Diffractive imaging of a rotational wavepacket in nitrogen molecules with femtosecond megaelectronvolt electron pulses

DOE PAGES

Yang, Jie; Guehr, Markus; Vecchione, Theodore; ...

2016-04-05

Imaging changes in molecular geometries on their natural femtosecond timescale with sub-Angström spatial precision is one of the critical challenges in the chemical sciences, as the nuclear geometry changes determine the molecular reactivity. For photoexcited molecules, the nuclear dynamics determine the photoenergy conversion path and efficiency. Here we report a gas-phase electron diffraction experiment using megaelectronvolt (MeV) electrons, where we captured the rotational wavepacket dynamics of nonadiabatically laser-aligned nitrogen molecules. We achieved a combination of 100 fs root-mean-squared temporal resolution and sub-Angstrom (0.76 Å) spatial resolution that makes it possible to resolve the position of the nuclei within the molecule.more » In addition, the diffraction patterns reveal the angular distribution of the molecules, which changes from prolate (aligned) to oblate (anti-aligned) in 300 fs. Lastly, our results demonstrate a significant and promising step towards making atomically resolved movies of molecular reactions.« less

The Rail Alignment Environmental Impact Statement: An Update

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

R. Sweeney

2005-01-20

On July 23,2002, the President of the United States signed into law a joint resolution of the United States Congress designating the Yucca Mountain site in Nye County, Nevada, for development as a geologic repository for the disposal of spent nuclear fuel and high-level radioactive waste. If the US. Nuclear Regulatory Commission authorizes construction of the repository and receipt and possession of spent nuclear fuel and high-level radioactive at Yucca Mountain, the U.S. Department of Energy (DOE) would be responsible for transporting these materials to the Yucca Mountain repository as part of its obligation under the Nuclear Waste Policy Act.more » Part of the site recommendation decision included the analysis of a nation-wide shipping campaign to the proposed repository site. The ''Final Environmental Impact Statement for a Geologic Repository for the Disposal of Spent Nuclear Fuel and High-Level Radioactive Waste at Yucca Mountain, Nye County, Nevada'' (February 2002) (Repository EIS) evaluated the potential impacts of the transportation of 70,000 Metric Tons of Heavy Metal spent nuclear fuel and high-level radioactive waste from 77 locations around the nation to the potential repository in Nevada over a 24 year shipping campaign. In the Repository EIS, DOE identified mostly rail as its preferred mode of transportation, both nationally and in the State of Nevada. In December 2003, based on public comments and the environmental analyses in the Repository EIS, DOE identified a preference for the Caliente rail corridor in Nevada. On April 8, 2004, DOE issued a Record of Decision (ROD) on the Mode of Transportation and Nevada Rail Corridor for the Disposal of Spent Nuclear Fuel and High-Level Radioactive Waste at Yucca Mountain, Nye County, Nevada. In this ROD, the DOE announced that it had decided to select the mostly rail scenario analyzed in the Repository EIS as the transportation mode both on a national basis and in the State of Nevada. Under the mostly rail scenario, the DOE would rely on a combination of rail, truck and possibly barge to transport to the repository site at Yucca Mountain up to 70,000 MTHM of spent nuclear fuel and high-level radioactive waste, with most of the spent nuclear fuel and high-level radioactive waste being transported by rail. This will ultimately require construction of a rail line in Nevada to the repository. In addition, the DOE has decided to select the Caliente rail corridor in which to examine potential alignments within which to construct that rail line. A corridor is a strip of land, approximately 400 meters (0.25 miles) wide, that encompasses one of several possible routes through which DOE could build a rail line. An alignment is the specific location of a rail line in a corridor, and would likely be 60 meters [200 feet] or less in width. Also on April 8, 2004, DOE issued a Notice of Intent to Prepare an Environmental Impact Statement for the Alignment, Construction, and Operation of a Rail Line to a Geologic Repository at Yucca Mountain, Nye County, NV. In the Notice of Intent, the Department announced its intent to prepare a Rail Alignment EIS to assist in selecting a possible alignment for construction of a rail line that would connect the repository at Yucca Mountain to an existing main rail line in Nevada. The Rail Alignment EIS also would consider the potential construction and operation of a rail-to-truck intermodal transfer facility, proposed to be located at the confluence of an existing mainline railroad and a highway, to support legal-weight truck transportation until the rail system is fully operational. This corridor is approximately 513 kilometers (319 miles) long and would cost an estimated $880 million (2001 dollars). Should DOE decide to build the Caliente corridor, it may be the longest rail line built in the United States since the Transcontinental Railroad was constructed in 1869. Some of the challenges in building this rail corridor are steep grades (the corridor crosses over 7 mountain ranges), isolated terrain, possible tunnels, and stakeholder acceptance.« less

Performance of automatic scanning microscope for nuclear emulsion experiments

NASA Astrophysics Data System (ADS)

Güler, A. Murat; Altınok, Özgür

2015-12-01

The impressive improvements in scanning technology and methods let nuclear emulsion to be used as a target in recent large experiments. We report the performance of an automatic scanning microscope for nuclear emulsion experiments. After successful calibration and alignment of the system, we have reached 99% tracking efficiency for the minimum ionizing tracks that penetrating through the emulsions films. The automatic scanning system is successfully used for the scanning of emulsion films in the OPERA experiment and plan to use for the next generation of nuclear emulsion experiments.

Performance of automatic scanning microscope for nuclear emulsion experiments

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

Güler, A. Murat, E-mail: mguler@newton.physics.metu.edu.tr; Altınok, Özgür; Tufts University, Medford, MA 02155

The impressive improvements in scanning technology and methods let nuclear emulsion to be used as a target in recent large experiments. We report the performance of an automatic scanning microscope for nuclear emulsion experiments. After successful calibration and alignment of the system, we have reached 99% tracking efficiency for the minimum ionizing tracks that penetrating through the emulsions films. The automatic scanning system is successfully used for the scanning of emulsion films in the OPERA experiment and plan to use for the next generation of nuclear emulsion experiments.

Multiaxial Polarity Determines Individual Cellular and Nuclear Chirality

PubMed Central

Raymond, Michael J.; Ray, Poulomi; Kaur, Gurleen; Fredericks, Michael; Singh, Ajay V.; Wan, Leo Q.

2016-01-01

Intrinsic cell chirality has been implicated in the left-right (LR) asymmetry of embryonic development. Impaired cell chirality could lead to severe birth defects in laterality. Previously, we detected cell chirality with an in vitro micropatterning system. Here, we demonstrate for the first time that chirality can be quantified as the coordination of multiaxial polarization of individual cells and nuclei. Using an object labeling, connected component based method, we characterized cell chirality based on cell and nuclear shape polarization and nuclear positioning of each cell in multicellular patterns of epithelial cells. We found that the cells adopted a LR bias the boundaries by positioning the sharp end towards the leading edge and leaving the nucleus at the rear. This behavior is consistent with the directional migration observed previously on the boundary of micropatterns. Although the nucleus is chirally aligned, it is not strongly biased towards or away from the boundary. As the result of the rear positioning of nuclei, the nuclear positioning has an opposite chirality to that of cell alignment. Overall, our results have revealed deep insights of chiral morphogenesis as the coordination of multiaxial polarization at the cellular and subcellular levels. PMID:28360944

Multiaxial Polarity Determines Individual Cellular and Nuclear Chirality.

PubMed

Raymond, Michael J; Ray, Poulomi; Kaur, Gurleen; Fredericks, Michael; Singh, Ajay V; Wan, Leo Q

2017-02-01

Intrinsic cell chirality has been implicated in the left-right (LR) asymmetry of embryonic development. Impaired cell chirality could lead to severe birth defects in laterality. Previously, we detected cell chirality with an in vitro micropatterning system. Here, we demonstrate for the first time that chirality can be quantified as the coordination of multiaxial polarization of individual cells and nuclei. Using an object labeling, connected component based method, we characterized cell chirality based on cell and nuclear shape polarization and nuclear positioning of each cell in multicellular patterns of epithelial cells. We found that the cells adopted a LR bias the boundaries by positioning the sharp end towards the leading edge and leaving the nucleus at the rear. This behavior is consistent with the directional migration observed previously on the boundary of micropatterns. Although the nucleus is chirally aligned, it is not strongly biased towards or away from the boundary. As the result of the rear positioning of nuclei, the nuclear positioning has an opposite chirality to that of cell alignment. Overall, our results have revealed deep insights of chiral morphogenesis as the coordination of multiaxial polarization at the cellular and subcellular levels.

Measurement of untruncated nuclear spin interactions via zero- to ultralow-field nuclear magnetic resonance

NASA Astrophysics Data System (ADS)

Blanchard, J. W.; Sjolander, T. F.; King, J. P.; Ledbetter, M. P.; Levine, E. H.; Bajaj, V. S.; Budker, D.; Pines, A.

2015-12-01

Zero- to ultralow-field nuclear magnetic resonance (ZULF NMR) provides a new regime for the measurement of nuclear spin-spin interactions free from the effects of large magnetic fields, such as truncation of terms that do not commute with the Zeeman Hamiltonian. One such interaction, the magnetic dipole-dipole coupling, is a valuable source of spatial information in NMR, though many terms are unobservable in high-field NMR, and the coupling averages to zero under isotropic molecular tumbling. Under partial alignment, this information is retained in the form of so-called residual dipolar couplings. We report zero- to ultralow-field NMR measurements of residual dipolar couplings in acetonitrile-2-13C aligned in stretched polyvinyl acetate gels. This permits the investigation of dipolar couplings as a perturbation on the indirect spin-spin J coupling in the absence of an applied magnetic field. As a consequence of working at zero magnetic field, we observe terms of the dipole-dipole coupling Hamiltonian that are invisible in conventional high-field NMR. This technique expands the capabilities of zero- to ultralow-field NMR and has potential applications in precision measurement of subtle physical interactions, chemical analysis, and characterization of local mesoscale structure in materials.

Dynamical Properties of Eccentric Nuclear Disks: Stability, Longevity, and Implications for Tidal Disruption Rates in Post-merger Galaxies

NASA Astrophysics Data System (ADS)

Madigan, Ann-Marie; Halle, Andrew; Moody, Mackenzie; McCourt, Michael; Nixon, Chris; Wernke, Heather

2018-02-01

In some galaxies, the stars orbiting the supermassive black hole take the form of an eccentric nuclear disk, in which every star is on a coherent, apsidally aligned orbit. The most famous example of an eccentric nuclear disk is the double nucleus of Andromeda, and there is strong evidence for many more in the local universe. Despite their apparent ubiquity, however, a dynamical explanation for their longevity has remained a mystery: differential precession should wipe out large-scale apsidal-alignment on a short timescale. Here we identify a new dynamical mechanism which stabilizes eccentric nuclear disks, and explain for the first time the negative eccentricity gradient seen in the Andromeda nucleus. The stabilizing mechanism drives oscillations of the eccentricity vectors of individual orbits, both in direction (about the mean body of the disk) and in magnitude. Combined with the negative eccentricity gradient, the eccentricity oscillations push some stars near the inner edge of the disk extremely close to the black hole, potentially leading to tidal disruption events (TDEs). Order of magnitude calculations predict extremely high rates in recently formed eccentric nuclear disks (∼0.1–1 {{yr}}-1 {{gal}}-1). Unless the stellar disks are replenished, these rates should decrease with time as the disk depletes in mass. If eccentric nuclear disks form during gas-rich major mergers, this may explain the preferential occurrence of TDEs in recently merged and post-merger (E+A/K+A) galaxies.

Securing Nuclear Materials: The 2010 Summit and Issues for Congress

DTIC Science & Technology

2011-04-27

Nigeria, Norway, Pakistan, Philippines, Poland, the Republic of Korea, the Russian Federation, Saudi Arabia, Singapore, Switzerland, South Africa...Spain, Sweden, Thailand, Turkey , United Arab Emirates, the United Kingdom, Ukraine, and Vietnam. White House Press Briefing, April 6, 2010. 8 “ The ...Non-Aligned Movement, where skepticism of the nuclear terrorism threat runs highest. In addition, the Russian Federation said it would be helping the

Electronic Measurement of Rock Stress

DTIC Science & Technology

atomic resonances that are pressure-sensitive. Nuclear quadrupole resonance ( NQR ) appeared clearly applicable, since no magnetic aligning field is needed...there are several common NQR -active nuclear species in major rock-forming minerals, and rf magnetic fields between 0.3 and 3 megahertz (the resonant...comprehensive literature search has been completed on NQR in minerals, which shows that aluminum-27 and a few other elements in feldspars are promising

NMR of (133)Cs(+) in stretched hydrogels: One-dimensional, z- and NOESY spectra, and probing the ion's environment in erythrocytes.

PubMed

Kuchel, Philip W; Shishmarev, Dmitry; Puckeridge, Max; Levitt, Malcolm H; Naumann, Christoph; Chapman, Bogdan E

2015-12-01

(133)Cs nuclear magnetic resonance (NMR) spectroscopy was conducted on (133)Cs(+) in gelatin hydrogels that were either relaxed or stretched. Stretching generated a septet from this spin-7/2 nucleus, and its nuclear magnetic relaxation was studied via z-spectra, and two-dimensional nuclear Overhauser (NOESY) spectroscopy. Various spectral features were well simulated by using Mathematica and the software package SpinDynamica. Spectra of CsCl in suspensions of human erythrocytes embedded in gelatin gel showed separation of the resonances from the cation inside and outside the cells. Upon stretching the sample, the extracellular (133)Cs(+) signal split into a septet, while the intracellular peak was unchanged, revealing different alignment/ordering properties of the environment inside and around the cells. Differential interference contrast light microscopy confirmed that the cells were stretched when the overall sample was elongated. Analysis of the various spectral features of (133)Cs(+) reported here opens up applications of this K(+) congener for studies of cation-handling by metabolically-active cells and tissues in aligned states. Copyright © 2015 Elsevier Inc. All rights reserved.

Phylogenetics of Pinus (Pinaceae) based on nuclear ribosomal DNA internal transcribed spacer region sequences.

PubMed

Liston, A; Robinson, W A; Piñero, D; Alvarez-Buylla, E R

1999-02-01

A 650-bp portion of the nuclear ribosomal DNA internal transcribed spacer region was sequenced in 47 species of Pinus, representing all recognized subsections of the genus, and 2 species of Picea and Cathaya as outgroups. Parsimony analyses of these length variable sequences were conducted using a manual alignment, 13 different automated alignments, elision of the automated alignments, and exclusion of all alignment ambiguous sites. High and moderately supported clades were consistently resolved across the different analyses, while poorly supported clades were inconsistently recovered. Comparison of the topologies highlights taxa of particularly problematic placement including Pinus nelsonii and P. aristata. Within subgenus Pinus, there is moderate support for the monophyly of a narrowly circumscribed subsect. Pinus (=subsect. Sylvestres) and strong support for a clade of North and Central American hard pines. The Himalayan P. roxburghii may be sister species to these "New World hard pines," which have two well-supported subgroups, subsect. Ponderosae and a clade of the remaining five subsections. The position of subsect. Contortae conflicts with its placement in a chloroplast DNA restriction site study. Within subgenus Strobus there is consistent support for the monophyly of a broadly circumscribed subsect. Strobi (including P. krempfii and a polyphyletic subsect. Cembrae) derived from a paraphyletic grade of the remaining soft pines. Relationships among subsects. Gerardianae, Cembroides, and Balfourianae are poorly resolved. Support for the monophyly of subgenus Pinus and subgenus Strobus is not consistently obtained. Copyright 1999 Academic Press.

Magnetic moment of the fragmentation-aligned 61Fe (9/2(+)) isomer.

PubMed

Matea, I; Georgiev, G; Daugas, J M; Hass, M; Neyens, G; Astabatyan, R; Baby, L T; Balabanski, D L; Bélier, G; Borremans, D; Goldring, G; Goutte, H; Himpe, P; Lewitowicz, M; Lukyanov, S; Méot, V; Santos, F de Oliveira; Penionzhkevich, Yu E; Roig, O; Sawicka, M

2004-10-01

We report on the g factor measurement of an isomer in the neutron-rich (61)(26)Fe (E(*)=861 keV and T(1/2)=239(5) ns). The isomer was produced and spin aligned via a projectile-fragmentation reaction at intermediate energy, the time dependent perturbed angular distribution method being used for the measurement of the g factor. For the first time, due to significant improvements of the experimental technique, an appreciable residual alignment of the nuclear spin ensemble has been observed, allowing a precise determination of its g factor, including the sign: g=-0.229(2). In this way we open the possibility to study moments of very neutron-rich short-lived isomers, not accessible via other production and spin-orientation methods.

Seeking an Anchorage. Stability and Variability in Tonal Alignment of Rising Prenuclear Pitch Accents in Cypriot Greek.

PubMed

Themistocleous, Charalambos

2016-12-01

Although tonal alignment constitutes a quintessential property of pitch accents, its exact characteristics remain unclear. This study, by exploring the timing of the Cypriot Greek L*+H prenuclear pitch accent, examines the predictions of three hypotheses about tonal alignment: the invariance hypothesis, the segmental anchoring hypothesis, and the segmental anchorage hypothesis. The study reports on two experiments: the first of which manipulates the syllable patterns of the stressed syllable, and the second of which modifies the distance of the L*+H from the following pitch accent. The findings on the alignment of the low tone (L) are illustrative of the segmental anchoring hypothesis predictions: the L persistently aligns inside the onset consonant, a few milliseconds before the stressed vowel. However, the findings on the alignment of the high tone (H) are both intriguing and unexpected: the alignment of the H depends on the number of unstressed syllables that follow the prenuclear pitch accent. The 'wandering' of the H over multiple syllables is extremely rare among languages, and casts doubt on the invariance hypothesis and the segmental anchoring hypothesis, as well as indicating the need for a modified version of the segmental anchorage hypothesis. To address the alignment of the H, we suggest that it aligns within a segmental anchorage-the area that follows the prenuclear pitch accent-in such a way as to protect the paradigmatic contrast between the L*+H prenuclear pitch accent and the L+H* nuclear pitch accent.

Rack for storing spent nuclear fuel elements

DOEpatents

Rubinstein, Herbert J.; Clark, Philip M.; Gilcrest, James D.

1978-06-20

A rack for storing spent nuclear fuel elements in which a plurality of aligned rows of upright enclosures of generally square cross-sectional areas contain vertically disposed fuel elements. The enclosures are fixed at the lower ends thereof to a base. Pockets are formed between confronting walls of adjacent enclosures for receiving high absorption neutron absorbers, such as Boral, cadmium, borated stainless steel and the like for the closer spacing of spent fuel elements.

Fission control system for nuclear reactor

DOEpatents

Conley, G.H.; Estes, G.P.

Control system for nuclear reactor comprises a first set of reactivity modifying rods fixed in a reactor core with their upper ends stepped in height across the core, and a second set of reactivity modifying rods movable vertically within the reactor core and having their lower ends stepped to correspond with the stepped arrangement of the first set of rods, pairs of the rods of the first and second sets being in coaxial alignment.

Rab5 GTPase controls chromosome alignment through Lamin disassembly and relocation of the NuMA-like protein Mud to the poles during mitosis

PubMed Central

Capalbo, Luisa; D'Avino, Pier Paolo; Archambault, Vincent; Glover, David M.

2011-01-01

The small GTPase Rab5 is a conserved regulator of membrane trafficking; it regulates the formation of early endosomes, their transport along microtubules, and the fusion to the target organelles. Although several members of the endocytic pathway were recently implicated in spindle organization, it is unclear whether Rab5 has any role during mitosis. Here, we describe that Rab5 is required for proper chromosome alignment during Drosophila mitoses. We also found that Rab5 associated in vivo with nuclear Lamin and mushroom body defect (Mud), the Drosophila counterpart of nuclear mitotic apparatus protein (NuMA). Consistent with this finding, Rab5 was required for the disassembly of the nuclear envelope at mitotic entry and the accumulation of Mud at the spindle poles. Furthermore, Mud depletion caused chromosome misalignment defects that resembled the defects of Rab5 RNAi cells, and double-knockdown experiments indicated that the two proteins function in a linear pathway. Our results indicate a role for Rab5 in mitosis and reinforce the emerging view of the contributions made by cell membrane dynamics to spindle function. PMID:21987826

Optical control of ground-state atomic orbital alignment: Cl(2P3/2) atoms from HCl(v=2,J=1) photodissociation.

PubMed

Sofikitis, Dimitris; Rubio-Lago, Luis; Martin, Marion R; Ankeny Brown, Davida J; Bartlett, Nathaniel C-M; Alexander, Andrew J; Zare, Richard N; Rakitzis, T Peter

2007-10-14

H(35)Cl(v=0,J=0) molecules in a supersonic expansion were excited to the H(35)Cl(v=2,J=1,M=0) state with linearly polarized laser pulses at about 1.7 microm. These rotationally aligned J=1 molecules were then selectively photodissociated with a linearly polarized laser pulse at 220 nm after a time delay, and the velocity-dependent alignment of the (35)Cl((2)P(32)) photofragments was measured using 2+1 REMPI and time-of-flight mass spectrometry. The (35)Cl((2)P(32)) atoms are aligned by two mechanisms: (1) the time-dependent transfer of rotational polarization of the H(35)Cl(v=2,J=1,M=0) molecule to the (35)Cl((2)P(32)) nuclear spin [which is conserved during the photodissociation and thus contributes to the total (35)Cl((2)P(32)) photofragment atomic polarization] and (2) the alignment of the (35)Cl((2)P(32)) electronic polarization resulting from the photoexcitation and dissociation process. The total alignment of the (35)Cl((2)P(32)) photofragments from these two mechanisms was found to vary as a function of time delay between the excitation and the photolysis laser pulses, in agreement with theoretical predictions. We show that the alignment of the ground-state (35)Cl((2)P(32)) atoms, with respect to the photodissociation recoil direction, can be controlled optically. Potential applications include the study of alignment-dependent collision effects.

Observation of γ-vibrations and alignments built on non-ground-state configurations in ¹⁵⁶Dy

DOE PAGES

Zhu, C. -H.; Hartley, D. J.; Riedinger, L. L.; ...

2015-03-26

The exact nature of the lowest K π=2⁺ rotational bands in all deformed nuclei remains obscure. Traditionally they are assumed to be collective vibrations of the nuclear shape in the γ degree of freedom perpendicular to the nuclear symmetry axis. Very few such γ-bands have been traced past the usual back-bending rotational alignments of high-j nucleons. We have investigated the structure of positive-parity bands in the N=90 nucleus ¹⁵⁶Dy, using the ¹⁴⁸Nd(¹²C,4n)¹⁵⁶Dy reaction at 65 MeV, observing the resulting γ-ray transitions with the Gammasphere array. The even- and odd-spin members of the π=2⁺ γ-band are observed to 32⁺ and 31⁺more » respectively. This rotational band faithfully tracks the ground-state configuration to the highest spins. The members of a possible γ-vibration built on the aligned yrast S-band are observed to spins 28⁺ and 27⁺. An even-spin positive-parity band, observed to spin 24⁺, is a candidate for an aligned S-band built on the seniority-zero configuration of the 0₂⁺ state at 676 keV. As a result, the crossing of this band with the 0₂⁺ band is at hw c = 0.28(1) MeV and is consistent with the configuration of the 0₂⁺ band not producing any blocking of the monopole pairing.« less

Jaw1/LRMP has a role in maintaining nuclear shape via interaction with SUN proteins.

PubMed

Kozono, Takuma; Tadahira, Kazuko; Okumura, Wataru; Itai, Nao; Tamura-Nakano, Miwa; Dohi, Taeko; Tonozuka, Takashi; Nishikawa, Atsushi

2018-06-06

Jaw1/LRMP is characterized as a type II integral membrane protein that is localized to endoplasmic reticulum (ER), however, its physiological functions have been poorly understood. An alignment of amino acid sequence of Jaw1 with KASH proteins, outer nuclear membrane proteins, revealed that Jaw1 has a partial homology to the KASH domain. Here, we show that the function of Jaw1 is to maintain nuclear shape in mouse melanoma cell line. The siRNA-mediated knockdown of Jaw1 caused a severe defect in nuclear shape, and the defect was rescued by ectopic expression of siRNA-resistant Jaw1. Since co-immunoprecipitation assay indicates that Jaw1 interacts with SUN proteins that are inner nuclear proteins and microtubules, this study suggests that Jaw1 has a role in maintaining nuclear shape via interactions with SUN proteins and microtubules.

Caenorhabditis elegans polo-like kinase PLK-1 is required for merging parental genomes into a single nucleus.

PubMed

Rahman, Mohammad M; Munzig, Mandy; Kaneshiro, Kiyomi; Lee, Brandon; Strome, Susan; Müller-Reichert, Thomas; Cohen-Fix, Orna

2015-12-15

Before the first zygotic division, the nuclear envelopes of the maternal and paternal pronuclei disassemble, allowing both sets of chromosomes to be incorporated into a single nucleus in daughter cells after mitosis. We found that in Caenorhabditis elegans, partial inactivation of the polo-like kinase PLK-1 causes the formation of two nuclei, containing either the maternal or paternal chromosomes, in each daughter cell. These two nuclei gave rise to paired nuclei in all subsequent cell divisions. The paired-nuclei phenotype was caused by a defect in forming a gap in the nuclear envelopes at the interface between the two pronuclei during the first mitotic division. This was accompanied by defects in chromosome congression and alignment of the maternal and paternal metaphase plates relative to each other. Perturbing chromosome congression by other means also resulted in failure to disassemble the nuclear envelope between the two pronuclei. Our data further show that PLK-1 is needed for nuclear envelope breakdown during early embryogenesis. We propose that during the first zygotic division, PLK-1-dependent chromosome congression and metaphase plate alignment are necessary for the disassembly of the nuclear envelope between the two pronuclei, ultimately allowing intermingling of the maternal and paternal chromosomes. © 2015 Rahman et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

A large-scale, higher-level, molecular phylogenetic study of the insect order Lepidoptera (moths and butterflies)

USDA-ARS?s Scientific Manuscript database

Higher-level relationships within the Lepidoptera, and particularly within the species-rich subclade Ditrysia, are generally not well understood, although recent studies have yielded progress. 483 taxa spanning 115 of 124 families were sampled for 19 protein-coding nuclear genes. Their aligned nucle...

29Si nuclear magnetic resonance study of URu 2Si 2 under pressure

DOE PAGES

Shirer, K. R.; Dioguardi, A. P.; Bush, B. T.; ...

2015-12-01

Here, we report 29Si nuclear magnetic resonance measurements of single crystals and aligned powders of URu 2Si 2 under pressure in the hidden order and paramagnetic phases. We find evidence for a reduction of the Knight shift with applied pressure, consistent with previous measurements of the static magnetic susceptibility. Previous measurements of the spin lattice relaxation time revealed a partial suppression of the density of states below 30 K. Here, we find that the temperature at which this suppression occurs is enhanced with applied pressure.

Developing an SSAC Self-Assessment Tool for Operators and Regulators

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

Frazar, Sarah L.; Innes-Jones, Gemma; Hamilton, Ian

Enabling an SSAC to understand why it is performing inefficiently can help it allocate resources more effectively to better support IAEA safeguards implementation. In collaboration with international consulting firm, Environmental Resources Management (ERM) and a U.S. based nuclear fuel cycle facility, the Pacific Northwest National Laboratory (PNNL) has been developing a framework for a future self-assessment tool for nuclear operators and regulators. This paper will describe the effort to date, with particular emphasis on the steps the team took to align the framework with relevant IAEA self-assessment tools.

Transient and Partial Nuclear Lamina Disruption Promotes Chromosome Movement in Early Meiotic Prophase.

PubMed

Link, Jana; Paouneskou, Dimitra; Velkova, Maria; Daryabeigi, Anahita; Laos, Triin; Labella, Sara; Barroso, Consuelo; Pacheco Piñol, Sarai; Montoya, Alex; Kramer, Holger; Woglar, Alexander; Baudrimont, Antoine; Markert, Sebastian Mathias; Stigloher, Christian; Martinez-Perez, Enrique; Dammermann, Alexander; Alsheimer, Manfred; Zetka, Monique; Jantsch, Verena

2018-04-23

Meiotic chromosome movement is important for the pairwise alignment of homologous chromosomes, which is required for correct chromosome segregation. Movement is driven by cytoplasmic forces, transmitted to chromosome ends by nuclear membrane-spanning proteins. In animal cells, lamins form a prominent scaffold at the nuclear periphery, yet the role lamins play in meiotic chromosome movement is unclear. We show that chromosome movement correlates with reduced lamin association with the nuclear rim, which requires lamin phosphorylation at sites analogous to those that open lamina network crosslinks in mitosis. Failure to remodel the lamina results in delayed meiotic entry, altered chromatin organization, unpaired or interlocked chromosomes, and slowed chromosome movement. The remodeling kinases are delivered to lamins via chromosome ends coupled to the nuclear envelope, potentially enabling crosstalk between the lamina and chromosomal events. Thus, opening the lamina network plays a role in modulating contacts between chromosomes and the nuclear periphery during meiosis. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Aligned interactions in cosmic rays

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

Kempa, J., E-mail: kempa@pw.plock.pl

2015-12-15

The first clean Centauro was found in cosmic rays years many ago at Mt Chacaltaya experiment. Since that time, many people have tried to find this type of interaction, both in cosmic rays and at accelerators. But no one has found a clean cases of this type of interaction.It happened finally in the last exposure of emulsion at Mt Chacaltaya where the second clean Centauro has been found. The experimental data for both the Centauros and STRANA will be presented and discussed in this paper. We also present our comments to the intriguing question of the existence of a typemore » of nuclear interactions at high energy with alignment.« less

Role of Nuclear Pools of Aminoacyl-tRNA Synthetases in tRNA Nuclear Export

PubMed Central

Azad, Abul K.; Stanford, David R.; Sarkar, Srimonti; Hopper, Anita K.

2001-01-01

Reports of nuclear tRNA aminoacylation and its role in tRNA nuclear export (Lund and Dahlberg, 1998; Sarkar et al., 1999; Grosshans et al., 2000a) have led to the prediction that there should be nuclear pools of aminoacyl-tRNA synthetases. We report that in budding yeast there are nuclear pools of tyrosyl-tRNA synthetase, Tys1p. By sequence alignments we predicted a Tys1p nuclear localization sequence and showed it to be sufficient for nuclear location of a passenger protein. Mutations of this nuclear localization sequence in endogenous Tys1p reduce nuclear Tys1p pools, indicating that the motif is also important for nucleus location. The mutations do not significantly affect catalytic activity, but they do cause defects in export of tRNAs to the cytosol. Despite export defects, the cells are viable, indicating that nuclear tRNA aminoacylation is not required for all tRNA nuclear export paths. Because the tRNA nuclear exportin, Los1p, is also unessential, we tested whether tRNA aminoacylation and Los1p operate in alternative tRNA nuclear export paths. No genetic interactions between aminoacyl-tRNA synthetases and Los1p were detected, indicating that tRNA nuclear aminoacylation and Los1p operate in the same export pathway or there are more than two pathways for tRNA nuclear export. PMID:11359929

Role of nuclear pools of aminoacyl-tRNA synthetases in tRNA nuclear export.

PubMed

Azad, A K; Stanford, D R; Sarkar, S; Hopper, A K

2001-05-01

Reports of nuclear tRNA aminoacylation and its role in tRNA nuclear export (Lund and Dahlberg, 1998; Sarkar et al., 1999; Grosshans et al., 20001) have led to the prediction that there should be nuclear pools of aminoacyl-tRNA synthetases. We report that in budding yeast there are nuclear pools of tyrosyl-tRNA synthetase, Tys1p. By sequence alignments we predicted a Tys1p nuclear localization sequence and showed it to be sufficient for nuclear location of a passenger protein. Mutations of this nuclear localization sequence in endogenous Tys1p reduce nuclear Tys1p pools, indicating that the motif is also important for nucleus location. The mutations do not significantly affect catalytic activity, but they do cause defects in export of tRNAs to the cytosol. Despite export defects, the cells are viable, indicating that nuclear tRNA aminoacylation is not required for all tRNA nuclear export paths. Because the tRNA nuclear exportin, Los1p, is also unessential, we tested whether tRNA aminoacylation and Los1p operate in alternative tRNA nuclear export paths. No genetic interactions between aminoacyl-tRNA synthetases and Los1p were detected, indicating that tRNA nuclear aminoacylation and Los1p operate in the same export pathway or there are more than two pathways for tRNA nuclear export.

Right-Angle Mechanized Electrical Connector

NASA Technical Reports Server (NTRS)

Collins, Clint A.; Blackler, David T.

1996-01-01

Right-angle electrical connector embedded in mechanism accommodates some initial misalignment and aligns itself. Connection and disconnection effected with relatively small forces and torques and simple movements. Actuated by one gloved hand or by robotic manipulator. Useful in underwater, nuclear, hot, cold, or toxic environments in which connections made or broken by heavily clothed technicians or by robots.

Argonne Physics Division - ATLAS

Science.gov Websites

Strategic Plan (2014) ATLAS Gus Savard Guy Savard, Director of ATLAS Welcome to ATLAS, the Argonne Tandem users. ATLAS mission statement and strategic plan guide the operation of the facility. The strategic plan defines the facilities main goals and is aligned with the US Nuclear Physics long-range plan

Nuclear Materials Focus Area Fiscal Year 2002 Mid Year Review

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

Thiel, Elizabeth Chilcote

2002-05-01

The Nuclear Materials Focus Area (NMFA) held its annual mid-year review on February 12 and 14, 2002, in Santa Fe, New Mexico. The purpose of this review was to examine both the technical aspects and the programmatic aspects of its technology development program. The focus area activities were reviewed by a panel consisting of personnel representing the end users of the technologies, and technical experts in nuclear materials. This year's review was somewhat different than in the past, as the stress was on how well the various projects being managed through the NMFA aligned with the two thrust areas andmore » nine key goals and priorities recently issued by the Deputy Assistant Secretary for DOE's Office of Environmental Management (EM).« less

Nuclear Materials Focus Area Fiscal Year 2002 Mid Year Review

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

Thiel, E.C.; Fuhrman, P.W.

2002-05-30

The Nuclear Materials Focus Area (NMFA) held its annual mid-year review on February 12 and 14, 2002, in Santa Fe, New Mexico. The purpose of this review was to examine both the technical aspects and the programmatic aspects of its technology development program. The focus area activities were reviewed by a panel consisting of personnel representing the end users of the technologies, and technical experts in nuclear materials. This year's review was somewhat different than in the past, as the stress was on how well the various projects being managed through the NMFA aligned with the two thrust areas andmore » nine key goals and priorities recently issued by the Deputy Assistant Secretary for DOE's Office of Environmental Management (EM).« less

Drosophila CTCF tandemly aligns with other insulator proteins at the borders of H3K27me3 domains.

PubMed

Van Bortle, Kevin; Ramos, Edward; Takenaka, Naomi; Yang, Jingping; Wahi, Jessica E; Corces, Victor G

2012-11-01

Several multiprotein DNA complexes capable of insulator activity have been identified in Drosophila melanogaster, yet only CTCF, a highly conserved zinc finger protein, and the transcription factor TFIIIC have been shown to function in mammals. CTCF is involved in diverse nuclear activities, and recent studies suggest that the proteins with which it associates and the DNA sequences that it targets may underlie these various roles. Here we show that the Drosophila homolog of CTCF (dCTCF) aligns in the genome with other Drosophila insulator proteins such as Suppressor of Hairy wing [SU(HW)] and Boundary Element Associated Factor of 32 kDa (BEAF-32) at the borders of H3K27me3 domains, which are also enriched for associated insulator proteins and additional cofactors. RNAi depletion of dCTCF and combinatorial knockdown of gene expression for other Drosophila insulator proteins leads to a reduction in H3K27me3 levels within repressed domains, suggesting that insulators are important for the maintenance of appropriate repressive chromatin structure in Polycomb (Pc) domains. These results shed new insights into the roles of insulators in chromatin domain organization and support recent models suggesting that insulators underlie interactions important for Pc-mediated repression. We reveal an important relationship between dCTCF and other Drosophila insulator proteins and speculate that vertebrate CTCF may also align with other nuclear proteins to accomplish similar functions.

Drosophila CTCF tandemly aligns with other insulator proteins at the borders of H3K27me3 domains

PubMed Central

Van Bortle, Kevin; Ramos, Edward; Takenaka, Naomi; Yang, Jingping; Wahi, Jessica E.; Corces, Victor G.

2012-01-01

Several multiprotein DNA complexes capable of insulator activity have been identified in Drosophila melanogaster, yet only CTCF, a highly conserved zinc finger protein, and the transcription factor TFIIIC have been shown to function in mammals. CTCF is involved in diverse nuclear activities, and recent studies suggest that the proteins with which it associates and the DNA sequences that it targets may underlie these various roles. Here we show that the Drosophila homolog of CTCF (dCTCF) aligns in the genome with other Drosophila insulator proteins such as Suppressor of Hairy wing [SU(HW)] and Boundary Element Associated Factor of 32 kDa (BEAF-32) at the borders of H3K27me3 domains, which are also enriched for associated insulator proteins and additional cofactors. RNAi depletion of dCTCF and combinatorial knockdown of gene expression for other Drosophila insulator proteins leads to a reduction in H3K27me3 levels within repressed domains, suggesting that insulators are important for the maintenance of appropriate repressive chromatin structure in Polycomb (Pc) domains. These results shed new insights into the roles of insulators in chromatin domain organization and support recent models suggesting that insulators underlie interactions important for Pc-mediated repression. We reveal an important relationship between dCTCF and other Drosophila insulator proteins and speculate that vertebrate CTCF may also align with other nuclear proteins to accomplish similar functions. PMID:22722341

Oocyte Polarization Is Coupled to the Chromosomal Bouquet, a Conserved Polarized Nuclear Configuration in Meiosis

PubMed Central

Elkouby, Yaniv M.; Jamieson-Lucy, Allison; Mullins, Mary C.

2016-01-01

The source of symmetry breaking in vertebrate oocytes is unknown. Animal—vegetal oocyte polarity is established by the Balbiani body (Bb), a conserved structure found in all animals examined that contains an aggregate of specific mRNAs, proteins, and organelles. The Bb specifies the oocyte vegetal pole, which is key to forming the embryonic body axes as well as the germline in most vertebrates. How Bb formation is regulated and how its asymmetric position is established are unknown. Using quantitative image analysis, we trace oocyte symmetry breaking in zebrafish to a nuclear asymmetry at the onset of meiosis called the chromosomal bouquet. The bouquet is a universal feature of meiosis where all telomeres cluster to one pole on the nuclear envelope, facilitating chromosomal pairing and meiotic recombination. We show that Bb precursor components first localize with the centrosome to the cytoplasm adjacent to the telomere cluster of the bouquet. They then aggregate around the centrosome in a specialized nuclear cleft that we identified, assembling the early Bb. We show that the bouquet nuclear events and the cytoplasmic Bb precursor localization are mechanistically coordinated by microtubules. Thus the animal—vegetal axis of the oocyte is aligned to the nuclear axis of the bouquet. We further show that the symmetry breaking events lay upstream to the only known regulator of Bb formation, the Bucky ball protein. Our findings link two universal features of oogenesis, the Bb and the chromosomal bouquet, to oocyte polarization. We propose that a meiotic—vegetal center couples meiosis and oocyte patterning. Our findings reveal a novel mode of cellular polarization in meiotic cells whereby cellular and nuclear polarity are aligned. We further reveal that in zygotene nests, intercellular cytoplasmic bridges remain between oocytes and that the position of the cytoplasmic bridge coincides with the location of the centrosome meiotic—vegetal organizing center. These results suggest that centrosome positioning is set by the last mitotic oogonial division plane. Thus, oocytes are polarized in two steps: first, mitotic divisions preset the centrosome with no obvious polarization yet, then the meiotic—vegetal center forms at zygotene bouquet stages, when symmetry is, in effect, broken. PMID:26741740

Laboratory Directed Research and Development LDRD-FY-2011

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

Dena Tomchak

2012-03-01

This report provides a summary of the research conducted at the Idaho National Laboratory (INL) during Fiscal Year (FY) 2011. This report demonstrates the types of cutting edge research the INL is performing to help ensure the nation's energy security. The research conducted under this program is aligned with our strategic direction, benefits the Department of Energy (DOE) and is in compliance with DOE order 413.2B. This report summarizes the diverse research and development portfolio with emphasis on the DOE Office of Nuclear Energy (DOE-NE) mission, encompassing both advanced nuclear science and technology and underlying technologies.

NUCLEAR REACTORS

DOEpatents

Long, E.; Ashley, J.W.

1958-12-16

A graphite moderator structure is described for a gas-cooled nuclear reactor having a vertical orlentation wherein the structure is physically stable with regard to dlmensional changes due to Wigner growth properties of the graphite, and leakage of coolant gas along spaces in the structure is reduced. The structure is comprised of stacks of unlform right prismatic graphite blocks positioned in layers extending in the direction of the lengths of the blocks, the adjacent end faces of the blocks being separated by pairs of tiles. The blocks and tiles have central bores which are in alignment when assembled and are provided with cooperatlng keys and keyways for physical stability.

A Ramsey’s Method With Pulsed Neutrons for a T-Violation Experiment

PubMed Central

Masuda, Y.; Ino, T.; Muto, S.; Skoy, V.

2005-01-01

A Ramsey’s method with pulsed neutrons is discussed for neutron spin manipulation in a time reversal (T) symmetry violation experiment. The neutron spin (sn) is aligned to the direction of a vector product of the nuclear spin (I) and the neutron momentum (kn) for the measurement of a T-odd correlation term, which is represented as sn · (kn × I), during propagation through a polarized nuclear target. The phase control and amplitude modulation of separated oscillatory fields are discussed for the measurement of the T-odd correlation term. PMID:27308171

A Ramsey's Method With Pulsed Neutrons for a T-Violation Experiment.

PubMed

Masuda, Y; Ino, T; Muto, S; Skoy, V

2005-01-01

A Ramsey's method with pulsed neutrons is discussed for neutron spin manipulation in a time reversal (T) symmetry violation experiment. The neutron spin (s n) is aligned to the direction of a vector product of the nuclear spin ( I ) and the neutron momentum ( k n) for the measurement of a T-odd correlation term, which is represented as s n · ( k n × I ), during propagation through a polarized nuclear target. The phase control and amplitude modulation of separated oscillatory fields are discussed for the measurement of the T-odd correlation term.

Development of single-copy nuclear intron markers for species-level phylogenetics: Case study with Paullinieae (Sapindaceae).

PubMed

Chery, Joyce G; Sass, Chodon; Specht, Chelsea D

2017-09-01

We developed a bioinformatic pipeline that leverages a publicly available genome and published transcriptomes to design primers in conserved coding sequences flanking targeted introns of single-copy nuclear loci. Paullinieae (Sapindaceae) is used to demonstrate the pipeline. Transcriptome reads phylogenetically closer to the lineage of interest are aligned to the closest genome. Single-nucleotide polymorphisms are called, generating a "pseudoreference" closer to the lineage of interest. Several filters are applied to meet the criteria of single-copy nuclear loci with introns of a desired size. Primers are designed in conserved coding sequences flanking introns. Using this pipeline, we developed nine single-copy nuclear intron markers for Paullinieae. This pipeline is highly flexible and can be used for any group with available genomic and transcriptomic resources. This pipeline led to the development of nine variable markers for phylogenetic study without generating sequence data de novo.

Germline Genetic Modification and Identity: the Mitochondrial and Nuclear Genomes.

PubMed

Scott, Rosamund; Wilkinson, Stephen

2017-12-01

In a legal 'first', the UK removed a prohibition against modifying embryos in human reproduction, to enable mitochondrial replacement techniques (MRTs), a move the Government distanced from 'germline genetic modification', which it aligned with modifying the nuclear genome. This paper (1) analyzes the uses and meanings of this term in UK/US legal and policy debates; and (2) evaluates related ethical concerns about identity. It shows that, with respect to identity, MRTs and nuclear genome editing techniques such as CRISPR/Cas-9 (now a policy topic), are not as different as has been supposed. While it does not follow that the two should be treated exactly alike, one of the central reasons offered for treating MRTs more permissively than nuclear genetic modification, and for not regarding MRTs as 'germline genetic modification', is thereby in doubt. Identity cannot, by itself, do the work thus far assigned to it, explicitly or otherwise, in law and policy.

icoshift: A versatile tool for the rapid alignment of 1D NMR spectra

NASA Astrophysics Data System (ADS)

Savorani, F.; Tomasi, G.; Engelsen, S. B.

2010-02-01

The increasing scientific and industrial interest towards metabonomics takes advantage from the high qualitative and quantitative information level of nuclear magnetic resonance (NMR) spectroscopy. However, several chemical and physical factors can affect the absolute and the relative position of an NMR signal and it is not always possible or desirable to eliminate these effects a priori. To remove misalignment of NMR signals a posteriori, several algorithms have been proposed in the literature. The icoshift program presented here is an open source and highly efficient program designed for solving signal alignment problems in metabonomic NMR data analysis. The icoshift algorithm is based on correlation shifting of spectral intervals and employs an FFT engine that aligns all spectra simultaneously. The algorithm is demonstrated to be faster than similar methods found in the literature making full-resolution alignment of large datasets feasible and thus avoiding down-sampling steps such as binning. The algorithm uses missing values as a filling alternative in order to avoid spectral artifacts at the segment boundaries. The algorithm is made open source and the Matlab code including documentation can be downloaded from www.models.life.ku.dk.

Automatic detection of left and right ventricles from CTA enables efficient alignment of anatomy with myocardial perfusion data.

PubMed

Piccinelli, Marina; Faber, Tracy L; Arepalli, Chesnal D; Appia, Vikram; Vinten-Johansen, Jakob; Schmarkey, Susan L; Folks, Russell D; Garcia, Ernest V; Yezzi, Anthony

2014-02-01

Accurate alignment between cardiac CT angiographic studies (CTA) and nuclear perfusion images is crucial for improved diagnosis of coronary artery disease. This study evaluated in an animal model the accuracy of a CTA fully automated biventricular segmentation algorithm, a necessary step for automatic and thus efficient PET/CT alignment. Twelve pigs with acute infarcts were imaged using Rb-82 PET and 64-slice CTA. Post-mortem myocardium mass measurements were obtained. Endocardial and epicardial myocardial boundaries were manually and automatically detected on the CTA and both segmentations used to perform PET/CT alignment. To assess the segmentation performance, image-based myocardial masses were compared to experimental data; the hand-traced profiles were used as a reference standard to assess the global and slice-by-slice robustness of the automated algorithm in extracting myocardium, LV, and RV. Mean distances between the automated and the manual 3D segmented surfaces were computed. Finally, differences in rotations and translations between the manual and automatic surfaces were estimated post-PET/CT alignment. The largest, smallest, and median distances between interactive and automatic surfaces averaged 1.2 ± 2.1, 0.2 ± 1.6, and 0.7 ± 1.9 mm. The average angular and translational differences in CT/PET alignments were 0.4°, -0.6°, and -2.3° about x, y, and z axes, and 1.8, -2.1, and 2.0 mm in x, y, and z directions. Our automatic myocardial boundary detection algorithm creates surfaces from CTA that are similar in accuracy and provide similar alignments with PET as those obtained from interactive tracing. Specific difficulties in a reliable segmentation of the apex and base regions will require further improvements in the automated technique.

