mesh model need to be divided into separate meaningful parts or surface patches based on certain standards to support reconstruction, compressing, texture mapping, model retrieval and etc. Therefore, segmentation is a key problem for 3D mesh model segmentation. In this paper, we propose a method to segment Collada (a type of mesh model 3D building models into meaningful parts using cluster analysis. Common clustering methods segment 3D mesh models by K-means, whose performance heavily depends on randomized initial seed points (i.e., centroid and different randomized centroid can get quite different results. Therefore, we improved the existing method and used K-means++ clustering algorithm to solve this problem. Our experiments show that K-means++ improves both the speed and the accuracy of K-means, and achieve good and meaningful results.

Implementation of the ALICE HLT hardware cluster finder algorithm in Vivado HLS

Energy Technology Data Exchange (ETDEWEB)

Gruell, Frederik; Engel, Heiko; Kebschull, Udo [Infrastructure and Computer Systems in Data Processing, Goethe University Frankfurt (Germany); Collaboration: ALICE-Collaboration

2016-07-01

The FastClusterFinder algorithm running in the ALICE High-Level Trigger (HLT) read-out boards extracts clusters from raw data from the Time Projection Chamber (TPC) detector and forwards them to the HLT data processing framework for tracking, event reconstruction and compression. It serves as an early stage of feature extraction in the FPGA of the board. Past and current implementations are written in VHDL on reconfigurable hardware for high throughput and low latency. We examine Vivado HLS, a high-level language that promises an increased developer productivity, as an alternative. The implementation of the application is compared to descriptions in VHDL and MaxJ in terms of productivity, resource usage and maximum clock frequency.

Robustness of the ATLAS pixel clustering neural network algorithm

CERN Document Server

AUTHOR|(INSPIRE)INSPIRE-00407780; The ATLAS collaboration

2016-01-01

Proton-proton collisions at the energy frontier puts strong constraints on track reconstruction algorithms. The algorithms depend heavily on accurate estimation of the position of particles as they traverse the inner detector elements. An artificial neural network algorithm is utilised to identify and split clusters of neighbouring read-out elements in the ATLAS pixel detector created by multiple charged particles. The method recovers otherwise lost tracks in dense environments where particles are separated by distances comparable to the size of the detector read-out elements. Such environments are highly relevant for LHC run 2, e.g. in searches for heavy resonances. Within the scope of run 2 track reconstruction performance and upgrades, the robustness of the neural network algorithm will be presented. The robustness has been studied by evaluating the stability of the algorithm’s performance under a range of variations in the pixel detector conditions.

Propagation stability of self-reconstructing Bessel beams enables contrast-enhanced imaging in thick media.

Science.gov (United States)

Fahrbach, Florian O; Rohrbach, Alexander

2012-01-17

Laser beams that can self-reconstruct their initial beam profile even in the presence of massive phase perturbations are able to propagate deeper into inhomogeneous media. This ability has crucial advantages for light sheet-based microscopy in thick media, such as cell clusters, embryos, skin or brain tissue or plants, as well as scattering synthetic materials. A ring system around the central intensity maximum of a Bessel beam enables its self-reconstruction, but at the same time illuminates out-of-focus regions and deteriorates image contrast. Here we present a detection method that minimizes the negative effect of the ring system. The beam's propagation stability along one straight line enables the use of a confocal line principle, resulting in a significant increase in image contrast. The axial resolution could be improved by nearly 100% relative to the standard light-sheet techniques using scanned Gaussian beams, while demonstrating self-reconstruction also for high propagation depths.

A high-throughput system for high-quality tomographic reconstruction of large datasets at Diamond Light Source.

Science.gov (United States)

Atwood, Robert C; Bodey, Andrew J; Price, Stephen W T; Basham, Mark; Drakopoulos, Michael

2015-06-13

Tomographic datasets collected at synchrotrons are becoming very large and complex, and, therefore, need to be managed efficiently. Raw images may have high pixel counts, and each pixel can be multidimensional and associated with additional data such as those derived from spectroscopy. In time-resolved studies, hundreds of tomographic datasets can be collected in sequence, yielding terabytes of data. Users of tomographic beamlines are drawn from various scientific disciplines, and many are keen to use tomographic reconstruction software that does not require a deep understanding of reconstruction principles. We have developed Savu, a reconstruction pipeline that enables users to rapidly reconstruct data to consistently create high-quality results. Savu is designed to work in an 'orthogonal' fashion, meaning that data can be converted between projection and sinogram space throughout the processing workflow as required. The Savu pipeline is modular and allows processing strategies to be optimized for users' purposes. In addition to the reconstruction algorithms themselves, it can include modules for identification of experimental problems, artefact correction, general image processing and data quality assessment. Savu is open source, open licensed and 'facility-independent': it can run on standard cluster infrastructure at any institution.

Implicit Regularization for Reconstructing 3D Building Rooftop Models Using Airborne LiDAR Data

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Jaewook Jung

2017-03-01

Full Text Available With rapid urbanization, highly accurate and semantically rich virtualization of building assets in 3D become more critical for supporting various applications, including urban planning, emergency response and location-based services. Many research efforts have been conducted to automatically reconstruct building models at city-scale from remotely sensed data. However, developing a fully-automated photogrammetric computer vision system enabling the massive generation of highly accurate building models still remains a challenging task. One the most challenging task for 3D building model reconstruction is to regularize the noises introduced in the boundary of building object retrieved from a raw data with lack of knowledge on its true shape. This paper proposes a data-driven modeling approach to reconstruct 3D rooftop models at city-scale from airborne laser scanning (ALS data. The focus of the proposed method is to implicitly derive the shape regularity of 3D building rooftops from given noisy information of building boundary in a progressive manner. This study covers a full chain of 3D building modeling from low level processing to realistic 3D building rooftop modeling. In the element clustering step, building-labeled point clouds are clustered into homogeneous groups by applying height similarity and plane similarity. Based on segmented clusters, linear modeling cues including outer boundaries, intersection lines, and step lines are extracted. Topology elements among the modeling cues are recovered by the Binary Space Partitioning (BSP technique. The regularity of the building rooftop model is achieved by an implicit regularization process in the framework of Minimum Description Length (MDL combined with Hypothesize and Test (HAT. The parameters governing the MDL optimization are automatically estimated based on Min-Max optimization and Entropy-based weighting method. The performance of the proposed method is tested over the International

Implicit Regularization for Reconstructing 3D Building Rooftop Models Using Airborne LiDAR Data.

Science.gov (United States)

Jung, Jaewook; Jwa, Yoonseok; Sohn, Gunho

2017-03-19

With rapid urbanization, highly accurate and semantically rich virtualization of building assets in 3D become more critical for supporting various applications, including urban planning, emergency response and location-based services. Many research efforts have been conducted to automatically reconstruct building models at city-scale from remotely sensed data. However, developing a fully-automated photogrammetric computer vision system enabling the massive generation of highly accurate building models still remains a challenging task. One the most challenging task for 3D building model reconstruction is to regularize the noises introduced in the boundary of building object retrieved from a raw data with lack of knowledge on its true shape. This paper proposes a data-driven modeling approach to reconstruct 3D rooftop models at city-scale from airborne laser scanning (ALS) data. The focus of the proposed method is to implicitly derive the shape regularity of 3D building rooftops from given noisy information of building boundary in a progressive manner. This study covers a full chain of 3D building modeling from low level processing to realistic 3D building rooftop modeling. In the element clustering step, building-labeled point clouds are clustered into homogeneous groups by applying height similarity and plane similarity. Based on segmented clusters, linear modeling cues including outer boundaries, intersection lines, and step lines are extracted. Topology elements among the modeling cues are recovered by the Binary Space Partitioning (BSP) technique. The regularity of the building rooftop model is achieved by an implicit regularization process in the framework of Minimum Description Length (MDL) combined with Hypothesize and Test (HAT). The parameters governing the MDL optimization are automatically estimated based on Min-Max optimization and Entropy-based weighting method. The performance of the proposed method is tested over the International Society for

Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection.

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Guthke, Reinhard; Möller, Ulrich; Hoffmann, Martin; Thies, Frank; Töpfer, Susanne

2005-04-15

The immune response to bacterial infection represents a complex network of dynamic gene and protein interactions. We present an optimized reverse engineering strategy aimed at a reconstruction of this kind of interaction networks. The proposed approach is based on both microarray data and available biological knowledge. The main kinetics of the immune response were identified by fuzzy clustering of gene expression profiles (time series). The number of clusters was optimized using various evaluation criteria. For each cluster a representative gene with a high fuzzy-membership was chosen in accordance with available physiological knowledge. Then hypothetical network structures were identified by seeking systems of ordinary differential equations, whose simulated kinetics could fit the gene expression profiles of the cluster-representative genes. For the construction of hypothetical network structures singular value decomposition (SVD) based methods and a newly introduced heuristic Network Generation Method here were compared. It turned out that the proposed novel method could find sparser networks and gave better fits to the experimental data. Reinhard.Guthke@hki-jena.de.

A Class of Manifold Regularized Multiplicative Update Algorithms for Image Clustering.

Science.gov (United States)

Yang, Shangming; Yi, Zhang; He, Xiaofei; Li, Xuelong

2015-12-01

Multiplicative update algorithms are important tools for information retrieval, image processing, and pattern recognition. However, when the graph regularization is added to the cost function, different classes of sample data may be mapped to the same subspace, which leads to the increase of data clustering error rate. In this paper, an improved nonnegative matrix factorization (NMF) cost function is introduced. Based on the cost function, a class of novel graph regularized NMF algorithms is developed, which results in a class of extended multiplicative update algorithms with manifold structure regularization. Analysis shows that in the learning, the proposed algorithms can efficiently minimize the rank of the data representation matrix. Theoretical results presented in this paper are confirmed by simulations. For different initializations and data sets, variation curves of cost functions and decomposition data are presented to show the convergence features of the proposed update rules. Basis images, reconstructed images, and clustering results are utilized to present the efficiency of the new algorithms. Last, the clustering accuracies of different algorithms are also investigated, which shows that the proposed algorithms can achieve state-of-the-art performance in applications of image clustering.

Robust fiber clustering of cerebral fiber bundles in white matter

Science.gov (United States)

Yao, Xufeng; Wang, Yongxiong; Zhuang, Songlin

2014-11-01

Diffusion tensor imaging fiber tracking (DTI-FT) has been widely accepted in the diagnosis and treatment of brain diseases. During the rendering pipeline of specific fiber tracts, the image noise and low resolution of DTI would lead to false propagations. In this paper, we propose a robust fiber clustering (FC) approach to diminish false fibers from one fiber tract. Our algorithm consists of three steps. Firstly, the optimized fiber assignment continuous tracking (FACT) is implemented to reconstruct one fiber tract; and then each curved fiber in the fiber tract is mapped to a point by kernel principal component analysis (KPCA); finally, the point clouds of fiber tract are clustered by hierarchical clustering which could distinguish false fibers from true fibers in one tract. In our experiment, the corticospinal tract (CST) in one case of human data in vivo was used to validate our method. Our method showed reliable capability in decreasing the false fibers in one tract. In conclusion, our method could effectively optimize the visualization of fiber bundles and would help a lot in the field of fiber evaluation.

Reconstruction of Orion Engineering Development Unit (EDU) Parachute Inflation Loads

Science.gov (United States)

Ray, Eric S.

2013-01-01

The process of reconstructing inflation loads of Capsule Parachute Assembly System (CPAS) has been updated as the program transitioned to testing Engineering Development Unit (EDU) hardware. The equations used to reduce the test data have been re-derived based on the same physical assumptions made by simulations. Due to instrumentation challenges, individual parachute loads are determined from complementary accelerometer and load cell measurements. Cluster inflations are now simulated by modeling each parachute individually to better represent different inflation times and non-synchronous disreefing. The reconstruction procedure is tailored to either infinite mass or finite mass events based on measurable characteristics from the test data. Inflation parameters are determined from an automated optimization routine to reduce subjectivity. Infinite mass inflation parameters have been re-defined to avoid unrealistic interactions in Monte Carlo simulations. Sample cases demonstrate how best-fit inflation parameters are used to generate simulated drag areas and loads which favorably agree with test data.

EnzDP: improved enzyme annotation for metabolic network reconstruction based on domain composition profiles.

Science.gov (United States)

Nguyen, Nam-Ninh; Srihari, Sriganesh; Leong, Hon Wai; Chong, Ket-Fah

2015-10-01

Determining the entire complement of enzymes and their enzymatic functions is a fundamental step for reconstructing the metabolic network of cells. High quality enzyme annotation helps in enhancing metabolic networks reconstructed from the genome, especially by reducing gaps and increasing the enzyme coverage. Currently, structure-based and network-based approaches can only cover a limited number of enzyme families, and the accuracy of homology-based approaches can be further improved. Bottom-up homology-based approach improves the coverage by rebuilding Hidden Markov Model (HMM) profiles for all known enzymes. However, its clustering procedure relies firmly on BLAST similarity score, ignoring protein domains/patterns, and is sensitive to changes in cut-off thresholds. Here, we use functional domain architecture to score the association between domain families and enzyme families (Domain-Enzyme Association Scoring, DEAS). The DEAS score is used to calculate the similarity between proteins, which is then used in clustering procedure, instead of using sequence similarity score. We improve the enzyme annotation protocol using a stringent classification procedure, and by choosing optimal threshold settings and checking for active sites. Our analysis shows that our stringent protocol EnzDP can cover up to 90% of enzyme families available in Swiss-Prot. It achieves a high accuracy of 94.5% based on five-fold cross-validation. EnzDP outperforms existing methods across several testing scenarios. Thus, EnzDP serves as a reliable automated tool for enzyme annotation and metabolic network reconstruction. Available at: www.comp.nus.edu.sg/~nguyennn/EnzDP .

Algebraic reconstruction techniques for spectral reconstruction in diffuse optical tomography

International Nuclear Information System (INIS)

Brendel, Bernhard; Ziegler, Ronny; Nielsen, Tim

2008-01-01

Reconstruction in diffuse optical tomography (DOT) necessitates solving the diffusion equation, which is nonlinear with respect to the parameters that have to be reconstructed. Currently applied solving methods are based on the linearization of the equation. For spectral three-dimensional reconstruction, the emerging equation system is too large for direct inversion, but the application of iterative methods is feasible. Computational effort and speed of convergence of these iterative methods are crucial since they determine the computation time of the reconstruction. In this paper, the iterative methods algebraic reconstruction technique (ART) and conjugated gradients (CGs) as well as a new modified ART method are investigated for spectral DOT reconstruction. The aim of the modified ART scheme is to speed up the convergence by considering the specific conditions of spectral reconstruction. As a result, it converges much faster to favorable results than conventional ART and CG methods

RMBNToolbox: random models for biochemical networks

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Niemi Jari

2007-05-01

Full Text Available Abstract Background There is an increasing interest to model biochemical and cell biological networks, as well as to the computational analysis of these models. The development of analysis methodologies and related software is rapid in the field. However, the number of available models is still relatively small and the model sizes remain limited. The lack of kinetic information is usually the limiting factor for the construction of detailed simulation models. Results We present a computational toolbox for generating random biochemical network models which mimic real biochemical networks. The toolbox is called Random Models for Biochemical Networks. The toolbox works in the Matlab environment, and it makes it possible to generate various network structures, stoichiometries, kinetic laws for reactions, and parameters therein. The generation can be based on statistical rules and distributions, and more detailed information of real biochemical networks can be used in situations where it is known. The toolbox can be easily extended. The resulting network models can be exported in the format of Systems Biology Markup Language. Conclusion While more information is accumulating on biochemical networks, random networks can be used as an intermediate step towards their better understanding. Random networks make it possible to study the effects of various network characteristics to the overall behavior of the network. Moreover, the construction of artificial network models provides the ground truth data needed in the validation of various computational methods in the fields of parameter estimation and data analysis.

Exploring biological network structure with clustered random networks

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Bansal Shweta

2009-12-01

Full Text Available Abstract Background Complex biological systems are often modeled as networks of interacting units. Networks of biochemical interactions among proteins, epidemiological contacts among hosts, and trophic interactions in ecosystems, to name a few, have provided useful insights into the dynamical processes that shape and traverse these systems. The degrees of nodes (numbers of interactions and the extent of clustering (the tendency for a set of three nodes to be interconnected are two of many well-studied network properties that can fundamentally shape a system. Disentangling the interdependent effects of the various network properties, however, can be difficult. Simple network models can help us quantify the structure of empirical networked systems and understand the impact of various topological properties on dynamics. Results Here we develop and implement a new Markov chain simulation algorithm to generate simple, connected random graphs that have a specified degree sequence and level of clustering, but are random in all other respects. The implementation of the algorithm (ClustRNet: Clustered Random Networks provides the generation of random graphs optimized according to a local or global, and relative or absolute measure of clustering. We compare our algorithm to other similar methods and show that ours more successfully produces desired network characteristics. Finding appropriate null models is crucial in bioinformatics research, and is often difficult, particularly for biological networks. As we demonstrate, the networks generated by ClustRNet can serve as random controls when investigating the impacts of complex network features beyond the byproduct of degree and clustering in empirical networks. Conclusion ClustRNet generates ensembles of graphs of specified edge structure and clustering. These graphs allow for systematic study of the impacts of connectivity and redundancies on network function and dynamics. This process is a key step in

TH-CD-207A-09: Stay On Target: Dynamic, Patient-Specific Templates of Fiducial Marker Clusters for IGRT

International Nuclear Information System (INIS)

Campbell, W; Miften, M; Jones, B

2016-01-01

Purpose: Pancreatic SBRT relies on extremely accurate delivery of ablative radiation doses to the target, and intra-fractional tracking of fiducial markers can facilitate improvements in dose delivery. However, this requires algorithms that are able to find fiducial markers with high speed and accuracy. The purpose of this study was to develop a novel marker tracking algorithm that is robust against many of the common errors seen with traditional template matching techniques. Methods: Using CBCT projection images, a method was developed to create detailed template images of fiducial marker clusters without prior knowledge of the number of markers, their positions, or their orientations. Briefly, the method (i) enhances markers in projection images, (ii) stabilizes the cluster’s position, (iii) reconstructs the cluster in 3D, and (iv) precomputes a set of static template images dependent on gantry angle. Furthermore, breathing data were used to produce 4D reconstructions of clusters, yielding dynamic template images dependent on gantry angle and breathing amplitude. To test these two approaches, static and dynamic templates were used to track the motion of marker clusters in more than 66,000 projection images from 75 CBCT scans of 15 pancreatic SBRT patients. Results: For both static and dynamic templates, the new technique was able to locate marker clusters present in projection images 100% of the time. The algorithm was also able to correctly locate markers in several instances where only some of the markers were visible due to insufficient field-of-view. In cases where clusters exhibited deformation and/or rotation during breathing, dynamic templates resulted in cross-correlation scores up to 70% higher than static templates. Conclusion: Patient-specific templates provided complete tracking of fiducial marker clusters in CBCT scans, and dynamic templates helped to provide higher cross-correlation scores for deforming/rotating clusters. This novel algorithm

TH-CD-207A-09: Stay On Target: Dynamic, Patient-Specific Templates of Fiducial Marker Clusters for IGRT

Energy Technology Data Exchange (ETDEWEB)

Campbell, W; Miften, M; Jones, B [Department of Radiation Oncology, University of Colorado School of Medicine, Aurora, CO (United States)

2016-06-15

Purpose: Pancreatic SBRT relies on extremely accurate delivery of ablative radiation doses to the target, and intra-fractional tracking of fiducial markers can facilitate improvements in dose delivery. However, this requires algorithms that are able to find fiducial markers with high speed and accuracy. The purpose of this study was to develop a novel marker tracking algorithm that is robust against many of the common errors seen with traditional template matching techniques. Methods: Using CBCT projection images, a method was developed to create detailed template images of fiducial marker clusters without prior knowledge of the number of markers, their positions, or their orientations. Briefly, the method (i) enhances markers in projection images, (ii) stabilizes the cluster’s position, (iii) reconstructs the cluster in 3D, and (iv) precomputes a set of static template images dependent on gantry angle. Furthermore, breathing data were used to produce 4D reconstructions of clusters, yielding dynamic template images dependent on gantry angle and breathing amplitude. To test these two approaches, static and dynamic templates were used to track the motion of marker clusters in more than 66,000 projection images from 75 CBCT scans of 15 pancreatic SBRT patients. Results: For both static and dynamic templates, the new technique was able to locate marker clusters present in projection images 100% of the time. The algorithm was also able to correctly locate markers in several instances where only some of the markers were visible due to insufficient field-of-view. In cases where clusters exhibited deformation and/or rotation during breathing, dynamic templates resulted in cross-correlation scores up to 70% higher than static templates. Conclusion: Patient-specific templates provided complete tracking of fiducial marker clusters in CBCT scans, and dynamic templates helped to provide higher cross-correlation scores for deforming/rotating clusters. This novel algorithm

Porous media: Analysis, reconstruction and percolation

DEFF Research Database (Denmark)

Rogon, Thomas Alexander

1995-01-01

functions of Gaussian fields and spatial autocorrelation functions of binary fields. An enhanced approach which embodies semi-analytical solutions for the conversions has been made. The scope and limitations of the method have been analysed in terms of realizability of different model correlation functions...... stereological methods. The measured sample autocorrelations are modeled by analytical correlation functions. A method for simulating porous networks from their porosity and spatial correlation originally developed by Joshi (14) is presented. This method is based on a conversion between spatial autocorrelation...... in binary fields. Percolation threshold of reconstructed porous media has been determined for different discretizations of a selected model correlation function. Also critical exponents such as the correlation length exponent v, the strength of the infinite network and the mean size of finite clusters have...

Real-time dynamics of RNA Polymerase II clustering in live human cells

Science.gov (United States)

Cisse, Ibrahim

2014-03-01

Transcription is the first step in the central dogma of molecular biology, when genetic information encoded on DNA is made into messenger RNA. How this fundamental process occurs within living cells (in vivo) is poorly understood,[1] despite extensive biochemical characterizations with isolated biomolecules (in vitro). For high-order organisms, like humans, transcription is reported to be spatially compartmentalized in nuclear foci consisting of clusters of RNA Polymerase II, the enzyme responsible for synthesizing all messenger RNAs. However, little is known of when these foci assemble or their relative stability. We developed an approach based on photo-activation localization microscopy (PALM) combined with a temporal correlation analysis, which we refer to as tcPALM. The tcPALM method enables the real-time characterization of biomolecular spatiotemporal organization, with single-molecule sensitivity, directly in living cells.[2] Using tcPALM, we observed that RNA Polymerase II clusters form transiently, with an average lifetime of 5.1 (+/- 0.4) seconds. Stimuli affecting transcription regulation yielded orders of magnitude changes in the dynamics of the polymerase clusters, implying that clustering is regulated and plays a role in the cells ability to effect rapid response to external signals. Our results suggest that the transient crowding of enzymes may aid in rate-limiting steps of genome regulation.

Digital breast tomosynthesis: computer-aided detection of clustered microcalcifications on planar projection images

International Nuclear Information System (INIS)

Samala, Ravi K; Chan, Heang-Ping; Lu, Yao; Hadjiiski, Lubomir M; Wei, Jun; Helvie, Mark A

2014-01-01

This paper describes a new approach to detect microcalcification clusters (MCs) in digital breast tomosynthesis (DBT) via its planar projection (PPJ) image. With IRB approval, two-view (cranio-caudal and mediolateral oblique views) DBTs of human subject breasts were obtained with a GE GEN2 prototype DBT system that acquires 21 projection angles spanning 60° in 3° increments. A data set of 307 volumes (154 human subjects) was divided by case into independent training (127 with MCs) and test sets (104 with MCs and 76 free of MCs). A simultaneous algebraic reconstruction technique with multiscale bilateral filtering (MSBF) regularization was used to enhance microcalcifications and suppress noise. During the MSBF regularized reconstruction, the DBT volume was separated into high frequency (HF) and low frequency components representing microcalcifications and larger structures. At the final iteration, maximum intensity projection was applied to the regularized HF volume to generate a PPJ image that contained MCs with increased contrast-to-noise ratio (CNR) and reduced search space. High CNR objects in the PPJ image were extracted and labeled as microcalcification candidates. Convolution neural network trained to recognize the image pattern of microcalcifications was used to classify the candidates into true calcifications and tissue structures and artifacts. The remaining microcalcification candidates were grouped into MCs by dynamic conditional clustering based on adaptive CNR threshold and radial distance criteria. False positive (FP) clusters were further reduced using the number of candidates in a cluster, CNR and size of microcalcification candidates. At 85% sensitivity an FP rate of 0.71 and 0.54 was achieved for view- and case-based sensitivity, respectively, compared to 2.16 and 0.85 achieved in DBT. The improvement was significant (p-value = 0.003) by JAFROC analysis. (paper)

Performance of the reconstruction algorithms of the FIRST experiment pixel sensors vertex detector

Energy Technology Data Exchange (ETDEWEB)

Rescigno, R., E-mail: regina.rescigno@iphc.cnrs.fr [Institut Pluridisciplinaire Hubert Curien, 23 rue du Loess, 67037 Strasbourg Cedex 2 (France); Finck, Ch.; Juliani, D. [Institut Pluridisciplinaire Hubert Curien, 23 rue du Loess, 67037 Strasbourg Cedex 2 (France); Spiriti, E. [Istituto Nazionale di Fisica Nucleare - Laboratori Nazionali di Frascati (Italy); Istituto Nazionale di Fisica Nucleare - Sezione di Roma 3 (Italy); Baudot, J. [Institut Pluridisciplinaire Hubert Curien, 23 rue du Loess, 67037 Strasbourg Cedex 2 (France); Abou-Haidar, Z. [CNA, Sevilla (Spain); Agodi, C. [Istituto Nazionale di Fisica Nucleare - Laboratori Nazionali del Sud (Italy); Alvarez, M.A.G. [CNA, Sevilla (Spain); Aumann, T. [GSI Helmholtzzentrum für Schwerionenforschung, Darmstadt (Germany); Battistoni, G. [Istituto Nazionale di Fisica Nucleare - Sezione di Milano (Italy); Bocci, A. [CNA, Sevilla (Spain); Böhlen, T.T. [European Organization for Nuclear Research CERN, Geneva (Switzerland); Medical Radiation Physics, Karolinska Institutet and Stockholm University, Stockholm (Sweden); Boudard, A. [CEA-Saclay, IRFU/SPhN, Gif sur Yvette Cedex (France); Brunetti, A.; Carpinelli, M. [Istituto Nazionale di Fisica Nucleare - Sezione di Cagliari (Italy); Università di Sassari (Italy); Cirrone, G.A.P. [Istituto Nazionale di Fisica Nucleare - Laboratori Nazionali del Sud (Italy); Cortes-Giraldo, M.A. [Departamento de Fisica Atomica, Molecular y Nuclear, University of Sevilla, 41080-Sevilla (Spain); Cuttone, G.; De Napoli, M. [Istituto Nazionale di Fisica Nucleare - Laboratori Nazionali del Sud (Italy); Durante, M. [GSI Helmholtzzentrum für Schwerionenforschung, Darmstadt (Germany); and others

2014-12-11

Hadrontherapy treatments use charged particles (e.g. protons and carbon ions) to treat tumors. During a therapeutic treatment with carbon ions, the beam undergoes nuclear fragmentation processes giving rise to significant yields of secondary charged particles. An accurate prediction of these production rates is necessary to estimate precisely the dose deposited into the tumours and the surrounding healthy tissues. Nowadays, a limited set of double differential carbon fragmentation cross-section is available. Experimental data are necessary to benchmark Monte Carlo simulations for their use in hadrontherapy. The purpose of the FIRST experiment is to study nuclear fragmentation processes of ions with kinetic energy in the range from 100 to 1000 MeV/u. Tracks are reconstructed using information from a pixel silicon detector based on the CMOS technology. The performances achieved using this device for hadrontherapy purpose are discussed. For each reconstruction step (clustering, tracking and vertexing), different methods are implemented. The algorithm performances and the accuracy on reconstructed observables are evaluated on the basis of simulated and experimental data.

USING THE BULLET CLUSTER AS A GRAVITATIONAL TELESCOPE TO STUDY z ∼> 7 LYMAN BREAK GALAXIES

International Nuclear Information System (INIS)

Hall, Nicholas; Bradač, Maruša; Gonzalez, Anthony H.; Treu, Tommaso; Clowe, Douglas; Jones, Christine; Stiavelli, Massimo; Zaritsky, Dennis; Cuby, Jean-Gabriel; Clément, Benjamin

2012-01-01

We use imaging obtained with the Hubble Space Telescope Wide Field Camera 3 to search for z 850 dropouts at z ∼ 7 and J 110 dropouts at z ∼ 9 lensed by the Bullet Cluster. In total we find 10 z 850 dropouts in our 8.27 arcmin 2 field. Using magnification maps from a combined weak- and strong-lensing mass reconstruction of the Bullet Cluster and correcting for estimated completeness levels, we calculate the surface density and luminosity function of our z 850 dropouts as a function of intrinsic (accounting for magnification) magnitude. We find results consistent with published blank field surveys, despite using much shallower data, and demonstrate the effectiveness of cluster surveys in the search for z ∼ 7 galaxies.

Collective Signal Processing in Cluster Chemotaxis: Roles of Adaptation, Amplification, and Co-attraction in Collective Guidance

Science.gov (United States)

Camley, Brian A.; Zimmermann, Juliane; Levine, Herbert; Rappel, Wouter-Jan

2016-01-01

Single eukaryotic cells commonly sense and follow chemical gradients, performing chemotaxis. Recent experiments and theories, however, show that even when single cells do not chemotax, clusters of cells may, if their interactions are regulated by the chemoattractant. We study this general mechanism of “collective guidance” computationally with models that integrate stochastic dynamics for individual cells with biochemical reactions within the cells, and diffusion of chemical signals between the cells. We show that if clusters of cells use the well-known local excitation, global inhibition (LEGI) mechanism to sense chemoattractant gradients, the speed of the cell cluster becomes non-monotonic in the cluster’s size—clusters either larger or smaller than an optimal size will have lower speed. We argue that the cell cluster speed is a crucial readout of how the cluster processes chemotactic signals; both amplification and adaptation will alter the behavior of cluster speed as a function of size. We also show that, contrary to the assumptions of earlier theories, collective guidance does not require persistent cell-cell contacts and strong short range adhesion. If cell-cell adhesion is absent, and the cluster cohesion is instead provided by a co-attraction mechanism, e.g. chemotaxis toward a secreted molecule, collective guidance may still function. However, new behaviors, such as cluster rotation, may also appear in this case. Co-attraction and adaptation allow for collective guidance that is robust to varying chemoattractant concentrations while not requiring strong cell-cell adhesion. PMID:27367541

Anatomical and Electrophysiological Clustering of Superficial Medial Entorhinal Cortex Interneurons

Science.gov (United States)

2017-01-01

Abstract Local GABAergic interneurons regulate the activity of spatially-modulated principal cells in the medial entorhinal cortex (MEC), mediating stellate-to-stellate connectivity and possibly enabling grid formation via recurrent inhibitory circuitry. Despite the important role interneurons seem to play in the MEC cortical circuit, the combination of low cell counts and functional diversity has made systematic electrophysiological studies of these neurons difficult. For these reasons, there remains a paucity of knowledge on the electrophysiological profiles of superficial MEC interneuron populations. Taking advantage of glutamic acid decarboxylase 2 (GAD2)-IRES-tdTomato and PV-tdTomato transgenic mice, we targeted GABAergic interneurons for whole-cell patch-clamp recordings and characterized their passive membrane features, basic input/output properties and action potential (AP) shape. These electrophysiologically characterized cells were then anatomically reconstructed, with emphasis on axonal projections and pial depth. K-means clustering of interneuron anatomical and electrophysiological data optimally classified a population of 106 interneurons into four distinct clusters. The first cluster is comprised of layer 2- and 3-projecting, slow-firing interneurons. The second cluster is comprised largely of PV+ fast-firing interneurons that project mainly to layers 2 and 3. The third cluster contains layer 1- and 2-projecting interneurons, and the fourth cluster is made up of layer 1-projecting horizontal interneurons. These results, among others, will provide greater understanding of the electrophysiological characteristics of MEC interneurons, help guide future in vivo studies, and may aid in uncovering the mechanism of grid field formation. PMID:29085901

Yeast identification by sequencing, biochemical kits, MALDI-TOF MS and rep-PCR DNA fingerprinting.

Science.gov (United States)

Zhao, Ying; Tsang, Chi-Ching; Xiao, Meng; Chan, Jasper F W; Lau, Susanna K P; Kong, Fanrong; Xu, Yingchun; Woo, Patrick C Y

2017-12-08

No study has comprehensively evaluated the performance of 28S nrDNA and ITS sequencing, commercial biochemical test kits, MALDI-TOF MS platforms, and the emerging rep-PCR DNA fingerprinting technology using a cohort of yeast strains collected from a clinical microbiology laboratory. In this study, using 71 clinically important yeast isolates (excluding Candida albicans) collected from a single centre, we determined the concordance of 28S nrDNA and ITS sequencing and evaluated the performance of two commercial test kits, two MALDI-TOF MS platforms, and rep-PCR DNA fingerprinting. 28S nrDNA and ITS sequencing showed complete agreement on the identities of the 71 isolates. Using sequencing results as the standard, 78.9% and 71.8% isolates were correctly identified using the API 20C AUX and Vitek 2 YST ID Card systems, respectively; and 90.1% and 80.3% isolates were correctly identified using the Bruker and Vitek MALDI-TOF MS platforms, respectively. Of the 18 strains belonging to the Candida parapsilosis species complex tested by DiversiLab automated rep-PCR DNA fingerprinting, all were identified only as Candida parapsilosis with similarities ≥93.2%, indicating the misidentification of Candida metapsilosis and Candida orthopsilosis. However, hierarchical cluster analysis of the rep-PCR DNA fingerprints of these three species within this species complex formed three different discrete clusters, indicating that this technology can potentially differentiate the three species. To achieve higher accuracies of identification, the databases of commercial biochemical test kits, MALDI-TOF MS platforms, and DiversiLab automated rep-PCR DNA fingerprinting needs further enrichment, particularly for uncommonly encountered yeast species. © The Author 2017. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

GASP. IX. Jellyfish galaxies in phase-space: an orbital study of intense ram-pressure stripping in clusters

Science.gov (United States)

Jaffé, Yara L.; Poggianti, Bianca M.; Moretti, Alessia; Gullieuszik, Marco; Smith, Rory; Vulcani, Benedetta; Fasano, Giovanni; Fritz, Jacopo; Tonnesen, Stephanie; Bettoni, Daniela; Hau, George; Biviano, Andrea; Bellhouse, Callum; McGee, Sean

2018-06-01

It is well known that galaxies falling into clusters can experience gas stripping due to ram pressure by the intra-cluster medium. The most spectacular examples are galaxies with extended tails of optically bright stripped material known as `jellyfish'. We use the first large homogeneous compilation of jellyfish galaxies in clusters from the WINGS and OmegaWINGS surveys, and follow-up MUSE observations from the GASP MUSE programme to investigate the orbital histories of jellyfish galaxies in clusters and reconstruct their stripping history through position versus velocity phase-space diagrams. We construct analytic models to define the regions in phase-space where ram-pressure stripping is at play. We then study the distribution of cluster galaxies in phase-space and find that jellyfish galaxies have on average higher peculiar velocities (and higher cluster velocity dispersion) than the overall population of cluster galaxies at all cluster-centric radii, which is indicative of recent infall into the cluster and radial orbits. In particular, the jellyfish galaxies with the longest gas tails reside very near the cluster cores (in projection) and are moving at very high speeds, which coincides with the conditions of the most intense ram pressure. We conclude that many of the jellyfish galaxies seen in clusters likely formed via fast (˜1-2 Gyr), incremental, outside-in ram-pressure stripping during first infall into the cluster in highly radial orbits.

Position Reconstruction and Charge Distribution in LHCb VELO Silicon Sensors

CERN Document Server

Versloot, TW; Akiba, K; Artuso, M; Van Beuzekom, M; Borel, J; Bowcock, TJV; Buytaert, J; Collins, P; Dumps, R; Dwyer, L; Eckstein, D; Eklund, L; Ferro-Luzzi, M; Frei, R; Gersabek M; Haefeli, G; Hennessy, K; Huse, T; Jans, E; John, M; Ketel, TJ; Keune, A; Lastoviicka, T; Mountain, R; Neufeld, N; Parkes, C; Stone, S; Szumlak, T; Tobin, M; Van Lysebetten, A; Viret, S; De Vries, H; Wang, J

2007-01-01

In 2006, a partially equipped LHCb VELO detector half was characterised in a test beam experiment (Alignment Challenge and Detector Commissioning, ACDC3). The position reconstruction and resolution for 2-strip R-sensor clusters was studied as a function of strip pitch and track inclination on the sensor surface. The Charge Density Distribution (CDD) is derived from the weighted charge distribution. It becomes asymmetric for tracks non-perpendicular to the strip surface. It is shown that the asymmetric broadening of the CDD around the track intercept position results in a linear eta-function at higher angles (>6 degrees). The sensor spatial resolution is determined both using a linear weighted mean of strip charges, as well as a third-order polynomial approximation via a eta-correction. The experimental results are in agreement with previous simulations. Future studies are underway to determine the angle and pitch dependent parameters which will be implemented in the LHCb VELO cluster position software tools.

Multiplatform serum metabolic phenotyping combined with pathway mapping to identify biochemical differences in smokers.

Science.gov (United States)

Kaluarachchi, Manuja R; Boulangé, Claire L; Garcia-Perez, Isabel; Lindon, John C; Minet, Emmanuel F

2016-10-01

Determining perturbed biochemical functions associated with tobacco smoking should be helpful for establishing causal relationships between exposure and adverse events. A multiplatform comparison of serum of smokers (n = 55) and never-smokers (n = 57) using nuclear magnetic resonance spectroscopy, UPLC-MS and statistical modeling revealed clustering of the classes, distinguished by metabolic biomarkers. The identified metabolites were subjected to metabolic pathway enrichment, modeling adverse biological events using available databases. Perturbation of metabolites involved in chronic obstructive pulmonary disease, cardiovascular diseases and cancer were identified and discussed. Combining multiplatform metabolic phenotyping with knowledge-based mapping gives mechanistic insights into disease development, which can be applied to next-generation tobacco and nicotine products for comparative risk assessment.

Reconstruction of Twist Torque in Main Parachute Risers

Science.gov (United States)

Day, Joshua D.

2015-01-01

The reconstruction of twist torque in the Main Parachute Risers of the Capsule Parachute Assembly System (CPAS) has been successfully used to validate CPAS Model Memo conservative twist torque equations. Reconstruction of basic, one degree of freedom drop tests was used to create a functional process for the evaluation of more complex, rigid body simulation. The roll, pitch, and yaw of the body, the fly-out angles of the parachutes, and the relative location of the parachutes to the body are inputs to the torque simulation. The data collected by the Inertial Measurement Unit (IMU) was used to calculate the true torque. The simulation then used photogrammetric and IMU data as inputs into the Model Memo equations. The results were then compared to the true torque results to validate the Model Memo equations. The Model Memo parameters were based off of steel risers and the parameters will need to be re-evaluated for different materials. Photogrammetric data was found to be more accurate than the inertial data in accounting for the relative rotation between payload and cluster. The Model Memo equations were generally a good match and when not matching were generally conservative.

A Proteomic Approach to Investigating Gene Cluster Expression and Secondary Metabolite Functionality in Aspergillus fumigatus

Science.gov (United States)

Owens, Rebecca A.; Hammel, Stephen; Sheridan, Kevin J.; Jones, Gary W.; Doyle, Sean

2014-01-01

A combined proteomics and metabolomics approach was utilised to advance the identification and characterisation of secondary metabolites in Aspergillus fumigatus. Here, implementation of a shotgun proteomic strategy led to the identification of non-redundant mycelial proteins (n = 414) from A. fumigatus including proteins typically under-represented in 2-D proteome maps: proteins with multiple transmembrane regions, hydrophobic proteins and proteins with extremes of molecular mass and pI. Indirect identification of secondary metabolite cluster expression was also achieved, with proteins (n = 18) from LaeA-regulated clusters detected, including GliT encoded within the gliotoxin biosynthetic cluster. Biochemical analysis then revealed that gliotoxin significantly attenuates H2O2-induced oxidative stress in A. fumigatus (p>0.0001), confirming observations from proteomics data. A complementary 2-D/LC-MS/MS approach further elucidated significantly increased abundance (pproteome and experimental strategies, plus mechanistic data pertaining to gliotoxin functionality in the organism. PMID:25198175

Top-down approach for nanophase reconstruction in bulk heterojunction solar cells.

Science.gov (United States)

Kong, Jaemin; Hwang, In-Wook; Lee, Kwanghee

2014-09-01

"Top-Down" nanophase reconstruction via a post-additive soaking process is first presented with various BHJ binary composites. By simply rinsing as-cast BHJ films with a solvent mixture containing a few traces of a nanophase-control reagent such as 1,8-diiodooctane, oversized fullerene-rich clusters (>100 nm in dia-meter) in the BHJ film are instataneously disassembled and entirely reorganized into finely intermixed donor/acceptor nanophases (ca. 10 nm) with a 3D compositional homogeneity, without surface segregation. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

On the Adaptive Design Rules of Biochemical Networks in Evolution

Directory of Open Access Journals (Sweden)

Bor-Sen Chen

2007-01-01

Full Text Available Biochemical networks are the backbones of physiological systems of organisms. Therefore, a biochemical network should be sufficiently robust (not sensitive to tolerate genetic mutations and environmental changes in the evolutionary process. In this study, based on the robustness and sensitivity criteria of biochemical networks, the adaptive design rules are developed for natural selection in the evolutionary process. This will provide insights into the robust adaptive mechanism of biochemical networks in the evolutionary process. We find that if a mutated biochemical network satisfies the robustness and sensitivity criteria of natural selection, there is a high probability for the biochemical network to prevail during natural selection in the evolutionary process. Since there are various mutated biochemical networks that can satisfy these criteria but have some differences in phenotype, the biochemical networks increase their diversities in the evolutionary process. The robustness of a biochemical network enables co-option so that new phenotypes can be generated in evolution. The proposed robust adaptive design rules of natural selection gain much insight into the evolutionary mechanism and provide a systematic robust biochemical circuit design method of biochemical networks for biotechnological and therapeutic purposes in the future.

Improving Marine Ecosystem Models with Biochemical Tracers

Science.gov (United States)

Pethybridge, Heidi R.; Choy, C. Anela; Polovina, Jeffrey J.; Fulton, Elizabeth A.

2018-01-01

Empirical data on food web dynamics and predator-prey interactions underpin ecosystem models, which are increasingly used to support strategic management of marine resources. These data have traditionally derived from stomach content analysis, but new and complementary forms of ecological data are increasingly available from biochemical tracer techniques. Extensive opportunities exist to improve the empirical robustness of ecosystem models through the incorporation of biochemical tracer data and derived indices, an area that is rapidly expanding because of advances in analytical developments and sophisticated statistical techniques. Here, we explore the trophic information required by ecosystem model frameworks (species, individual, and size based) and match them to the most commonly used biochemical tracers (bulk tissue and compound-specific stable isotopes, fatty acids, and trace elements). Key quantitative parameters derived from biochemical tracers include estimates of diet composition, niche width, and trophic position. Biochemical tracers also provide powerful insight into the spatial and temporal variability of food web structure and the characterization of dominant basal and microbial food web groups. A major challenge in incorporating biochemical tracer data into ecosystem models is scale and data type mismatches, which can be overcome with greater knowledge exchange and numerical approaches that transform, integrate, and visualize data.

The GALAH survey: chemical tagging of star clusters and new members in the Pleiades

Science.gov (United States)

Kos, Janez; Bland-Hawthorn, Joss; Freeman, Ken; Buder, Sven; Traven, Gregor; De Silva, Gayandhi M.; Sharma, Sanjib; Asplund, Martin; Duong, Ly; Lin, Jane; Lind, Karin; Martell, Sarah; Simpson, Jeffrey D.; Stello, Dennis; Zucker, Daniel B.; Zwitter, Tomaž; Anguiano, Borja; Da Costa, Gary; D'Orazi, Valentina; Horner, Jonathan; Kafle, Prajwal R.; Lewis, Geraint; Munari, Ulisse; Nataf, David M.; Ness, Melissa; Reid, Warren; Schlesinger, Katie; Ting, Yuan-Sen; Wyse, Rosemary

2018-02-01

The technique of chemical tagging uses the elemental abundances of stellar atmospheres to 'reconstruct' chemically homogeneous star clusters that have long since dispersed. The GALAH spectroscopic survey - which aims to observe one million stars using the Anglo-Australian Telescope - allows us to measure up to 30 elements or dimensions in the stellar chemical abundance space, many of which are not independent. How to find clustering reliably in a noisy high-dimensional space is a difficult problem that remains largely unsolved. Here, we explore t-distributed stochastic neighbour embedding (t-SNE) - which identifies an optimal mapping of a high-dimensional space into fewer dimensions - whilst conserving the original clustering information. Typically, the projection is made to a 2D space to aid recognition of clusters by eye. We show that this method is a reliable tool for chemical tagging because it can: (i) resolve clustering in chemical space alone, (ii) recover known open and globular clusters with high efficiency and low contamination, and (iii) relate field stars to known clusters. t-SNE also provides a useful visualization of a high-dimensional space. We demonstrate the method on a data set of 13 abundances measured in the spectra of 187 000 stars by the GALAH survey. We recover seven of the nine observed clusters (six globular and three open clusters) in chemical space with minimal contamination from field stars and low numbers of outliers. With chemical tagging, we also identify two Pleiades supercluster members (which we confirm kinematically), one as far as 6° - one tidal radius away from the cluster centre.

Fast group matching for MR fingerprinting reconstruction.

Science.gov (United States)

Cauley, Stephen F; Setsompop, Kawin; Ma, Dan; Jiang, Yun; Ye, Huihui; Adalsteinsson, Elfar; Griswold, Mark A; Wald, Lawrence L

2015-08-01

MR fingerprinting (MRF) is a technique for quantitative tissue mapping using pseudorandom measurements. To estimate tissue properties such as T1 , T2 , proton density, and B0 , the rapidly acquired data are compared against a large dictionary of Bloch simulations. This matching process can be a very computationally demanding portion of MRF reconstruction. We introduce a fast group matching algorithm (GRM) that exploits inherent correlation within MRF dictionaries to create highly clustered groupings of the elements. During matching, a group specific signature is first used to remove poor matching possibilities. Group principal component analysis (PCA) is used to evaluate all remaining tissue types. In vivo 3 Tesla brain data were used to validate the accuracy of our approach. For a trueFISP sequence with over 196,000 dictionary elements, 1000 MRF samples, and image matrix of 128 × 128, GRM was able to map MR parameters within 2s using standard vendor computational resources. This is an order of magnitude faster than global PCA and nearly two orders of magnitude faster than direct matching, with comparable accuracy (1-2% relative error). The proposed GRM method is a highly efficient model reduction technique for MRF matching and should enable clinically relevant reconstruction accuracy and time on standard vendor computational resources. © 2014 Wiley Periodicals, Inc.

The ALICE Software Release Validation cluster

International Nuclear Information System (INIS)

Berzano, D; Krzewicki, M

2015-01-01

One of the most important steps of software lifecycle is Quality Assurance: this process comprehends both automatic tests and manual reviews, and all of them must pass successfully before the software is approved for production. Some tests, such as source code static analysis, are executed on a single dedicated service: in High Energy Physics, a full simulation and reconstruction chain on a distributed computing environment, backed with a sample “golden” dataset, is also necessary for the quality sign off. The ALICE experiment uses dedicated and virtualized computing infrastructures for the Release Validation in order not to taint the production environment (i.e. CVMFS and the Grid) with non-validated software and validation jobs: the ALICE Release Validation cluster is a disposable virtual cluster appliance based on CernVM and the Virtual Analysis Facility, capable of deploying on demand, and with a single command, a dedicated virtual HTCondor cluster with an automatically scalable number of virtual workers on any cloud supporting the standard EC2 interface. Input and output data are externally stored on EOS, and a dedicated CVMFS service is used to provide the software to be validated. We will show how the Release Validation Cluster deployment and disposal are completely transparent for the Release Manager, who simply triggers the validation from the ALICE build system's web interface. CernVM 3, based entirely on CVMFS, permits to boot any snapshot of the operating system in time: we will show how this allows us to certify each ALICE software release for an exact CernVM snapshot, addressing the problem of Long Term Data Preservation by ensuring a consistent environment for software execution and data reprocessing in the future. (paper)

Raman spectroscopic biochemical mapping of tissues

Science.gov (United States)

Stone, Nicholas; Hart Prieto, Maria C.; Kendall, Catherine A.; Shetty, Geeta; Barr, Hugh

2006-02-01

Advances in technologies have brought us closer to routine spectroscopic diagnosis of early malignant disease. However, there is still a poor understanding of the carcinogenesis process. For example it is not known whether many cancers follow a logical sequence from dysplasia, to carcinoma in situ, to invasion. Biochemical tissue changes, triggered by genetic mutations, precede morphological and structural changes. These can be probed using Raman or FTIR microspectroscopy and the spectra analysed for biochemical constituents. Local microscopic distribution of various constituents can then be visualised. Raman mapping has been performed on a number of tissues including oesophagus, breast, bladder and prostate. The biochemical constituents have been calculated at each point using basis spectra and least squares analysis. The residual of the least squares fit indicates any unfit spectral components. The biochemical distribution will be compared with the defined histopathological boundaries. The distribution of nucleic acids, glycogen, actin, collagen I, III, IV, lipids and others appear to follow expected patterns.

Protein clustering and RNA phylogenetic reconstruction of the influenza A [corrected] virus NS1 protein allow an update in classification and identification of motif conservation.

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Sevilla-Reyes, Edgar E; Chavaro-Pérez, David A; Piten-Isidro, Elvira; Gutiérrez-González, Luis H; Santos-Mendoza, Teresa

2013-01-01

The non-structural protein 1 (NS1) of influenza A virus (IAV), coded by its third most diverse gene, interacts with multiple molecules within infected cells. NS1 is involved in host immune response regulation and is a potential contributor to the virus host range. Early phylogenetic analyses using 50 sequences led to the classification of NS1 gene variants into groups (alleles) A and B. We reanalyzed NS1 diversity using 14,716 complete NS IAV sequences, downloaded from public databases, without host bias. Removal of sequence redundancy and further structured clustering at 96.8% amino acid similarity produced 415 clusters that enhanced our capability to detect distinct subgroups and lineages, which were assigned a numerical nomenclature. Maximum likelihood phylogenetic reconstruction using RNA sequences indicated the previously identified deep branching separating group A from group B, with five distinct subgroups within A as well as two and five lineages within the A4 and A5 subgroups, respectively. Our classification model proposes that sequence patterns in thirteen amino acid positions are sufficient to fit >99.9% of all currently available NS1 sequences into the A subgroups/lineages or the B group. This classification reduces host and virus bias through the prioritization of NS1 RNA phylogenetics over host or virus phenetics. We found significant sequence conservation within the subgroups and lineages with characteristic patterns of functional motifs, such as the differential binding of CPSF30 and crk/crkL or the availability of a C-terminal PDZ-binding motif. To understand selection pressures and evolution acting on NS1, it is necessary to organize the available data. This updated classification may help to clarify and organize the study of NS1 interactions and pathogenic differences and allow the drawing of further functional inferences on sequences in each group, subgroup and lineage rather than on a strain-by-strain basis.

Simulation studies in biochemical signaling and enzyme reactions

Science.gov (United States)

Nelatury, Sudarshan R.; Vagula, Mary C.

2014-06-01

Biochemical pathways characterize various biochemical reaction schemes that involve a set of species and the manner in which they are connected. Determination of schematics that represent these pathways is an important task in understanding metabolism and signal transduction. Examples of these Pathways are: DNA and protein synthesis, and production of several macro-molecules essential for cell survival. A sustained feedback mechanism arises in gene expression and production of mRNA that lead to protein synthesis if the protein so synthesized serves as a transcription factor and becomes a repressor of the gene expression. The cellular regulations are carried out through biochemical networks consisting of reactions and regulatory proteins. Systems biology is a relatively new area that attempts to describe the biochemical pathways analytically and develop reliable mathematical models for the pathways. A complete understanding of chemical reaction kinetics is prohibitively hard thanks to the nonlinear and highly complex mechanisms that regulate protein formation, but attempting to numerically solve some of the governing differential equations seems to offer significant insight about their biochemical picture. To validate these models, one can perform simple experiments in the lab. This paper introduces fundamental ideas in biochemical signaling and attempts to take first steps into the understanding of biochemical oscillations. Initially, the two-pool model of calcium is used to describe the dynamics behind the oscillations. Later we present some elementary results showing biochemical oscillations arising from solving differential equations of Elowitz and Leibler using MATLAB software.

A scale invariant clustering of genes on human chromosome 7

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Kendal Wayne S

2004-01-01

Full Text Available Abstract Background Vertebrate genes often appear to cluster within the background of nontranscribed genomic DNA. Here an analysis of the physical distribution of gene structures on human chromosome 7 was performed to confirm the presence of clustering, and to elucidate possible underlying statistical and biological mechanisms. Results Clustering of genes was confirmed by virtue of a variance of the number of genes per unit physical length that exceeded the respective mean. Further evidence for clustering came from a power function relationship between the variance and mean that possessed an exponent of 1.51. This power function implied that the spatial distribution of genes on chromosome 7 was scale invariant, and that the underlying statistical distribution had a Poisson-gamma (PG form. A PG distribution for the spatial scattering of genes was validated by stringent comparisons of both the predicted variance to mean power function and its cumulative distribution function to data derived from chromosome 7. Conclusion The PG distribution was consistent with at least two different biological models: In the microrearrangement model, the number of genes per unit length of chromosome represented the contribution of a random number of smaller chromosomal segments that had originated by random breakage and reconstruction of more primitive chromosomes. Each of these smaller segments would have necessarily contained (on average a gamma distributed number of genes. In the gene cluster model, genes would be scattered randomly to begin with. Over evolutionary timescales, tandem duplication, mutation, insertion, deletion and rearrangement could act at these gene sites through a stochastic birth death and immigration process to yield a PG distribution. On the basis of the gene position data alone it was not possible to identify the biological model which best explained the observed clustering. However, the underlying PG statistical model implicated neutral

Statistical analysis and data mining of digital reconstructions of dendritic morphologies

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Sridevi ePolavaram

2014-12-01

Full Text Available Neuronal morphology is diverse among animal species, developmental stages, brain regions, and cell types. The geometry of individual neurons also varies substantially even within the same cell class. Moreover, specific histological, imaging, and reconstruction methodologies can differentially affect morphometric measures. The quantitative characterization of neuronal arbors is necessary for in-depth understanding of the structure-function relationship in nervous systems. The large collection of community-contributed digitally reconstructed neurons available at NeuroMorpho.Org constitutes a big data research opportunity for neuroscience discovery beyond the approaches typically pursued in single laboratories. To illustrate these potential and related challenges, we present a database-wide statistical analysis of dendritic arbors enabling the quantification of major morphological similarities and differences across broadly adopted metadata categories. Furthermore, we adopt a complementary unsupervised approach based on clustering and dimensionality reduction to identify the main morphological parameters leading to the most statistically informative structural classification. We find that specific combinations of measures related to branching density, overall size, tortuosity, bifurcation angles, arbor flatness, and topological asymmetry can capture anatomically and functionally relevant features of dendritic trees. The reported results only represent a small fraction of the relationships available for data exploration and hypothesis testing enabled by digital sharing of morphological reconstructions.

Statistical analysis and data mining of digital reconstructions of dendritic morphologies.

Science.gov (United States)

Polavaram, Sridevi; Gillette, Todd A; Parekh, Ruchi; Ascoli, Giorgio A

2014-01-01

Neuronal morphology is diverse among animal species, developmental stages, brain regions, and cell types. The geometry of individual neurons also varies substantially even within the same cell class. Moreover, specific histological, imaging, and reconstruction methodologies can differentially affect morphometric measures. The quantitative characterization of neuronal arbors is necessary for in-depth understanding of the structure-function relationship in nervous systems. The large collection of community-contributed digitally reconstructed neurons available at NeuroMorpho.Org constitutes a "big data" research opportunity for neuroscience discovery beyond the approaches typically pursued in single laboratories. To illustrate these potential and related challenges, we present a database-wide statistical analysis of dendritic arbors enabling the quantification of major morphological similarities and differences across broadly adopted metadata categories. Furthermore, we adopt a complementary unsupervised approach based on clustering and dimensionality reduction to identify the main morphological parameters leading to the most statistically informative structural classification. We find that specific combinations of measures related to branching density, overall size, tortuosity, bifurcation angles, arbor flatness, and topological asymmetry can capture anatomically and functionally relevant features of dendritic trees. The reported results only represent a small fraction of the relationships available for data exploration and hypothesis testing enabled by sharing of digital morphological reconstructions.

Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea

OpenAIRE

Wolf Yuri I; Novichkov Pavel S; Sorokin Alexander V; Makarova Kira S; Koonin Eugene V

2007-01-01

Abstract Background An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. Shortly after multiple genome sequences of bacteria, archaea, and unicellular eukaryotes became available, an attempt on such a classification was implemented in Clusters of Orthologous Groups of proteins (COGs). Rapid accumulation of genome sequences creates opportunities for refining COGs ...

Automated analysis of information processing, kinetic independence and modular architecture in biochemical networks using MIDIA.

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Bowsher, Clive G

2011-02-15

Understanding the encoding and propagation of information by biochemical reaction networks and the relationship of such information processing properties to modular network structure is of fundamental importance in the study of cell signalling and regulation. However, a rigorous, automated approach for general biochemical networks has not been available, and high-throughput analysis has therefore been out of reach. Modularization Identification by Dynamic Independence Algorithms (MIDIA) is a user-friendly, extensible R package that performs automated analysis of how information is processed by biochemical networks. An important component is the algorithm's ability to identify exact network decompositions based on both the mass action kinetics and informational properties of the network. These modularizations are visualized using a tree structure from which important dynamic conditional independence properties can be directly read. Only partial stoichiometric information needs to be used as input to MIDIA, and neither simulations nor knowledge of rate parameters are required. When applied to a signalling network, for example, the method identifies the routes and species involved in the sequential propagation of information between its multiple inputs and outputs. These routes correspond to the relevant paths in the tree structure and may be further visualized using the Input-Output Path Matrix tool. MIDIA remains computationally feasible for the largest network reconstructions currently available and is straightforward to use with models written in Systems Biology Markup Language (SBML). The package is distributed under the GNU General Public License and is available, together with a link to browsable Supplementary Material, at http://code.google.com/p/midia. Further information is at www.maths.bris.ac.uk/~macgb/Software.html.

Investigations of Calorimeter Clustering in ATLAS using Machine Learning

CERN Document Server

AUTHOR|(CDS)2153685

The Large Hadron Collider (LHC) at CERN is designed to search for new physics by colliding protons with a center-of-mass energy of 13 TeV. The ATLAS detector is a multipurpose particle detector built to record these proton-proton collisions. In order to improve sensitivity to new physics at the LHC, luminosity increases are planned for 2018 and beyond. With this greater luminosity comes an increase in the number of simultaneous proton-proton collisions per bunch crossing (pile-up). This extra pile- up has adverse effects on algorithms for clustering the ATLAS detector's calorimeter cells. These adverse effects stem from overlapping energy deposits originating from distinct particles and could lead to diffculties in accurately reconstructing events. Machine learning algorithms provide a new tool that has potential to clustering per- formance. Recent developments in computer science have given rise to new set of machine learning algorithms that, in many circumstances, out-perform more conven- tional algorithms....

Brightest Cluster Galaxies in REXCESS Clusters

Science.gov (United States)

Haarsma, Deborah B.; Leisman, L.; Bruch, S.; Donahue, M.

2009-01-01

Most galaxy clusters contain a Brightest Cluster Galaxy (BCG) which is larger than the other cluster ellipticals and has a more extended profile. In the hierarchical model, the BCG forms through many galaxy mergers in the crowded center of the cluster, and thus its properties give insight into the assembly of the cluster as a whole. In this project, we are working with the Representative XMM-Newton Cluster Structure Survey (REXCESS) team (Boehringer et al 2007) to study BCGs in 33 X-ray luminous galaxy clusters, 0.055 < z < 0.183. We are imaging the BCGs in R band at the Southern Observatory for Astrophysical Research (SOAR) in Chile. In this poster, we discuss our methods and give preliminary measurements of the BCG magnitudes, morphology, and stellar mass. We compare these BCG properties with the properties of their host clusters, particularly of the X-ray emitting gas.

An Effective Tri-Clustering Algorithm Combining Expression Data with Gene Regulation Information

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Ao Li

2009-04-01

Full Text Available Motivation: Bi-clustering algorithms aim to identify sets of genes sharing similar expression patterns across a subset of conditions. However direct interpretation or prediction of gene regulatory mechanisms may be difficult as only gene expression data is used. Information about gene regulators may also be available, most commonly about which transcription factors may bind to the promoter region and thus control the expression level of a gene. Thus a method to integrate gene expression and gene regulation information is desirable for clustering and analyzing. Methods: By incorporating gene regulatory information with gene expression data, we define regulated expression values (REV as indicators of how a gene is regulated by a specific factor. Existing bi-clustering methods are extended to a three dimensional data space by developing a heuristic TRI-Clustering algorithm. An additional approach named Automatic Boundary Searching algorithm (ABS is introduced to automatically determine the boundary threshold. Results: Results based on incorporating ChIP-chip data representing transcription factor-gene interactions show that the algorithms are efficient and robust for detecting tri-clusters. Detailed analysis of the tri-cluster extracted from yeast sporulation REV data shows genes in this cluster exhibited significant differences during the middle and late stages. The implicated regulatory network was then reconstructed for further study of defined regulatory mechanisms. Topological and statistical analysis of this network demonstrated evidence of significant changes of TF activities during the different stages of yeast sporulation, and suggests this approach might be a general way to study regulatory networks undergoing transformations.

Continuous osteological characters in the reconstruction of phylogenetic relationships of the six Euro-Mediterranean mullet species (Mugilidae).

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Antović, Ivanka

2013-09-01

Sixty-three continuous osteological characters (18 skull continuous characters and the total length of neurocranium, 45 continuous characters of 15 elements of the viscerodermal skeleton) were analyzed and included in the reconstruction of phylogenetic relationships of the six Euro-Mediterranean mullet species from the South Adriatic Sea: Mugil cephalus Linnaeus, 1758; Liza saliens Risso, 1810; Liza aurata Risso, 1810; Liza ramada Risso, 1826; Chelon labrosus Risso, 1826 and Oedalechilus labeo Cuvier, 1829. The study reveals that Sphyraenidae was separated clearly from Mugilidae, C. labrosus and three Liza species form a common cluster (L. ramada and L. saliens being the closest), while O. labeo and M. cephalus cluster together.

Breast reconstruction after mastectomy

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Daniel eSchmauss

2016-01-01

Full Text Available Breast cancer is the leading cause of cancer death in women worldwide. Its surgical approach has become less and less mutilating in the last decades. However, the overall number of breast reconstructions has significantly increased lately. Nowadays breast reconstruction should be individualized at its best, first of all taking into consideration oncological aspects of the tumor, neo-/adjuvant treatment and genetic predisposition, but also its timing (immediate versus delayed breast reconstruction, as well as the patient’s condition and wish. This article gives an overview over the various possibilities of breast reconstruction, including implant- and expander-based reconstruction, flap-based reconstruction (vascularized autologous tissue, the combination of implant and flap, reconstruction using non-vascularized autologous fat, as well as refinement surgery after breast reconstruction.

Breast reconstruction - implants

Science.gov (United States)

Breast implants surgery; Mastectomy - breast reconstruction with implants; Breast cancer - breast reconstruction with implants ... harder to find a tumor if your breast cancer comes back. Getting breast implants does not take as long as breast reconstruction ...

Massively parallel unsupervised single-particle cryo-EM data clustering via statistical manifold learning.

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Jiayi Wu

Full Text Available Structural heterogeneity in single-particle cryo-electron microscopy (cryo-EM data represents a major challenge for high-resolution structure determination. Unsupervised classification may serve as the first step in the assessment of structural heterogeneity. However, traditional algorithms for unsupervised classification, such as K-means clustering and maximum likelihood optimization, may classify images into wrong classes with decreasing signal-to-noise-ratio (SNR in the image data, yet demand increased computational costs. Overcoming these limitations requires further development of clustering algorithms for high-performance cryo-EM data processing. Here we introduce an unsupervised single-particle clustering algorithm derived from a statistical manifold learning framework called generative topographic mapping (GTM. We show that unsupervised GTM clustering improves classification accuracy by about 40% in the absence of input references for data with lower SNRs. Applications to several experimental datasets suggest that our algorithm can detect subtle structural differences among classes via a hierarchical clustering strategy. After code optimization over a high-performance computing (HPC environment, our software implementation was able to generate thousands of reference-free class averages within hours in a massively parallel fashion, which allows a significant improvement on ab initio 3D reconstruction and assists in the computational purification of homogeneous datasets for high-resolution visualization.

Massively parallel unsupervised single-particle cryo-EM data clustering via statistical manifold learning.

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Wu, Jiayi; Ma, Yong-Bei; Congdon, Charles; Brett, Bevin; Chen, Shuobing; Xu, Yaofang; Ouyang, Qi; Mao, Youdong

2017-01-01

Structural heterogeneity in single-particle cryo-electron microscopy (cryo-EM) data represents a major challenge for high-resolution structure determination. Unsupervised classification may serve as the first step in the assessment of structural heterogeneity. However, traditional algorithms for unsupervised classification, such as K-means clustering and maximum likelihood optimization, may classify images into wrong classes with decreasing signal-to-noise-ratio (SNR) in the image data, yet demand increased computational costs. Overcoming these limitations requires further development of clustering algorithms for high-performance cryo-EM data processing. Here we introduce an unsupervised single-particle clustering algorithm derived from a statistical manifold learning framework called generative topographic mapping (GTM). We show that unsupervised GTM clustering improves classification accuracy by about 40% in the absence of input references for data with lower SNRs. Applications to several experimental datasets suggest that our algorithm can detect subtle structural differences among classes via a hierarchical clustering strategy. After code optimization over a high-performance computing (HPC) environment, our software implementation was able to generate thousands of reference-free class averages within hours in a massively parallel fashion, which allows a significant improvement on ab initio 3D reconstruction and assists in the computational purification of homogeneous datasets for high-resolution visualization.

Metal cluster compounds - chemistry and importance; clusters containing isolated main group element atoms, large metal cluster compounds, cluster fluxionality

International Nuclear Information System (INIS)

Walther, B.

1988-01-01

This part of the review on metal cluster compounds deals with clusters containing isolated main group element atoms, with high nuclearity clusters and metal cluster fluxionality. It will be obvious that main group element atoms strongly influence the geometry, stability and reactivity of the clusters. High nuclearity clusters are of interest in there own due to the diversity of the structures adopted, but their intermediate position between molecules and the metallic state makes them a fascinating research object too. These both sites of the metal cluster chemistry as well as the frequently observed ligand and core fluxionality are related to the cluster metal and surface analogy. (author)

Adaptive algebraic reconstruction technique

International Nuclear Information System (INIS)

Lu Wenkai; Yin Fangfang

2004-01-01

Algebraic reconstruction techniques (ART) are iterative procedures for reconstructing objects from their projections. It is proven that ART can be computationally efficient by carefully arranging the order in which the collected data are accessed during the reconstruction procedure and adaptively adjusting the relaxation parameters. In this paper, an adaptive algebraic reconstruction technique (AART), which adopts the same projection access scheme in multilevel scheme algebraic reconstruction technique (MLS-ART), is proposed. By introducing adaptive adjustment of the relaxation parameters during the reconstruction procedure, one-iteration AART can produce reconstructions with better quality, in comparison with one-iteration MLS-ART. Furthermore, AART outperforms MLS-ART with improved computational efficiency

Activation and clustering of a Plasmodium falciparum var gene are affected by subtelomeric sequences.

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Duffy, Michael F; Tang, Jingyi; Sumardy, Fransisca; Nguyen, Hanh H T; Selvarajah, Shamista A; Josling, Gabrielle A; Day, Karen P; Petter, Michaela; Brown, Graham V

2017-01-01

The Plasmodium falciparum var multigene family encodes the cytoadhesive, variant antigen PfEMP1. P. falciparum antigenic variation and cytoadhesion specificity are controlled by epigenetic switching between the single, or few, simultaneously expressed var genes. Most var genes are maintained in perinuclear clusters of heterochromatic telomeres. The active var gene(s) occupy a single, perinuclear var expression site. It is unresolved whether the var expression site forms in situ at a telomeric cluster or whether it is an extant compartment to which single chromosomes travel, thus controlling var switching. Here we show that transcription of a var gene did not require decreased colocalisation with clusters of telomeres, supporting var expression site formation in situ. However following recombination within adjacent subtelomeric sequences, the same var gene was persistently activated and did colocalise less with telomeric clusters. Thus, participation in stable, heterochromatic, telomere clusters and var switching are independent but are both affected by subtelomeric sequences. The var expression site colocalised with the euchromatic mark H3K27ac to a greater extent than it did with heterochromatic H3K9me3. H3K27ac was enriched within the active var gene promoter even when the var gene was transiently repressed in mature parasites and thus H3K27ac may contribute to var gene epigenetic memory. © 2016 Federation of European Biochemical Societies.

PREFACE: Nuclear Cluster Conference; Cluster'07

Science.gov (United States)

Freer, Martin

2008-05-01

The Cluster Conference is a long-running conference series dating back to the 1960's, the first being initiated by Wildermuth in Bochum, Germany, in 1969. The most recent meeting was held in Nara, Japan, in 2003, and in 2007 the 9th Cluster Conference was held in Stratford-upon-Avon, UK. As the name suggests the town of Stratford lies upon the River Avon, and shortly before the conference, due to unprecedented rainfall in the area (approximately 10 cm within half a day), lay in the River Avon! Stratford is the birthplace of the `Bard of Avon' William Shakespeare, and this formed an intriguing conference backdrop. The meeting was attended by some 90 delegates and the programme contained 65 70 oral presentations, and was opened by a historical perspective presented by Professor Brink (Oxford) and closed by Professor Horiuchi (RCNP) with an overview of the conference and future perspectives. In between, the conference covered aspects of clustering in exotic nuclei (both neutron and proton-rich), molecular structures in which valence neutrons are exchanged between cluster cores, condensates in nuclei, neutron-clusters, superheavy nuclei, clusters in nuclear astrophysical processes and exotic cluster decays such as 2p and ternary cluster decay. The field of nuclear clustering has become strongly influenced by the physics of radioactive beam facilities (reflected in the programme), and by the excitement that clustering may have an important impact on the structure of nuclei at the neutron drip-line. It was clear that since Nara the field had progressed substantially and that new themes had emerged and others had crystallized. Two particular topics resonated strongly condensates and nuclear molecules. These topics are thus likely to be central in the next cluster conference which will be held in 2011 in the Hungarian city of Debrechen. Martin Freer Participants and Cluster'07

Online Plasma Shape Reconstruction for EAST Tokamak

International Nuclear Information System (INIS)

Luo Zhengping; Xiao Bingjia; Zhu Yingfei; Yang Fei

2010-01-01

An online plasma shape reconstruction, based on the offline version of the EFIT code and MPI library, can be carried out between two adjacent shots in EAST. It combines online data acquisition, parallel calculation, and data storage together. The program on the master node of the cluster detects the termination of the discharge promptly, reads diagnostic data from the EAST mdsplus server on the completion of data storing, and writes the results onto the EFIT mdsplus server after the calculation is finished. These processes run automatically on a nine-nodes IBM blade center. The total time elapsed is about 1 second to several minutes, depending on the duration of the shot. With the results stored in the mdsplus server, it is convenient for operators and physicists to analyze the behavior of plasma using visualization tools.

Soft Measurement Modeling Based on Chaos Theory for Biochemical Oxygen Demand (BOD

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Junfei Qiao

2016-12-01

Full Text Available The precision of soft measurement for biochemical oxygen demand (BOD is always restricted due to various factors in the wastewater treatment plant (WWTP. To solve this problem, a new soft measurement modeling method based on chaos theory is proposed and is applied to BOD measurement in this paper. Phase space reconstruction (PSR based on Takens embedding theorem is used to extract more information from the limited datasets of the chaotic system. The WWTP is first testified as a chaotic system by the correlation dimension (D, the largest Lyapunov exponents (λ1, the Kolmogorov entropy (K of the BOD and other water quality parameters time series. Multivariate chaotic time series modeling method with principal component analysis (PCA and artificial neural network (ANN is then adopted to estimate the value of the effluent BOD. Simulation results show that the proposed approach has higher accuracy and better prediction ability than the corresponding modeling approaches not based on chaos theory.

Use of FPGA embedded processors for fast cluster reconstruction in the NA62 liquid krypton electromagnetic calorimeter

Science.gov (United States)

Badoni, D.; Bizzarri, M.; Bonaiuto, V.; Checcucci, B.; De Simone, N.; Federici, L.; Fucci, A.; Paoluzzi, G.; Papi, A.; Piccini, M.; Salamon, A.; Salina, G.; Santovetti, E.; Sargeni, F.; Venditti, S.

2014-01-01

The goal of the NA62 experiment at the CERN SPS is the measurement of the Branching Ratio of the very rare kaon decay K+→π+ ν bar nu with a 10% accuracy by collecting 100 events in two years of data taking. An efficient photon veto system is needed to reject the K+→π+ π0 background and a liquid krypton electromagnetic calorimeter will be used for this purpose in the 1-10 mrad angular region. The L0 trigger system for the calorimeter consists of a peak reconstruction algorithm implemented on FPGA by using a mixed parallel architecture based on soft core Altera NIOS II embedded processors together with custom VHDL modules. This solution allows an efficient and flexible reconstruction of the energy-deposition peak. The system will be totally composed of 36 TEL62 boards, 108 mezzanine cards and 215 high-performance FPGAs. We describe the design, current status and the results of the first performance tests.

Use of FPGA embedded processors for fast cluster reconstruction in the NA62 liquid krypton electromagnetic calorimeter

International Nuclear Information System (INIS)

Badoni, D; Fucci, A; Paoluzzi, G; Salamon, A; Salina, G; Bizzarri, M; Bonaiuto, V; Simone, N De; Federici, L; Sargeni, F; Checcucci, B; Papi, A; Piccini, M; Santovetti, E; Venditti, S

2014-01-01

The goal of the NA62 experiment at the CERN SPS is the measurement of the Branching Ratio of the very rare kaon decay K + →π +  ν ν-bar with a 10% accuracy by collecting 100 events in two years of data taking. An efficient photon veto system is needed to reject the K + →π +  π 0 background and a liquid krypton electromagnetic calorimeter will be used for this purpose in the 1-10 mrad angular region. The L0 trigger system for the calorimeter consists of a peak reconstruction algorithm implemented on FPGA by using a mixed parallel architecture based on soft core Altera NIOS II embedded processors together with custom VHDL modules. This solution allows an efficient and flexible reconstruction of the energy-deposition peak. The system will be totally composed of 36 TEL62 boards, 108 mezzanine cards and 215 high-performance FPGAs. We describe the design, current status and the results of the first performance tests

Application of 2D and 3D image technologies to characterise morphological attributes of grapevine clusters.