A Compass in Need of Alignment: Does United States Air Force Fighter Doctrine Adequately Cover Contingency Operations?

DTIC Science & Technology

1989-12-13

New York: Harcourt Brace Jovancv’.ch, 1983. Ben-Porat, Yeshayahu, Haber , Eitan and Schiff, Zeev. Entebbe Rescue. Trans. Louis Williams. New York...Times 25 Sept.e:ner 1989: pp. 16-17, 22-24, 84. Barth, Fritz J., Captain, USMC. "Stemming Nuclear Terrorism.- U.S. Naval Institute Proceedings, December

DNA nanotubes for NMR structure determination of membrane proteins.

PubMed

Bellot, Gaëtan; McClintock, Mark A; Chou, James J; Shih, William M

2013-04-01

Finding a way to determine the structures of integral membrane proteins using solution nuclear magnetic resonance (NMR) spectroscopy has proved to be challenging. A residual-dipolar-coupling-based refinement approach can be used to resolve the structure of membrane proteins up to 40 kDa in size, but to do this you need a weak-alignment medium that is detergent-resistant and it has thus far been difficult to obtain such a medium suitable for weak alignment of membrane proteins. We describe here a protocol for robust, large-scale synthesis of detergent-resistant DNA nanotubes that can be assembled into dilute liquid crystals for application as weak-alignment media in solution NMR structure determination of membrane proteins in detergent micelles. The DNA nanotubes are heterodimers of 400-nm-long six-helix bundles, each self-assembled from a M13-based p7308 scaffold strand and >170 short oligonucleotide staple strands. Compatibility with proteins bearing considerable positive charge as well as modulation of molecular alignment, toward collection of linearly independent restraints, can be introduced by reducing the negative charge of DNA nanotubes using counter ions and small DNA-binding molecules. This detergent-resistant liquid-crystal medium offers a number of properties conducive for membrane protein alignment, including high-yield production, thermal stability, buffer compatibility and structural programmability. Production of sufficient nanotubes for four or five NMR experiments can be completed in 1 week by a single individual.

Integration of 3D Printed and Micropatterned Polycaprolactone Scaffolds for Guidance of Oriented Collagenous Tissue Formation In Vivo.

PubMed

Pilipchuk, Sophia P; Monje, Alberto; Jiao, Yizu; Hao, Jie; Kruger, Laura; Flanagan, Colleen L; Hollister, Scott J; Giannobile, William V

2016-03-01

Scaffold design incorporating multiscale cues for clinically relevant, aligned tissue regeneration has potential to improve structural and functional integrity of multitissue interfaces. The objective of this preclinical study is to develop poly(ε-caprolactone) (PCL) scaffolds with mesoscale and microscale architectural cues specific to human ligament progenitor cells and assess their ability to form aligned bone-ligament-cementum complexes in vivo. PCL scaffolds are designed to integrate a 3D printed bone region with a micropatterned PCL thin film consisting of grooved pillars. The patterned film region is seeded with human ligament cells, fibroblasts transduced with bone morphogenetic protein-7 genes seeded within the bone region, and a tooth dentin segment positioned on the ligament region prior to subcutaneous implantation into a murine model. Results indicate increased tissue alignment in vivo using micropatterned PCL films, compared to random-porous PCL. At week 6, 30 μm groove depth significantly enhances oriented collagen fiber thickness, overall cell alignment, and nuclear elongation relative to 10 μm groove depth. This study demonstrates for the first time that scaffolds with combined hierarchical mesoscale and microscale features can align cells in vivo for oral tissue repair with potential for improving the regenerative response of other bone-ligament complexes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Collective and non-collective structures in nuclei of mass region A ≈ 125

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

Singh, A. K.; Collaboration: INGA Collaboration; Gammasphere Collaboration

Generation of angular momentum in nuclei is a key question in nuclear structure studies. In single particle model, it is due to alignment of spin of individual nucleon available in the valence space, whereas coherent motion of nucleons are assumed in the collective model. The nuclei near the closed shell at Z = 50 with mass number A ≈ 120-125 represent ideal cases to explore the interplay between these competing mechanisms and the transition from non-collective to collective behavior or vice versa. Recent spectroscopic studies of nuclei in this region reveal several non-collective maximally aligned states representing the first kindmore » of excitation mechanism, where 8-12 particles above the {sup 114}Sn align their spins to generate these states. Deformed rotational bands feeding the non-collective states in the spin range I=20-25 and excitation energies around 10 MeV have also been observed. Structure of the collective and non-collective states are discussed in the framework of Cranked-Nilsson-Strutinsky model.« less

Nuclear congression and membrane fusion: two distinct events in the yeast karyogamy pathway

PubMed Central

1994-01-01

Karyogamy is the process where haploid nuclei fuse to form a diploid nucleus during yeast mating. We devised a novel genetic screen that identified five new karyogamy (KAR) genes and three new cell fusion (FUS) genes. The kar mutants fell into two classes that represent distinct events in the yeast karyogamy pathway. Class I mutations blocked congression of the nuclei due to cytoplasmic microtubule defects. In Class II mutants, nuclear congression proceeded and the membranes of apposed nuclei were closely aligned but unfused. In vitro, Class II mutant membranes were defective in a homotypic ER/nuclear membrane fusion assay. We propose that Class II mutants define components of a novel membrane fusion complex which functions during vegetative growth and is recruited for karyogamy. PMID:8051211

Trajectories of Cepheid variable stars in the Galactic nuclear bulge

NASA Astrophysics Data System (ADS)

Matsunaga, Noriyuki

2012-06-01

The central region of our Galaxy provides us with a good opportunity to study the evolution of galactic nuclei and bulges because we can observe various phenomena in detail at the proximity of 8 kpc. There is a hierarchical alignment of stellar systems with different sizes; from the extended bulge, the nuclear bulge, down to the compact cluster around the central supermassive blackhole. The nuclear bulge contains stars as young as a few Myr, and even hosts the ongoing star formation. These are in contrast to the more extended bulge which are dominated by old stars, 10Gyr. It is considered that the star formation in the nuclear bulge is caused by fresh gas provided from the inner disk. In this picture, the nuclear bulge plays an important role as the interface between the gas supplier, the inner disk, and the galactic nucleus. Kinematics of young stars in the nuclear bulge is important to discuss the star forming process and the gas circulation in the Galactic Center. We here propose spectroscopic observations of Cepheid variable stars, 25 Myr, which we recently discovered in the nuclear bulge. The spectra taken in this proposal will allow timely estimates of the systemic velocities of the variable stars.

Connecting apparatus for limited rotary or rectilinear motion

DOEpatents

Hardin, Jr., Roy T.

1981-11-10

Apparatus for providing connection between two members movable in a horizontal plane with respect to each other in a rotary or linear fashion. The apparatus includes a set of horizontal shelves affixed to each of the two members, vertically aligned across a selected gap. A number of cables or hoses, for electrical, hydraulic or pneumatic connection are arranged on the aligned shelves in a U-shaped loop, connected through their extremities to the two members, so that through a sliding motion portions of the cable are transferred from one shelf to the other, across the gap, upon relative motion of the members. The apparatus is particularly adaptable to the rotating plugs of the reactor vessel head of a nuclear reactor.

BATMAN--an R package for the automated quantification of metabolites from nuclear magnetic resonance spectra using a Bayesian model.

PubMed

Hao, Jie; Astle, William; De Iorio, Maria; Ebbels, Timothy M D

2012-08-01

Nuclear Magnetic Resonance (NMR) spectra are widely used in metabolomics to obtain metabolite profiles in complex biological mixtures. Common methods used to assign and estimate concentrations of metabolites involve either an expert manual peak fitting or extra pre-processing steps, such as peak alignment and binning. Peak fitting is very time consuming and is subject to human error. Conversely, alignment and binning can introduce artefacts and limit immediate biological interpretation of models. We present the Bayesian automated metabolite analyser for NMR spectra (BATMAN), an R package that deconvolutes peaks from one-dimensional NMR spectra, automatically assigns them to specific metabolites from a target list and obtains concentration estimates. The Bayesian model incorporates information on characteristic peak patterns of metabolites and is able to account for shifts in the position of peaks commonly seen in NMR spectra of biological samples. It applies a Markov chain Monte Carlo algorithm to sample from a joint posterior distribution of the model parameters and obtains concentration estimates with reduced error compared with conventional numerical integration and comparable to manual deconvolution by experienced spectroscopists. http://www1.imperial.ac.uk/medicine/people/t.ebbels/ t.ebbels@imperial.ac.uk.

Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals

PubMed Central

Yuri, Tamaki; Kimball, Rebecca T.; Harshman, John; Bowie, Rauri C. K.; Braun, Michael J.; Chojnowski, Jena L.; Han, Kin-Lan; Hackett, Shannon J.; Huddleston, Christopher J.; Moore, William S.; Reddy, Sushma; Sheldon, Frederick H.; Steadman, David W.; Witt, Christopher C.; Braun, Edward L.

2013-01-01

Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP) and a simple maximum likelihood (ML) framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven difficult to recover in previous studies. Moreover, independent lines of evidence typically corroborated the nucleotide topology instead of the gap topology when they disagreed, although the number of conflicting nodes with high bootstrap support was limited. Filtering to remove short indels did not substantially reduce homoplasy or reduce conflict. Combined analyses of nucleotides and gaps resulted in the nucleotide topology, but with increased support, suggesting that gap data may prove most useful when analyzed in combination with nucleotide substitutions. PMID:24832669

An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data.

PubMed

Vu, Trung N; Valkenborg, Dirk; Smets, Koen; Verwaest, Kim A; Dommisse, Roger; Lemière, Filip; Verschoren, Alain; Goethals, Bart; Laukens, Kris

2011-10-20

Nuclear magnetic resonance spectroscopy (NMR) is a powerful technique to reveal and compare quantitative metabolic profiles of biological tissues. However, chemical and physical sample variations make the analysis of the data challenging, and typically require the application of a number of preprocessing steps prior to data interpretation. For example, noise reduction, normalization, baseline correction, peak picking, spectrum alignment and statistical analysis are indispensable components in any NMR analysis pipeline. We introduce a novel suite of informatics tools for the quantitative analysis of NMR metabolomic profile data. The core of the processing cascade is a novel peak alignment algorithm, called hierarchical Cluster-based Peak Alignment (CluPA). The algorithm aligns a target spectrum to the reference spectrum in a top-down fashion by building a hierarchical cluster tree from peak lists of reference and target spectra and then dividing the spectra into smaller segments based on the most distant clusters of the tree. To reduce the computational time to estimate the spectral misalignment, the method makes use of Fast Fourier Transformation (FFT) cross-correlation. Since the method returns a high-quality alignment, we can propose a simple methodology to study the variability of the NMR spectra. For each aligned NMR data point the ratio of the between-group and within-group sum of squares (BW-ratio) is calculated to quantify the difference in variability between and within predefined groups of NMR spectra. This differential analysis is related to the calculation of the F-statistic or a one-way ANOVA, but without distributional assumptions. Statistical inference based on the BW-ratio is achieved by bootstrapping the null distribution from the experimental data. The workflow performance was evaluated using a previously published dataset. Correlation maps, spectral and grey scale plots show clear improvements in comparison to other methods, and the down-to-earth quantitative analysis works well for the CluPA-aligned spectra. The whole workflow is embedded into a modular and statistically sound framework that is implemented as an R package called "speaq" ("spectrum alignment and quantitation"), which is freely available from http://code.google.com/p/speaq/.

Microtesla SABRE enables 10% nitrogen-15 nuclear spin polarization.

PubMed

Theis, Thomas; Truong, Milton L; Coffey, Aaron M; Shchepin, Roman V; Waddell, Kevin W; Shi, Fan; Goodson, Boyd M; Warren, Warren S; Chekmenev, Eduard Y

2015-02-04

Parahydrogen is demonstrated to efficiently transfer its nuclear spin hyperpolarization to nitrogen-15 in pyridine and nicotinamide (vitamin B(3) amide) by conducting "signal amplification by reversible exchange" (SABRE) at microtesla fields within a magnetic shield. Following transfer of the sample from the magnetic shield chamber to a conventional NMR spectrometer, the (15)N NMR signals for these molecules are enhanced by ∼30,000- and ∼20,000-fold at 9.4 T, corresponding to ∼10% and ∼7% nuclear spin polarization, respectively. This method, dubbed "SABRE in shield enables alignment transfer to heteronuclei" or "SABRE-SHEATH", promises to be a simple, cost-effective way to hyperpolarize heteronuclei. It may be particularly useful for in vivo applications because of longer hyperpolarization lifetimes, lack of background signal, and facile chemical-shift discrimination of different species.

Microtesla SABRE Enables 10% Nitrogen-15 Nuclear Spin Polarization

PubMed Central

2016-01-01

Parahydrogen is demonstrated to efficiently transfer its nuclear spin hyperpolarization to nitrogen-15 in pyridine and nicotinamide (vitamin B3 amide) by conducting “signal amplification by reversible exchange” (SABRE) at microtesla fields within a magnetic shield. Following transfer of the sample from the magnetic shield chamber to a conventional NMR spectrometer, the 15N NMR signals for these molecules are enhanced by ∼30,000- and ∼20,000-fold at 9.4 T, corresponding to ∼10% and ∼7% nuclear spin polarization, respectively. This method, dubbed “SABRE in shield enables alignment transfer to heteronuclei” or “SABRE-SHEATH”, promises to be a simple, cost-effective way to hyperpolarize heteronuclei. It may be particularly useful for in vivo applications because of longer hyperpolarization lifetimes, lack of background signal, and facile chemical-shift discrimination of different species. PMID:25583142

High resolution microscopy reveals the nuclear shape of budding yeast during cell cycle and in various biological states

PubMed Central

Kamgoue, Alain; Normand, Christophe; Léger-Silvestre, Isabelle; Mangeat, Thomas

2016-01-01

ABSTRACT How spatial organization of the genome depends on nuclear shape is unknown, mostly because accurate nuclear size and shape measurement is technically challenging. In large cell populations of the yeast Saccharomyces cerevisiae, we assessed the geometry (size and shape) of nuclei in three dimensions with a resolution of 30 nm. We improved an automated fluorescence localization method by implementing a post-acquisition correction of the spherical microscopic aberration along the z-axis, to detect the three dimensional (3D) positions of nuclear pore complexes (NPCs) in the nuclear envelope. Here, we used a method called NucQuant to accurately estimate the geometry of nuclei in 3D throughout the cell cycle. To increase the robustness of the statistics, we aggregated thousands of detected NPCs from a cell population in a single representation using the nucleolus or the spindle pole body (SPB) as references to align nuclei along the same axis. We could detect asymmetric changes of the nucleus associated with modification of nucleolar size. Stereotypical modification of the nucleus toward the nucleolus further confirmed the asymmetric properties of the nuclear envelope. PMID:27831493

Low-Field Nuclear Polarization Using Nitrogen Vacancy Centers in Diamonds

NASA Astrophysics Data System (ADS)

Hovav, Y.; Naydenov, B.; Jelezko, F.; Bar-Gill, N.

2018-02-01

It was recently demonstrated that bulk nuclear polarization can be obtained using nitrogen vacancy (NV) color centers in diamonds, even at ambient conditions. This is based on the optical polarization of the NV electron spin, and using several polarization transfer methods. One such method is the nuclear orientation via electron spin locking (NOVEL) sequence, where a spin-locked sequence is applied on the NV spin, with a microwave power equal to the nuclear precession frequency. This was performed at relatively high fields, to allow for both polarization transfer and noise decoupling. As a result, this scheme requires accurate magnetic field alignment in order preserve the NV properties. Such a requirement may be undesired or impractical in many practical scenarios. Here we present a new sequence, termed the refocused NOVEL, which can be used for polarization transfer (and detection) even at low fields. Numerical simulations are performed, taking into account both the spin Hamiltonian and spin decoherence, and we show that, under realistic parameters, it can outperform the NOVEL sequence.

Germline Genetic Modification and Identity: the Mitochondrial and Nuclear Genomes

PubMed Central

Scott, Rosamund; Wilkinson, Stephen

2017-01-01

Abstract In a legal ‘first’, the UK removed a prohibition against modifying embryos in human reproduction, to enable mitochondrial replacement techniques (MRTs), a move the Government distanced from ‘germline genetic modification’, which it aligned with modifying the nuclear genome. This paper (1) analyzes the uses and meanings of this term in UK/US legal and policy debates; and (2) evaluates related ethical concerns about identity. It shows that, with respect to identity, MRTs and nuclear genome editing techniques such as CRISPR/Cas-9 (now a policy topic), are not as different as has been supposed. While it does not follow that the two should be treated exactly alike, one of the central reasons offered for treating MRTs more permissively than nuclear genetic modification, and for not regarding MRTs as ‘germline genetic modification’, is thereby in doubt. Identity cannot, by itself, do the work thus far assigned to it, explicitly or otherwise, in law and policy. PMID:29670305

The role of 3D microenvironmental organization in MCF-7 epithelial–mesenchymal transition after 7 culture days

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

Foroni, Laura; Vasuri, Francesco, E-mail: vasurifrancesco@libero.it; Chair of Vascular Surgery, Department of Specialistic Surgery and Anaesthesiological Sciences, S. Orsola-Malpighi Hospital, Bologna University

2013-06-10

We present a multi-technique study on in vitro epithelial–mesenchymal transition (EMT) in human MCF-7 cells cultured on electrospun scaffolds of poly(L-lactic acid) (PLA), with random and aligned fiber orientations. Our aim is to investigate the morphological and genetic characteristics induced by extracellular matrix in tumor cells cultured in different 3D environments, and at different time points. Cell vitality was assessed with AlamarBlue at days 1, 3, 5 and 7. Scanning electron microscopy was performed at culture days 3 and 7. Immunohistochemistry (for E-cadherin, β-catenin, cytokeratins, nucleophosmin, tubulin, Ki-67 and vimentin), immunofluorescence (for F-actin) western blot (for E-cadherin, β-catenin and vimentin)more » and transmission electron microscopy were carried out at day 7. An EMT gene array followed by PCR analysis confirmed the regulation of selected genes. At day 7, scanning electron microscopy on aligned-PLA revealed spindle-shaped cells gathered in buds and ribbon-like structures, with a higher nucleolar/nuclear ratio and a loss in E-cadherin and β-catenin at immunohistochemistry and western blot. An up-regulation of SMAD2, TGF-β2, TFPI2 and SOX10 was found in aligned-PLA compared to random-PLA cultured cells. The topography of the extracellular matrix has a role in tumor EMT, and a more aggressive phenotype characterizes MCF-7 cells cultured on aligned-PLA scaffold. -- Highlights: • After 7 culture days an aligned-PLA scaffold induces a spindle shape to MCF-7 cells. • Despite these changes, the aligned MCF-7 cells keep an epithelial phenotype. • The extracellular environment alone influences the E-cadherin/β-catenin axis. • The extracellular environment can promote the epithelial–mesenchymal transition.« less

CONCENTRIC TUBE FUEL ELEMENT SPRING ALIGNMENT SPACER DEVICE

DOEpatents

Weems, S.J.

1963-09-24

A rib construction for a nuclear-fuel element is described, in which one of three peripherally spaced ribs adjacent to each end of the fuel element is mounted on a radially yielding spring that embraces the fuel element. This spring enables the fuel element to have a good fit with a coolant tube and yet to be easily inserted in and withdrawn from the tube. (AEC)

The Nuclear Spectroscopic Telescope Array (NuSTAR)

NASA Technical Reports Server (NTRS)

Harrison, Fiona A.; Boggs, Steven; Christensen, Finn; Craig, William; Hailey, Charles; Stern, Daniel; Zhang, William; Angelini, Lorella; An, Hong Jun; Bhalereo, Varun;

Assessment of phylogenetic relationship of rare plant species collected from Saudi Arabia using internal transcribed spacer sequences of nuclear ribosomal DNA.

PubMed

Al-Qurainy, F; Khan, S; Nadeem, M; Tarroum, M; Alaklabi, A

2013-03-11

The rare and endangered plants of any country are important genetic resources that often require urgent conservation measures. Assessment of phylogenetic relationships and evaluation of genetic diversity is very important prior to implementation of conservation strategies for saving rare and endangered plant species. We used internal transcribed spacer sequences of nuclear ribosomal DNA for the evaluation of sequence identity from the available taxa in the GenBank database by using the Basic Local Alignment Search Tool (BLAST). Two rare plant species viz, Heliotropium strigosum claded with H. pilosum (98% branch support) and Pancratium tortuosum claded with P. tenuifolium (61% branch support) clearly. However, some species, viz Scadoxus multiflorus, Commiphora myrrha and Senecio hadiensis showed close relationships with more than one species. We conclude that nuclear ribosomal internal transcribed spacer sequences are useful markers for phylogenetic study of these rare plant species in Saudi Arabia.

Kerman's Problem in the Continuum

NASA Astrophysics Data System (ADS)

Macchiavelli, A. O.; Casten, R. F.; Clark, R. M.; Campbell, C. M.; Crawford, H. L.; Cromaz, M.; Fallon, P.; Jones, M. D.; Salathe, M.

2017-09-01

In 1956 Kerman published a seminal paper on rotational perturbations in nuclei. Since then, Coriolis and rotational alignment effects have been extensively studied and are rather well understood. With the development of exotic beam facilities and advanced instrumentation it is becoming possible to access regions of deformation in the nuclear chart, near the neutron drip-line. Here, the effects of weak binding are expected to play an important role, affecting the dynamics of the nuclear motion. In this work we study Kerman's problem when the single-particle levels involved are resonant states. We will present results showing the behavior of the kinematic and dynamic moments of inertia as a function of the state widths. Connection to possible experiments will be discussed. This material is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Nuclear Physics under Contract No. DE-AC02-05CH11231 (LBNL).

Spectroscopic characterizations of a mixed surfactant mesophase and its application in materials synthesis

NASA Astrophysics Data System (ADS)

Liu, Limin

A viscous lyotropic crystalline mesophase containing bis (2-ethylhexyl) sodium sulfosuccinate (AOT), alpha-phosphatidylcholine (lecithin), with comparable volume fractions of isooctane and water was characterized by Fourier-transform 31P and 1H nuclear magnetic resonance (NMR) spectroscopy. Shear alignment on the reverse hexagonal mesophase was reflected through both 31P NMR and 1H NMR spectra. A complicated 31P spectrum was observed as a result of superposition of chemical shifts according to the distribution of crystalline domains prior to shear. The initially disordered samples with polydomain structures became macroscopically aligned after Couette shear and the alignment retained for a long period of time. 31P NMR chemical shift anisotropy characteristics were used to elucidate orientation of the hexagonal phase. Interestingly, 1H NMR of the water, methyl and methylene groups exhibited spectral changes upon shear alignment closely corresponding with that of 31P NMR spectra. A reverse hexagonal to lamellar phase transition was manifested as an expanding of the expressed 31P NMR chemical shift anisotropy and an apparent reversal of the powder pattern with increasing water content and/or temperature. Correspondingly, 1H NMR spectra also experienced a spectral pattern transition as the water content or temperature was increased. These observations complement the findings of mesophase alignment obtained using small angle neutron scattering (SANS) and imply that 31P and 1H NMR spectroscopy can be used as probes to define microstructure and monitor orientation changes in this binary surfactant system. This is especially beneficial if these mesophases are used as templates for materials synthesis. The mesophase retains its alignment for extended periods allowing materials synthesis to be decoupled from the application of shear. Highly aligned string-like silica nanostructures were obtained through templated synthesis in the columnar hexagonal structure of the viscous lyotropic crystalline mesophase. A two-step procedure was used to first shear-align the surfactant mesophase, and then conduct synthesis under quiescent conditions in the mesophase. Polystyrene was post-grafted to the silica surface without disturbing its nanostring morphology. The coupling of materials synthesis in surfactant mesophases with processing techniques (e.g. extrusion) may result in functional materials, such as new catalyst support and membrane nanoarchitectures.

Double-spiral magnetic structure of the Fe/Cr multilayer revealed by nuclear resonance reflectivity

NASA Astrophysics Data System (ADS)

Andreeva, M. A.; Baulin, R. A.; Chumakov, A. I.; Rüffer, R.; Smirnov, G. V.; Babanov, Y. A.; Devyaterikov, D. I.; Milyaev, M. A.; Ponomarev, D. A.; Romashev, L. N.; Ustinov, V. V.

2018-01-01

We have studied the magnetization depth profiles in a [57Fe (dFe) /Cr (dCr) ]30 multilayer with ultrathin Fe layers and nominal thickness of the chromium spacers dCr≈2.0 nm using nuclear resonance scattering of synchrotron radiation. The presence of a broad pure-magnetic half-order (1/2) Bragg reflection has been detected at zero external field. The joint fit of the reflectivity curves and Mössbauer spectra of reflectivity measured near the critical angle and at the "magnetic" peak reveals that the magnetic structure of the multilayer is formed by two spirals, one in the odd and another one in the even iron layers, with the opposite signs of rotation. The double-spiral structure starts from the surface with the almost-antiferromagnetic alignment of the adjacent Fe layers. The rotation of the two spirals leads to nearly ferromagnetic alignment of the two magnetic subsystems at some depth, where the sudden turn of the magnetic vectors by ˜180∘ (spin flop) appears, and both spirals start to rotate in opposite directions. The observation of this unusual double-spiral magnetic structure suggests that the unique properties of giant magnetoresistance devices can be further tailored using ultrathin magnetic layers.

Bilinear Factor Matrix Norm Minimization for Robust PCA: Algorithms and Applications.

PubMed

Shang, Fanhua; Cheng, James; Liu, Yuanyuan; Luo, Zhi-Quan; Lin, Zhouchen

2017-09-04

The heavy-tailed distributions of corrupted outliers and singular values of all channels in low-level vision have proven effective priors for many applications such as background modeling, photometric stereo and image alignment. And they can be well modeled by a hyper-Laplacian. However, the use of such distributions generally leads to challenging non-convex, non-smooth and non-Lipschitz problems, and makes existing algorithms very slow for large-scale applications. Together with the analytic solutions to Lp-norm minimization with two specific values of p, i.e., p=1/2 and p=2/3, we propose two novel bilinear factor matrix norm minimization models for robust principal component analysis. We first define the double nuclear norm and Frobenius/nuclear hybrid norm penalties, and then prove that they are in essence the Schatten-1/2 and 2/3 quasi-norms, respectively, which lead to much more tractable and scalable Lipschitz optimization problems. Our experimental analysis shows that both our methods yield more accurate solutions than original Schatten quasi-norm minimization, even when the number of observations is very limited. Finally, we apply our penalties to various low-level vision problems, e.g. moving object detection, image alignment and inpainting, and show that our methods usually outperform the state-of-the-art methods.

Phylogenetic relationships within the cyst-forming nematodes (Nematoda, Heteroderidae) based on analysis of sequences from the ITS regions of ribosomal DNA.

PubMed

Subbotin, S A; Vierstraete, A; De Ley, P; Rowe, J; Waeyenberge, L; Moens, M; Vanfleteren, J R

2001-10-01

The ITS1, ITS2, and 5.8S gene sequences of nuclear ribosomal DNA from 40 taxa of the family Heteroderidae (including the genera Afenestrata, Cactodera, Heterodera, Globodera, Punctodera, Meloidodera, Cryphodera, and Thecavermiculatus) were sequenced and analyzed. The ITS regions displayed high levels of sequence divergence within Heteroderinae and compared to outgroup taxa. Unlike recent findings in root knot nematodes, ITS sequence polymorphism does not appear to complicate phylogenetic analysis of cyst nematodes. Phylogenetic analyses with maximum-parsimony, minimum-evolution, and maximum-likelihood methods were performed with a range of computer alignments, including elision and culled alignments. All multiple alignments and phylogenetic methods yielded similar basic structure for phylogenetic relationships of Heteroderidae. The cyst-forming nematodes are represented by six main clades corresponding to morphological characters and host specialization, with certain clades assuming different positions depending on alignment procedure and/or method of phylogenetic inference. Hypotheses of monophyly of Punctoderinae and Heteroderinae are, respectively, strongly and moderately supported by the ITS data across most alignments. Close relationships were revealed between the Avenae and the Sacchari groups and between the Humuli group and the species H. salixophila within Heteroderinae. The Goettingiana group occupies a basal position within this subfamily. The validity of the genera Afenestrata and Bidera was tested and is discussed based on molecular data. We conclude that ITS sequence data are appropriate for studies of relationships within the different species groups and less so for recovery of more ancient speciations within Heteroderidae. Copyright 2001 Academic Press.

Nuclear Fabrication Consortium

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

Levesque, Stephen

2013-04-05

This report summarizes the activities undertaken by EWI while under contract from the Department of Energy (DOE) Office of Nuclear Energy (NE) for the management and operation of the Nuclear Fabrication Consortium (NFC). The NFC was established by EWI to independently develop, evaluate, and deploy fabrication approaches and data that support the re-establishment of the U.S. nuclear industry: ensuring that the supply chain will be competitive on a global stage, enabling more cost-effective and reliable nuclear power in a carbon constrained environment. The NFC provided a forum for member original equipment manufactures (OEM), fabricators, manufacturers, and materials suppliers to effectivelymore » engage with each other and rebuild the capacity of this supply chain by : Identifying and removing impediments to the implementation of new construction and fabrication techniques and approaches for nuclear equipment, including system components and nuclear plants. Providing and facilitating detailed scientific-based studies on new approaches and technologies that will have positive impacts on the cost of building of nuclear plants. Analyzing and disseminating information about future nuclear fabrication technologies and how they could impact the North American and the International Nuclear Marketplace. Facilitating dialog and initiate alignment among fabricators, owners, trade associations, and government agencies. Supporting industry in helping to create a larger qualified nuclear supplier network. Acting as an unbiased technology resource to evaluate, develop, and demonstrate new manufacturing technologies. Creating welder and inspector training programs to help enable the necessary workforce for the upcoming construction work. Serving as a focal point for technology, policy, and politically interested parties to share ideas and concepts associated with fabrication across the nuclear industry. The report the objectives and summaries of the Nuclear Fabrication Consortium projects. Full technical reports for each of the projects have been submitted as well.« less

A High Resolution View of Galactic Centers: Arp 220 and M31

NASA Astrophysics Data System (ADS)

Lockhart, Kelly E.

The centers of galaxy are small in size and yet incredibly complex. They play host to supermassive black holes and nuclear star clusters (NSCs) and are subject to large gas inows, nuclear starbursts, and active galactic nuclear (AGN) activity. They can also be the launching site for large-scale galactic outows. However, though these systems are quite important to galactic evolution, observations are quite difficult due to their small size. Using high spatial resolution narrowband imaging with HST/WFC3 of Arp 220, a latestage galaxy merger, I discover an ionized gas bubble feature ( r = 600 pc) just off the nucleus. The bubble is aligned with both the western nucleus and with the large-scale galactic outflow. Using energetics arguments, I link the bubble with a young, obscured AGN or with an intense nuclear starburst. Given its alignment along the large-scale outflow axis, I argue that the bubble presents evidence for a link between the galactic center and the large-scale outflow. I also present new observations of the NSC in M31, the closest large spiral galaxy to our own. Using the OSIRIS near-infrared integral field spectrograph (IFS) on Keck, I map the kinematics of the old stellar population in the eccentric disk of the NSC. I compare the observations to models to derive a precession speed of the disk of 0+/-5 km s-1 pc-1 , and hence confirm that winds from the old stellar population may be the source of gas needed to form the young stellar population in the NSC. Studies of galactic centers are dependent on high spatial resolution observations. In particular, IFSs are ideal instruments for these studies as they provide two-dimensional spectroscopy of the field of view, enabling 2D kinematic studies. I report on work to characterize and improve the data reduction pipeline of the OSIRIS IFS, and discuss implications for future generations of IFS instrumentation.

Nuclear Thermal Propulsion Mars Mission Systems Analysis and Requirements Definition

NASA Technical Reports Server (NTRS)

Mulqueen, Jack; Chiroux, Robert C.; Thomas, Dan; Crane, Tracie

2007-01-01

This paper describes the Mars transportation vehicle design concepts developed by the Marshall Space Flight Center (MSFC) Advanced Concepts Office. These vehicle design concepts provide an indication of the most demanding and least demanding potential requirements for nuclear thermal propulsion systems for human Mars exploration missions from years 2025 to 2035. Vehicle concept options vary from large "all-up" vehicle configurations that would transport all of the elements for a Mars mission on one vehicle. to "split" mission vehicle configurations that would consist of separate smaller vehicles that would transport cargo elements and human crew elements to Mars separately. Parametric trades and sensitivity studies show NTP stage and engine design options that provide the best balanced set of metrics based on safety, reliability, performance, cost and mission objectives. Trade studies include the sensitivity of vehicle performance to nuclear engine characteristics such as thrust, specific impulse and nuclear reactor type. Tbe associated system requirements are aligned with the NASA Exploration Systems Mission Directorate (ESMD) Reference Mars mission as described in the Explorations Systems Architecture Study (ESAS) report. The focused trade studies include a detailed analysis of nuclear engine radiation shield requirements for human missions and analysis of nuclear thermal engine design options for the ESAS reference mission.

Nuclear organization in human sperm: preliminary evidence for altered sex chromosome centromere position in infertile males.

PubMed

Finch, K A; Fonseka, K G L; Abogrein, A; Ioannou, D; Handyside, A H; Thornhill, A R; Hickson, N; Griffin, D K

2008-06-01

Many genetic defects with a chromosomal basis affect male reproduction via a range of different mechanisms. Chromosome position is a well-known marker of nuclear organization, and alterations in standard patterns can lead to disease phenotypes such as cancer, laminopathies and epilepsy. It has been demonstrated that normal mammalian sperm adopt a pattern with the centromeres aligning towards the nuclear centre. The purpose of this study was to test the hypothesis that altered chromosome position in the sperm head is associated with male infertility. The average nuclear positions of fluorescence in-situ hybridization signals for three centromeric probes (for chromosomes X, Y and 18) were compared in normoozoospermic men and in men with compromised semen parameters. In controls, the centromeres of chromosomes X, Y and 18 all occupied a central nuclear location. In infertile men the sex chromosomes appeared more likely to be distributed in a pattern not distinguishable from a random model. Our findings cast doubt on the reliability of centromeric probes for aneuploidy screening. The analysis of chromosome position in sperm heads should be further investigated for the screening of infertile men.

Books Noted

NASA Astrophysics Data System (ADS)

Walsh, Edward J.

1999-10-01

The Colloidal Domain: Where Physics, Chemistry, Biology, and Technology Meet, 2nd edition

D. Fennell Evans and Hakan Wennerstroem. Advances in Interfacial Engineering Series. Wiley-VCH: New York, 1999. xl + 632 pp. ISBN 0-471-24247-0. 89.95.

Commercial Nuclear Power: Assuring Safety for the Future

Charles B. Ramsey and Mohammed Modarres. Wiley-Interscience: New York, 1998. xxviii + 508 pp. ISBN 0-471-29186-2. 79.95.

Advances in Medicinal Chemistry, Vol. 4

Bruce E. Maryanoff and Allen B. Reitz, Eds. JAI Press: Stamford, CT, 1999. ISBN 1-7623-0064-7. 109.50.

Advances in Strained and Interesting Organic Molecules, Vol. 7

Brian Halton, Ed. JAI Press: Stamford, CT, 1999. xii + 259 pp. ISBN 0-7623-0530-4. 109.50.

Advances in Electron Transfer Chemistry, Vol. 6

Patrick S. Mariano, Ed. JAI Press: Stamford, CT, 1999. x + 171 pp. ISBN 0-7623-0213-5. 109.50.

Automating Science and Engineering Laboratories with Visual Basic

Mark F. Russo and Martin M. Echols. Wiley-Interscience Series on Laboratory Automation. Wiley-Interscience: New York, 1999. xx + 355 pp. ISBN 0-471-25493-2. 49.95.

Plantwide Process Control

Kelvin T. Erickson and John L. Hedrick. Wiley Series in Chemical Engineering. Wiley-Interscience: New York, 1999. xii + 547 pp. ISBN 0-471-17835-7. 89.95.

Heme Peroxidases

H. Brian Dunford. Wiley-VCH: New York, 1999. xiii + 507 pp. ISBN 0-471-24244-6. 195.00.

Industrial Ecology: Environmental Chemistry and Hazardous Wastes

Stanley E. Manahan. Lewis: Boca Raton, FL, 1999. 318 pp. ISBN 1-56670-381-6. 69.95.

Reviews in Computational Chemistry, Vol. 13

Kenny B. Lipkowitz and Donald B. Boyd. Wiley-VCH: New York, 1999. xxxiii + 426 pp. ISBN 0-471-33135-x. 135.00.

Surfaces, Interfaces, and Colloids: Principles and Applications, 2nd edition

Drew Myers. Wiley-VCH: New York, 1999. xx + 501 pp. ISBN 0-471-33060-4. 94.95.

Onium Ions

George A. Olah, Kenneth K. Laali, Qi Wang, and G. K. Surya Prakash. Wiley-Interscience: New York, 1998. xv + 509 pp. ISBN 0-471-14877-6. 110.00.

Environmental Soil and Water Chemistry: Principles and Applications V. P. Evangelou. Wiley-Interscience: New York, 1998. xix + 564 pp. ISBN 0-471-16515-8. 79.95.

1001 Chemicals in Everyday Products, 2nd edition

Grace Ross Lewis. Wiley-Interscience: New York, 1999. x + 388 pp. ISBN 0-471-29212-5. 39.95.

Organic Coatings: Science and Technology, 2nd edition

Zeno W. Wicks Jr., Frank N. Jones, and S. Peter Pappas. Wiley-Interscience: New York, 1999. xxi + 630 pp. ISBN 0-471-24507-0. 125.00.

Progress in Inorganic Chemistry, Vol. 48

Kenneth D. Karlin, Ed. Wiley-Interscience: New York, 1999. vi + 603 pp. ISBN 0-471-32623-2. 145.00.

Occupational Biomechanics, 3rd edition

Don B. Chaffin, Gunnar B. Andersson, and Bernard J. Martin. Wiley-Interscience: New York, 1999. xvii + 579 pp. ISBN 0-471-24697-2. 69.95.

Advances in Photochemistry, Vol. 25

Douglas C. Neckers, David H. Volman, and Gunther Von Bünau. Wiley-Interscience: New York, 1999. xi + 238 pp. ISBN 0-471-32708-5. 110.00.

Distillation

Johann G. Stichlmair and James R. Fair. Wiley-VCH: New York, 1998. xiii + 524 pp. ISBN 0-471-25241-7. 94.95.

Ammonia - Principles and Industrial Practice

Maz Appl. Wiley-VCH: New York, 1999. ix + 301 pp. ISBN 3-527-29593-3. 160.00.

Precursor-Derived Ceramics: Synthesis, Structure, and High-Temperature Mechanical Properties

Fritz Aldinger, Fumihiro Wakai, and Joachim Bill, Eds. Wiley-VCH: New York, 1999. xv + 298 pp. ISBN 3-527-29814-2. 180.00.

Advances in Sonochemisty, Vol. 5

Timothy J. Mason. JAI Press: Stamford, CT, 1999. xi + 311 pp. ISBN 0-7623-0331-x. 109.50.

Fluid Metals: The Liquid-Vapor Transition of Metals

Friedrich Hensel and William W. Warren Jr. Princeton University Press: Princeton, NJ. 1999. xvii + 243 pp. ISBN 0-691-05830-x. 69.50.

Direct Phasing in Crystallography: Fundamentals and Applications

Carmelo Giacovazzo. Oxford University Press: New York, 1999. xxiii + 767 pp. ISBN 0-19-850072-6. 140.00.

Practical Environmental Analysis

M. Radojevic and V. N. Bashkin. Royal Society of Chemistry: Cambridge, UK. 1999. xx + 466 pp. ISBN 0-85404-594-5. £32.00.

Advances in Dendritic Macromolecules, Vol. 4 George R. Newkome, Ed. JAI Press: Stamford, CT, 1999. x + 207 pp. ISBN 0-7623-0347-6. 109.50.

Advances in Quantitative Structure-Property Relationships, Vol. 2

Marvin Charton. JAI Press: Stamford, CT, 1999. ix + 257 pp. ISBN 0-7623-0067-1. 109.50.

Pesticide Residues in Foods: Methods, Techniques, and Regulations

W. George Fong, H. Anson Moye, James N. Seiber, and John P. Toth. Chemical Analysis, Vol. 151.Wiley-Interscience: New York, 1999. xiv + 358 pp. ISBN 0-471-57400-7. $84.95.

Nuclear resonance reflectivity from a [57Fe/Cr]30 multilayer with the Synchrotron Mössbauer Source.

PubMed

Andreeva, Marina A; Baulin, Roman A; Chumakov, Aleksandr I; Rüffer, Rudolf; Smirnov, Gennadii V; Babanov, Yurii A; Devyaterikov, Denis I; Milyaev, Mikhail A; Ponomarev, Dmitrii A; Romashev, Lazar N; Ustinov, Vladimir V

2018-03-01

Mössbauer reflectivity spectra and nuclear resonance reflectivity (NRR) curves have been measured using the Synchrotron Mössbauer Source (SMS) for a [ 57 Fe/Cr] 30 periodic multilayer, characterized by the antiferromagnetic interlayer coupling between adjacent 57 Fe layers. Specific features of the Mössbauer reflectivity spectra measured with π-polarized radiation of the SMS near the critical angle and at the `magnetic' maximum on the NRR curve are analyzed. The variation of the ratio of lines in the Mössbauer reflectivity spectra and the change of the intensity of the `magnetic' maximum under an applied external field has been used to reveal the transformation of the magnetic alignment in the investigated multilayer.

Nuclear magnetic resonance studies of pseudospin fluctuations in URu 2 Si 2

DOE PAGES

Shirer, K. R.; Haraldsen, J. T.; Dioguardi, A. P.; ...

2013-09-26

Here, we report 29Si nuclear magnetic resonance measurements in single crystals and aligned powders of URu 2Si 2 in the hidden order and paramagnetic phases. The spin-lattice relaxation data reveal evidence of pseudospin fluctuations of U moments in the paramagnetic phase. We find evidence for partial suppression of the density of states below 30 K and analyze the data in terms of a two-component spin-fermion model. We propose that this behavior is a realization of a pseudogap between the hidden-order transition T HO and 30 K. This behavior is then compared to other materials that demonstrate precursor fluctuations in amore » pseudogap regime above a ground state with long-range order.« less

Development of undergraduate nuclear security curriculum at College of Engineering, Universiti Tenaga Nasional

NASA Astrophysics Data System (ADS)

Hamid, Nasri A.; Mujaini, Madihah; Mohamed, Abdul Aziz

2017-01-01

The Center for Nuclear Energy (CNE), College of Engineering, Universiti Tenaga Nasional (UNITEN) has a great responsibility to undertake educational activities that promote developing human capital in the area of nuclear engineering and technology. Developing human capital in nuclear through education programs is necessary to support the implementation of nuclear power projects in Malaysia in the near future. In addition, the educational program must also meet the nuclear power industry needs and requirements. In developing a certain curriculum, the contents must comply with the university's Outcomes Based Education (OBE) philosophy. One of the important courses in the nuclear curriculum is in the area of nuclear security. Basically the nuclear security course covers the current issues of law, politics, military strategy, and technology with regard to weapons of mass destruction and related topics in international security, and review legal regulations and political relationship that determine the state of nuclear security at the moment. In addition, the course looks into all aspects of the nuclear safeguards, builds basic knowledge and understanding of nuclear non-proliferation, nuclear forensics and nuclear safeguards in general. The course also discusses tools used to combat nuclear proliferation such as treaties, institutions, multilateral arrangements and technology controls. In this paper, we elaborate the development of undergraduate nuclear security course at the College of Engineering, Universiti Tenaga Nasional. Since the course is categorized as mechanical engineering subject, it must be developed in tandem with the program educational objectives (PEO) of the Bachelor of Mechanical Engineering program. The course outcomes (CO) and transferrable skills are also identified. Furthermore, in aligning the CO with program outcomes (PO), the PO elements need to be emphasized through the CO-PO mapping. As such, all assessments and distribution of Bloom Taxonomy levels are assigned in accordance with the CO-PO mapping. Finally, the course has to fulfill the International Engineering Alliance (IEA) Graduate Attributes of the Washington Accord.

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

Walter, Andrew

National policymakers are currently considering a dilemma of critical importance to the continued security of the United States: how can U.S. nuclear weapons policies be leveraged to benefit U.S. nuclear nonproliferation goals in the near-term, without sacrificing U.S. national security? In its role supporting U.S. nuclear weapons policy, Sandia National Laboratories has a responsibility to provide objective technical advice to support policy deliberations on this question. However, to best fulfill this duty Sandia must have a broader understanding of the context of the problem. To help develop this understanding, this paper analyzes the two predominant analytical perspectives of international relationsmore » theory to explore their prescriptions for how nuclear weapons and nonproliferation policies interact. As lenses with which to view and make sense of the world, theories of international relations must play a crucial role in framing the trade-offs at the intersection of the nuclear weapons and nonproliferation policy domains. An analysis of what these theories suggest as courses of action to leverage nuclear weapons policies to benefit nonproliferation goals is then offered, with particular emphasis on where the policy prescriptions resulting from the respective theories align to offer near-term policy changes with broad theoretical support. These policy prescriptions are then compared to the 2001 Nuclear Posture Review to understand what the theories indicate policymakers may have gotten right in their dealing with the nuclear dilemma, and where they may have gone wrong. Finally, a brief international relations research agenda is proposed to help address the dilemma between nuclear deterrence and nuclear nonproliferation policies, with particular emphasis on how such an agenda can best support the needs of the policy community and a potential 'all things nuclear' policy deliberation and decision-support framework.« less

Robust techniques for polarization and detection of nuclear spin ensembles

NASA Astrophysics Data System (ADS)

Scheuer, Jochen; Schwartz, Ilai; Müller, Samuel; Chen, Qiong; Dhand, Ish; Plenio, Martin B.; Naydenov, Boris; Jelezko, Fedor

2017-11-01

Highly sensitive nuclear spin detection is crucial in many scientific areas including nuclear magnetic resonance spectroscopy, magnetic resonance imaging (MRI), and quantum computing. The tiny thermal nuclear spin polarization represents a major obstacle towards this goal which may be overcome by dynamic nuclear spin polarization (DNP) methods. The latter often rely on the transfer of the thermally polarized electron spins to nearby nuclear spins, which is limited by the Boltzmann distribution of the former. Here we utilize microwave dressed states to transfer the high (>92 % ) nonequilibrium electron spin polarization of a single nitrogen-vacancy center (NV) induced by short laser pulses to the surrounding 13C carbon nuclear spins. The NV is repeatedly repolarized optically, thus providing an effectively infinite polarization reservoir. A saturation of the polarization of the nearby nuclear spins is achieved, which is confirmed by the decay of the polarization transfer signal and shows an excellent agreement with theoretical simulations. Hereby we introduce the polarization readout by polarization inversion method as a quantitative magnetization measure of the nuclear spin bath, which allows us to observe by ensemble averaging macroscopically hidden polarization dynamics like Landau-Zener-Stückelberg oscillations. Moreover, we show that using the integrated solid effect both for single- and double-quantum transitions nuclear spin polarization can be achieved even when the static magnetic field is not aligned along the NV's crystal axis. This opens a path for the application of our DNP technique to spins in and outside of nanodiamonds, enabling their application as MRI tracers. Furthermore, the methods reported here can be applied to other solid state systems where a central electron spin is coupled to a nuclear spin bath, e.g., phosphor donors in silicon and color centers in silicon carbide.