Science.gov (United States)

Tello, Javier; Cubero, Sergio; Blasco, José; Tardaguila, Javier; Aleixos, Nuria; Ibáñez, Javier

2016-10-01

Grapevine cluster morphology influences the quality and commercial value of wine and table grapes. It is routinely evaluated by subjective and inaccurate methods that do not meet the requirements set by the food industry. Novel two-dimensional (2D) and three-dimensional (3D) machine vision technologies emerge as promising tools for its automatic and fast evaluation. The automatic evaluation of cluster length, width and elongation was successfully achieved by the analysis of 2D images, significant and strong correlations with the manual methods being found (r = 0.959, 0.861 and 0.852, respectively). The classification of clusters according to their shape can be achieved by evaluating their conicity in different sections of the cluster. The geometric reconstruction of the morphological volume of the cluster from 2D features worked better than the direct 3D laser scanning system, showing a high correlation (r = 0.956) with the manual approach (water displacement method). In addition, we constructed and validated a simple linear regression model for cluster compactness estimation. It showed a high predictive capacity for both the training and validation subsets of clusters (R(2)  = 84.5 and 71.1%, respectively). The methodologies proposed in this work provide continuous and accurate data for the fast and objective characterisation of cluster morphology. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Architecture of the Yeast Mitochondrial Iron-Sulfur Cluster Assembly Machinery

Science.gov (United States)

Ranatunga, Wasantha; Gakh, Oleksandr; Galeano, Belinda K.; Smith, Douglas Y.; Söderberg, Christopher A. G.; Al-Karadaghi, Salam; Thompson, James R.; Isaya, Grazia

2016-01-01

The biosynthesis of Fe-S clusters is a vital process involving the delivery of elemental iron and sulfur to scaffold proteins via molecular interactions that are still poorly defined. We reconstituted a stable, functional complex consisting of the iron donor, Yfh1 (yeast frataxin homologue 1), and the Fe-S cluster scaffold, Isu1, with 1:1 stoichiometry, [Yfh1]24·[Isu1]24. Using negative staining transmission EM and single particle analysis, we obtained a three-dimensional reconstruction of this complex at a resolution of ∼17 Å. In addition, via chemical cross-linking, limited proteolysis, and mass spectrometry, we identified protein-protein interaction surfaces within the complex. The data together reveal that [Yfh1]24·[Isu1]24 is a roughly cubic macromolecule consisting of one symmetric Isu1 trimer binding on top of one symmetric Yfh1 trimer at each of its eight vertices. Furthermore, molecular modeling suggests that two subunits of the cysteine desulfurase, Nfs1, may bind symmetrically on top of two adjacent Isu1 trimers in a manner that creates two putative [2Fe-2S] cluster assembly centers. In each center, conserved amino acids known to be involved in sulfur and iron donation by Nfs1 and Yfh1, respectively, are in close proximity to the Fe-S cluster-coordinating residues of Isu1. We suggest that this architecture is suitable to ensure concerted and protected transfer of potentially toxic iron and sulfur atoms to Isu1 during Fe-S cluster assembly. PMID:26941001

MCBT: Multi-Hop Cluster Based Stable Backbone Trees for Data Collection and Dissemination in WSNs

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Tae-Jin Lee

2009-07-01

Full Text Available We propose a stable backbone tree construction algorithm using multi-hop clusters for wireless sensor networks (WSNs. The hierarchical cluster structure has advantages in data fusion and aggregation. Energy consumption can be decreased by managing nodes with cluster heads. Backbone nodes, which are responsible for performing and managing multi-hop communication, can reduce the communication overhead such as control traffic and minimize the number of active nodes. Previous backbone construction algorithms, such as Hierarchical Cluster-based Data Dissemination (HCDD and Multicluster, Mobile, Multimedia radio network (MMM, consume energy quickly. They are designed without regard to appropriate factors such as residual energy and degree (the number of connections or edges to other nodes of a node for WSNs. Thus, the network is quickly disconnected or has to reconstruct a backbone. We propose a distributed algorithm to create a stable backbone by selecting the nodes with higher energy or degree as the cluster heads. This increases the overall network lifetime. Moreover, the proposed method balances energy consumption by distributing the traffic load among nodes around the cluster head. In the simulation, the proposed scheme outperforms previous clustering schemes in terms of the average and the standard deviation of residual energy or degree of backbone nodes, the average residual energy of backbone nodes after disseminating the sensed data, and the network lifetime.

Discriminative clustering on manifold for adaptive transductive classification.

Science.gov (United States)

Zhang, Zhao; Jia, Lei; Zhang, Min; Li, Bing; Zhang, Li; Li, Fanzhang

2017-10-01

In this paper, we mainly propose a novel adaptive transductive label propagation approach by joint discriminative clustering on manifolds for representing and classifying high-dimensional data. Our framework seamlessly combines the unsupervised manifold learning, discriminative clustering and adaptive classification into a unified model. Also, our method incorporates the adaptive graph weight construction with label propagation. Specifically, our method is capable of propagating label information using adaptive weights over low-dimensional manifold features, which is different from most existing studies that usually predict the labels and construct the weights in the original Euclidean space. For transductive classification by our formulation, we first perform the joint discriminative K-means clustering and manifold learning to capture the low-dimensional nonlinear manifolds. Then, we construct the adaptive weights over the learnt manifold features, where the adaptive weights are calculated through performing the joint minimization of the reconstruction errors over features and soft labels so that the graph weights can be joint-optimal for data representation and classification. Using the adaptive weights, we can easily estimate the unknown labels of samples. After that, our method returns the updated weights for further updating the manifold features. Extensive simulations on image classification and segmentation show that our proposed algorithm can deliver the state-of-the-art performance on several public datasets. Copyright © 2017 Elsevier Ltd. All rights reserved.

Genetic Variability among Lucerne Cultivars Based on Biochemical (SDS-PAGE) and Morphological Markers

Science.gov (United States)

Farshadfar, M.; Farshadfar, E.

The present research was conducted to determine the genetic variability of 18 Lucerne cultivars, based on morphological and biochemical markers. The traits studied were plant height, tiller number, biomass, dry yield, dry yield/biomass, dry leaf/dry yield, macro and micro elements, crude protein, dry matter, crude fiber and ash percentage and SDS- PAGE in seed and leaf samples. Field experiments included 18 plots of two meter rows. Data based on morphological, chemical and SDS-PAGE markers were analyzed using SPSSWIN soft ware and the multivariate statistical procedures: cluster analysis (UPGMA), principal component. Analysis of analysis of variance and mean comparison for morphological traits reflected significant differences among genotypes. Genotype 13 and 15 had the greatest values for most traits. The Genotypic Coefficient of Variation (GCV), Phenotypic Coefficient of Variation (PCV) and Heritability (Hb) parameters for different characters raged from 12.49 to 26.58% for PCV, hence the GCV ranged from 6.84 to 18.84%. The greatest value of Hb was 0.94 for stem number. Lucerne genotypes could be classified, based on morphological traits, into four clusters and 94% of the variance among the genotypes was explained by two PCAs: Based on chemical traits they were classified into five groups and 73.492% of variance was explained by four principal components: Dry matter, protein, fiber, P, K, Na, Mg and Zn had higher variance. Genotypes based on the SDS-PAGE patterns all genotypes were classified into three clusters. The greatest genetic distance was between cultivar 10 and others, therefore they would be suitable parent in a breeding program.

Formation of stable products from cluster-cluster collisions

International Nuclear Information System (INIS)

Alamanova, Denitsa; Grigoryan, Valeri G; Springborg, Michael

2007-01-01

The formation of stable products from copper cluster-cluster collisions is investigated by using classical molecular-dynamics simulations in combination with an embedded-atom potential. The dependence of the product clusters on impact energy, relative orientation of the clusters, and size of the clusters is studied. The structures and total energies of the product clusters are analysed and compared with those of the colliding clusters before impact. These results, together with the internal temperature, are used in obtaining an increased understanding of cluster fusion processes

Biochemical Process Development and Integration | Bioenergy | NREL

Science.gov (United States)

Biochemical Process Development and Integration Biochemical Process Development and Integration Our conversion and separation processes to pilot-scale integrated process development and scale up. We also Publications Accounting for all sugar produced during integrated production of ethanol from lignocellulosic

Document clustering methods, document cluster label disambiguation methods, document clustering apparatuses, and articles of manufacture

Science.gov (United States)

Sanfilippo, Antonio [Richland, WA; Calapristi, Augustin J [West Richland, WA; Crow, Vernon L [Richland, WA; Hetzler, Elizabeth G [Kennewick, WA; Turner, Alan E [Kennewick, WA

2009-12-22

Document clustering methods, document cluster label disambiguation methods, document clustering apparatuses, and articles of manufacture are described. In one aspect, a document clustering method includes providing a document set comprising a plurality of documents, providing a cluster comprising a subset of the documents of the document set, using a plurality of terms of the documents, providing a cluster label indicative of subject matter content of the documents of the cluster, wherein the cluster label comprises a plurality of word senses, and selecting one of the word senses of the cluster label.

Robust water fat separated dual-echo MRI by phase-sensitive reconstruction.

Science.gov (United States)

Romu, Thobias; Dahlström, Nils; Leinhard, Olof Dahlqvist; Borga, Magnus

2017-09-01

The purpose of this work was to develop and evaluate a robust water-fat separation method for T1-weighted symmetric two-point Dixon data. A method for water-fat separation by phase unwrapping of the opposite-phase images by phase-sensitive reconstruction (PSR) is introduced. PSR consists of three steps; (1), identification of clusters of tissue voxels; (2), unwrapping of the phase in each cluster by solving Poisson's equation; and (3), finding the correct sign of each unwrapped opposite-phase cluster, so that the water-fat images are assigned the correct identities. Robustness was evaluated by counting the number of water-fat swap artifacts in a total of 733 image volumes. The method was also compared to commercial software. In the water-fat separated image volumes, the PSR method failed to unwrap the phase of one cluster and misclassified 10. One swap was observed in areas affected by motion and was constricted to the affected area. Twenty swaps were observed surrounding susceptibility artifacts, none of which spread outside the artifact affected regions. The PSR method had fewer swaps when compared to commercial software. The PSR method can robustly produce water-fat separated whole-body images based on symmetric two-echo spoiled gradient echo images, under both ideal conditions and in the presence of common artifacts. Magn Reson Med 78:1208-1216, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Performance of the reconstruction algorithms of the FIRST experiment pixel sensors vertex detector

CERN Document Server

Rescigno, R; Juliani, D; Spiriti, E; Baudot, J; Abou-Haidar, Z; Agodi, C; Alvarez, M A G; Aumann, T; Battistoni, G; Bocci, A; Böhlen, T T; Boudard, A; Brunetti, A; Carpinelli, M; Cirrone, G A P; Cortes-Giraldo, M A; Cuttone, G; De Napoli, M; Durante, M; Gallardo, M I; Golosio, B; Iarocci, E; Iazzi, F; Ickert, G; Introzzi, R; Krimmer, J; Kurz, N; Labalme, M; Leifels, Y; Le Fevre, A; Leray, S; Marchetto, F; Monaco, V; Morone, M C; Oliva, P; Paoloni, A; Patera, V; Piersanti, L; Pleskac, R; Quesada, J M; Randazzo, N; Romano, F; Rossi, D; Rousseau, M; Sacchi, R; Sala, P; Sarti, A; Scheidenberger, C; Schuy, C; Sciubba, A; Sfienti, C; Simon, H; Sipala, V; Tropea, S; Vanstalle, M; Younis, H

2014-01-01

Hadrontherapy treatments use charged particles (e.g. protons and carbon ions) to treat tumors. During a therapeutic treatment with carbon ions, the beam undergoes nuclear fragmentation processes giving rise to significant yields of secondary charged particles. An accurate prediction of these production rates is necessary to estimate precisely the dose deposited into the tumours and the surrounding healthy tissues. Nowadays, a limited set of double differential carbon fragmentation cross-section is available. Experimental data are necessary to benchmark Monte Carlo simulations for their use in hadrontherapy. The purpose of the FIRST experiment is to study nuclear fragmentation processes of ions with kinetic energy in the range from 100 to 1000 MeV/u. Tracks are reconstructed using information from a pixel silicon detector based on the CMOS technology. The performances achieved using this device for hadrontherapy purpose are discussed. For each reconstruction step (clustering, tracking and vertexing), different...

Proteomic Assessment of Biochemical Pathways That Are Critical to Nickel-Induced Toxicity Responses in Human Epithelial Cells

Science.gov (United States)

Ge, Yue; Bruno, Maribel; Haykal-Coates, Najwa; Wallace, Kathleen; Andrews, Debora; Swank, Adam; Winnik, Witold; Ross, Jeffrey A.

2016-01-01

Understanding the mechanisms underlying toxicity initiated by nickel, a ubiquitous environmental contaminant and known human carcinogen is necessary for proper assessment of its risks to human and environment. Among a variety of toxic mechanisms, disruption of protein responses and protein response-based biochemical pathways represents a key mechanism through which nickel induces cytotoxicity and carcinogenesis. To identify protein responses and biochemical pathways that are critical to nickel-induced toxicity responses, we measured cytotoxicity and changes in expression and phosphorylation status of 14 critical biochemical pathway regulators in human BEAS-2B cells exposed to four concentrations of nickel using an integrated proteomic approach. A subset of the pathway regulators, including interleukin-6, and JNK, were found to be linearly correlated with cell viability, and may function as molecular determinants of cytotoxic responses of BEAS-2B cells to nickel exposures. In addition, 128 differentially expressed proteins were identified by two dimensional electrophoresis (2-DE) and mass spectrometry. Principal component analysis, hierarchical cluster analyses, and ingenuity signaling pathway analysis (IPA) identified putative nickel toxicity pathways. Some of the proteins and pathways identified have not previously been linked to nickel toxicity. Based on the consistent results obtained from both ELISA and 2-DE proteomic analysis, we propose a core signaling pathway regulating cytotoxic responses of human BEAS-2B cells to nickel exposures, which integrates a small set of proteins involved in glycolysis and gluconeogenesis pathways, apoptosis, protein degradation, and stress responses including inflammation and oxidative stress. PMID:27626938

Biochemical and structural insights into xylan utilization by the thermophilic bacterium Caldanaerobius polysaccharolyticus.

Science.gov (United States)

Han, Yejun; Agarwal, Vinayak; Dodd, Dylan; Kim, Jason; Bae, Brian; Mackie, Roderick I; Nair, Satish K; Cann, Isaac K O

2012-10-12

Hemicellulose is the next most abundant plant cell wall component after cellulose. The abundance of hemicellulose such as xylan suggests that their hydrolysis and conversion to biofuels can improve the economics of bioenergy production. In an effort to understand xylan hydrolysis at high temperatures, we sequenced the genome of the thermophilic bacterium Caldanaerobius polysaccharolyticus. Analysis of the partial genome sequence revealed a gene cluster that contained both hydrolytic enzymes and also enzymes key to the pentose-phosphate pathway. The hydrolytic enzymes in the gene cluster were demonstrated to convert products from a large endoxylanase (Xyn10A) predicted to anchor to the surface of the bacterium. We further use structural and calorimetric studies to demonstrate that the end products of Xyn10A hydrolysis of xylan are recognized and bound by XBP1, a putative solute-binding protein, likely for transport into the cell. The XBP1 protein showed preference for xylo-oligosaccharides as follows: xylotriose > xylobiose > xylotetraose. To elucidate the structural basis for the oligosaccharide preference, we solved the co-crystal structure of XBP1 complexed with xylotriose to a 1.8-Å resolution. Analysis of the biochemical data in the context of the co-crystal structure reveals the molecular underpinnings of oligosaccharide length specificity.

Planck intermediate results: V. Pressure profiles of galaxy clusters from the Sunyaev-Zeldovich effect

DEFF Research Database (Denmark)

Bartlett, J.G.; Cardoso, J.-F.; Castex, G.

2013-01-01

that most clusters are individually detected at least out to R500. By stacking the radial profiles, we have statistically detected the radial SZ signal out to 3 × R500, i.e., at a density contrast of about 50-100, though the dispersion about the mean profile dominates the statistical errors across the whole......Taking advantage of the all-sky coverage and broadfrequency range of the Planck satellite, we study the Sunyaev-Zeldovich (SZ) and pressure profiles of 62 nearby massive clusters detected at high significance in the 14-month nominal survey. Careful reconstruction of the SZ signal indicates...... flatter than most predictions from numerical simulations. Combining the SZ and X-ray observed profiles into a joint fit to a generalised pressure profile gives best-fit parameters [P0,c500,γ, α,β] = [6.41,1.81,0.31,1.33,4.13]. Using a reasonable hypothesis for the gas temperature in the cluster outskirts...

Ge clusters and wetting layers forming from granular films on the Si(001) surface

International Nuclear Information System (INIS)

Storozhevykh, M S; Arapkina, L V; Yuryev, V A

2016-01-01

The report studies the transformation of a Ge granular film deposited on the Si(001) surface at room temperature into a Ge/Si(001) heterostructure as a result of rapid heating and annealing at 600 °C. As a result of the short-term annealing at 600 °C in conditions of a closed system, the Ge granular film transforms into a usual wetting layer and Ge clusters with multimodal size distribution and Ge oval drops having the highest number density. After the long-term thermal treatment of the Ge film at the same temperature, Ge drops disappear; the large clusters increase their sizes at the expense of the smaller ones. The total density of Ge clusters on the surface drastically decreases. The wetting layer mixed c(4 x 2) + p(2 x 2) reconstruction transforms into a single c(4 x 2) one which is likely to be thermodynamically favoured. Pyramids or domes are not observed on the surface after any annealing. (paper)

Computed Tomography Image Quality Evaluation of a New Iterative Reconstruction Algorithm in the Abdomen (Adaptive Statistical Iterative Reconstruction-V) a Comparison With Model-Based Iterative Reconstruction, Adaptive Statistical Iterative Reconstruction, and Filtered Back Projection Reconstructions.

Science.gov (United States)

Goodenberger, Martin H; Wagner-Bartak, Nicolaus A; Gupta, Shiva; Liu, Xinming; Yap, Ramon Q; Sun, Jia; Tamm, Eric P; Jensen, Corey T

The purpose of this study was to compare abdominopelvic computed tomography images reconstructed with adaptive statistical iterative reconstruction-V (ASIR-V) with model-based iterative reconstruction (Veo 3.0), ASIR, and filtered back projection (FBP). Abdominopelvic computed tomography scans for 36 patients (26 males and 10 females) were reconstructed using FBP, ASIR (80%), Veo 3.0, and ASIR-V (30%, 60%, 90%). Mean ± SD patient age was 32 ± 10 years with mean ± SD body mass index of 26.9 ± 4.4 kg/m. Images were reviewed by 2 independent readers in a blinded, randomized fashion. Hounsfield unit, noise, and contrast-to-noise ratio (CNR) values were calculated for each reconstruction algorithm for further comparison. Phantom evaluation of low-contrast detectability (LCD) and high-contrast resolution was performed. Adaptive statistical iterative reconstruction-V 30%, ASIR-V 60%, and ASIR 80% were generally superior qualitatively compared with ASIR-V 90%, Veo 3.0, and FBP (P ASIR-V 60% with respective CNR values of 5.54 ± 2.39, 8.78 ± 3.15, and 3.49 ± 1.77 (P ASIR 80% had the best and worst spatial resolution, respectively. Adaptive statistical iterative reconstruction-V 30% and ASIR-V 60% provided the best combination of qualitative and quantitative performance. Adaptive statistical iterative reconstruction 80% was equivalent qualitatively, but demonstrated inferior spatial resolution and LCD.

List-mode PET image reconstruction for motion correction using the Intel XEON PHI co-processor

Science.gov (United States)

Ryder, W. J.; Angelis, G. I.; Bashar, R.; Gillam, J. E.; Fulton, R.; Meikle, S.

2014-03-01

List-mode image reconstruction with motion correction is computationally expensive, as it requires projection of hundreds of millions of rays through a 3D array. To decrease reconstruction time it is possible to use symmetric multiprocessing computers or graphics processing units. The former can have high financial costs, while the latter can require refactoring of algorithms. The Xeon Phi is a new co-processor card with a Many Integrated Core architecture that can run 4 multiple-instruction, multiple data threads per core with each thread having a 512-bit single instruction, multiple data vector register. Thus, it is possible to run in the region of 220 threads simultaneously. The aim of this study was to investigate whether the Xeon Phi co-processor card is a viable alternative to an x86 Linux server for accelerating List-mode PET image reconstruction for motion correction. An existing list-mode image reconstruction algorithm with motion correction was ported to run on the Xeon Phi coprocessor with the multi-threading implemented using pthreads. There were no differences between images reconstructed using the Phi co-processor card and images reconstructed using the same algorithm run on a Linux server. However, it was found that the reconstruction runtimes were 3 times greater for the Phi than the server. A new version of the image reconstruction algorithm was developed in C++ using OpenMP for mutli-threading and the Phi runtimes decreased to 1.67 times that of the host Linux server. Data transfer from the host to co-processor card was found to be a rate-limiting step; this needs to be carefully considered in order to maximize runtime speeds. When considering the purchase price of a Linux workstation with Xeon Phi co-processor card and top of the range Linux server, the former is a cost-effective computation resource for list-mode image reconstruction. A multi-Phi workstation could be a viable alternative to cluster computers at a lower cost for medical imaging

Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea

Directory of Open Access Journals (Sweden)

Wolf Yuri I

2007-11-01

Full Text Available Abstract Background An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. Shortly after multiple genome sequences of bacteria, archaea, and unicellular eukaryotes became available, an attempt on such a classification was implemented in Clusters of Orthologous Groups of proteins (COGs. Rapid accumulation of genome sequences creates opportunities for refining COGs but also represents a challenge because of error amplification. One of the practical strategies involves construction of refined COGs for phylogenetically compact subsets of genomes. Results New Archaeal Clusters of Orthologous Genes (arCOGs were constructed for 41 archaeal genomes (13 Crenarchaeota, 27 Euryarchaeota and one Nanoarchaeon using an improved procedure that employs a similarity tree between smaller, group-specific clusters, semi-automatically partitions orthology domains in multidomain proteins, and uses profile searches for identification of remote orthologs. The annotation of arCOGs is a consensus between three assignments based on the COGs, the CDD database, and the annotations of homologs in the NR database. The 7538 arCOGs, on average, cover ~88% of the genes in a genome compared to a ~76% coverage in COGs. The finer granularity of ortholog identification in the arCOGs is apparent from the fact that 4538 arCOGs correspond to 2362 COGs; ~40% of the arCOGs are new. The archaeal gene core (protein-coding genes found in all 41 genome consists of 166 arCOGs. The arCOGs were used to reconstruct gene loss and gene gain events during archaeal evolution and gene sets of ancestral forms. The Last Archaeal Common Ancestor (LACA is conservatively estimated to possess 996 genes compared to 1245 and 1335 genes for the last common ancestors of Crenarchaeota and Euryarchaeota, respectively. It is inferred that LACA was a chemoautotrophic hyperthermophile

Nuclear clustering - a cluster core model study

International Nuclear Information System (INIS)

Paul Selvi, G.; Nandhini, N.; Balasubramaniam, M.

2015-01-01

Nuclear clustering, similar to other clustering phenomenon in nature is a much warranted study, since it would help us in understanding the nature of binding of the nucleons inside the nucleus, closed shell behaviour when the system is highly deformed, dynamics and structure at extremes. Several models account for the clustering phenomenon of nuclei. We present in this work, a cluster core model study of nuclear clustering in light mass nuclei

Analysis of protein-protein docking decoys using interaction fingerprints: application to the reconstruction of CaM-ligand complexes

Directory of Open Access Journals (Sweden)

Uchikoga Nobuyuki

2010-05-01

Full Text Available Abstract Background Protein-protein docking for proteins with large conformational changes was analyzed by using interaction fingerprints, one of the scales for measuring similarities among complex structures, utilized especially for searching near-native protein-ligand or protein-protein complex structures. Here, we have proposed a combined method for analyzing protein-protein docking by taking large conformational changes into consideration. This combined method consists of ensemble soft docking with multiple protein structures, refinement of complexes, and cluster analysis using interaction fingerprints and energy profiles. Results To test for the applicability of this combined method, various CaM-ligand complexes were reconstructed from the NMR structures of unbound CaM. For the purpose of reconstruction, we used three known CaM-ligands, namely, the CaM-binding peptides of cyclic nucleotide gateway (CNG, CaM kinase kinase (CaMKK and the plasma membrane Ca2+ ATPase pump (PMCA, and thirty-one structurally diverse CaM conformations. For each ligand, 62000 CaM-ligand complexes were generated in the docking step and the relationship between their energy profiles and structural similarities to the native complex were analyzed using interaction fingerprint and RMSD. Near-native clusters were obtained in the case of CNG and CaMKK. Conclusions The interaction fingerprint method discriminated near-native structures better than the RMSD method in cluster analysis. We showed that a combined method that includes the interaction fingerprint is very useful for protein-protein docking analysis of certain cases.

Detecting groups of coevolving positions in a molecule: a clustering approach

Directory of Open Access Journals (Sweden)

Galtier Nicolas

2007-11-01

Full Text Available Abstract Background Although the patterns of co-substitutions in RNA is now well characterized, detection of coevolving positions in proteins remains a difficult task. It has been recognized that the signal is typically weak, due to the fact that (i amino-acid are characterized by various biochemical properties, so that distinct amino acids changes are not functionally equivalent, and (ii a given mutation can be compensated by more than one mutation, at more than one position. Results We present a new method based on phylogenetic substitution mapping. The two above-mentioned problems are addressed by (i the introduction of a weighted mapping, which accounts for the biochemical effects (volume, polarity, charge of amino-acid changes, (ii the use of a clustering approach to detect groups of coevolving sites of virtually any size, and (iii the distinction between biochemical compensation and other coevolutionary mechanisms. We apply this methodology to a previously studied data set of bacterial ribosomal RNA, and to three protein data sets (myoglobin of vertebrates, S-locus Receptor Kinase and Methionine Amino-Peptidase. Conclusion We succeed in detecting groups of sites which significantly depart the null hypothesis of independence. Group sizes range from pairs to groups of size ≃ 10, depending on the substitution weights used. The structural and functional relevance of these groups of sites are assessed, and the various evolutionary processes potentially generating correlated substitution patterns are discussed.

Cluster fusion algorithm: application to Lennard-Jones clusters

DEFF Research Database (Denmark)

Solov'yov, Ilia; Solov'yov, Andrey V.; Greiner, Walter

2006-01-01

paths up to the cluster size of 150 atoms. We demonstrate that in this way all known global minima structures of the Lennard-Jones clusters can be found. Our method provides an efficient tool for the calculation and analysis of atomic cluster structure. With its use we justify the magic number sequence......We present a new general theoretical framework for modelling the cluster structure and apply it to description of the Lennard-Jones clusters. Starting from the initial tetrahedral cluster configuration, adding new atoms to the system and absorbing its energy at each step, we find cluster growing...... for the clusters of noble gas atoms and compare it with experimental observations. We report the striking correspondence of the peaks in the dependence of the second derivative of the binding energy per atom on cluster size calculated for the chain of the Lennard-Jones clusters based on the icosahedral symmetry...

Cluster fusion algorithm: application to Lennard-Jones clusters

DEFF Research Database (Denmark)

Solov'yov, Ilia; Solov'yov, Andrey V.; Greiner, Walter

2008-01-01

paths up to the cluster size of 150 atoms. We demonstrate that in this way all known global minima structures of the Lennard-Jones clusters can be found. Our method provides an efficient tool for the calculation and analysis of atomic cluster structure. With its use we justify the magic number sequence......We present a new general theoretical framework for modelling the cluster structure and apply it to description of the Lennard-Jones clusters. Starting from the initial tetrahedral cluster configuration, adding new atoms to the system and absorbing its energy at each step, we find cluster growing...... for the clusters of noble gas atoms and compare it with experimental observations. We report the striking correspondence of the peaks in the dependence of the second derivative of the binding energy per atom on cluster size calculated for the chain of the Lennard-Jones clusters based on the icosahedral symmetry...

Biochemical basis for the action of radioprotective drugs

International Nuclear Information System (INIS)

Romantsev, E.F.; Blokhina, V.D.; Zhulanova, Z.I.; Koshcheenko, N.N.; Filippovich, I.V.

1977-01-01

The hypothesis of complex biochemical mechanism of action of radioprotective drugs is described. Shortly after injection of radioprotective aminothiols into animals the inhibition of radiosensitive biochemical processes: DNA and RNA synthesis, protein synthesis and oxidative phosphorylation has been observed. The molecular mechanism of these phenomena consists of radioprotectors ability to form adsorption, thioester, amide, and disulphide bonds with appropriate enzymes. The curve reflecting the formation and breakdown of mixed disulphides between radioprotectors and proteins coincides well with that reflecting the radioprotective effect dependence on time. The radiobiological significance of molecular interactions observed may be interpreted as the diminution in ''spoiled'' molecules formation (inhibition of replication) and elevation in repartion rate. The inhibition of biochemical processes has the reversible nature and last for short time. The drugs acting according to so-called oxygen effect protect also by means of biochemical mechanisms. The molecular mechanism is mediated through their ability to bind to receptors, and biologically important molecules and macromolecules. As a result the inhibition of radiosensitive processes occurs, the ''spoiled'' molecules number is diminished and reparation takes place more easily. The idea on the complex biochemical mechanism of action of radioprotectors correlates with the proposal on complex biochemical mechanism responsible for interphase death occured after irradiation

Biochemical reactions of the organism

International Nuclear Information System (INIS)

Fedorova, A.V.

1984-01-01

Effects of mercury, strontium chloride, GMDA, trichlorfon as well as some radionuclides ( 89 Sr, 137 Cs, 203 Hg) were studied on rats. Changes in biochemical parameters (histamine content, activity of cholinesterase and histaminase) are noted. Most noticeable changes were observed in enzymatic activity. Distortion of enzymatic systems and accumulation of intermediate exchange and decay products of tissues in excess quantities affecting other systems can be the reason for changes in the organism. The observed changes in biochemical parameters should be necessarily taken into account at hygienic regulations of harmful effects of enviroment

Image Reconstruction. Chapter 13

Energy Technology Data Exchange (ETDEWEB)

Nuyts, J. [Department of Nuclear Medicine and Medical Imaging Research Center, Katholieke Universiteit Leuven, Leuven (Belgium); Matej, S. [Medical Image Processing Group, Department of Radiology, University of Pennsylvania, Philadelphia, PA (United States)

2014-12-15

This chapter discusses how 2‑D or 3‑D images of tracer distribution can be reconstructed from a series of so-called projection images acquired with a gamma camera or a positron emission tomography (PET) system [13.1]. This is often called an ‘inverse problem’. The reconstruction is the inverse of the acquisition. The reconstruction is called an inverse problem because making software to compute the true tracer distribution from the acquired data turns out to be more difficult than the ‘forward’ direction, i.e. making software to simulate the acquisition. There are basically two approaches to image reconstruction: analytical reconstruction and iterative reconstruction. The analytical approach is based on mathematical inversion, yielding efficient, non-iterative reconstruction algorithms. In the iterative approach, the reconstruction problem is reduced to computing a finite number of image values from a finite number of measurements. That simplification enables the use of iterative instead of mathematical inversion. Iterative inversion tends to require more computer power, but it can cope with more complex (and hopefully more accurate) models of the acquisition process.

Coordinate reconstruction using box reconstruction and projection of X-ray photo

International Nuclear Information System (INIS)

Achmad Suntoro

2011-01-01

Some mathematical formula have been derived for a process of reconstruction to define the coordinate of any point relative to a pre set coordinate system. The process of reconstruction uses a reconstruction box in which each edge's length of the box is known, each top-bottom face and left-right face of the box having a cross marker, and the top face and the right face of the box as plane projections by X-ray source in perspective projection -system. Using the data of the two X-ray projection images, any point inside the reconstruction box, as long as its projection is recorded in the two photos, will be determined its coordinate relative to the midpoint of the reconstruction box as the central point coordinates. (author)

Modelling of Track Reconstruction Inside Jets with the 2016 ATLAS $\\sqrt{s}= 13$ TeV pp dataset

CERN Document Server

The ATLAS collaboration

2017-01-01

Inside the core of high transverse momentum jets, the particle density is so high that the tracks of charged particles begin to overlap, and due to the different charged particles, pixel clusters in the ATLAS inner detector begin to merge. This high density environment results in a degradation of track reconstruction. Recent innovations to the ambiguity solving in the charged particle pattern recognition partially mitigate the loss in performance. However, it is critical for all physics results using tracks inside jets that the algorithms be well modeled by simulation. This note presents new measurements of the charged particle reconstruction inefficiency and fake rate inside jets with the $\\sqrt{s}=13$ TeV $pp$ dataset collected by the ATLAS experiment at the LHC in 2016.

Segmentation-DrivenTomographic Reconstruction

DEFF Research Database (Denmark)

Kongskov, Rasmus Dalgas

such that the segmentation subsequently can be carried out by use of a simple segmentation method, for instance just a thresholding method. We tested the advantages of going from a two-stage reconstruction method to a one stage segmentation-driven reconstruction method for the phase contrast tomography reconstruction......The tomographic reconstruction problem is concerned with creating a model of the interior of an object from some measured data, typically projections of the object. After reconstructing an object it is often desired to segment it, either automatically or manually. For computed tomography (CT...

Hierarchical model generation for architecture reconstruction using laser-scanned point clouds

Science.gov (United States)

Ning, Xiaojuan; Wang, Yinghui; Zhang, Xiaopeng

2014-06-01

Architecture reconstruction using terrestrial laser scanner is a prevalent and challenging research topic. We introduce an automatic, hierarchical architecture generation framework to produce full geometry of architecture based on a novel combination of facade structures detection, detailed windows propagation, and hierarchical model consolidation. Our method highlights the generation of geometric models automatically fitting the design information of the architecture from sparse, incomplete, and noisy point clouds. First, the planar regions detected in raw point clouds are interpreted as three-dimensional clusters. Then, the boundary of each region extracted by projecting the points into its corresponding two-dimensional plane is classified to obtain detailed shape structure elements (e.g., windows and doors). Finally, a polyhedron model is generated by calculating the proposed local structure model, consolidated structure model, and detailed window model. Experiments on modeling the scanned real-life buildings demonstrate the advantages of our method, in which the reconstructed models not only correspond to the information of architectural design accurately, but also satisfy the requirements for visualization and analysis.

Prevalence of biochemical and immunological abnormalities in ...

African Journals Online (AJOL)

Tile prevalence of biochemical and immunological abnormalities was studied in a group of 256 patients with rheumatoid arthritis (104 coloureds, 100 whites and 52 blacks). The most common biochemical abnormalities detected were a reduction in the serum creatinine value (43,4%), raised globulins (39,7%), raised serum ...

[Biochemical diagnostics of fatal opium intoxication].

Science.gov (United States)

Papyshev, I P; Astashkina, O G; Tuchik, E S; Nikolaev, B S; Cherniaev, A L

2013-01-01

Biochemical diagnostics of fatal opium intoxication remains a topical problem in forensic medical science and practice. We investigated materials obtained in the course of forensic medical expertise of the cases of fatal opium intoxication. The study revealed significant differences between myoglobin levels in blood, urine, myocardium, and skeletal muscles. The proposed approach to biochemical diagnostics of fatal opium intoxication enhances the accuracy and the level of evidence of expert conclusions.

Comprehensive cluster analysis with Transitivity Clustering.

Science.gov (United States)

Wittkop, Tobias; Emig, Dorothea; Truss, Anke; Albrecht, Mario; Böcker, Sebastian; Baumbach, Jan

2011-03-01

Transitivity Clustering is a method for the partitioning of biological data into groups of similar objects, such as genes, for instance. It provides integrated access to various functions addressing each step of a typical cluster analysis. To facilitate this, Transitivity Clustering is accessible online and offers three user-friendly interfaces: a powerful stand-alone version, a web interface, and a collection of Cytoscape plug-ins. In this paper, we describe three major workflows: (i) protein (super)family detection with Cytoscape, (ii) protein homology detection with incomplete gold standards and (iii) clustering of gene expression data. This protocol guides the user through the most important features of Transitivity Clustering and takes ∼1 h to complete.

Adsorption behavior and electronic properties of Pdn (n ≤ 10) clusters on silicon carbide nanotubes: a first-principles study

International Nuclear Information System (INIS)

Wang Jianguang; Ma Li; Wang Guanghou

2013-01-01

First-principles calculations have been carried out to investigate the adsorption of Pd n (n ≤ 10) clusters on the single-walled (8, 0) and (5, 5) SiC nanotubes (SiCNTs). We find that the Pd n clusters can be stably adsorbed on the outer surfaces of both SiCNTs through an exothermic adsorption process. The adsorption energies of the Pd n clusters on the (8, 0) SiCNT are generally larger than those of clusters on the (5, 5) SiCNT. The number of bonds between the Pd n clusters and the SiCNTs increases with increasing cluster size. The Pd atoms adjacent to the SiCNTs adsorb preferentially on the bridge sites over an axial Si–C bond. The adsorption leads to elongation of the Pd–Pd bond lengths and structural reconstruction for the Pd n clusters. Moreover, the adsorbed Pd n clusters show two-layered structures at the cluster size n ≥ 4. We also find that the adsorbed Pd n clusters induce some impurity states within the band gap of the pristine SiCNTs and the strong pd hybridization near the Fermi level, thereby reducing the band gap. The charge transfer from the SiCNTs to the Pd atoms that occurs is observed for all the systems considered. Due to the strong interactions between the Pd n clusters and the SiCNTs, most adsorbed Pd n clusters exhibit zero magnetic moment. (paper)

Cluster-cluster correlations and constraints on the correlation hierarchy

Science.gov (United States)

Hamilton, A. J. S.; Gott, J. R., III

1988-01-01

The hypothesis that galaxies cluster around clusters at least as strongly as they cluster around galaxies imposes constraints on the hierarchy of correlation amplitudes in hierachical clustering models. The distributions which saturate these constraints are the Rayleigh-Levy random walk fractals proposed by Mandelbrot; for these fractal distributions cluster-cluster correlations are all identically equal to galaxy-galaxy correlations. If correlation amplitudes exceed the constraints, as is observed, then cluster-cluster correlations must exceed galaxy-galaxy correlations, as is observed.

Analysis of NFU-1 metallocofactor binding-site substitutions-impacts on iron-sulfur cluster coordination and protein structure and function.

Science.gov (United States)

Wesley, Nathaniel A; Wachnowsky, Christine; Fidai, Insiya; Cowan, J A

2017-11-01

Iron-sulfur (Fe/S) clusters are ancient prosthetic groups found in numerous metalloproteins and are conserved across all kingdoms of life due to their diverse, yet essential functional roles. Genetic mutations to a specific subset of mitochondrial Fe/S cluster delivery proteins are broadly categorized as disease-related under multiple mitochondrial dysfunction syndrome (MMDS), with symptoms indicative of a general failure of the metabolic system. Multiple mitochondrial dysfunction syndrome 1 (MMDS1) arises as a result of the missense mutation in NFU1, an Fe/S cluster scaffold protein, which substitutes a glycine near the Fe/S cluster-binding pocket to a cysteine (p.Gly208Cys). This substitution has been shown to promote protein dimerization such that cluster delivery to NFU1 is blocked, preventing downstream cluster trafficking. However, the possibility of this additional cysteine, located adjacent to the cluster-binding site, serving as an Fe/S cluster ligand has not yet been explored. To fully understand the consequences of this Gly208Cys replacement, complementary substitutions at the Fe/S cluster-binding pocket for native and Gly208Cys NFU1 were made, along with six other variants. Herein, we report the results of an investigation on the effect of these substitutions on both cluster coordination and NFU1 structure and function. The data suggest that the G208C substitution does not contribute to cluster binding. Rather, replacement of the glycine at position 208 changes the oligomerization state as a result of global structural alterations that result in the downstream effects manifest as MMDS1, but does not perturb the coordination chemistry of the Fe-S cluster. © 2017 Federation of European Biochemical Societies.

CONSTRAINING CLUSTER PHYSICS WITH THE SHAPE OF X-RAY CLUSTERS: COMPARISON OF LOCAL X-RAY CLUSTERS VERSUS ΛCDM CLUSTERS

International Nuclear Information System (INIS)

Lau, Erwin T.; Nagai, Daisuke; Kravtsov, Andrey V.; Vikhlinin, Alexey; Zentner, Andrew R.

2012-01-01

Recent simulations of cluster formation have demonstrated that condensation of baryons into central galaxies during cluster formation can drive the shape of the gas distribution in galaxy clusters significantly rounder out to their virial radius. These simulations generally predict stellar fractions within cluster virial radii that are ∼2-3 times larger than the stellar masses deduced from observations. In this paper, we compare ellipticity profiles of simulated clusters performed with varying input physics (radiative cooling, star formation, and supernova feedback) to the cluster ellipticity profiles derived from Chandra and ROSAT observations, in an effort to constrain the fraction of gas that cools and condenses into the central galaxies within clusters. We find that local relaxed clusters have an average ellipticity of ε = 0.18 ± 0.05 in the radial range of 0.04 ≤ r/r 500 ≤ 1. At larger radii r > 0.1r 500 , the observed ellipticity profiles agree well with the predictions of non-radiative simulations. In contrast, the ellipticity profiles of simulated clusters that include dissipative gas physics deviate significantly from the observed ellipticity profiles at all radii. The dissipative simulations overpredict (underpredict) ellipticity in the inner (outer) regions of galaxy clusters. By comparing simulations with and without dissipative gas physics, we show that gas cooling causes the gas distribution to be more oblate in the central regions, but makes the outer gas distribution more spherical. We find that late-time gas cooling and star formation are responsible for the significantly oblate gas distributions in cluster cores, but the gas shapes outside of cluster cores are set primarily by baryon dissipation at high redshift (z ≥ 2). Our results indicate that the shapes of X-ray emitting gas in galaxy clusters, especially at large radii, can be used to place constraints on cluster gas physics, making it potential probes of the history of baryonic

Genomic analysis of thermophilic Bacillus coagulans strains: efficient producers for platform bio-chemicals.

Science.gov (United States)

Su, Fei; Xu, Ping

2014-01-29

Microbial strains with high substrate efficiency and excellent environmental tolerance are urgently needed for the production of platform bio-chemicals. Bacillus coagulans has these merits; however, little genetic information is available about this species. Here, we determined the genome sequences of five B. coagulans strains, and used a comparative genomic approach to reconstruct the central carbon metabolism of this species to explain their fermentation features. A novel xylose isomerase in the xylose utilization pathway was identified in these strains. Based on a genome-wide positive selection scan, the selection pressure on amino acid metabolism may have played a significant role in the thermal adaptation. We also researched the immune systems of B. coagulans strains, which provide them with acquired resistance to phages and mobile genetic elements. Our genomic analysis provides comprehensive insights into the genetic characteristics of B. coagulans and paves the way for improving and extending the uses of this species.

Vaginal reconstruction

International Nuclear Information System (INIS)

Lesavoy, M.A.

1985-01-01

Vaginal reconstruction can be an uncomplicated and straightforward procedure when attention to detail is maintained. The Abbe-McIndoe procedure of lining the neovaginal canal with split-thickness skin grafts has become standard. The use of the inflatable Heyer-Schulte vaginal stent provides comfort to the patient and ease to the surgeon in maintaining approximation of the skin graft. For large vaginal and perineal defects, myocutaneous flaps such as the gracilis island have been extremely useful for correction of radiation-damaged tissue of the perineum or for the reconstruction of large ablative defects. Minimal morbidity and scarring ensue because the donor site can be closed primarily. With all vaginal reconstruction, a compliant patient is a necessity. The patient must wear a vaginal obturator for a minimum of 3 to 6 months postoperatively and is encouraged to use intercourse as an excellent obturator. In general, vaginal reconstruction can be an extremely gratifying procedure for both the functional and emotional well-being of patients

Convex Clustering: An Attractive Alternative to Hierarchical Clustering

Science.gov (United States)

Chen, Gary K.; Chi, Eric C.; Ranola, John Michael O.; Lange, Kenneth

2015-01-01

The primary goal in cluster analysis is to discover natural groupings of objects. The field of cluster analysis is crowded with diverse methods that make special assumptions about data and address different scientific aims. Despite its shortcomings in accuracy, hierarchical clustering is the dominant clustering method in bioinformatics. Biologists find the trees constructed by hierarchical clustering visually appealing and in tune with their evolutionary perspective. Hierarchical clustering operates on multiple scales simultaneously. This is essential, for instance, in transcriptome data, where one may be interested in making qualitative inferences about how lower-order relationships like gene modules lead to higher-order relationships like pathways or biological processes. The recently developed method of convex clustering preserves the visual appeal of hierarchical clustering while ameliorating its propensity to make false inferences in the presence of outliers and noise. The solution paths generated by convex clustering reveal relationships between clusters that are hidden by static methods such as k-means clustering. The current paper derives and tests a novel proximal distance algorithm for minimizing the objective function of convex clustering. The algorithm separates parameters, accommodates missing data, and supports prior information on relationships. Our program CONVEXCLUSTER incorporating the algorithm is implemented on ATI and nVidia graphics processing units (GPUs) for maximal speed. Several biological examples illustrate the strengths of convex clustering and the ability of the proximal distance algorithm to handle high-dimensional problems. CONVEXCLUSTER can be freely downloaded from the UCLA Human Genetics web site at http://www.genetics.ucla.edu/software/ PMID:25965340

Breast Reconstruction After Mastectomy

Science.gov (United States)

... Cancer Prevention Genetics of Breast & Gynecologic Cancers Breast Cancer Screening Research Breast Reconstruction After Mastectomy On This Page What is breast reconstruction? How do surgeons use implants to reconstruct a woman’s breast? How do surgeons ...

Cluster management.

Science.gov (United States)

Katz, R

1992-11-01

Cluster management is a management model that fosters decentralization of management, develops leadership potential of staff, and creates ownership of unit-based goals. Unlike shared governance models, there is no formal structure created by committees and it is less threatening for managers. There are two parts to the cluster management model. One is the formation of cluster groups, consisting of all staff and facilitated by a cluster leader. The cluster groups function for communication and problem-solving. The second part of the cluster management model is the creation of task forces. These task forces are designed to work on short-term goals, usually in response to solving one of the unit's goals. Sometimes the task forces are used for quality improvement or system problems. Clusters are groups of not more than five or six staff members, facilitated by a cluster leader. A cluster is made up of individuals who work the same shift. For example, people with job titles who work days would be in a cluster. There would be registered nurses, licensed practical nurses, nursing assistants, and unit clerks in the cluster. The cluster leader is chosen by the manager based on certain criteria and is trained for this specialized role. The concept of cluster management, criteria for choosing leaders, training for leaders, using cluster groups to solve quality improvement issues, and the learning process necessary for manager support are described.

Determination of Arctic sea ice variability modes on interannual timescales via nonhierarchical clustering

Science.gov (United States)

Fučkar, Neven-Stjepan; Guemas, Virginie; Massonnet, François; Doblas-Reyes, Francisco

2015-04-01

Over the modern observational era, the northern hemisphere sea ice concentration, age and thickness have experienced a sharp long-term decline superimposed with strong internal variability. Hence, there is a crucial need to identify robust patterns of Arctic sea ice variability on interannual timescales and disentangle them from the long-term trend in noisy datasets. The principal component analysis (PCA) is a versatile and broadly used method for the study of climate variability. However, the PCA has several limiting aspects because it assumes that all modes of variability have symmetry between positive and negative phases, and suppresses nonlinearities by using a linear covariance matrix. Clustering methods offer an alternative set of dimension reduction tools that are more robust and capable of taking into account possible nonlinear characteristics of a climate field. Cluster analysis aggregates data into groups or clusters based on their distance, to simultaneously minimize the distance between data points in a given cluster and maximize the distance between the centers of the clusters. We extract modes of Arctic interannual sea-ice variability with nonhierarchical K-means cluster analysis and investigate the mechanisms leading to these modes. Our focus is on the sea ice thickness (SIT) as the base variable for clustering because SIT holds most of the climate memory for variability and predictability on interannual timescales. We primarily use global reconstructions of sea ice fields with a state-of-the-art ocean-sea-ice model, but we also verify the robustness of determined clusters in other Arctic sea ice datasets. Applied cluster analysis over the 1958-2013 period shows that the optimal number of detrended SIT clusters is K=3. Determined SIT cluster patterns and their time series of occurrence are rather similar between different seasons and months. Two opposite thermodynamic modes are characterized with prevailing negative or positive SIT anomalies over the

Evidence-Based ACL Reconstruction

Directory of Open Access Journals (Sweden)

E. Carlos RODRIGUEZ-MERCHAN

2015-01-01

Full Text Available There is controversy in the literature regarding a number of topics related to anterior cruciate ligament (ACLreconstruction. The purpose of this article is to answer the following questions: 1 Bone patellar tendon bone (BPTB reconstruction or hamstring reconstruction (HR; 2 Double bundle or single bundle; 3 Allograft or authograft; 4 Early or late reconstruction; 5 Rate of return to sports after ACL reconstruction; 6 Rate of osteoarthritis after ACL reconstruction. A Cochrane Library and PubMed (MEDLINE search of systematic reviews and meta-analysis related to ACL reconstruction was performed. The key words were: ACL reconstruction, systematic reviews and meta-analysis. The main criteria for selection were that the articles were systematic reviews and meta-analysesfocused on the aforementioned questions. Sixty-nine articles were found, but only 26 were selected and reviewed because they had a high grade (I-II of evidence. BPTB-R was associated with better postoperative knee stability but with a higher rate of morbidity. However, the results of both procedures in terms of functional outcome in the long-term were similar. The double-bundle ACL reconstruction technique showed better outcomes in rotational laxity, although functional recovery was similar between single-bundle and double-bundle. Autograft yielded better results than allograft. There was no difference between early and delayed reconstruction. 82% of patients were able to return to some kind of sport participation. 28% of patients presented radiological signs of osteoarthritis with a follow-up of minimum 10 years.

Analysis of ligand-protein exchange by Clustering of Ligand Diffusion Coefficient Pairs (CoLD-CoP)

Science.gov (United States)

Snyder, David A.; Chantova, Mihaela; Chaudhry, Saadia

2015-06-01

NMR spectroscopy is a powerful tool in describing protein structures and protein activity for pharmaceutical and biochemical development. This study describes a method to determine weak binding ligands in biological systems by using hierarchic diffusion coefficient clustering of multidimensional data obtained with a 400 MHz Bruker NMR. Comparison of DOSY spectrums of ligands of the chemical library in the presence and absence of target proteins show translational diffusion rates for small molecules upon interaction with macromolecules. For weak binders such as compounds found in fragment libraries, changes in diffusion rates upon macromolecular binding are on the order of the precision of DOSY diffusion measurements, and identifying such subtle shifts in diffusion requires careful statistical analysis. The "CoLD-CoP" (Clustering of Ligand Diffusion Coefficient Pairs) method presented here uses SAHN clustering to identify protein-binders in a chemical library or even a not fully characterized metabolite mixture. We will show how DOSY NMR and the "CoLD-CoP" method complement each other in identifying the most suitable candidates for lysozyme and wheat germ acid phosphatase.

Biochemical and toxicological studies of aqueous extract of ...

African Journals Online (AJOL)

Biochemical and toxicological studies of aqueous extract of Syzigium ... tract diseases and also used as food spices), on some biochemical indices, such as ... liver functions and blood parameters were studied in adult albino rats of both sexes.

eQuilibrator--the biochemical thermodynamics calculator.

Science.gov (United States)

Flamholz, Avi; Noor, Elad; Bar-Even, Arren; Milo, Ron

2012-01-01

The laws of thermodynamics constrain the action of biochemical systems. However, thermodynamic data on biochemical compounds can be difficult to find and is cumbersome to perform calculations with manually. Even simple thermodynamic questions like 'how much Gibbs energy is released by ATP hydrolysis at pH 5?' are complicated excessively by the search for accurate data. To address this problem, eQuilibrator couples a comprehensive and accurate database of thermodynamic properties of biochemical compounds and reactions with a simple and powerful online search and calculation interface. The web interface to eQuilibrator (http://equilibrator.weizmann.ac.il) enables easy calculation of Gibbs energies of compounds and reactions given arbitrary pH, ionic strength and metabolite concentrations. The eQuilibrator code is open-source and all thermodynamic source data are freely downloadable in standard formats. Here we describe the database characteristics and implementation and demonstrate its use.

eQuilibrator—the biochemical thermodynamics calculator

Science.gov (United States)

Flamholz, Avi; Noor, Elad; Bar-Even, Arren; Milo, Ron

2012-01-01

The laws of thermodynamics constrain the action of biochemical systems. However, thermodynamic data on biochemical compounds can be difficult to find and is cumbersome to perform calculations with manually. Even simple thermodynamic questions like ‘how much Gibbs energy is released by ATP hydrolysis at pH 5?’ are complicated excessively by the search for accurate data. To address this problem, eQuilibrator couples a comprehensive and accurate database of thermodynamic properties of biochemical compounds and reactions with a simple and powerful online search and calculation interface. The web interface to eQuilibrator (http://equilibrator.weizmann.ac.il) enables easy calculation of Gibbs energies of compounds and reactions given arbitrary pH, ionic strength and metabolite concentrations. The eQuilibrator code is open-source and all thermodynamic source data are freely downloadable in standard formats. Here we describe the database characteristics and implementation and demonstrate its use. PMID:22064852

Lifting to cluster-tilting objects in higher cluster categories

OpenAIRE

Liu, Pin

2008-01-01

In this note, we consider the $d$-cluster-tilted algebras, the endomorphism algebras of $d$-cluster-tilting objects in $d$-cluster categories. We show that a tilting module over such an algebra lifts to a $d$-cluster-tilting object in this $d$-cluster category.

Snapshot Survey of the Globular Cluster Populations of Isolated Early Type Galaxies

Science.gov (United States)

Gregg, Michael

2017-08-01

We propose WFC3/UVIS snapshot observations of a sample of 75 isolated early type galaxiesresiding in cosmic voids or extremely low density regions. The primary aim is to usetheir globular cluster populations to reconstruct their evolutionary history, revealingif, how, and why void ellipticals differ from cluster ellipticals. The galaxies span arange of luminosities, providing a varied sample for comparison with the well-documentedglobular cluster populations in denser environments. This proposed WFC3 study of isolatedearly type galaxies breaks new ground by targeting a sample which has thus far receivedlittle attention, and, significantly, this will be the first such study with HST.Characterizing early type galaxies in voids and their GC systems promises to increase ourunderstanding of galaxy formation and evolution of galaxies in general because isolatedobjects are the best approximation to a control sample that we have for understanding theinfluence of environment on formation and evolution. Whether these isolated objects turnout to be identical to or distinct from counterparts in other regions of the Universe,they will supply insight into the formation and evolution of all galaxies. Parallel ACSimaging will help to characterize the near field environments of the sample.

Proper Motions and Structural Parameters of the Galactic Globular Cluster M71

Energy Technology Data Exchange (ETDEWEB)

Cadelano, M.; Dalessandro, E.; Ferraro, F. R.; Miocchi, P.; Lanzoni, B.; Pallanca, C. [Dipartimento di Fisica e Astronomia, Università di Bologna, Viale Berti Pichat 6/2, I-40127 Bologna (Italy); Massari, D. [INAF—Osservatorio Astronomico di Bologna, Via Ranzani 1, I-40127 Bologna (Italy)

2017-02-20

By exploiting two ACS/ HST data sets separated by a temporal baseline of ∼7 years, we have determined the relative stellar proper motions (PMs; providing membership) and the absolute PM of the Galactic globular cluster M71. The absolute PM has been used to reconstruct the cluster orbit within a Galactic, three-component, axisymmetric potential. M71 turns out to be in a low-latitude disk-like orbit inside the Galactic disk, further supporting the scenario in which it lost a significant fraction of its initial mass. Since large differential reddening is known to affect this system, we took advantage of near-infrared, ground-based observations to re-determine the cluster center and density profile from direct star counts. The new structural parameters turn out to be significantly different from the ones quoted in the literature. In particular, M71 has a core and a half-mass radii almost 50% larger than previously thought. Finally, we estimate that the initial mass of M71 was likely one order of magnitude larger than its current value, thus helping to solve the discrepancy with the observed number of X-ray sources.

Data Clustering

Science.gov (United States)

Wagstaff, Kiri L.

2012-03-01

On obtaining a new data set, the researcher is immediately faced with the challenge of obtaining a high-level understanding from the observations. What does a typical item look like? What are the dominant trends? How many distinct groups are included in the data set, and how is each one characterized? Which observable values are common, and which rarely occur? Which items stand out as anomalies or outliers from the rest of the data? This challenge is exacerbated by the steady growth in data set size [11] as new instruments push into new frontiers of parameter space, via improvements in temporal, spatial, and spectral resolution, or by the desire to "fuse" observations from different modalities and instruments into a larger-picture understanding of the same underlying phenomenon. Data clustering algorithms provide a variety of solutions for this task. They can generate summaries, locate outliers, compress data, identify dense or sparse regions of feature space, and build data models. It is useful to note up front that "clusters" in this context refer to groups of items within some descriptive feature space, not (necessarily) to "galaxy clusters" which are dense regions in physical space. The goal of this chapter is to survey a variety of data clustering methods, with an eye toward their applicability to astronomical data analysis. In addition to improving the individual researcher’s understanding of a given data set, clustering has led directly to scientific advances, such as the discovery of new subclasses of stars [14] and gamma-ray bursts (GRBs) [38]. All clustering algorithms seek to identify groups within a data set that reflect some observed, quantifiable structure. Clustering is traditionally an unsupervised approach to data analysis, in the sense that it operates without any direct guidance about which items should be assigned to which clusters. There has been a recent trend in the clustering literature toward supporting semisupervised or constrained

[Reconstructive methods after Fournier gangrene].

Science.gov (United States)

Wallner, C; Behr, B; Ring, A; Mikhail, B D; Lehnhardt, M; Daigeler, A

2016-04-01

Fournier's gangrene is a variant of the necrotizing fasciitis restricted to the perineal and genital region. It presents as an acute life-threatening disease and demands rapid surgical debridement, resulting in large soft tissue defects. Various reconstructive methods have to be applied to reconstitute functionality and aesthetics. The objective of this work is to identify different reconstructive methods in the literature and compare them to our current concepts for reconstructing defects caused by Fournier gangrene. Analysis of the current literature and our reconstructive methods on Fournier gangrene. The Fournier gangrene is an emergency requiring rapid, calculated antibiotic treatment and radical surgical debridement. After the acute phase of the disease, appropriate reconstructive methods are indicated. The planning of the reconstruction of the defect depends on many factors, especially functional and aesthetic demands. Scrotal reconstruction requires a higher aesthetic and functional reconstructive degree than perineal cutaneous wounds. In general, thorough wound hygiene, proper pre-operative planning, and careful consideration of the patient's demands are essential for successful reconstruction. In the literature, various methods for reconstruction after Fournier gangrene are described. Reconstruction with a flap is required for a good functional result in complex regions as the scrotum and penis, while cutaneous wounds can be managed through skin grafting. Patient compliance and tissue demand are crucial factors in the decision-making process.

Dense Fe cluster-assembled films by energetic cluster deposition

International Nuclear Information System (INIS)

Peng, D.L.; Yamada, H.; Hihara, T.; Uchida, T.; Sumiyama, K.

2004-01-01

High-density Fe cluster-assembled films were produced at room temperature by an energetic cluster deposition. Though cluster-assemblies are usually sooty and porous, the present Fe cluster-assembled films are lustrous and dense, revealing a soft magnetic behavior. Size-monodispersed Fe clusters with the mean cluster size d=9 nm were synthesized using a plasma-gas-condensation technique. Ionized clusters are accelerated electrically and deposited onto the substrate together with neutral clusters from the same cluster source. Packing fraction and saturation magnetic flux density increase rapidly and magnetic coercivity decreases remarkably with increasing acceleration voltage. The Fe cluster-assembled film obtained at the acceleration voltage of -20 kV has a packing fraction of 0.86±0.03, saturation magnetic flux density of 1.78±0.05 Wb/m 2 , and coercivity value smaller than 80 A/m. The resistivity at room temperature is ten times larger than that of bulk Fe metal

Ultrafast and scalable cone-beam CT reconstruction using MapReduce in a cloud computing environment.

Science.gov (United States)

Meng, Bowen; Pratx, Guillem; Xing, Lei

2011-12-01

Four-dimensional CT (4DCT) and cone beam CT (CBCT) are widely used in radiation therapy for accurate tumor target definition and localization. However, high-resolution and dynamic image reconstruction is computationally demanding because of the large amount of data processed. Efficient use of these imaging techniques in the clinic requires high-performance computing. The purpose of this work is to develop a novel ultrafast, scalable and reliable image reconstruction technique for 4D CBCT∕CT using a parallel computing framework called MapReduce. We show the utility of MapReduce for solving large-scale medical physics problems in a cloud computing environment. In this work, we accelerated the Feldcamp-Davis-Kress (FDK) algorithm by porting it to Hadoop, an open-source MapReduce implementation. Gated phases from a 4DCT scans were reconstructed independently. Following the MapReduce formalism, Map functions were used to filter and backproject subsets of projections, and Reduce function to aggregate those partial backprojection into the whole volume. MapReduce automatically parallelized the reconstruction process on a large cluster of computer nodes. As a validation, reconstruction of a digital phantom and an acquired CatPhan 600 phantom was performed on a commercial cloud computing environment using the proposed 4D CBCT∕CT reconstruction algorithm. Speedup of reconstruction time is found to be roughly linear with the number of nodes employed. For instance, greater than 10 times speedup was achieved using 200 nodes for all cases, compared to the same code executed on a single machine. Without modifying the code, faster reconstruction is readily achievable by allocating more nodes in the cloud computing environment. Root mean square error between the images obtained using MapReduce and a single-threaded reference implementation was on the order of 10(-7). Our study also proved that cloud computing with MapReduce is fault tolerant: the reconstruction completed

Possible Biochemical Markers in Protein-Energy Malnutrition and ...

African Journals Online (AJOL)

This study was carried out to determine possible biochemical markers in children suffering from Plasmodium falciparum malaria and Protein-Energy Malnutrition in a Hospital setting in Western Kenya. Spectrophotometric assays of selected biochemical parameters namely, albumin, total proteins, glucose, glutamate ...

Shaping the breast in secondary microsurgical breast reconstruction: single- vs. two-esthetic unit reconstruction.

Science.gov (United States)

Gravvanis, Andreas; Smith, Roger W

2010-10-01

The esthetic outcome is dictated essentially not only by the position, size, and shape of the reconstructed breast, but also by the extra scaring involved. In the present study, we conducted a visual analog scale survey to compare the esthetic outcome in delayed autologous breast reconstruction following two different abdominal flaps inset. Twenty-five patients had their reconstruction using the Single-esthetic Unit principle and were compared with 25 patients that their breast was reconstructed using the Two-Esthetic Unit principle. Photographic images were formulated to a PowerPoint presentation and cosmetic outcomes were assessed from 30 physicians, by means of a Questionnaire and a visual analog scale. Our data showed that the single-esthetic unit breast reconstruction presents significant advantages over the traditional two-esthetic units, due to inconspicuous flap reconstruction, better position of the inframammary fold, and more natural transition from native and reconstructed tissues. Moreover, patient self-evaluation of esthetic outcome and quality of life showed that single-esthetic unit reconstruction is associated with higher patient satisfaction, therefore should be considered the method of choice. © 2010 Wiley-Liss, Inc.

Cluster Physics with Merging Galaxy Clusters

Directory of Open Access Journals (Sweden)

Sandor M. Molnar

2016-02-01

Full Text Available Collisions between galaxy clusters provide a unique opportunity to study matter in a parameter space which cannot be explored in our laboratories on Earth. In the standard LCDM model, where the total density is dominated by the cosmological constant ($Lambda$ and the matter density by cold dark matter (CDM, structure formation is hierarchical, and clusters grow mostly by merging.Mergers of two massive clusters are the most energetic events in the universe after the Big Bang,hence they provide a unique laboratory to study cluster physics.The two main mass components in clusters behave differently during collisions:the dark matter is nearly collisionless, responding only to gravity, while the gas is subject to pressure forces and dissipation, and shocks and turbulenceare developed during collisions. In the present contribution we review the different methods used to derive the physical properties of merging clusters. Different physical processes leave their signatures on different wavelengths, thusour review is based on a multifrequency analysis. In principle, the best way to analyze multifrequency observations of merging clustersis to model them using N-body/HYDRO numerical simulations. We discuss the results of such detailed analyses.New high spatial and spectral resolution ground and space based telescopeswill come online in the near future. Motivated by these new opportunities,we briefly discuss methods which will be feasible in the near future in studying merging clusters.

Globular clusters in high-redshift dwarf galaxies: a case study from the Local Group

Science.gov (United States)

Zick, Tom O.; Weisz, Daniel R.; Boylan-Kolchin, Michael

2018-06-01

We present the reconstructed evolution of rest-frame ultraviolet (UV) luminosities of the most massive Milky Way dwarf spheroidal satellite galaxy, Fornax, and its five globular clusters (GCs) across redshift, based on analysis of the stellar fossil record and stellar population synthesis modelling. We find that (1) Fornax's (proto-)GCs can generate 10-100 times more UV flux than the field population, despite comprising 3. (3) GC formation can introduce order-of-magnitude errors in abundance matching. We also find that some compact HFF objects are consistent with the reconstructed properties of Fornax's GCs at the same redshifts (e.g. surface brightness, star formation rate), suggesting we may have already detected proto-GCs in the early Universe. Finally, we discuss the prospects for improving the connections between local GCs and proto-GCs detected in the early Universe.

Our Clinical Experience in Lower Eyelid Reconstruction and Comparison of Reconstruction Techniques.

Directory of Open Access Journals (Sweden)

Erol Kesiktas

2011-03-01

Full Text Available Lower eyelid reconstruction after tumor resection or trauma is extremely important in order to obtain the protection of the globe and it requires extra care. The aim of this study is to evaluate the techniques that we use in lower eyelid reconstruction. Between the years of 1999-2009, a total of 23 patients who had lower eyelid defects due to tumor resection (21 patients or trauma (2 patients were reconstructed by the use of various flaps. Eleven of the patients were women and twelve of them were men. Average age was 60.7. For the reconstruction 13 Mustarde flap, 9 bipedicled Tripier flap, 1 Tenzel flap and 1 bipedicled infraorbital flaps were used. Average postoperative follow up interval was 35 months. (18-47 months. Flap necrosis, function loss in the lower lid were not experienced in any of the patients. Cosmetically satisfactory results were obtained. In lower eyelid reconstruction, the size of the defect and the amount of skin around must be carefully evaluated and should be considered while planning the reconstruction. [Cukurova Med J 2011; 36(1: 15-23

GPI-anchored proteins are confined in subdiffraction clusters at the apical surface of polarized epithelial cells.

Science.gov (United States)

Paladino, Simona; Lebreton, Stéphanie; Lelek, Mickaël; Riccio, Patrizia; De Nicola, Sergio; Zimmer, Christophe; Zurzolo, Chiara

2017-12-01

Spatio-temporal compartmentalization of membrane proteins is critical for the regulation of diverse vital functions in eukaryotic cells. It was previously shown that, at the apical surface of polarized MDCK cells, glycosylphosphatidylinositol (GPI)-anchored proteins (GPI-APs) are organized in small cholesterol-independent clusters of single GPI-AP species (homoclusters), which are required for the formation of larger cholesterol-dependent clusters formed by multiple GPI-AP species (heteroclusters). This clustered organization is crucial for the biological activities of GPI-APs; hence, understanding the spatio-temporal properties of their membrane organization is of fundamental importance. Here, by using direct stochastic optical reconstruction microscopy coupled to pair correlation analysis (pc-STORM), we were able to visualize and measure the size of these clusters. Specifically, we show that they are non-randomly distributed and have an average size of 67 nm. We also demonstrated that polarized MDCK and non-polarized CHO cells have similar cluster distribution and size, but different sensitivity to cholesterol depletion. Finally, we derived a model that allowed a quantitative characterization of the cluster organization of GPI-APs at the apical surface of polarized MDCK cells for the first time. Experimental FRET (fluorescence resonance energy transfer)/FLIM (fluorescence-lifetime imaging microscopy) data were correlated to the theoretical predictions of the model. © 2017 The Author(s).

Defining the Architecture of the Core Machinery for the Assembly of Fe-S Clusters in Human Mitochondria.

Science.gov (United States)

Gakh, Oleksandr; Ranatunga, Wasantha; Galeano, Belinda K; Smith, Douglas S; Thompson, James R; Isaya, Grazia

2017-01-01

Although Fe-S clusters may assemble spontaneously from elemental iron and sulfur in protein-free systems, the potential toxicity of free Fe 2+ , Fe 3+ , and S 2- ions in aerobic environments underscores the requirement for specialized proteins to oversee the safe assembly of Fe-S clusters in living cells. Prokaryotes first developed multiprotein systems for Fe-S cluster assembly, from which mitochondria later derived their own system and became the main Fe-S cluster suppliers for eukaryotic cells. Early studies in yeast and human mitochondria indicated that Fe-S cluster assembly in eukaryotes is centered around highly conserved Fe-S proteins (human ISCU) that serve as scaffolds upon which new Fe-S clusters are assembled from (i) elemental sulfur, provided by a pyridoxal phosphate-dependent cysteine desulfurase (human NFS1) and its stabilizing-binding partner (human ISD11), and (ii) elemental iron, provided by an iron-binding protein of the frataxin family (human FXN). Further studies revealed that all of these proteins could form stable complexes that could reach molecular masses of megadaltons. However, the protein-protein interaction surfaces, catalytic mechanisms, and overall architecture of these macromolecular machines remained undefined for quite some time. The delay was due to difficulties inherent in reconstituting these very large multiprotein complexes in vitro or isolating them from cells in sufficient quantities to enable biochemical and structural studies. Here, we describe approaches we developed to reconstitute the human Fe-S cluster assembly machinery in Escherichia coli and to define its remarkable architecture. © 2017 Elsevier Inc. All rights reserved.

Possibilities and methods for biochemical assessment of radiation injury

Energy Technology Data Exchange (ETDEWEB)

Minkova, M [Meditsinska Akademiya, Sofia (Bulgaria). Nauchen Inst. po Rentgenologiya i Radiobiologiya

1986-01-01

An extensitive review (77 references) is made of the application of biochemical diagnostic methods for assessment of radiation diseases. A brief characteristics of several biochemical indicators is given: deoxycytidine, thymidine, rho-aminoisocarboxylic acid, DNA-ase, nucleic acids. Influence of such factors as age, sex, season etc. is studied by means of functional biochemical indicators as: creatine, triptophanic metabolites, 5-hydroxy-indolacetic acid, biogenic amines, serum proteins, enzymes, etc.

Contribution of radiation chemistry to the study of metal clusters.

Science.gov (United States)

Belloni, J

1998-11-01

Radiation chemistry dates from the discovery of radioactivity one century ago by H. Becquerel and P. and M. Curie. The complex phenomena induced by ionizing radiation have been explained progressively. At present, the methodology of radiation chemistry, particularly in the pulsed mode, provides a powerful means to study not only the early processes after the energy absorption, but more generally a broad diversity of chemical and biochemical reaction mechanisms. Among them, the new area of metal cluster chemistry illustrates how radiation chemistry contributed to this field in suggesting fruitful original concepts, in guiding and controlling specific syntheses, and in the detailed elaboration of the mechanisms of complex and long-unsolved processes, such as the dynamics of nucleation, electron transfer catalysis and photographic development.

Are clusters of dietary patterns and cluster membership stable over time? Results of a longitudinal cluster analysis study.

Science.gov (United States)

Walthouwer, Michel Jean Louis; Oenema, Anke; Soetens, Katja; Lechner, Lilian; de Vries, Hein

2014-11-01

Developing nutrition education interventions based on clusters of dietary patterns can only be done adequately when it is clear if distinctive clusters of dietary patterns can be derived and reproduced over time, if cluster membership is stable, and if it is predictable which type of people belong to a certain cluster. Hence, this study aimed to: (1) identify clusters of dietary patterns among Dutch adults, (2) test the reproducibility of these clusters and stability of cluster membership over time, and (3) identify sociodemographic predictors of cluster membership and cluster transition. This study had a longitudinal design with online measurements at baseline (N=483) and 6 months follow-up (N=379). Dietary intake was assessed with a validated food frequency questionnaire. A hierarchical cluster analysis was performed, followed by a K-means cluster analysis. Multinomial logistic regression analyses were conducted to identify the sociodemographic predictors of cluster membership and cluster transition. At baseline and follow-up, a comparable three-cluster solution was derived, distinguishing a healthy, moderately healthy, and unhealthy dietary pattern. Male and lower educated participants were significantly more likely to have a less healthy dietary pattern. Further, 251 (66.2%) participants remained in the same cluster, 45 (11.9%) participants changed to an unhealthier cluster, and 83 (21.9%) participants shifted to a healthier cluster. Men and people living alone were significantly more likely to shift toward a less healthy dietary pattern. Distinctive clusters of dietary patterns can be derived. Yet, cluster membership is unstable and only few sociodemographic factors were associated with cluster membership and cluster transition. These findings imply that clusters based on dietary intake may not be suitable as a basis for nutrition education interventions. Copyright © 2014 Elsevier Ltd. All rights reserved.

Identification and manipulation of the pleuromutilin gene cluster from Clitopilus passeckerianus for increased rapid antibiotic production

Science.gov (United States)

Bailey, Andy M.; Alberti, Fabrizio; Kilaru, Sreedhar; Collins, Catherine M.; de Mattos-Shipley, Kate; Hartley, Amanda J.; Hayes, Patrick; Griffin, Alison; Lazarus, Colin M.; Cox, Russell J.; Willis, Christine L.; O'Dwyer, Karen; Spence, David W.; Foster, Gary D.

2016-05-01

Semi-synthetic derivatives of the tricyclic diterpene antibiotic pleuromutilin from the basidiomycete Clitopilus passeckerianus are important in combatting bacterial infections in human and veterinary medicine. These compounds belong to the only new class of antibiotics for human applications, with novel mode of action and lack of cross-resistance, representing a class with great potential. Basidiomycete fungi, being dikaryotic, are not generally amenable to strain improvement. We report identification of the seven-gene pleuromutilin gene cluster and verify that using various targeted approaches aimed at increasing antibiotic production in C. passeckerianus, no improvement in yield was achieved. The seven-gene pleuromutilin cluster was reconstructed within Aspergillus oryzae giving production of pleuromutilin in an ascomycete, with a significant increase (2106%) in production. This is the first gene cluster from a basidiomycete to be successfully expressed in an ascomycete, and paves the way for the exploitation of a metabolically rich but traditionally overlooked group of fungi.

Improving Weak Lensing Mass Map Reconstructions using Gaussian and Sparsity Priors: Application to DES SV

Energy Technology Data Exchange (ETDEWEB)

Jeffrey, N.; et al.

2018-01-26

Mapping the underlying density field, including non-visible dark matter, using weak gravitational lensing measurements is now a standard tool in cosmology. Due to its importance to the science results of current and upcoming surveys, the quality of the convergence reconstruction methods should be well understood. We compare three different mass map reconstruction methods: Kaiser-Squires (KS), Wiener filter, and GLIMPSE. KS is a direct inversion method, taking no account of survey masks or noise. The Wiener filter is well motivated for Gaussian density fields in a Bayesian framework. The GLIMPSE method uses sparsity, with the aim of reconstructing non-linearities in the density field. We compare these methods with a series of tests on the public Dark Energy Survey (DES) Science Verification (SV) data and on realistic DES simulations. The Wiener filter and GLIMPSE methods offer substantial improvement on the standard smoothed KS with a range of metrics. For both the Wiener filter and GLIMPSE convergence reconstructions we present a 12% improvement in Pearson correlation with the underlying truth from simulations. To compare the mapping methods' abilities to find mass peaks, we measure the difference between peak counts from simulated {\\Lambda}CDM shear catalogues and catalogues with no mass fluctuations. This is a standard data vector when inferring cosmology from peak statistics. The maximum signal-to-noise value of these peak statistic data vectors was increased by a factor of 3.5 for the Wiener filter and by a factor of 9 using GLIMPSE. With simulations we measure the reconstruction of the harmonic phases, showing that the concentration of the phase residuals is improved 17% by GLIMPSE and 18% by the Wiener filter. We show that the correlation between the reconstructions from data and the foreground redMaPPer clusters is increased 18% by the Wiener filter and 32% by GLIMPSE. [Abridged

Aerodynamic Reconstruction Applied to Parachute Test Vehicle Flight Data Analysis

Science.gov (United States)

Cassady, Leonard D.; Ray, Eric S.; Truong, Tuan H.

2013-01-01

The aerodynamics, both static and dynamic, of a test vehicle are critical to determining the performance of the parachute cluster in a drop test and for conducting a successful test. The Capsule Parachute Assembly System (CPAS) project is conducting tests of NASA's Orion Multi-Purpose Crew Vehicle (MPCV) parachutes at the Army Yuma Proving Ground utilizing the Parachute Test Vehicle (PTV). The PTV shape is based on the MPCV, but the height has been reduced in order to fit within the C-17 aircraft for extraction. Therefore, the aerodynamics of the PTV are similar, but not the same as, the MPCV. A small series of wind tunnel tests and computational fluid dynamics cases were run to modify the MPCV aerodynamic database for the PTV, but aerodynamic reconstruction of the flights has proven an effective source for further improvements to the database. The acceleration and rotational rates measured during free flight, before parachute inflation but during deployment, were used to con rm vehicle static aerodynamics. A multibody simulation is utilized to reconstruct the parachute portions of the flight. Aerodynamic or parachute parameters are adjusted in the simulation until the prediction reasonably matches the flight trajectory. Knowledge of the static aerodynamics is critical in the CPAS project because the parachute riser load measurements are scaled based on forebody drag. PTV dynamic damping is critical because the vehicle has no reaction control system to maintain attitude - the vehicle dynamics must be understood and modeled correctly before flight. It will be shown here that aerodynamic reconstruction has successfully contributed to the CPAS project.