Cellular and Nuclear Alignment Analysis for Determining Epithelial Cell Chirality

PubMed Central

Raymond, Michael J.; Ray, Poulomi; Kaur, Gurleen; Singh, Ajay V.; Wan, Leo Q.

2015-01-01

Left-right (LR) asymmetry is a biologically conserved property in living organisms that can be observed in the asymmetrical arrangement of organs and tissues and in tissue morphogenesis, such as the directional looping of the gastrointestinal tract and heart. The expression of LR asymmetry in embryonic tissues can be appreciated in biased cell alignment. Previously an in vitro chirality assay was reported by patterning multiple cells on microscale defined geometries and quantified the cell phenotype–dependent LR asymmetry, or cell chirality. However, morphology and chirality of individual cells on micropatterned surfaces has not been well characterized. Here, a Python-based algorithm was developed to identify and quantify immunofluorescence stained individual epithelial cells on multicellular patterns. This approach not only produces results similar to the image intensity gradient-based method reported previously, but also can capture properties of single cells such as area and aspect ratio. We also found that cell nuclei exhibited biased alignment. Around 35% cells were misaligned and were typically smaller and less elongated. This new imaging analysis approach is an effective tool for measuring single cell chirality inside multicellular structures and can potentially help unveil biophysical mechanisms underlying cellular chiral bias both in vitro and in vivo. PMID:26294010

Alignment-independent technique for 3D QSAR analysis

NASA Astrophysics Data System (ADS)

Wilkes, Jon G.; Stoyanova-Slavova, Iva B.; Buzatu, Dan A.

2016-04-01

Molecular biochemistry is controlled by 3D phenomena but structure-activity models based on 3D descriptors are infrequently used for large data sets because of the computational overhead for determining molecular conformations. A diverse dataset of 146 androgen receptor binders was used to investigate how different methods for defining molecular conformations affect the performance of 3D-quantitative spectral data activity relationship models. Molecular conformations tested: (1) global minimum of molecules' potential energy surface; (2) alignment-to-templates using equal electronic and steric force field contributions; (3) alignment using contributions "Best-for-Each" template; (4) non-energy optimized, non-aligned (2D > 3D). Aggregate predictions from models were compared. Highest average coefficients of determination ranged from R Test 2 = 0.56 to 0.61. The best model using 2D > 3D (imported directly from ChemSpider) produced R Test 2 = 0.61. It was superior to energy-minimized and conformation-aligned models and was achieved in only 3-7 % of the time required using the other conformation strategies. Predictions averaged from models built on different conformations achieved a consensus R Test 2 = 0.65. The best 2D > 3D model was analyzed for underlying structure-activity relationships. For the compound strongest binding to the androgen receptor, 10 substructural features contributing to binding were flagged. Utility of 2D > 3D was compared for two other activity endpoints, each modeling a medium sized data set. Results suggested that large scale, accurate predictions using 2D > 3D SDAR descriptors may be produced for interactions involving endocrine system nuclear receptors and other data sets in which strongest activities are produced by fairly inflexible substrates.

MetalS2: a tool for the structural alignment of minimal functional sites in metal-binding proteins and nucleic acids.

PubMed

Andreini, Claudia; Cavallaro, Gabriele; Rosato, Antonio; Valasatava, Yana

2013-11-25

We developed a new software tool, MetalS(2), for the structural alignment of Minimal Functional Sites (MFSs) in metal-binding biological macromolecules. MFSs are 3D templates that describe the local environment around the metal(s) independently of the larger context of the macromolecular structure. Such local environment has a determinant role in tuning the chemical reactivity of the metal, ultimately contributing to the functional properties of the whole system. On our example data sets, MetalS(2) unveiled structural similarities that other programs for protein structure comparison do not consistently point out and overall identified a larger number of structurally similar MFSs. MetalS(2) supports the comparison of MFSs harboring different metals and/or with different nuclearity and is available both as a stand-alone program and a Web tool ( http://metalweb.cerm.unifi.it/tools/metals2/).

The Implications of the Rise of China’s Military for Mongolian Security

DTIC Science & Technology

2010-06-01

Regional Forum ASAT – Anti-satellite ASUW – Anti- surface warfare ASW – Antisubmarine Warfare AWACS – Airborne Warning and Control System CCP – Chinese...Military Region NAM – Non-Aligned Movements NATO – North Atlantic Treaty Organization NCO – Non-commissioned Officer NWFZ – Nuclear-Weapon- Free Zone...currency ROC – Republic of China RRU – Rapid Reaction Units SAM – Surface to Air Missile SCO – Shanghai Cooperation Organization SIPRI – Stockholm

LOADING MACHINE FOR REACTORS

DOEpatents

Simon, S.L.

1959-07-01

An apparatus is described for loading or charging slugs of fissionable material into a nuclear reactor. The apparatus of the invention is a "muzzle loading" type comprising a delivery tube or muzzle designed to be brought into alignment with any one of a plurality of fuel channels. The delivery tube is located within the pressure shell and it is also disposed within shielding barriers while the fuel cantridges or slugs are forced through the delivery tube by an externally driven flexible ram.

CDS Re Mix

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

None

CDS (Change Detection Systems) is a mechanism for rapid visual analysis using complex image alignment algorithms. CDS is controlled with a simple interface that has been designed for use for anyone that can operate a digital camera. A challenge of complex industrial systems like nuclear power plants is to accurately identify changes in systems, structures and components that may critically impact the operation of the facility. CDS can provide a means of early intervention before the issues evolve into safety and production challenges.

HAL-2 Promotes Homologous Pairing during Caenorhabditis elegans Meiosis by Antagonizing Inhibitory Effects of Synaptonemal Complex Precursors

PubMed Central

Zhang, Weibin; Miley, Natasha; Zastrow, Michael S.; MacQueen, Amy J.; Sato, Aya; Nabeshima, Kentaro; Martinez-Perez, Enrique; Mlynarczyk-Evans, Susanna; Carlton, Peter M.; Villeneuve, Anne M.

2012-01-01

During meiosis, chromosomes align with their homologous pairing partners and stabilize this alignment through assembly of the synaptonemal complex (SC). Since the SC assembles cooperatively yet is indifferent to homology, pairing and SC assembly must be tightly coordinated. We identify HAL-2 as a key mediator in this coordination, showing that HAL-2 promotes pairing largely by preventing detrimental effects of SC precursors (SYP proteins). hal-2 mutants fail to establish pairing and lack multiple markers of chromosome movement mediated by pairing centers (PCs), chromosome sites that link chromosomes to cytoplasmic microtubules through nuclear envelope-spanning complexes. Moreover, SYP proteins load inappropriately along individual unpaired chromosomes in hal-2 mutants, and markers of PC-dependent movement and function are restored in hal-2; syp double mutants. These and other data indicate that SYP proteins can impede pairing and that HAL-2 promotes pairing predominantly but not exclusively by counteracting this inhibition, thereby enabling activation and regulation of PC function. HAL-2 concentrates in the germ cell nucleoplasm and colocalizes with SYP proteins in nuclear aggregates when SC assembly is prevented. We propose that HAL-2 functions to shepherd SYP proteins prior to licensing of SC assembly, preventing untimely interactions between SC precursors and chromosomes and allowing sufficient accumulation of precursors for rapid cooperative assembly upon homology verification. PMID:22912597

HAL-2 promotes homologous pairing during Caenorhabditis elegans meiosis by antagonizing inhibitory effects of synaptonemal complex precursors.

PubMed

Zhang, Weibin; Miley, Natasha; Zastrow, Michael S; MacQueen, Amy J; Sato, Aya; Nabeshima, Kentaro; Martinez-Perez, Enrique; Mlynarczyk-Evans, Susanna; Carlton, Peter M; Villeneuve, Anne M

2012-01-01

During meiosis, chromosomes align with their homologous pairing partners and stabilize this alignment through assembly of the synaptonemal complex (SC). Since the SC assembles cooperatively yet is indifferent to homology, pairing and SC assembly must be tightly coordinated. We identify HAL-2 as a key mediator in this coordination, showing that HAL-2 promotes pairing largely by preventing detrimental effects of SC precursors (SYP proteins). hal-2 mutants fail to establish pairing and lack multiple markers of chromosome movement mediated by pairing centers (PCs), chromosome sites that link chromosomes to cytoplasmic microtubules through nuclear envelope-spanning complexes. Moreover, SYP proteins load inappropriately along individual unpaired chromosomes in hal-2 mutants, and markers of PC-dependent movement and function are restored in hal-2; syp double mutants. These and other data indicate that SYP proteins can impede pairing and that HAL-2 promotes pairing predominantly but not exclusively by counteracting this inhibition, thereby enabling activation and regulation of PC function. HAL-2 concentrates in the germ cell nucleoplasm and colocalizes with SYP proteins in nuclear aggregates when SC assembly is prevented. We propose that HAL-2 functions to shepherd SYP proteins prior to licensing of SC assembly, preventing untimely interactions between SC precursors and chromosomes and allowing sufficient accumulation of precursors for rapid cooperative assembly upon homology verification.

A genomic landscape of mitochondrial DNA insertions in the pig nuclear genome provides evolutionary signatures of interspecies admixture.

PubMed

Schiavo, Giuseppina; Hoffmann, Orsolya Ivett; Ribani, Anisa; Utzeri, Valerio Joe; Ghionda, Marco Ciro; Bertolini, Francesca; Geraci, Claudia; Bovo, Samuele; Fontanesi, Luca

2017-10-01

Nuclear DNA sequences of mitochondrial origin (numts) are derived by insertion of mitochondrial DNA (mtDNA), into the nuclear genome. In this study, we provide, for the first time, a genome picture of numts inserted in the pig nuclear genome. The Sus scrofa reference nuclear genome (Sscrofa10.2) was aligned with circularized and consensus mtDNA sequences using LAST software. A total of 430 numt sequences that may represent 246 different numt integration events (57 numt regions determined by at least two numt sequences and 189 singletons) were identified, covering about 0.0078% of the nuclear genome. Numt integration events were correlated (0.99) to the chromosome length. The longest numt sequence (about 11 kbp) was located on SSC2. Six numts were sequenced and PCR amplified in pigs of European commercial and local pig breeds, of the Chinese Meishan breed and in European wild boars. Three of them were polymorphic for the presence or absence of the insertion. Surprisingly, the estimated age of insertion of two of the three polymorphic numts was more ancient than that of the speciation time of the Sus scrofa, supporting that these polymorphic sites were originated from interspecies admixture that contributed to shape the pig genome. © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Update on DOE’s Nuclear Energy University Program

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

M. J. Lambregts

2009-04-01

The Center for Advanced Energy Studies (CAES) Nuclear Energy University Program Office assists the U.S. Department of Energy Office of Nuclear Energy (DOE-NE) by administering its University Program. To promote accountable relationships between universities and the TIOs/TDOs, a process was designed and administered which includes two competitive Requests for Proposals (RFP’s) and two FOAs in the following areas: (1)Research and Development Grants, (2)Infrastructure improvement, and (3)Scholarships and Fellowships. NEUP will also host periodic reviews of university mission-specific R&D that document progress, reinforce accountability, and assess return on investment; sponsor workshops that inform universities of the Department’s research needs to facilitatemore » continued alignment of university R&D with NE missions; and conduct communications activities that foster stakeholder trust, serve as a catalyst for accomplishing NEUP objectives, and provide national visibility of NEUP activities and accomplishments. Year to date efforts to achieve these goals will be discussed.« less

Update on DOE's Nuclear Energy University Program

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

Lambregts, Marsha J.

2009-08-19

The Nuclear Energy University Program (NEUP) Office assists the U.S. Department of Energy Office of Nuclear Energy (DOE-NE) by administering its University Program. To promote accountable relationships between universities and the Technical Integration Offices (TIOs)/Technology Development Offices (TDOs), a process was designed and administered which includes two competitive Requests for Proposals (RFPs) and two Funding Opportunity Announcements (FOAs) in the following areas: (1) Research and Development (R and D) Grants, (2) Infrastructure improvement, and (3) Scholarships and Fellowships. NEUP will also host periodic reviews of university mission-specific R and D that document progress, reinforce accountability, and assess return on investment;more » sponsor workshops that inform universities of the Department's research needs to facilitate continued alignment of university R and D with NE missions; and conduct communications activities that foster stakeholder trust, serve as a catalyst for accomplishing NEUP objectives, and provide national visibility of NEUP activities and accomplishments. Year to date efforts to achieve these goals will be discussed.« less

ELECTRON MICROSCOPY OF MITOSIS IN A RADIOSENSITIVE GIANT AMOEBA

PubMed Central

Daniels, E. W.; Roth, L. E.

1964-01-01

Various aspects of the ultrastructure of the dividing nuclei in the large radiosensitive amoeba Pelomyxa illinoisensis are demonstrated. Evidence of nuclear envelope breakdown is presented, and membrane fragments are traced throughout metaphase to envelope reconstruction in anaphase and telophase. Annuli in the nuclear envelope and its fragments are shown throughout mitosis. During metaphase and anaphase some 15 to 20 mitochondria are aligned at each end of the spindle, and are called polar mitochondria. The radioresistant amoebae Pelomyxa carolinensis and Amoeba proteus do not have polar mitochondria, and Pelomyxa illinoisensis is unique in this regard. The shape of the P. illinoisensis interphase nucleoli differs from that in the two radioresistant species, and certain aspects of nucleolar dissolution in the prophase vary. Helical coils in the interphase nucleoplasm are similar to those in the radioresistant amoebae. A "blister" phase in the flatly shaped telophase nuclei of P. illinoisensis is described which is interpreted to be the result of a rapid nuclear expansion leading to the formation of the normal spherical interphase nuclei. PMID:14105218

The Nuclear Option: Evidence Implicating the Cell Nucleus in Mechanotransduction.

PubMed

Szczesny, Spencer E; Mauck, Robert L

2017-02-01

Biophysical stimuli presented to cells via microenvironmental properties (e.g., alignment and stiffness) or external forces have a significant impact on cell function and behavior. Recently, the cell nucleus has been identified as a mechanosensitive organelle that contributes to the perception and response to mechanical stimuli. However, the specific mechanotransduction mechanisms that mediate these effects have not been clearly established. Here, we offer a comprehensive review of the evidence supporting (and refuting) three hypothetical nuclear mechanotransduction mechanisms: physical reorganization of chromatin, signaling at the nuclear envelope, and altered cytoskeletal structure/tension due to nuclear remodeling. Our goal is to provide a reference detailing the progress that has been made and the areas that still require investigation regarding the role of nuclear mechanotransduction in cell biology. Additionally, we will briefly discuss the role that mathematical models of cell mechanics can play in testing these hypotheses and in elucidating how biophysical stimulation of the nucleus drives changes in cell behavior. While force-induced alterations in signaling pathways involving lamina-associated polypeptides (LAPs) (e.g., emerin and histone deacetylase 3 (HDAC3)) and transcription factors (TFs) located at the nuclear envelope currently appear to be the most clearly supported mechanism of nuclear mechanotransduction, additional work is required to examine this process in detail and to more fully test alternative mechanisms. The combination of sophisticated experimental techniques and advanced mathematical models is necessary to enhance our understanding of the role of the nucleus in the mechanotransduction processes driving numerous critical cell functions.

The Nuclear Option: Evidence Implicating the Cell Nucleus in Mechanotransduction

PubMed Central

Szczesny, Spencer E.; Mauck, Robert L.

2017-01-01

Biophysical stimuli presented to cells via microenvironmental properties (e.g., alignment and stiffness) or external forces have a significant impact on cell function and behavior. Recently, the cell nucleus has been identified as a mechanosensitive organelle that contributes to the perception and response to mechanical stimuli. However, the specific mechanotransduction mechanisms that mediate these effects have not been clearly established. Here, we offer a comprehensive review of the evidence supporting (and refuting) three hypothetical nuclear mechanotransduction mechanisms: physical reorganization of chromatin, signaling at the nuclear envelope, and altered cytoskeletal structure/tension due to nuclear remodeling. Our goal is to provide a reference detailing the progress that has been made and the areas that still require investigation regarding the role of nuclear mechanotransduction in cell biology. Additionally, we will briefly discuss the role that mathematical models of cell mechanics can play in testing these hypotheses and in elucidating how biophysical stimulation of the nucleus drives changes in cell behavior. While force-induced alterations in signaling pathways involving lamina-associated polypeptides (LAPs) (e.g., emerin and histone deacetylase 3 (HDAC3)) and transcription factors (TFs) located at the nuclear envelope currently appear to be the most clearly supported mechanism of nuclear mechanotransduction, additional work is required to examine this process in detail and to more fully test alternative mechanisms. The combination of sophisticated experimental techniques and advanced mathematical models is necessary to enhance our understanding of the role of the nucleus in the mechanotransduction processes driving numerous critical cell functions. PMID:27918797

Dynamic nuclear polarisation via the integrated solid effect II: experiments on naphthalene-h8 doped with pentacene-d14

NASA Astrophysics Data System (ADS)

Eichhorn, T. R.; van den Brandt, B.; Hautle, P.; Henstra, A.; Wenckebach, W. Th.

2014-07-01

In dynamic nuclear polarisation (DNP), also called hyperpolarisation, a small amount of unpaired electron spins is added to the sample containing the nuclear spins, and the polarisation of these unpaired electron spins is transferred to the nuclear spins by means of a microwave field. Traditional DNP polarises the electron spin of stable paramagnetic centres by cooling down to low temperature and applying a strong magnetic field. Then weak continuous wave microwave fields are used to induce the polarisation transfer. Complicated cryogenic equipment and strong magnets can be avoided using short-lived photo-excited triplet states that are strongly aligned in the optical excitation process. However, a much faster transfer of the electron spin polarisation is needed and pulsed DNP methods like nuclear orientation via electron spin locking (NOVEL) and the integrated solid effect (ISE) are used. To describe the polarisation transfer with the strong microwave fields in NOVEL and ISE, the usual perturbation methods cannot be used anymore. In the previous paper, we presented a theoretical approach to calculate the polarisation transfer in ISE. In the present paper, the theory is applied to the system naphthalene-h8 doped with pentacene-d14 yielding the photo-excited triplet states and compared with experimental results.

Spin coherent states phenomena probed by quantum state tomography in Zeeman perturbed nuclear quadrupole resonance

NASA Astrophysics Data System (ADS)

Teles, João; Auccaise, Ruben; Rivera-Ascona, Christian; Araujo-Ferreira, Arthur G.; Andreeta, José P.; Bonagamba, Tito J.

2018-07-01

Recently, we reported an experimental implementation of quantum information processing (QIP) by nuclear quadrupole resonance (NQR). In this work, we present the first quantum state tomography (QST) experimental implementation in the NQR QIP context. Two approaches are proposed, employing coherence selection by temporal and spatial averaging. Conditions for reduction in the number of cycling steps are analyzed, which can be helpful for larger spin systems. The QST method was applied to the study of spin coherent states, where the alignment-to-orientation phenomenon and the evolution of squeezed spin states show the effect of the nonlinear quadrupole interaction intrinsic to the NQR system. The quantum operations were implemented using a single-crystal sample of KClO3 and observing ^{35}Cl nuclei, which posses spin 3/2.

The nuclear high excitation outflow cone in NGC 1365

NASA Astrophysics Data System (ADS)

Per Lindblad, Olof; Hjelm, Maja; Jörsäter, Steven; Kristen, Helmuth

The morphology and kinematics of the high excitation outflow cone in the nuclear region of the Seyfert 1.5 galaxy NGC 1365 is investigated. An empirical model based on ground-based [OIII] emission line data consists of a somewhat hollow double cone with its apex at the Seyfert nucleus. The cone axis is well aligned in space with the normal to the symmetry plane of the galaxy and the position angle of its projection on the sky coincides closely with that of a jet-like radio feature. The opening angle of the cone is 100° and the orientation such that the line of sight to the Seyfert 1.5 nucleus falls inside the cone. The outflow velocities within the cone are accelerated and fall off towards the edge.

Nuclear counterparts of the cytoplasmic mitochondrial 12S rRNA gene: a problem of ancient DNA and molecular phylogenies.

PubMed

van der Kuyl, A C; Kuiken, C L; Dekker, J T; Perizonius, W R; Goudsmit, J

1995-06-01

Monkey mummy bones and teeth originating from the North Saqqara Baboon Galleries (Egypt), soft tissue from a mummified baboon in a museum collection, and nineteenth/twentieth-century skin fragments from mangabeys were used for DNA extraction and PCR amplification of part of the mitochondrial 12S rRNA gene. Sequences aligning with the 12S rRNA gene were recovered but were only distantly related to contemporary monkey mitochondrial 12S rRNA sequences. However, many of these sequences were identical or closely related to human nuclear DNA sequences resembling mitochondrial 12S rRNA (isolated from a cell line depleted in mitochondria) and therefore have to be considered contamination. Subsequently in a separate study we were able to recover genuine mitochondrial 12S rRNA sequences from many extant species of nonhuman Old World primates and sequences closely resembling the human nuclear integrations. Analysis of all sequences by the neighbor-joining (NJ) method indicated that mitochondrial DNA sequences and their nuclear counterparts can be divided into two distinct clusters. One cluster contained all temporary cytoplasmic mitochondrial DNA sequences and approximately half of the monkey nuclear mitochondriallike sequences. A second cluster contained most human nuclear sequences and the other half of monkey nuclear sequences with a separate branch leading to human and gorilla mitochondrial and nuclear sequences. Sequences recovered from ancient materials were equally divided between the two clusters. These results constitute a warning for when working with ancient DNA or performing phylogenetic analysis using mitochondrial DNA as a target sequence: Nuclear counterparts of mitochondrial genes may lead to faulty interpretation of results.

Nuclear fuel element with axially aligned fuel pellets and fuel microspheres therein

DOEpatents

Sease, J.D.; Harrington, F.E.

1973-12-11

Elongated single- and multi-region fuel elements are prepared by replacing within a cladding container a coarse fraction of fuel material which includes plutonium and uranium in the appropriate regions of the fuel element and then infiltrating with vibration a fine-sized fraction of uranium-containing microspheres throughout all interstices in the coarse material in a single loading. The fine, rigid material defines a thin annular layer between the coarse fraction and the cladding to reduce adverse mechanical and chemical interactions. (Official Gazette)

Useful diagnostic biometabolic data obtained by PET/CT and MR fusion imaging using open source software.

PubMed

Antonica, Filippo; Asabella, Artor Niccoli; Ferrari, Cristina; Rubini, Domenico; Notaristefano, Antonio; Nicoletti, Adriano; Altini, Corinna; Merenda, Nunzio; Mossa, Emilio; Guarini, Attilio; Rubini, Giuseppe

2014-01-01

In the last decade numerous attempts were considered to co-register and integrate different imaging data. Like PET/CT the integration of PET to MR showed great interest. PET/MR scanners are recently tested on different distrectual or systemic pathologies. Unfortunately PET/MR scanners are expensive and diagnostic protocols are still under studies and investigations. Nuclear Medicine imaging highlights functional and biometabolic information but has poor anatomic details. The aim of this study is to integrate MR and PET data to produce distrectual or whole body fused images acquired from different scanners even in different days. We propose an offline method to fuse PET with MR data using an open-source software that has to be inexpensive, reproducible and capable to exchange data over the network. We also evaluate global quality, alignment quality, and diagnostic confidence of fused PET-MR images. We selected PET/CT studies performed in our Nuclear Medicine unit, MR studies provided by patients on DICOM CD media or network received. We used Osirix 5.7 open source version. We aligned CT slices with the first MR slice, pointed and marked for co-registration using MR-T1 sequence and CT as reference and fused with PET to produce a PET-MR image. A total of 100 PET/CT studies were fused with the following MR studies: 20 head, 15 thorax, 24 abdomen, 31 pelvis, 10 whole body. An interval of no more than 15 days between PET and MR was the inclusion criteria. PET/CT, MR and fused studies were evaluated by two experienced radiologist and two experienced nuclear medicine physicians. Each one filled a five point based evaluation scoring scheme based on image quality, image artifacts, segmentation errors, fusion misalignment and diagnostic confidence. Our fusion method showed best results for head, thorax and pelvic districts in terms of global quality, alignment quality and diagnostic confidence,while for the abdomen and pelvis alignement quality and global quality resulted poor due to internal organs filling variation and time shifting beetwen examinations. PET/CT images with time of flight reconstruction and real attenuation correction were combined with anatomical detailed MRI images. We used Osirix, an image processing Open Source Software dedicated to DICOM images. No additional costs, to buy and upgrade proprietary software are required for combining data. No high technology or very expensive PET/MR scanner, that requires dedicated shielded room spaces and personnel to be employed or to be trained, are needed. Our method allows to share patient PET/MR fused data with different medical staff using dedicated networks. The proposed method may be applied to every MR sequence (MR-DWI and MR-STIR, magnet enhanced sequences) to characterize soft tissue alterations and improve discrimination diseases. It can be applied not only to PET with MR but virtually to every DICOM study.

Dynamic localization of Mps1 kinase to kinetochores is essential for accurate spindle microtubule attachment

PubMed Central

Dou, Zhen; Liu, Xing; Wang, Wenwen; Zhu, Tongge; Wang, Xinghui; Xu, Leilei; Abrieu, Ariane; Fu, Chuanhai; Hill, Donald L.; Yao, Xuebiao

2015-01-01

The spindle assembly checkpoint (SAC) is a conserved signaling pathway that monitors faithful chromosome segregation during mitosis. As a core component of SAC, the evolutionarily conserved kinase monopolar spindle 1 (Mps1) has been implicated in regulating chromosome alignment, but the underlying molecular mechanism remains unclear. Our molecular delineation of Mps1 activity in SAC led to discovery of a previously unidentified structural determinant underlying Mps1 function at the kinetochores. Here, we show that Mps1 contains an internal region for kinetochore localization (IRK) adjacent to the tetratricopeptide repeat domain. Importantly, the IRK region determines the kinetochore localization of inactive Mps1, and an accumulation of inactive Mps1 perturbs accurate chromosome alignment and mitotic progression. Mechanistically, the IRK region binds to the nuclear division cycle 80 complex (Ndc80C), and accumulation of inactive Mps1 at the kinetochores prevents a dynamic interaction between Ndc80C and spindle microtubules (MTs), resulting in an aberrant kinetochore attachment. Thus, our results present a previously undefined mechanism by which Mps1 functions in chromosome alignment by orchestrating Ndc80C–MT interactions and highlight the importance of the precise spatiotemporal regulation of Mps1 kinase activity and kinetochore localization in accurate mitotic progression. PMID:26240331

Dynamic localization of Mps1 kinase to kinetochores is essential for accurate spindle microtubule attachment.

PubMed

Dou, Zhen; Liu, Xing; Wang, Wenwen; Zhu, Tongge; Wang, Xinghui; Xu, Leilei; Abrieu, Ariane; Fu, Chuanhai; Hill, Donald L; Yao, Xuebiao

2015-08-18

The spindle assembly checkpoint (SAC) is a conserved signaling pathway that monitors faithful chromosome segregation during mitosis. As a core component of SAC, the evolutionarily conserved kinase monopolar spindle 1 (Mps1) has been implicated in regulating chromosome alignment, but the underlying molecular mechanism remains unclear. Our molecular delineation of Mps1 activity in SAC led to discovery of a previously unidentified structural determinant underlying Mps1 function at the kinetochores. Here, we show that Mps1 contains an internal region for kinetochore localization (IRK) adjacent to the tetratricopeptide repeat domain. Importantly, the IRK region determines the kinetochore localization of inactive Mps1, and an accumulation of inactive Mps1 perturbs accurate chromosome alignment and mitotic progression. Mechanistically, the IRK region binds to the nuclear division cycle 80 complex (Ndc80C), and accumulation of inactive Mps1 at the kinetochores prevents a dynamic interaction between Ndc80C and spindle microtubules (MTs), resulting in an aberrant kinetochore attachment. Thus, our results present a previously undefined mechanism by which Mps1 functions in chromosome alignment by orchestrating Ndc80C-MT interactions and highlight the importance of the precise spatiotemporal regulation of Mps1 kinase activity and kinetochore localization in accurate mitotic progression.

Fabrication Procedures and Birefringence Measurements for Designing Magnetically Responsive Lanthanide Ion Chelating Phospholipid Assemblies.

PubMed

Isabettini, Stéphane; Baumgartner, Mirjam E; Fischer, Peter; Windhab, Erich J; Liebi, Marianne; Kuster, Simon

2018-01-03

Bicelles are tunable disk-like polymolecular assemblies formed from a large variety of lipid mixtures. Applications range from membrane protein structural studies by nuclear magnetic resonance (NMR) to nanotechnological developments including the formation of optically active and magnetically switchable gels. Such technologies require high control of the assembly size, magnetic response and thermal resistance. Mixtures of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and its lanthanide ion (Ln 3+ ) chelating phospholipid conjugate, 1,2-dimyristoyl-sn-glycero-3-phospho-ethanolamine-diethylene triaminepentaacetate (DMPE-DTPA), assemble into highly magnetically responsive assemblies such as DMPC/DMPE-DTPA/Ln 3+ (molar ratio 4:1:1) bicelles. Introduction of cholesterol (Chol-OH) and steroid derivatives in the bilayer results in another set of assemblies offering unique physico-chemical properties. For a given lipid composition, the magnetic alignability is proportional to the bicelle size. The complexation of Ln 3+ results in unprecedented magnetic responses in terms of both magnitude and alignment direction. The thermo-reversible collapse of the disk-like structures into vesicles upon heating allows tailoring of the assemblies' dimensions by extrusion through membrane filters with defined pore sizes. The magnetically alignable bicelles are regenerated by cooling to 5 °C, resulting in assembly dimensions defined by the vesicle precursors. Herein, this fabrication procedure is explained and the magnetic alignability of the assemblies is quantified by birefringence measurements under a 5.5 T magnetic field. The birefringence signal, originating from the phospholipid bilayer, further enables monitoring of polymolecular changes occurring in the bilayer. This simple technique is complementary to NMR experiments that are commonly employed to characterize bicelles.

Dynamic interaction between actin and nesprin2 maintain the cell nucleus in a prestressed state

NASA Astrophysics Data System (ADS)

Kumar, Abhishek; Shivashankar, G. V.

2016-12-01

Mechanical coupling between the nucleus and the cytoskeleton is indispensable for direct force transduction from the extra cellular matrix (ECM) to the chromatin. Although this physical coupling has been shown to be crucial for nuclear positioning and its function, the quantification of nuclear-cytoskeleton interaction has been lacking. In this paper, using various quantitative fluorescence spectroscopy techniques, we investigate the nature of this connection. High-resolution 3D imaging shows that nesprin2G forms short linear structures along actin stress fibers (ASFs) in the apical region of the nucleus. Fluorescence recovery after photobleaching (FRAP) revealed that the alignment of nesprin2G becomes heterogeneous when cell shape is engineered from elongated rectangular shape to square using micropatterned substrates. Further, fluorescence cross-correlation spectroscopy (FCCS) revealed that actin interacts transiently with outer nuclear membrane protein nesprin2G with a time scale of 12 ms. In addition, fluorescence resonance energy transfer (FRET) experiments show that the apical ASFs and nesprin2G are in close physical proximity. This interaction is spatially heterogeneous with high FRET along the ASFs. Lastly, we show that the disruption of actin to nuclear connection by over-expression of Dominant Negative Klarsicht, ANC-1, Syne Homology (DNKASH) leads to an increase in nuclear height. These results not only reveal the characteristics of actin-nesprin2G interaction and its significance in regulating nuclear morphology, but also validate the utility of quantitative fluorescence techniques in deciphering physical connections that are essential for mechanotransduction.

γ-Particle coincidence technique for the study of nuclear reactions

NASA Astrophysics Data System (ADS)

Zagatto, V. A. B.; Oliveira, J. R. B.; Allegro, P. R. P.; Chamon, L. C.; Cybulska, E. W.; Medina, N. H.; Ribas, R. V.; Seale, W. A.; Silva, C. P.; Gasques, L. R.; Zahn, G. S.; Genezini, F. A.; Shorto, J. M. B.; Lubian, J.; Linares, R.; Toufen, D. L.; Silveira, M. A. G.; Rossi, E. S.; Nobre, G. P.

2014-06-01

The Saci-Perere γ ray spectrometer (located at the Pelletron AcceleratorLaboratory - IFUSP) was employed to implement the γ-particle coincidence technique for the study of nuclear reaction mechanisms. For this, the 18O+110Pd reaction has been studied in the beam energy range of 45-54 MeV. Several corrections to the data due to various effects (energy and angle integrations, beam spot size, γ detector finite size and the vacuum de-alignment) are small and well controlled. The aim of this work was to establish a proper method to analyze the data and identify the reaction mechanisms involved. To achieve this goal the inelastic scattering to the first excited state of 110Pd has been extracted and compared to coupled channel calculations using the São Paulo Potential (PSP), being reasonably well described by it.

Ultra-stable sub-meV monochromator for hard X-rays

DOE PAGES

Toellner, T. S.; Collins, J.; Goetze, K.; ...

2015-07-17

A high-resolution silicon monochromator suitable for 21.541 keV synchrotron radiation is presented that produces a bandwidth of 0.27 meV. The operating energy corresponds to a nuclear transition in 151Eu. The first-of-its-kind, fully cryogenic design achieves an energy-alignment stability of 0.017 meV r.m.s. per day, or a 100-fold improvement over other meV-monochromators, and can tolerate higher X-ray power loads than room-temperature designs of comparable resolution. This offers the potential for significantly more accurate measurements of lattice excitation energies using nuclear resonant vibrational spectroscopy if combined with accurate energy calibration using, for example, high-speed Doppler shifting. The design of the monochromator alongmore » with its performance and impact on transmitted beam properties are presented.« less

Jacking mechanism for upper internals structure of a liquid metal nuclear reactor

DOEpatents

Gillett, James E.; Wineman, Arthur L.

1984-01-01

A jacking mechanism for raising the upper internals structure of a liquid metal nuclear reactor which jacking mechanism uses a system of gears and drive shafts to transmit force from a single motor to four mechanically synchronized ball jacks to raise and lower support columns which support the upper internals structure. The support columns have a pin structure which rides up and down in a slot in a housing fixed to the reactor head. The pin has two locking plates which can be rotated around the pin to bring bolt holes through the locking plates into alignment with a set of bolt holes in the housing, there being a set of such housing bolt holes corresponding to both a raised and a lowered position of the support column. When the locking plate is so aligned, a surface of the locking plate mates with a surface in the housing such that the support column is then supported by the locking plate and not by the ball jacks. Since the locking plates are to be installed and bolted to the housing during periods of reactor operation, the ball jacks need not be sized to react the large forces which occur or potentially could occur on the upper internals structure of the reactor during operation. The locking plates react these loads. The ball jacks, used only during refueling, can be smaller, which enable conventionally available equipment to fulfill the precision requirements for the task within available space.

Toward Simultaneous Real-Time Fluoroscopic and Nuclear Imaging in the Intervention Room.

PubMed

Beijst, Casper; Elschot, Mattijs; Viergever, Max A; de Jong, Hugo W A M

2016-01-01

To investigate the technical feasibility of hybrid simultaneous fluoroscopic and nuclear imaging. An x-ray tube, an x-ray detector, and a gamma camera were positioned in one line, enabling imaging of the same field of view. Since a straightforward combination of these elements would block the lines of view, a gamma camera setup was developed to be able to view around the x-ray tube. A prototype was built by using a mobile C-arm and a gamma camera with a four-pinhole collimator. By using the prototype, test images were acquired and sensitivity, resolution, and coregistration error were analyzed. Nuclear images (two frames per second) were acquired simultaneously with fluoroscopic images. Depending on the distance from point source to detector, the system resolution was 1.5-1.9-cm full width at half maximum, the sensitivity was (0.6-1.5) × 10(-5) counts per decay, and the coregistration error was -0.13 to 0.15 cm. With good spatial and temporal alignment of both modalities throughout the field of view, fluoroscopic images can be shown in grayscale and corresponding nuclear images in color overlay. Measurements obtained with the hybrid imaging prototype device that combines simultaneous fluoroscopic and nuclear imaging of the same field of view have demonstrated the feasibility of real-time simultaneous hybrid imaging in the intervention room. © RSNA, 2015

Nuclear reactor fuel assembly duct-tube-to-handling-socket attachment system

DOEpatents

Christiansen, David W.; Smith, Bob G.

1982-01-01

A reusable system for removably attaching the upper end 10of a nuclear reactor duct tube to the lower end 30 of a nuclear reactor fuel assembly handling socket. A transition ring 20, fixed to the duct tube's upper end 10, has an interior-threaded section 22 with a first locking hole segment 24. An adaptor ring 40, fixed to the handling socket's lower end 30 has an outside-threaded section 42 with a second locking hole segment 44. The inside 22 and outside 42 threaded sections match and can be joined so that the first 24 and second 44 locking hole segments can be aligned to form a locking hole. A locking ring 50, with a locking pin 52, slides over the adaptor ring 40 so that the locking pin 52 fits in the locking hole. A swage lock 60 or a cantilever finger lock 70 is formed from the locking cup collar 26 to fit in a matching groove 54 or 56 in the locking ring 50 to prevent the locking ring's locking pin 52 from backing out of the locking hole.

An X-ray image of the Seyfert galaxy NGC 1068

NASA Technical Reports Server (NTRS)

Wilson, A. S.; Elvis, M.; Lawrence, A.; Bland-Hawthorn, J.

1992-01-01

An image of NGC 1068 with 4-5 arcsec obtained with the High Resolution Imager on the Rosat X-ray Observatory in the energy band 0.1-2.4 keV is presented and discussed. The map reveals an unresolved nuclear source, extended (about 1.5 kpc) emission around the nucleus, and extended (about 13 kpc) emission from the starburst disk. The extended circumnuclear emission aligns toward the NE, the same direction as found for the resolved emission of the active nucleus in several other wavebands. Thermal emission from a hot wind is argued to be the source of the steep-spectrum, nuclear, and circumnuclear emission. The disk of NGC 1068 has ratios of soft X-ray to B band and soft X-ray to 60-micron luminosities which are similar to those found for other starburst systems. The X-ray spectrum of the starburst disk is harder than that of the nuclear emission. By adopting a plausible spectrum and extrapolating the present measured flux, it is concluded that the starburst disk contributes most of the hard component seen in the 2-10 keV band.

Connecting apparatus for limited rotary of rectilinear motion (II)

DOEpatents

Hardin, Jr., Roy T.; Kurinko, Carl D.

1981-01-01

Apparatus for providing connection between two members having relative movement in a horizontal plane in a rotary or linear fashion. The apparatus includes a set of vertical surfaces affixed to each of the members, laterally aligned across a selected vertical gap. A number of cables or hoses, for electrical, hydraulic, or pneumatic connection are arranged between consecutive surfaces in a C-shaped traveling loop, connected through their end portions to the two respective members, so that through a sliding motion portions of the cable are transferred from between one set of surfaces to the other aligned set, across the gap, upon relative motion of the members. A number of flexible devices are affixed to the upper set of surfaces for supporting the upper portion of each looped cable. The apparatus is particularly adaptable to an area having limited lateral clearances and requiring signal level separation between electrical cables, such as found in the rotating plugs and associated equipment of the reactor vessel head of a nuclear reactor.

Actin realignment and cofilin regulation are essential for barrier integrity during shear stress

PubMed Central

Slee, Joshua B.; Lowe-Krentz, Linda J.

2014-01-01

Vascular endothelial cells and their actin microfilaments align in the direction of fluid shear stress (FSS) in vitro and in vivo. To determine whether cofilin, an actin severing protein, is required in this process, the levels of phospho-cofilin (serine-3) were evaluated in cells exposed to FSS. Phospho-cofilin levels decreased in the cytoplasm and increased in the nucleus during FSS exposure. This was accompanied by increased nuclear staining for activated LIMK, a cofilin kinase. Blocking stress kinases JNK and p38, known to play roles in actin realignment during FSS, decreased cofilin phosphorylation under static conditions, and JNK inhibition also resulted in decreased phospho-cofilin during FSS exposure. Inhibition of dynamic changes in cofilin phosphorylation through cofilin mutants decreased correct actin realignment. The mutants also decreased barrier integrity as did inhibition of the stress kinases. These results identify the importance of cofilin in the process of actin alignment and the requirement for actin realignment in endothelial barrier integrity during FSS. PMID:23060131

Neutron diffraction study of Tb0.5Ho0.5Mn2Si2

NASA Astrophysics Data System (ADS)

Pandey, Swati; Siruguri, Vasudeva; Rawat, Rajeev

2018-02-01

The magnetic properties of tetragonal polycrystalline intermetallic compound Tb0.5Ho0.5Mn2Si2 have been investigated using temperature dependent dc magnetic susceptibility and neutron powder diffraction studies. Results of high temperature susceptibility data shows anomaly at TN = 510 K while low temperature susceptibility data indicate two successive anomalies at T1 = 11 K and T2 = 25 K. Metamagnetic transition is observed in magnetization versus field curves. Our neutron diffraction results indicate three different magnetic regions with different magnetic structures. Neutron diffraction data shows that below T2, the intensities of some of the nuclear peaks get enhanced indicating ferromagnetic ordering, while additional magnetic reflections are observed below T1, indicating antiferromagnetic order. Ordering of rare earth sublattice at low temperature rearranges the ordering of Mn sublattice and results in reorientation of Mn spins at T1. At 2 K Tb/Ho moments are aligned along c-axis while Mn moments are aligned perpendicular to c-axis.

Injection method of barrier bucket supported by off-aligned electron cooling for CRing of HIAF

NASA Astrophysics Data System (ADS)

Shen, Guo-Dong; Yang, Jian-Cheng; Xia, Jia-Wen; Mao, Li-Jun; Yin, Da-Yu; Chai, Wei-Ping; Shi, Jian; Sheng, Li-Na; Smirnov, A.; Wu, Bo; Zhao, He

2016-08-01

A new accelerator complex, HIAF (the High Intensity Heavy Ion Accelerator Facility), has been approved in China. It is designed to provide intense primary and radioactive ion beams for research in high energy density physics, nuclear physics, atomic physics as well as other applications. In order to achieve a high intensity of up to 5×1011 ppp 238U34+, the Compression Ring (CRing) needs to stack more than 5 bunches transferred from the Booster Ring (BRing). However, the normal bucket to bucket injection scheme can only achieve an intensity gain of 2, so an injection method, fixed barrier bucket (BB) supported by electron cooling, is proposed. To suppress the severe space charge effect during the stacking process, off-alignment is adopted in the cooler to control the transverse emittance. In this paper, simulation and optimization with the BETACOOL program are presented. Supported by New Interdisciplinary and Advanced Pilot Fund of Chinese Academy of Sciences

Phylogenetic analysis of 47 chloroplast genomes clarifies the contribution of wild species to the domesticated apple maternal line.

PubMed

Nikiforova, Svetlana V; Cavalieri, Duccio; Velasco, Riccardo; Goremykin, Vadim

2013-08-01

Both the origin of domesticated apple and the overall phylogeny of the genus Malus are still not completely resolved. Having this as a target, we built a 134,553-position-long alignment including two previously published chloroplast DNAs (cpDNAs) and 45 de novo sequenced, fully colinear chloroplast genomes from cultivated apple varieties and wild apple species. The data produced are free from compositional heterogeneity and from substitutional saturation, which can adversely affect phylogeny reconstruction. Phylogenetic analyses based on this alignment recovered a branch, having the maximum bootstrap support, subtending a large group of the cultivated apple sorts together with all analyzed European wild apple (Malus sylvestris) accessions. One apple cultivar was embedded in a monophylum comprising wild M. sieversii accessions and other Asian apple species. The data demonstrate that M. sylvestris has contributed chloroplast genome to a substantial fraction of domesticated apple varieties, supporting the conclusion that different wild species should have contributed the organelle and nuclear genomes to the domesticated apple.

Reactor shroud joint

DOEpatents

Ballas, Gary J.; Fife, Alex Blair; Ganz, Israel

1998-01-01

A shroud for a nuclear reactor is described. In one embodiment, the shroud includes first and second shroud sections, and each shroud section includes a substantially cylindrical main body having a first end and a second end. With respect to each shroud section, a flange is located at the main body first end, and the flange has a plurality of bolt openings therein and a plurality of scalloped regions. The first shroud section is welded to the second shroud section, and at least some of the bolt openings in the first shroud section flange align with respective bolt openings in the second shroud section flange. In the event that the onset of inter-granular stress corrosion cracking is ever detected in the weld between the shroud section, bolts are inserted through bolt openings in the first shroud section flange and through aligned bolt openings the second shroud section flange. Each bolt, in one embodiment, has a shank section and first and second threaded end sections. Nuts are threadedly engaged to the threaded end sections and tightened against the respective flanges.

ELECTRON MICROSCOPY OF MITOSIS IN A RADIOSENSITIVE GIANT AMOEBA

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

Daniels, E.W.; Roth, L.E.

1962-10-01

Pelomyxa illinoisensis amoebae, the large radiosensitive species, were fixed in OsO/sub 4/ and embedded in either Epon 812 or methacrylate. Ultrastructural morphology is demonstrated in subnuclear structures at interphase and during specific times in mitosis. Evidence of nuclear envelope breakdown and reconstruction is presented. Fragments of nuclear envelope membranes are traced throughout metaphase and anaphase to telophase. Annuli in the nuclear envelope and its fragments are demonstrated. P. illinoisensis is unique in mitochondrial arrangement during metaphase and anaphase-- mitochondria are aligned at the ends of fibrils distal to the chromosomes at the positions occupied by centrioles in other types ofmore » cells; there they remain until the end of anaphase. The radioresistant amoebae, Pelomyxa carolinensis and Amoeba proteus do not have polar mitochondria. P. illinoisensis also differs from the two radioresistant species in nucleolar morphology during interphase, and in the manner of nucleolar dissolution during prophase. On the other hand, helical coils are shown in the interphase nucleoplasm which appear similar to those in the radioresistant amoebae, P. carolinensis and A. groteus. A blister stage in the telophase of P. illinoisensis is described which is interpreted to be the result of a rapid nuclear expansion leading to interphase. This has not been observed in the radioresistant amoebae. (auth)« less

Subcellular localization of calcium and Ca-ATPase activity during nuclear maturation in Bufo arenarum oocytes.

PubMed

Ramos, Inés; Cisint, Susana B; Crespo, Claudia A; Medina, Marcela F; Fernández, Silvia N

2009-08-01

The localization of calcium and Ca-ATPase activity in Bufo arenarum oocytes was investigated by ultracytochemical techniques during progesterone-induced nuclear maturation, under in vitro conditions. No Ca2+ deposits were detected in either control oocytes or progesterone-treated ones for 1-2 h. At the time when nuclear migration started, electron dense deposits of Ca2+ were visible in vesicles, endoplasmic reticulum cisternae and in the space between the annulate lamellae membranes. Furthermore, Ca-ATPase activity was also detected in these membrane structures. As maturation progressed, the cation deposits were observed in the cytomembrane structures, which underwent an important reorganization and redistribution. Thus, they moved from the subcortex and became located predominantly in the oocyte cortex area when nuclear maturation ended. Ca2+ stores were observed in vesicles surrounding or between the cortical granules, which are aligned close to the plasma membrane. The positive Ca-ATPase reaction in these membrane structures could indicate that the calcium deposit is an ATP-dependent process. Our results suggest that during oocyte maturation calcium would be stored in membrane structures where it remains available for release at the time of fertilization. Data obtained under our experimental conditions indicate that calcium from the extracellular medium would be important for the oocyte maturation process.

Cerebellar Nuclear Neurons Use Time and Rate Coding to Transmit Purkinje Neuron Pauses.

PubMed

Sudhakar, Shyam Kumar; Torben-Nielsen, Benjamin; De Schutter, Erik

2015-12-01

Neurons of the cerebellar nuclei convey the final output of the cerebellum to their targets in various parts of the brain. Within the cerebellum their direct upstream connections originate from inhibitory Purkinje neurons. Purkinje neurons have a complex firing pattern of regular spikes interrupted by intermittent pauses of variable length. How can the cerebellar nucleus process this complex input pattern? In this modeling study, we investigate different forms of Purkinje neuron simple spike pause synchrony and its influence on candidate coding strategies in the cerebellar nuclei. That is, we investigate how different alignments of synchronous pauses in synthetic Purkinje neuron spike trains affect either time-locking or rate-changes in the downstream nuclei. We find that Purkinje neuron synchrony is mainly represented by changes in the firing rate of cerebellar nuclei neurons. Pause beginning synchronization produced a unique effect on nuclei neuron firing, while the effect of pause ending and pause overlapping synchronization could not be distinguished from each other. Pause beginning synchronization produced better time-locking of nuclear neurons for short length pauses. We also characterize the effect of pause length and spike jitter on the nuclear neuron firing. Additionally, we find that the rate of rebound responses in nuclear neurons after a synchronous pause is controlled by the firing rate of Purkinje neurons preceding it.

Automated fuel pin loading system

DOEpatents

Christiansen, David W.; Brown, William F.; Steffen, Jim M.

1985-01-01

An automated loading system for nuclear reactor fuel elements utilizes a gravity feed conveyor which permits individual fuel pins to roll along a constrained path perpendicular to their respective lengths. The individual lengths of fuel cladding are directed onto movable transports, where they are aligned coaxially with the axes of associated handling equipment at appropriate production stations. Each fuel pin can be reciprocated axially and/or rotated about its axis as required during handling steps. The fuel pins are inserted as a batch prior to welding of end caps by one of two disclosed welding systems.

Automated fuel pin loading system

DOEpatents

Christiansen, D.W.; Brown, W.F.; Steffen, J.M.

An automated loading system for nuclear reactor fuel elements utilizes a gravity feed conveyor which permits individual fuel pins to roll along a constrained path perpendicular to their respective lengths. The individual lengths of fuel cladding are directed onto movable transports, where they are aligned coaxially with the axes of associated handling equipment at appropriate production stations. Each fuel pin can be be reciprocated axially and/or rotated about its axis as required during handling steps. The fuel pins are inerted as a batch prior to welding of end caps by one of two disclosed welding systems.

NMR spectrum analysis for CrAs at ambient pressure

NASA Astrophysics Data System (ADS)

Kotegawa, H.; Nakahara, S.; Matsushima, K.; Tou, H.; Matsuoka, E.; Sugawara, H.; Harima, H.

2018-05-01

We report NMR spectrum analysis for CrAs, which was recently reported to be superconducting under pressure. The NMR spectrum obtained by the powdered single crystals shows a typical powder pattern reproduced by the electric field gradient (EFG) parameters and isotropic Knight shift, indicating anisotropy of Knight shift is not remarkable in CrAs. For the oriented sample, the spectrum can be understood by considering that the crystals are aligned for H ∥ b . The temperature dependence of Knight shift was successfully obtained from NMR spectrum with large nuclear quadrupole interaction.

Finite-volume scheme for anisotropic diffusion

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

Es, Bram van, E-mail: bramiozo@gmail.com; FOM Institute DIFFER, Dutch Institute for Fundamental Energy Research, The Netherlands"1; Koren, Barry

In this paper, we apply a special finite-volume scheme, limited to smooth temperature distributions and Cartesian grids, to test the importance of connectivity of the finite volumes. The area of application is nuclear fusion plasma with field line aligned temperature gradients and extreme anisotropy. We apply the scheme to the anisotropic heat-conduction equation, and compare its results with those of existing finite-volume schemes for anisotropic diffusion. Also, we introduce a general model adaptation of the steady diffusion equation for extremely anisotropic diffusion problems with closed field lines.

Nuclear component horizontal seismic restraint

DOEpatents

Snyder, Glenn J.

1988-01-01

A nuclear component horizontal seismic restraint. Small gaps limit horizontal displacement of components during a seismic occurrence and therefore reduce dynamic loadings on the free lower end. The reactor vessel and reactor guard vessel use thicker section roll-forged rings welded between the vessel straight shell sections and the bottom hemispherical head sections. The inside of the reactor guard vessel ring forging contains local vertical dovetail slots and upper ledge pockets to mount and retain field fitted and installed blocks. As an option, the horizontal displacement of the reactor vessel core support cone can be limited by including shop fitted/installed local blocks in opposing alignment with the reactor vessel forged ring. Beams embedded in the wall of the reactor building protrude into apertures in the thermal insulation shell adjacent the reactor guard vessel ring and have motion limit blocks attached thereto to provide to a predetermined clearance between the blocks and reactor guard vessel ring.

Centromere pairing precedes meiotic chromosome pairing in plants.

PubMed

Zhang, Jing; Han, Fangpu

2017-11-01

Meiosis is a specialized eukaryotic cell division, in which diploid cells undergo a single round of DNA replication and two rounds of nuclear division to produce haploid gametes. In most eukaryotes, the core events of meiotic prophase I are chromosomal pairing, synapsis and recombination. To ensure accurate chromosomal segregation, homologs have to identify and align along each other at the onset of meiosis. Although much progress has been made in elucidating meiotic processes, information on the mechanisms underlying chromosome pairing is limited in contrast to the meiotic recombination and synapsis events. Recent research in many organisms indicated that centromere interactions during early meiotic prophase facilitate homologous chromosome pairing, and functional centromere is a prerequisite for centromere pairing such as in maize. Here, we summarize the recent achievements of chromosome pairing research on plants and other organisms, and outline centromere interactions, nuclear chromosome orientation, and meiotic cohesin, as main determinants of chromosome pairing in early meiotic prophase.

Method for testing the strength and structural integrity of nuclear fuel particles

DOEpatents

Lessing, P.A.

1995-10-17

An accurate method for testing the strength of nuclear fuel particles is disclosed. Each particle includes an upper and lower portion, and is placed within a testing apparatus having upper and lower compression members. The upper compression member includes a depression therein which is circular and sized to receive only part of the upper portion of the particle. The lower compression member also includes a similar depression. The compression members are parallel to each other with the depressions therein being axially aligned. The fuel particle is then placed between the compression members and engaged within the depressions. The particle is then compressed between the compression members until it fractures. The amount of force needed to fracture the particle is thereafter recorded. This technique allows a broader distribution of forces and provides more accurate results compared with systems which distribute forces at singular points on the particle. 13 figs.

Method for testing the strength and structural integrity of nuclear fuel particles

DOEpatents

Lessing, Paul A.

1995-01-01

An accurate method for testing the strength of nuclear fuel particles. Each particle includes an upper and lower portion, and is placed within a testing apparatus having upper and lower compression members. The upper compression member includes a depression therein which is circular and sized to receive only part of the upper portion of the particle. The lower compression member also includes a similar depression. The compression members are parallel to each other with the depressions therein being axially aligned. The fuel particle is then placed between the compression members and engaged within the depressions. The particle is then compressed between the compression members until it fractures. The amount of force needed to fracture the particle is thereafter recorded. This technique allows a broader distribution of forces and provides more accurate results compared with systems which distribute forces at singular points on the particle.

Ahp2 (Hop2) function in Arabidopsis thaliana (Ler) is required for stabilization of close alignment and synaptonemal complex formation except for the two short arms that contain nucleolus organizer regions.

PubMed

Stronghill, P; Pathan, N; Ha, H; Supijono, E; Hasenkampf, C

2010-08-01

A cytological comparative analysis of male meiocytes was performed for Arabidopsis wild type and the ahp2 (hop2) mutant with emphasis on ahp2's largely uncharacterized prophase I. Leptotene progression appeared normal in ahp2 meiocytes; chromosomes exhibited regular axis formation and assumed a typical polarized nuclear organization. In contrast, 4',6'-diamidino-2-phenylindole-stained ahp2 pachytene chromosome spreads demonstrated a severe reduction in stabilized pairing. However, transmission electron microscopy (TEM) analysis of sections from meiocytes revealed that ahp2 chromosome axes underwent significant amounts of close alignment (44% of total axis). This apparent paradox strongly suggests that the Ahp2 protein is involved in the stabilization of homologous chromosome close alignment. Fluorescent in situ hybridization in combination with Zyp1 immunostaining revealed that ahp2 mutants undergo homologous synapsis of the nucleolus-organizer-region-bearing short arms of chromosomes 2 and 4, despite the otherwise "nucleus-wide" lack of stabilized pairing. The duration of ahp2 zygotene was significantly prolonged and is most likely due to difficulties in chromosome alignment stabilization and subsequent synaptonemal complex formation. Ahp2 and Mnd1 proteins have previously been shown, "in vitro," to form a heterodimer. Here we show, "in situ," that the Ahp2 and Mnd1 proteins are synchronous in their appearance and disappearance from meiotic chromosomes. Both the Ahp2 and Mnd1 proteins localize along the chromosomal axis. However, localization of the Ahp2 protein was entirely foci-based whereas Mnd1 protein exhibited an immunostaining pattern with some foci along the axis and a diffuse staining for the rest of the chromosome.

Backbendings of superdeformed bands in 36;40Ar

NASA Astrophysics Data System (ADS)

Xiang, Xu-Hui; He, Xiao-Tao

2018-05-01

Experimentally observed superdeformed (SD) rotational bands in 36Ar and 40Ar are studied by the cranked shell model (CSM) with the pairing correlations treated by a particle-number-conserving (PNC) method. This is the first time that PNC-CSM calculations have been performed on the light nuclear mass region around A=40. The experimental kinematic moments of inertia J (1) versus rotational frequency are reproduced well. The backbending of the SD band at frequency around ℏω=1.5 MeV in 36Ar is attributed to the sharp rise of the simultaneous alignments of the neutron and proton 1d 5/2[202]5/2 pairs and 1f 7/2[321]3/2 pairs, which is a consequence of the band crossing between the 1d 5/2[202]5/2 and 1f 7/2[321]3/2 configuration states. The gentle upbending at low frequency of the SD band in 40Ar is mainly affected by the alignments of the neutron 1f 7/2[321]3/2 pairs and proton 1d 5/2[202]5/2 pairs. The PNC-CSM calculations show that besides the diagonal parts, the off-diagonal parts of the alignments play an important role in the rotational behavior of the SD bands. Supported by National Natural Science Foundation of China (11775112 and 11275098) and the Priority Academic Program Development of Jiangsu Higher Education Institutions

Intimal cushions and endothelial nuclear elongation around mouse aortic branches and their spatial correspondence with patterns of lipid deposition

PubMed Central

Bond, Andrew R.; Ni, Chih-Wen; Jo, Hanjoong

2010-01-01

Spatial variation in hemodynamic stresses acting on the arterial wall may explain the nonuniform distribution of atherosclerosis. In thoracic aortas of LDL receptor/apolipoprotein E double knockout mice, lesions develop preferentially around the entire circumference of intercostal branch ostia, regardless of age, with the highest prevalence occurring upstream. Additional chevron-shaped lesions occur further upstream of the ostia. This pattern differs from the age-related ones occurring in people and rabbits. In the present study, patterns of near-wall blood flow around intercostal ostia in wild-type mice were estimated from the morphology of endothelial nuclei, which were shown in vitro to elongate in response to elevated shear stress and to align with the flow, and wall structure was assessed from confocal and scanning electron microscopy. A triangular intimal cushion surrounded the upstream part of most ostia. Nuclear length-to-width ratios were lowest over this cushion and highest at the sides of branches, regardless of age. Nuclear orientations were consistent with flow diverging around the branch. The pattern of nuclear morphology differed from the age-related ones observed in rabbits. The intimal cushion and the distribution of shear stress inferred from these observations can partly account for the pattern of lesions observed in knockout mice. Nuclear elongation in nonbranch regions was approximately constant across animals of different size, demonstrating the existence of a mechanism by which endothelial cells compensate for the dependence of mean aortic wall shear stress on body mass. PMID:19933414

The reorientation of cell nucleus promotes the establishment of front-rear polarity in migrating fibroblasts.

PubMed

Maninová, Miloslava; Klímová, Zuzana; Parsons, J Thomas; Weber, Michael J; Iwanicki, Marcin P; Vomastek, Tomáš

2013-06-12

The establishment of cell polarity is an essential step in the process of cell migration. This process requires precise spatiotemporal coordination of signaling pathways that in most cells create the typical asymmetrical profile of a polarized cell with nucleus located at the cell rear and the microtubule organizing center (MTOC) positioned between the nucleus and the leading edge. During cell polarization, nucleus rearward positioning promotes correct microtubule organizing center localization and thus the establishment of front-rear polarity and directional migration. We found that cell polarization and directional migration require also the reorientation of the nucleus. Nuclear reorientation is manifested as temporally restricted nuclear rotation that aligns the nuclear axis with the axis of cell migration. We also found that nuclear reorientation requires physical connection between the nucleus and cytoskeleton mediated by the LINC (linker of nucleoskeleton and cytoskeleton) complex. Nuclear reorientation is controlled by coordinated activity of lysophosphatidic acid (LPA)-mediated activation of GTPase Rho and the activation of integrin, FAK (focal adhesion kinase), Src, and p190RhoGAP signaling pathway. Integrin signaling is spatially induced at the leading edge as FAK and p190RhoGAP are predominantly activated or localized at this location. We suggest that integrin activation within lamellipodia defines cell front, and subsequent FAK, Src, and p190RhoGAP signaling represents the polarity signal that induces reorientation of the nucleus and thus promotes the establishment of front-rear polarity. Copyright © 2013 Elsevier Ltd. All rights reserved.

Heterogeneous nuclear ribonucleoprotein K upregulates the kinetochore complex component NUF2 and promotes the tumorigenicity of colon cancer cells

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

Sugimasa, Hironobu; Taniue, Kenzui; Kurimoto, Akiko

2015-03-27

Heterogeneous nuclear ribonucleoprotein K (hnRNP K) is a multi-functional protein involved in transcription, mRNA splicing, mRNA stabilization and translation. Although hnRNP K has been suggested to play a role in the development of many cancers, its molecular function in colorectal cancer has remained elusive. Here we show that hnRNP K plays an important role in the mitotic process in HCT116 colon cancer cells. Furthermore, we demonstrate that hnRNP K directly transactivates the NUF2 gene, the product of which is a component of the NDC80 kinetochore complex and which is known to be critical for a stable spindle microtubule-kinetochore attachment. Inmore » addition, knockdown of both hnRNP K and NUF2 caused failure in metaphase chromosome alignment and drastic decrease in the growth of colon cancer cells. These results suggest that the hnRNP K-NUF2 axis is important for the mitotic process and proliferation of colon cancer cells and that this axis could be a target for the therapy of colon cancer. - Highlights: • hnRNP K is required for the tumorigenicity of colon cancer cells. • hnRNP K binds to the promoter region of NUF2 and activates its transcription. • NUF2 expression is correlated with hnRNP K expression in colorectal cancer tissue. • hnRNP K and NUF2 are required for metaphase chromosome alignment. • The hnRNP K-NUF2 axis is important for the proliferation of colon cancer cells.« less

The US nuclear weapon infrastructure and a stable global nuclear weapon regime

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

Immele, John D; Wagner, Richard L

2009-01-01

US nuclear weapons capabilities -- extant force structure and nuclear weapons infrastructure as well as declared policy -- influence other nations' nuclear weapons postures, at least to some extent. This influence can be desirable or undesirable, and is, of course, a mixture of both. How strong the influence is, and its nature, are complicated, controversial, and -- in our view -- not well understood but often overstated. Divergent views about this influence and how it might shape the future global nuclear weapons regime seem to us to be the most serious impediment to reaching a national consensus on US weaponsmore » policy, force structure and supporting infrastructure. We believe that a paradigm shift to capability-based deterrence and dissuasion is not only consistent with the realities of the world and how it has changed, but also a desirable way for nuclear weapon postures and infrastructures to evolve. The US and other nuclear states could not get to zero nor even reduce nuclear arms and the nuclear profile much further without learning to manage latent capability. This paper has defined three principles for designing NW infrastructure both at the 'next plateau' and 'near zero.' The US can be a leader in reducing weapons and infrastructure and in creating an international regime in which capability gradually substitutes for weapons in being and is transparent. The current 'strategy' of not having policy or a Congressionally-approved plan for transforming the weapons complex is not leadership. If we can conform the US infrastructure to the next plateau and architect it in such a way that it is aligned with further arms reductions, it will have these benefits: The extant stockpile can be reduced in size, while the smaller stockpile still deters attack on the US and Allies. The capabilities of the infrastructure will dissuade emergence of new challenges/threats; if they emerge, nevertheless, the US will be able to deal with them in time. We will begin to transform the way other major powers view their nuclear capability. Finally, and though of less cosmic importance, it will save money in the long run.« less

Generalized Nuclear Data: A New Structure (with Supporting Infrastructure) for Handling Nuclear Data

NASA Astrophysics Data System (ADS)

Mattoon, C. M.; Beck, B. R.; Patel, N. R.; Summers, N. C.; Hedstrom, G. W.; Brown, D. A.

2012-12-01

The Evaluated Nuclear Data File (ENDF) format was designed in the 1960s to accommodate neutron reaction data to support nuclear engineering applications in power, national security and criticality safety. Over the years, the scope of the format has been extended to handle many other kinds of data including charged particle, decay, atomic, photo-nuclear and thermal neutron scattering. Although ENDF has wide acceptance and support for many data types, its limited support for correlated particle emission, limited numeric precision, and general lack of extensibility mean that the nuclear data community cannot take advantage of many emerging opportunities. More generally, the ENDF format provides an unfriendly environment that makes it difficult for new data evaluators and users to create and access nuclear data. The Cross Section Evaluation Working Group (CSEWG) has begun the design of a new Generalized Nuclear Data (or 'GND') structure, meant to replace older formats with a hierarchy that mirrors the underlying physics, and is aligned with modern coding and database practices. In support of this new structure, Lawrence Livermore National Laboratory (LLNL) has updated its nuclear data/reactions management package Fudge to handle GND structured nuclear data. Fudge provides tools for converting both the latest ENDF format (ENDF-6) and the LLNL Evaluated Nuclear Data Library (ENDL) format to and from GND, as well as for visualizing, modifying and processing (i.e., converting evaluated nuclear data into a form more suitable to transport codes) GND structured nuclear data. GND defines the structure needed for storing nuclear data evaluations and the type of data that needs to be stored. But unlike ENDF and ENDL, GND does not define how the data are to be stored in a file. Currently, Fudge writes the structured GND data to a file using the eXtensible Markup Language (XML), as it is ASCII based and can be viewed with any text editor. XML is a meta-language, meaning that it has a primitive set of definitions for representing hierarchical data/text in a file. Other meta-languages, like HDF5 which stores the data in binary form, can also be used to store GND in a file. In this paper, we will present an overview of the new GND data structures along with associated tools in Fudge.

Modular structural elements in the replication origin region of Tetrahymena rDNA.

PubMed Central

Du, C; Sanzgiri, R P; Shaiu, W L; Choi, J K; Hou, Z; Benbow, R M; Dobbs, D L

1995-01-01

Computer analyses of the DNA replication origin region in the amplified rRNA genes of Tetrahymena thermophila identified a potential initiation zone in the 5'NTS [Dobbs, Shaiu and Benbow (1994), Nucleic Acids Res. 22, 2479-2489]. This region consists of a putative DNA unwinding element (DUE) aligned with predicted bent DNA segments, nuclear matrix or scaffold associated region (MAR/SAR) consensus sequences, and other common modular sequence elements previously shown to be clustered in eukaryotic chromosomal origin regions. In this study, two mung bean nuclease-hypersensitive sites in super-coiled plasmid DNA were localized within the major DUE-like element predicted by thermodynamic analyses. Three restriction fragments of the 5'NTS region predicted to contain bent DNA segments exhibited anomalous migration characteristic of bent DNA during electrophoresis on polyacrylamide gels. Restriction fragments containing the 5'NTS region bound Tetrahymena nuclear matrices in an in vitro binding assay, consistent with an association of the replication origin region with the nuclear matrix in vivo. The direct demonstration in a protozoan origin region of elements previously identified in Drosophila, chick and mammalian origin regions suggests that clusters of modular structural elements may be a conserved feature of eukaryotic chromosomal origins of replication. Images PMID:7784181

Deuteron NMR (Nuclear Magnetic Resonance) in relation to the glass transition in polymers

NASA Technical Reports Server (NTRS)

Roessler, E.; Sillescu, H.; Spiess, H. W.; Wallwitz, R.

1983-01-01

H-2NMR is introduced as a tool for investigating slow molecular motion in the glass transition region of amorphous polymers. In particular, we compare H-2 spin alignment echo spectra of chain deuterated polystyrene with model calculations for restricted rotational Brownian motion. Molecular motion in the polyztyrene-toluene system has been investigated by analyzing H-2NMR of partially deuterated polystyrene and toluene, respectively. The diluent mobility in the mixed glass has been decomposed into solid and liquid components where the respective average correlation times differ by more than 5 decades.

Tribal Colleges and Universitie/American Indian Higher Education Consortium Advanced Manufacturing Technical Assistance Project.

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

Atcitty, Stanley

The National Nuclear Security Agency (NNSA) created a Minority Serving Institution Partnership Plan (MSIPP) to 1) align investments in a university capacity and workforce development with the NNSA mission to develop the needed skills and talent for NNSA’s enduring technical workforce at the laboratories and production plants and 2) to enhance research and education at under-represented colleges and universities. Out of this effort, MSIPP launched a new program in early FY17 focused on Tribal Colleges and Universities (TCUs). The following report summarizes the project focus and status update during this reporting period.

Tribal Colleges and Universitie/American Indian Higher Education Consortium Advanced Manufacturing Technical Assistance Project

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

Atcitty, Stanley

The National Nuclear Security Agency (NNSA) created a Minority Serving Institution Partnership Plan (MSIPP) to 1) align investments in a university capacity and workforce development with the NNSA mission to develop the needed skills and talent for NNSA’s enduring technical workforce at the laboratories and production plants and 2) to enhance research and education at under-represented colleges and universities. Out of this effort, MSIPP launched a new program in early FY17 focused on Tribal Colleges and Universities (TCUs). The following report summarizes the project focus and status update during this reporting period.

Few mitochondrial DNA sequences are inserted into the turkey (Meleagris gallopavo) nuclear genome: evolutionary analyses and informativity in the domestic lineage.

PubMed

Schiavo, G; Strillacci, M G; Ribani, A; Bovo, S; Roman-Ponce, S I; Cerolini, S; Bertolini, F; Bagnato, A; Fontanesi, L

2018-06-01

Mitochondrial DNA (mtDNA) insertions have been detected in the nuclear genome of many eukaryotes. These sequences are pseudogenes originated by horizontal transfer of mtDNA fragments into the nuclear genome, producing nuclear DNA sequences of mitochondrial origin (numt). In this study we determined the frequency and distribution of mtDNA-originated pseudogenes in the turkey (Meleagris gallopavo) nuclear genome. The turkey reference genome (Turkey_2.01) was aligned with the reference linearized mtDNA sequence using last. A total of 32 numt sequences (corresponding to 18 numt regions derived by unique insertional events) were identified in the turkey nuclear genome (size ranging from 66 to 1415 bp; identity against the modern turkey mtDNA corresponding region ranging from 62% to 100%). Numts were distributed in nine chromosomes and in one scaffold. They derived from parts of 10 mtDNA protein-coding genes, ribosomal genes, the control region and 10 tRNA genes. Seven numt regions reported in the turkey genome were identified in orthologues positions in the Gallus gallus genome and therefore were present in the ancestral genome that in the Cretaceous originated the lineages of the modern crown Galliformes. Five recently integrated turkey numts were validated by PCR in 168 turkeys of six different domestic populations. None of the analysed numts were polymorphic (i.e. absence of the inserted sequence, as reported in numts of recent integration in other species), suggesting that the reticulate speciation model is not useful for explaining the origin of the domesticated turkey lineage. © 2018 Stichting International Foundation for Animal Genetics.

Orientational alignment in solids from bidimensional isotropic-anisotropic nuclear magnetic resonance spectroscopy: applications to the analysis of aramide fibers.

PubMed

Sachleben, J R; Frydman, L

1997-02-01

The use of two-dimensional isotropic-anisotropic correlation spectroscopy for the analysis of orientational alignment in solids is presented. The theoretical background and advantages of this natural-abundance 13C NMR method of measurement are discussed, and demonstrated with a series of powder and single-crystal variable-angle correlation spectroscopy (VACSY) experiments on model systems. The technique is subsequently employed to analyze the orientational distributions of three polymer fibers: Kevlar 29, Kevlar 49 and Kevlar 149. Using complementary two-dimensional NMR data recorded on synthetic samples of poly(p-phenyleneterephthalamide), the precursor of Kevlar, it was found that these commercial fibers possess molecules distributed over a very narrow orientational range with respect to the macroscopic director. The widths measured for these director distribution arrangements were (12 +/- 1.5) degrees for Kevlar 29, (15 +/- 1.5) degrees for Kevlar 49, and (8 +/- 1.5) degrees for Kevlar 149. These figures compare well with previous results obtained for non-commercial fiber samples derived from the same polymer.

Reactor shroud joint

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

Ballas, G.J.; Fife, A.B.; Ganz, I.

1998-04-07

A shroud for a nuclear reactor is described. In one embodiment, the shroud includes first and second shroud sections, and each shroud section includes a substantially cylindrical main body having a first end and a second end. With respect to each shroud section, a flange is located at the main body first end, and the flange has a plurality of bolt openings therein and a plurality of scalloped regions. The first shroud section is welded to the second shroud section, and at least some of the bolt openings in the first shroud section flange align with respective bolt openings inmore » the second shroud section flange. In the event that the onset of inter-granular stress corrosion cracking is ever detected in the weld between the shroud section, bolts are inserted through bolt openings in the first shroud section flange and through aligned bolt openings the second shroud section flange. Each bolt, in one embodiment, has a shank section and first and second threaded end sections. Nuts are threadedly engaged to the threaded end sections and tightened against the respective flanges. 4 figs.« less

Reactor shroud joint

DOEpatents

Ballas, G.J.; Fife, A.B.; Ganz, I.

1998-04-07

A shroud for a nuclear reactor is described. In one embodiment, the shroud includes first and second shroud sections, and each shroud section includes a substantially cylindrical main body having a first end and a second end. With respect to each shroud section, a flange is located at the main body first end, and the flange has a plurality of bolt openings therein and a plurality of scalloped regions. The first shroud section is welded to the second shroud section, and at least some of the bolt openings in the first shroud section flange align with respective bolt openings in the second shroud section flange. In the event that the onset of inter-granular stress corrosion cracking is ever detected in the weld between the shroud section, bolts are inserted through bolt openings in the first shroud section flange and through aligned bolt openings the second shroud section flange. Each bolt, in one embodiment, has a shank section and first and second threaded end sections. Nuts are threadedly engaged to the threaded end sections and tightened against the respective flanges. 4 figs.

Human retroviruses and AIDS 1996. A compilation and analysis of nucleic acid and amino acid sequences

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

Myers, G.; Foley, B.; Korber, B.

1997-04-01

This compendium and the accompanying floppy diskettes are the result of an effort to compile and rapidly publish all relevant molecular data concerning the human immunodeficiency viruses (HIV) and related retroviruses. The scope of the compendium and database is best summarized by the five parts that it comprises: (1) Nuclear Acid Alignments and Sequences; (2) Amino Acid Alignments; (3) Analysis; (4) Related Sequences; and (5) Database Communications. Information within all the parts is updated throughout the year on the Web site, http://hiv-web.lanl.gov. While this publication could take the form of a review or sequence monograph, it is not so conceived.more » Instead, the literature from which the database is derived has simply been summarized and some elementary computational analyses have been performed upon the data. Interpretation and commentary have been avoided insofar as possible so that the reader can form his or her own judgments concerning the complex information. In addition to the general descriptions of the parts of the compendium, the user should read the individual introductions for each part.« less

Wavelet analysis of poorly-focused ultrasonic signal of pressure tube inspection in nuclear industry

NASA Astrophysics Data System (ADS)

Zhao, Huan; Gachagan, Anthony; Dobie, Gordon; Lardner, Timothy

2018-04-01

Pressure tube fabrication and installment challenges combined with natural sagging over time can produce issues with probe alignment for pressure tube inspection of the primary circuit of CANDU reactors. The ability to extract accurate defect depth information from poorly focused ultrasonic signals would reduce additional inspection procedures, which leads to a significant time and cost saving. Currently, the defect depth measurement protocol is to simply calculate the time difference between the peaks of the echo signals from the tube surface and the defect from a single element probe focused at the back-wall depth. When alignment issues are present, incorrect focusing results in interference within the returning echo signal. This paper proposes a novel wavelet analysis method that employs the Haar wavelet to decompose the original poorly focused A-scan signal and reconstruct detailed information based on a selected high frequency component range within the bandwidth of the transducer. Compared to the original signal, the wavelet analysis method provides additional characteristic defect information and an improved estimate of defect depth with errors less than 5%.

YAP is essential for tissue tension to ensure vertebrate 3D body shape.

PubMed

Porazinski, Sean; Wang, Huijia; Asaoka, Yoichi; Behrndt, Martin; Miyamoto, Tatsuo; Morita, Hitoshi; Hata, Shoji; Sasaki, Takashi; Krens, S F Gabriel; Osada, Yumi; Asaka, Satoshi; Momoi, Akihiro; Linton, Sarah; Miesfeld, Joel B; Link, Brian A; Senga, Takeshi; Shimizu, Nobuyoshi; Nagase, Hideaki; Matsuura, Shinya; Bagby, Stefan; Kondoh, Hisato; Nishina, Hiroshi; Heisenberg, Carl-Philipp; Furutani-Seiki, Makoto

2015-05-14

Vertebrates have a unique 3D body shape in which correct tissue and organ shape and alignment are essential for function. For example, vision requires the lens to be centred in the eye cup which must in turn be correctly positioned in the head. Tissue morphogenesis depends on force generation, force transmission through the tissue, and response of tissues and extracellular matrix to force. Although a century ago D'Arcy Thompson postulated that terrestrial animal body shapes are conditioned by gravity, there has been no animal model directly demonstrating how the aforementioned mechano-morphogenetic processes are coordinated to generate a body shape that withstands gravity. Here we report a unique medaka fish (Oryzias latipes) mutant, hirame (hir), which is sensitive to deformation by gravity. hir embryos display a markedly flattened body caused by mutation of YAP, a nuclear executor of Hippo signalling that regulates organ size. We show that actomyosin-mediated tissue tension is reduced in hir embryos, leading to tissue flattening and tissue misalignment, both of which contribute to body flattening. By analysing YAP function in 3D spheroids of human cells, we identify the Rho GTPase activating protein ARHGAP18 as an effector of YAP in controlling tissue tension. Together, these findings reveal a previously unrecognised function of YAP in regulating tissue shape and alignment required for proper 3D body shape. Understanding this morphogenetic function of YAP could facilitate the use of embryonic stem cells to generate complex organs requiring correct alignment of multiple tissues.

Regulation of adipose-tissue-derived stromal cell orientation and motility in 2D- and 3D-cultures by direct-current electrical field.

PubMed

Yang, Gang; Long, Haiyan; Ren, Xiaomei; Ma, Kunlong; Xiao, Zhenghua; Wang, Ying; Guo, Yingqiang

2017-02-01

Cell alignment and motility play a critical role in a variety of cell behaviors, including cytoskeleton reorganization, membrane-protein relocation, nuclear gene expression, and extracellular matrix remodeling. Direct current electric field (EF) in vitro can direct many types of cells to align vertically to EF vector. In this work, we investigated the effects of EF stimulation on rat adipose-tissue-derived stromal cells (ADSCs) in 2D-culture on plastic culture dishes and in 3D-culture on various scaffold materials, including collagen hydrogels, chitosan hydrogels and poly(L-lactic acid)/gelatin electrospinning fibers. Rat ADSCs were exposed to various physiological-strength EFs in a homemade EF-bioreactor. Changes of morphology and movements of cells affected by applied EFs were evaluated by time-lapse microphotography, and cell survival rates and intracellular calcium oscillations were also detected. Results showed that EF facilitated ADSC morphological changes, under 6 V/cm EF strength, and that ADSCs in 2D-culture aligned vertically to EF vector and kept a good cell survival rate. In 3D-culture, cell galvanotaxis responses were subject to the synergistic effect of applied EF and scaffold materials. Fast cell movement and intracellular calcium activities were observed in the cells of 3D-culture. We believe our research will provide some experimental references for the future study in cell galvanotaxis behaviors. © 2017 Japanese Society of Developmental Biologists.

Distribution and morphology of cholinergic, putative catecholaminergic and serotonergic neurons in the brain of the Egyptian rousette flying fox, Rousettus aegyptiacus.

PubMed

Maseko, Busisiwe C; Bourne, James A; Manger, Paul R

2007-11-01

Over the past decade much controversy has surrounded the hypothesis that the megachiroptera, or megabats, share unique neural characteristics with the primates. These observations, which include similarities in visual pathways, have suggested that the megabats are more closely related to the primates than to the other group of the Chiropteran order, the microbats, and suggests a diphyletic origin of the Chiroptera. To contribute data relevant to this debate, we used immunohistochemical techniques to reveal the architecture of the neuromodulatory systems of the Egyptian rousette (Rousettus aegypticus), an echolocating megabat. Our findings revealed many similarities in the nuclear parcellation of the cholinergic, putative catecholaminergic and serotonergic systems with that seen in other mammals including the microbat. However, there were 11 discrete nuclei forming part of these systems in the brain of the megabat studied that were not evident in an earlier study of a microbat. The occurrence of these nuclei align the megabat studied more closely with primates than any other mammalian group and clearly distinguishes them from the microbat, which aligns with the insectivores. The neural systems investigated are not related to such Chiropteran specializations as echolocation, flight, vision or olfaction. If neural characteristics are considered strong indicators of phylogenetic relationships, then the data of the current study strongly supports the diphyletic origin of Chiroptera and aligns the megabat most closely with primates in agreement with studies of other neural characters.

Mission Analysis for Using Preventive Radiological/Nuclear Detection Equipment for Consequence Management

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

Buddemeier, Brooke R.; Wood-Zika, Annmarie R.; Haynes, Daniel

The overall objective of this project is to research, evaluate, and test first responder preventive radiological/nuclear detection (PRND) equipment to provide state and local agencies with scientific guidance on how to effectively use this equipment for response after a radiological/nuclear release or detonation. While the equipment being tested in this effort has been specifically designed by technology manufacturers and purchased by responders for preventive detection and source interdiction operations, the fleet of PRND equipment can help fill critical needs for radiological instrumentation should a consequence management (CM) response take place, as it is currently the most widely available and fieldedmore » radiological instrumentation by state and local agencies. This effort will provide scientific guidance on the most effective way to utilize this class of equipment for consequence management missions. Gaining a better understanding of how PRND equipment can operate and perform for these missions will allow for recommendations on the tactical approach responders can use for consequence management operations. PRND equipment has been placed into service by federal, state, and local agencies throughout the nation. If the equipment capability and limitations are taken into account, this large inventory can be leveraged to support the emergency response in the aftermath of a radiological or nuclear event. With several hundred makes and models of PRND equipment, often with significantly different detection capabilities that do not align with their nominal PRND equipment type, development of a streamlined categorization scheme with respect to consequence management missions was the first step to identifying safe and effective uses of PRND equipment for radiological/nuclear incident response.« less

Identification and qualification of 500 nuclear, single-copy, orthologous genes for the Eupulmonata (Gastropoda) using transcriptome sequencing and exon capture.

PubMed

Teasdale, Luisa C; Köhler, Frank; Murray, Kevin D; O'Hara, Tim; Moussalli, Adnan

2016-09-01

The qualification of orthology is a significant challenge when developing large, multiloci phylogenetic data sets from assembled transcripts. Transcriptome assemblies have various attributes, such as fragmentation, frameshifts and mis-indexing, which pose problems to automated methods of orthology assessment. Here, we identify a set of orthologous single-copy genes from transcriptome assemblies for the land snails and slugs (Eupulmonata) using a thorough approach to orthology determination involving manual alignment curation, gene tree assessment and sequencing from genomic DNA. We qualified the orthology of 500 nuclear, protein-coding genes from the transcriptome assemblies of 21 eupulmonate species to produce the most complete phylogenetic data matrix for a major molluscan lineage to date, both in terms of taxon and character completeness. Exon capture targeting 490 of the 500 genes (those with at least one exon >120 bp) from 22 species of Australian Camaenidae successfully captured sequences of 2825 exons (representing all targeted genes), with only a 3.7% reduction in the data matrix due to the presence of putative paralogs or pseudogenes. The automated pipeline Agalma retrieved the majority of the manually qualified 500 single-copy gene set and identified a further 375 putative single-copy genes, although it failed to account for fragmented transcripts resulting in lower data matrix completeness when considering the original 500 genes. This could potentially explain the minor inconsistencies we observed in the supported topologies for the 21 eupulmonate species between the manually curated and 'Agalma-equivalent' data set (sharing 458 genes). Overall, our study confirms the utility of the 500 gene set to resolve phylogenetic relationships at a range of evolutionary depths and highlights the importance of addressing fragmentation at the homolog alignment stage for probe design. © 2016 John Wiley & Sons Ltd.

Chromosome painting reveals asynaptic full alignment of homologs and HIM-8-dependent remodeling of X chromosome territories during Caenorhabditis elegans meiosis.

PubMed

Nabeshima, Kentaro; Mlynarczyk-Evans, Susanna; Villeneuve, Anne M

2011-08-01

During early meiotic prophase, a nucleus-wide reorganization leads to sorting of chromosomes into homologous pairs and to establishing associations between homologous chromosomes along their entire lengths. Here, we investigate global features of chromosome organization during this process, using a chromosome painting method in whole-mount Caenorhabditis elegans gonads that enables visualization of whole chromosomes along their entire lengths in the context of preserved 3D nuclear architecture. First, we show that neither spatial proximity of premeiotic chromosome territories nor chromosome-specific timing is a major factor driving homolog pairing. Second, we show that synaptonemal complex-independent associations can support full lengthwise juxtaposition of homologous chromosomes. Third, we reveal a prominent elongation of chromosome territories during meiotic prophase that initiates prior to homolog association and alignment. Mutant analysis indicates that chromosome movement mediated by association of chromosome pairing centers (PCs) with mobile patches of the nuclear envelope (NE)-spanning SUN-1/ZYG-12 protein complexes is not the primary driver of territory elongation. Moreover, we identify new roles for the X chromosome PC (X-PC) and X-PC binding protein HIM-8 in promoting elongation of X chromosome territories, separable from their role(s) in mediating local stabilization of pairing and association of X chromosomes with mobile SUN-1/ZYG-12 patches. Further, we present evidence that HIM-8 functions both at and outside of PCs to mediate chromosome territory elongation. These and other data support a model in which synapsis-independent elongation of chromosome territories, driven by PC binding proteins, enables lengthwise juxtaposition of chromosomes, thereby facilitating assessment of their suitability as potential pairing partners.

Chromosome Painting Reveals Asynaptic Full Alignment of Homologs and HIM-8–Dependent Remodeling of X Chromosome Territories during Caenorhabditis elegans Meiosis

PubMed Central

Nabeshima, Kentaro; Mlynarczyk-Evans, Susanna; Villeneuve, Anne M.

2011-01-01

During early meiotic prophase, a nucleus-wide reorganization leads to sorting of chromosomes into homologous pairs and to establishing associations between homologous chromosomes along their entire lengths. Here, we investigate global features of chromosome organization during this process, using a chromosome painting method in whole-mount Caenorhabditis elegans gonads that enables visualization of whole chromosomes along their entire lengths in the context of preserved 3D nuclear architecture. First, we show that neither spatial proximity of premeiotic chromosome territories nor chromosome-specific timing is a major factor driving homolog pairing. Second, we show that synaptonemal complex-independent associations can support full lengthwise juxtaposition of homologous chromosomes. Third, we reveal a prominent elongation of chromosome territories during meiotic prophase that initiates prior to homolog association and alignment. Mutant analysis indicates that chromosome movement mediated by association of chromosome pairing centers (PCs) with mobile patches of the nuclear envelope (NE)–spanning SUN-1/ZYG-12 protein complexes is not the primary driver of territory elongation. Moreover, we identify new roles for the X chromosome PC (X-PC) and X-PC binding protein HIM-8 in promoting elongation of X chromosome territories, separable from their role(s) in mediating local stabilization of pairing and association of X chromosomes with mobile SUN-1/ZYG-12 patches. Further, we present evidence that HIM-8 functions both at and outside of PCs to mediate chromosome territory elongation. These and other data support a model in which synapsis-independent elongation of chromosome territories, driven by PC binding proteins, enables lengthwise juxtaposition of chromosomes, thereby facilitating assessment of their suitability as potential pairing partners. PMID:21876678

Tutorial: Neural networks and their potential application in nuclear power plants

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

Uhrig, R.E.

A neural network is a data processing system consisting of a number of simple, highly interconnected processing elements in an architecture inspired by the structure of the cerebral cortex portion of the brain. Hence, neural networks are often capable of doing things which humans or animals do well but which conventional computers often do poorly. Neural networks have emerged in the past few years as an area of unusual opportunity for research, development and application to a variety of real world problems. Indeed, neural networks exhibit characteristics and capabilities not provided by any other technology. Examples include reading Japanese Kanjimore » characters and human handwriting, reading a typewritten manuscript aloud, compensating for alignment errors in robots, interpreting very noise'' signals (e.g. electroencephalograms), modeling complex systems that cannot be modelled mathematically, and predicting whether proposed loans will be good or fail. This paper presents a brief tutorial on neural networks and describes research on the potential applications to nuclear power plants.« less

High-order-harmonic generation from H2+ molecular ions near plasmon-enhanced laser fields

NASA Astrophysics Data System (ADS)

Yavuz, I.; Tikman, Y.; Altun, Z.

2015-08-01

Simulations of plasmon-enhanced high-order-harmonic generation are performed for a H2+ molecular cation near the metallic nanostructures. We employ the numerical solution of the time-dependent Schrödinger equation in reduced coordinates. We assume that the main axis of H2+ is aligned perfectly with the polarization direction of the plasmon-enhanced field. We perform systematic calculations on plasmon-enhanced harmonic generation based on an infinite-mass approximation, i.e., pausing nuclear vibrations. Our simulations show that molecular high-order-harmonic generation from plasmon-enhanced laser fields is possible. We observe the dispersion of a plateau of harmonics when the laser field is plasmon enhanced. We find that the maximum kinetic energy of the returning electron follows 4 Up . We also find that when nuclear vibrations are enabled, the efficiency of the harmonics is greatly enhanced relative to that of static nuclei. However, the maximum kinetic energy 4 Up is largely maintained.

A study of small impact parameter ion channeling effects in thin crystals

NASA Astrophysics Data System (ADS)

Motapothula, Mallikarjuna Rao; Breese, Mark B. H.

2018-03-01

We have recorded channeling patterns produced by 1-2 MeV protons aligned with ⟨1 1 1⟩ axes in 55 nm thick silicon crystals which exhibit characteristic angular structure for deflection angles up to and beyond the axial critical angle, ψ a . Such large angular deflections are produced by ions incident on atomic strings with small impact parameters, resulting in trajectories which pass through several radial rings of atomic strings before exiting the thin crystal. Each ring may focus, steer or scatter the channeled ions in the transverse direction and the resulting characteristic angular structure beyond 0.6 ψ a at different depths can be related to peaks and troughs in the nuclear encounter probability. Such "radial focusing" underlies other axial channeling phenomena in thin crystals including planar channeling of small impact parameter trajectories, peaks around the azimuthal distribution at small tilts and large shoulders in the nuclear encounter probability at tilts beyond ψ a .