Breast Reconstruction Following Cancer Treatment.

Science.gov (United States)

Gerber, Bernd; Marx, Mario; Untch, Michael; Faridi, Andree

2015-08-31

About 8000 breast reconstructions after mastectomy are per - formed in Germany each year. It has become more difficult to advise patients because of the wide variety of heterologous and autologous techniques that are now available and because of changes in the recommendations about radiotherapy. This article is based on a review of pertinent articles (2005-2014) that were retrieved by a selective search employing the search terms "mastectomy" and "breast reconstruction." The goal of reconstruction is to achieve an oncologically safe and aestically satisfactory result for the patient over the long term. Heterologous, i.e., implant-based, breast reconstruction (IBR) and autologous breast reconstruction (ABR) are complementary techniques. Immediate reconstruction preserves the skin of the breast and its natural form and prevents the psychological trauma associated with mastectomy. If post-mastectomy radiotherapy (PMRT) is not indicated, implant-based reconstruction with or without a net/acellular dermal matrix (ADM) is a common option. Complications such as seroma formation, infection, and explantation are significantly more common when an ADM is used (15.3% vs. 5.4% ). If PMRT is performed, then the complication rate of implant-based breast reconstruction is 1 to 48% ; in particular, Baker grade III/IV capsular fibrosis occurs in 7 to 22% of patients, and the prosthesis must be explanted in 9 to 41% . Primary or, preferably, secondary autologous reconstruction is an alternative. The results of ABR are more stable over the long term, but the operation is markedly more complex. Autologous breast reconstruction after PMRT does not increase the risk of serious complications (20.5% vs. 17.9% without radiotherapy). No randomized controlled trials have yet been conducted to compare the reconstructive techniques with each other. If radiotherapy will not be performed, immediate reconstruction with an implant is recommended. On the other hand, if post-mastectomy radiotherapy

Clusters and how to make it work : Cluster Strategy Toolkit

NARCIS (Netherlands)

Manickam, Anu; van Berkel, Karel

2014-01-01

Clusters are the magic answer to regional economic development. Firms in clusters are more innovative; cluster policy dominates EU policy; ‘top-sectors’ and excellence are the choice of national policy makers; clusters are ‘in’. But, clusters are complex, clusters are ‘messy’; there is no clear

Cluster dynamics at different cluster size and incident laser wavelengths

International Nuclear Information System (INIS)

Desai, Tara; Bernardinello, Andrea

2002-01-01

X-ray emission spectra from aluminum clusters of diameter -0.4 μm and gold clusters of dia. ∼1.25 μm are experimentally studied by irradiating the cluster foil targets with 1.06 μm laser, 10 ns (FWHM) at an intensity ∼10 12 W/cm 2 . Aluminum clusters show a different spectra compared to bulk material whereas gold cluster evolve towards bulk gold. Experimental data are analyzed on the basis of cluster dimension, laser wavelength and pulse duration. PIC simulations are performed to study the behavior of clusters at higher intensity I≥10 17 W/cm 2 for different size of the clusters irradiated at different laser wavelengths. Results indicate the dependence of cluster dynamics on cluster size and incident laser wavelength

Permutationally invariant state reconstruction

DEFF Research Database (Denmark)

Moroder, Tobias; Hyllus, Philipp; Tóth, Géza

2012-01-01

Feasible tomography schemes for large particle numbers must possess, besides an appropriate data acquisition protocol, an efficient way to reconstruct the density operator from the observed finite data set. Since state reconstruction typically requires the solution of a nonlinear large-scale opti...... optimization, which has clear advantages regarding speed, control and accuracy in comparison to commonly employed numerical routines. First prototype implementations easily allow reconstruction of a state of 20 qubits in a few minutes on a standard computer.......-scale optimization problem, this is a major challenge in the design of scalable tomography schemes. Here we present an efficient state reconstruction scheme for permutationally invariant quantum state tomography. It works for all common state-of-the-art reconstruction principles, including, in particular, maximum...

Text Clustering Algorithm Based on Random Cluster Core

Directory of Open Access Journals (Sweden)

Huang Long-Jun

2016-01-01

Full Text Available Nowadays clustering has become a popular text mining algorithm, but the huge data can put forward higher requirements for the accuracy and performance of text mining. In view of the performance bottleneck of traditional text clustering algorithm, this paper proposes a text clustering algorithm with random features. This is a kind of clustering algorithm based on text density, at the same time using the neighboring heuristic rules, the concept of random cluster is introduced, which effectively reduces the complexity of the distance calculation.

Haematological and blood biochemical indices of West African ...

African Journals Online (AJOL)

Haematological and blood biochemical indices of West African dwarf goats vaccinated against Pestes des petit ruminants (PPR) ... blood biochemical indices of forty randomly selected West African dwarf (WAD) goats were studied. Packed cell volume ... neutrophil/lymphocyte ratio and white blood cells (WBC) than females.

BioNessie - a grid enabled biochemical networks simulation environment

OpenAIRE

Liu, X.; Jiang, J.; Ajayi, O.; Gu, X.; Gilbert, D.; Sinnott, R.O.

2008-01-01

The simulation of biochemical networks provides insight and understanding about the underlying biochemical processes and pathways used by cells and organisms. BioNessie is a biochemical network simulator which has been developed at the University of Glasgow. This paper describes the simulator and focuses in particular on how it has been extended to benefit from a wide variety of high performance compute resources across the UK through Grid technologies to support larger scale simulations.

Fast implementations of reconstruction-based scatter compensation in fully 3D SPECT image reconstruction

International Nuclear Information System (INIS)

Kadrmas, Dan J.; Karimi, Seemeen S.; Frey, Eric C.; Tsui, Benjamin M.W.

1998-01-01

Accurate scatter compensation in SPECT can be performed by modelling the scatter response function during the reconstruction process. This method is called reconstruction-based scatter compensation (RBSC). It has been shown that RBSC has a number of advantages over other methods of compensating for scatter, but using RBSC for fully 3D compensation has resulted in prohibitively long reconstruction times. In this work we propose two new methods that can be used in conjunction with existing methods to achieve marked reductions in RBSC reconstruction times. The first method, coarse-grid scatter modelling, significantly accelerates the scatter model by exploiting the fact that scatter is dominated by low-frequency information. The second method, intermittent RBSC, further accelerates the reconstruction process by limiting the number of iterations during which scatter is modelled. The fast implementations were evaluated using a Monte Carlo simulated experiment of the 3D MCAT phantom with 99m Tc tracer, and also using experimentally acquired data with 201 Tl tracer. Results indicated that these fast methods can reconstruct, with fully 3D compensation, images very similar to those obtained using standard RBSC methods, and in reconstruction times that are an order of magnitude shorter. Using these methods, fully 3D iterative reconstruction with RBSC can be performed well within the realm of clinically realistic times (under 10 minutes for 64x64x24 image reconstruction). (author)

Update on orbital reconstruction.

Science.gov (United States)

Chen, Chien-Tzung; Chen, Yu-Ray

2010-08-01

Orbital trauma is common and frequently complicated by ocular injuries. The recent literature on orbital fracture is analyzed with emphasis on epidemiological data assessment, surgical timing, method of approach and reconstruction materials. Computed tomographic (CT) scan has become a routine evaluation tool for orbital trauma, and mobile CT can be applied intraoperatively if necessary. Concomitant serious ocular injury should be carefully evaluated preoperatively. Patients presenting with nonresolving oculocardiac reflex, 'white-eyed' blowout fracture, or diplopia with a positive forced duction test and CT evidence of orbital tissue entrapment require early surgical repair. Otherwise, enophthalmos can be corrected by late surgery with a similar outcome to early surgery. The use of an endoscope-assisted approach for orbital reconstruction continues to grow, offering an alternative method. Advances in alloplastic materials have improved surgical outcome and shortened operating time. In this review of modern orbital reconstruction, several controversial issues such as surgical indication, surgical timing, method of approach and choice of reconstruction material are discussed. Preoperative fine-cut CT image and thorough ophthalmologic examination are key elements to determine surgical indications. The choice of surgical approach and reconstruction materials much depends on the surgeon's experience and the reconstruction area. Prefabricated alloplastic implants together with image software and stereolithographic models are significant advances that help to more accurately reconstruct the traumatized orbit. The recent evolution of orbit reconstruction improves functional and aesthetic results and minimizes surgical complications.

Identification of hadronic {tau} decays using the {tau} lepton flight path and reconstruction and identification of jets with a low transverse energy at intermediate luminosities with an application to the search for the Higgs boson in vector boson fusion with the ATLAS experiment at the LHC

Energy Technology Data Exchange (ETDEWEB)

Ruwiedel, Christoph

2010-06-15

Three studies of different components of the object reconstruction with the ATLAS experiment using simulated data are presented. In each study, a method for the improvement of the reconstruction is developed and the improvements are evaluated. The reconstruction of observables sensitive to the {tau} lepton lifetime and their use for the identification of hadronic {tau} decays are the subject of the first study. In the second study, a method for the identification of jets from the signal interaction in the presence of additional minimum bias interactions is developed and applied to the central jet veto in the vector boson fusion Higgs analysis. In the third study, the effects of additional minimum bias interactions close in time to the triggered event on the cluster formation and the determination of the jet energy are evaluated and the cluster formation is modified in a way such that the bias of the reconstructed jet energy is minimized. (orig.)

Definitions of biochemical failure in prostate cancer following radiation therapy

International Nuclear Information System (INIS)

Taylor, Jeremy M.G.; Griffith, Kent A.; Sandler, Howard M.

2001-01-01

Purpose: The American Society for Therapeutic Radiology and Oncology (ASTRO) published a consensus panel definition of biochemical failure following radiation therapy for prostate cancer. In this paper, we develop a series of alternative definitions of biochemical failure. Using data from 688 patients, we evaluated the sensitivity and specificity of the various definitions, with respect to a defined 'clinically meaningful' outcome. Methods and Materials: The ASTRO definition of biochemical failure requires 3 consecutive rises in prostate-specific antigen (PSA). We considered several modifications to the standard definition: to require PSA rises of a certain magnitude, to consider 2 instead of 3 rises, to require the final PSA value to be greater than a fixed cutoff level, and to define biochemical failure based on the slope of PSA over 1, 1.5, or 2 years. A clinically meaningful failure is defined as local recurrence, distant metastases, initiation of unplanned hormonal therapy, unplanned radical prostatectomy, or a PSA>25 later than 6 months after radiation. Results: Requiring the final PSA in a series of consecutive rises to be larger than 1.5 ng/mL increased the specificity of biochemical failure. For a fixed specificity, defining biochemical failure based on 2 consecutive rises, or the slope over the last year, could increase the sensitivity by up to approximately 20%, compared to the ASTRO definition. Using a rule based on the slope over the previous year or 2 rises leads to a slightly earlier detection of biochemical failure than does the ASTRO definition. Even with the best rule, only approximately 20% of true failures are biochemically detected more than 1 year before the clinically meaningful event time. Conclusion: There is potential for improvement in the ASTRO consensus definition of biochemical failure. Further research is needed, in studies with long follow-up times, to evaluate the relationship between various definitions of biochemical failure and

On clusters and clustering from atoms to fractals

CERN Document Server

Reynolds, PJ

1993-01-01

This book attempts to answer why there is so much interest in clusters. Clusters occur on all length scales, and as a result occur in a variety of fields. Clusters are interesting scientifically, but they also have important consequences technologically. The division of the book into three parts roughly separates the field into small, intermediate, and large-scale clusters. Small clusters are the regime of atomic and molecular physics and chemistry. The intermediate regime is the transitional regime, with its characteristics including the onset of bulk-like behavior, growth and aggregation, a

Temperature reconstruction and volcanic eruption signal from tree-ring width and maximum latewood density over the past 304 years in the southeastern Tibetan Plateau.

Science.gov (United States)

Li, Mingqi; Huang, Lei; Yin, Zhi-Yong; Shao, Xuemei

2017-11-01

This study presents a 304-year mean July-October maximum temperature reconstruction for the southeastern Tibetan Plateau based on both tree-ring width and maximum latewood density data. The reconstruction explained 58% of the variance in July-October maximum temperature during the calibration period (1958-2005). On the decadal scale, we identified two prominent cold periods during AD 1801-1833 and 1961-2003 and two prominent warm periods during AD 1730-1800 and 1928-1960, which are consistent with other reconstructions from the nearby region. Based on the reconstructed temperature series and volcanic eruption chronology, we found that most extreme cold years were in good agreement with major volcanic eruptions, such as 1816 after the Tambora eruption in 1815. Also, clusters of volcanic eruptions probably made the 1810s the coldest decade in the past 300 years. Our results indicated that fingerprints of major volcanic eruptions can be found in the reconstructed temperature records, while the responses of regional climate to these eruption events varied in space and time in the southeastern Tibetan Plateau.

Design and Application of the Reconstruction Software for the BaBar Calorimeter

International Nuclear Information System (INIS)

Strother, Philip David; Imperial Coll., London

2006-01-01

The BaBar high energy physics experiment will be in operation at the PEP-II asymmetric e + e - collider in Spring 1999. The primary purpose of the experiment is the investigation of CP violation in the neutral B meson system. The electromagnetic calorimeter forms a central part of the experiment and new techniques are employed in data acquisition and reconstruction software to maximize the capability of this device. The use of a matched digital filter in the feature extraction in the front end electronics is presented. The performance of the filter in the presence of the expected high levels of soft photon background from the machine is evaluated. The high luminosity of the PEP-II machine and the demands on the precision of the calorimeter require reliable software that allows for increased physics capability. BaBar has selected C++ as its primary programming language and object oriented analysis and design as its coding paradigm. The application of this technology to the reconstruction software for the calorimeter is presented. The design of the systems for clustering, cluster division, track matching, particle identification and global calibration is discussed with emphasis on the provisions in the design for increased physics capability as levels of understanding of the detector increase. The CP violating channel B 0 → J/Ψ K s 0 has been studied in the two lepton, two π 0 final state. The contribution of this channel to the evaluation of the angle sin 2β of the unitarity triangle is compared to that from the charged pion final state. An error of 0.34 on this quantity is expected after 1 year of running at design luminosity

Intra-specific genetic relationship analyses of Elaeagnus angustifolia based on RP-HPLC biochemical markers

Institute of Scientific and Technical Information of China (English)

无

2006-01-01

Elaeagnus angustifolia Linn. has various ecological, medicinal and economical uses. An approach was established using RP-HPLC (reversed-phase high-performance liquid chromatography) to classify and analyse the intra-specific genetic relationships of seventeen populations of E. angustifolia, collected from the Xinjiang areas of China. Chromatograms of alcohol-soluble proteins produced by seventeen populations ofE. angustifolia, were compared. Each chromatogram of alcohol-soluble proteins came from a single seed of one wild plant only. The results showed that when using a Waters Delta Pak. C18, 5 μm particle size reversed phase column (150 mm×3.9 mm), a linear gradient of 25%～60% solvent B with flow rate of 1 ml/min and run time of 67 min, the chromatography yielded optimum separation ofE. angustifolia alcohol-soluble proteins. Representative peaks in each population were chosen according to peak area and occurrence in every seed. The converted data on the elution peaks of each population were different and could be used to represent those populations. GSC (genetic similarity coefficients) of 41% to 62% showed a medium degree of genetic diversity among the populations in these eco-areas. Cluster analysis showed that the seventeen populations ofE. angustifolia could be divided into six clusters at the GSC=0.535 level and indicated the general and unique biochemical markers of these clusters. We suggest that E. angustifolia distribution in these eco-areas could be classified into six variable species. RP-HPLC was shown to be a rapid, repeatable and reliable method for E. angustifolia classification and identification and for analysis of genetic diversity.

Functional Diversity of Haloacid Dehalogenase Superfamily Phosphatases from Saccharomyces cerevisiae: BIOCHEMICAL, STRUCTURAL, AND EVOLUTIONARY INSIGHTS.

Science.gov (United States)

Kuznetsova, Ekaterina; Nocek, Boguslaw; Brown, Greg; Makarova, Kira S; Flick, Robert; Wolf, Yuri I; Khusnutdinova, Anna; Evdokimova, Elena; Jin, Ke; Tan, Kemin; Hanson, Andrew D; Hasnain, Ghulam; Zallot, Rémi; de Crécy-Lagard, Valérie; Babu, Mohan; Savchenko, Alexei; Joachimiak, Andrzej; Edwards, Aled M; Koonin, Eugene V; Yakunin, Alexander F

2015-07-24

The haloacid dehalogenase (HAD)-like enzymes comprise a large superfamily of phosphohydrolases present in all organisms. The Saccharomyces cerevisiae genome encodes at least 19 soluble HADs, including 10 uncharacterized proteins. Here, we biochemically characterized 13 yeast phosphatases from the HAD superfamily, which includes both specific and promiscuous enzymes active against various phosphorylated metabolites and peptides with several HADs implicated in detoxification of phosphorylated compounds and pseudouridine. The crystal structures of four yeast HADs provided insight into their active sites, whereas the structure of the YKR070W dimer in complex with substrate revealed a composite substrate-binding site. Although the S. cerevisiae and Escherichia coli HADs share low sequence similarities, the comparison of their substrate profiles revealed seven phosphatases with common preferred substrates. The cluster of secondary substrates supporting significant activity of both S. cerevisiae and E. coli HADs includes 28 common metabolites that appear to represent the pool of potential activities for the evolution of novel HAD phosphatases. Evolution of novel substrate specificities of HAD phosphatases shows no strict correlation with sequence divergence. Thus, evolution of the HAD superfamily combines the conservation of the overall substrate pool and the substrate profiles of some enzymes with remarkable biochemical and structural flexibility of other superfamily members. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

GibbsCluster: unsupervised clustering and alignment of peptide sequences

DEFF Research Database (Denmark)

Andreatta, Massimo; Alvarez, Bruno; Nielsen, Morten

2017-01-01

motif characterizing each cluster. Several parameters are available to customize cluster analysis, including adjustable penalties for small clusters and overlapping groups and a trash cluster to remove outliers. As an example application, we used the server to deconvolute multiple specificities in large......-scale peptidome data generated by mass spectrometry. The server is available at http://www.cbs.dtu.dk/services/GibbsCluster-2.0....

Diametrical clustering for identifying anti-correlated gene clusters.

Science.gov (United States)

Dhillon, Inderjit S; Marcotte, Edward M; Roshan, Usman

2003-09-01

Clustering genes based upon their expression patterns allows us to predict gene function. Most existing clustering algorithms cluster genes together when their expression patterns show high positive correlation. However, it has been observed that genes whose expression patterns are strongly anti-correlated can also be functionally similar. Biologically, this is not unintuitive-genes responding to the same stimuli, regardless of the nature of the response, are more likely to operate in the same pathways. We present a new diametrical clustering algorithm that explicitly identifies anti-correlated clusters of genes. Our algorithm proceeds by iteratively (i). re-partitioning the genes and (ii). computing the dominant singular vector of each gene cluster; each singular vector serving as the prototype of a 'diametric' cluster. We empirically show the effectiveness of the algorithm in identifying diametrical or anti-correlated clusters. Testing the algorithm on yeast cell cycle data, fibroblast gene expression data, and DNA microarray data from yeast mutants reveals that opposed cellular pathways can be discovered with this method. We present systems whose mRNA expression patterns, and likely their functions, oppose the yeast ribosome and proteosome, along with evidence for the inverse transcriptional regulation of a number of cellular systems.

Partitional clustering algorithms

CERN Document Server

2015-01-01

This book summarizes the state-of-the-art in partitional clustering. Clustering, the unsupervised classification of patterns into groups, is one of the most important tasks in exploratory data analysis. Primary goals of clustering include gaining insight into, classifying, and compressing data. Clustering has a long and rich history that spans a variety of scientific disciplines including anthropology, biology, medicine, psychology, statistics, mathematics, engineering, and computer science. As a result, numerous clustering algorithms have been proposed since the early 1950s. Among these algorithms, partitional (nonhierarchical) ones have found many applications, especially in engineering and computer science. This book provides coverage of consensus clustering, constrained clustering, large scale and/or high dimensional clustering, cluster validity, cluster visualization, and applications of clustering. Examines clustering as it applies to large and/or high-dimensional data sets commonly encountered in reali...

40 CFR 158.2080 - Experimental use permit data requirements-biochemical pesticides.

Science.gov (United States)

2010-07-01

... requirements-biochemical pesticides. 158.2080 Section 158.2080 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Biochemical Pesticides § 158.2080 Experimental use permit data requirements—biochemical pesticides. (a) Sections 158.2081...

Incomplete projection reconstruction of computed tomography based on the modified discrete algebraic reconstruction technique

Science.gov (United States)

Yang, Fuqiang; Zhang, Dinghua; Huang, Kuidong; Gao, Zongzhao; Yang, YaFei

2018-02-01

Based on the discrete algebraic reconstruction technique (DART), this study aims to address and test a new improved algorithm applied to incomplete projection data to generate a high quality reconstruction image by reducing the artifacts and noise in computed tomography. For the incomplete projections, an augmented Lagrangian based on compressed sensing is first used in the initial reconstruction for segmentation of the DART to get higher contrast graphics for boundary and non-boundary pixels. Then, the block matching 3D filtering operator was used to suppress the noise and to improve the gray distribution of the reconstructed image. Finally, simulation studies on the polychromatic spectrum were performed to test the performance of the new algorithm. Study results show a significant improvement in the signal-to-noise ratios (SNRs) and average gradients (AGs) of the images reconstructed from incomplete data. The SNRs and AGs of the new images reconstructed by DART-ALBM were on average 30%-40% and 10% higher than the images reconstructed by DART algorithms. Since the improved DART-ALBM algorithm has a better robustness to limited-view reconstruction, which not only makes the edge of the image clear but also makes the gray distribution of non-boundary pixels better, it has the potential to improve image quality from incomplete projections or sparse projections.

Reconstructing genealogies of serial samples under the assumption of a molecular clock using serial-sample UPGMA.

Science.gov (United States)

Drummond, A; Rodrigo, A G

2000-12-01

Reconstruction of evolutionary relationships from noncontemporaneous molecular samples provides a new challenge for phylogenetic reconstruction methods. With recent biotechnological advances there has been an increase in molecular sequencing throughput, and the potential to obtain serial samples of sequences from populations, including rapidly evolving pathogens, is fast being realized. A new method called the serial-sample unweighted pair grouping method with arithmetic means (sUPGMA) is presented that reconstructs a genealogy or phylogeny of sequences sampled serially in time using a matrix of pairwise distances. The resulting tree depicts the terminal lineages of each sample ending at a different level consistent with the sample's temporal order. Since sUPGMA is a variant of UPGMA, it will perform best when sequences have evolved at a constant rate (i.e., according to a molecular clock). On simulated data, this new method performs better than standard cluster analysis under a variety of longitudinal sampling strategies. Serial-sample UPGMA is particularly useful for analysis of longitudinal samples of viruses and bacteria, as well as ancient DNA samples, with the minimal requirement that samples of sequences be ordered in time.

The Molecular Bases of the Dual Regulation of Bacterial Iron Sulfur Cluster Biogenesis by CyaY and IscX

Directory of Open Access Journals (Sweden)

Salvatore Adinolfi

2018-02-01

Full Text Available IscX (or YfhJ is a protein of unknown function which takes part in the iron-sulfur cluster assembly machinery, a highly specialized and essential metabolic pathway. IscX binds to iron with low affinity and interacts with IscS, the desulfurase central to cluster assembly. Previous studies have suggested a competition between IscX and CyaY, the bacterial ortholog of frataxin, for the same binding surface of IscS. This competition could suggest a link between the two proteins with a functional significance. Using a hybrid approach based on nuclear magnetic resonance, small angle scattering and biochemical methods, we show here that IscX is a modulator of the inhibitory properties of CyaY: by competing for the same site on IscS, the presence of IscX rescues the rates of enzymatic cluster formation which are inhibited by CyaY. The effect is stronger at low iron concentrations, whereas it becomes negligible at high iron concentrations. These results strongly suggest the mechanism of the dual regulation of iron sulfur cluster assembly under the control of iron as the effector.

Reconstructing Sessions from Data Discovery and Access Logs to Build a Semantic Knowledge Base for Improving Data Discovery

Directory of Open Access Journals (Sweden)

Yongyao Jiang

2016-04-01

Full Text Available Big geospatial data are archived and made available through online web discovery and access. However, finding the right data for scientific research and application development is still a challenge. This paper aims to improve the data discovery by mining the user knowledge from log files. Specifically, user web session reconstruction is focused upon in this paper as a critical step for extracting usage patterns. However, reconstructing user sessions from raw web logs has always been difficult, as a session identifier tends to be missing in most data portals. To address this problem, we propose two session identification methods, including time-clustering-based and time-referrer-based methods. We also present the workflow of session reconstruction and discuss the approach of selecting appropriate thresholds for relevant steps in the workflow. The proposed session identification methods and workflow are proven to be able to extract data access patterns for further pattern analyses of user behavior and improvement of data discovery for more relevancy data ranking, suggestion, and navigation.

A phenanthrene derived PARP inhibitor is an extra-centrosomes de-clustering agent exclusively eradicating human cancer cells

Directory of Open Access Journals (Sweden)

Izraeli Shai

2011-09-01

Full Text Available Abstract Background Cells of most human cancers have supernumerary centrosomes. To enable an accurate chromosome segregation and cell division, these cells developed a yet unresolved molecular mechanism, clustering their extra centrosomes at two poles, thereby mimicking mitosis in normal cells. Failure of this bipolar centrosome clustering causes multipolar spindle structures and aberrant chromosomes segregation that prevent normal cell division and lead to 'mitotic catastrophe cell death'. Methods We used cell biology and biochemical methods, including flow cytometry, immunocytochemistry and live confocal imaging. Results We identified a phenanthrene derived PARP inhibitor, known for its activity in neuroprotection under stress conditions, which exclusively eradicated multi-centrosomal human cancer cells (mammary, colon, lung, pancreas, ovarian while acting as extra-centrosomes de-clustering agent in mitosis. Normal human proliferating cells (endothelial, epithelial and mesenchymal cells were not impaired. Despite acting as PARP inhibitor, the cytotoxic activity of this molecule in cancer cells was not attributed to PARP inhibition alone. Conclusion We identified a water soluble phenanthridine that exclusively targets the unique dependence of most human cancer cells on their supernumerary centrosomes bi-polar clustering for their survival. This paves the way for a new selective cancer-targeting therapy, efficient in a wide range of human cancers.

Improving Weak Lensing Mass Map Reconstructions using Gaussian and Sparsity Priors: Application to DES SV

Science.gov (United States)

Jeffrey, N.; Abdalla, F. B.; Lahav, O.; Lanusse, F.; Starck, J.-L.; Leonard, A.; Kirk, D.; Chang, C.; Baxter, E.; Kacprzak, T.; Seitz, S.; Vikram, V.; Whiteway, L.; Abbott, T. M. C.; Allam, S.; Avila, S.; Bertin, E.; Brooks, D.; Rosell, A. Carnero; Kind, M. Carrasco; Carretero, J.; Castander, F. J.; Crocce, M.; Cunha, C. E.; D'Andrea, C. B.; da Costa, L. N.; Davis, C.; De Vicente, J.; Desai, S.; Doel, P.; Eifler, T. F.; Evrard, A. E.; Flaugher, B.; Fosalba, P.; Frieman, J.; García-Bellido, J.; Gerdes, D. W.; Gruen, D.; Gruendl, R. A.; Gschwend, J.; Gutierrez, G.; Hartley, W. G.; Honscheid, K.; Hoyle, B.; James, D. J.; Jarvis, M.; Kuehn, K.; Lima, M.; Lin, H.; March, M.; Melchior, P.; Menanteau, F.; Miquel, R.; Plazas, A. A.; Reil, K.; Roodman, A.; Sanchez, E.; Scarpine, V.; Schubnell, M.; Sevilla-Noarbe, I.; Smith, M.; Soares-Santos, M.; Sobreira, F.; Suchyta, E.; Swanson, M. E. C.; Tarle, G.; Thomas, D.; Walker, A. R.

2018-05-01

Mapping the underlying density field, including non-visible dark matter, using weak gravitational lensing measurements is now a standard tool in cosmology. Due to its importance to the science results of current and upcoming surveys, the quality of the convergence reconstruction methods should be well understood. We compare three methods: Kaiser-Squires (KS), Wiener filter, and GLIMPSE. KS is a direct inversion, not accounting for survey masks or noise. The Wiener filter is well-motivated for Gaussian density fields in a Bayesian framework. GLIMPSE uses sparsity, aiming to reconstruct non-linearities in the density field. We compare these methods with several tests using public Dark Energy Survey (DES) Science Verification (SV) data and realistic DES simulations. The Wiener filter and GLIMPSE offer substantial improvements over smoothed KS with a range of metrics. Both the Wiener filter and GLIMPSE convergence reconstructions show a 12% improvement in Pearson correlation with the underlying truth from simulations. To compare the mapping methods' abilities to find mass peaks, we measure the difference between peak counts from simulated ΛCDM shear catalogues and catalogues with no mass fluctuations (a standard data vector when inferring cosmology from peak statistics); the maximum signal-to-noise of these peak statistics is increased by a factor of 3.5 for the Wiener filter and 9 for GLIMPSE. With simulations we measure the reconstruction of the harmonic phases; the phase residuals' concentration is improved 17% by GLIMPSE and 18% by the Wiener filter. The correlation between reconstructions from data and foreground redMaPPer clusters is increased 18% by the Wiener filter and 32% by GLIMPSE.

A dynamic evolutionary clustering perspective: Community detection in signed networks by reconstructing neighbor sets

Science.gov (United States)

Chen, Jianrui; Wang, Hua; Wang, Lina; Liu, Weiwei

2016-04-01

Community detection in social networks has been intensively studied in recent years. In this paper, a novel similarity measurement is defined according to social balance theory for signed networks. Inter-community positive links are found and deleted due to their low similarity. The positive neighbor sets are reconstructed by this method. Then, differential equations are proposed to imitate the constantly changing states of nodes. Each node will update its state based on the difference between its state and average state of its positive neighbors. Nodes in the same community will evolve together with time and nodes in the different communities will evolve far away. Communities are detected ultimately when states of nodes are stable. Experiments on real world and synthetic networks are implemented to verify detection performance. The thorough comparisons demonstrate the presented method is more efficient than two acknowledged better algorithms.

Identification and functional analysis of gene cluster involvement in biosynthesis of the cyclic lipopeptide antibiotic pelgipeptin produced by Paenibacillus elgii

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Qian Chao-Dong

2012-09-01

Full Text Available Abstract Background Pelgipeptin, a potent antibacterial and antifungal agent, is a non-ribosomally synthesised lipopeptide antibiotic. This compound consists of a β-hydroxy fatty acid and nine amino acids. To date, there is no information about its biosynthetic pathway. Results A potential pelgipeptin synthetase gene cluster (plp was identified from Paenibacillus elgii B69 through genome analysis. The gene cluster spans 40.8 kb with eight open reading frames. Among the genes in this cluster, three large genes, plpD, plpE, and plpF, were shown to encode non-ribosomal peptide synthetases (NRPSs, with one, seven, and one module(s, respectively. Bioinformatic analysis of the substrate specificity of all nine adenylation domains indicated that the sequence of the NRPS modules is well collinear with the order of amino acids in pelgipeptin. Additional biochemical analysis of four recombinant adenylation domains (PlpD A1, PlpE A1, PlpE A3, and PlpF A1 provided further evidence that the plp gene cluster involved in pelgipeptin biosynthesis. Conclusions In this study, a gene cluster (plp responsible for the biosynthesis of pelgipeptin was identified from the genome sequence of Paenibacillus elgii B69. The identification of the plp gene cluster provides an opportunity to develop novel lipopeptide antibiotics by genetic engineering.

Cluster Matters

DEFF Research Database (Denmark)

Gulati, Mukesh; Lund-Thomsen, Peter; Suresh, Sangeetha

2018-01-01

sell their products successfully in international markets, but there is also an increasingly large consumer base within India. Indeed, Indian industrial clusters have contributed to a substantial part of this growth process, and there are several hundred registered clusters within the country...... of this handbook, which focuses on the role of CSR in MSMEs. Hence we contribute to the literature on CSR in industrial clusters and specifically CSR in Indian industrial clusters by investigating the drivers of CSR in India’s industrial clusters....

Weighted Clustering

DEFF Research Database (Denmark)

Ackerman, Margareta; Ben-David, Shai; Branzei, Simina

2012-01-01

We investigate a natural generalization of the classical clustering problem, considering clustering tasks in which different instances may have different weights.We conduct the first extensive theoretical analysis on the influence of weighted data on standard clustering algorithms in both...... the partitional and hierarchical settings, characterizing the conditions under which algorithms react to weights. Extending a recent framework for clustering algorithm selection, we propose intuitive properties that would allow users to choose between clustering algorithms in the weighted setting and classify...

Cluster implementation for parallel computation within MATLAB software environment

International Nuclear Information System (INIS)

Santana, Antonio O. de; Dantas, Carlos C.; Charamba, Luiz G. da R.; Souza Neto, Wilson F. de; Melo, Silvio B. Melo; Lima, Emerson A. de O.

2013-01-01

A cluster for parallel computation with MATLAB software the COCGT - Cluster for Optimizing Computing in Gamma ray Transmission methods, is implemented. The implementation correspond to creation of a local net of computers, facilities and configurations of software, as well as the accomplishment of cluster tests for determine and optimizing of performance in the data processing. The COCGT implementation was required by data computation from gamma transmission measurements applied to fluid dynamic and tomography reconstruction in a FCC-Fluid Catalytic Cracking cold pilot unity, and simulation data as well. As an initial test the determination of SVD - Singular Values Decomposition - of random matrix with dimension (n , n), n=1000, using the Girco's law modified, revealed that COCGT was faster in comparison to the literature [1] cluster, which is similar and operates at the same conditions. Solution of a system of linear equations provided a new test for the COCGT performance by processing a square matrix with n=10000, computing time was 27 s and for square matrix with n=12000, computation time was 45 s. For determination of the cluster behavior in relation to 'parfor' (parallel for-loop) and 'spmd' (single program multiple data), two codes were used containing those two commands and the same problem: determination of SVD of a square matrix with n= 1000. The execution of codes by means of COCGT proved: 1) for the code with 'parfor', the performance improved with the labs number from 1 to 8 labs; 2) for the code 'spmd', just 1 lab (core) was enough to process and give results in less than 1 s. In similar situation, with the difference that now the SVD will be determined from square matrix with n1500, for code with 'parfor', and n=7000, for code with 'spmd'. That results take to conclusions: 1) for the code with 'parfor', the behavior was the same already described above; 2) for code with 'spmd', the same besides having produced a larger performance, it supports a

Accurate atom-mapping computation for biochemical reactions.

Science.gov (United States)

Latendresse, Mario; Malerich, Jeremiah P; Travers, Mike; Karp, Peter D

2012-11-26

The complete atom mapping of a chemical reaction is a bijection of the reactant atoms to the product atoms that specifies the terminus of each reactant atom. Atom mapping of biochemical reactions is useful for many applications of systems biology, in particular for metabolic engineering where synthesizing new biochemical pathways has to take into account for the number of carbon atoms from a source compound that are conserved in the synthesis of a target compound. Rapid, accurate computation of the atom mapping(s) of a biochemical reaction remains elusive despite significant work on this topic. In particular, past researchers did not validate the accuracy of mapping algorithms. We introduce a new method for computing atom mappings called the minimum weighted edit-distance (MWED) metric. The metric is based on bond propensity to react and computes biochemically valid atom mappings for a large percentage of biochemical reactions. MWED models can be formulated efficiently as Mixed-Integer Linear Programs (MILPs). We have demonstrated this approach on 7501 reactions of the MetaCyc database for which 87% of the models could be solved in less than 10 s. For 2.1% of the reactions, we found multiple optimal atom mappings. We show that the error rate is 0.9% (22 reactions) by comparing these atom mappings to 2446 atom mappings of the manually curated Kyoto Encyclopedia of Genes and Genomes (KEGG) RPAIR database. To our knowledge, our computational atom-mapping approach is the most accurate and among the fastest published to date. The atom-mapping data will be available in the MetaCyc database later in 2012; the atom-mapping software will be available within the Pathway Tools software later in 2012.

New experimental investigation of cluster structures in 10 Be and 16 C neutron-rich nuclei

Science.gov (United States)

Dell'Aquila, L.; Acosta, D.; Auditore, L.; Cardella, G.; De Filippo, E.; De Luca, S.; Francalanza, L.; Gnoffo, B.; Lanzalone, G.; Lombardo, I.; Martorana, N. S.; Norella, S.; Pagano, A.; Pagano, E. V.; Papa, M.; Pirrone, S.; Politi, G.; Quattrocchi, L.; Rizzo, F.; Russotto, P.; Trifirò, A.; Trimarchi, M.; Verde, G.; Vigilante, M.

2017-11-01

The existence of cluster structures in ^{10} Be and ^{16} C neutron-rich isotopes is investigated via projectile break-up reactions induced on polyethylene (CH _2 target. We used a fragmentation beam constituted by 55MeV/u ^{10} Be and 49MeV/u ^{16} C beams provided by the FRIBs facility at INFN-LNS. Invariant mass spectra of 4{He}+ 6 He and 6{He} + ^{10} Be breakup fragments are reconstructed by means of the CHIMERA 4π detector to investigate the presence of excited states of projectile nuclei characterized by cluster structure. In the first case, we suggest the presence of a new state in ^{10} Be at 13.5MeV. A non-vanishing yield corresponding to 20.6MeV excitation energy of ^{16} C was observed in the 6{He} + ^{10} Be cluster decay channel. To improve the results of the present analysis, a new experiment has been performed recently, taking advantage of the coupling of CHIMERA and FARCOS. In the paper we describe the data reduction process of the new experiment together with preliminary results.