Peptide backbone orientation and dynamics in spider dragline silk and two-photon excitation in nuclear magnetic and quadrupole resonance

NASA Astrophysics Data System (ADS)

Eles, Philip Thomas

2005-07-01

In the first part of the dissertation, spider dragline silk is studied by solid state NMR techniques. The dependence of NMR frequency on molecular orientation is exploited using the DECODER experiment to determine the orientation of the protein backbone within the silk fibre. Practical experimental considerations require that the silk fibres be wound about a cylindrical axis perpendicular to the external magnetic field, complicating the reconstruction of the underlying orientation distribution and necess-itating the development of numerical techniques for this purpose. A two-component model of silk incorporating static b-sheets and polyglycine II helices adequately fits the NMR data and suggests that the b-sheets are well aligned along the silk axis (20 FWHM) while the helices are poorly aligned (68 FWHM). The effects of fibre strain, draw rate and hydration on orientation are measured. Measurements of the time-scale for peptide backbone motion indicate that when wet, a strain-dependent frac-tion of the poorly aligned component becomes mobile. This suggests a mechanism for the supercontraction of silk involving latent entropic springs that undergo a local strain-dependent phase transition, driving supercontraction. In the second part of this dissertation a novel method is developed for exciting NMR and nuclear quadrupole resonance (NQR) by rf irradiation at multiple frequencies that sum to (or differ by) the resonance frequency. This is fundamentally different than traditional NMR experiments where irradiation is applied on-resonance. With excitation outside the detection bandwidth, two-photon excitation allows for detection of free induction signals during excitation, completely eliminating receiver dead-time. A theoretical approach to describing two-photon excitation is developed based on average Hamiltonian theory. An intuition for two-photon excitation is gained by analogy to the coherent absorption of multiple photons requiring conservation of total energy and momentum. It is shown that two-photon excitation efficiency impro-ves when the two applied rf frequencies deviate from half-resonance. For two-photon NQR, it is shown that observable magnetization appears perpendicular to the excita-tion coil, requiring a second coil for detection, and that double quantum coherences are also generated. Several model systems and experimental geometries are used to demonstrate the peculiarities of two-photon excitation in NMR and NQR.

Hydraulic balancing of a control component within a nuclear reactor

DOEpatents

Marinos, D.; Ripfel, H.C.F.

1975-10-14

A reactor control component includes an inner conduit, for instance containing neutron absorber elements, adapted for longitudinal movement within an outer guide duct. A transverse partition partially encloses one end of the conduit and meets a transverse wall within the guide duct when the conduit is fully inserted into the reactor core. A tube piece extends from the transverse partition and is coaxially aligned to be received within a tubular receptacle which extends from the transverse wall. The tube piece and receptacle cooperate in engagement to restrict the flow and pressure of coolant beneath the transverse partition and thereby minimize upward forces tending to expel the inner conduit.

Relativistic fluid dynamics with spin

NASA Astrophysics Data System (ADS)

Florkowski, Wojciech; Friman, Bengt; Jaiswal, Amaresh; Speranza, Enrico

2018-04-01

Using the conservation laws for charge, energy, momentum, and angular momentum, we derive hydrodynamic equations for the charge density, local temperature, and fluid velocity, as well as for the polarization tensor, starting from local equilibrium distribution functions for particles and antiparticles with spin 1/2. The resulting set of differential equations extends the standard picture of perfect-fluid hydrodynamics with a conserved entropy current in a minimal way. This framework can be used in space-time analyses of the evolution of spin and polarization in various physical systems including high-energy nuclear collisions. We demonstrate that a stationary vortex, which exhibits vorticity-spin alignment, corresponds to a special solution of the spin-hydrodynamical equations.

The effect of static magnetic fields and tat peptides on cellular and nuclear uptake of magnetic nanoparticles.

PubMed

Smith, Carol-Anne M; de la Fuente, Jesus; Pelaz, Beatriz; Furlani, Edward P; Mullin, Margaret; Berry, Catherine C

2010-05-01

Magnetic nanoparticles are widely used in bioapplications such as imaging (MRI), targeted delivery (drugs/genes) and cell transfection (magnetofection). Historically, the impermeable nature of both the plasma and nuclear membranes hinder potential. Researchers combat this by developing techniques to enhance cellular and nuclear uptake. Two current popular methods are using external magnetic fields to remotely control particle direction or functionalising the nanoparticles with a cell penetrating peptide (e.g. tat); both of which facilitate cell entry. This paper compares the success of both methods in terms of nanoparticle uptake, analysing the type of magnetic forces the particles experience, and determines gross cell response in terms of morphology and structure and changes at the gene level via microarray analysis. Results indicated that both methods enhanced uptake via a caveolin dependent manner, with tat peptide being the more efficient and achieving nuclear uptake. On comparison to control cells, many groups of gene changes were observed in response to the particles. Importantly, the magnetic field also caused many change in gene expression, regardless of the nanoparticles, and appeared to cause F-actin alignment in the cells. Results suggest that static fields should be modelled and analysed prior to application in culture as cells clearly respond appropriately. Furthermore, the use of cell penetrating peptides may prove more beneficial in terms of enhancing uptake and maintaining cell homeostasis than a magnetic field. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Identifying Functional Neighborhoods within the Cell Nucleus: Proximity Analysis of Early S-Phase Replicating Chromatin Domains to Sites of Transcription, RNA Polymerase II, HP1γ, Matrin 3 and SAF-A

PubMed Central

Malyavantham, Kishore S; Bhattacharya, Sambit; Barbeitos, Marcos; Mukherjee, Lopamudra; Xu, Jinhui; Fackelmayer, Frank O; Berezney, Ronald

2009-01-01

Higher order chromatin organization in concert with epigenetic regulation is a key process that determines gene expression at the global level. The organization of dynamic chromatin domains and their associated protein factors is intertwined with nuclear function to create higher levels of functional zones within the cell nucleus. As a step towards elucidating the organization and dynamics of these functional zones, we have investigated the spatial proximities among a constellation of functionally related sites that are found within euchromatic regions of the cell nucleus including: HP1γ, nascent transcript sites (TS), active DNA replicating sites in early S phase (PCNA) and RNA polymerase II sites. We report close associations among these different sites with proximity values specific for each combination. Analysis of matrin 3 and SAF-A sites demonstrates that these nuclear matrix proteins are highly proximal with the functionally related sites as well as to each other and display closely aligned and overlapping regions following application of the minimal spanning tree (MST) algorithm to visualize higher order network-like patterns. Our findings suggest that multiple factors within the nuclear microenvironment collectively form higher order combinatorial arrays of function. We propose a model for the organization of these functional neighborhoods which takes into account the proximity values of the individual sites and their spatial organization within the nuclear architecture. PMID:18618731

Nuclear structure research at the Triangle Universities Nuclear Laboratory

NASA Astrophysics Data System (ADS)

Mitchell, G. E.

1992-10-01

Studies of fundamental symmetries by the TRIPLE collaboration using the unique capabilities at LAMTF have found unexpected systematics in the parity-violating amplitudes for epithermal-neutron scattering. Tests to lower the present limits on time-reversal-invariance violation in the strong interaction are being made at in experiments on the scattering of polarized fast neutrons from aligned holmium targets. Studies of few-nucleon systems have received increasing emphasis over the past year, involving a broad program for testing the low- to medium-energy internucleon interactions, from the tensor component in n-p scattering and the n-n scattering lengths, through three-nucleon systems and the alpha particle, on up to Be-8. Of particular interest are three-nucleon systems, both in elastic scattering and in three-body breakup. Beam requirements range from production of intense and highly-polarized neutron beams to tensor-polarized beams for measurements at both very low energies (25-80 keV) and at tandem energies for definitive measurements of D-state components of the triton, He-3, and He-4 obtained from transfer reactions. The program in nuclear astrophysics expanded during 1991-1992. Several facets of the nuclear many-body problem and of excitation mechanisms of the nucleus are being elucidated, including measurements and analyses to elucidate the neutron-nucleus elastic-scattering interaction over a wide range of nuclei and energies. Several projects involved developments in electronuclear physics, instrumentation, RF-transition units, and low-temperature bolometric particle detectors.

Nuclear genomes distinguish cryptic species suggested by their DNA barcodes and ecology

PubMed Central

Janzen, Daniel H.; Burns, John M.; Cong, Qian; Hallwachs, Winnie; Dapkey, Tanya; Manjunath, Ramya; Hajibabaei, Mehrdad; Hebert, Paul D. N.; Grishin, Nick V.

2017-01-01

DNA sequencing brings another dimension to exploration of biodiversity, and large-scale mitochondrial DNA cytochrome oxidase I barcoding has exposed many potential new cryptic species. Here, we add complete nuclear genome sequencing to DNA barcoding, ecological distribution, natural history, and subtleties of adult color pattern and size to show that a widespread neotropical skipper butterfly known as Udranomia kikkawai (Weeks) comprises three different species in Costa Rica. Full-length barcodes obtained from all three century-old Venezuelan syntypes of U. kikkawai show that it is a rainforest species occurring from Costa Rica to Brazil. The two new species are Udranomia sallydaleyae Burns, a dry forest denizen occurring from Costa Rica to Mexico, and Udranomia tomdaleyi Burns, which occupies the junction between the rainforest and dry forest and currently is known only from Costa Rica. Whereas the three species are cryptic, differing but slightly in appearance, their complete nuclear genomes totaling 15 million aligned positions reveal significant differences consistent with their 0.00065-Mbp (million base pair) mitochondrial barcodes and their ecological diversification. DNA barcoding of tropical insects reared by a massive inventory suggests that the presence of cryptic species is a widespread phenomenon and that further studies will substantially increase current estimates of insect species richness. PMID:28716927

(1)H-(13)C Hetero-nuclear dipole-dipole couplings of methyl groups in stationary and magic angle spinning solid-state NMR experiments of peptides and proteins.

PubMed

Wu, Chin H; Das, Bibhuti B; Opella, Stanley J

2010-02-01

(13)C NMR of isotopically labeled methyl groups has the potential to combine spectroscopic simplicity with ease of labeling for protein NMR studies. However, in most high resolution separated local field experiments, such as polarization inversion spin exchange at the magic angle (PISEMA), that are used to measure (1)H-(13)C hetero-nuclear dipolar couplings, the four-spin system of the methyl group presents complications. In this study, the properties of the (1)H-(13)C hetero-nuclear dipolar interactions of (13)C-labeled methyl groups are revealed through solid-state NMR experiments on a range of samples, including single crystals, stationary powders, and magic angle spinning of powders, of (13)C(3) labeled alanine alone and incorporated into a protein. The spectral simplifications resulting from proton detected local field (PDLF) experiments are shown to enhance resolution and simplify the interpretation of results on single crystals, magnetically aligned samples, and powders. The complementarity of stationary sample and magic angle spinning (MAS) measurements of dipolar couplings is demonstrated by applying polarization inversion spin exchange at the magic angle and magic angle spinning (PISEMAMAS) to unoriented samples. Copyright 2009 Elsevier Inc. All rights reserved.

Cellular Mechanosensing: Getting to the nucleus of it all

PubMed Central

Fedorchak, Gregory R.; Kaminski, Ashley; Lammerding, Jan

2014-01-01

Cells respond to mechanical forces by activating specific genes and signaling pathways that allow the cells to adapt to their physical environment. Examples include muscle growth in response to exercise, bone remodeling based on their mechanical load, or endothelial cells aligning under fluid shear stress. While the involved downstream signaling pathways and mechanoresponsive genes are generally well characterized, many of the molecular mechanisms of the initiating ‘mechanosensing’ remain still elusive. In this review, we discuss recent findings and accumulating evidence suggesting that the cell nucleus plays a crucial role in cellular mechanotransduction, including processing incoming mechanoresponsive signals and even directly responding to mechanical forces. Consequently, mutations in the involved proteins or changes in nuclear envelope composition can directly impact mechanotransduction signaling and contribute to the development and progression of a variety of human diseases, including muscular dystrophy, cancer, and the focus of this review, dilated cardiomyopathy. Improved insights into the molecular mechanisms underlying nuclear mechanotransduction, brought in part by the emergence of new technologies to study intracellular mechanics at high spatial and temporal resolution, will not only result in a better understanding of cellular mechanosensing in normal cells but may also lead to the development of novel therapies in the many diseases linked to defects in nuclear envelope proteins. PMID:25008017

Management and non-supervisory perceptions surrounding the implementation and significance of high-performance work practices in a nuclear power plant

NASA Astrophysics Data System (ADS)

Ashbridge, Gayle Ann

Change management has become an imperative for organizations as they move into the 21st century; up to 75 percent of change initiatives fail. Nuclear power plants face the same challenges as industrial firms with the added challenge of deregulation. Faced with this challenge, restructuring the electric utility has raised a number of complex issues. Under traditional cost-of-service regulation, electric utilities were able to pass on their costs to consumers who absorbed them. In the new competitive environment, customers will now choose their suppliers based on the most competitive price. The purpose of this study is to determine the degree of congruence between non-supervisory and supervisory personnel regarding the perceived implementation of high performance workplace practices at a nuclear power plant. This study used as its foundation the practices identified in the Road to High Performance Workplaces: A Guide to Better Jobs and Better Business Results by the U.S. Department of Labor's Office of the American Workplace (1994). The population for this study consisted of organizational members at one nuclear power plant. Over 300 individuals completed surveys on high performance workplace practices. Two surveys were administered, one to non-supervisory personnel and one to first line supervisors and above. The determination of implementation levels was accomplished through descriptive statistical analysis. Results of the study revealed 32 areas of noncongruence between non-supervisory and supervisory personnel in regard to the perceived implementation level of the high performance workplace practices. Factor analysis further revealed that the order in which the respondents place emphasis on the variables varies between the two groups. This study provides recommendations that may improve the nuclear power plants alignment of activities. Recommendations are also provided for additional research on high-performance work practices.

r-Process nucleosynthesis from three-dimensional jet-driven core-collapse supernovae with magnetic misalignments

NASA Astrophysics Data System (ADS)

Halevi, Goni; Mösta, Philipp

2018-06-01

We investigate r-process nucleosynthesis in three-dimensional general relativistic magnetohydrodynamic simulations of jet-driven supernovae resulting from rapidly rotating, strongly magnetized core-collapse. We explore the effect of misaligning the pre-collapse magnetic field with respect to the rotation axis by performing four simulations: one aligned model and models with 15°, 30°, and 45° misalignments. The simulations we present employ a microphysical finite-temperature equation of state and a leakage scheme that captures the overall energetics and lepton number exchange due to post-bounce neutrino emission and absorption. We track the thermodynamic properties of the ejected material with Lagrangian tracer particles and analyse its composition with the nuclear reaction network SKYNET. By using different neutrino luminosities in post-processing the tracer data with SKYNET, we constrain the impact of uncertainties in neutrino luminosities. We find that, for the aligned model considered here, the use of an approximate leakage scheme results in neutrino luminosity uncertainties corresponding to a factor of 100-1000 uncertainty in the abundance of third peak r-process elements. Our results show that for misalignments of 30° or less, r-process elements are robustly produced as long as neutrino luminosities are reasonably low (≲ 5 × 1052 erg s-1). For a more extreme misalignment of 45°, we find the production of r-process elements beyond the second peak significantly reduced. We conclude that robust r-process nucleosynthesis in magnetorotational supernovae requires a progenitor stellar core with a large poloidal magnetic field component that is at least moderately (within ˜30°) aligned with the rotation axis.

Study of Image Quality From CT Scanner Multi-Detector by using Americans College of Radiology (ACR) Phantom

NASA Astrophysics Data System (ADS)

Mulyadin; Dewang, Syamsir; Abdullah, Bualkar; Tahir, Dahlang

2018-03-01

In this study, the image quality of CT scan using phantom American College of Radiology (ACR) was determined. Scanning multidetector CT is used to know the image quality parameters by using a solid phantom containing four modules and primarily from materials that are equivalent to water. Each module is 4 cm in diameter and 20 cm in diameter. There is white alignment marks painted white to reflect the alignment laser and there are also “HEAD”, “FOOT”, and “TOP” marks on the phantom to help align. This test obtains CT images of each module according to the routine inspection protocol of the head. Acceptance of image quality obtained for determination: CT Number Accuracy (CTN), CT Number Uniformity and Noise, Linearity CT Number, Slice Technique, Low Contrast Resolution and High Contrast Resolution represent image quality parameters. In testing CT Number Accuracy (CTN), CT Uniform number and Noise are in the range of tolerable values allowed. In the test, Linearity CT Number obtained correlation value above 0.99 is the relationship between electron density and CT Number. In a low contrast resolution test, the smallest contrast groups are visible. In contrast, the high resolution is seen up to 7 lp/cm. The quality of GE CT Scan is very high, as all the image quality tests obtained are within the tolerance brackets of values permitted by the Nuclear Power Control Agency (BAPETEN). Image quality test is a way to get very important information about the accuracy of snoring result by using phantom ACR.

Science and Technology Review October/November 2009

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

Bearinger, J P

2009-08-21

This month's issue has the following articles: (1) Award-Winning Collaborations Provide Solutions--Commentary by Steven D. Liedle; (2) Light-Speed Spectral Analysis of a Laser Pulse--An optical device inspects and stops potentially damaging laser pulses; (3) Capturing Waveforms in a Quadrillionth of a Second--The femtoscope, a time microscope, improves the temporal resolution and dynamic range of conventional recording instruments; (4) Gamma-Ray Spectroscopy in the Palm of Your Hand--A miniature gamma-ray spectrometer provides increased resolution at a reduced cost; (5) Building Fusion Targets with Precision Robotics--A robotic system assembles tiny fusion targets with nanometer precision; (6) ROSE: Making Compiler Technology More Accessible--An open-sourcemore » software infrastructure makes powerful compiler techniques available to all programmers; (7) Restoring Sight to the Blind with an Artificial Retina--A retinal prosthesis could restore vision to people suffering from eye diseases; (8) Eradicating the Aftermath of War--A remotely operated system precisely locates buried land mines; (9) Compact Alignment for Diagnostic Laser Beams--A smaller, less expensive device aligns diagnostic laser beams onto targets; and (10) Securing Radiological Sources in Africa--Livermore and other national laboratories are helping African countries secure their nuclear materials.« less

Natural convection heat transfer for a staggered array of heated, horizontal cylinders within a rectangular enclosure

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

Triplett, C.E.

1996-12-01

This thesis presents the results of an experimental investigation of natural convection heat transfer in a staggered array of heated cylinders, oriented horizontally within a rectangular enclosure. The main purpose of this research was to extend the knowledge of heat transfer within enclosed bundles of spent nuclear fuel rods sealed within a shipping or storage container. This research extends Canaan`s investigation of an aligned array of heated cylinders that thermally simulated a boiling water reactor (BWR) spent fuel assembly sealed within a shipping or storage cask. The results are presented in terms of piecewise Nusselt-Rayleigh number correlations of the formmore » Nu = C(Ra){sup n}, where C and n are constants. Correlations are presented both for individual rods within the array and for the array as a whole. The correlations are based only on the convective component of the heat transfer. The radiative component was calculated with a finite-element code that used measured surface temperatures, rod array geometry, and measured surface emissivities as inputs. The correlation results are compared to Canaan`s aligned array results and to other studies of natural convection in horizontal tube arrays.« less

Construction, characterization, and environmental testing of a Laue lens prototype using Fe and Al crystals

NASA Astrophysics Data System (ADS)

Wade, C.; Barrière, N. M.; Tomsick, J. A.; Hanlon, L.; Boggs, S. E.; Lowell, A.; von Ballmoos, P.; Massahi, S.

2018-07-01

Laue lenses use Bragg diffraction to concentrate soft γ-rays onto a detector. This decoupling of the collecting area from the detector volume can generate a significant increase in sensitivity for applications in astrophysics and nuclear medicine. A demonstrator lens was constructed at the UC Berkeley's Space Sciences Laboratory in 2014 by gluing 48 Fe and Al diffracting crystals to an aluminium substrate. The goal was to demonstrate a fast and accurate assembly technique that is compatible with the large number of crystals required to fabricate a Laue lens telescope for astronomical observations. We present here the lens design, the assembly technique we used, and the results of measurements of the angular misalignments before and after curing of the glue and during environmental testing (thermal, vacuum, and vibration). We conclude that our alignment technique is fast enough to assemble a full lens made of several thousand crystals. The achieved alignment accuracy had an average of 32.7‧‧ and a standard deviation of 44.1‧‧. The accuracy could be improved by using an alternative glue or by having better control over the asymmetry angle resulting from the crystal cut.

Spatially resolved elemental distributions in articular cartilage

NASA Astrophysics Data System (ADS)

Reinert, T.; Reibetanz, U.; Vogt, J.; Butz, T.; Werner, A.; Gründer, W.

2001-07-01

In this study, the nuclear microprobe technique is employed to analyse the chemistry of joint cartilage in order to correlate internal structures of the collagen network with the elemental distribution. The samples were taken from pig's knee joint. 30 μm thick coronar cross-sections were prepared by means of cryosectioning and freeze-drying. We performed simultaneously particle induced X-ray emission (PIXE), Rutherford backscattering spectrometry (RBS) and elastic recoil detection analysis (ERDA). Thus we obtained spatially resolved distributions of the elements H, C, N, O, P, S, Cl, K and Ca. The main components of the organic matrix are H, C, N and O. It was shown that their relations vary with the cartilage structures. It could be shown that zones with aligned collagen fibrils contain less sulphur and potassium but more chlorine. The higher chlorine concentration is remarkable because newest biochemical studies found that hypochloric acid is involved in cartilage degradation. Furthermore, the calcium distribution is still of great interest. Its correlation to structural changes inside the cartilage is still being discussed. It could be disproved that zones of higher calcium concentration are related to the aligned structures of the collagen network.

Twenty-Five Year Site Plan FY2013 - FY2037

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

Jones, William H.

2012-07-12

Los Alamos National Laboratory (the Laboratory) is the nation's premier national security science laboratory. Its mission is to develop and apply science and technology to ensure the safety, security, and reliability of the United States (U.S.) nuclear stockpile; reduce the threat of weapons of mass destruction, proliferation, and terrorism; and solve national problems in defense, energy, and the environment. The fiscal year (FY) 2013-2037 Twenty-Five Year Site Plan (TYSP) is a vital component for planning to meet the National Nuclear Security Administration (NNSA) commitment to ensure the U.S. has a safe, secure, and reliable nuclear deterrent. The Laboratory also usesmore » the TYSP as an integrated planning tool to guide development of an efficient and responsive infrastructure that effectively supports the Laboratory's missions and workforce. Emphasizing the Laboratory's core capabilities, this TYSP reflects the Laboratory's role as a prominent contributor to NNSA missions through its programs and campaigns. The Laboratory is aligned with Nuclear Security Enterprise (NSE) modernization activities outlined in the NNSA Strategic Plan (May 2011) which include: (1) ensuring laboratory plutonium space effectively supports pit manufacturing and enterprise-wide special nuclear materials consolidation; (2) constructing the Chemistry and Metallurgy Research Replacement Nuclear Facility (CMRR-NF); (3) establishing shared user facilities to more cost effectively manage high-value, experimental, computational and production capabilities; and (4) modernizing enduring facilities while reducing the excess facility footprint. Th is TYSP is viewed by the Laboratory as a vital planning tool to develop an effi cient and responsive infrastructure. Long range facility and infrastructure development planning are critical to assure sustainment and modernization. Out-year re-investment is essential for sustaining existing facilities, and will be re-evaluated on an annual basis. At the same time, major modernization projects will require new line-item funding. This document is, in essence, a roadmap that defines a path forward for the Laboratory to modernize, streamline, consolidate, and sustain its infrastructure to meet its national security mission.« less

Host Galaxies, Obscuration, and Nuclear Structure of Three Nearby Compact Symmetric Objects

NASA Astrophysics Data System (ADS)

Perlman, Eric S.; Stocke, John T.; Conway, John; Reynolds, Chris

2001-08-01

We present three-band Hubble Space Telescope imaging of three nearby (z<=0.1) compact symmetric objects: 4C 31.04, 1946+708, and 1146+596. These objects were chosen on the basis of proximity to Earth as well as H I 21 cm line absorption. The inner H-band isophotes of these galaxies are well fitted by Nuker models, typical of nearby elliptical galaxies. Each shows a significant flattening in the isophotal profile at radii ~0.5", as well as significant variations in ellipticity and P.A. However, as previous authors have noted, neither is uncommon for elliptical galaxies. All three objects show modest departures from Nuker law models at radii of 1-5 h-160 kpc. Each galaxy shows large well-distributed dust features, which are somewhat concentrated in the nuclear regions in features that resemble disks or tori. We find that the amount of dust in these galaxies is about 10 times higher than normal for elliptical galaxies and radio galaxy hosts. The major axes of the nuclear dust disks tend to be oriented roughly perpendicular to the radio axis. One galaxy, 4C 31.04, exhibits bright nuclear regions well aligned with the radio axis, while another, 1146+596, shows a significant near-IR excess resembling a stellar bar along its dust disk. The combination of outwardly normal isophotal profiles with significant variations in P.A. and ellipticity is consistent with the host galaxies being relatively recent merger remnants and the mergers having occurred >~108 yr ago. Such a merger could have ``triggered'' the onset of the current active phase seen in these objects, but our data require a significant time delay between the merger event and the onset of nuclear activity. However, these data are also consistent with the hypothesis that the onset of nuclear activity in radio galaxies is due to relatively minor ``feeding'' events and/or the formation of ``bars within bars,'' events which would disturb the internal kinematics only slightly.

Trails of Kilovolt Ions Created by Subsurface Channeling

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

Redinger, Alex; Standop, Sebastian; Michely, Thomas

2010-02-19

Using scanning tunneling microscopy, we observe the damage trails produced by keV noble-gas ions incident at glancing angles onto Pt(111). Surface vacancies and adatoms aligned along the ion trajectory constitute the ion trails. Atomistic simulations reveal that these straight trails are produced by nuclear (elastic) collisions with surface layer atoms during subsurface channeling of the projectiles. In a small energy window around 5 keV, Xe{sup +} ions create vacancy grooves that mark the ion trajectory with atomic precision. The asymmetry of the adatom production on the two sides of the projectile path is traced back to the asymmetry of themore » ion's subsurface channel.« less

2013 SRNL LDRD Annual Report

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

McWhorter, S.

2014-03-07

This report demonstrates the execution of our LDRD program within the objectives and guidelines outlined by the Department of Energy (DOE) through the DOE Order 413.2b. The projects described within the report align purposefully with SRNL’s strategic vision and provide great value to the DOE. The diversity exhibited in the research and development projects underscores the DOE Office of Environmental Management (DOE-EM) mission and enhances that mission by developing the technical capabilities and human capital necessary to support future DOE-EM national needs. As a multiprogram national laboratory, SRNL is applying those capabilities to achieve tangible results for the nation inmore » National Security, Environmental Stewardship, Clean Energy and Nuclear Materials Management.« less

Preliminary experimental results from a MARS Micro-CT system.

PubMed

He, Peng; Yu, Hengyong; Thayer, Patrick; Jin, Xin; Xu, Qiong; Bennett, James; Tappenden, Rachael; Wei, Biao; Goldstein, Aaron; Renaud, Peter; Butler, Anthony; Butler, Phillip; Wang, Ge

2012-01-01

The Medipix All Resolution System (MARS) system is a commercial spectral/multi-energy micro-CT scanner designed and assembled by the MARS Bioimaging, Ltd. in New Zealand. This system utilizes the state-of-the-art Medipix photon-counting, energy-discriminating detector technology developed by a collaboration at European Organization for Nuclear Research (CERN). In this paper, we report our preliminary experimental results using this system, including geometrical alignment, photon energy characterization, protocol optimization, and spectral image reconstruction. We produced our scan datasets with a multi-material phantom, and then applied ordered subset-simultaneous algebraic reconstruction technique (OS-SART) to reconstruct images in different energy ranges and principal component analysis (PCA) to evaluate spectral deviation among the energy ranges.

J/ψ Suppression in In-In Collisions at 158 GeV/n

NASA Astrophysics Data System (ADS)

Arnaldi, Roberta; NA60 Collaboration

2007-02-01

The NA60 experiment has studied J/ψ production in Indium-Indium collisions at 158 AṡGeV. In this paper we present an updated set of results obtained with the complete set of available statistics and an improved alignment of the vertex tracker. The centrality dependence of the J/ψ production, obtained with an analysis technique based only on the J/ψ sample, indicates that a suppression beyond that induced by nuclear absorption is present in In-In collisions, setting in at ˜80 participant nucleons. A first study of the systematic errors related with this measurement is discussed. We also present preliminary results on the J/ψ azimuthal distributions.

Cardiac muscle organization revealed in 3-D by imaging whole-mount mouse hearts using two-photon fluorescence and confocal microscopy.

PubMed

Sivaguru, Mayandi; Fried, Glenn; Sivaguru, Barghav S; Sivaguru, Vignesh A; Lu, Xiaochen; Choi, Kyung Hwa; Saif, M Taher A; Lin, Brian; Sadayappan, Sakthivel

2015-11-01

The ability to image the entire adult mouse heart at high resolution in 3-D would provide enormous advantages in the study of heart disease. However, a technique for imaging nuclear/cellular detail as well as the overall structure of the entire heart in 3-D with minimal effort is lacking. To solve this problem, we modified the benzyl alcohol:benzyl benzoate (BABB) clearing technique by labeling mouse hearts with periodic acid Schiff (PAS) stain. We then imaged the hearts with a combination of two-photon fluorescence microscopy and automated tile-scan imaging/stitching. Utilizing the differential spectral properties of PAS, we could identify muscle and nuclear compartments in the heart. We were also able to visualize the differences between a 3-month-old normal mouse heart and a mouse heart that had undergone heart failure due to the expression of cardiac myosin binding protein-C (cMyBP-C) gene mutation (t/t). Using 2-D and 3-D morphometric analysis, we found that the t/t heart had anomalous ventricular shape, volume, and wall thickness, as well as a disrupted sarcomere pattern. We further validated our approach using decellularized hearts that had been cultured with 3T3 fibroblasts, which were tracked using a nuclear label. We were able to detect the 3T3 cells inside the decellularized intact heart tissue, achieving nuclear/cellular resolution in 3-D. The combination of labeling, clearing, and two-photon microscopy together with tiling eliminates laborious and time-consuming physical sectioning, alignment, and 3-D reconstruction.

MitoNuc: a database of nuclear genes coding for mitochondrial proteins. Update 2002.

PubMed

Attimonelli, Marcella; Catalano, Domenico; Gissi, Carmela; Grillo, Giorgio; Licciulli, Flavio; Liuni, Sabino; Santamaria, Monica; Pesole, Graziano; Saccone, Cecilia

2002-01-01

Mitochondria, besides their central role in energy metabolism, have recently been found to be involved in a number of basic processes of cell life and to contribute to the pathogenesis of many degenerative diseases. All functions of mitochondria depend on the interaction of nuclear and organelle genomes. Mitochondrial genomes have been extensively sequenced and analysed and data have been collected in several specialised databases. In order to collect information on nuclear coded mitochondrial proteins we developed MitoNuc, a database containing detailed information on sequenced nuclear genes coding for mitochondrial proteins in Metazoa. The MitoNuc database can be retrieved through SRS and is available via the web site http://bighost.area.ba.cnr.it/mitochondriome where other mitochondrial databases developed by our group, the complete list of the sequenced mitochondrial genomes, links to other mitochondrial sites and related information, are available. The MitoAln database, related to MitoNuc in the previous release, reporting the multiple alignments of the relevant homologous protein coding regions, is no longer supported in the present release. In order to keep the links among entries in MitoNuc from homologous proteins, a new field in the database has been defined: the cluster identifier, an alpha numeric code used to identify each cluster of homologous proteins. A comment field derived from the corresponding SWISS-PROT entry has been introduced; this reports clinical data related to dysfunction of the protein. The logic scheme of MitoNuc database has been implemented in the ORACLE DBMS. This will allow the end-users to retrieve data through a friendly interface that will be soon implemented.

Method and apparatus for reading lased bar codes on shiny-finished fuel rod cladding tubes

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

Goldenfield, M.P.; Lambert, D.V.

1990-10-02

This patent describes, in a nuclear fuel rod identification system, a method of reading a bar code etched directly on a surface of a nuclear fuel rod. It comprises: defining a pair of light diffuser surfaces adjacent one another but in oppositely inclined relation to a beam of light emitted from a light reader; positioning a fuel rod, having a cylindrical surface portion with a bar code etched directly thereon, relative to the light diffuser surfaces such that the surfaces are disposed adjacent to and in oppositely inclined relation along opposite sides of the fuel rod surface portion and themore » fuel rod surface portion is aligned with the beam of light emitted from the light reader; directing the beam of light on the bar code on fuel rod cylindrical surface portion such that the light is reflected therefrom onto one of the light diffuser surfaces; and receiving and reading the reflected light from the bar code via the one of the light diffuser surfaces to the light reader.« less

Nuclear reactor having a polyhedral primary shield and removable vessel insulation

DOEpatents

Ekeroth, Douglas E.; Orr, Richard

1993-01-01

A nuclear reactor is provided having a generally cylindrical reactor vessel disposed within an opening in a primary shield. The opening in the primary shield is defined by a plurality of generally planar side walls forming a generally polyhedral-shaped opening. The reactor vessel is supported within the opening in the primary shield by reactor vessel supports which are in communication and aligned with central portions of some of the side walls. The reactor vessel is connected to the central portions of the reactor vessel supports. A thermal insulation polyhedron formed from a plurality of slidably insertable and removable generally planar insulation panels substantially surrounds at least a portion of the reactor vessel and is disposed between the reactor vessel and the side walls of the primary shield. The shape of the insulation polyhedron generally corresponds to the shape of the opening in the primary shield. Reactor monitoring instrumentation may be mounted in the corners of the opening in the primary shield between the side walls and the reactor vessel such that insulation is not disposed between the instrumentation and the reactor vessel.

Nuclear reactor having a polyhedral primary shield and removable vessel insulation

DOEpatents

Ekeroth, D.E.; Orr, R.

1993-12-07

A nuclear reactor is provided having a generally cylindrical reactor vessel disposed within an opening in a primary shield. The opening in the primary shield is defined by a plurality of generally planar side walls forming a generally polyhedral-shaped opening. The reactor vessel is supported within the opening in the primary shield by reactor vessel supports which are in communication and aligned with central portions of some of the side walls. The reactor vessel is connected to the central portions of the reactor vessel supports. A thermal insulation polyhedron formed from a plurality of slidably insertable and removable generally planar insulation panels substantially surrounds at least a portion of the reactor vessel and is disposed between the reactor vessel and the side walls of the primary shield. The shape of the insulation polyhedron generally corresponds to the shape of the opening in the primary shield. Reactor monitoring instrumentation may be mounted in the corners of the opening in the primary shield between the side walls and the reactor vessel such that insulation is not disposed between the instrumentation and the reactor vessel. 5 figures.

Level anti-crossings are a key factor for understanding para-hydrogen-induced hyperpolarization in SABRE experiments.

PubMed

Pravdivtsev, Andrey N; Yurkovskaya, Alexandra V; Vieth, Hans-Martin; Ivanov, Konstantin L; Kaptein, Robert

2013-10-07

Various hyperpolarization methods are able to enhance the sensitivity of nuclear magnetic resonance (NMR) spectroscopy and magnetic resonance imaging (MRI) by several orders of magnitude. Among these methods are para-hydrogen-induced polarization (PHIP) and signal amplification by reversible exchange (SABRE), which exploit the strong nuclear alignment of para-hydrogen. Several SABRE experiments have been reported but, so far, it has not been possible to account for the experimentally observed sign and magnetic-field dependence of substrate polarization. Herein, we present an analysis based on level anti-crossings (LACs), which provides a complete understanding of the SABRE effect. The field-dependence of both net and anti-phase polarization is measured for several ligands, which can be reproduced by the theory. The similar SABRE field-dependence for different ligands is also explained. In general, the LAC concept allows complex spin dynamics to be unraveled, and is crucial for optimizing the performance of novel hyperpolarization methods in NMR and MRI techniques. Copyright © 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim.

133Cs-NMR study on aligned powder of competing spin chain compound Cs2Cu2Mo3O12

NASA Astrophysics Data System (ADS)

Yagi, A.; Matsui, K.; Goto, T.; Hase, M.; Sasaki, T.

2018-03-01

S = 1/2 competing spin chain compound Cs2Cu2Mo3O12 has two dominant exchange interactions of the nearest neighbouring ferromagnetic J 1 = 93 K and the second nearest neighbouring antiferromagnetic J 2 = +33 K, and is expected to show the nematic Tomonaga-Luttinger liquid (TLL) state under high magnetic field region. The recent theoretical study by Sato et al. has shown that in the nematic TLL state, the spin fluctuations are expected to be highly anisotropic, that is, its transverse component is suppressed. Our previous NMR study on the present system showed that the dominant contribution to nuclear spin relaxation comes from the longitudinal component. In order to conclude that the transverse component of spin fluctuations is suppressed, the knowledge of hyperfine coupling is indispensable. This article is solely devoted to investigate the hyperfine coupling of 133Cs-NMR site to prove that the anisotropic part of hyperfine coupling, which connects the nuclear spin relaxation with the transverse spin fluctuations is considerably large to be A an = +770 Oe/μB.

Molecular basis of Kar9-Bim1 complex function during mating and spindle positioning

PubMed Central

Manatschal, Cristina; Farcas, Ana-Maria; Degen, Miriam Steiner; Bayer, Mathias; Kumar, Anil; Landgraf, Christiane; Volkmer, Rudolf; Barral, Yves; Steinmetz, Michel O.

2016-01-01

The Kar9 pathway promotes nuclear fusion during mating and spindle alignment during metaphase in budding yeast. How Kar9 supports the different outcome of these two divergent processes is an open question. Here, we show that three sites in the C-terminal disordered domain of Kar9 mediate tight Kar9 interaction with the C-terminal dimerization domain of Bim1 (EB1 orthologue). Site1 and Site2 contain SxIP motifs; however, Site3 defines a novel type of EB1-binding site. Whereas Site2 and Site3 mediate Kar9 recruitment to microtubule tips, nuclear movement, and karyogamy, only Site2 functions in spindle positioning during metaphase. Site1 in turn plays an inhibitory role during mating. Additionally, the Kar9-Bim1 complex is involved in microtubule-independent activities during mating. Together, our data reveal how multiple and partially redundant EB1-binding sites provide a microtubule-associated protein with the means to modulate its biochemical properties to promote different molecular processes during cell proliferation and differentiation. PMID:27682587

Study of the 28Si(d,α)26Al Nuclear Reaction at Low Energies

NASA Astrophysics Data System (ADS)

Araujo-Escalona, Victoria; Acosta, L.; Andrade, E.; Barrón-Palos, L.; de Lucio, O.; Favela, F.; Huerta, A.; Lopez, E.; Rita, P. Santa; Solis, C.; Chávez, E.

26Al is known as a γ-ray emitter in the universe. Since its half-life is only 0.72 My it's the obvious evidence of ongoing nucleosynthesis. This isotope is also known as an origin of an abundance-anomaly of 26Mg observed in meteorites. There is also 26Al production on Earth due to the continuous cosmic ray bombardment. Therefore, a precise knowledge of the production rates for 26Al are needed. In this paper, we present a progress report on our measurements of the 28Si(d,α)26Al nuclear reaction. The experimental protocol consists of three steps: i) target preparation, ii) deuteron irradiations and iii) 26Al off line counting using Accelerator Mass Spectrometry (AMS). Due to accelerator failure, deuteron irradiations had to be interrupted and the number or 26Al produced was insufficient to extract cross sections as expected. In step (ii), given our special geometry requirements we ended up facing the old problem of a goat tethered inside a circular field, which we turned into a tool to fine-tune the beam-target alignment in the micron range.

Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements

PubMed Central

Gillespie, J J; Johnston, J S; Cannone, J J; Gutell, R R

2006-01-01

As an accompanying manuscript to the release of the honey bee genome, we report the entire sequence of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) ribosomal RNA (rRNA)-encoding gene sequences (rDNA) and related internally and externally transcribed spacer regions of Apis mellifera (Insecta: Hymenoptera: Apocrita). Additionally, we predict secondary structures for the mature rRNA molecules based on comparative sequence analyses with other arthropod taxa and reference to recently published crystal structures of the ribosome. In general, the structures of honey bee rRNAs are in agreement with previously predicted rRNA models from other arthropods in core regions of the rRNA, with little additional expansion in non-conserved regions. Our multiple sequence alignments are made available on several public databases and provide a preliminary establishment of a global structural model of all rRNAs from the insects. Additionally, we provide conserved stretches of sequences flanking the rDNA cistrons that comprise the externally transcribed spacer regions (ETS) and part of the intergenic spacer region (IGS), including several repetitive motifs. Finally, we report the occurrence of retrotransposition in the nuclear large subunit rDNA, as R2 elements are present in the usual insertion points found in other arthropods. Interestingly, functional R1 elements usually present in the genomes of insects were not detected in the honey bee rRNA genes. The reverse transcriptase products of the R2 elements are deduced from their putative open reading frames and structurally aligned with those from another hymenopteran insect, the jewel wasp Nasonia (Pteromalidae). Stretches of conserved amino acids shared between Apis and Nasonia are illustrated and serve as potential sites for primer design, as target amplicons within these R2 elements may serve as novel phylogenetic markers for Hymenoptera. Given the impending completion of the sequencing of the Nasonia genome, we expect our report eventually to shed light on the evolution of the hymenopteran genome within higher insects, particularly regarding the relative maintenance of conserved rDNA genes, related variable spacer regions and retrotransposable elements. PMID:17069639

Mathematical Investigation of Gamma Ray and Neutron Absorption Grid Patterns for Homeland Defense Related Fourier Imaging Systems

NASA Technical Reports Server (NTRS)

Boccio, Dona

2003-01-01

Terrorist suitcase nuclear devices typically using converted Soviet tactical nuclear warheads contain several kilograms of plutonium. This quantity of plutonium emits a significant number of gamma rays and neutrons as it undergoes radioactive decay. These gamma rays and neutrons normally penetrate ordinary matter to a significant distance. Unfortunately this penetrating quality of the radiation makes imaging with classical optics impractical. However, this radiation signature emitted by the nuclear source may be sufficient to be imaged from low-flying aerial platforms carrying Fourier imaging systems. The Fourier imaging system uses a pair of co-aligned absorption grids to measure a selected range of spatial frequencies from an object. These grids typically measure the spatial frequency in only one direction at a time. A grid pair that looks in all directions simultaneously would be an improvement over existing technology. A number of grid pairs governed by various parameters were investigated to solve this problem. By examining numerous configurations, it became apparent that an appropriate spiral pattern could be made to work. A set of equations was found to describe a grid pattern that produces straight fringes. Straight fringes represent a Fourier transform of a point source at infinity. An inverse Fourier transform of this fringe pattern would provide an accurate image (location and intensity) of a point source.

Mechanisms of Chromosome Congression during Mitosis

PubMed Central

Maiato, Helder; Gomes, Ana Margarida; Sousa, Filipe; Barisic, Marin

2017-01-01

Chromosome congression during prometaphase culminates with the establishment of a metaphase plate, a hallmark of mitosis in metazoans. Classical views resulting from more than 100 years of research on this topic have attempted to explain chromosome congression based on the balance between opposing pulling and/or pushing forces that reach an equilibrium near the spindle equator. However, in mammalian cells, chromosome bi-orientation and force balance at kinetochores are not required for chromosome congression, whereas the mechanisms of chromosome congression are not necessarily involved in the maintenance of chromosome alignment after congression. Thus, chromosome congression and maintenance of alignment are determined by different principles. Moreover, it is now clear that not all chromosomes use the same mechanism for congressing to the spindle equator. Those chromosomes that are favorably positioned between both poles when the nuclear envelope breaks down use the so-called “direct congression” pathway in which chromosomes align after bi-orientation and the establishment of end-on kinetochore-microtubule attachments. This favors the balanced action of kinetochore pulling forces and polar ejection forces along chromosome arms that drive chromosome oscillatory movements during and after congression. The other pathway, which we call “peripheral congression”, is independent of end-on kinetochore microtubule-attachments and relies on the dominant and coordinated action of the kinetochore motors Dynein and Centromere Protein E (CENP-E) that mediate the lateral transport of peripheral chromosomes along microtubules, first towards the poles and subsequently towards the equator. How the opposite polarities of kinetochore motors are regulated in space and time to drive congression of peripheral chromosomes only now starts to be understood. This appears to be regulated by position-dependent phosphorylation of both Dynein and CENP-E and by spindle microtubule diversity by means of tubulin post-translational modifications. This so-called “tubulin code” might work as a navigation system that selectively guides kinetochore motors with opposite polarities along specific spindle microtubule populations, ultimately leading to the congression of peripheral chromosomes. We propose an integrated model of chromosome congression in mammalian cells that depends essentially on the following parameters: (1) chromosome position relative to the spindle poles after nuclear envelope breakdown; (2) establishment of stable end-on kinetochore-microtubule attachments and bi-orientation; (3) coordination between kinetochore- and arm-associated motors; and (4) spatial signatures associated with post-translational modifications of specific spindle microtubule populations. The physiological consequences of abnormal chromosome congression, as well as the therapeutic potential of inhibiting chromosome congression are also discussed. PMID:28218637

Astrocytes Increase ATP Exocytosis Mediated Calcium Signaling in Response to Microgroove Structures

PubMed Central

Singh, Ajay V.; Raymond, Michael; Pace, Fabiano; Certo, Anthony; Zuidema, Jonathan M.; McKay, Christopher A.; Gilbert, Ryan J.; Lu, X. Lucas; Wan, Leo Q.

2015-01-01

Following central nervous system (CNS) injury, activated astrocytes form glial scars, which inhibit axonal regeneration, leading to long-term functional deficits. Engineered nanoscale scaffolds guide cell growth and enhance regeneration within models of spinal cord injury. However, the effects of micro-/nanosize scaffolds on astrocyte function are not well characterized. In this study, a high throughput (HTP) microscale platform was developed to study astrocyte cell behavior on micropatterned surfaces containing 1 μm spacing grooves with a depth of 250 or 500 nm. Significant changes in cell and nuclear elongation and alignment on patterned surfaces were observed, compared to on flat surfaces. The cytoskeleton components (particularly actin filaments and focal adhesions) and nucleus-centrosome axis were aligned along the grooved direction as well. More interestingly, astrocytes on micropatterned surfaces showed enhanced mitochondrial activity with lysosomes localized at the lamellipodia of the cells, accompanied by enhanced adenosine triphosphate (ATP) release and calcium activities. These data indicate that the lysosome-mediated ATP exocytosis and calcium signaling may play an important role in astrocytic responses to substrate topology. These new findings have furthered our understanding of the biomechanical regulation of astrocyte cell–substrate interactions, and may benefit the optimization of scaffold design for CNS healing. PMID:25597401

Measuring mechanodynamics in an unsupported epithelial monolayer grown at an air–water interface

PubMed Central

Gullekson, Corinne; Walker, Matthew; Harden, James L.; Pelling, Andrew E.

2017-01-01

Actomyosin contraction and relaxation in a monolayer is a fundamental biophysical process in development and homeostasis. Current methods used to characterize the mechanodynamics of monolayers often involve cells grown on solid supports such as glass or gels. The results of these studies are fundamentally influenced by these supporting structures. Here we describe a new method for measuring the mechanodynamics of epithelial monolayers by culturing cells at an air–liquid interface. These model monolayers are grown in the absence of any supporting structures, removing cell–substrate effects. This method’s potential was evaluated by observing and quantifying the generation and release of internal stresses upon actomyosin contraction (800 ± 100 Pa) and relaxation (600 ± 100 Pa) in response to chemical treatments. Although unsupported monolayers exhibited clear major and minor strain axes, they were not correlated with nuclear alignment as observed when the monolayers were grown on soft deformable gels. It was also observed that both gels and glass substrates led to the promotion of long-range cell nuclei alignment not seen in the hanging-drop model. This new approach provides us with a picture of basal actomyosin mechanodynamics in a simplified system, allowing us to infer how the presence of a substrate affects contractility and long-range multicellular organization and dynamics. PMID:28035043

Engineering an in vitro organotypic model for studying cardiac hypertrophy.

PubMed

Jain, Aditi; Hasan, Jafar; Desingu, Perumal Arumugam; Sundaresan, Nagalingam R; Chatterjee, Kaushik

2018-05-01

Neonatal cardiomyocytes cultured on flat surfaces are commonly used as a model to study cardiac failure of diverse origin. A major drawback of such a system is that the cardiomyocytes do not exhibit alignment, organization and calcium transients, similar to the native heart. Therefore, there is a need to develop in vitro platforms that recapitulate the cellular microenvironment of the murine heart as organotypic models to study cardiovascular diseases. In this study, we report an engineered platform that mimics cardiac cell organization and function of the heart. For this purpose, microscale ridges were fabricated on silicon using ultraviolet lithography and reactive ion etching techniques. Physical characterization of the microstructures was done using scanning electron microscopy and atomic force microscopy. Cardiomyocytes grown on these micro-ridges showed global parallel alignment and elliptical nuclear morphology as observed in the heart. Interestingly, calcium currents traversed the engineered cardiomyocytes in a coordinated and directional manner. Moreover, the cardiomyocytes on the engineered substrates were found to be responsive to hypertrophic stimuli, as observed by the expression of a fetal gene, atrial natriuretic peptide and increase in calcium transients upon agonist treatment. Taken together, our work demonstrates that micro-ridges can be used to obtain cardiomyocyte response in vitro, which closely resembles mammalian heart. Copyright © 2018 Elsevier B.V. All rights reserved.

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

Webb, Aaron P.; Carlson, Charles T.; Weaver, William T.

A mask alignment system for providing precise and repeatable alignment between ion implantation masks and workpieces. The system includes a mask frame having a plurality of ion implantation masks loosely connected thereto. The mask frame is provided with a plurality of frame alignment cavities, and each mask is provided with a plurality of mask alignment cavities. The system further includes a platen for holding workpieces. The platen may be provided with a plurality of mask alignment pins and frame alignment pins configured to engage the mask alignment cavities and frame alignment cavities, respectively. The mask frame can be lowered ontomore » the platen, with the frame alignment cavities moving into registration with the frame alignment pins to provide rough alignment between the masks and workpieces. The mask alignment cavities are then moved into registration with the mask alignment pins, thereby shifting each individual mask into precise alignment with a respective workpiece.« less

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

Wedding, Jason L.; Harris, Hugh H.; Bader, Christie A.

Optical fluorescence microscopy was used in conjunction with X-ray fluorescence microscopy to monitor the stability and intracellular distribution of the luminescent rhenium(I) complex fac-[Re(CO) 3(phen)L], where phen = 1,10-phenathroline and L = 5-(4-iodophenyl)tetrazolato, in 22Rv1 cells. The rhenium complex showed no signs of ancillary ligand dissociation, a conclusion based on data obtained via X-ray fluorescence imaging aligning iodine and rhenium distributions. A diffuse reticular localisation was detected for the complex, in the nuclear/perinuclear region of cells, by either optical or X-ray fluorescence techniques. Furthermore, X-ray fluorescence also showed that the Re-I complex disrupted the homeostasis of some biologically relevant elements,more » such as chlorine, potassium and zinc.« less

HD{sup +} in a short strong laser pulse: Practical consideration of the observability of carrier-envelope phase effects

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

Roudnev, V.; Esry, B. D.

2007-08-15

We summarize the results of numerical calculations of HD{sup +} in a 7.1 fs (intensity full width at half maximum) 790 nm laser pulse. The molecule is assumed to be aligned with the linearly polarized laser field and includes two electronic and one nuclear degrees of freedom. We report total dissociation and ionization probabilities from the lowest 10 vibrational states for a range of intensities from 10{sup 13} to 7x10{sup 14} W/cm{sup 2}. The conditions for the observability of carrier-envelope phase (CEP) effects for a mixed initial state and for intensity averaging over the laser focal volume are discussed inmore » detail.« less

The nuclear activity and central structure of the elliptical galaxy NGC 5322

NASA Astrophysics Data System (ADS)

Dullo, Bililign T.; Knapen, Johan H.; Williams, David R. A.; Beswick, Robert J.; Bendo, George; Baldi, Ranieri D.; Argo, Megan; McHardy, Ian M.; Muxlow, Tom; Westcott, J.

2018-04-01

We have analysed a new high-resolution e-MERLIN 1.5 GHz radio continuum map together with HST and SDSS imaging of NGC 5322, an elliptical galaxy hosting radio jets, aiming to understand the galaxy's central structure and its connection to the nuclear activity. We decomposed the composite HST + SDSS surface brightness profile of the galaxy into an inner stellar disc, a spheroid, and an outer stellar halo. Past works showed that this embedded disc counter-rotates rapidly with respect to the spheroid. The HST images reveal an edge-on nuclear dust disc across the centre, aligned along the major-axis of the galaxy and nearly perpendicular to the radio jets. After careful masking of this dust disc, we find a central stellar mass deficit Mdef in the spheroid, scoured by SMBH binaries with final mass MBH such that Mdef/MBH ˜ 1.3-3.4. We propose a three-phase formation scenario for NGC 5322, where a few (2-7) `dry' major mergers involving SMBHs built the spheroid with a depleted core. The cannibalism of a gas-rich satellite subsequently creates the faint counter-rotating disc and funnels gaseous material directly on to the AGN, powering the radio core with a brightness temperature of TB, core ˜ 4.5 × 107 K and the low-power radio jets (Pjets ˜ 7.04 × 1020 W Hz-1), which extend ˜1.6 kpc. The outer halo can later grow via minor mergers and the accretion of tidal debris. The low-luminosity AGN/jet-driven feedback may have quenched the late-time nuclear star formation promptly, which could otherwise have replenished the depleted core.

Initial high-resolution microscopic mapping of active and inactive regulatory sequences proves non-random 3D arrangements in chromatin domain clusters.

PubMed

Cremer, Marion; Schmid, Volker J; Kraus, Felix; Markaki, Yolanda; Hellmann, Ines; Maiser, Andreas; Leonhardt, Heinrich; John, Sam; Stamatoyannopoulos, John; Cremer, Thomas

2017-08-07

The association of active transcription regulatory elements (TREs) with DNAse I hypersensitivity (DHS[+]) and an 'open' local chromatin configuration has long been known. However, the 3D topography of TREs within the nuclear landscape of individual cells in relation to their active or inactive status has remained elusive. Here, we explored the 3D nuclear topography of active and inactive TREs in the context of a recently proposed model for a functionally defined nuclear architecture, where an active and an inactive nuclear compartment (ANC-INC) form two spatially co-aligned and functionally interacting networks. Using 3D structured illumination microscopy, we performed 3D FISH with differently labeled DNA probe sets targeting either sites with DHS[+], apparently active TREs, or DHS[-] sites harboring inactive TREs. Using an in-house image analysis tool, DNA targets were quantitatively mapped on chromatin compaction shaped 3D nuclear landscapes. Our analyses present evidence for a radial 3D organization of chromatin domain clusters (CDCs) with layers of increasing chromatin compaction from the periphery to the CDC core. Segments harboring active TREs are significantly enriched at the decondensed periphery of CDCs with loops penetrating into interchromatin compartment channels, constituting the ANC. In contrast, segments lacking active TREs (DHS[-]) are enriched toward the compacted interior of CDCs (INC). Our results add further evidence in support of the ANC-INC network model. The different 3D topographies of DHS[+] and DHS[-] sites suggest positional changes of TREs between the ANC and INC depending on their functional state, which might provide additional protection against an inappropriate activation. Our finding of a structural organization of CDCs based on radially arranged layers of different chromatin compaction levels indicates a complex higher-order chromatin organization beyond a dichotomic classification of chromatin into an 'open,' active and 'closed,' inactive state.

Transcriptome-Mining for Single-Copy Nuclear Markers in Ferns

PubMed Central

Rothfels, Carl J.; Larsson, Anders; Li, Fay-Wei; Sigel, Erin M.; Huiet, Layne; Burge, Dylan O.; Ruhsam, Markus; Graham, Sean W.; Stevenson, Dennis W.; Wong, Gane Ka-Shu; Korall, Petra; Pryer, Kathleen M.

2013-01-01

Background Molecular phylogenetic investigations have revolutionized our understanding of the evolutionary history of ferns—the second-most species-rich major group of vascular plants, and the sister clade to seed plants. The general absence of genomic resources available for this important group of plants, however, has resulted in the strong dependence of these studies on plastid data; nuclear or mitochondrial data have been rarely used. In this study, we utilize transcriptome data to design primers for nuclear markers for use in studies of fern evolutionary biology, and demonstrate the utility of these markers across the largest order of ferns, the Polypodiales. Principal Findings We present 20 novel single-copy nuclear regions, across 10 distinct protein-coding genes: ApPEFP_C, cryptochrome 2, cryptochrome 4, DET1, gapCpSh, IBR3, pgiC, SQD1, TPLATE, and transducin. These loci, individually and in combination, show strong resolving power across the Polypodiales phylogeny, and are readily amplified and sequenced from our genomic DNA test set (from 15 diploid Polypodiales species). For each region, we also present transcriptome alignments of the focal locus and related paralogs—curated broadly across ferns—that will allow researchers to develop their own primer sets for fern taxa outside of the Polypodiales. Analyses of sequence data generated from our genomic DNA test set reveal strong effects of partitioning schemes on support levels and, to a much lesser extent, on topology. A model partitioned by codon position is strongly favored, and analyses of the combined data yield a Polypodiales phylogeny that is well-supported and consistent with earlier studies of this group. Conclusions The 20 single-copy regions presented here more than triple the single-copy nuclear regions available for use in ferns. They provide a much-needed opportunity to assess plastid-derived hypotheses of relationships within the ferns, and increase our capacity to explore aspects of fern evolution previously unavailable to scientific investigation. PMID:24116189

Physics division annual report 2000.

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

Thayer, K., ed.

2001-10-04

This report summarizes the research performed in 2000 in the Physics Division of Argonne National Laboratory. The Division's programs include operation of ATLAS as a national user facility, nuclear structure and reaction research, nuclear theory and medium energy physics research, and accelerator research and development. As the Nuclear Science Advisory Committee and the nuclear science community create a new long range plan for the field in 2001, it is clear that the research of the Division is closely aligned with and continues to help define the national goals of our field. The NSAC 2001 Long Range Plan recommends as themore » highest priority for major new construction the Rare Isotope Accelerator (RIA), a bold step forward for nuclear structure and nuclear astrophysics. The accelerator R&D in the Physics Division has made major contributions to almost all aspects of the RIA design concept and the community was convinced that this project is ready to move forward. 2000 saw the end of the first Gammasphere epoch at ATLAS, One hundred Gammasphere experiments were completed between January 1998 and March 2000, 60% of which used the Fragment Mass Analyzer to provide mass identification in the reaction. The experimental program at ATLAS then shifted to other important research avenues including proton radioactivity, mass measurements with the Canadian Penning Trap and measurements of high energy gamma-rays in nuclear reactions with the MSU/ORNL/Texas A&M BaF{sub 2} array. ATLAS provided 5460 beam-research hours for user experiments and maintained an operational reliability of 95%. Radioactive beams accounted for 7% of the beam time. ATLAS also provided a crucial test of a key RIA concept, the ability to accelerate multiple charge states in a superconducting heavy-ion linac. This new capability was immediately used to increase the performance for a scheduled experiment. The medium energy program continued to make strides in examining how the quark-gluon structure of matter impacts the structure of nuclei and extended the exquisite sensitivity of the Atom-Trap-Trace-Analysis technique to new species and applications. All of this progress was built on advances in nuclear theory, which the Division pursues at the quark, hadron, and nuclear collective degrees of freedom levels. These are just a few of the highlights in the Division's research program. The results reflect the talents and dedication of the Physics Division staff and the visitors, guests and students who bring so much to the research.« less

COACH: profile-profile alignment of protein families using hidden Markov models.

PubMed

Edgar, Robert C; Sjölander, Kimmen

2004-05-22

Alignments of two multiple-sequence alignments, or statistical models of such alignments (profiles), have important applications in computational biology. The increased amount of information in a profile versus a single sequence can lead to more accurate alignments and more sensitive homolog detection in database searches. Several profile-profile alignment methods have been proposed and have been shown to improve sensitivity and alignment quality compared with sequence-sequence methods (such as BLAST) and profile-sequence methods (e.g. PSI-BLAST). Here we present a new approach to profile-profile alignment we call Comparison of Alignments by Constructing Hidden Markov Models (HMMs) (COACH). COACH aligns two multiple sequence alignments by constructing a profile HMM from one alignment and aligning the other to that HMM. We compare the alignment accuracy of COACH with two recently published methods: Yona and Levitt's prof_sim and Sadreyev and Grishin's COMPASS. On two sets of reference alignments selected from the FSSP database, we find that COACH is able, on average, to produce alignments giving the best coverage or the fewest errors, depending on the chosen parameter settings. COACH is freely available from www.drive5.com/lobster

The variations in the nuclear proteome reveal new transcription factors and mechanisms involved in UV stress response in Pinus radiata.

PubMed

Pascual, Jesús; Alegre, Sara; Nagler, Matthias; Escandón, Mónica; Annacondia, María Luz; Weckwerth, Wolfram; Valledor, Luis; Cañal, María Jesús

2016-06-30

The importance of UV stress and its side-effects over the loss of plant productivity in forest species demands a deeper understanding of how pine trees respond to UV irradiation. Although the response to UV stress has been characterized at system and cellular levels, the dynamics within the nuclear proteome triggered by UV is still unknown despite that they are essential for gene expression and regulation of plant physiology. To fill this gap this work aims to characterize the variations in the nuclear proteome as a response to UV irradiation by using state-of-the-art mass spectrometry-based methods combined with novel bioinformatics workflows. The combination of SEQUEST, de novo sequencing, and novel annotation pipelines allowed cover sensing and transduction pathways, endoplasmic reticulum-related mechanisms and the regulation of chromatin dynamism and gene expression by histones, histone-like NF-Ys, and other transcription factors previously unrelated to this stress source, as well as the role of alternative splicing and other mechanisms involved in RNA translation and protein synthesis. The determination of 33 transcription factors, including NF-YB13, Pp005698_3 (NF-YB) and Pr009668_2 (WD-40), which are correlated to stress responsive mechanisms like an increased accumulation of photoprotective pigments and reduced photosynthesis, pointing them as strong candidate biomarkers for breeding programs aimed to improve UV resistance of pine trees. The description of the nuclear proteome of Pinus radiata combining a classic approach based on the use of SEQUEST and the use of a mass accuracy precursor alignment (MAPA) allowed an unprecedented protein coverage. This workflow provided the methodological basis for characterizing the changes in the nuclear proteome triggered by UV irradiation, allowing the depiction of the nuclear events involved in stress response and adaption. The relevance of some of the discovered proteins will suppose a major advance in stress biology field, also providing a set of transcription factors that can be considered as strong biomarker candidates to select trees more tolerant to UV radiation in forest upgrade programs. Copyright © 2016 Elsevier B.V. All rights reserved.

CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.

PubMed

Terashi, Genki; Takeda-Shitaka, Mayuko

2015-01-01

Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein structure alignment methods treat protein structures as rigid bodies. Thus, these methods fail to identify the equivalences of residue pairs in regions with flexibility. In this study, we considered that the evolutionary relationship between proteins corresponds directly to the residue-residue physical contacts rather than the three-dimensional (3D) coordinates of proteins. Thus, we developed a new protein structure alignment method, contact area-based alignment (CAB-align), which uses the residue-residue contact area to identify regions of similarity. The main purpose of CAB-align is to identify homologous relationships at the residue level between related protein structures. The CAB-align procedure comprises two main steps: First, a rigid-body alignment method based on local and global 3D structure superposition is employed to generate a sufficient number of initial alignments. Then, iterative dynamic programming is executed to find the optimal alignment. We evaluated the performance and advantages of CAB-align based on four main points: (1) agreement with the gold standard alignment, (2) alignment quality based on an evolutionary relationship without 3D coordinate superposition, (3) consistency of the multiple alignments, and (4) classification agreement with the gold standard classification. Comparisons of CAB-align with other state-of-the-art protein structure alignment methods (TM-align, FATCAT, and DaliLite) using our benchmark dataset showed that CAB-align performed robustly in obtaining high-quality alignments and generating consistent multiple alignments with high coverage and accuracy rates, and it performed extremely well when discriminating between homologous and nonhomologous pairs of proteins in both single and multi-domain comparisons. The CAB-align software is freely available to academic users as stand-alone software at http://www.pharm.kitasato-u.ac.jp/bmd/bmd/Publications.html.

IUS prerelease alignment

NASA Technical Reports Server (NTRS)

Evans, F. A.

1978-01-01

Space shuttle orbiter/IUS alignment transfer was evaluated. Although the orbiter alignment accuracy was originally believed to be the major contributor to the overall alignment transfer error, it was shown that orbiter alignment accuracy is not a factor affecting IUS alignment accuracy, if certain procedures are followed. Results are reported of alignment transfer accuracy analysis.

Evaluative Assay of Nuclear and Mitochondrial Genes to Diagnose Leishmania Species in Clinical Specimens.

PubMed

Esmaeili Rastaghi, Ahmad Reza; Spotin, Adel; Khataminezhad, Mohammad Reza; Jafarpour, Mostafa; Alaeenovin, Elnaz; Najafzadeh, Narmin; Samei, Neda; Taleshi, Neda; Mohammadi, Somayeh; Parvizi, Parviz

2017-10-01

Leishmaniasis as an emerging and reemerging disease is increasing worldwide with high prevalence and new incidence in recent years. For epidemiological investigation and accurate identification of Leishmania species, three nuclear and mitochondrial genes (ITS-rDNA, Hsp70, and Cyt b ) were employed and analyzed from clinical samples in three important Zoonotic Cutaneous Leishmaniasis (ZCL) foci of Iran. In this cross-sectional/descriptive study conducted in 2014-15, serous smears of lesions were directly prepared from suspected patients of ZCL in Turkmen in northeast, Abarkouh in center and Shush district in southwest of Iran. They were directly prepared from suspected patients and DNA was extracted. Two nuclear genes of ITS-rDNA, Hsp70 and one mitochondrial gene of Cyt b within Leishmania parasites were amplified. RFLP was performed on PCR-positive samples. PCR products were sequenced, aligned and edited with sequencher 4.1.4 and phylogenic analyses performed using MEGA 5.05 software. Overall, 203 out of 360 clinical samples from suspected patients were Leishmania positive using routine laboratory methods and 231 samples were positive by molecular techniques. L. major L. tropica , and L. turanica were firmly identified by employing different molecular genes and phylogenic analyses. By combining different molecular genes, Leishmania parasites were identified accurately. The sensitivity and specificity three genes were evaluated and had more advantages to compare routine laboratory methods. ITS-rDNA gene is more appropriate for firm identification of Leishmania species.

The 4-Celled Tetrabaena socialis Nuclear Genome Reveals the Essential Components for Genetic Control of Cell Number at the Origin of Multicellularity in the Volvocine Lineage.

PubMed

Featherston, Jonathan; Arakaki, Yoko; Hanschen, Erik R; Ferris, Patrick J; Michod, Richard E; Olson, Bradley J S C; Nozaki, Hisayoshi; Durand, Pierre M

2018-04-01

Multicellularity is the premier example of a major evolutionary transition in individuality and was a foundational event in the evolution of macroscopic biodiversity. The volvocine chlorophyte lineage is well suited for studying this process. Extant members span unicellular, simple colonial, and obligate multicellular taxa with germ-soma differentiation. Here, we report the nuclear genome sequence of one of the most morphologically simple organisms in this lineage-the 4-celled colonial Tetrabaena socialis and compare this to the three other complete volvocine nuclear genomes. Using conservative estimates of gene family expansions a minimal set of expanded gene families was identified that associate with the origin of multicellularity. These families are rich in genes related to developmental processes. A subset of these families is lineage specific, which suggests that at a genomic level the evolution of multicellularity also includes lineage-specific molecular developments. Multiple points of evidence associate modifications to the ubiquitin proteasomal pathway (UPP) with the beginning of coloniality. Genes undergoing positive or accelerating selection in the multicellular volvocines were found to be enriched in components of the UPP and gene families gained at the origin of multicellularity include components of the UPP. A defining feature of colonial/multicellular life cycles is the genetic control of cell number. The genomic data presented here, which includes diversification of cell cycle genes and modifications to the UPP, align the genetic components with the evolution of this trait.

Characterization of nuclear graphite elastic properties using laser ultrasonic methods

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

Zeng, Fan W; Han, Karen; Olasov, Lauren R

2015-01-01

Laser ultrasonic methods have been used to characterize the elastic behaviors of commercially-available and legacy nuclear graphites. Since ultrasonic techniques are sensitive to various aspects of graphite microstructure including preferred grain orientation, microcrack orientation and porosity, laser ultrasonics is a candidate technique for monitoring graphite degradation and structural integrity in environments expected in high-temperature, gas-cooled nuclear reactors. Aspects of materials texture can be assessed by studying ultrasonic wavespeeds as a function of propagation direction and polarization. Shear wave birefringence measurements, in particular, can be used to evaluate elastic anisotropy. In this work, laser ultrasonic measurements of graphite moduli have beenmore » made to provide insight into the relationship between the microstructures and the macroscopic stiffnesses of these materials. In particular, laser ultrasonic measurements have been made using laser line sources to produce shear waves with specific polarizations. By varying the line orientation relative to the sample, shear wave birefringence measurements have been recorded. Results from shear wave birefringence measurements show that an isostatically molded graphite, such as PCIB, behaves isotropically, while an extruded graphite, such as H-451, displays significant ultrasonic texture. Graphites have complicated microstructures that depend on the manufacturing processes used, and ultrasonic texture in these materials could originate from grain orientation and preferred microcrack alignment. Effects on material isotropy due to service related microstructural changes are possible and the ultimate aim of this work is to determine the degree to which these changes can be assessed nondestructively using laser ultrasonics measurements« less

The gene coding for small ribosomal subunit RNA in the basidiomycete Ustilago maydis contains a group I intron.

PubMed Central

De Wachter, R; Neefs, J M; Goris, A; Van de Peer, Y

1992-01-01

The nucleotide sequence of the gene coding for small ribosomal subunit RNA in the basidiomycete Ustilago maydis was determined. It revealed the presence of a group I intron with a length of 411 nucleotides. This is the third occurrence of such an intron discovered in a small subunit rRNA gene encoded by a eukaryotic nuclear genome. The other two occurrences are in Pneumocystis carinii, a fungus of uncertain taxonomic status, and Ankistrodesmus stipitatus, a green alga. The nucleotides of the conserved core structure of 101 group I intron sequences present in different genes and genome types were aligned and their evolutionary relatedness was examined. This revealed a cluster including all group I introns hitherto found in eukaryotic nuclear genes coding for small and large subunit rRNAs. A secondary structure model was designed for the area of the Ustilago maydis small ribosomal subunit RNA precursor where the intron is situated. It shows that the internal guide sequence pairing with the intron boundaries fits between two helices of the small subunit rRNA, and that minimal rearrangement of base pairs suffices to achieve the definitive secondary structure of the 18S rRNA upon splicing. PMID:1561081

[Phenotypic and genetic characterization of nuclear polyhedrosis virus isolated from gypsy moth (Lymantria dispar L.) larvae from the natural populations of Western Siberia].

PubMed

Bakhvalov, S A; Bakhvalova, V N; Martem'ianov, V V; Morozova, O V

2010-01-01

Six nuclear polyhedrosis virus (NPV) isolates have been isolated from dead larvae of gypsy moth in Western Siberia. Heterogeneity of virulence and reproduction activity was revealed for the NPV isolated by bioassay with Lymantria dispar L. larvae. The findings may suggest phenotypic variation of the NPV isolates. No correlation was found between virulence and reproductive activity with the only exception--the isolate Karassuk with a high virulence and a high reproductive activity. Nucleotide sequences of PCR products with primers specific to the polyhedrin gene were determined for NPV isolated Karassuk and Tatarskyi with the maximum and minimal virulence, respectively. Alignment of the nucleotide sequences demonstrated a high homology of the study polyhedrin gene fragment between NPV Western-Siberian isolates and NPV strains from the USA with two point mutations. The mutations were identical for the NPV isolated from Russia but were different from the known structures of the polyhedrin gene of the American strains. The only one from two found mutations resulted in amino acid substitution in polyhedrin protein. Consequently, the structure of both polyhedrin and encoded protein did not influence on the NPV virulence and reproductive activity.

The vertical disk structure of the edge-on spiral galaxy NGC 3079

NASA Technical Reports Server (NTRS)

Veilleux, S.; Bland-Hawthorn, Jonathan; Cecil, G.; Tully, R. B.

1993-01-01

NGC 3079 is an edge-on SB(s)c galaxy at a redshift of 1225 km/s relative to the Local Group. Earlier researchers found a spectacular 'figure-eight' radio structure aligned along the minor axis of the galaxy, centered on the nucleus, and extending 3 kpc above and below the plane. The geometry of this structure and the evidence of unusually high nuclear gas velocities suggest that a wind-type outflow from the nucleus is taking place. The disk of NGC 3079 is also remarkable: it is extremely rich in H 2 regions and is the only unambiguous example of a galaxy outside M31 and our own Galaxy to exhibit 'Heiles-like' shells. Other researchers have also identified a nebulosity with a ragged X-shaped morphology formed by a system of lumpy filaments with individual lengths of 3 - 5 kpc. They suggest that this material is ambient halo gas entrained into the boundary layers of the nuclear outflow. The complex structure of the line emission in NGC 3079 makes this object an ideal target for an imaging spectroscopic study. The present paper reports the preliminary results of such a study.

SFESA: a web server for pairwise alignment refinement by secondary structure shifts.

PubMed

Tong, Jing; Pei, Jimin; Grishin, Nick V

2015-09-03

Protein sequence alignment is essential for a variety of tasks such as homology modeling and active site prediction. Alignment errors remain the main cause of low-quality structure models. A bioinformatics tool to refine alignments is needed to make protein alignments more accurate. We developed the SFESA web server to refine pairwise protein sequence alignments. Compared to the previous version of SFESA, which required a set of 3D coordinates for a protein, the new server will search a sequence database for the closest homolog with an available 3D structure to be used as a template. For each alignment block defined by secondary structure elements in the template, SFESA evaluates alignment variants generated by local shifts and selects the best-scoring alignment variant. A scoring function that combines the sequence score of profile-profile comparison and the structure score of template-derived contact energy is used for evaluation of alignments. PROMALS pairwise alignments refined by SFESA are more accurate than those produced by current advanced alignment methods such as HHpred and CNFpred. In addition, SFESA also improves alignments generated by other software. SFESA is a web-based tool for alignment refinement, designed for researchers to compute, refine, and evaluate pairwise alignments with a combined sequence and structure scoring of alignment blocks. To our knowledge, the SFESA web server is the only tool that refines alignments by evaluating local shifts of secondary structure elements. The SFESA web server is available at http://prodata.swmed.edu/sfesa.

A novel approach to multiple sequence alignment using hadoop data grids.

PubMed

Sudha Sadasivam, G; Baktavatchalam, G

2010-01-01

Multiple alignment of protein sequences helps to determine evolutionary linkage and to predict molecular structures. The factors to be considered while aligning multiple sequences are speed and accuracy of alignment. Although dynamic programming algorithms produce accurate alignments, they are computation intensive. In this paper we propose a time efficient approach to sequence alignment that also produces quality alignment. The dynamic nature of the algorithm coupled with data and computational parallelism of hadoop data grids improves the accuracy and speed of sequence alignment. The principle of block splitting in hadoop coupled with its scalability facilitates alignment of very large sequences.

Fabrication of high temperature superconductors

DOEpatents

Balachandran, Uthamalingam; Dorris, Stephen E.; Ma, Beihai; Li, Meiya

2003-06-17

A method of forming a biaxially aligned superconductor on a non-biaxially aligned substrate substantially chemically inert to the biaxially aligned superconductor comprising is disclosed. A non-biaxially aligned substrate chemically inert to the superconductor is provided and a biaxially aligned superconductor material is deposited directly on the non-biaxially aligned substrate. A method forming a plume of superconductor material and contacting the plume and the non-biaxially aligned substrate at an angle greater than 0.degree. and less than 90.degree. to deposit a biaxially aligned superconductor on the non-biaxially aligned substrate is also disclosed. Various superconductors and substrates are illustrated.

Triangular Alignment (TAME). A Tensor-based Approach for Higher-order Network Alignment

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

Mohammadi, Shahin; Gleich, David F.; Kolda, Tamara G.

2015-11-01

Network alignment is an important tool with extensive applications in comparative interactomics. Traditional approaches aim to simultaneously maximize the number of conserved edges and the underlying similarity of aligned entities. We propose a novel formulation of the network alignment problem that extends topological similarity to higher-order structures and provide a new objective function that maximizes the number of aligned substructures. This objective function corresponds to an integer programming problem, which is NP-hard. Consequently, we approximate this objective function as a surrogate function whose maximization results in a tensor eigenvalue problem. Based on this formulation, we present an algorithm called Triangularmore » AlignMEnt (TAME), which attempts to maximize the number of aligned triangles across networks. We focus on alignment of triangles because of their enrichment in complex networks; however, our formulation and resulting algorithms can be applied to general motifs. Using a case study on the NAPABench dataset, we show that TAME is capable of producing alignments with up to 99% accuracy in terms of aligned nodes. We further evaluate our method by aligning yeast and human interactomes. Our results indicate that TAME outperforms the state-of-art alignment methods both in terms of biological and topological quality of the alignments.« less

Unified Alignment of Protein-Protein Interaction Networks.

PubMed

Malod-Dognin, Noël; Ban, Kristina; Pržulj, Nataša

2017-04-19

Paralleling the increasing availability of protein-protein interaction (PPI) network data, several network alignment methods have been proposed. Network alignments have been used to uncover functionally conserved network parts and to transfer annotations. However, due to the computational intractability of the network alignment problem, aligners are heuristics providing divergent solutions and no consensus exists on a gold standard, or which scoring scheme should be used to evaluate them. We comprehensively evaluate the alignment scoring schemes and global network aligners on large scale PPI data and observe that three methods, HUBALIGN, L-GRAAL and NATALIE, regularly produce the most topologically and biologically coherent alignments. We study the collective behaviour of network aligners and observe that PPI networks are almost entirely aligned with a handful of aligners that we unify into a new tool, Ulign. Ulign enables complete alignment of two networks, which traditional global and local aligners fail to do. Also, multiple mappings of Ulign define biologically relevant soft clusterings of proteins in PPI networks, which may be used for refining the transfer of annotations across networks. Hence, PPI networks are already well investigated by current aligners, so to gain additional biological insights, a paradigm shift is needed. We propose such a shift come from aligning all available data types collectively rather than any particular data type in isolation from others.

Accelerating large-scale protein structure alignments with graphics processing units

PubMed Central

2012-01-01

Background Large-scale protein structure alignment, an indispensable tool to structural bioinformatics, poses a tremendous challenge on computational resources. To ensure structure alignment accuracy and efficiency, efforts have been made to parallelize traditional alignment algorithms in grid environments. However, these solutions are costly and of limited accessibility. Others trade alignment quality for speedup by using high-level characteristics of structure fragments for structure comparisons. Findings We present ppsAlign, a parallel protein structure Alignment framework designed and optimized to exploit the parallelism of Graphics Processing Units (GPUs). As a general-purpose GPU platform, ppsAlign could take many concurrent methods, such as TM-align and Fr-TM-align, into the parallelized algorithm design. We evaluated ppsAlign on an NVIDIA Tesla C2050 GPU card, and compared it with existing software solutions running on an AMD dual-core CPU. We observed a 36-fold speedup over TM-align, a 65-fold speedup over Fr-TM-align, and a 40-fold speedup over MAMMOTH. Conclusions ppsAlign is a high-performance protein structure alignment tool designed to tackle the computational complexity issues from protein structural data. The solution presented in this paper allows large-scale structure comparisons to be performed using massive parallel computing power of GPU. PMID:22357132

AlignMe—a membrane protein sequence alignment web server

PubMed Central

Stamm, Marcus; Staritzbichler, René; Khafizov, Kamil; Forrest, Lucy R.

2014-01-01

We present a web server for pair-wise alignment of membrane protein sequences, using the program AlignMe. The server makes available two operational modes of AlignMe: (i) sequence to sequence alignment, taking two sequences in fasta format as input, combining information about each sequence from multiple sources and producing a pair-wise alignment (PW mode); and (ii) alignment of two multiple sequence alignments to create family-averaged hydropathy profile alignments (HP mode). For the PW sequence alignment mode, four different optimized parameter sets are provided, each suited to pairs of sequences with a specific similarity level. These settings utilize different types of inputs: (position-specific) substitution matrices, secondary structure predictions and transmembrane propensities from transmembrane predictions or hydrophobicity scales. In the second (HP) mode, each input multiple sequence alignment is converted into a hydrophobicity profile averaged over the provided set of sequence homologs; the two profiles are then aligned. The HP mode enables qualitative comparison of transmembrane topologies (and therefore potentially of 3D folds) of two membrane proteins, which can be useful if the proteins have low sequence similarity. In summary, the AlignMe web server provides user-friendly access to a set of tools for analysis and comparison of membrane protein sequences. Access is available at http://www.bioinfo.mpg.de/AlignMe PMID:24753425

Overcoming low-alignment signal contrast induced alignment failure by alignment signal enhancement

NASA Astrophysics Data System (ADS)

Lee, Byeong Soo; Kim, Young Ha; Hwang, Hyunwoo; Lee, Jeongjin; Kong, Jeong Heung; Kang, Young Seog; Paarhuis, Bart; Kok, Haico; de Graaf, Roelof; Weichselbaum, Stefan; Droste, Richard; Mason, Christopher; Aarts, Igor; de Boeij, Wim P.

2016-03-01

Overlay is one of the key factors which enables optical lithography extension to 1X node DRAM manufacturing. It is natural that accurate wafer alignment is a prerequisite for good device overlay. However, alignment failures or misalignments are commonly observed in a fab. There are many factors which could induce alignment problems. Low alignment signal contrast is one of the main issues. Alignment signal contrast can be degraded by opaque stack materials or by alignment mark degradation due to processes like CMP. This issue can be compounded by mark sub-segmentation from design rules in combination with double or quadruple spacer process. Alignment signal contrast can be improved by applying new material or process optimization, which sometimes lead to the addition of another process-step with higher costs. If we can amplify the signal components containing the position information and reduce other unwanted signal and background contributions then we can improve alignment performance without process change. In this paper we use ASML's new alignment sensor (as was introduced and released on the NXT:1980Di) and sample wafers with special stacks which can induce poor alignment signal to demonstrate alignment and overlay improvement.

MaxAlign: maximizing usable data in an alignment.

PubMed

Gouveia-Oliveira, Rodrigo; Sackett, Peter W; Pedersen, Anders G

2007-08-28

The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. In phylogenetic and other analyses, for instance, gapped columns are often discarded entirely from the alignment. MaxAlign is a program that optimizes the alignment prior to such analyses. Specifically, it maximizes the number of nucleotide (or amino acid) symbols that are present in gap-free columns - the alignment area - by selecting the optimal subset of sequences to exclude from the alignment. MaxAlign can be used prior to phylogenetic and bioinformatical analyses as well as in other situations where this form of alignment improvement is useful. In this work we test MaxAlign's performance in these tasks and compare the accuracy of phylogenetic estimates including and excluding gapped columns from the analysis, with and without processing with MaxAlign. In this paper we also introduce a new simple measure of tree similarity, Normalized Symmetric Similarity (NSS) that we consider useful for comparing tree topologies. We demonstrate how MaxAlign is helpful in detecting misaligned or defective sequences without requiring manual inspection. We also show that it is not advisable to exclude gapped columns from phylogenetic analyses unless MaxAlign is used first. Finally, we find that the sequences removed by MaxAlign from an alignment tend to be those that would otherwise be associated with low phylogenetic accuracy, and that the presence of gaps in any given sequence does not seem to disturb the phylogenetic estimates of other sequences. The MaxAlign web-server is freely available online at http://www.cbs.dtu.dk/services/MaxAlign where supplementary information can also be found. The program is also freely available as a Perl stand-alone package.

Alignment methods: strategies, challenges, benchmarking, and comparative overview.

PubMed

Löytynoja, Ari

2012-01-01

Comparative evolutionary analyses of molecular sequences are solely based on the identities and differences detected between homologous characters. Errors in this homology statement, that is errors in the alignment of the sequences, are likely to lead to errors in the downstream analyses. Sequence alignment and phylogenetic inference are tightly connected and many popular alignment programs use the phylogeny to divide the alignment problem into smaller tasks. They then neglect the phylogenetic tree, however, and produce alignments that are not evolutionarily meaningful. The use of phylogeny-aware methods reduces the error but the resulting alignments, with evolutionarily correct representation of homology, can challenge the existing practices and methods for viewing and visualising the sequences. The inter-dependency of alignment and phylogeny can be resolved by joint estimation of the two; methods based on statistical models allow for inferring the alignment parameters from the data and correctly take into account the uncertainty of the solution but remain computationally challenging. Widely used alignment methods are based on heuristic algorithms and unlikely to find globally optimal solutions. The whole concept of one correct alignment for the sequences is questionable, however, as there typically exist vast numbers of alternative, roughly equally good alignments that should also be considered. This uncertainty is hidden by many popular alignment programs and is rarely correctly taken into account in the downstream analyses. The quest for finding and improving the alignment solution is complicated by the lack of suitable measures of alignment goodness. The difficulty of comparing alternative solutions also affects benchmarks of alignment methods and the results strongly depend on the measure used. As the effects of alignment error cannot be predicted, comparing the alignments' performance in downstream analyses is recommended.

System and method for 2D workpiece alignment

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

Weaver, William T.; Carlson, Charles T.; Smith, Scott A.

2015-07-14

A carrier capable of holding one or more workpieces is disclosed. The carrier includes movable projections located along the sides of each cell in the carrier. This carrier, in conjunction with a separate alignment apparatus, aligns each workpiece within its respective cell against several alignment pins, using a multiple step alignment process to guarantee proper positioning of the workpiece in the cell. First, the workpieces are moved toward one side of the cell. Once the workpieces have been aligned against this side, the workpieces are then moved toward an adjacent orthogonal side such that the workpieces are aligned to twomore » sides of the cell. Once aligned, the workpiece is held in place by the projections located along each side of each cell. In addition, the alignment pins are also used to align the associated mask, thereby guaranteeing that the mask is properly aligned to the workpiece.« less

The power of change: interpersonal attraction as a function of attitude similarity and attitude alignment.

PubMed

Reid, Chelsea A; Davis, Jody L; Green, Jeffrey D

2013-01-01

Does attitude alignment predict attraction? Would you like a stranger more who shifts her/his attitudes to more closely align with yours? In pairs, participants (N = 77) discussed social issues about which they disagreed and received false feedback on whether the partner engaged in attitude alignment (shifted her/his attitudes toward the participant's attitude) following discussion. Participants also received false feedback about the proportion of similarity to the partner on a set of issues (i.e., 25%, 50%, or 75%). Participants reported greater attraction to partners who engaged in attitude alignment and who were more similar. Moreover, similarity and attitude alignment interacted. Similarity predicted attraction when attitude alignment did not occur, but did not predict attraction when attitude alignment did occur. Finally, partner attitude alignment led to participant attitude alignment, and perceived reasoning ability mediated the attitude alignment-attraction relationship.

Aligned Single Wall Carbon Nanotube Polymer Composites Using an Electric Field

NASA Technical Reports Server (NTRS)

Park, Cheol; Wiklinson, John; Banda, Sumanth; Ounaies, Zoubeida; Wise, Kristopher E.; Sauti, Godfrey; Lillehei, Peter T.; Harrison, Joycelyn S.

2005-01-01

While high shear alignment has been shown to improve the mechanical properties of single wall carbon nanotubes (SWNT)-polymer composites, it is difficult to control and often results in degradation of the electrical and dielectric properties of the composite. Here, we report a novel method to actively align SWNTs in a polymer matrix, which allows for control over the degree of alignment of SWNTs without the side effects of shear alignment. In this process, SWNTs are aligned via field-induced dipolar interactions among the nanotubes under an AC electric field in a liquid matrix followed by immobilization by photopolymerization while maintaining the electric field. Alignment of SWNTs was controlled as a function of magnitude, frequency, and application time of the applied electric field. The degree of SWNT alignment was assessed using optical microscopy and polarized Raman spectroscopy and the morphology of the aligned nanocomposites was investigated by high resolution scanning electron microscopy. The structure of the field induced aligned SWNTs is intrinsically different from that of shear aligned SWNTs. In the present work, SWNTs are not only aligned along the field, but also migrate laterally to form thick, aligned SWNT percolative columns between the electrodes. The actively aligned SWNTs amplify the electrical and dielectric properties in addition to improving the mechanical properties of the composite. All of these properties of the aligned nanocomposites exhibited anisotropic characteristics, which were controllable by tuning the applied field conditions.

ALMA observations of feeding and feedback in nearby Seyfert galaxies: an AGN-driven outflow in NGC 1433

NASA Astrophysics Data System (ADS)

Combes, F.; García-Burillo, S.; Casasola, V.; Hunt, L.; Krips, M.; Baker, A. J.; Boone, F.; Eckart, A.; Marquez, I.; Neri, R.; Schinnerer, E.; Tacconi, L. J.

2013-10-01

We report ALMA observations of CO(3-2) emission in the Seyfert 2 galaxy NGC 1433 at the unprecedented spatial resolution of 0.''5 = 24 pc. Our aim is to probe active galactic nucleus (AGN) feeding and feedback phenomena through the morphology and dynamics of the gas inside the central kpc. The galaxy NGC 1433 is a strongly barred spiral with three resonant rings: one at the ultra-harmonic resonance near corotation, and the others at the outer and inner Lindblad resonances (OLR and ILR). A nuclear bar of 400 pc radius is embedded in the large-scale primary bar. The CO map, which covers the whole nuclear region (nuclear bar and ring), reveals a nuclear gaseous spiral structure, inside the nuclear ring encircling the nuclear stellar bar. This gaseous spiral is well correlated with the dusty spiral seen in Hubble Space Telescope (HST) images. The nuclear spiral winds up in a pseudo-ring at ~200 pc radius, which might correspond to the inner ILR. Continuum emission is detected at 0.87 mm only at the very centre, and its origin is more likely thermal dust emission than non-thermal emission from the AGN. It might correspond to the molecular torus expected to exist in this Seyfert 2 galaxy. The HCN(4-3) and HCO+(4-3) lines were observed simultaneously, but only upper limits are derived, with a ratio to the CO(3-2) line lower than 1/60 at 3σ, indicating a relatively low abundance of very dense gas. The kinematics of the gas over the nuclear disk reveal rather regular rotation only slightly perturbed by streaming motions due to the spiral; the primary and secondary bars are too closely aligned with the galaxy major or minor axis to leave a signature in the projected velocities. Near the nucleus, there is an intense high-velocity CO emission feature redshifted to 200 km s-1 (if located in the plane), with a blue-shifted counterpart, at 2'' (100 pc) from the centre. While the CO spectra are quite narrow in the centre, this wide component is interpreted as an outflow involving a molecular mass of 3.6 × 106 M⊙ and a flow rate ~7 M⊙/yr. The flow could be in part driven by the central star formation, but is mainly boosted by the AGN through its radio jets. Based on observations carried out with ALMA in Cycle 0.

Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner.

PubMed

Lu, David V; Brown, Randall H; Arumugam, Manimozhiyan; Brent, Michael R

2009-07-01

The most accurate way to determine the intron-exon structures in a genome is to align spliced cDNA sequences to the genome. Thus, cDNA-to-genome alignment programs are a key component of most annotation pipelines. The scoring system used to choose the best alignment is a primary determinant of alignment accuracy, while heuristics that prevent consideration of certain alignments are a primary determinant of runtime and memory usage. Both accuracy and speed are important considerations in choosing an alignment algorithm, but scoring systems have received much less attention than heuristics. We present Pairagon, a pair hidden Markov model based cDNA-to-genome alignment program, as the most accurate aligner for sequences with high- and low-identity levels. We conducted a series of experiments testing alignment accuracy with varying sequence identity. We first created 'perfect' simulated cDNA sequences by splicing the sequences of exons in the reference genome sequences of fly and human. The complete reference genome sequences were then mutated to various degrees using a realistic mutation simulator and the perfect cDNAs were aligned to them using Pairagon and 12 other aligners. To validate these results with natural sequences, we performed cross-species alignment using orthologous transcripts from human, mouse and rat. We found that aligner accuracy is heavily dependent on sequence identity. For sequences with 100% identity, Pairagon achieved accuracy levels of >99.6%, with one quarter of the errors of any other aligner. Furthermore, for human/mouse alignments, which are only 85% identical, Pairagon achieved 87% accuracy, higher than any other aligner. Pairagon source and executables are freely available at http://mblab.wustl.edu/software/pairagon/

Image-based quantification of fiber alignment within electrospun tissue engineering scaffolds is related to mechanical anisotropy.