Support Policies in Clusters: Prioritization of Support Needs by Cluster Members According to Cluster Life Cycle

Directory of Open Access Journals (Sweden)

Gulcin Salıngan

2012-07-01

Full Text Available Economic development has always been a moving target. Both the national and local governments have been facing the challenge of implementing the effective and efficient economic policy and program in order to best utilize their limited resources. One of the recent approaches in this area is called cluster-based economic analysis and strategy development. This study reviews key literature and some of the cluster based economic policies adopted by different governments. Based on this review, it proposes “the cluster life cycle” as a determining factor to identify the support requirements of clusters. A survey, designed based on literature review of International Cluster support programs, was conducted with 30 participants from 3 clusters with different maturity stage. This paper discusses the results of this study conducted among the cluster members in Eskişehir- Bilecik-Kütahya Region in Turkey on the requirement of the support to foster the development of related clusters.

Biochemical Removal of HAP Precursors From Coal

Energy Technology Data Exchange (ETDEWEB)

Olson, G.; Tucker, L.; Richards, J.

1997-07-01

This project addresses DOE`s interest in advanced concepts for controlling emissions of air toxics from coal-fired utility boilers. We are determining the feasibility of developing a biochemical process for the precombustion removal of substantial percentages of 13 inorganic hazardous air pollutant (HAP) precursors from coal. These HAP precursors are Sb, As, Be, Cd, Cr, Cl, Co, F, Pb, Hg, Mn, Ni, and Se. Although rapid physical coal cleaning is done routinely in preparation plants, biochemical processes for removal of HAP precursors from coal potentially offer advantages of deeper cleaning, more specificity, and less coal loss. Compared to chemical processes for coal cleaning, biochemical processes potentially offer lower costs and milder process conditions. Pyrite oxidizing bacteria, most notably Thiobacillusferrooxidans, are being evaluated in this project for their ability to remove HAP precursors from U.S. coals.

Biochemical Removal of HAP Precursors From Coal

International Nuclear Information System (INIS)

Olson, G.; Tucker, L.; Richards, J.

1997-07-01

This project addresses DOE's interest in advanced concepts for controlling emissions of air toxics from coal-fired utility boilers. We are determining the feasibility of developing a biochemical process for the precombustion removal of substantial percentages of 13 inorganic hazardous air pollutant (HAP) precursors from coal. These HAP precursors are Sb, As, Be, Cd, Cr, Cl, Co, F, Pb, Hg, Mn, Ni, and Se. Although rapid physical coal cleaning is done routinely in preparation plants, biochemical processes for removal of HAP precursors from coal potentially offer advantages of deeper cleaning, more specificity, and less coal loss. Compared to chemical processes for coal cleaning, biochemical processes potentially offer lower costs and milder process conditions. Pyrite oxidizing bacteria, most notably Thiobacillusferrooxidans, are being evaluated in this project for their ability to remove HAP precursors from U.S. coals

Sharing the Burden? Assessing the Lithuanian Decision to Establish a Provincial Reconstruction Team in Afghanistan

Directory of Open Access Journals (Sweden)

Maskaliūnaitė Asta

2014-12-01

Full Text Available The paper assesses theories explaining the states’ burden-sharing decisions in an alliance and uses them to evaluate the Lithuanian decision to establish a Provincial Reconstruction Team (PRT in Afghanistan. In the literature, several influences on such decision-making are identified. These fall into two broad categories of systemic and domestic factors. From the former, threat perception, alliance dependence, systemic pressures of alliance politics are analysed; and from the latter three clusters of aspects such as: state autonomy, elite consensus, space of manoeuver of the executive; bureaucratic politics and organizational interests, and third, some additional elements of strategic culture/state identity. While most factors have some explanatory value, the analysis invites the conclusion that in case of the decision to lead a PRT, the two most important elements were alliance dependence from the first cluster and strategic culture and bureaucratic politics from the second.

Ultra fast, accurate PET image reconstruction for the Siemens hybrid MR/BrainPET scanner using raw LOR data

International Nuclear Information System (INIS)

Scheins, Juergen; Lerche, Christoph; Shah, Jon

2015-01-01

Fast PET image reconstruction algorithms usually use a Line-of-Response (LOR) preprocessing step where the detected raw LOR data are interpolated either to evenly spaced sinogram projection bins or alternatively to a generic projection space as for example proposed by the PET Reconstruction Software Toolkit (PRESTO) [1]. In this way, speed-optimised, versatile geometrical projectors can be implemented for iterative image reconstruction independent of the underlying scanner geometry. However, all strategies of projection data interpolation unavoidably lead to a loss of original information and result in some degradation of image quality. Here, direct LOR reconstructions overcome this evident drawback at cost of a massively enhanced computational burden. Therefore, computational optimisation techniques are essential to make such demanding approaches attractive and economical for widespread usage in the clinical environment. In this paper, we demonstrate for the Siemens Hybrid MR/BrainPET with 240 million physical LORs that a very fast quantitative direct LOR reconstruction can be realized using a modified version of PRESTO. Now, PRESTO is also capable to directly use sets of symmetric physical LORs instead of interpolating LORs to a generic projection space. Exploiting basic scanner symmetries together with the technique of Single Instruction Multipe Data (SIMD) and Simultaneous Multi-Threading (SMT) results in an overall calculation time of 2-3 minutes per frame on a single multi-core machine, i.e. neither requiring a cluster of mutliple machines nor Graphics Processing Units (GPUs).

Ultra fast, accurate PET image reconstruction for the Siemens hybrid MR/BrainPET scanner using raw LOR data

Energy Technology Data Exchange (ETDEWEB)

Scheins, Juergen; Lerche, Christoph; Shah, Jon [Forschungszentrum Jülich GmbH, Jülich (Germany)

2015-05-18

Fast PET image reconstruction algorithms usually use a Line-of-Response (LOR) preprocessing step where the detected raw LOR data are interpolated either to evenly spaced sinogram projection bins or alternatively to a generic projection space as for example proposed by the PET Reconstruction Software Toolkit (PRESTO) [1]. In this way, speed-optimised, versatile geometrical projectors can be implemented for iterative image reconstruction independent of the underlying scanner geometry. However, all strategies of projection data interpolation unavoidably lead to a loss of original information and result in some degradation of image quality. Here, direct LOR reconstructions overcome this evident drawback at cost of a massively enhanced computational burden. Therefore, computational optimisation techniques are essential to make such demanding approaches attractive and economical for widespread usage in the clinical environment. In this paper, we demonstrate for the Siemens Hybrid MR/BrainPET with 240 million physical LORs that a very fast quantitative direct LOR reconstruction can be realized using a modified version of PRESTO. Now, PRESTO is also capable to directly use sets of symmetric physical LORs instead of interpolating LORs to a generic projection space. Exploiting basic scanner symmetries together with the technique of Single Instruction Multipe Data (SIMD) and Simultaneous Multi-Threading (SMT) results in an overall calculation time of 2-3 minutes per frame on a single multi-core machine, i.e. neither requiring a cluster of mutliple machines nor Graphics Processing Units (GPUs).

Formation of a homocitrate-free iron-molybdenum cluster on NifEN: implications for the role of homocitrate in nitrogenase assembly.

Science.gov (United States)

Fay, Aaron Wolfe; Blank, Michael Aaron; Yoshizawa, Janice Mariko; Lee, Chi Chung; Wiig, Jared Andrew; Hu, Yilin; Hodgson, Keith Owen; Hedman, Britt; Ribbe, Markus Walter

2010-03-28

Molybdenum (Mo)-dependent nitrogenase is a complex metalloprotein that catalyzes the biological reduction of dinitrogen (N(2)) to ammonia (NH(3)) at the molybdenum-iron cofactor (FeMoco) site of its molybdenum-iron (MoFe) protein component. Here we report the formation of a homocitrate-free, iron-molybdenum ("FeMo") cluster on the biosynthetic scaffold of FeMoco, NifEN. Such a NifEN-associated "FeMo" cluster exhibits EPR features similar to those of the NifEN-associated, fully-complemented "FeMoco", which originate from the presence of Mo in both cluster species; however, "FeMo" cluster and "FeMoco" display different temperature-dependent changes in the line shape and the signal intensity of their respective EPR features, which reflect the impact of homocitrate on the redox properties of these clusters. XAS/EXAFS analysis reveals that the Mo centers in both "FeMo" cluster and "FeMoco" are present in a similar coordination environment, although Mo in "FeMo" cluster is more loosely coordinated as compared to that in "FeMoco" with respect to the Mo-O distances in the cluster, likely due to the absence of homocitrate that normally serves as an additional ligand for the Mo in the cluster. Subsequent biochemical investigation of the "FeMo" cluster not only facilitates the determination of the sequence of events in the mobilization of Mo and homocitrate during FeMoco maturation, but also permits the examination of the role of homocitrate in the transfer of FeMoco between NifEN and MoFe protein. Combined outcome of these studies establishes a platform for future structural analysis of the interactions between NifEN and MoFe protein, which will provide useful insights into the mechanism of cluster transfer between the two proteins.

Output ordering and prioritisation system (OOPS): ranking biosynthetic gene clusters to enhance bioactive metabolite discovery.

Science.gov (United States)

Peña, Alejandro; Del Carratore, Francesco; Cummings, Matthew; Takano, Eriko; Breitling, Rainer

2017-12-18

The rapid increase of publicly available microbial genome sequences has highlighted the presence of hundreds of thousands of biosynthetic gene clusters (BGCs) encoding valuable secondary metabolites. The experimental characterization of new BGCs is extremely laborious and struggles to keep pace with the in silico identification of potential BGCs. Therefore, the prioritisation of promising candidates among computationally predicted BGCs represents a pressing need. Here, we propose an output ordering and prioritisation system (OOPS) which helps sorting identified BGCs by a wide variety of custom-weighted biological and biochemical criteria in a flexible and user-friendly interface. OOPS facilitates a judicious prioritisation of BGCs using G+C content, coding sequence length, gene number, cluster self-similarity and codon bias parameters, as well as enabling the user to rank BGCs based upon BGC type, novelty, and taxonomic distribution. Effective prioritisation of BGCs will help to reduce experimental attrition rates and improve the breadth of bioactive metabolites characterized.

Clusters and how to make it work : toolkit for cluster strategy

NARCIS (Netherlands)

Manickam, Anu; van Berkel, Karel

2013-01-01

Clusters are the magic answer to regional economic development. Firms in clusters are more innovative; cluster policy dominates EU policy; ‘top-sectors’ and excellence are the choice of national policy makers; clusters are ‘in’. But, clusters are complex, clusters are ‘messy’; there is no clear

Hybrid spectral CT reconstruction.

Directory of Open Access Journals (Sweden)

Darin P Clark

Full Text Available Current photon counting x-ray detector (PCD technology faces limitations associated with spectral fidelity and photon starvation. One strategy for addressing these limitations is to supplement PCD data with high-resolution, low-noise data acquired with an energy-integrating detector (EID. In this work, we propose an iterative, hybrid reconstruction technique which combines the spectral properties of PCD data with the resolution and signal-to-noise characteristics of EID data. Our hybrid reconstruction technique is based on an algebraic model of data fidelity which substitutes the EID data into the data fidelity term associated with the PCD reconstruction, resulting in a joint reconstruction problem. Within the split Bregman framework, these data fidelity constraints are minimized subject to additional constraints on spectral rank and on joint intensity-gradient sparsity measured between the reconstructions of the EID and PCD data. Following a derivation of the proposed technique, we apply it to the reconstruction of a digital phantom which contains realistic concentrations of iodine, barium, and calcium encountered in small-animal micro-CT. The results of this experiment suggest reliable separation and detection of iodine at concentrations ≥ 5 mg/ml and barium at concentrations ≥ 10 mg/ml in 2-mm features for EID and PCD data reconstructed with inherent spatial resolutions of 176 μm and 254 μm, respectively (point spread function, FWHM. Furthermore, hybrid reconstruction is demonstrated to enhance spatial resolution within material decomposition results and to improve low-contrast detectability by as much as 2.6 times relative to reconstruction with PCD data only. The parameters of the simulation experiment are based on an in vivo micro-CT experiment conducted in a mouse model of soft-tissue sarcoma. Material decomposition results produced from this in vivo data demonstrate the feasibility of distinguishing two K-edge contrast agents with

Hybrid spectral CT reconstruction

Science.gov (United States)

Clark, Darin P.

2017-01-01

Current photon counting x-ray detector (PCD) technology faces limitations associated with spectral fidelity and photon starvation. One strategy for addressing these limitations is to supplement PCD data with high-resolution, low-noise data acquired with an energy-integrating detector (EID). In this work, we propose an iterative, hybrid reconstruction technique which combines the spectral properties of PCD data with the resolution and signal-to-noise characteristics of EID data. Our hybrid reconstruction technique is based on an algebraic model of data fidelity which substitutes the EID data into the data fidelity term associated with the PCD reconstruction, resulting in a joint reconstruction problem. Within the split Bregman framework, these data fidelity constraints are minimized subject to additional constraints on spectral rank and on joint intensity-gradient sparsity measured between the reconstructions of the EID and PCD data. Following a derivation of the proposed technique, we apply it to the reconstruction of a digital phantom which contains realistic concentrations of iodine, barium, and calcium encountered in small-animal micro-CT. The results of this experiment suggest reliable separation and detection of iodine at concentrations ≥ 5 mg/ml and barium at concentrations ≥ 10 mg/ml in 2-mm features for EID and PCD data reconstructed with inherent spatial resolutions of 176 μm and 254 μm, respectively (point spread function, FWHM). Furthermore, hybrid reconstruction is demonstrated to enhance spatial resolution within material decomposition results and to improve low-contrast detectability by as much as 2.6 times relative to reconstruction with PCD data only. The parameters of the simulation experiment are based on an in vivo micro-CT experiment conducted in a mouse model of soft-tissue sarcoma. Material decomposition results produced from this in vivo data demonstrate the feasibility of distinguishing two K-edge contrast agents with a spectral

Craniometaphyseal dysplasia with obvious biochemical abnormality and rickets-like features.

Science.gov (United States)

Wu, Bo; Jiang, Yan; Wang, Ou; Li, Mei; Xing, Xiao-Ping; Xia, Wei-Bo

2016-05-01

Craniometaphyseal dysplasia (CMD) is a rare genetic disorder that is characterized by progressive sclerosis of the craniofacial bones and metaphyseal widening of long bones, and biochemical indexes were mostly normal. To further the understanding of the disease from a biochemical perspective, we reported a CMD case with obviously abnormal biochemical indexes. A 1-year-old boy was referred to our clinic. Biochemical test showed obviously increased alkaline phosphatase (ALP) and parathyroid hormone (PTH), mild hypocalcemia and hypophosphatemia. Moreover, significant elevated receptor activator of nuclear factor kappa-B ligand (RANKL) level, but normal β-C-terminal telopeptide of type I collagen (β-CTX) concentration were revealed. He was initially suspected of rickets, because the radiological examination also showed broadened epiphysis in his long bones. Supplementation with calcium and calcitriol alleviated biochemical abnormality. However, the patient gradually developed osteosclerosis which was inconformity with rickets. Considering that he was also presented with facial paralysis and nasal obstruction symptom, the diagnosis of craniometaphyseal dysplasia was suspected, and then was confirmed by the mutation analysis of ANKH of the proband and his family, which showed a de novo heterozygous mutation (C1124-1126delCCT) on exon 9. Our study revealed that obvious biochemical abnormality and rickets-like features might present as uncommon characteristics in CMD patients, and the calcium and calcitriol supplementation could alleviate biochemical abnormalities. Furthermore, although early osteoclast differentiation factor was excited in CMD patient, activity of osteoclast was still inert. Copyright © 2016. Published by Elsevier B.V.

Determination of atomic cluster structure with cluster fusion algorithm

DEFF Research Database (Denmark)

Obolensky, Oleg I.; Solov'yov, Ilia; Solov'yov, Andrey V.

2005-01-01

We report an efficient scheme of global optimization, called cluster fusion algorithm, which has proved its reliability and high efficiency in determination of the structure of various atomic clusters.......We report an efficient scheme of global optimization, called cluster fusion algorithm, which has proved its reliability and high efficiency in determination of the structure of various atomic clusters....

Large-Scale Multi-Dimensional Document Clustering on GPU Clusters

Energy Technology Data Exchange (ETDEWEB)

Cui, Xiaohui [ORNL; Mueller, Frank [North Carolina State University; Zhang, Yongpeng [ORNL; Potok, Thomas E [ORNL

2010-01-01

Document clustering plays an important role in data mining systems. Recently, a flocking-based document clustering algorithm has been proposed to solve the problem through simulation resembling the flocking behavior of birds in nature. This method is superior to other clustering algorithms, including k-means, in the sense that the outcome is not sensitive to the initial state. One limitation of this approach is that the algorithmic complexity is inherently quadratic in the number of documents. As a result, execution time becomes a bottleneck with large number of documents. In this paper, we assess the benefits of exploiting the computational power of Beowulf-like clusters equipped with contemporary Graphics Processing Units (GPUs) as a means to significantly reduce the runtime of flocking-based document clustering. Our framework scales up to over one million documents processed simultaneously in a sixteennode GPU cluster. Results are also compared to a four-node cluster with higher-end GPUs. On these clusters, we observe 30X-50X speedups, which demonstrates the potential of GPU clusters to efficiently solve massive data mining problems. Such speedups combined with the scalability potential and accelerator-based parallelization are unique in the domain of document-based data mining, to the best of our knowledge.

Membership determination of open clusters based on a spectral clustering method

Science.gov (United States)

Gao, Xin-Hua

2018-06-01

We present a spectral clustering (SC) method aimed at segregating reliable members of open clusters in multi-dimensional space. The SC method is a non-parametric clustering technique that performs cluster division using eigenvectors of the similarity matrix; no prior knowledge of the clusters is required. This method is more flexible in dealing with multi-dimensional data compared to other methods of membership determination. We use this method to segregate the cluster members of five open clusters (Hyades, Coma Ber, Pleiades, Praesepe, and NGC 188) in five-dimensional space; fairly clean cluster members are obtained. We find that the SC method can capture a small number of cluster members (weak signal) from a large number of field stars (heavy noise). Based on these cluster members, we compute the mean proper motions and distances for the Hyades, Coma Ber, Pleiades, and Praesepe clusters, and our results are in general quite consistent with the results derived by other authors. The test results indicate that the SC method is highly suitable for segregating cluster members of open clusters based on high-precision multi-dimensional astrometric data such as Gaia data.

Developments in commercially produced microbials at Biochem Products

Science.gov (United States)

John Lublinkhof; Douglas H. Ross

1985-01-01

Biochem Products is part of a large industrial and scientific family - the Solvay Group. Solvay, headquartered in Brussels, Belgium is a multinational company with 46,000 employees worldwide. In the U.S., our working partners include a large polymer manufacturer, a peroxygen producer and a leading poultry and animal health products company. Biochem Products is a...

Kombucha tea fermentation: Microbial and biochemical dynamics.

Science.gov (United States)

Chakravorty, Somnath; Bhattacharya, Semantee; Chatzinotas, Antonis; Chakraborty, Writachit; Bhattacharya, Debanjana; Gachhui, Ratan

2016-03-02

Kombucha tea, a non-alcoholic beverage, is acquiring significant interest due to its claimed beneficial properties. The microbial community of Kombucha tea consists of bacteria and yeast which thrive in two mutually non-exclusive compartments: the soup or the beverage and the biofilm floating on it. The microbial community and the biochemical properties of the beverage have so far mostly been described in separate studies. This, however, may prevent understanding the causal links between the microbial communities and the beneficial properties of Kombucha tea. Moreover, an extensive study into the microbial and biochemical dynamics has also been missing. In this study, we thus explored the structure and dynamics of the microbial community along with the biochemical properties of Kombucha tea at different time points up to 21 days of fermentation. We hypothesized that several biochemical properties will change during the course of fermentation along with the shifts in the yeast and bacterial communities. The yeast community of the biofilm did not show much variation over time and was dominated by Candida sp. (73.5-83%). The soup however, showed a significant shift in dominance from Candida sp. to Lachancea sp. on the 7th day of fermentation. This is the first report showing Candida as the most dominating yeast genus during Kombucha fermentation. Komagateibacter was identified as the single largest bacterial genus present in both the biofilm and the soup (~50%). The bacterial diversity was higher in the soup than in the biofilm with a peak on the seventh day of fermentation. The biochemical properties changed with the progression of the fermentation, i.e., beneficial properties of the beverage such as the radical scavenging ability increased significantly with a maximum increase at day 7. We further observed a significantly higher D-saccharic acid-1,4-lactone content and caffeine degradation property compared to previously described Kombucha tea fermentations. Our

Biochemical markers of bone turnover

International Nuclear Information System (INIS)

Kim, Deog Yoon

1999-01-01

Biochemical markers of bone turnover has received increasing attention over the past few years, because of the need for sensitivity and specific tool in the clinical investigation of osteoporosis. Bone markers should be unique to bone, reflect changes of bone less, and should be correlated with radiocalcium kinetics, histomorphometry, or changes in bone mass. The markers also should be useful in monitoring treatment efficacy. Although no bone marker has been established to meet all these criteria, currently osteocalcin and pyridinium crosslinks are the most efficient markers to assess the level of bone turnover in the menopausal and senile osteoporosis. Recently, N-terminal telopeptide (NTX), C-terminal telopeptide (CTX) and bone specific alkaline phosphatase are considered as new valid markers of bone turnover. Recent data suggest that CTX and free deoxypyridinoline could predict the subsequent risk of hip fracture of elderly women. Treatment of postmenopausal women with estrogen, calcitonin and bisphosphonates demonstrated rapid decrease of the levels of bone markers that correlated with the long-term increase of bone mass. Factors such as circadian rhythms, diet, age, sex, bone mass and renal function affect the results of biochemical markers and should be appropriately adjusted whenever possible. Each biochemical markers of bone turnover may have its own specific advantages and limitations. Recent advances in research will provide more sensitive and specific assays

Cluster headache

Science.gov (United States)

Histamine headache; Headache - histamine; Migrainous neuralgia; Headache - cluster; Horton's headache; Vascular headache - cluster ... Doctors do not know exactly what causes cluster headaches. They ... (chemical in the body released during an allergic response) or ...

Tomographic reconstruction by using FPSIRT (Fast Particle System Iterative Reconstruction Technique)

Energy Technology Data Exchange (ETDEWEB)

Moreira, Icaro Valgueiro M.; Melo, Silvio de Barros; Dantas, Carlos; Lima, Emerson Alexandre; Silva, Ricardo Martins; Cardoso, Halisson Alberdan C., E-mail: ivmm@cin.ufpe.br, E-mail: sbm@cin.ufpe.br, E-mail: rmas@cin.ufpe.br, E-mail: hacc@cin.ufpe.br, E-mail: ccd@ufpe.br, E-mail: eal@cin.ufpe.br [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil)

2015-07-01

The PSIRT (Particle System Iterative Reconstruction Technique) is a method of tomographic image reconstruction primarily designed to work with configurations suitable for industrial applications. A particle system is an optimization technique inspired in real physical systems that associates to the reconstructing material a set of particles with certain physical features, subject to a force eld, which can produce movement. The system constantly updates the set of particles by repositioning them in such a way as to approach the equilibrium. The elastic potential along a trajectory is a function of the difference between the attenuation coefficient in the current configuration and the corresponding input data. PSIRT has been successfully used to reconstruct simulated and real objects subject to sets of parallel and fanbeam lines in different angles, representing typical gamma-ray tomographic arrangements. One of PSIRT's limitation was its performance, too slow for real time scenarios. In this work, it is presented a reformulation in PSIRT's computational model, which is able to grant the new algorithm, the FPSIRT - Fast System Iterative Reconstruction Technique, a performance up to 200-time faster than PSIRT's. In this work a comparison of their application to real and simulated data from the HSGT, High Speed Gamma Tomograph, is presented. (author)

Tomographic reconstruction by using FPSIRT (Fast Particle System Iterative Reconstruction Technique)

International Nuclear Information System (INIS)

Moreira, Icaro Valgueiro M.; Melo, Silvio de Barros; Dantas, Carlos; Lima, Emerson Alexandre; Silva, Ricardo Martins; Cardoso, Halisson Alberdan C.

2015-01-01

The PSIRT (Particle System Iterative Reconstruction Technique) is a method of tomographic image reconstruction primarily designed to work with configurations suitable for industrial applications. A particle system is an optimization technique inspired in real physical systems that associates to the reconstructing material a set of particles with certain physical features, subject to a force eld, which can produce movement. The system constantly updates the set of particles by repositioning them in such a way as to approach the equilibrium. The elastic potential along a trajectory is a function of the difference between the attenuation coefficient in the current configuration and the corresponding input data. PSIRT has been successfully used to reconstruct simulated and real objects subject to sets of parallel and fanbeam lines in different angles, representing typical gamma-ray tomographic arrangements. One of PSIRT's limitation was its performance, too slow for real time scenarios. In this work, it is presented a reformulation in PSIRT's computational model, which is able to grant the new algorithm, the FPSIRT - Fast System Iterative Reconstruction Technique, a performance up to 200-time faster than PSIRT's. In this work a comparison of their application to real and simulated data from the HSGT, High Speed Gamma Tomograph, is presented. (author)

The evolving breast reconstruction

DEFF Research Database (Denmark)

Thomsen, Jørn Bo; Gunnarsson, Gudjon Leifur

2014-01-01

The aim of this editorial is to give an update on the use of the propeller thoracodorsal artery perforator flap (TAP/TDAP-flap) within the field of breast reconstruction. The TAP-flap can be dissected by a combined use of a monopolar cautery and a scalpel. Microsurgical instruments are generally...... not needed. The propeller TAP-flap can be designed in different ways, three of these have been published: (I) an oblique upwards design; (II) a horizontal design; (III) an oblique downward design. The latissimus dorsi-flap is a good and reliable option for breast reconstruction, but has been criticized...... for oncoplastic and reconstructive breast surgery and will certainly become an invaluable addition to breast reconstructive methods....

Reconstructing see-saw models

International Nuclear Information System (INIS)

Ibarra, Alejandro

2007-01-01

In this talk we discuss the prospects to reconstruct the high-energy see-saw Lagrangian from low energy experiments in supersymmetric scenarios. We show that the model with three right-handed neutrinos could be reconstructed in theory, but not in practice. Then, we discuss the prospects to reconstruct the model with two right-handed neutrinos, which is the minimal see-saw model able to accommodate neutrino observations. We identify the relevant processes to achieve this goal, and comment on the sensitivity of future experiments to them. We find the prospects much more promising and we emphasize in particular the importance of the observation of rare leptonic decays for the reconstruction of the right-handed neutrino masses

Silver-induced reconstruction of an adeninate-based metal-organic framework for encapsulation of luminescent adenine-stabilized silver clusters.

Science.gov (United States)

Jonckheere, Dries; Coutino-Gonzalez, Eduardo; Baekelant, Wouter; Bueken, Bart; Reinsch, Helge; Stassen, Ivo; Fenwick, Oliver; Richard, Fanny; Samorì, Paolo; Ameloot, Rob; Hofkens, Johan; Roeffaers, Maarten B J; De Vos, Dirk E

2016-05-21

Bright luminescent silver-adenine species were successfully stabilized in the pores of the MOF-69A (zinc biphenyldicarboxylate) metal-organic framework, starting from the intrinsically blue luminescent bio-MOF-1 (zinc adeninate 4,4'-biphenyldicarboxylate). Bio-MOF-1 is transformed to the MOF-69A framework by selectively leaching structural adenine linkers from the original framework using silver nitrate solutions in aqueous ethanol. Simultaneously, bright blue-green luminescent silver-adenine clusters are formed inside the pores of the recrystallized MOF-69A matrix in high local concentrations. The structural transition and concurrent changes in optical properties were characterized using a range of structural, physicochemical and spectroscopic techniques (steady-state and time-resolved luminescence, quantum yield determination, fluorescence microscopy). The presented results open new avenues for exploring the use of MOFs containing luminescent silver clusters for solid-state lighting and sensor applications.

Measures of Biochemical Sociology

Science.gov (United States)

Snell, Joel; Marsh, Mitchell

2008-01-01

In a previous article, the authors introduced a new sub field in sociology that we labeled "biochemical sociology." We introduced the definition of a sociology that encompasses sociological measures, psychological measures, and biological indicators Snell & Marsh (2003). In this article, we want to demonstrate a research strategy that would assess…

Simulations of the Response of the Cluster Detector/Scintillator Wall for the 4π facility at SIS/ESR using the GEANT Detector program

International Nuclear Information System (INIS)

Herrmann, N.; Maguire, C.F.; Cerruti, C.; Coffin, J.P.; Fintz, P.; Guillaume, G.; Jundt, F.; Rami, F.; Tezkratt, R.; Wagner, P.

1990-01-01

The expected response of the cluster detector/scintillator wall of the SIS/ESR 4π facility has been investigated with the use of the GEANT detector program and the FREESCO event generator code. Results are presented and discussed. It is shown in particular that the efficiency of the track reconstruction method should be acceptable

Single-cluster dynamics for the random-cluster model

NARCIS (Netherlands)

Deng, Y.; Qian, X.; Blöte, H.W.J.

2009-01-01

We formulate a single-cluster Monte Carlo algorithm for the simulation of the random-cluster model. This algorithm is a generalization of the Wolff single-cluster method for the q-state Potts model to noninteger values q>1. Its results for static quantities are in a satisfactory agreement with those

Discovering Reliable Sources of Biochemical Thermodynamic Data to Aid Students' Understanding

Science.gov (United States)

Me´ndez, Eduardo; Cerda´, María F.

2016-01-01

Students of physical chemistry in biochemical disciplines need biochemical examples to capture the need, not always understood, of a difficult area in their studies. The use of thermodynamic data in the chemical reference state may lead to incorrect interpretations in the analysis of biochemical examples when the analysis does not include relevant…

Design and Application of the Reconstruction Software for the BaBar Calorimeter

Energy Technology Data Exchange (ETDEWEB)

Strother, Philip David; /Imperial Coll., London

2006-07-07

The BaBar high energy physics experiment will be in operation at the PEP-II asymmetric e{sup +}e{sup -} collider in Spring 1999. The primary purpose of the experiment is the investigation of CP violation in the neutral B meson system. The electromagnetic calorimeter forms a central part of the experiment and new techniques are employed in data acquisition and reconstruction software to maximize the capability of this device. The use of a matched digital filter in the feature extraction in the front end electronics is presented. The performance of the filter in the presence of the expected high levels of soft photon background from the machine is evaluated. The high luminosity of the PEP-II machine and the demands on the precision of the calorimeter require reliable software that allows for increased physics capability. BaBar has selected C++ as its primary programming language and object oriented analysis and design as its coding paradigm. The application of this technology to the reconstruction software for the calorimeter is presented. The design of the systems for clustering, cluster division, track matching, particle identification and global calibration is discussed with emphasis on the provisions in the design for increased physics capability as levels of understanding of the detector increase. The CP violating channel B{sup 0} {yields} J/{Psi}K{sub S}{sup 0} has been studied in the two lepton, two {pi}{sup 0} final state. The contribution of this channel to the evaluation of the angle sin 2{beta} of the unitarity triangle is compared to that from the charged pion final state. An error of 0.34 on this quantity is expected after 1 year of running at design luminosity.

'BioNessie(G) - a grid enabled biochemical networks simulation environment

OpenAIRE

Liu, X; Jiang, J; Ajayi, O; Gu, X; Gilbert, D; Sinnott, R

2008-01-01

The simulation of biochemical networks provides insight and understanding about the underlying biochemical processes and pathways used by cells and organisms. BioNessie is a biochemical network simulator which has been developed at the University of Glasgow. This paper describes the simulator and focuses in particular on how it has been extended to benefit from a wide variety of high performance compute resources across the UK through Grid technologies to support larger scal...

Mass Profile Decomposition of the Frontier Fields Cluster MACS J0416-2403: Insights on the Dark-matter Inner Profile

Science.gov (United States)

Annunziatella, M.; Bonamigo, M.; Grillo, C.; Mercurio, A.; Rosati, P.; Caminha, G.; Biviano, A.; Girardi, M.; Gobat, R.; Lombardi, M.; Munari, E.

2017-12-01

We present a high-resolution dissection of the two-dimensional total mass distribution in the core of the Hubble Frontier Fields galaxy cluster MACS J0416.1‑2403, at z = 0.396. We exploit HST/WFC3 near-IR (F160W) imaging, VLT/Multi Unit Spectroscopic Explorer spectroscopy, and Chandra data to separate the stellar, hot gas, and dark-matter mass components in the inner 300 kpc of the cluster. We combine the recent results of our refined strong lensing analysis, which includes the contribution of the intracluster gas, with the modeling of the surface brightness and stellar mass distributions of 193 cluster members, of which 144 are spectroscopically confirmed. We find that, moving from 10 to 300 kpc from the cluster center, the stellar to total mass fraction decreases from 12% to 1% and the hot gas to total mass fraction increases from 3% to 9%, resulting in a baryon fraction of approximatively 10% at the outermost radius. We measure that the stellar component represents ∼30%, near the cluster center, and 15%, at larger clustercentric distances, of the total mass in the cluster substructures. We subtract the baryonic mass component from the total mass distribution and conclude that within 30 kpc (∼3 times the effective radius of the brightest cluster galaxy) from the cluster center the surface mass density profile of the total mass and global (cluster plus substructures) dark-matter are steeper and that of the diffuse (cluster) dark-matter is shallower than an NFW profile. Our current analysis does not point to a significant offset between the cluster stellar and dark-matter components. This detailed and robust reconstruction of the inner dark-matter distribution in a larger sample of galaxy clusters will set a new benchmark for different structure formation scenarios.

Pre-operative planning for mandibular reconstruction - A full digital planning workflow resulting in a patient specific reconstruction

Science.gov (United States)

2011-01-01

Objectives Reconstruction of large mandiblular defects following ablative oncologic surgery could be done by using vascularized bone transfer or, more often, primarily with simultaneous or delayed bone grafting, using load bearing reconstruction plates. Bending of these reconstruction plates is typically directed along the outer contour of the original mandible. Simultaneously or in a second operation vascularized or non-vascularized bone is fixed to the reconstruction plate. However, the prosthodontic-driven backward planning to ease bony reconstruction of the mandible in terms of dental rehabilitation using implant-retained overdentures might be an eligible solution. The purpose of this work was to develop, establish and clinically evaluate a novel 3D planning procedure for mandibular reconstruction. Materials and methods Three patients with tumors involving the mandible, which included squamous cell carcinoma in the floor of the mouth and keratocystic odontogenic tumor, were treated surgically by hemimandibulectomy. Results In primary alloplastic mandible reconstruction, shape and size of the reconstruction plate could be predefined and prebent prior to surgery. Clinical relevance This study provides modern treatment strategies for mandibular reconstruction. PMID:21968330

Track reconstruction at the ILC: the ILD tracking software

International Nuclear Information System (INIS)

Gaede, Frank; Aplin, Steven; Rosemann, Christoph; Voutsinas, Georgios; Glattauer, Robin

2014-01-01

One of the key requirements for Higgs physics at the International Linear Collider ILC is excellent track reconstruction with very good momentum and impact parameter resolution. ILD is one of the two detector concepts at the ILC. Its central tracking system comprises of an outer Si-tracker, a highly granular TPC, an intermediate silicon tracker and a pixel vertex detector, and it is complemented by silicon tracking disks in the forward direction. Large hit densities from beam induced coherent electron-positron pairs at the ILC pose an additional challenge to the pattern recognition algorithms. We present the recently developed new ILD tracking software, the pattern recognition algorithms that are using clustering techniques, Cellular Automatons and Kalman filter based track extrapolation. The performance of the ILD tracking system is evaluated using a detailed simulation including dead material, gaps and imperfections.

clusterMaker: a multi-algorithm clustering plugin for Cytoscape

Directory of Open Access Journals (Sweden)

Morris John H

2011-11-01

Full Text Available Abstract Background In the post-genomic era, the rapid increase in high-throughput data calls for computational tools capable of integrating data of diverse types and facilitating recognition of biologically meaningful patterns within them. For example, protein-protein interaction data sets have been clustered to identify stable complexes, but scientists lack easily accessible tools to facilitate combined analyses of multiple data sets from different types of experiments. Here we present clusterMaker, a Cytoscape plugin that implements several clustering algorithms and provides network, dendrogram, and heat map views of the results. The Cytoscape network is linked to all of the other views, so that a selection in one is immediately reflected in the others. clusterMaker is the first Cytoscape plugin to implement such a wide variety of clustering algorithms and visualizations, including the only implementations of hierarchical clustering, dendrogram plus heat map visualization (tree view, k-means, k-medoid, SCPS, AutoSOME, and native (Java MCL. Results Results are presented in the form of three scenarios of use: analysis of protein expression data using a recently published mouse interactome and a mouse microarray data set of nearly one hundred diverse cell/tissue types; the identification of protein complexes in the yeast Saccharomyces cerevisiae; and the cluster analysis of the vicinal oxygen chelate (VOC enzyme superfamily. For scenario one, we explore functionally enriched mouse interactomes specific to particular cellular phenotypes and apply fuzzy clustering. For scenario two, we explore the prefoldin complex in detail using both physical and genetic interaction clusters. For scenario three, we explore the possible annotation of a protein as a methylmalonyl-CoA epimerase within the VOC superfamily. Cytoscape session files for all three scenarios are provided in the Additional Files section. Conclusions The Cytoscape plugin cluster

Characterization and detection of a widely distributed gene cluster that predicts anaerobic choline utilization by human gut bacteria.