PubMed

Fee, Timothy; Downs, Crawford; Eberhardt, Alan; Zhou, Yong; Berry, Joel

2016-07-01

It is well documented that electrospun tissue engineering scaffolds can be fabricated with variable degrees of fiber alignment to produce scaffolds with anisotropic mechanical properties. Several attempts have been made to quantify the degree of fiber alignment within an electrospun scaffold using image-based methods. However, these methods are limited by the inability to produce a quantitative measure of alignment that can be used to make comparisons across publications. Therefore, we have developed a new approach to quantifying the alignment present within a scaffold from scanning electron microscopic (SEM) images. The alignment is determined by using the Sobel approximation of the image gradient to determine the distribution of gradient angles with an image. This data was fit to a Von Mises distribution to find the dispersion parameter κ, which was used as a quantitative measure of fiber alignment. We fabricated four groups of electrospun polycaprolactone (PCL) + Gelatin scaffolds with alignments ranging from κ = 1.9 (aligned) to κ = 0.25 (random) and tested our alignment quantification method on these scaffolds. It was found that our alignment quantification method could distinguish between scaffolds of different alignments more accurately than two other published methods. Additionally, the alignment parameter κ was found to be a good predictor the mechanical anisotropy of our electrospun scaffolds. The ability to quantify fiber alignment within and make direct comparisons of scaffold fiber alignment across publications can reduce ambiguity between published results where cells are cultured on "highly aligned" fibrous scaffolds. This could have important implications for characterizing mechanics and cellular behavior on aligned tissue engineering scaffolds. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1680-1686, 2016. © 2016 Wiley Periodicals, Inc.

Aligning for accountable care: Strategic practices for change in accountable care organizations.

PubMed

Hilligoss, Brian; Song, Paula H; McAlearney, Ann Scheck

Alignment within accountable care organizations (ACOs) is crucial if these new entities are to achieve their lofty goals. However, the concept of alignment remains underexamined, and we know little about the work entailed in creating alignment. The aim of this study was to develop the concept of aligning by identifying and describing the strategic practices administrators use to align the structures, processes, and behaviors of their organizations and individual providers in pursuit of accountable care. We conducted 2-year qualitative case studies of four ACOs that have assumed full risk for the costs and quality of care for defined populations. Five strategic aligning practices were used by all four ACOs. Informing both aligns providers' understandings with the goals and value proposition of the ACO and aligns the providers' attention with the drivers of performance. Involving both aligns ACO leaders' understandings with the realities facing providers and aligns the policies of the ACO with the needs of providers. Enhancing both aligns the operations of individual provider practices with the operations of the ACO and aligns the trust of providers with the ACO. Motivating aligns what providers value with the goals of the ACO. Finally, evolving is a metapractice of learning and adapting that guides the execution of the other four practices. Our findings suggest that there are second-order cognitive (e.g., understandings and attention) and cultural (e.g., trust and values) levels of alignment, as well as a first-order operational level (organizational structures, processes, and incentives). A well-aligned organization may require ongoing repositioning at each of these levels, as well as attention to both cooperative and coordinative dimensions of alignment. Implications for research and practice are discussed.

Using structure to explore the sequence alignment space of remote homologs.

PubMed

Kuziemko, Andrew; Honig, Barry; Petrey, Donald

2011-10-01

Protein structure modeling by homology requires an accurate sequence alignment between the query protein and its structural template. However, sequence alignment methods based on dynamic programming (DP) are typically unable to generate accurate alignments for remote sequence homologs, thus limiting the applicability of modeling methods. A central problem is that the alignment that is "optimal" in terms of the DP score does not necessarily correspond to the alignment that produces the most accurate structural model. That is, the correct alignment based on structural superposition will generally have a lower score than the optimal alignment obtained from sequence. Variations of the DP algorithm have been developed that generate alternative alignments that are "suboptimal" in terms of the DP score, but these still encounter difficulties in detecting the correct structural alignment. We present here a new alternative sequence alignment method that relies heavily on the structure of the template. By initially aligning the query sequence to individual fragments in secondary structure elements and combining high-scoring fragments that pass basic tests for "modelability", we can generate accurate alignments within a small ensemble. Our results suggest that the set of sequences that can currently be modeled by homology can be greatly extended.

Choosing and Using Introns in Molecular Phylogenetics

PubMed Central

Creer, Simon

2007-01-01

Introns are now commonly used in molecular phylogenetics in an attempt to recover gene trees that are concordant with species trees, but there are a range of genomic, logistical and analytical considerations that are infrequently discussed in empirical studies that utilize intron data. This review outlines expedient approaches for locus selection, overcoming paralogy problems, recombination detection methods and the identification and incorporation of LVHs in molecular systematics. A range of parsimony and Bayesian analytical approaches are also described in order to highlight the methods that can currently be employed to align sequences and treat indels in subsequent analyses. By covering the main points associated with the generation and analysis of intron data, this review aims to provide a comprehensive introduction to using introns (or any non-coding nuclear data partition) in contemporary phylogenetics. PMID:19461984

Aeromagnetic Expression of Buried Basaltic Volcanoes Near Yucca Mountain, Nevada

USGS Publications Warehouse

O'Leary, Dennis W.; Mankinen, E.A.; Blakely, R.J.; Langenheim, V.E.; Ponce, D.A.

2002-01-01

A high-resolution aeromagnetic survey has defined a number of small dipolar anomalies indicating the presence of magnetic bodies buried beneath the surface of Crater Flat and the Amargosa Desert. Results of potential-field modeling indicate that isolated, small-volume, highly magnetic bodies embedded within the alluvial deposits of both areas produce the anomalies. Their physical characteristics and the fact that they tend to be aligned along major structural trends provide strong support for the hypothesis that the anomalies reflect buried basaltic volcanic centers. Other, similar anomalies are identified as possible targets for further investigation. High-resolution gravity and ground-magnetic surveys, perhaps along with drilling sources of selected anomalies and radiometric age determinations, can provide valuable constraints in estimating potential volcanic hazard to the potential nuclear waste repository at Yucca Mountain.

Xylopsora canopeorum (Umbilicariaceae), a new lichen species from the canopy of Sequoia sempervirens.

PubMed

Bendiksby, Mika; Næsborg, Rikke Reese; Timdal, Einar

2018-01-01

Xylopsora canopeorum Timdal, Reese Næsborg & Bendiksby is described as a new species occupying the crowns of large Sequoia sempervirens trees in California, USA. The new species is supported by morphology, anatomy, secondary chemistry and DNA sequence data. While similar in external appearance to X. friesii , it is distinguished by forming smaller, partly coralloid squamules, by the occurrence of soralia and, in some specimens, by the presence of thamnolic acid in addition to friesiic acid in the thallus. Molecular phylogenetic results are based on nuclear (ITS and LSU) as well as mitochondrial (SSU) ribosomal DNA sequence alignments. Phylogenetic hypotheses obtained using Bayesian Inference, Maximum Likelihood and Maximum Parsimony all support X. canopeorum as a distinct evolutionary lineage belonging to the X. caradocensis - X. friesii clade.

Xylopsora canopeorum (Umbilicariaceae), a new lichen species from the canopy of Sequoia sempervirens

PubMed Central

Bendiksby, Mika; Næsborg, Rikke Reese; Timdal, Einar

2018-01-01

Abstract Xylopsora canopeorum Timdal, Reese Næsborg & Bendiksby is described as a new species occupying the crowns of large Sequoia sempervirens trees in California, USA. The new species is supported by morphology, anatomy, secondary chemistry and DNA sequence data. While similar in external appearance to X. friesii, it is distinguished by forming smaller, partly coralloid squamules, by the occurrence of soralia and, in some specimens, by the presence of thamnolic acid in addition to friesiic acid in the thallus. Molecular phylogenetic results are based on nuclear (ITS and LSU) as well as mitochondrial (SSU) ribosomal DNA sequence alignments. Phylogenetic hypotheses obtained using Bayesian Inference, Maximum Likelihood and Maximum Parsimony all support X. canopeorum as a distinct evolutionary lineage belonging to the X. caradocensis–X. friesii clade. PMID:29559828

Irradiation setup at the U-120M cyclotron facility

NASA Astrophysics Data System (ADS)

Křížek, F.; Ferencei, J.; Matlocha, T.; Pospíšil, J.; Príbeli, P.; Raskina, V.; Isakov, A.; Štursa, J.; Vaňát, T.; Vysoká, K.

2018-06-01

This paper describes parameters of the proton beams provided by the U-120M cyclotron and the related irradiation setup at the open access irradiation facility at the Nuclear Physics Institute of the Czech Academy of Sciences. The facility is suitable for testing radiation hardness of various electronic components. The use of the setup is illustrated by a measurement of an error rate for errors caused by Single Event Transients in an SRAM-based Xilinx XC3S200 FPGA. This measurement provides an estimate of a possible occurrence of Single Event Transients. Data suggest that the variation of error rate of the Single Event Effects for different clock phase shifts is not significant enough to use clock phase alignment with the beam as a fault mitigation technique.

A trajectory generation and system characterization model for cislunar low-thrust spacecraft. Volume 2: Technical manual

NASA Technical Reports Server (NTRS)

Korsmeyer, David J.; Pinon, Elfego, III; Oconnor, Brendan M.; Bilby, Curt R.

1990-01-01

The documentation of the Trajectory Generation and System Characterization Model for the Cislunar Low-Thrust Spacecraft is presented in Technical and User's Manuals. The system characteristics and trajectories of low thrust nuclear electric propulsion spacecraft can be generated through the use of multiple system technology models coupled with a high fidelity trajectory generation routine. The Earth to Moon trajectories utilize near Earth orbital plane alignment, midcourse control dependent upon the spacecraft's Jacobian constant, and capture to target orbit utilizing velocity matching algorithms. The trajectory generation is performed in a perturbed two-body equinoctial formulation and the restricted three-body formulation. A single control is determined by the user for the interactive midcourse portion of the trajectory. The full spacecraft system characteristics and trajectory are provided as output.

Evidence for Coherent Transfer of para-Hydrogen-Induced Polarization at Low Magnetic Fields.

PubMed

Kiryutin, Alexey S; Yurkovskaya, Alexandra V; Kaptein, Robert; Vieth, Hans-Martin; Ivanov, Konstantin L

2013-08-01

We have investigated the mechanism of para-hydrogen-induced polarization (PHIP) transfer from the original strongly aligned protons to other nuclei at low external magnetic fields. Although it is known that PHIP is efficiently transferred at low fields, the nature of the transfer mechanism, that is, coherent spin mixing or cross-relaxation, is not well established. Polarization transfer kinetics for individual protons of styrene was, for the first time, measured and modeled theoretically. Pronounced oscillations were observed indicating a coherent transfer mechanism. Spin coherences were excited by passing through an avoided level crossing of the nuclear spin energy levels. Transfer at avoided level crossings is selective with respect to spin order. Our work provides evidence that the coherent PHIP transfer mechanism is dominant at low magnetic fields.

Medical image registration: basic science and clinical implications.

PubMed

Imran, Muhammad Babar; Meo, Sultan Ayoub; Yousuf, Mohammad; Othman, Saleh; Shahid, Abubakar

2010-01-01

Image Registration is a process of aligning two or more images so that corresponding feature can be related objectively. Integration of corresponding and complementary information from various images has become an important area of computation in medical imaging. Merging different images of the same patient taken by different modalities or acquired at different times is quite useful in interpreting lower resolution functional images, such as those provided by nuclear medicine, in determining spatial relationships of structures seen in different modalities. This will help in planning surgery and longitudinal follow up. The aim of this article was to introduce image registration to all those who are working in field of medical sciences in general and medical doctors in particular; and indicate how and where this specialty is moving to provide better health care services.

Intracellular distribution and stability of a luminescent rhenium(i) tricarbonyl tetrazolato complex using epifluorescence microscopy in conjunction with X-ray fluorescence imaging.

PubMed

Wedding, J L; Harris, H H; Bader, C A; Plush, S E; Mak, R; Massi, M; Brooks, D A; Lai, B; Vogt, S; Werrett, M V; Simpson, P V; Skelton, B W; Stagni, S

2017-04-19

Optical epifluorescence microscopy was used in conjunction with X-ray fluorescence imaging to monitor the stability and intracellular distribution of the luminescent rhenium(i) complex fac-[Re(CO) 3 (phen)L], where phen = 1,10-phenathroline and L = 5-(4-iodophenyl)tetrazolato, in 22Rv1 cells. The rhenium complex showed no signs of ancillary ligand dissociation, a conclusion based on data obtained via X-ray fluorescence imaging aligning iodine and rhenium distributions. A diffuse reticular localisation was detected for the complex in the nuclear/perinuclear region of cells, by either optical or X-ray fluorescence imaging techniques. X-ray fluorescence also showed that the rhenium complex disrupted the homeostasis of some biologically relevant elements, such as chlorine, potassium and zinc.

Intrinsic alignments of galaxies in the EAGLE and cosmo-OWLS simulations

NASA Astrophysics Data System (ADS)

Velliscig, Marco; Cacciato, Marcello; Schaye, Joop; Hoekstra, Henk; Bower, Richard G.; Crain, Robert A.; van Daalen, Marcel P.; Furlong, Michelle; McCarthy, I. G.; Schaller, Matthieu; Theuns, Tom

2015-12-01

We report results for the alignments of galaxies in the EAGLE and cosmo-OWLS hydrodynamical cosmological simulations as a function of galaxy separation (-1 ≤ log10(r/[ h-1 Mpc]) ≤ 2) and halo mass (10.7 ≤ log10(M200/[h-1 M⊙]) ≤ 15). We focus on two classes of alignments: the orientations of galaxies with respect to either the directions to, or the orientations of, surrounding galaxies. We find that the strength of the alignment is a strongly decreasing function of the distance between galaxies. For galaxies hosted by the most massive haloes in our simulations the alignment can remain significant up to ˜100 Mpc. Galaxies hosted by more massive haloes show stronger alignment. At a fixed halo mass, more aspherical or prolate galaxies exhibit stronger alignments. The spatial distribution of satellites is anisotropic and significantly aligned with the major axis of the main host halo. The major axes of satellite galaxies, when all stars are considered, are preferentially aligned towards the centre of the main host halo. The predicted projected direction-orientation alignment, ɛg+(rp), is in broad agreement with recent observations. We find that the orientation-orientation alignment is weaker than the orientation-direction alignment on all scales. Overall, the strength of galaxy alignments depends strongly on the subset of stars that are used to measure the orientations of galaxies and it is always weaker than the alignment of dark matter haloes. Thus, alignment models that use halo orientation as a direct proxy for galaxy orientation overestimate the impact of intrinsic galaxy alignments.

Cerebellar Purkinje Cells Generate Highly Correlated Spontaneous Slow-Rate Fluctuations.

PubMed

Cao, Ying; Liu, Yu; Jaeger, Dieter; Heck, Detlef H

2017-01-01

Cerebellar Purkinje cells (PC) fire action potentials at high, sustained rates. Changes in spike rate that last a few tens of milliseconds encode sensory and behavioral events. Here we investigated spontaneous fluctuations of PC simple spike rate at a slow time scale of the order of 1 s. Simultaneous recordings from pairs of PCs that were aligned either along the sagittal or transversal axis of the cerebellar cortex revealed that simple spike rate fluctuations at the 1 s time scale were highly correlated. Each pair of PCs had either a predominantly positive or negative slow-rate correlation, with negative correlations observed only in PC pairs aligned along the transversal axis. Slow-rate correlations were independent of faster rate changes that were correlated with fluid licking behavior. Simultaneous recordings from PCs and cerebellar nuclear (CN) neurons showed that slow-rate fluctuations in PC and CN activity were also highly correlated, but their correlations continually alternated between periods of positive and negative correlation. The functional significance of this new aspect of cerebellar spike activity remains to be determined. Correlated slow-rate fluctuations seem too slow to be involved in the real-time control of ongoing behavior. However, slow-rate fluctuations of PCs converging on the same CN neuron are likely to modulate the excitability of the CN neuron, thus introduce a possible slow modulation of cerebellar output activity.

Formation mechanism of gas bubble superlattice in UMo metal fuels: Phase-field modeling investigation

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

Hu, Shenyang; Burkes, Douglas E.; Lavender, Curt A.

2016-07-08

Nano-gas bubble superlattices are often observed in irradiated UMo nuclear fuels. However, the for- mation mechanism of gas bubble superlattices is not well understood. A number of physical processes may affect the gas bubble nucleation and growth; hence, the morphology of gas bubble microstructures including size and spatial distributions. In this work, a phase-field model integrating a first-passage Monte Carlo method to investigate the formation mechanism of gas bubble superlattices was devel- oped. Six physical processes are taken into account in the model: 1) heterogeneous generation of gas atoms, vacancies, and interstitials informed from atomistic simulations; 2) one-dimensional (1-D) migration of interstitials; 3) irradiation-induced dissolution of gas atoms; 4) recombination between vacancies and interstitials; 5) elastic interaction; and 6) heterogeneous nucleation of gas bubbles. We found that the elastic interaction doesn’t cause the gas bubble alignment, and fast 1-D migration of interstitials alongmore » $$\\langle$$110$$\\rangle$$ directions in the body-centered cubic U matrix causes the gas bubble alignment along $$\\langle$$110$$\\rangle$$ directions. It implies that 1-D interstitial migration along [110] direction should be the primary mechanism of a fcc gas bubble superlattice which is observed in bcc UMo alloys. Simulations also show that fission rates, saturated gas concentration, and elastic interaction all affect the morphology of gas bubble microstructures.« less

Investigations of the local environment and macroscopic alignment behavior of novel polymerizeable lyotropic liquid crystals using nuclear magnetic resonance

NASA Astrophysics Data System (ADS)

Juang, Elizabeth

In this dissertation, a variety of NMR techniques were used to explore the local environment of novel polymerizeable lyotropic liquid crystals (LLC). The LLC monomers examined in this study self-assemble in the presence of a small amount of water to form uniform, nanometer-scale tubes with aqueous interiors. The phase architecture is retained upon photopolymerization to yield the resulting nanoporous material. By dissolving reactive precursors into the aqueous phase, well- structured nancomposite materials have also been formed. Proposed uses for these novel polymerizeable LLCs are as porous water filtration membranes, as heterogeneous organic catalysts, and as nanocomposite materials for load bearing and optical applications. In order to better exploit these polymerizeable LLCs for materials development, the local environment must be examined. In addition, the macroscopic orientation of these materials remains an important step in their advancement. Various NMR studies were conducted on these novel LLCs. NMR T1 relaxation measurements were conducted to elucidate the local environment and dynamics of the 23Na counterions located inside the aqueous channels. 2H NMR line shape analyses were used to characterize the local structure and dynamics near the hydrophilic headgroup. 29 Si NMR studies were performed on silica nanocomposites formed with these LLC structures. Finally, the macroscopic alignment behavior of these novel LLCs using shear and magnetic fields was examined.

Superimposition of protein structures with dynamically weighted RMSD.

PubMed

Wu, Di; Wu, Zhijun

2010-02-01

In protein modeling, one often needs to superimpose a group of structures for a protein. A common way to do this is to translate and rotate the structures so that the square root of the sum of squares of coordinate differences of the atoms in the structures, called the root-mean-square deviation (RMSD) of the structures, is minimized. While it has provided a general way of aligning a group of structures, this approach has not taken into account the fact that different atoms may have different properties and they should be compared differently. For this reason, when superimposed with RMSD, the coordinate differences of different atoms should be evaluated with different weights. The resulting RMSD is called the weighted RMSD (wRMSD). Here we investigate the use of a special wRMSD for superimposing a group of structures with weights assigned to the atoms according to certain thermal motions of the atoms. We call such an RMSD the dynamically weighted RMSD (dRMSD). We show that the thermal motions of the atoms can be obtained from several sources such as the mean-square fluctuations that can be estimated by Gaussian network model analysis. We show that the superimposition of structures with dRMSD can successfully identify protein domains and protein motions, and that it has important implications in practice, e.g., in aligning the ensemble of structures determined by nuclear magnetic resonance.

Alignment method for parabolic trough solar concentrators

DOEpatents

Diver, Richard B [Albuquerque, NM

2010-02-23

A Theoretical Overlay Photographic (TOP) alignment method uses the overlay of a theoretical projected image of a perfectly aligned concentrator on a photographic image of the concentrator to align the mirror facets of a parabolic trough solar concentrator. The alignment method is practical and straightforward, and inherently aligns the mirror facets to the receiver. When integrated with clinometer measurements for which gravity and mechanical drag effects have been accounted for and which are made in a manner and location consistent with the alignment method, all of the mirrors on a common drive can be aligned and optimized for any concentrator orientation.

Increased alignment sensitivity improves the usage of genome alignments for comparative gene annotation.

PubMed

Sharma, Virag; Hiller, Michael

2017-08-21

Genome alignments provide a powerful basis to transfer gene annotations from a well-annotated reference genome to many other aligned genomes. The completeness of these annotations crucially depends on the sensitivity of the underlying genome alignment. Here, we investigated the impact of the genome alignment parameters and found that parameters with a higher sensitivity allow the detection of thousands of novel alignments between orthologous exons that have been missed before. In particular, comparisons between species separated by an evolutionary distance of >0.75 substitutions per neutral site, like human and other non-placental vertebrates, benefit from increased sensitivity. To systematically test if increased sensitivity improves comparative gene annotations, we built a multiple alignment of 144 vertebrate genomes and used this alignment to map human genes to the other 143 vertebrates with CESAR. We found that higher alignment sensitivity substantially improves the completeness of comparative gene annotations by adding on average 2382 and 7440 novel exons and 117 and 317 novel genes for mammalian and non-mammalian species, respectively. Our results suggest a more sensitive alignment strategy that should generally be used for genome alignments between distantly-related species. Our 144-vertebrate genome alignment and the comparative gene annotations (https://bds.mpi-cbg.de/hillerlab/144VertebrateAlignment_CESAR/) are a valuable resource for comparative genomics. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

HubAlign: an accurate and efficient method for global alignment of protein-protein interaction networks.

PubMed

Hashemifar, Somaye; Xu, Jinbo

2014-09-01

High-throughput experimental techniques have produced a large amount of protein-protein interaction (PPI) data. The study of PPI networks, such as comparative analysis, shall benefit the understanding of life process and diseases at the molecular level. One way of comparative analysis is to align PPI networks to identify conserved or species-specific subnetwork motifs. A few methods have been developed for global PPI network alignment, but it still remains challenging in terms of both accuracy and efficiency. This paper presents a novel global network alignment algorithm, denoted as HubAlign, that makes use of both network topology and sequence homology information, based upon the observation that topologically important proteins in a PPI network usually are much more conserved and thus, more likely to be aligned. HubAlign uses a minimum-degree heuristic algorithm to estimate the topological and functional importance of a protein from the global network topology information. Then HubAlign aligns topologically important proteins first and gradually extends the alignment to the whole network. Extensive tests indicate that HubAlign greatly outperforms several popular methods in terms of both accuracy and efficiency, especially in detecting functionally similar proteins. HubAlign is available freely for non-commercial purposes at http://ttic.uchicago.edu/∼hashemifar/software/HubAlign.zip. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Phylogenic inference using alignment-free methods for applications in microbial community surveys using 16s rRNA gene

PubMed Central

2017-01-01

The diversity of microbiota is best explored by understanding the phylogenetic structure of the microbial communities. Traditionally, sequence alignment has been used for phylogenetic inference. However, alignment-based approaches come with significant challenges and limitations when massive amounts of data are analyzed. In the recent decade, alignment-free approaches have enabled genome-scale phylogenetic inference. Here we evaluate three alignment-free methods: ACS, CVTree, and Kr for phylogenetic inference with 16s rRNA gene data. We use a taxonomic gold standard to compare the accuracy of alignment-free phylogenetic inference with that of common microbiome-wide phylogenetic inference pipelines based on PyNAST and MUSCLE alignments with FastTree and RAxML. We re-simulate fecal communities from Human Microbiome Project data to evaluate the performance of the methods on datasets with properties of real data. Our comparisons show that alignment-free methods are not inferior to alignment-based methods in giving accurate and robust phylogenic trees. Moreover, consensus ensembles of alignment-free phylogenies are superior to those built from alignment-based methods in their ability to highlight community differences in low power settings. In addition, the overall running times of alignment-based and alignment-free phylogenetic inference are comparable. Taken together our empirical results suggest that alignment-free methods provide a viable approach for microbiome-wide phylogenetic inference. PMID:29136663

CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments.

PubMed

Zhou, Carol L Ecale

2015-01-01

In order to better define regions of similarity among related protein structures, it is useful to identify the residue-residue correspondences among proteins. Few codes exist for constructing a one-to-many multiple sequence alignment derived from a set of structure or sequence alignments, and a need was evident for creating such a tool for combining pairwise structure alignments that would allow for insertion of gaps in the reference structure. This report describes a new Python code, CombAlign, which takes as input a set of pairwise sequence alignments (which may be structure based) and generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA). The use and utility of CombAlign was demonstrated by generating gapped MSSAs using sets of pairwise structure-based sequence alignments between structure models of the matrix protein (VP40) and pre-small/secreted glycoprotein (sGP) of Reston Ebolavirus and the corresponding proteins of several other filoviruses. The gapped MSSAs revealed structure-based residue-residue correspondences, which enabled identification of structurally similar versus differing regions in the Reston proteins compared to each of the other corresponding proteins. CombAlign is a new Python code that generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA) given a set of pairwise sequence alignments (which may be structure based). CombAlign has utility in assisting the user in distinguishing structurally conserved versus divergent regions on a reference protein structure relative to other closely related proteins. CombAlign was developed in Python 2.6, and the source code is available for download from the GitHub code repository.

Health care's new game changer. Thinking like a health plan.

PubMed

Eggbeer, Bill; Bowers, Krista

2014-10-01

The transition for hospitals from having only a provider's perspective to thinking more like a health plan will require strategic alignment on four fronts: Health plan alignment. Hospital and physician alignment. Leadership alignment. Organizational alignment.

Iterative non-sequential protein structural alignment.

PubMed

Salem, Saeed; Zaki, Mohammed J; Bystroff, Christopher

2009-06-01

Structural similarity between proteins gives us insights into their evolutionary relationships when there is low sequence similarity. In this paper, we present a novel approach called SNAP for non-sequential pair-wise structural alignment. Starting from an initial alignment, our approach iterates over a two-step process consisting of a superposition step and an alignment step, until convergence. We propose a novel greedy algorithm to construct both sequential and non-sequential alignments. The quality of SNAP alignments were assessed by comparing against the manually curated reference alignments in the challenging SISY and RIPC datasets. Moreover, when applied to a dataset of 4410 protein pairs selected from the CATH database, SNAP produced longer alignments with lower rmsd than several state-of-the-art alignment methods. Classification of folds using SNAP alignments was both highly sensitive and highly selective. The SNAP software along with the datasets are available online at http://www.cs.rpi.edu/~zaki/software/SNAP.

Electric-field-induced flow-aligning state in a nematic liquid crystal.

PubMed

Fatriansyah, Jaka Fajar; Orihara, Hiroshi

2015-04-01

The response of shear stress to a weak ac electric field as a probe is measured in a nematic liquid crystal under shear flow and dc electric fields. Two states with different responses are clearly observed when the dc electric field is changed at a constant shear rate: the flow aligning and non-flow aligning states. The director lies in the shear plane in the flow aligning state and out of the plane in the non-flow aligning state. Through application of dc electric field, the non-flow aligning state can be changed to the flow aligning state. In the transition from the flow aligning state to the non-flow aligning state, it is found that the response increases and the relaxation time becomes longer. Here, the experimental results in the flow aligning state are discussed on the basis of the Ericksen-Leslie theory.

Use of the BINP HLS to measure vertical changes in the locations of the building and ground at the PAL-XFEL

NASA Astrophysics Data System (ADS)

Choi, Hyo-Jin; Seo, Kwang-Won; Gil, Kye-Hwan; Kim, Seung-Hwan; Kang, Heung-Sik

2016-09-01

The Pohang Accelerator Laboratory's X-ray free-electron laser (PAL-XFEL), a 4 th generation light source, is currently being installed and will be completed by December 2015 so that users can be supported beginning in 2016. The PAL-XFEL equipment must continuously maintain the bunch-tobunch beam parameters (60 Hz, Energy: 10 GeV, Charge: 200 pC, Bunch Length: 60 fs, Emittance X/Y: 0.481/0.256 mm rad) in order to supply stable photons with the energy and flux appropriate for tests by beamline users. To this end, the PAL-XFEL equipment has to be kept precisely aligned (Linear Accelerator: +/- 100 μm, Undulator: +/- 50 μm). As a part of the process for installing the PAL-XFEL, a GPS-using surface geodetic network is being constructed for precise equipment measurement and alignment, and the installation of a tunnel measurement network inside the buildings is in the preparation stage; additionally, the fiducialization of major equipment is underway. After the PAL-XFEL equipment is optimized and aligned, if the ground and the buildings go through vertical changes during operation, misalignment (and tilt) of the equipment, including various magnets and RF structures, will cause errors in the electron beam's trajectory, which will lead to changes to the beam parameters. For continuous and systemic measurement of vertical changes in the buildings and monitoring of ground sinking and uplifting, the Budker Institute of Nuclear Physics (BINP) Ultrasonic-type Hydrostatic Levelling System (HLS) is to be installed and operated in all sections of the PAL-XFEL for the linear accelerator, the insertion device (undulator) and the beamline. This study will introduce the operation principle, design concept, and advantages (self-calibration) of the HLS and will outline its installation plan and operation plan.

AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework.

PubMed

Zheng, Qi; Grice, Elizabeth A

2016-10-01

Accurate mapping of next-generation sequencing (NGS) reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely) mapped reads. Most available NGS aligners attempt to address this by either removing all non-uniquely mapping reads, or reporting one random or "best" hit based on simple heuristics. Accurate estimation of the mapping quality of NGS reads is therefore critical albeit completely lacking at present. Here we developed a generalized software toolkit "AlignerBoost", which utilizes a Bayesian-based framework to accurately estimate mapping quality of ambiguously mapped NGS reads. We tested AlignerBoost with both simulated and real DNA-seq and RNA-seq datasets at various thresholds. In most cases, but especially for reads falling within repetitive regions, AlignerBoost dramatically increases the mapping precision of modern NGS aligners without significantly compromising the sensitivity even without mapping quality filters. When using higher mapping quality cutoffs, AlignerBoost achieves a much lower false mapping rate while exhibiting comparable or higher sensitivity compared to the aligner default modes, therefore significantly boosting the detection power of NGS aligners even using extreme thresholds. AlignerBoost is also SNP-aware, and higher quality alignments can be achieved if provided with known SNPs. AlignerBoost's algorithm is computationally efficient, and can process one million alignments within 30 seconds on a typical desktop computer. AlignerBoost is implemented as a uniform Java application and is freely available at https://github.com/Grice-Lab/AlignerBoost.

Alignment of the femoral component in a mobile-bearing unicompartmental knee arthroplasty: a study in 10 cadaver femora.

PubMed

Kort, N P; van Raay, J J A M; Thomassen, B J W

2007-08-01

Use of an intramedullary rod is advised for the alignment of the femoral component of an Oxford phase-III prosthesis. There are users moving toward extramedullary alignment, which is merely an indicator of frustration with accuracy of intramedullary alignment. The results of our study with 10 cadaver femora demonstrate that use of a short and long intramedullary femoral rod may result in excessive flexion alignment error of the femoral component. Understanding of the extramedullary alignment possibility and experience with the visual alignment of the femoral drill guide is essential toward minimizing potential errors in the alignment of the femoral component.

Desktop aligner for fabrication of multilayer microfluidic devices.

PubMed

Li, Xiang; Yu, Zeta Tak For; Geraldo, Dalton; Weng, Shinuo; Alve, Nitesh; Dun, Wu; Kini, Akshay; Patel, Karan; Shu, Roberto; Zhang, Feng; Li, Gang; Jin, Qinghui; Fu, Jianping

2015-07-01

Multilayer assembly is a commonly used technique to construct multilayer polydimethylsiloxane (PDMS)-based microfluidic devices with complex 3D architecture and connectivity for large-scale microfluidic integration. Accurate alignment of structure features on different PDMS layers before their permanent bonding is critical in determining the yield and quality of assembled multilayer microfluidic devices. Herein, we report a custom-built desktop aligner capable of both local and global alignments of PDMS layers covering a broad size range. Two digital microscopes were incorporated into the aligner design to allow accurate global alignment of PDMS structures up to 4 in. in diameter. Both local and global alignment accuracies of the desktop aligner were determined to be about 20 μm cm(-1). To demonstrate its utility for fabrication of integrated multilayer PDMS microfluidic devices, we applied the desktop aligner to achieve accurate alignment of different functional PDMS layers in multilayer microfluidics including an organs-on-chips device as well as a microfluidic device integrated with vertical passages connecting channels located in different PDMS layers. Owing to its convenient operation, high accuracy, low cost, light weight, and portability, the desktop aligner is useful for microfluidic researchers to achieve rapid and accurate alignment for generating multilayer PDMS microfluidic devices.

Desktop aligner for fabrication of multilayer microfluidic devices

PubMed Central

Li, Xiang; Yu, Zeta Tak For; Geraldo, Dalton; Weng, Shinuo; Alve, Nitesh; Dun, Wu; Kini, Akshay; Patel, Karan; Shu, Roberto; Zhang, Feng; Li, Gang; Jin, Qinghui; Fu, Jianping

2015-01-01

Multilayer assembly is a commonly used technique to construct multilayer polydimethylsiloxane (PDMS)-based microfluidic devices with complex 3D architecture and connectivity for large-scale microfluidic integration. Accurate alignment of structure features on different PDMS layers before their permanent bonding is critical in determining the yield and quality of assembled multilayer microfluidic devices. Herein, we report a custom-built desktop aligner capable of both local and global alignments of PDMS layers covering a broad size range. Two digital microscopes were incorporated into the aligner design to allow accurate global alignment of PDMS structures up to 4 in. in diameter. Both local and global alignment accuracies of the desktop aligner were determined to be about 20 μm cm−1. To demonstrate its utility for fabrication of integrated multilayer PDMS microfluidic devices, we applied the desktop aligner to achieve accurate alignment of different functional PDMS layers in multilayer microfluidics including an organs-on-chips device as well as a microfluidic device integrated with vertical passages connecting channels located in different PDMS layers. Owing to its convenient operation, high accuracy, low cost, light weight, and portability, the desktop aligner is useful for microfluidic researchers to achieve rapid and accurate alignment for generating multilayer PDMS microfluidic devices. PMID:26233409

Nuclear Forensics: A Capability at Risk (Abbreviated Version)

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

National Research Council of the National Academies

Nuclear forensics is important to our national security. Actions, including provision of appropriate funding, are needed now to sustain and improve the nation's nuclear forensics capabilities. The Department of Homeland Security (DHS), working with cooperating agencies and national laboratories, should plan and implement a sustainable, effective nuclear forensics program. Nuclear forensics is the examination and evaluation of discovered or seized nuclear materials and devices or, in cases of nuclear explosions or radiological dispersals, of detonation signals and post-detonation debris. Nuclear forensic evidence helps law enforcement and intelligence agencies work toward preventing, mitigating, and attributing a nuclear or radiological incident. Thismore » report, requested by DHS, the National Nuclear Security Administration, and the Department of Defense, makes recommendations on how to sustain and improve U.S. nuclear forensics capabilities. The United States has developed a nuclear forensics capability that has been demonstrated in real-world incidents of interdicted materials and in exercises of actions required after a nuclear detonation. The committee, however, has concerns about the program and finds that without strong leadership, careful planning, and additional funds, these capabilities will decline. Major areas of concern include: Organization. The responsibility for nuclear forensics is shared by several agencies without central authority and with no consensus on strategic requirements to guide the program. This organizational complexity hampers the program and could prove to be a major hindrance operationally. Sustainability. The nation's current nuclear forensics capabilities are available primarily because the system of laboratories, equipment, and personnel upon which they depend was developed and funded by the nuclear weapons program. However, the weapons program's funds are declining. Workforce and Infrastructure. Personnel skilled in nuclear forensics are too few and are spread too thinly. Some key facilities are in need of replacement because they are old, outdated, and not built to modern environmental, health, and safety standards. Procedures and Tools. Most nuclear forensics techniques were developed to carry out Cold War missions and to satisfy a different, less restrictive set of environmental, health, and safety standards. Some of the equipment also does not reflect today's technical capabilities. The Executive Office of the President established the National Technical Nuclear Forensics Center under the direction of the Secretary of Homeland Security, to coordinate nuclear forensics in the United States. DHS's responsibility can only be carried out with the cooperation and support of the other agencies involved. The committee recommends that DHS and the other cooperating agencies should: 1. Streamline the organizational structure, aligning authority and responsibility; and develop and issue appropriate requirements documents. 2. Issue a coordinated and integrated implementation plan for fulfilling the requirements and sustaining and improving the program's capabilities. This plan would form the basis for the agencies' multi-year program budget requests. 3. Implement a plan to build and maintain an appropriately sized and composed nuclear forensics workforce, ensuring sufficient staffing at the national laboratories and support for university research, training programs, and collaborative relationships among the national laboratories and other organizations. 4. Adapt nuclear forensics to the challenges of real emergency situations, including, for example, conducting more realistic exercises that are unannounced and that challenge regulations and procedures followed in the normal work environment, and implementing lessons learned. The national laboratories should: 5. Optimize procedures and equipment through R&D to meet program requirements. Modeling and simulation should play an increased role in research, development, and planning. The nuclear forensics community should: 6. Develop standards and procedures for nuclear forensics that are rooted in the same underlying principles that have been recommended to guide modern forensic science. DHS and the other cooperating agencies should: 7. Devise and implement a plan that enables access to relevant information in databases including classified and proprietary databases for nuclear forensics missions. The Executive Office of the President and the Department of State, working with the community of nuclear forensics experts, should: 8. Determine the classes of data and methods that are to be shared internationally and explore mechanisms to accomplish that sharing.« less

Iterative refinement of structure-based sequence alignments by Seed Extension

PubMed Central

Kim, Changhoon; Tai, Chin-Hsien; Lee, Byungkook

2009-01-01

Background Accurate sequence alignment is required in many bioinformatics applications but, when sequence similarity is low, it is difficult to obtain accurate alignments based on sequence similarity alone. The accuracy improves when the structures are available, but current structure-based sequence alignment procedures still mis-align substantial numbers of residues. In order to correct such errors, we previously explored the possibility of replacing the residue-based dynamic programming algorithm in structure alignment procedures with the Seed Extension algorithm, which does not use a gap penalty. Here, we describe a new procedure called RSE (Refinement with Seed Extension) that iteratively refines a structure-based sequence alignment. Results RSE uses SE (Seed Extension) in its core, which is an algorithm that we reported recently for obtaining a sequence alignment from two superimposed structures. The RSE procedure was evaluated by comparing the correctly aligned fractions of residues before and after the refinement of the structure-based sequence alignments produced by popular programs. CE, DaliLite, FAST, LOCK2, MATRAS, MATT, TM-align, SHEBA and VAST were included in this analysis and the NCBI's CDD root node set was used as the reference alignments. RSE improved the average accuracy of sequence alignments for all programs tested when no shift error was allowed. The amount of improvement varied depending on the program. The average improvements were small for DaliLite and MATRAS but about 5% for CE and VAST. More substantial improvements have been seen in many individual cases. The additional computation times required for the refinements were negligible compared to the times taken by the structure alignment programs. Conclusion RSE is a computationally inexpensive way of improving the accuracy of a structure-based sequence alignment. It can be used as a standalone procedure following a regular structure-based sequence alignment or to replace the traditional iterative refinement procedures based on residue-level dynamic programming algorithm in many structure alignment programs. PMID:19589133

Torsional stress impedance and magneto-impedance in (Co0.95Fe0.05)72.5 Si12.5B15 amorphous wire with helical induced anisotropy

NASA Astrophysics Data System (ADS)

Blanco, J. M.; Zhukov, A. P.; González, J.

1999-12-01

The magneto-impedance effect icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/ZH = [Z(H)-Z(Hmax)]/Z(Hmax) has been measured in (Fe0.95Co0.05)72.5B15Si12.5 wire under torsion stress, icons/Journals/Common/xi" ALT="xi" ALIGN="TOP"/> (torsion angle per unit length) with axial magnetic field (H) as parameter. Without stress (icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/Z)H(H) dependence has a non-monotonous shape with first an increase of total impedance Z and then a decrease, i.e. shows a maximum at certain axial magnetic field Hm. It was found that the torsion stress dependence of electrical impedance (torsion impedance), (icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/Z)icons/Journals/Common/xi" ALT="xi" ALIGN="MIDDLE"/> = [Z(icons/Journals/Common/xi" ALT="xi" ALIGN="TOP"/>)-Z(icons/Journals/Common/xi" ALT="xi" ALIGN="TOP"/>max)]/Z(icons/Journals/Common/xi" ALT="xi" ALIGN="TOP"/>max), has asymmetric character with a clear maximum at torsion angle, icons/Journals/Common/xi" ALT="xi" ALIGN="TOP"/> around 7icons/Journals/Common/pi" ALT="pi" ALIGN="TOP"/> rad m-1 in as-cast wire, while (icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/Z)icons/Journals/Common/xi" ALT="xi" ALIGN="MIDDLE"/> reaches a maximum around 170%. Thermal treatments under torsion stress (without and with a previous annealing stage) develop a helical anisotropy on the amorphous wire, which drastically modifies the (icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/Z)icons/Journals/Common/xi" ALT="xi" ALIGN="MIDDLE"/> response. Such treatments were carried out by using current annealing which resulted in a drastic increase of the maximum (icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/Z)icons/Journals/Common/xi" ALT="xi" ALIGN="MIDDLE"/> up to 225%, and a change of torsion dependence of icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/Z with a tendency to a finally symmetric dependence of (icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/Z)icons/Journals/Common/xi" ALT="xi" ALIGN="MIDDLE"/>(icons/Journals/Common/xi" ALT="xi" ALIGN="TOP"/>). The maximum (icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/Z)icons/Journals/Common/xi" ALT="xi" ALIGN="MIDDLE"/> ratio, (icons/Journals/Common/Delta" ALT="Delta" ALIGN="TOP"/> Z/Z)icons/Journals/Common/xi" ALT="xi" ALIGN="TOP"/> m, was obtained under torsion stress of icons/Journals/Common/xi" ALT="xi" ALIGN="TOP"/> = 20icons/Journals/Common/pi" ALT="pi" ALIGN="TOP"/> rad m-1 (in a torsion annealed sample) and = 11 rad m-1 (with pre-annealing and torsion annealing). Observed dependences were explained taking into account the frozen-in magneto-elastic anisotropy owing to the internal stress distribution during the fabrication process, the helical anisotropies induced by the torsion strain and that developed by thermal treatment under torsion stress (torsion annealing). The differences in the shape and intensity of the maximum ( Z/Z) m between the torsion annealed and pre-annealed and torsion annealed samples should be ascribed to the visco-elastic character of the helical anisotropy induced by torsion stress.

Reverse alignment "mirror image" visualization as a laparoscopic training tool improves task performance.

PubMed

Dunnican, Ward J; Singh, T Paul; Ata, Ashar; Bendana, Emma E; Conlee, Thomas D; Dolce, Charles J; Ramakrishnan, Rakesh

2010-06-01

Reverse alignment (mirror image) visualization is a disconcerting situation occasionally faced during laparoscopic operations. This occurs when the camera faces back at the surgeon in the opposite direction from which the surgeon's body and instruments are facing. Most surgeons will attempt to optimize trocar and camera placement to avoid this situation. The authors' objective was to determine whether the intentional use of reverse alignment visualization during laparoscopic training would improve performance. A standard box trainer was configured for reverse alignment, and 34 medical students and junior surgical residents were randomized to train with either forward alignment (DIRECT) or reverse alignment (MIRROR) visualization. Enrollees were tested on both modalities before and after a 4-week structured training program specific to their modality. Student's t test was used to determine differences in task performance between the 2 groups. Twenty-one participants completed the study (10 DIRECT, 11 MIRROR). There were no significant differences in performance time between DIRECT or MIRROR participants during forward or reverse alignment initial testing. At final testing, DIRECT participants had improved times only in forward alignment performance; they demonstrated no significant improvement in reverse alignment performance. MIRROR participants had significant time improvement in both forward and reverse alignment performance at final testing. Reverse alignment imaging for laparoscopic training improves task performance for both reverse alignment and forward alignment tasks. This may be translated into improved performance in the operating room when faced with reverse alignment situations. Minimal lab training can account for drastic adaptation to this environment.

Photoresist thin-film effects on alignment process capability

NASA Astrophysics Data System (ADS)

Flores, Gary E.; Flack, Warren W.

1993-08-01

Two photoresists were selected for alignment characterization based on their dissimilar coating properties and observed differences on alignment capability. The materials are Dynachem OFPR-800 and Shipley System 8. Both photoresists were examined on two challenging alignment levels in a submicron CMOS process, a nitride level and a planarized second level metal. An Ultratech Stepper model 1500 which features a darkfield alignment system with a broadband green light for alignment signal detection was used for this project. Initially, statistically designed linear screening experiments were performed to examine six process factors for each photoresist: viscosity, spin acceleration, spin speed, spin time, softbake time, and softbake temperature. Using the results derived from the screening experiments, a more thorough examination of the statistically significant process factors was performed. A full quadratic experimental design was conducted to examine viscosity, spin speed, and spin time coating properties on alignment. This included a characterization of both intra and inter wafer alignment control and alignment process capability. Insight to the different alignment behavior is analyzed in terms of photoresist material properties and the physical nature of the alignment detection system.