Science.gov (United States)

Martínez-del Campo, Ana; Bodea, Smaranda; Hamer, Hilary A; Marks, Jonathan A; Haiser, Henry J; Turnbaugh, Peter J; Balskus, Emily P

2015-04-14

Elucidation of the molecular mechanisms underlying the human gut microbiota's effects on health and disease has been complicated by difficulties in linking metabolic functions associated with the gut community as a whole to individual microorganisms and activities. Anaerobic microbial choline metabolism, a disease-associated metabolic pathway, exemplifies this challenge, as the specific human gut microorganisms responsible for this transformation have not yet been clearly identified. In this study, we established the link between a bacterial gene cluster, the choline utilization (cut) cluster, and anaerobic choline metabolism in human gut isolates by combining transcriptional, biochemical, bioinformatic, and cultivation-based approaches. Quantitative reverse transcription-PCR analysis and in vitro biochemical characterization of two cut gene products linked the entire cluster to growth on choline and supported a model for this pathway. Analyses of sequenced bacterial genomes revealed that the cut cluster is present in many human gut bacteria, is predictive of choline utilization in sequenced isolates, and is widely but discontinuously distributed across multiple bacterial phyla. Given that bacterial phylogeny is a poor marker for choline utilization, we were prompted to develop a degenerate PCR-based method for detecting the key functional gene choline TMA-lyase (cutC) in genomic and metagenomic DNA. Using this tool, we found that new choline-metabolizing gut isolates universally possessed cutC. We also demonstrated that this gene is widespread in stool metagenomic data sets. Overall, this work represents a crucial step toward understanding anaerobic choline metabolism in the human gut microbiota and underscores the importance of examining this microbial community from a function-oriented perspective. Anaerobic choline utilization is a bacterial metabolic activity that occurs in the human gut and is linked to multiple diseases. While bacterial genes responsible for

Reconstruction of emission coefficients for a non-axisymmetric coupling arc by algebraic reconstruction technique

International Nuclear Information System (INIS)

Zhang Guangjun; Xiong Jun; Gao Hongming; Wu Lin

2011-01-01

A preliminary investigation of tomographic reconstruction of an asymmetric arc plasma has been carried out. The objective of this work aims at reconstructing emission coefficients of a non-axisymmetric coupling arc from measured intensities by means of an algebraic reconstruction technique (ART). In order to define the optimal experimental scheme for good quality with limited views, the dependence of the reconstruction quality on three configurations (four, eight, ten projection angles) are presented and discussed via a displaced Gaussian model. Then, the emission coefficients of a free burning arc are reconstructed by the ART with the ten-view configuration and an Abel inversion, respectively, and good agreement is obtained. Finally, the emission coefficient profiles of the coupling arc are successfully achieved with the ten-view configuration. The results show that the distribution of emission coefficient for the coupling arc is different from centrosymmetric shape. The ART is perfectly suitable for reconstructing emission coefficients of the coupling arc with the ten-view configuration, proving the feasibility and utility of the ART to characterize an asymmetric arc.

Exploring basic biochemical constituents in the body tissues of ...

African Journals Online (AJOL)

Feeding regime did not influence susceptibility to mass loss during export. Animal age influenced the biochemical composition and export performance of abalone. Keywords: abalone; aquaculture; feeds; Haliotis midae; live export; mass loss; tissue biochemical constituents. African Journal of Marine Science 2010, 32(1): ...

Predicting and analyzing DNA-binding domains using a systematic approach to identifying a set of informative physicochemical and biochemical properties

Science.gov (United States)

2011-01-01

Background Existing methods of predicting DNA-binding proteins used valuable features of physicochemical properties to design support vector machine (SVM) based classifiers. Generally, selection of physicochemical properties and determination of their corresponding feature vectors rely mainly on known properties of binding mechanism and experience of designers. However, there exists a troublesome problem for designers that some different physicochemical properties have similar vectors of representing 20 amino acids and some closely related physicochemical properties have dissimilar vectors. Results This study proposes a systematic approach (named Auto-IDPCPs) to automatically identify a set of physicochemical and biochemical properties in the AAindex database to design SVM-based classifiers for predicting and analyzing DNA-binding domains/proteins. Auto-IDPCPs consists of 1) clustering 531 amino acid indices in AAindex into 20 clusters using a fuzzy c-means algorithm, 2) utilizing an efficient genetic algorithm based optimization method IBCGA to select an informative feature set of size m to represent sequences, and 3) analyzing the selected features to identify related physicochemical properties which may affect the binding mechanism of DNA-binding domains/proteins. The proposed Auto-IDPCPs identified m=22 features of properties belonging to five clusters for predicting DNA-binding domains with a five-fold cross-validation accuracy of 87.12%, which is promising compared with the accuracy of 86.62% of the existing method PSSM-400. For predicting DNA-binding sequences, the accuracy of 75.50% was obtained using m=28 features, where PSSM-400 has an accuracy of 74.22%. Auto-IDPCPs and PSSM-400 have accuracies of 80.73% and 82.81%, respectively, applied to an independent test data set of DNA-binding domains. Some typical physicochemical properties discovered are hydrophobicity, secondary structure, charge, solvent accessibility, polarity, flexibility, normalized Van Der

Relevant Subspace Clustering

DEFF Research Database (Denmark)

Müller, Emmanuel; Assent, Ira; Günnemann, Stephan

2009-01-01

Subspace clustering aims at detecting clusters in any subspace projection of a high dimensional space. As the number of possible subspace projections is exponential in the number of dimensions, the result is often tremendously large. Recent approaches fail to reduce results to relevant subspace...... clusters. Their results are typically highly redundant, i.e. many clusters are detected multiple times in several projections. In this work, we propose a novel model for relevant subspace clustering (RESCU). We present a global optimization which detects the most interesting non-redundant subspace clusters...... achieves top clustering quality while competing approaches show greatly varying performance....

Identification of a large, fast-expanding HIV-1 subtype B transmission cluster among MSM in Valencia, Spain.

Directory of Open Access Journals (Sweden)

Juan Ángel Patiño-Galindo

Full Text Available We describe and characterize an exceptionally large HIV-1 subtype B transmission cluster occurring in the Comunidad Valenciana (CV, Spain. A total of 1806 HIV-1 protease-reverse transcriptase (PR/RT sequences from different patients were obtained in the CV between 2004 and 2014. After subtyping and generating a phylogenetic tree with additional HIV-1 subtype B sequences, a very large transmission cluster which included almost exclusively sequences from the CV was detected (n = 143 patients. This cluster was then validated and characterized with further maximum-likelihood phylogenetic analyses and Bayesian coalescent reconstructions. With these analyses, the CV cluster was delimited to 113 patients, predominately men who have sex with men (MSM. Although it was significantly located in the city of Valencia (n = 105, phylogenetic analyses suggested this cluster derives from a larger HIV lineage affecting other Spanish localities (n = 194. Coalescent analyses estimated its expansion in Valencia to have started between 1998 and 2004. From 2004 to 2009, members of this cluster represented only 1.46% of the HIV-1 subtype B samples studied in Valencia (n = 5/143, whereas from 2010 onwards its prevalence raised to 12.64% (n = 100/791. In conclusion, we have detected a very large transmission cluster in the CV where it has experienced a very fast growth in the recent years in the city of Valencia, thus contributing significantly to the HIV epidemic in this locality. Its transmission efficiency evidences shortcomings in HIV control measures in Spain and particularly in Valencia.

Identification of a large, fast-expanding HIV-1 subtype B transmission cluster among MSM in Valencia, Spain.

Science.gov (United States)

Patiño-Galindo, Juan Ángel; Torres-Puente, Manoli; Bracho, María Alma; Alastrué, Ignacio; Juan, Amparo; Navarro, David; Galindo, María José; Gimeno, Concepción; Ortega, Enrique; González-Candelas, Fernando

2017-01-01

We describe and characterize an exceptionally large HIV-1 subtype B transmission cluster occurring in the Comunidad Valenciana (CV, Spain). A total of 1806 HIV-1 protease-reverse transcriptase (PR/RT) sequences from different patients were obtained in the CV between 2004 and 2014. After subtyping and generating a phylogenetic tree with additional HIV-1 subtype B sequences, a very large transmission cluster which included almost exclusively sequences from the CV was detected (n = 143 patients). This cluster was then validated and characterized with further maximum-likelihood phylogenetic analyses and Bayesian coalescent reconstructions. With these analyses, the CV cluster was delimited to 113 patients, predominately men who have sex with men (MSM). Although it was significantly located in the city of Valencia (n = 105), phylogenetic analyses suggested this cluster derives from a larger HIV lineage affecting other Spanish localities (n = 194). Coalescent analyses estimated its expansion in Valencia to have started between 1998 and 2004. From 2004 to 2009, members of this cluster represented only 1.46% of the HIV-1 subtype B samples studied in Valencia (n = 5/143), whereas from 2010 onwards its prevalence raised to 12.64% (n = 100/791). In conclusion, we have detected a very large transmission cluster in the CV where it has experienced a very fast growth in the recent years in the city of Valencia, thus contributing significantly to the HIV epidemic in this locality. Its transmission efficiency evidences shortcomings in HIV control measures in Spain and particularly in Valencia.

Horticultural cluster

OpenAIRE

SHERSTIUK S.V.; POSYLAYEVA K.I.

2013-01-01

In the article there are the theoretical and methodological approaches to the nature and existence of the cluster. The cluster differences from other kinds of cooperative and integration associations. Was develop by scientific-practical recommendations for forming a competitive horticultur cluster.

TreeCluster: Massively scalable transmission clustering using phylogenetic trees

OpenAIRE

Moshiri, Alexander

2018-01-01

Background: The ability to infer transmission clusters from molecular data is critical to designing and evaluating viral control strategies. Viral sequencing datasets are growing rapidly, but standard methods of transmission cluster inference do not scale well beyond thousands of sequences. Results: I present TreeCluster, a cross-platform tool that performs transmission cluster inference on a given phylogenetic tree orders of magnitude faster than existing inference methods and supports multi...

Technical basis for dose reconstruction

International Nuclear Information System (INIS)

Anspaugh, L.R.

1996-01-01

The purpose of this paper is to consider two general topics: Technical considerations of why dose-reconstruction studies should or should not be performed and methods of dose reconstruction. The first topic is of general and growing interest as the number of dose-reconstruction studies increases, and one asks the question whether it is necessary to perform a dose reconstruction for virtually every site at which, for example, the Department of Energy (DOE) has operated a nuclear-related facility. And there is the broader question of how one might logically draw the line at performing or not performing dose-reconstruction (radiological and chemical) studies for virtually every industrial complex in the entire country. The second question is also of general interest. There is no single correct way to perform a dose-reconstruction study, and it is important not to follow blindly a single method to the point that cheaper, faster, more accurate, and more transparent methods might not be developed and applied. 90 refs., 4 tabs

Technical basis for dose reconstruction

International Nuclear Information System (INIS)

Anspaugh, L.R.

1996-01-01

The purpose of this paper is to consider two general topics: technical considerations of why dose-reconstruction studies should or should not be performed and methods of dose reconstruction. The first topic is of general and growing interest as the number of dose-reconstruction studies increases, and one asks the question whether it is necessary to perform a dose reconstruction for virtually every site at which, for example, the Department of Energy (DOE) has operated a nuclear-related facility. And there is the broader question of how one might logically draw the line at performing or not performing dose-reconstruction (radiological and chemical) studies for virtually every industrial complex in the entire country. The second question is also of general interest. There is no single correct way to perform a dose-reconstruction study, and it is important not to follow blindly a single method to the point that cheaper, faster, more accurate, and more transparent methods might not be developed and applied

Voting-based consensus clustering for combining multiple clusterings of chemical structures

Directory of Open Access Journals (Sweden)

Saeed Faisal

2012-12-01

Full Text Available Abstract Background Although many consensus clustering methods have been successfully used for combining multiple classifiers in many areas such as machine learning, applied statistics, pattern recognition and bioinformatics, few consensus clustering methods have been applied for combining multiple clusterings of chemical structures. It is known that any individual clustering method will not always give the best results for all types of applications. So, in this paper, three voting and graph-based consensus clusterings were used for combining multiple clusterings of chemical structures to enhance the ability of separating biologically active molecules from inactive ones in each cluster. Results The cumulative voting-based aggregation algorithm (CVAA, cluster-based similarity partitioning algorithm (CSPA and hyper-graph partitioning algorithm (HGPA were examined. The F-measure and Quality Partition Index method (QPI were used to evaluate the clusterings and the results were compared to the Ward’s clustering method. The MDL Drug Data Report (MDDR dataset was used for experiments and was represented by two 2D fingerprints, ALOGP and ECFP_4. The performance of voting-based consensus clustering method outperformed the Ward’s method using F-measure and QPI method for both ALOGP and ECFP_4 fingerprints, while the graph-based consensus clustering methods outperformed the Ward’s method only for ALOGP using QPI. The Jaccard and Euclidean distance measures were the methods of choice to generate the ensembles, which give the highest values for both criteria. Conclusions The results of the experiments show that consensus clustering methods can improve the effectiveness of chemical structures clusterings. The cumulative voting-based aggregation algorithm (CVAA was the method of choice among consensus clustering methods.

Focusing Cosmic Telescopes: Exploring Redshift z ~ 5-6 Galaxies with the Bullet Cluster 1E0657 - 56

Science.gov (United States)

Bradač, Maruša; Treu, Tommaso; Applegate, Douglas; Gonzalez, Anthony H.; Clowe, Douglas; Forman, William; Jones, Christine; Marshall, Phil; Schneider, Peter; Zaritsky, Dennis

2009-12-01

The gravitational potential of clusters of galaxies acts as a cosmic telescope allowing us to find and study galaxies at fainter limits than otherwise possible and thus probe closer to the epoch of formation of the first galaxies. We use the Bullet cluster 1E0657 - 56 (z = 0.296) as a case study, because its high mass and merging configuration makes it one of the most efficient cosmic telescopes we know. We develop a new algorithm to reconstruct the gravitational potential of the Bullet cluster based on a non-uniform adaptive grid, combining strong and weak gravitational lensing data derived from deep Hubble Space Telescope/Advanced Camera for Surveys F606W-F775W-F850LP and ground-based imaging. We exploit this improved mass map to study z ~ 5-6 Lyman break galaxies (LBGs), which we detect as dropouts. One of the LBGs is multiply imaged, providing a geometric confirmation of its high redshift, and is used to further improve our mass model. We quantify the uncertainties in the magnification map reconstruction in the intrinsic source luminosity, and in the volume surveyed, and show that they are negligible compared to sample variance when determining the luminosity function of high-redshift galaxies. With shallower and comparable magnitude limits to Hubble Ultra Deep Field (HUDF) and Great Observatories Origins Deep Survey (GOODS), the Bullet cluster observations, after correcting for magnification, probe deeper into the luminosity function of the high-redshift galaxies than GOODS and only slightly shallower than HUDF. We conclude that accurately focused cosmic telescopes are the most efficient way to sample the bright end of the luminosity function of high-redshift galaxies and—in case they are multiply imaged—confirm their redshifts. Based on observations made with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5

OBSERVED SCALING RELATIONS FOR STRONG LENSING CLUSTERS: CONSEQUENCES FOR COSMOLOGY AND CLUSTER ASSEMBLY

International Nuclear Information System (INIS)

Comerford, Julia M.; Moustakas, Leonidas A.; Natarajan, Priyamvada

2010-01-01

Scaling relations of observed galaxy cluster properties are useful tools for constraining cosmological parameters as well as cluster formation histories. One of the key cosmological parameters, σ 8 , is constrained using observed clusters of galaxies, although current estimates of σ 8 from the scaling relations of dynamically relaxed galaxy clusters are limited by the large scatter in the observed cluster mass-temperature (M-T) relation. With a sample of eight strong lensing clusters at 0.3 8 , but combining the cluster concentration-mass relation with the M-T relation enables the inclusion of unrelaxed clusters as well. Thus, the resultant gains in the accuracy of σ 8 measurements from clusters are twofold: the errors on σ 8 are reduced and the cluster sample size is increased. Therefore, the statistics on σ 8 determination from clusters are greatly improved by the inclusion of unrelaxed clusters. Exploring cluster scaling relations further, we find that the correlation between brightest cluster galaxy (BCG) luminosity and cluster mass offers insight into the assembly histories of clusters. We find preliminary evidence for a steeper BCG luminosity-cluster mass relation for strong lensing clusters than the general cluster population, hinting that strong lensing clusters may have had more active merging histories.

Three-dimensional ICT reconstruction

International Nuclear Information System (INIS)

Zhang Aidong; Li Ju; Chen Fa; Sun Lingxia

2005-01-01

The three-dimensional ICT reconstruction method is the hot topic of recent ICT technology research. In the context, qualified visual three-dimensional ICT pictures are achieved through multi-piece two-dimensional images accumulation by, combining with thresholding method and linear interpolation. Different direction and different position images of the reconstructed pictures are got by rotation and interception respectively. The convenient and quick method is significantly instructive to more complicated three-dimensional reconstruction of ICT images. (authors)

Three-dimensional ICT reconstruction

International Nuclear Information System (INIS)

Zhang Aidong; Li Ju; Chen Fa; Sun Lingxia

2004-01-01

The three-dimensional ICT reconstruction method is the hot topic of recent ICT technology research. In the context qualified visual three-dimensional ICT pictures are achieved through multi-piece two-dimensional images accumulation by order, combining with thresholding method and linear interpolation. Different direction and different position images of the reconstructed pictures are got by rotation and interception respectively. The convenient and quick method is significantly instructive to more complicated three-dimensional reconstruction of ICT images. (authors)

ClbM is a versatile, cation-promiscuous MATE transporter found in the colibactin biosynthetic gene cluster.

Science.gov (United States)

Mousa, Jarrod J; Newsome, Rachel C; Yang, Ye; Jobin, Christian; Bruner, Steven D

2017-01-22

Multidrug transporters play key roles in cellular drug resistance to toxic molecules, yet these transporters are also involved in natural product transport as part of biosynthetic clusters in bacteria and fungi. The genotoxic molecule colibactin is produced by strains of virulent and pathobiont Escherichia coli and Klebsiella pneumoniae. In the biosynthetic cluster is a multidrug and toxic compound extrusion protein (MATE) proposed to transport the prodrug molecule precolibactin across the cytoplasmic membrane, for subsequent cleavage by the peptidase ClbP and cellular export. We recently determined the X-ray structure of ClbM, and showed preliminary data suggesting its specific role in precolibactin transport. Here, we define a functional role of ClbM by examining transport capabilities under various biochemical conditions. Our data indicate ClbM responds to sodium, potassium, and rubidium ion gradients, while also having substantial transport activity in the absence of alkali cations. Copyright © 2016 Elsevier Inc. All rights reserved.

Cluster Headache

OpenAIRE

Pearce, Iris

1985-01-01

Cluster headache is the most severe primary headache with recurrent pain attacks described as worse than giving birth. The aim of this paper was to make an overview of current knowledge on cluster headache with a focus on pathophysiology and treatment. This paper presents hypotheses of cluster headache pathophysiology, current treatment options and possible future therapy approaches. For years, the hypothalamus was regarded as the key structure in cluster headache, but is now thought to be pa...

Biochemical Stimulus-Based Strategies for Meniscus Tissue Engineering and Regeneration

Science.gov (United States)

Chen, Mingxue; Guo, Weimin; Gao, Shunag; Hao, Chunxiang; Shen, Shi; Zhang, Zengzeng; Wang, Zhenyong; Wang, Zehao; Li, Xu; Jing, Xiaoguang; Zhang, Xueliang; Yuan, Zhiguo; Wang, Mingjie; Zhang, Yu; Peng, Jiang; Wang, Aiyuan; Wang, Yu; Sui, Xiang

2018-01-01

Meniscus injuries are very common and still pose a challenge for the orthopedic surgeon. Meniscus injuries in the inner two-thirds of the meniscus remain incurable. Tissue-engineered meniscus strategies seem to offer a new approach for treating meniscus injuries with a combination of seed cells, scaffolds, and biochemical or biomechanical stimulation. Cell- or scaffold-based strategies play a pivotal role in meniscus regeneration. Similarly, biochemical and biomechanical stimulation are also important. Seed cells and scaffolds can be used to construct a tissue-engineered tissue; however, stimulation to enhance tissue maturation and remodeling is still needed. Such stimulation can be biomechanical or biochemical, but this review focuses only on biochemical stimulation. Growth factors (GFs) are one of the most important forms of biochemical stimulation. Frequently used GFs always play a critical role in normal limb development and growth. Further understanding of the functional mechanism of GFs will help scientists to design the best therapy strategies. In this review, we summarize some of the most important GFs in tissue-engineered menisci, as well as other types of biological stimulation. PMID:29581987

Thermodynamically consistent Bayesian analysis of closed biochemical reaction systems

Directory of Open Access Journals (Sweden)

Goutsias John

2010-11-01

Full Text Available Abstract Background Estimating the rate constants of a biochemical reaction system with known stoichiometry from noisy time series measurements of molecular concentrations is an important step for building predictive models of cellular function. Inference techniques currently available in the literature may produce rate constant values that defy necessary constraints imposed by the fundamental laws of thermodynamics. As a result, these techniques may lead to biochemical reaction systems whose concentration dynamics could not possibly occur in nature. Therefore, development of a thermodynamically consistent approach for estimating the rate constants of a biochemical reaction system is highly desirable. Results We introduce a Bayesian analysis approach for computing thermodynamically consistent estimates of the rate constants of a closed biochemical reaction system with known stoichiometry given experimental data. Our method employs an appropriately designed prior probability density function that effectively integrates fundamental biophysical and thermodynamic knowledge into the inference problem. Moreover, it takes into account experimental strategies for collecting informative observations of molecular concentrations through perturbations. The proposed method employs a maximization-expectation-maximization algorithm that provides thermodynamically feasible estimates of the rate constant values and computes appropriate measures of estimation accuracy. We demonstrate various aspects of the proposed method on synthetic data obtained by simulating a subset of a well-known model of the EGF/ERK signaling pathway, and examine its robustness under conditions that violate key assumptions. Software, coded in MATLAB®, which implements all Bayesian analysis techniques discussed in this paper, is available free of charge at http://www.cis.jhu.edu/~goutsias/CSS%20lab/software.html. Conclusions Our approach provides an attractive statistical methodology for

Raw-data display and visual reconstruction validation in ALICE

International Nuclear Information System (INIS)

Tadel, M

2008-01-01

ALICE Event Visualization Environment (AliEVE) is based on ROOT and its GUI, 2D and 3D graphics classes. A small application kernel provides for registration and management of visualization objects. CINT scripts are used as an extensible mechanism for data extraction, selection and processing as well as for steering of frequent event-related tasks. AliEVE is used for event visualization in offline and high-level trigger frameworks. Mechanisms and base-classes provided for visual representation of raw-data for different detector-types are described. Common infrastructure for thresholding and color-coding of signal/time information, placement of detector-modules in various 2D/3D layouts and for user-interaction with displayed data is presented. Methods for visualization of raw-data on different levels of detail are discussed as they are expected to play an important role during early detector operation with poorly understood detector calibration, occupancy and noise-levels. Since September 2006 ALICE applies a regular visual-scanning procedure to simulated proton-proton data to detect any shortcomings in cluster finding, tracking and primary and secondary vertex reconstruction. A high-level of interactivity is required to allow in-depth exploration of event-structure. Navigation back to simulation records is supported for debugging purposes. Standard 2D projections and transformations are available for clusters, tracks and simplified detector geometry

Investigation of various reconstruction parameters for algebraic reconstruction technique in a newly developed chest digital tomosynthesis

International Nuclear Information System (INIS)

Lee, H.; Choi, S.; Kim, Y.-S.; Park, H.-S.; Seo, C.-W.; Kim, H.-J.; Lee, D.; Lee, Y.

2017-01-01

Chest digital tomosynthesis (CDT) is a promising new modality that provides 3D information by reconstructing limited projection views. CDT systems have been developed to improve the limitations of conventional radiography such as image degradation and low sensitivity. However, the development of reconstruction methods is challenging because of the limited projection views within various angular ranges. Optimization of reconstruction parameters for various reconsturction methods in CDT system also is needed. The purpose of this study was to investigate the feasibility of algebraic reconstruction technique (ART) method, and to evaluate the effect of the reconstruction parameters for our newly developed CDT system. We designed ART method with 41 projection views over an angular range of ±20°. To investigate the effect of reconstruction parameters, we measured the contrast-to-noise ratio (CNR), artifact spread function (ASF), and quality factor (QF) using LUNGMAN phantom included tumors. We found that the proper choice of reconstruction parameters such as relaxation parameter, initial guess, and number of iterations improved the quality of reconstructed images from the same projection views. Optimal values of ART relaxation parameter with uniform (UI) and back-projection (BP) initial guesses were 0.4 and 0.6, respectively. BP initial guess improved image quality in comparison with UI initial guess, in terms of providing a higher CNR and QF values with a faster speed. CNR and QF values improved with increasing number of iteration. Particularly, ART method with BP initial guess (when β = 0.6) after 3-terations provide satisfactory reconstructed image. In conclusion, the use of ART method with proper reconstruction parameters provided better image quality than FBP method as well as conventional radiography. These results indicated that the ART method with optimal reconstruction parameters could improve image quality for nodule detection using the CDT system.

Investigation of various reconstruction parameters for algebraic reconstruction technique in a newly developed chest digital tomosynthesis

Science.gov (United States)

Lee, H.; Choi, S.; Lee, D.; Kim, Y.-s.; Park, H.-S.; Lee, Y.; Seo, C.-W.; Kim, H.-J.

2017-08-01

Chest digital tomosynthesis (CDT) is a promising new modality that provides 3D information by reconstructing limited projection views. CDT systems have been developed to improve the limitations of conventional radiography such as image degradation and low sensitivity. However, the development of reconstruction methods is challenging because of the limited projection views within various angular ranges. Optimization of reconstruction parameters for various reconsturction methods in CDT system also is needed. The purpose of this study was to investigate the feasibility of algebraic reconstruction technique (ART) method, and to evaluate the effect of the reconstruction parameters for our newly developed CDT system. We designed ART method with 41 projection views over an angular range of ±20°. To investigate the effect of reconstruction parameters, we measured the contrast-to-noise ratio (CNR), artifact spread function (ASF), and quality factor (QF) using LUNGMAN phantom included tumors. We found that the proper choice of reconstruction parameters such as relaxation parameter, initial guess, and number of iterations improved the quality of reconstructed images from the same projection views. Optimal values of ART relaxation parameter with uniform (UI) and back-projection (BP) initial guesses were 0.4 and 0.6, respectively. BP initial guess improved image quality in comparison with UI initial guess, in terms of providing a higher CNR and QF values with a faster speed. CNR and QF values improved with increasing number of iteration. Particularly, ART method with BP initial guess (when β = 0.6) after 3-terations provide satisfactory reconstructed image. In conclusion, the use of ART method with proper reconstruction parameters provided better image quality than FBP method as well as conventional radiography. These results indicated that the ART method with optimal reconstruction parameters could improve image quality for nodule detection using the CDT system.

Biochemical toxicology of environmental agents

International Nuclear Information System (INIS)

Bruin, A. de

1976-01-01

A thorough and up-to-date account of the molecular-biological aspects of harmful agents - both chemical and physical - is given. This current treatise is principally intended to serve as an informative reference work for researchers in various areas of the field. In the pursuit of this aim, a devision of the entire field into 42 chapters has been made. Each chapter starts with a short introductory account dealing with the biochemical essentials of the particular subject. Radiation effects are discussed briefly at the end of each treatise. In order to make the treatise useful as a source book, a substantial collection of pertinent literature references is provided which are numbered in order of citation in the text. Initial chapters are devoted to the metabolic fate of the major classes of xenobiotic compounds. Peripheral topics, closely related to metabolism and dealing with modification of xenobiotic-metabolizing ability, as well as interaction phenomena follow (chs. 5-8). Subjects that draw heavily on the practical field of occupational hygiene are dealt with in chapters 9 and 10. The systematic treatment of how chemical and physical agents interact with the various biochemical and enzymatic systems they encounter during their passage through the organism occupies quantitatively the main part of the book (chs. 11-36). Finally, radiation biochemistry is discussed from the viewpoint of its high degree of scientific advancement, and secondly because the type of biochemical changes produced in vivo by X-rays closely parallel those evoked by chemical agents

Properties of an ionised-cluster beam from a vaporised-cluster ion source

International Nuclear Information System (INIS)

Takagi, T.; Yamada, I.; Sasaki, A.

1978-01-01

A new type of ion source vaporised-metal cluster ion source, has been developed for deposition and epitaxy. A cluster consisting of 10 2 to 10 3 atoms coupled loosely together is formed by adiabatic expansion ejecting the vapour of materials into a high-vacuum region through the nozzle of a heated crucible. The clusters are ionised by electron bombardment and accelerated with neutral clusters toward a substrate. In this paper, mechanisms of cluster formation experimental results of the cluster size (atoms/cluster) and its distribution, and characteristics of the cluster ion beams are reported. The size is calculated from the kinetic equation E = (1/2)mNVsub(ej) 2 , where E is the cluster beam energy, Vsub(ej) is the ejection velocity, m is the mass of atom and N is the cluster size. The energy and the velocity of the cluster are measured by an electrostatic 127 0 energy analyser and a rotating disc system, respectively. The cluster size obtained for Ag is about 5 x 10 2 to 2 x 10 3 atoms. The retarding potential method is used to confirm the results for Ag. The same dependence on cluster size for metals such as Ag, Cu and Pb has been obtained in previous experiments. In the cluster state the cluster ion beam is easily produced by electron bombardment. About 50% of ionised clusters are obtained under typical operation conditions, because of the large ionisation cross sections of the clusters. To obtain a uniform spatial distribution, the ionising electrode system is also discussed. The new techniques are termed ionised-cluster beam deposition (ICBD) and epitaxy (ICBE). (author)

Enzyme and biochemical producing fungi

DEFF Research Database (Denmark)

Lübeck, Peter Stephensen; Lübeck, Mette; Nilsson, Lena

2010-01-01

factories for sustainable production of important molecules. For developing fungi into efficient cell factories, the project includes identification of important factors that control the flux through the pathways using metabolic flux analysis and metabolic engineering of biochemical pathways....

Feasibility Study of Parallel Finite Element Analysis on Cluster-of-Clusters

Science.gov (United States)

Muraoka, Masae; Okuda, Hiroshi

With the rapid growth of WAN infrastructure and development of Grid middleware, it's become a realistic and attractive methodology to connect cluster machines on wide-area network for the execution of computation-demanding applications. Many existing parallel finite element (FE) applications have been, however, designed and developed with a single computing resource in mind, since such applications require frequent synchronization and communication among processes. There have been few FE applications that can exploit the distributed environment so far. In this study, we explore the feasibility of FE applications on the cluster-of-clusters. First, we classify FE applications into two types, tightly coupled applications (TCA) and loosely coupled applications (LCA) based on their communication pattern. A prototype of each application is implemented on the cluster-of-clusters. We perform numerical experiments executing TCA and LCA on both the cluster-of-clusters and a single cluster. Thorough these experiments, by comparing the performances and communication cost in each case, we evaluate the feasibility of FEA on the cluster-of-clusters.

Interplay between experiments and calculations for organometallic clusters and caged clusters

International Nuclear Information System (INIS)

Nakajima, Atsushi

2015-01-01

Clusters consisting of 10-1000 atoms exhibit size-dependent electronic and geometric properties. In particular, composite clusters consisting of several elements and/or components provide a promising way for a bottom-up approach for designing functional advanced materials, because the functionality of the composite clusters can be optimized not only by the cluster size but also by their compositions. In the formation of composite clusters, their geometric symmetry and dimensionality are emphasized to control the physical and chemical properties, because selective and anisotropic enhancements for optical, chemical, and magnetic properties can be expected. Organometallic clusters and caged clusters are demonstrated as a representative example of designing the functionality of the composite clusters. Organometallic vanadium-benzene forms a one dimensional sandwich structure showing ferromagnetic behaviors and anomalously large HOMO-LUMO gap differences of two spin orbitals, which can be regarded as spin-filter components for cluster-based spintronic devices. Caged clusters of aluminum (Al) are well stabilized both geometrically and electronically at Al 12 X, behaving as a “superatom”

Soft Sensor Modeling Based on Multiple Gaussian Process Regression and Fuzzy C-mean Clustering

Directory of Open Access Journals (Sweden)

Xianglin ZHU

2014-06-01

Full Text Available In order to overcome the difficulties of online measurement of some crucial biochemical variables in fermentation processes, a new soft sensor modeling method is presented based on the Gaussian process regression and fuzzy C-mean clustering. With the consideration that the typical fermentation process can be distributed into 4 phases including lag phase, exponential growth phase, stable phase and dead phase, the training samples are classified into 4 subcategories by using fuzzy C- mean clustering algorithm. For each sub-category, the samples are trained using the Gaussian process regression and the corresponding soft-sensing sub-model is established respectively. For a new sample, the membership between this sample and sub-models are computed based on the Euclidean distance, and then the prediction output of soft sensor is obtained using the weighting sum. Taking the Lysine fermentation as example, the simulation and experiment are carried out and the corresponding results show that the presented method achieves better fitting and generalization ability than radial basis function neutral network and single Gaussian process regression model.

Formation of clusters composed of C60 molecules via self-assembly in critical fluids

International Nuclear Information System (INIS)

Fukuda, Takahiro; Ishii, Koji; Kurosu, Shunji; Whitby, Raymond; Maekawa, Toru

2007-01-01

Fullerenes are promising candidates for intelligent, functional nanomaterials because of their unique mechanical, electronic and chemical properties. However, it is necessary to invent some efficient but relatively simple methods of producing structures composed of fullerenes for the development of nanomechatronic, nanoelectronic and biochemical devices and sensors. In this paper, we show that various structures such as straight fibres, networks formed by fibres, wide sheets and helical structures, which are composed of C 60 molecules, are created by placing C 60 -crystals in critical ethane, carbon dioxide and xenon even though C 60 molecules do not dissolve or disperse in the above fluids. It is supposed, judging by the intermolecular potentials between C 60 and C 60 , between C 60 and ethane, and between ethane and ethane, that C 60 -clusters grow with the assistance of solvent molecules, which are trapped between C 60 molecules under critical conditions. This room-temperature self-assembly cluster growth process in critical fluids may open up a new methodology of forming structures built up with fullerenes without the need for any ultra-fine processing technologies

Categorias Cluster

OpenAIRE

Queiroz, Dayane Andrade

2015-01-01

Neste trabalho apresentamos as categorias cluster, que foram introduzidas por Aslak Bakke Buan, Robert Marsh, Markus Reineke, Idun Reiten e Gordana Todorov, com o objetivo de categoriíicar as algebras cluster criadas em 2002 por Sergey Fomin e Andrei Zelevinsky. Os autores acima, em [4], mostraram que existe uma estreita relação entre algebras cluster e categorias cluster para quivers cujo grafo subjacente é um diagrama de Dynkin. Para isto desenvolveram uma teoria tilting na estrutura triang...

BRIGHTEST CLUSTER GALAXIES AND CORE GAS DENSITY IN REXCESS CLUSTERS

International Nuclear Information System (INIS)

Haarsma, Deborah B.; Leisman, Luke; Donahue, Megan; Bruch, Seth; Voit, G. Mark; Boehringer, Hans; Pratt, Gabriel W.; Pierini, Daniele; Croston, Judith H.; Arnaud, Monique

2010-01-01

We investigate the relationship between brightest cluster galaxies (BCGs) and their host clusters using a sample of nearby galaxy clusters from the Representative XMM-Newton Cluster Structure Survey. The sample was imaged with the Southern Observatory for Astrophysical Research in R band to investigate the mass of the old stellar population. Using a metric radius of 12 h -1 kpc, we found that the BCG luminosity depends weakly on overall cluster mass as L BCG ∝ M 0.18±0.07 cl , consistent with previous work. We found that 90% of the BCGs are located within 0.035 r 500 of the peak of the X-ray emission, including all of the cool core (CC) clusters. We also found an unexpected correlation between the BCG metric luminosity and the core gas density for non-cool-core (non-CC) clusters, following a power law of n e ∝ L 2.7±0.4 BCG (where n e is measured at 0.008 r 500 ). The correlation is not easily explained by star formation (which is weak in non-CC clusters) or overall cluster mass (which is not correlated with core gas density). The trend persists even when the BCG is not located near the peak of the X-ray emission, so proximity is not necessary. We suggest that, for non-CC clusters, this correlation implies that the same process that sets the central entropy of the cluster gas also determines the central stellar density of the BCG, and that this underlying physical process is likely to be mergers.

Entropy and transverse section reconstruction

International Nuclear Information System (INIS)

Gullberg, G.T.

1976-01-01

A new approach to the reconstruction of a transverse section using projection data from multiple views incorporates the concept of maximum entropy. The principle of maximizing information entropy embodies the assurance of minimizing bias or prejudice in the reconstruction. Using maximum entropy is a necessary condition for the reconstructed image. This entropy criterion is most appropriate for 3-D reconstruction of objects from projections where the system is underdetermined or the data are limited statistically. This is the case in nuclear medicine time limitations in patient studies do not yield sufficient projections

Reconstructing recent human phylogenies with forensic STR loci: A statistical approach

Directory of Open Access Journals (Sweden)

Khan Faisal

2005-09-01

Full Text Available Abstract Background Forensic Short Tandem Repeat (STR loci are effective for the purpose of individual identification, and other forensic applications. Most of these markers have high allelic variability and mutation rate because of which they have limited use in the phylogenetic reconstruction. In the present study, we have carried out a meta-analysis to explore the possibility of using only five STR loci (TPOX, FES, vWA, F13A and Tho1 to carry out phylogenetic assessment based on the allele frequency profile of 20 world population and north Indian Hindus analyzed in the present study. Results Phylogenetic analysis based on two different approaches – genetic distance and maximum likelihood along with statistical bootstrapping procedure involving 1000 replicates was carried out. The ensuing tree topologies and PC plots were further compared with those obtained in earlier phylogenetic investigations. The compiled database of 21 populations got segregated and finely resolved into three basal clusters with very high bootstrap values corresponding to three geo-ethnic groups of African, Orientals, and Caucasians. Conclusion Based on this study we conclude that if appropriate and logistic statistical approaches are followed then even lesser number of forensic STR loci are powerful enough to reconstruct the recent human phylogenies despite of their relatively high mutation rates.

Breast reconstruction - natural tissue

Science.gov (United States)

... flap; TRAM; Latissimus muscle flap with a breast implant; DIEP flap; DIEAP flap; Gluteal free flap; Transverse upper gracilis flap; TUG; Mastectomy - breast reconstruction with natural tissue; Breast cancer - breast reconstruction with natural tissue

PCA based clustering for brain tumor segmentation of T1w MRI images.

Science.gov (United States)

Kaya, Irem Ersöz; Pehlivanlı, Ayça Çakmak; Sekizkardeş, Emine Gezmez; Ibrikci, Turgay

2017-03-01

Medical images are huge collections of information that are difficult to store and process consuming extensive computing time. Therefore, the reduction techniques are commonly used as a data pre-processing step to make the image data less complex so that a high-dimensional data can be identified by an appropriate low-dimensional representation. PCA is one of the most popular multivariate methods for data reduction. This paper is focused on T1-weighted MRI images clustering for brain tumor segmentation with dimension reduction by different common Principle Component Analysis (PCA) algorithms. Our primary aim is to present a comparison between different variations of PCA algorithms on MRIs for two cluster methods. Five most common PCA algorithms; namely the conventional PCA, Probabilistic Principal Component Analysis (PPCA), Expectation Maximization Based Principal Component Analysis (EM-PCA), Generalize Hebbian Algorithm (GHA), and Adaptive Principal Component Extraction (APEX) were applied to reduce dimensionality in advance of two clustering algorithms, K-Means and Fuzzy C-Means. In the study, the T1-weighted MRI images of the human brain with brain tumor were used for clustering. In addition to the original size of 512 lines and 512 pixels per line, three more different sizes, 256 × 256, 128 × 128 and 64 × 64, were included in the study to examine their effect on the methods. The obtained results were compared in terms of both the reconstruction errors and the Euclidean distance errors among the clustered images containing the same number of principle components. According to the findings, the PPCA obtained the best results among all others. Furthermore, the EM-PCA and the PPCA assisted K-Means algorithm to accomplish the best clustering performance in the majority as well as achieving significant results with both clustering algorithms for all size of T1w MRI images. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

TH-AB-207A-05: A Fully-Automated Pipeline for Generating CT Images Across a Range of Doses and Reconstruction Methods

International Nuclear Information System (INIS)

Young, S; Lo, P; Hoffman, J; Wahi-Anwar, M; Brown, M; McNitt-Gray, M; Noo, F

2016-01-01

Purpose: To evaluate the robustness of CAD or Quantitative Imaging methods, they should be tested on a variety of cases and under a variety of image acquisition and reconstruction conditions that represent the heterogeneity encountered in clinical practice. The purpose of this work was to develop a fully-automated pipeline for generating CT images that represent a wide range of dose and reconstruction conditions. Methods: The pipeline consists of three main modules: reduced-dose simulation, image reconstruction, and quantitative analysis. The first two modules of the pipeline can be operated in a completely automated fashion, using configuration files and running the modules in a batch queue. The input to the pipeline is raw projection CT data; this data is used to simulate different levels of dose reduction using a previously-published algorithm. Filtered-backprojection reconstructions are then performed using FreeCT_wFBP, a freely-available reconstruction software for helical CT. We also added support for an in-house, model-based iterative reconstruction algorithm using iterative coordinate-descent optimization, which may be run in tandem with the more conventional recon methods. The reduced-dose simulations and image reconstructions are controlled automatically by a single script, and they can be run in parallel on our research cluster. The pipeline was tested on phantom and lung screening datasets from a clinical scanner (Definition AS, Siemens Healthcare). Results: The images generated from our test datasets appeared to represent a realistic range of acquisition and reconstruction conditions that we would expect to find clinically. The time to generate images was approximately 30 minutes per dose/reconstruction combination on a hybrid CPU/GPU architecture. Conclusion: The automated research pipeline promises to be a useful tool for either training or evaluating performance of quantitative imaging software such as classifiers and CAD algorithms across the range

TH-AB-207A-05: A Fully-Automated Pipeline for Generating CT Images Across a Range of Doses and Reconstruction Methods

Energy Technology Data Exchange (ETDEWEB)

Young, S; Lo, P; Hoffman, J; Wahi-Anwar, M; Brown, M; McNitt-Gray, M [UCLA School of Medicine, Los Angeles, CA (United States); Noo, F [University of Utah, Salt Lake City, UT (United States)

2016-06-15

Purpose: To evaluate the robustness of CAD or Quantitative Imaging methods, they should be tested on a variety of cases and under a variety of image acquisition and reconstruction conditions that represent the heterogeneity encountered in clinical practice. The purpose of this work was to develop a fully-automated pipeline for generating CT images that represent a wide range of dose and reconstruction conditions. Methods: The pipeline consists of three main modules: reduced-dose simulation, image reconstruction, and quantitative analysis. The first two modules of the pipeline can be operated in a completely automated fashion, using configuration files and running the modules in a batch queue. The input to the pipeline is raw projection CT data; this data is used to simulate different levels of dose reduction using a previously-published algorithm. Filtered-backprojection reconstructions are then performed using FreeCT-wFBP, a freely-available reconstruction software for helical CT. We also added support for an in-house, model-based iterative reconstruction algorithm using iterative coordinate-descent optimization, which may be run in tandem with the more conventional recon methods. The reduced-dose simulations and image reconstructions are controlled automatically by a single script, and they can be run in parallel on our research cluster. The pipeline was tested on phantom and lung screening datasets from a clinical scanner (Definition AS, Siemens Healthcare). Results: The images generated from our test datasets appeared to represent a realistic range of acquisition and reconstruction conditions that we would expect to find clinically. The time to generate images was approximately 30 minutes per dose/reconstruction combination on a hybrid CPU/GPU architecture. Conclusion: The automated research pipeline promises to be a useful tool for either training or evaluating performance of quantitative imaging software such as classifiers and CAD algorithms across the range

Probabilistic sensitivity analysis of biochemical reaction systems.

Science.gov (United States)

Zhang, Hong-Xuan; Dempsey, William P; Goutsias, John

2009-09-07

Sensitivity analysis is an indispensable tool for studying the robustness and fragility properties of biochemical reaction systems as well as for designing optimal approaches for selective perturbation and intervention. Deterministic sensitivity analysis techniques, using derivatives of the system response, have been extensively used in the literature. However, these techniques suffer from several drawbacks, which must be carefully considered before using them in problems of systems biology. We develop here a probabilistic approach to sensitivity analysis of biochemical reaction systems. The proposed technique employs a biophysically derived model for parameter fluctuations and, by using a recently suggested variance-based approach to sensitivity analysis [Saltelli et al., Chem. Rev. (Washington, D.C.) 105, 2811 (2005)], it leads to a powerful sensitivity analysis methodology for biochemical reaction systems. The approach presented in this paper addresses many problems associated with derivative-based sensitivity analysis techniques. Most importantly, it produces thermodynamically consistent sensitivity analysis results, can easily accommodate appreciable parameter variations, and allows for systematic investigation of high-order interaction effects. By employing a computational model of the mitogen-activated protein kinase signaling cascade, we demonstrate that our approach is well suited for sensitivity analysis of biochemical reaction systems and can produce a wealth of information about the sensitivity properties of such systems. The price to be paid, however, is a substantial increase in computational complexity over derivative-based techniques, which must be effectively addressed in order to make the proposed approach to sensitivity analysis more practical.

Characterizing multistationarity regimes in biochemical reaction networks.

Directory of Open Access Journals (Sweden)

Irene Otero-Muras

Full Text Available Switch like responses appear as common strategies in the regulation of cellular systems. Here we present a method to characterize bistable regimes in biochemical reaction networks that can be of use to both direct and reverse engineering of biological switches. In the design of a synthetic biological switch, it is important to study the capability for bistability of the underlying biochemical network structure. Chemical Reaction Network Theory (CRNT may help at this level to decide whether a given network has the capacity for multiple positive equilibria, based on their structural properties. However, in order to build a working switch, we also need to ensure that the bistability property is robust, by studying the conditions leading to the existence of two different steady states. In the reverse engineering of biological switches, knowledge collected about the bistable regimes of the underlying potential model structures can contribute at the model identification stage to a drastic reduction of the feasible region in the parameter space of search. In this work, we make use and extend previous results of the CRNT, aiming not only to discriminate whether a biochemical reaction network can exhibit multiple steady states, but also to determine the regions within the whole space of parameters capable of producing multistationarity. To that purpose we present and justify a condition on the parameters of biochemical networks for the appearance of multistationarity, and propose an efficient and reliable computational method to check its satisfaction through the parameter space.

Scientific Cluster Deployment and Recovery - Using puppet to simplify cluster management

Science.gov (United States)

Hendrix, Val; Benjamin, Doug; Yao, Yushu

2012-12-01

Deployment, maintenance and recovery of a scientific cluster, which has complex, specialized services, can be a time consuming task requiring the assistance of Linux system administrators, network engineers as well as domain experts. Universities and small institutions that have a part-time FTE with limited time for and knowledge of the administration of such clusters can be strained by such maintenance tasks. This current work is the result of an effort to maintain a data analysis cluster (DAC) with minimal effort by a local system administrator. The realized benefit is the scientist, who is the local system administrator, is able to focus on the data analysis instead of the intricacies of managing a cluster. Our work provides a cluster deployment and recovery process (CDRP) based on the puppet configuration engine allowing a part-time FTE to easily deploy and recover entire clusters with minimal effort. Puppet is a configuration management system (CMS) used widely in computing centers for the automatic management of resources. Domain experts use Puppet's declarative language to define reusable modules for service configuration and deployment. Our CDRP has three actors: domain experts, a cluster designer and a cluster manager. The domain experts first write the puppet modules for the cluster services. A cluster designer would then define a cluster. This includes the creation of cluster roles, mapping the services to those roles and determining the relationships between the services. Finally, a cluster manager would acquire the resources (machines, networking), enter the cluster input parameters (hostnames, IP addresses) and automatically generate deployment scripts used by puppet to configure it to act as a designated role. In the event of a machine failure, the originally generated deployment scripts along with puppet can be used to easily reconfigure a new machine. The cluster definition produced in our CDRP is an integral part of automating cluster deployment

Jini service to reconstruct tomographic data

Science.gov (United States)

Knoll, Peter; Mirzaei, S.; Koriska, K.; Koehn, H.

2002-06-01

A number of imaging systems rely on the reconstruction of a 3- dimensional model from its projections through the process of computed tomography (CT). In medical imaging, for example magnetic resonance imaging (MRI), positron emission tomography (PET), and Single Computer Tomography (SPECT) acquire two-dimensional projections of a three dimensional projections of a three dimensional object. In order to calculate the 3-dimensional representation of the object, i.e. its voxel distribution, several reconstruction algorithms have been developed. Currently, mainly two reconstruct use: the filtered back projection(FBP) and iterative methods. Although the quality of iterative reconstructed SPECT slices is better than that of FBP slices, such iterative algorithms are rarely used for clinical routine studies because of their low availability and increased reconstruction time. We used Jini and a self-developed iterative reconstructions algorithm to design and implement a Jini reconstruction service. With this service, the physician selects the patient study from a database and a Jini client automatically discovers the registered Jini reconstruction services in the department's Intranet. After downloading the proxy object the this Jini service, the SPECT acquisition data are reconstructed. The resulting transaxial slices are visualized using a Jini slice viewer, which can be used for various imaging modalities.

Cluster-cluster correlations in the two-dimensional stationary Ising-model

International Nuclear Information System (INIS)

Klassmann, A.

1997-01-01

In numerical integration of the Cahn-Hillard equation, which describes Oswald rising in a two-phase matrix, N. Masbaum showed that spatial correlations between clusters scale with respect to the mean cluster size (itself a function of time). T. B. Liverpool showed by Monte Carlo simulations for the Ising model that the analogous correlations have a similar form. Both demonstrated that immediately around each cluster there is some depletion area followed by something like a ring of clusters of the same size as the original one. More precisely, it has been shown that the distribution of clusters around a given cluster looks like a sinus-curve decaying exponentially with respect to the distance to a constant value

概率密度函数法研究重构吸引子的结构%Probability Density Function Method for Observing Reconstructed Attractor Structure

Institute of Scientific and Technical Information of China (English)

陆宏伟; 陈亚珠; 卫青

2004-01-01

Probability density function (PDF) method is proposed for analysing the structure of the reconstructed attractor in computing the correlation dimensions of RR intervals of ten normal old men.PDF contains important information about the spatial distribution of the phase points in the reconstructed attractor.To the best of our knowledge, it is the first time that the PDF method is put forward for the analysis of the reconstructed attractor structure.Numerical simulations demonstrate that the cardiac systems of healthy old men are about 6-6.5 dimensional complex dynamical systems.It is found that PDF is not symmetrically distributed when time delay is small, while PDF satisfies Gaussian distribution when time delay is big enough.A cluster effect mechanism is presented to explain this phenomenon.By studying the shape of PDFs, that the roles played by time delay are more important than embedding dimension in the reconstruction is clearly indicated.Results have demonstrated that the PDF method represents a promising numerical approach for the observation of the reconstructed attractor structure and may provide more information and new diagnostic potential of the analyzed cardiac system.

Meaningful Clusters

Energy Technology Data Exchange (ETDEWEB)

Sanfilippo, Antonio P.; Calapristi, Augustin J.; Crow, Vernon L.; Hetzler, Elizabeth G.; Turner, Alan E.

2004-05-26

We present an approach to the disambiguation of cluster labels that capitalizes on the notion of semantic similarity to assign WordNet senses to cluster labels. The approach provides interesting insights on how document clustering can provide the basis for developing a novel approach to word sense disambiguation.

Macroeconomic Dimensions in the Clusterization Processes: Lithuanian Biomass Cluster Case

Directory of Open Access Journals (Sweden)

Navickas Valentinas

2017-03-01

Full Text Available The Future production systems’ increasing significance will impose work, which maintains not a competitive, but a collaboration basis, with concentrated resources and expertise, which can help to reach the general purpose. One form of collaboration among medium-size business organizations is work in clusters. Clusterization as a phenomenon has been known from quite a long time, but it offers simple benefits to researches at micro and medium levels. The clusterization process evaluation in macroeconomic dimensions has been comparatively little investigated. Thereby, in this article, the clusterization processes is analysed by concentrating our attention on macroeconomic factor researches. The authors analyse clusterization’s influence on country’s macroeconomic growth; they apply a structure research methodology for clusterization’s macroeconomic influence evaluation and propose that clusterization processes benefit macroeconomic analysis. The theoretical model of clusterization processes was validated by referring to a biomass cluster case. Because biomass cluster case is a new phenomenon, currently there are no other scientific approaches to them. The authors’ accomplished researches show that clusterization allows the achievement of a large positive slip in macroeconomics, which proves to lead to a high value added to creation, a faster country economic growth, and social situation amelioration.

Clustering Dycom

KAUST Repository

Minku, Leandro L.

2017-10-06

Background: Software Effort Estimation (SEE) can be formulated as an online learning problem, where new projects are completed over time and may become available for training. In this scenario, a Cross-Company (CC) SEE approach called Dycom can drastically reduce the number of Within-Company (WC) projects needed for training, saving the high cost of collecting such training projects. However, Dycom relies on splitting CC projects into different subsets in order to create its CC models. Such splitting can have a significant impact on Dycom\\'s predictive performance. Aims: This paper investigates whether clustering methods can be used to help finding good CC splits for Dycom. Method: Dycom is extended to use clustering methods for creating the CC subsets. Three different clustering methods are investigated, namely Hierarchical Clustering, K-Means, and Expectation-Maximisation. Clustering Dycom is compared against the original Dycom with CC subsets of different sizes, based on four SEE databases. A baseline WC model is also included in the analysis. Results: Clustering Dycom with K-Means can potentially help to split the CC projects, managing to achieve similar or better predictive performance than Dycom. However, K-Means still requires the number of CC subsets to be pre-defined, and a poor choice can negatively affect predictive performance. EM enables Dycom to automatically set the number of CC subsets while still maintaining or improving predictive performance with respect to the baseline WC model. Clustering Dycom with Hierarchical Clustering did not offer significant advantage in terms of predictive performance. Conclusion: Clustering methods can be an effective way to automatically generate Dycom\\'s CC subsets.

BREAST RECONSTRUCTIONS AFTER BREAST CANCER TREATING

Directory of Open Access Journals (Sweden)

Erik Vrabič

2018-02-01

Full Text Available Background. Breasts are an important symbol of physical beauty, feminity, mothering and sexual desire through the entire history of mankind. Lost of the whole or part of the breast is functional and aesthetic disturbance for woman. It is understandable, that the woman, who is concerned over breast loss, is as appropriate as another person´s concern over the loss of a limb or other body part. Before the 1960, breast reconstruction was considered as a dangerous procedure and it was almost prohibited. Considering the psychological importance of the breast in modern society, the possibility of breast reconstruction for the woman about to undergo a mastectomy is a comforting alternative. We can perform breast reconstruction with autologous tissue (autologous reconstruction, with breast implants and combination of both methods. For autologous reconstruction we can use local tissue (local flaps, or tissue from distant parts of the body (free vascular tissue transfer. Tissue expansion must be performed first, in many cases of breast reconstructions with breast implants. Conclusions. Possibility of breast reconstruction made a big progress last 3 decades. Today we are able to reconstruct almost every defect of the breast and the entire breast. Breast reconstruction rise the quality of life for breast cancer patients. Breast reconstruction is a team work of experts from many medicine specialites. In Slovenia we can offer breast reconstruction for breast cancer patients in Ljubljana, where plastic surgeons from Clinical Department for Plastic Surgery and Burns cooperate with oncologic surgeons. Ten years ago a similar cooperation between plastic surgeons and surgeons of the Centre for Breast Diseases was established in Maribor.

Reconstruction of a ring applicator using CT imaging: impact of the reconstruction method and applicator orientation

International Nuclear Information System (INIS)

Hellebust, Taran Paulsen; Tanderup, Kari; Bergstrand, Eva Stabell; Knutsen, Bjoern Helge; Roeislien, Jo; Olsen, Dag Rune

2007-01-01

The purpose of this study is to investigate whether the method of applicator reconstruction and/or the applicator orientation influence the dose calculation to points around the applicator for brachytherapy of cervical cancer with CT-based treatment planning. A phantom, containing a fixed ring applicator set and six lead pellets representing dose points, was used. The phantom was CT scanned with the ring applicator at four different angles related to the image plane. In each scan the applicator was reconstructed by three methods: (1) direct reconstruction in each image (DR) (2) reconstruction in multiplanar reconstructed images (MPR) and (3) library plans, using pre-defined applicator geometry (LIB). The doses to the lead pellets were calculated. The relative standard deviation (SD) for all reconstruction methods was less than 3.7% in the dose points. The relative SD for the LIB method was significantly lower (p < 0.05) than for the DR and MPR methods for all but two points. All applicator orientations had similar dose calculation reproducibility. Using library plans for applicator reconstruction gives the most reproducible dose calculation. However, with restrictive guidelines for applicator reconstruction the uncertainties for all methods are low compared to other factors influencing the accuracy of brachytherapy

Delayed vaginal reconstruction in the fibrotic pelvis following radiation or previous reconstruction

International Nuclear Information System (INIS)

Berek, J.S.; Hacker, N.F.; Lagasse, L.D.; Smith, M.L.

1983-01-01

Vaginal reconstruction was performed in 14 patients who had developed vaginal stenosis secondary to extensive pelvic fibrosis after pelvic radiation therapy (12 patients) or prior vaginal reconstruction (2 patients). Sixteen procedures were performed using a split-thickness skin graft. All patients had satisfactory vaginal restoration, and 12 patients reported good vaginal function. No fistula developed as a result of the operative procedure, but one patient later developed a rectovaginal fistula resulting from tumor recurrence. Successful vaginal reconstruction can be achieved even years after initial therapy in patients who develop an obliterated vagina from previous radiation or surgery

SABIO-RK: A data warehouse for biochemical reactions and their kinetics

Directory of Open Access Journals (Sweden)

Krebs Olga

2007-03-01

Full Text Available Systems biology is an emerging field that aims at obtaining a system-level understanding of biological processes. The modelling and simulation of networks of biochemical reactions have great and promising application potential but require reliable kinetic data. In order to support the systems biology community with such data we have developed SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics, a curated database with information about biochemical reactions and their kinetic properties, which allows researchers to obtain and compare kinetic data and to integrate them into models of biochemical networks. SABIO-RK is freely available for academic use at http://sabio.villa-bosch.de/SABIORK/.

LMC clusters: young

International Nuclear Information System (INIS)

Freeman, K.C.

1980-01-01

The young globular clusters of the LMC have ages of 10 7 -10 8 y. Their masses and structure are similar to those of the smaller galactic globular clusters. Their stellar mass functions (in the mass range 6 solar masses to 1.2 solar masses) vary greatly from cluster to cluster, although the clusters are similar in total mass, age, structure and chemical composition. It would be very interesting to know why these clusters are forming now in the LMC and not in the Galaxy. The author considers the 'young globular' or 'blue populous' clusters of the LMC. The ages of these objects are 10 7 to 10 8 y, and their masses are 10 4 to 10 5 solar masses, so they are populous enough to be really useful for studying the evolution of massive stars. The author concentrates on the structure and stellar content of these young clusters. (Auth.)

Major cluster mergers and the location of the brightest cluster galaxy

International Nuclear Information System (INIS)

Martel, Hugo; Robichaud, Fidèle; Barai, Paramita

2014-01-01

Using a large N-body cosmological simulation combined with a subgrid treatment of galaxy formation, merging, and tidal destruction, we study the formation and evolution of the galaxy and cluster population in a comoving volume (100 Mpc) 3 in a ΛCDM universe. At z = 0, our computational volume contains 1788 clusters with mass M cl > 1.1 × 10 12 M ☉ , including 18 massive clusters with M cl > 10 14 M ☉ . It also contains 1, 088, 797 galaxies with mass M gal ≥ 2 × 10 9 M ☉ and luminosity L > 9.5 × 10 5 L ☉ . For each cluster, we identified the brightest cluster galaxy (BCG). We then computed two separate statistics: the fraction f BNC of clusters in which the BCG is not the closest galaxy to the center of the cluster in projection, and the ratio Δv/σ, where Δv is the difference in radial velocity between the BCG and the whole cluster and σ is the radial velocity dispersion of the cluster. We found that f BNC increases from 0.05 for low-mass clusters (M cl ∼ 10 12 M ☉ ) to 0.5 for high-mass clusters (M cl > 10 14 M ☉ ) with very little dependence on cluster redshift. Most of this result turns out to be a projection effect and when we consider three-dimensional distances instead of projected distances, f BNC increases only to 0.2 at high-cluster mass. The values of Δv/σ vary from 0 to 1.8, with median values in the range 0.03-0.15 when considering all clusters, and 0.12-0.31 when considering only massive clusters. These results are consistent with previous observational studies and indicate that the central galaxy paradigm, which states that the BCG should be at rest at the center of the cluster, is usually valid, but exceptions are too common to be ignored. We built merger trees for the 18 most massive clusters in the simulation. Analysis of these trees reveal that 16 of these clusters have experienced 1 or several major or semi-major mergers in the past. These mergers leave each cluster in a non-equilibrium state, but eventually the cluster

Changing cluster composition in cluster randomised controlled trials: design and analysis considerations

Science.gov (United States)

2014-01-01

Background There are many methodological challenges in the conduct and analysis of cluster randomised controlled trials, but one that has received little attention is that of post-randomisation changes to cluster composition. To illustrate this, we focus on the issue of cluster merging, considering the impact on the design, analysis and interpretation of trial outcomes. Methods We explored the effects of merging clusters on study power using standard methods of power calculation. We assessed the potential impacts on study findings of both homogeneous cluster merges (involving clusters randomised to the same arm of a trial) and heterogeneous merges (involving clusters randomised to different arms of a trial) by simulation. To determine the impact on bias and precision of treatment effect estimates, we applied standard methods of analysis to different populations under analysis. Results Cluster merging produced a systematic reduction in study power. This effect depended on the number of merges and was most pronounced when variability in cluster size was at its greatest. Simulations demonstrate that the impact on analysis was minimal when cluster merges were homogeneous, with impact on study power being balanced by a change in observed intracluster correlation coefficient (ICC). We found a decrease in study power when cluster merges were heterogeneous, and the estimate of treatment effect was attenuated. Conclusions Examples of cluster merges found in previously published reports of cluster randomised trials were typically homogeneous rather than heterogeneous. Simulations demonstrated that trial findings in such cases would be unbiased. However, simulations also showed that any heterogeneous cluster merges would introduce bias that would be hard to quantify, as well as having negative impacts on the precision of estimates obtained. Further methodological development is warranted to better determine how to analyse such trials appropriately. Interim recommendations

Pin count-aware biochemical application compilation for mVLSI biochips

DEFF Research Database (Denmark)

Lander Raagaard, Michael; Pop, Paul

2015-01-01

Microfluidic biochips are replacing the conventional biochemical analyzers and are able to integrate the necessary functions for biochemical analysis on-chip. In this paper we are interested in flow-based biochips, in which the fluidic flow manipulated using integrated microvalves, which are cont...... a biochemical application. We focus on the compilation task, where the strategy is to delay operations, without missing their deadlines, such that the sharing of control signals is maximized. The evaluation shows a significant reduction in the number of control pins required....

Breast reconstruction following mastectomy: current status in Australia.

Science.gov (United States)

Sandelin, Kerstin; King, Elizabeth; Redman, Sally

2003-09-01

Although breast reconstruction provides some advantages for women following mastectomy, few Australian breast cancer patients currently receive reconstruction. In Australia, the routine provision of breast reconstruction will require the development of specific health service delivery models. The present paper reports an analysis of the provision of breast reconstruction in eight sites in Australia. A semi-structured telephone interview was conducted with 10 surgeons offering breast reconstruction as part of their practice, including nine breast or general surgeons and one plastic surgeon. Surgeons reported offering breast reconstruction to all women facing mastectomy; the proportion of women deciding to have breast reconstruction varied between sites with up to 50% of women having a reconstruction at some sites. Most sites offered three types of reconstruction. Two pathways emerged: either the breast surgeon performed the breast surgery in a team with the plastic surgeon who undertook the breast reconstruction or the breast surgeon provided both the breast surgery and the reconstruction. Considerable waiting times for breast reconstruction were reported in the public sector particularly for delayed reconstruction. Surgeons reported receiving training in breast reconstruction from plastic surgeons or from a breast surgery team that performed reconstructions; a number had been trained overseas. No audits of breast reconstruction were being undertaken. Breast reconstruction can be offered on a routine basis in Australia in both the private and public sectors. Women may be more readily able to access breast reconstruction when it is provided by a breast surgeon alone, but the range of reconstruction options may be more limited. If access to breast reconstruction is to be increased, there will be a need to: (i) develop effective models for the rural sector taking account of the lack of plastic surgeons; (ii) address waiting times for reconstruction surgery in the

Diagnostics of subtropical plants functional state by cluster analysis

Directory of Open Access Journals (Sweden)

Oksana Belous

2016-05-01

Full Text Available The article presents an application example of statistical methods for data analysis on diagnosis of the adaptive capacity of subtropical plants varieties. We depicted selection indicators and basic physiological parameters that were defined as diagnostic. We used evaluation on a set of parameters of water regime, there are: determination of water deficit of the leaves, determining the fractional composition of water and detection parameters of the concentration of cell sap (CCS (for tea culture flushes. These settings are characterized by high liability and high responsiveness to the effects of many abiotic factors that determined the particular care in the selection of plant material for analysis and consideration of the impact on sustainability. On the basis of the experimental data calculated the coefficients of pair correlation between climatic factors and used physiological indicators. The result was a selection of physiological and biochemical indicators proposed to assess the adaptability and included in the basis of methodical recommendations on diagnostics of the functional state of the studied cultures. Analysis of complex studies involving a large number of indicators is quite difficult, especially does not allow to quickly identify the similarity of new varieties for their adaptive responses to adverse factors, and, therefore, to set general requirements to conditions of cultivation. Use of cluster analysis suggests that in the analysis of only quantitative data; define a set of variables used to assess varieties (and the more sampling, the more accurate the clustering will happen, be sure to ascertain the measure of similarity (or difference between objects. It is shown that the identification of diagnostic features, which are subjected to statistical processing, impact the accuracy of the varieties classification. Selection in result of the mono-clusters analysis (variety tea Kolhida; hazelnut Lombardsky red; variety kiwi Monty

Petz recovery versus matrix reconstruction

Science.gov (United States)

Holzäpfel, Milan; Cramer, Marcus; Datta, Nilanjana; Plenio, Martin B.

2018-04-01

The reconstruction of the state of a multipartite quantum mechanical system represents a fundamental task in quantum information science. At its most basic, it concerns a state of a bipartite quantum system whose subsystems are subjected to local operations. We compare two different methods for obtaining the original state from the state resulting from the action of these operations. The first method involves quantum operations called Petz recovery maps, acting locally on the two subsystems. The second method is called matrix (or state) reconstruction and involves local, linear maps that are not necessarily completely positive. Moreover, we compare the quantities on which the maps employed in the two methods depend. We show that any state that admits Petz recovery also admits state reconstruction. However, the latter is successful for a strictly larger set of states. We also compare these methods in the context of a finite spin chain. Here, the state of a finite spin chain is reconstructed from the reduced states of a few neighbouring spins. In this setting, state reconstruction is the same as the matrix product operator reconstruction proposed by Baumgratz et al. [Phys. Rev. Lett. 111, 020401 (2013)]. Finally, we generalize both these methods so that they employ long-range measurements instead of relying solely on short-range correlations embodied in such local reduced states. Long-range measurements enable the reconstruction of states which cannot be reconstructed from measurements of local few-body observables alone and hereby we improve existing methods for quantum state tomography of quantum many-body systems.

Cluster evolution

International Nuclear Information System (INIS)

Schaeffer, R.

1987-01-01

The galaxy and cluster luminosity functions are constructed from a model of the mass distribution based on hierarchical clustering at an epoch where the matter distribution is non-linear. These luminosity functions are seen to reproduce the present distribution of objects as can be inferred from the observations. They can be used to deduce the redshift dependence of the cluster distribution and to extrapolate the observations towards the past. The predicted evolution of the cluster distribution is quite strong, although somewhat less rapid than predicted by the linear theory

PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories.

Directory of Open Access Journals (Sweden)

Victor Hanson-Smith

2016-07-01

Full Text Available The method of phylogenetic ancestral sequence reconstruction is a powerful approach for studying evolutionary relationships among protein sequence, structure, and function. In particular, this approach allows investigators to (1 reconstruct and "resurrect" (that is, synthesize in vivo or in vitro extinct proteins to study how they differ from modern proteins, (2 identify key amino acid changes that, over evolutionary timescales, have altered the function of the protein, and (3 order historical events in the evolution of protein function. Widespread use of this approach has been slow among molecular biologists, in part because the methods require significant computational expertise. Here we present PhyloBot, a web-based software tool that makes ancestral sequence reconstruction easy. Designed for non-experts, it integrates all the necessary software into a single user interface. Additionally, PhyloBot provides interactive tools to explore evolutionary trajectories between ancestors, enabling the rapid generation of hypotheses that can be tested using genetic or biochemical approaches. Early versions of this software were used in previous studies to discover genetic mechanisms underlying the functions of diverse protein families, including V-ATPase ion pumps, DNA-binding transcription regulators, and serine/threonine protein kinases. PhyloBot runs in a web browser, and is available at the following URL: http://www.phylobot.com. The software is implemented in Python using the Django web framework, and runs on elastic cloud computing resources from Amazon Web Services. Users can create and submit jobs on our free server (at the URL listed above, or use our open-source code to launch their own PhyloBot server.

Development of a new first-aid biochemical detector

Science.gov (United States)

Hu, Jingfei; Liao, Haiyang; Su, Shilin; Ding, Hao; Liu, Suquan

2016-10-01

The traditional biochemical detector exhibits poor adaptability, inconvenient carrying and slow detection, which can't meet the needs of first-aid under field condition like natural or man-made disasters etc. Therefore a scheme of first-aid biochemical detector based on MOMES Micro Spectrometer, UV LED and Photodiode was proposed. An optical detection structure combined continuous spectrum sweep with fixed wavelength measurement was designed, which adopted mobile detection optical path consisting of Micro Spectrometer and Halogen Lamp to detect Chloride (Cl-), Creatinine (Cre), Glucose (Glu), Hemoglobin (Hb). The UV LED and Photodiode were designed to detect Potassium (K-), Carbon dioxide (CO2), Sodium (Na+). According to the field diagnosis and treatment requirements, we designed the embedded control hardware circuit and software system, the prototype of first-aid biochemical detector was developed and the clinical trials were conducted. Experimental results show that the sample's absorbance repeatability is less than 2%, the max coefficient of variation (CV) in the batch repeatability test of all 7 biochemical parameters in blood samples is 4.68%, less than the clinical requirements 10%, the correlation coefficient (R2) in the clinical contrast test with AU5800 is almost greater than 0.97. To sum up, the prototype meets the requirements of clinical application.

Regulation of human Nfu activity in Fe-S cluster delivery-characterization of the interaction between Nfu and the HSPA9/Hsc20 chaperone complex.

Science.gov (United States)

Wachnowsky, Christine; Liu, Yushi; Yoon, Taejin; Cowan, J A

2018-01-01

Iron-sulfur cluster biogenesis is a complex, but highly regulated process that involves de novo cluster formation from iron and sulfide ions on a scaffold protein, and subsequent delivery to final targets via a series of Fe-S cluster-binding carrier proteins. The process of cluster release from the scaffold/carrier for transfer to the target proteins may be mediated by a dedicated Fe-S cluster chaperone system. In human cells, the chaperones include heat shock protein HSPA9 and the J-type chaperone Hsc20. While the role of chaperones has been somewhat clarified in yeast and bacterial systems, many questions remain over their functional roles in cluster delivery and interactions with a variety of human Fe-S cluster proteins. One such protein, Nfu, has recently been recognized as a potential interaction partner of the chaperone complex. Herein, we examined the ability of human Nfu to function as a carrier by interacting with the human chaperone complex. Human Nfu is shown to bind to both chaperone proteins with binding affinities similar to those observed for IscU binding to the homologous HSPA9 and Hsc20, while Nfu can also stimulate the ATPase activity of HSPA9. Additionally, the chaperone complex was able to promote Nfu function by enhancing the second-order rate constants for Fe-S cluster transfer to target proteins and providing directionality in cluster transfer from Nfu by eliminating promiscuous transfer reactions. Together, these data support a hypothesis in which Nfu can serve as an alternative carrier protein for chaperone-mediated cluster release and delivery in Fe-S cluster biogenesis and trafficking. © 2017 Federation of European Biochemical Societies.

Biochemical failure after radical external beam radiotherapy for prostate cancer

International Nuclear Information System (INIS)

Nomoto, Satoshi; Imada, Hajime; Kato, Fumio; Yahara, Katsuya; Morioka, Tomoaki; Ohguri, Takayuki; Nakano, Keita; Korogi, Yukunori

2005-01-01

The purpose of this study was to evaluate biochemical failures after radical external beam radiotherapy for prostate cancer. A total of 143 patients with prostate cancer (5 cases in stage A2, 95 in stage B and 43 in stage C; 18 in low risk group, 37 in intermediate risk group, 67 in high risk group and 21 in unknown group) were included in this study. Patients of stage A2 and B underwent external irradiation of 46 Gy to the prostate gland and seminal vesicle and additional 20 Gy to the prostate gland, while patients of stage C underwent external irradiation of 66 Gy to the prostate gland and seminal vesicle including 46 Gy to the pelvis. Neoadjuvant hormonal therapy was done in 66 cases, and long-term hormonal therapy in 75 cases; two cases were treated with radiation therapy alone. The 3-year relapse free survival rates by stage A2, B and C were 100%, 96.7% and 88.1%, respectively. The 3-year relapse free survival rates by low, intermediate and high risk groups were 100%, 92.3% and 89.7%, respectively. Biochemical failure was noted in nine cases during the average observation term of 32.2 months; in this group the median of prostate specific antigen (PSA) value was 2.6 ng/ml, the doubling time was 8.6 months, and the term of biochemical failure was 33.2 months. Six of eight cases with biochemical failure were the neoadjuvant hormonal therapy group, but biochemical no evidence of disease (bNED) curve showed no significant difference between neoadjuvant and long-term hormonal groups. It is supposed that unnecessary hormonal therapies were performed based on the nonspecific diagnosis of biochemical failure after radical radiotherapy in our group of patients. A precise criterion of biochemical failure after radical radiotherapy for prostate cancer is necessary. (author)

Breast Reconstruction After Solid Organ Transplant.

Science.gov (United States)

Koonce, Stephanie L; Giles, Brian; McLaughlin, Sarah A; Perdikis, Galen; Waldorf, James; Lemaine, Valerie; TerKonda, Sarvam

2015-09-01

Solid organ transplant patients frequently develop posttransplant malignancies including breast cancer. They may desire breast reconstruction after mastectomy, which could potentially be complicated by their transplant status, immunosuppressive regimen, and previous operations. We review our experience with patients who have undergone solid organ transplant and subsequent breast reconstruction after mastectomy After institutional review board approval, we queried our prospective breast reconstruction and solid organ transplant databases for corresponding patients. Inclusion criteria comprised breast reconstruction after solid organ transplant. A chart review was conducted of identified patients. Seventeen patients were identified: 1 pulmonary transplant, 4 cardiac transplants, 2 liver transplants, 1 pancreas transplant, 2 combined kidney/pancreas transplants, and 7 kidney transplants. Indications for mastectomy included posttransplant malignancy and prophylaxis. Median time from transplant to completion of reconstruction was 186 months (range, 11-336 months). Median age at transplant was 34.5 years (range, 21-65 years) with the median age of the patients at reconstructive surgery 51.5 years (range, 34-71 years). Median body mass index was 25.3 (range, 21.3-46.5). No significant complications were noted after reconstructive surgery. All patients were on full immunosuppression at time of reconstruction. Breast reconstruction is a viable option for transplant patients after mastectomy and should not be refused based on their transplant status. Close coordination with the transplant team and careful preoperative planning is essential for optimal outcomes.

Cluster-cluster aggregation of Ising dipolar particles under thermal noise

KAUST Repository

Suzuki, Masaru

2009-08-14

The cluster-cluster aggregation processes of Ising dipolar particles under thermal noise are investigated in the dilute condition. As the temperature increases, changes in the typical structures of clusters are observed from chainlike (D1) to crystalline (D2) through fractal structures (D1.45), where D is the fractal dimension. By calculating the bending energy of the chainlike structure, it is found that the transition temperature is associated with the energy gap between the chainlike and crystalline configurations. The aggregation dynamics changes from being dominated by attraction to diffusion involving changes in the dynamic exponent z=0.2 to 0.5. In the region of temperature where the fractal clusters grow, different growth rates are observed between charged and neutral clusters. Using the Smoluchowski equation with a twofold kernel, this hetero-aggregation process is found to result from two types of dynamics: the diffusive motion of neutral clusters and the weak attractive motion between charged clusters. The fact that changes in structures and dynamics take place at the same time suggests that transitions in the structure of clusters involve marked changes in the dynamics of the aggregation processes. © 2009 The American Physical Society.

Multidimensional biochemical information processing of dynamical patterns.

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