A Polar Initial Alignment Algorithm for Unmanned Underwater Vehicles

PubMed Central

Yan, Zheping; Wang, Lu; Wang, Tongda; Zhang, Honghan; Zhang, Xun; Liu, Xiangling

2017-01-01

Due to its highly autonomy, the strapdown inertial navigation system (SINS) is widely used in unmanned underwater vehicles (UUV) navigation. Initial alignment is crucial because the initial alignment results will be used as the initial SINS value, which might affect the subsequent SINS results. Due to the rapid convergence of Earth meridians, there is a calculation overflow in conventional initial alignment algorithms, making conventional initial algorithms are invalid for polar UUV navigation. To overcome these problems, a polar initial alignment algorithm for UUV is proposed in this paper, which consists of coarse and fine alignment algorithms. Based on the principle of the conical slow drift of gravity, the coarse alignment algorithm is derived under the grid frame. By choosing the velocity and attitude as the measurement, the fine alignment with the Kalman filter (KF) is derived under the grid frame. Simulation and experiment are realized among polar, conventional and transversal initial alignment algorithms for polar UUV navigation. Results demonstrate that the proposed polar initial alignment algorithm can complete the initial alignment of UUV in the polar region rapidly and accurately. PMID:29168735

Relation between film character and wafer alignment: critical alignment issues on HV device for VLSI manufacturing

NASA Astrophysics Data System (ADS)

Lo, Yi-Chuan; Lee, Chih-Hsiung; Lin, Hsun-Peng; Peng, Chiou-Shian

1998-06-01

Several continuous splits for wafer alignment target topography conditions to improve epitaxy film alignment were applied. The alignment evaluation among former layer pad oxide thickness (250 angstrom - 500 angstrom), drive oxide thickness (6000 angstrom - 10000 angstrom), nitride film thickness (600 angstrom - 1500 angstrom), initial oxide etch (fully wet etch, fully dry etch and dry plus wet etch) will be split to this experiment. Also various epitaxy deposition recipe such as: epitaxy source (SiHCl2 or SiCHCl3) and growth rate (1.3 micrometer/min approximately 2.0 micrometer/min) will be used to optimize the process window for alignment issue. All the reflectance signal and cross section photography of alignment target during NIKON stepper alignment process will be examined. Experimental results show epitaxy recipe plays an important role to wafer alignment. Low growth rate with good performance conformity epitaxy lead to alignment target avoid washout, pattern shift and distortion. All the results (signal monitor and film character) combined with NIKON's stepper standard laser scanning alignment system will be discussed in this paper.

R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.

PubMed

Rahrig, Ryan R; Petrov, Anton I; Leontis, Neocles B; Zirbel, Craig L

2013-07-01

The R3D Align web server provides online access to 'RNA 3D Align' (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/.

Evolution of the nuclear receptor superfamily: early diversification from an ancestral orphan receptor.

PubMed

Laudet, V

1997-12-01

From a database containing the published nuclear hormone receptor (NR) sequences I constructed an alignment of the C, D and E domains of these molecules. Using this alignment, I have performed tree reconstruction using both distance matrix and parsimony analysis. The robustness of each branch was estimated using bootstrap resampling methods. The trees constructed by these two methods gave congruent topologies. From these analyses I defined six NR subfamilies: (i) a large one clustering thyroid hormone receptors (TRs), retinoic acid receptors (RARs), peroxisome proliferator-activated receptors (PPARs), vitamin D receptors (VDRs) and ecdysone receptors (EcRs) as well as numerous orphan receptors such as RORs or Rev-erbs; (ii) one containing retinoid X receptors (RXRs) together with COUP, HNF4, tailless, TR2 and TR4 orphan receptors; (iii) one containing steroid receptors; (iv) one containing the NGFIB orphan receptors; (v) one containing FTZ-F1 orphan receptors; and finally (vi) one containing to date only one gene, the GCNF1 orphan receptor. The relationships between the six subfamilies are not known except for subfamilies I and IV which appear to be related. Interestingly, most of the liganded receptors appear to be derived when compared with orphan receptors. This suggests that the ligand-binding ability of NRs has been gained by orphan receptors during the course of evolution to give rise to the presently known receptors. The distribution into six subfamilies correlates with the known abilities of the various NRs to bind to DNA as homo- or heterodimers. For example, receptors heterodimerizing efficiently with RXR belong to the first or the fourth subfamilies. I suggest that the ability to heterodimerize evolved once, just before the separation of subfamilies I and IV and that the first NR was able to bind to DNA as a homodimer. From the study of NR sequences existing in vertebrates, arthropods and nematodes, I define two major steps of NR diversification: one that took place very early, probably during the multicellularization event leading to all the metazoan phyla, and a second occurring later on, corresponding to the advent of vertebrates. Finally, I show that in vertebrate species the various groups of NRs accumulated mutations at very different rates.

How genome complexity can explain the difficulty of aligning reads to genomes.

PubMed

Phan, Vinhthuy; Gao, Shanshan; Tran, Quang; Vo, Nam S

2015-01-01

Although it is frequently observed that aligning short reads to genomes becomes harder if they contain complex repeat patterns, there has not been much effort to quantify the relationship between complexity of genomes and difficulty of short-read alignment. Existing measures of sequence complexity seem unsuitable for the understanding and quantification of this relationship. We investigated several measures of complexity and found that length-sensitive measures of complexity had the highest correlation to accuracy of alignment. In particular, the rate of distinct substrings of length k, where k is similar to the read length, correlated very highly to alignment performance in terms of precision and recall. We showed how to compute this measure efficiently in linear time, making it useful in practice to estimate quickly the difficulty of alignment for new genomes without having to align reads to them first. We showed how the length-sensitive measures could provide additional information for choosing aligners that would align consistently accurately on new genomes. We formally established a connection between genome complexity and the accuracy of short-read aligners. The relationship between genome complexity and alignment accuracy provides additional useful information for selecting suitable aligners for new genomes. Further, this work suggests that the complexity of genomes sometimes should be thought of in terms of specific computational problems, such as the alignment of short reads to genomes.

Aligned Layers of Silver Nano-Fibers.

PubMed

Golovin, Andrii B; Stromer, Jeremy; Kreminska, Liubov

2012-02-01

We describe a new dichroic polarizers made by ordering silver nano-fibers to aligned layers. The aligned layers consist of nano-fibers and self-assembled molecular aggregates of lyotropic liquid crystals. Unidirectional alignment of the layers is achieved by means of mechanical shearing. Aligned layers of silver nano-fibers are partially transparent to a linearly polarized electromagnetic radiation. The unidirectional alignment and density of the silver nano-fibers determine degree of polarization of transmitted light. The aligned layers of silver nano-fibers might be used in optics, microwave applications, and organic electronics.

Aligning the unalignable: bacteriophage whole genome alignments.

PubMed

Bérard, Sèverine; Chateau, Annie; Pompidor, Nicolas; Guertin, Paul; Bergeron, Anne; Swenson, Krister M

2016-01-13

In recent years, many studies focused on the description and comparison of large sets of related bacteriophage genomes. Due to the peculiar mosaic structure of these genomes, few informative approaches for comparing whole genomes exist: dot plots diagrams give a mostly qualitative assessment of the similarity/dissimilarity between two or more genomes, and clustering techniques are used to classify genomes. Multiple alignments are conspicuously absent from this scene. Indeed, whole genome aligners interpret lack of similarity between sequences as an indication of rearrangements, insertions, or losses. This behavior makes them ill-prepared to align bacteriophage genomes, where even closely related strains can accomplish the same biological function with highly dissimilar sequences. In this paper, we propose a multiple alignment strategy that exploits functional collinearity shared by related strains of bacteriophages, and uses partial orders to capture mosaicism of sets of genomes. As classical alignments do, the computed alignments can be used to predict that genes have the same biological function, even in the absence of detectable similarity. The Alpha aligner implements these ideas in visual interactive displays, and is used to compute several examples of alignments of Staphylococcus aureus and Mycobacterium bacteriophages, involving up to 29 genomes. Using these datasets, we prove that Alpha alignments are at least as good as those computed by standard aligners. Comparison with the progressive Mauve aligner - which implements a partial order strategy, but whose alignments are linearized - shows a greatly improved interactive graphic display, while avoiding misalignments. Multiple alignments of whole bacteriophage genomes work, and will become an important conceptual and visual tool in comparative genomics of sets of related strains. A python implementation of Alpha, along with installation instructions for Ubuntu and OSX, is available on bitbucket (https://bitbucket.org/thekswenson/alpha).

AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework

PubMed Central

Zheng, Qi; Grice, Elizabeth A.

2016-01-01

Accurate mapping of next-generation sequencing (NGS) reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely) mapped reads. Most available NGS aligners attempt to address this by either removing all non-uniquely mapping reads, or reporting one random or "best" hit based on simple heuristics. Accurate estimation of the mapping quality of NGS reads is therefore critical albeit completely lacking at present. Here we developed a generalized software toolkit "AlignerBoost", which utilizes a Bayesian-based framework to accurately estimate mapping quality of ambiguously mapped NGS reads. We tested AlignerBoost with both simulated and real DNA-seq and RNA-seq datasets at various thresholds. In most cases, but especially for reads falling within repetitive regions, AlignerBoost dramatically increases the mapping precision of modern NGS aligners without significantly compromising the sensitivity even without mapping quality filters. When using higher mapping quality cutoffs, AlignerBoost achieves a much lower false mapping rate while exhibiting comparable or higher sensitivity compared to the aligner default modes, therefore significantly boosting the detection power of NGS aligners even using extreme thresholds. AlignerBoost is also SNP-aware, and higher quality alignments can be achieved if provided with known SNPs. AlignerBoost’s algorithm is computationally efficient, and can process one million alignments within 30 seconds on a typical desktop computer. AlignerBoost is implemented as a uniform Java application and is freely available at https://github.com/Grice-Lab/AlignerBoost. PMID:27706155

Multiple DNA and protein sequence alignment on a workstation and a supercomputer.

PubMed

Tajima, K

1988-11-01

This paper describes a multiple alignment method using a workstation and supercomputer. The method is based on the alignment of a set of aligned sequences with the new sequence, and uses a recursive procedure of such alignment. The alignment is executed in a reasonable computation time on diverse levels from a workstation to a supercomputer, from the viewpoint of alignment results and computational speed by parallel processing. The application of the algorithm is illustrated by several examples of multiple alignment of 12 amino acid and DNA sequences of HIV (human immunodeficiency virus) env genes. Colour graphic programs on a workstation and parallel processing on a supercomputer are discussed.

The evolutionary history of ferns inferred from 25 low-copy nuclear genes.

PubMed

Rothfels, Carl J; Li, Fay-Wei; Sigel, Erin M; Huiet, Layne; Larsson, Anders; Burge, Dylan O; Ruhsam, Markus; Deyholos, Michael; Soltis, Douglas E; Stewart, C Neal; Shaw, Shane W; Pokorny, Lisa; Chen, Tao; dePamphilis, Claude; DeGironimo, Lisa; Chen, Li; Wei, Xiaofeng; Sun, Xiao; Korall, Petra; Stevenson, Dennis W; Graham, Sean W; Wong, Gane K-S; Pryer, Kathleen M

2015-07-01

• Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data.• Here we take a curated phylogenomics approach to infer the first broad fern phylogeny from multiple nuclear loci, by combining broad taxon sampling (73 ferns and 12 outgroup species) with focused character sampling (25 loci comprising 35877 bp), along with rigorous alignment, orthology inference and model selection.• Our phylogeny corroborates some earlier inferences and provides novel insights; in particular, we find strong support for Equisetales as sister to the rest of ferns, Marattiales as sister to leptosporangiate ferns, and Dennstaedtiaceae as sister to the eupolypods. Our divergence-time analyses reveal that divergences among the extant fern orders all occurred prior to ∼200 MYA. Finally, our species-tree inferences are congruent with analyses of concatenated data, but generally with lower support. Those cases where species-tree support values are higher than expected involve relationships that have been supported by smaller plastid datasets, suggesting that deep coalescence may be reducing support from the concatenated nuclear data.• Our study demonstrates the utility of a curated phylogenomics approach to inferring fern phylogeny, and highlights the need to consider underlying data characteristics, along with data quantity, in phylogenetic studies. © 2015 Botanical Society of America, Inc.

A Novel Partial Sequence Alignment Tool for Finding Large Deletions

PubMed Central

Aruk, Taner; Ustek, Duran; Kursun, Olcay

2012-01-01

Finding large deletions in genome sequences has become increasingly more useful in bioinformatics, such as in clinical research and diagnosis. Although there are a number of publically available next generation sequencing mapping and sequence alignment programs, these software packages do not correctly align fragments containing deletions larger than one kb. We present a fast alignment software package, BinaryPartialAlign, that can be used by wet lab scientists to find long structural variations in their experiments. For BinaryPartialAlign, we make use of the Smith-Waterman (SW) algorithm with a binary-search-based approach for alignment with large gaps that we called partial alignment. BinaryPartialAlign implementation is compared with other straight-forward applications of SW. Simulation results on mtDNA fragments demonstrate the effectiveness (runtime and accuracy) of the proposed method. PMID:22566777

Development and applications of retro-reflective surfaces for ultrasound in LBE

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

NONE

The Belgian Nuclear Research Centre SCK-CEN is in the process of developing MYRRHA - a fast flux research reactor to replace the aging BR2. MYRRHA is conceptualized as an accelerator driven system cooled by lead bismuth eutectic mixture (LBE). As LBE is opaque to visual light, ultrasonic measurement techniques are employed as the main technology to provide feedback to submerged operations when needed. Conceptually, MYRRHA is a pool type reactor divided in a cold lower plenum and hot upper plenum separated by a diaphragm that forces the main flow through the core. The main flow is cooled by four heatmore » exchangers and driven by two liquid metal pumps. One of the tasks tackled using ultrasound is locating a potentially lost fuel assembly to assist a recovery operation. As all fuel manipulations in MYRRHA are performed in the lower plenum, a potentially lost fuel assembly is located in the lower plenum. Buoyancy will force the lost fuel assembly to float against the diaphragm unless it is still partially inserted in the core. Because of the latter situation, an ultrasonic scan localizing the fuel assembly should be performed from a large distance to avoid a collision with such a partially inserted fuel assembly. Unfortunately, standard machined stainless steel objects, such as a fuel assembly, reflect an ultrasonic pulse in a specular way which induces stringent requirements on the alignment of the ultrasonic sensor with respect to the fuel assembly as we cannot rely on diffuse reflections and/or scattering of the ultrasonic pulse. Moreover, increasing the distance also increases geometric spreading and absorption of the pulse weakening the signal amplitude even faster to noise levels when deviating from perfect alignment. An alternative approach consists in relying on reflections from the known surroundings: a lost fuel assembly will block the line-of-sight to the diaphragm resulting in an anomaly in the reflection - either a shorter than expected time-of-flight of the pulse or a complete absence of a reflection like a shadow. In that way, it suffices to align the sensor with the diaphragm instead of the fuel assembly which is much easier to achieve as the robotics on which the sensor is mounted move parallel with the diaphragm. The alignment requirement in the latter approach can be further relaxed by using a tiling of retro-reflectors on the lower surface of the diaphragm. In that way, alignment becomes less vital and the main source of acoustic energy loss - geometric spread of the beam - is almost completely removed, leaving only absorption losses. In this paper, we present the first results in developing a retro reflectance surface for ultrasound in LBE. We present experimental results for different designs of retro-reflectors in both water and LBE. We discuss both linear and array retro-reflectors of different sizes and investigate the influence of the main relevant ultrasonic parameters such as wavelength and spot size on the strength of the received reflection under different alignment angles. We also demonstrate how retro-reflective surfaces can be exploited when localizing objects using linear and rotating scanning methods. (authors)« less

Alignment system for SGII-Up laser facility

NASA Astrophysics Data System (ADS)

Gao, Yanqi; Cui, Yong; Li, Hong; Gong, Lei; Lin, Qiang; Liu, Daizhong; Zhu, Baoqiang; Ma, Weixin; Zhu, Jian; Lin, Zunqi

2018-03-01

The SGII-Up laser facility in Shanghai is one of the most important high-power laser facilities in China. It is designed to obtain 24 kJ (3ω) of energy with a square pulse of 3 ns using eight laser beams (two bundles). To satisfy the requirements for the safety, efficiency, and quality, an alignment system is developed for this facility. This alignment system can perform automatic alignment of the preamplifier system, main amplifier system, and harmonic conversion system within 30 min before every shot during the routine operation of the facility. In this article, an overview of the alignment system is first presented. Then, its alignment characteristics are discussed, along with the alignment process. Finally, experimental results, including the alignment results and the facility performance, are reported. The results show that the far-field beam pointing alignment accuracy is better than 3 μrad, and the alignment error of the near-field beam centering is no larger than 1 mm. These satisfy the design requirements very well.

Fine-tuning structural RNA alignments in the twilight zone.

PubMed

Bremges, Andreas; Schirmer, Stefanie; Giegerich, Robert

2010-04-30

A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score based on thermodynamics and covariance. This method works best around 75% sequence similarity. However, in a "twilight zone" below 55% similarity, the sequence alignment tends to obscure the covariance signal used in the second phase. Therefore, while the overall shape of the consensus structure may still be found, the degree of conservation cannot be estimated reliably. Based on a combination of available methods, we present a method named planACstar for improving structure conservation in structural alignments in the twilight zone. After constructing a consensus structure by alignment folding, planACstar abandons the original sequence alignment, refolds the sequences individually, but consistent with the consensus, aligns the structures, irrespective of sequence, by a pure structure alignment method, and derives an improved sequence alignment from the alignment of structures, to be re-submitted to alignment folding, etc.. This circle may be iterated as long as structural conservation improves, but normally, one step suffices. Employing the tools ClustalW, RNAalifold, and RNAforester, we find that for sequences with 30-55% sequence identity, structural conservation can be improved by 10% on average, with a large variation, measured in terms of RNAalifold's own criterion, the structure conservation index.

Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies.

PubMed

Joseph, Agnel Praveen; Srinivasan, Narayanaswamy; de Brevern, Alexandre G

2012-09-01

Comparison of multiple protein structures has a broad range of applications in the analysis of protein structure, function and evolution. Multiple structure alignment tools (MSTAs) are necessary to obtain a simultaneous comparison of a family of related folds. In this study, we have developed a method for multiple structure comparison largely based on sequence alignment techniques. A widely used Structural Alphabet named Protein Blocks (PBs) was used to transform the information on 3D protein backbone conformation as a 1D sequence string. A progressive alignment strategy similar to CLUSTALW was adopted for multiple PB sequence alignment (mulPBA). Highly similar stretches identified by the pairwise alignments are given higher weights during the alignment. The residue equivalences from PB based alignments are used to obtain a three dimensional fit of the structures followed by an iterative refinement of the structural superposition. Systematic comparisons using benchmark datasets of MSTAs underlines that the alignment quality is better than MULTIPROT, MUSTANG and the alignments in HOMSTRAD, in more than 85% of the cases. Comparison with other rigid-body and flexible MSTAs also indicate that mulPBA alignments are superior to most of the rigid-body MSTAs and highly comparable to the flexible alignment methods. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

Modified alignment CGHs for aspheric surface test

NASA Astrophysics Data System (ADS)

Song, Jae-Bong; Yang, Ho-Soon; Rhee, Hyug-Gyo; Lee, Yun-Woo

2009-08-01

Computer Generated Holograms (CGH) for optical test are commonly consisted of one main pattern for testing aspheric surface and some alignment patterns for aligning the interferometer, CGH, and the test optics. To align the CGH plate and the test optics, we designed the alignment CGHs modified from the cat's eye alignment method, which are consisted of a couple of CGH patterns. The incident beam passed through the one part of the alignment CGH pattern is focused onto the one radius position of the test aspheric surface, and is reflected to the other part, and vice versa. This method has several merits compared to the conventional cat's eye alignment method. First, this method can be used in testing optics with a center hole, and the center part of CGH plate can be assigned to the alignment pattern. Second, the alignment pattern becomes a concentric circular arc pattern. The whole CGH patterns including the main pattern and alignment patterns are consisted of only concentric circular fringes. This concentric circular pattern can be easily made by the polar coordinated writer with circular scanning. The required diffraction angle becomes relatively small, so the 1st order diffraction beams instead of the 3rd order diffraction beam can be used as alignment beams, and the visibility can be improved. This alignment method also is more sensitive to the tilt and the lateral shift of the test aspheric surface. Using this alignment pattern, a 200 mm diameter F/0.5 aspheric mirror and a 600 mm diameter F/0.9 mirror were tested.

Effects of whole spine alignment patterns on neck responses in rear end impact.

PubMed

Sato, Fusako; Odani, Mamiko; Miyazaki, Yusuke; Yamazaki, Kunio; Östh, Jonas; Svensson, Mats

2017-02-17

The aim of this study was to investigate the whole spine alignment in automotive seated postures for both genders and the effects of the spinal alignment patterns on cervical vertebral motion in rear impact using a human finite element (FE) model. Image data for 8 female and 7 male subjects in a seated posture acquired by an upright open magnetic resonance imaging (MRI) system were utilized. Spinal alignment was determined from the centers of the vertebrae and average spinal alignment patterns for both genders were estimated by multidimensional scaling (MDS). An occupant FE model of female average size (162 cm, 62 kg; the AF 50 size model) was developed by scaling THUMS AF 05. The average spinal alignment pattern for females was implemented in the model, and model validation was made with respect to female volunteer sled test data from rear end impacts. Thereafter, the average spinal alignment pattern for males and representative spinal alignments for all subjects were implemented in the validated female model, and additional FE simulations of the sled test were conducted to investigate effects of spinal alignment patterns on cervical vertebral motion. The estimated average spinal alignment pattern was slight kyphotic, or almost straight cervical and less-kyphotic thoracic spine for the females and lordotic cervical and more pronounced kyphotic thoracic spine for the males. The AF 50 size model with the female average spinal alignment exhibited spine straightening from upper thoracic vertebra level and showed larger intervertebral angular displacements in the cervical spine than the one with the male average spinal alignment. The cervical spine alignment is continuous with the thoracic spine, and a trend of the relationship between cervical spine and thoracic spinal alignment was shown in this study. Simulation results suggested that variations in thoracic spinal alignment had a potential impact on cervical spine motion as well as cervical spinal alignment in rear end impact condition.

Kinematically aligned TKA can align knee joint line to horizontal.

PubMed

Ji, Hyung-Min; Han, Jun; Jin, Dong San; Seo, Hyunseok; Won, Ye-Yeon

2016-08-01

The joint line of the native knee is horizontal to the floor and perpendicular to the vertical weight-bearing axis of the patient in a bipedal stance. The purposes of this study were as follows: (1) to find out the distribution of the native joint line in a population of normal patients with normal knees; (2) to compare the native joint line orientation between patients receiving conventional mechanically aligned total knee arthroplasty (TKA), navigated mechanically aligned TKA, and kinematically aligned TKA; and (3) to determine which of the three TKA methods aligns the postoperative knee joint perpendicular to the weight-bearing axis of the limb in bipedal stance. To determine the joint line orientation of a native knee, 50 full-length standing hip-to-ankle digital radiographs were obtained in 50 young, healthy individuals. The angle between knee joint line and the line parallel to the floor was measured and defined as joint line orientation angle (JLOA). JLOA was also measured prior to and after conventional mechanically aligned TKA (65 knees), mechanically aligned TKA using imageless navigation (65 knees), and kinematically aligned TKA (65 knees). The proportion of the knees similar to the native joint line was calculated for each group. The mean JLOA in healthy individuals was parallel to the floor (0.2° ± 1.1°). The pre-operative JLOA of all treatment groups slanted down to the lateral side. Postoperative JLOA slanted down to the lateral side in conventional mechanically aligned TKA (-3.3° ± 2.2°) and in navigation mechanically aligned TKA (-2.6° ± 1.8°), while it was horizontal to the floor in kinematically aligned TKA (0.6° ± 1.7°). Only 6.9 % of the conventional mechanically aligned TKA and 16.9 % of the navigation mechanically aligned TKA were within one SD of the mean JLOA of the native knee, while the proportion was significantly higher (50.8 %) in kinematically aligned TKA. The portion was statistically greater in mechanically aligned TKA group than the other two. Postoperative joint line orientation after kinematically aligned TKA was more similar to that of native knees than that of mechanically aligned TKA and horizontal to the floor. Kinematically aligned TKA can restore pre-arthritic knee joint line orientation, while mechanically aligned TKA is inefficient in achieving the purpose even if navigation TKA is employed. III.

Analyzing the Curriculum Alignment of Teachers

ERIC Educational Resources Information Center

Turan-Özpolat, Esen; Bay, Erdal

2017-01-01

The purpose of this research was to analyze the curriculum alignment of teachers in secondary education 5th grade Science course. Alignment levels of teachers in dimensions of acquisition, content, teaching methods and techniques, activity, material and measurement - assessment, and the reasons for their alignment/non-alignment to the curriculum…

Alignment of Standards and Assessments as an Accountability Criterion.

ERIC Educational Resources Information Center

La Marca, Paul M.

2001-01-01

Provides an overview of the concept of alignment and the role it plays in assessment and accountability systems. Discusses some methodological issues affecting the study of alignment and explores the relationship between alignment and test score interpretation. Alignment is not only a methodological requirement but also an ethical requirement.…

Sandia Corporation (Albuquerque, NM)

DOEpatents

Diver, Richard B.

2010-02-23

A Theoretical Overlay Photographic (TOP) alignment method uses the overlay of a theoretical projected image of a perfectly aligned concentrator on a photographic image of the concentrator to align the mirror facets of a parabolic trough solar concentrator. The alignment method is practical and straightforward, and inherently aligns the mirror facets to the receiver. When integrated with clinometer measurements for which gravity and mechanical drag effects have been accounted for and which are made in a manner and location consistent with the alignment method, all of the mirrors on a common drive can be aligned and optimized for any concentrator orientation.

The post-genomic era of biological network alignment.

PubMed

Faisal, Fazle E; Meng, Lei; Crawford, Joseph; Milenković, Tijana

2015-12-01

Biological network alignment aims to find regions of topological and functional (dis)similarities between molecular networks of different species. Then, network alignment can guide the transfer of biological knowledge from well-studied model species to less well-studied species between conserved (aligned) network regions, thus complementing valuable insights that have already been provided by genomic sequence alignment. Here, we review computational challenges behind the network alignment problem, existing approaches for solving the problem, ways of evaluating their alignment quality, and the approaches' biomedical applications. We discuss recent innovative efforts of improving the existing view of network alignment. We conclude with open research questions in comparative biological network research that could further our understanding of principles of life, evolution, disease, and therapeutics.

SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments

PubMed Central

Di Tommaso, Paolo; Bussotti, Giovanni; Kemena, Carsten; Capriotti, Emidio; Chatzou, Maria; Prieto, Pablo; Notredame, Cedric

2014-01-01

This article introduces the SARA-Coffee web server; a service allowing the online computation of 3D structure based multiple RNA sequence alignments. The server makes it possible to combine sequences with and without known 3D structures. Given a set of sequences SARA-Coffee outputs a multiple sequence alignment along with a reliability index for every sequence, column and aligned residue. SARA-Coffee combines SARA, a pairwise structural RNA aligner with the R-Coffee multiple RNA aligner in a way that has been shown to improve alignment accuracy over most sequence aligners when enough structural data is available. The server can be accessed from http://tcoffee.crg.cat/apps/tcoffee/do:saracoffee. PMID:24972831

Implementation of a parallel protein structure alignment service on cloud.

PubMed

Hung, Che-Lun; Lin, Yaw-Ling

2013-01-01

Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform.

Implementation of a Parallel Protein Structure Alignment Service on Cloud

PubMed Central

Hung, Che-Lun; Lin, Yaw-Ling

2013-01-01

Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform. PMID:23671842

Diffractive optics for precision alignment of Euclid space telescope optics (Conference Presentation)

NASA Astrophysics Data System (ADS)

Asfour, Jean-Michel; Weidner, Frank; Bodendorf, Christof; Bode, Andreas; Poleshchuk, Alexander G.; Nasyrov, Ruslan K.; Grupp, Frank; Bender, Ralf

2017-09-01

We present a method for precise alignment of lens elements using specific Computer Generated Hologram (CGH) with an integrated Fizeau reference flat surface and a Fizeau interferometer. The method is used for aligning the so called Camera Lens Assembly for ESAs Euclid telescope. Each lens has a corresponding annular area on the diffractive optics, which is used to control the position of each lens. The lenses are subsequently positioned using individual annular rings of the CGH. The overall alignment accuracy is below 1 µm, the alignment sensitivity is in the range of 0.1 µm. The achieved alignment accuracy of the lenses relative to each other is mainly depending on the stability in time of the alignment tower. Error budgets when using computer generated holograms and physical limitations are explained. Calibration measurements of the alignment system and the typically reached alignment accuracies will be shown and discussed.

SIM Lite: Ground Alignment of the Instrument

NASA Technical Reports Server (NTRS)

Dekens, Frank G.; Goullioud, Renaud; Nicaise, Fabien; Kuan, Gary; Morales, Mauricio

2010-01-01

We present the start of the ground alignment plan for the SIM Lite Instrument. We outline the integration and alignment of the individual benches on which all the optics are mounted, and then the alignment of the benches to form the Science and Guide interferometers. The Instrument has a guide interferometer with only a 40 arc-seconds field of regard, and 200 arc-seconds of alignment adjustability. This requires each sides of the interferometer to be aligned to a fraction of that, while at the same time be orthogonal to the baseline defined by the External Metrology Truss. The baselines of the Science and Guide interferometers must also be aligned to be parallel. The start of these alignment plans is captured in a SysML Instrument System model, in the form of activity diagrams. These activity diagrams are then related to the hardware design and requirements. We finish with future plans for the alignment and integration activities and requirements.

SIM Lite: ground alignment of the instrument

NASA Astrophysics Data System (ADS)

Dekens, Frank G.; Goullioud, Renaud; Nicaise, Fabien; Kuan, Gary; Morales, Mauricio

2010-07-01

We present the start of the ground alignment plan for the SIM Lite Instrument. We outline the integration and alignment of the individual benches on which all the optics are mounted, and then the alignment of the benches to form the Science and Guide interferometers. The Instrument has a guide interferometer with only a 40 arc-seconds field of regard, and 200 arc-seconds of alignment adjustability. This requires each sides of the interferometer to be aligned to a fraction of that, while at the same time be orthogonal to the baseline defined by the External Metrology Truss. The baselines of the Science and Guide interferometers must also be aligned to be parallel. The start of these alignment plans is captured in a SysML Instrument System model, in the form of activity diagrams. These activity diagrams are then related to the hardware design and requirements. We finish with future plans for the alignment and integration activities and requirements.

Multiple network alignment via multiMAGNA+.

PubMed

Vijayan, Vipin; Milenkovic, Tijana

2017-08-21

Network alignment (NA) aims to find a node mapping that identifies topologically or functionally similar network regions between molecular networks of different species. Analogous to genomic sequence alignment, NA can be used to transfer biological knowledge from well- to poorly-studied species between aligned network regions. Pairwise NA (PNA) finds similar regions between two networks while multiple NA (MNA) can align more than two networks. We focus on MNA. Existing MNA methods aim to maximize total similarity over all aligned nodes (node conservation). Then, they evaluate alignment quality by measuring the amount of conserved edges, but only after the alignment is constructed. Directly optimizing edge conservation during alignment construction in addition to node conservation may result in superior alignments. Thus, we present a novel MNA method called multiMAGNA++ that can achieve this. Indeed, multiMAGNA++ outperforms or is on par with existing MNA methods, while often completing faster than existing methods. That is, multiMAGNA++ scales well to larger network data and can be parallelized effectively. During method evaluation, we also introduce new MNA quality measures to allow for more fair MNA method comparison compared to the existing alignment quality measures. MultiMAGNA++ code is available on the method's web page at http://nd.edu/~cone/multiMAGNA++/.

Text-image alignment for historical handwritten documents

NASA Astrophysics Data System (ADS)

Zinger, S.; Nerbonne, J.; Schomaker, L.

2009-01-01

We describe our work on text-image alignment in context of building a historical document retrieval system. We aim at aligning images of words in handwritten lines with their text transcriptions. The images of handwritten lines are automatically segmented from the scanned pages of historical documents and then manually transcribed. To train automatic routines to detect words in an image of handwritten text, we need a training set - images of words with their transcriptions. We present our results on aligning words from the images of handwritten lines and their corresponding text transcriptions. Alignment based on the longest spaces between portions of handwriting is a baseline. We then show that relative lengths, i.e. proportions of words in their lines, can be used to improve the alignment results considerably. To take into account the relative word length, we define the expressions for the cost function that has to be minimized for aligning text words with their images. We apply right to left alignment as well as alignment based on exhaustive search. The quality assessment of these alignments shows correct results for 69% of words from 100 lines, or 90% of partially correct and correct alignments combined.

Rapid Quantification of 3D Collagen Fiber Alignment and Fiber Intersection Correlations with High Sensitivity

PubMed Central

Sun, Meng; Bloom, Alexander B.; Zaman, Muhammad H.

2015-01-01

Metastatic cancers aggressively reorganize collagen in their microenvironment. For example, radially orientated collagen fibers have been observed surrounding tumor cell clusters in vivo. The degree of fiber alignment, as a consequence of this remodeling, has often been difficult to quantify. In this paper, we present an easy to implement algorithm for accurate detection of collagen fiber orientation in a rapid pixel-wise manner. This algorithm quantifies the alignment of both computer generated and actual collagen fiber networks of varying degrees of alignment within 5°°. We also present an alternative easy method to calculate the alignment index directly from the standard deviation of fiber orientation. Using this quantitative method for determining collagen alignment, we demonstrate that the number of collagen fiber intersections has a negative correlation with the degree of fiber alignment. This decrease in intersections of aligned fibers could explain why cells move more rapidly along aligned fibers than unaligned fibers, as previously reported. Overall, our paper provides an easier, more quantitative and quicker way to quantify fiber orientation and alignment, and presents a platform in studying effects of matrix and cellular properties on fiber alignment in complex 3D environments. PMID:26158674

Physician-Hospital Alignment in Orthopedic Surgery.

PubMed

Bushnell, Brandon D

2015-09-01

The concept of "alignment" between physicians and hospitals is a popular buzzword in the age of health care reform. Despite their often tumultuous histories, physicians and hospitals find themselves under increasing pressures to work together toward common goals. However, effective alignment is more than just simple cooperation between parties. The process of achieving alignment does not have simple, universal steps. Alignment will differ based on individual situational factors and the type of specialty involved. Ultimately, however, there are principles that underlie the concept of alignment and should be a part of any physician-hospital alignment efforts. In orthopedic surgery, alignment involves the clinical, administrative, financial, and even personal aspects of a surgeon's practice. It must be based on the principles of financial interest, clinical authority, administrative participation, transparency, focus on the patient, and mutual necessity. Alignment can take on various forms as well, with popular models consisting of shared governance and comanagement, gainsharing, bundled payments, accountable care organizations, and other methods. As regulatory and financial pressures continue to motivate physicians and hospitals to develop alignment relationships, new and innovative methods of alignment will also appear. Existing models will mature and evolve, with individual variability based on local factors. However, certain trends seem to be appearing as time progresses and alignment relationships deepen, including regional and national collaboration, population management, and changes in the legal system. This article explores the history, principles, and specific methods of physician-hospital alignment and its critical importance for the future of health care delivery. Copyright 2015, SLACK Incorporated.

Simultaneous phylogeny reconstruction and multiple sequence alignment

PubMed Central

Yue, Feng; Shi, Jian; Tang, Jijun

2009-01-01

Background A phylogeny is the evolutionary history of a group of organisms. To date, sequence data is still the most used data type for phylogenetic reconstruction. Before any sequences can be used for phylogeny reconstruction, they must be aligned, and the quality of the multiple sequence alignment has been shown to affect the quality of the inferred phylogeny. At the same time, all the current multiple sequence alignment programs use a guide tree to produce the alignment and experiments showed that good guide trees can significantly improve the multiple alignment quality. Results We devise a new algorithm to simultaneously align multiple sequences and search for the phylogenetic tree that leads to the best alignment. We also implemented the algorithm as a C program package, which can handle both DNA and protein data and can take simple cost model as well as complex substitution matrices, such as PAM250 or BLOSUM62. The performance of the new method are compared with those from other popular multiple sequence alignment tools, including the widely used programs such as ClustalW and T-Coffee. Experimental results suggest that this method has good performance in terms of both phylogeny accuracy and alignment quality. Conclusion We present an algorithm to align multiple sequences and reconstruct the phylogenies that minimize the alignment score, which is based on an efficient algorithm to solve the median problems for three sequences. Our extensive experiments suggest that this method is very promising and can produce high quality phylogenies and alignments. PMID:19208110

Structural re-alignment in an immunologic surface region of ricin A chain

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

Zemla, A T; Zhou, C E

2007-07-24

We compared structure alignments generated by several protein structure comparison programs to determine whether existing methods would satisfactorily align residues at a highly conserved position within an immunogenic loop in ribosome inactivating proteins (RIPs). Using default settings, structure alignments generated by several programs (CE, DaliLite, FATCAT, LGA, MAMMOTH, MATRAS, SHEBA, SSM) failed to align the respective conserved residues, although LGA reported correct residue-residue (R-R) correspondences when the beta-carbon (Cb) position was used as the point of reference in the alignment calculations. Further tests using variable points of reference indicated that points distal from the beta carbon along a vector connectingmore » the alpha and beta carbons yielded rigid structural alignments in which residues known to be highly conserved in RIPs were reported as corresponding residues in structural comparisons between ricin A chain, abrin-A, and other RIPs. Results suggest that approaches to structure alignment employing alternate point representations corresponding to side chain position may yield structure alignments that are more consistent with observed conservation of functional surface residues than do standard alignment programs, which apply uniform criteria for alignment (i.e., alpha carbon (Ca) as point of reference) along the entirety of the peptide chain. We present the results of tests that suggest the utility of allowing user-specified points of reference in generating alternate structural alignments, and we present a web server for automatically generating such alignments.« less

Evolution of physician-hospital alignment models: a case study of comanagement.

PubMed

Sowers, Kevin W; Newman, Paul R; Langdon, Jeffrey C

2013-06-01

Recently, quality, financial, and regulatory demands have driven physicians to seek alignment opportunities with hospitals. The motivation for alignment on the part of physicians and hospitals is now accelerating because the new paradigm under healthcare reform requires an increased focus on improving quality, cost, and efficiency. We (1) identify the key drivers for physician-hospital alignment models; (2) summarize comanagement as a physician-hospital alignment model; and (3) explore a detailed case study of comanagement as an option to better align physicians with hospital goals on quality, safety, and outcomes. A Medline abstract review was performed that identified 45 references that discuss options for physician-hospital alignment. None of the articles identified provide a detailed example of successful alignment structures. A detailed case study of a successful comanagement alignment program is reviewed. The key drivers for alignment are inpatient growth rates, declining reimbursements, and the opportunity to improve quality, decrease costs, and increase efficiency. Two general strategies of alignment involve noneconomic and/or economic integration. In our example, comanagement with economic integration was chosen as the preferred structure for physician-hospital alignment. The choice of structure will vary depending on the existing relationships and governance of the hospital and the physicians in the targeted area of focus. The measure of success in building physician-hospital alignment is measured in improvements in care for the patient, reduced cost of care delivery, and improved relations between physicians and hospital leadership.

Matt: local flexibility aids protein multiple structure alignment.

PubMed

Menke, Matthew; Berger, Bonnie; Cowen, Lenore

2008-01-01

Even when there is agreement on what measure a protein multiple structure alignment should be optimizing, finding the optimal alignment is computationally prohibitive. One approach used by many previous methods is aligned fragment pair chaining, where short structural fragments from all the proteins are aligned against each other optimally, and the final alignment chains these together in geometrically consistent ways. Ye and Godzik have recently suggested that adding geometric flexibility may help better model protein structures in a variety of contexts. We introduce the program Matt (Multiple Alignment with Translations and Twists), an aligned fragment pair chaining algorithm that, in intermediate steps, allows local flexibility between fragments: small translations and rotations are temporarily allowed to bring sets of aligned fragments closer, even if they are physically impossible under rigid body transformations. After a dynamic programming assembly guided by these "bent" alignments, geometric consistency is restored in the final step before the alignment is output. Matt is tested against other recent multiple protein structure alignment programs on the popular Homstrad and SABmark benchmark datasets. Matt's global performance is competitive with the other programs on Homstrad, but outperforms the other programs on SABmark, a benchmark of multiple structure alignments of proteins with more distant homology. On both datasets, Matt demonstrates an ability to better align the ends of alpha-helices and beta-strands, an important characteristic of any structure alignment program intended to help construct a structural template library for threading approaches to the inverse protein-folding problem. The related question of whether Matt alignments can be used to distinguish distantly homologous structure pairs from pairs of proteins that are not homologous is also considered. For this purpose, a p-value score based on the length of the common core and average root mean squared deviation (RMSD) of Matt alignments is shown to largely separate decoys from homologous protein structures in the SABmark benchmark dataset. We postulate that Matt's strong performance comes from its ability to model proteins in different conformational states and, perhaps even more important, its ability to model backbone distortions in more distantly related proteins.

Highly Enhanced Gas Adsorption Properties in Vertically Aligned MoS2 Layers.

PubMed

Cho, Soo-Yeon; Kim, Seon Joon; Lee, Youhan; Kim, Jong-Seon; Jung, Woo-Bin; Yoo, Hae-Wook; Kim, Jihan; Jung, Hee-Tae

2015-09-22

In this work, we demonstrate that gas adsorption is significantly higher in edge sites of vertically aligned MoS2 compared to that of the conventional basal plane exposed MoS2 films. To compare the effect of the alignment of MoS2 on the gas adsorption properties, we synthesized three distinct MoS2 films with different alignment directions ((1) horizontally aligned MoS2 (basal plane exposed), (2) mixture of horizontally aligned MoS2 and vertically aligned layers (basal and edge exposed), and (3) vertically aligned MoS2 (edge exposed)) by using rapid sulfurization method of CVD process. Vertically aligned MoS2 film shows about 5-fold enhanced sensitivity to NO2 gas molecules compared to horizontally aligned MoS2 film. Vertically aligned MoS2 has superior resistance variation compared to horizontally aligned MoS2 even with same surface area exposed to identical concentration of gas molecules. We found that electrical response to target gas molecules correlates directly with the density of the exposed edge sites of MoS2 due to high adsorption of gas molecules onto edge sites of vertically aligned MoS2. Density functional theory (DFT) calculations corroborate the experimental results as stronger NO2 binding energies are computed for multiple configurations near the edge sites of MoS2, which verifies that electrical response to target gas molecules (NO2) correlates directly with the density of the exposed edge sites of MoS2 due to high adsorption of gas molecules onto edge sites of vertically aligned MoS2. We believe that this observation extends to other 2D TMD materials as well as MoS2 and can be applied to significantly enhance the gas sensor performance in these materials.

Preliminary CFD study of Pebble Size and its Effect on Heat Transfer in a Pebble Bed Reactor

NASA Astrophysics Data System (ADS)

Jones, Andrew; Enriquez, Christian; Spangler, Julian; Yee, Tein; Park, Jungkyu; Farfan, Eduardo

2017-11-01

In pebble bed reactors, the typical pebble diameter used is 6cm, and within each pebble is are thousands of nuclear fuel kernels. However, efficiency of the reactor does not solely depend on the number of kernels of fuel within each graphite sphere, but also depends on the type and motion of the coolant within the voids between the spheres and the reactor itself. In this work a physical analysis of the pebble bed nuclear reactor's fluid dynamics is undertaken using Computational Fluid Dynamics software. The primary goal of this work is to observe the relationship between the different pebble diameters in an idealized alignment and the thermal transport efficiency of the reactor. The model constructed of our idealized argument will consist on stacked 8 pebble columns that fixed at the inlet on the reactor. Two different pebble sizes 4 cm and 6 cm will be studied and helium will be supplied as coolant with a fixed flow rate of 96 kg/s, also a fixed pebble surface temperatures will be used. Comparison will then be made to evaluate the efficiency of coolant to transport heat due to the varying sizes of the pebbles. Assistant Professor for the Department of Civil and Construction Engineering PhD.

On the intonation of German intonation questions: the role of the prenuclear region.

PubMed

Petrone, Caterina; Niebuhr, Oliver

2014-03-01

German questions and statements are distinguished not only by lexical and syntactic but also by intonational means. This study revisits, for Northern Standard German, how questions are signalled intonationally in utterances that have neither lexical nor syntactic cues. Starting from natural productions of such 'intonation questions', two perception experiments were run. Experiment 1 is based on a gating paradigm, which was applied to naturally produced questions and statements. Experiment 11 includes two indirect-identification tasks. Resynthesized stimuli were judged in relation to two context utterances, each of which was compatible with only one sentence mode interpretation. Results show that utterances with a finally falling nuclear pitch-accent contour can also trigger question perception. An utterance-final rise is not mandatory. Also, question and statement cues are not restricted to the intonational nucleus. Rather, listeners can refer to shape, slope, and alignment differences of the preceding prenuclear pitch accent to identify sentence mode. These findings are in line with studies suggesting that the utterance-final rise versus fall contrast is not directly related to sentence modality, but represents a separate attitudinal meaning dimension. Moreover, the findings support that both prenuclear and nuclear fundamental frequency (F0) patterns must be taken into account in the analysis of tune meaning.

Thrust Vector Control for Nuclear Thermal Rockets

NASA Technical Reports Server (NTRS)

Ensworth, Clinton B. F.

2013-01-01

Future space missions may use Nuclear Thermal Rocket (NTR) stages for human and cargo missions to Mars and other destinations. The vehicles are likely to require engine thrust vector control (TVC) to maintain desired flight trajectories. This paper explores requirements and concepts for TVC systems for representative NTR missions. Requirements for TVC systems were derived using 6 degree-of-freedom models of NTR vehicles. Various flight scenarios were evaluated to determine vehicle attitude control needs and to determine the applicability of TVC. Outputs from the models yielded key characteristics including engine gimbal angles, gimbal rates and gimbal actuator power. Additional factors such as engine thrust variability and engine thrust alignment errors were examined for impacts to gimbal requirements. Various technologies are surveyed for TVC systems for the NTR applications. A key factor in technology selection is the unique radiation environment present in NTR stages. Other considerations including mission duration and thermal environments influence the selection of optimal TVC technologies. Candidate technologies are compared to see which technologies, or combinations of technologies best fit the requirements for selected NTR missions. Representative TVC systems are proposed and key properties such as mass and power requirements are defined. The outputs from this effort can be used to refine NTR system sizing models, providing higher fidelity definition for TVC systems for future studies.

What can the past of pay-for-performance tell us about the future of Value-Based Purchasing in Medicare?

PubMed

Ryan, Andrew M; Damberg, Cheryl L

2013-06-01

The Medicare program has implemented pay-for-performance (P4P), or Value-Based Purchasing, for inpatient care and for Medicare Advantage plans, and plans to implement a program for physicians in 2015. In this paper, we review evidence on the effectiveness of P4P and identify design criteria deemed to be best practice in P4P. We then assess the extent to which Medicare's existing and planned Value-Based Purchasing programs align with these best practices. Of the seven identified best practices in P4P program design, the Hospital Value-Based Purchasing program is strongly aligned with two of the best practices, moderately aligned with three, weakly aligned with one, and has unclear alignment with one best practice. The Physician Value-Based Purchasing Modifier is strongly aligned with two of the best practices, moderately aligned with one, weakly aligned with three, and has unclear alignment with one of the best practices. The Medicare Advantage Quality Bonus Program is strongly aligned with four of the best practices, moderately aligned with two, and weakly aligned with one of the best practices. We identify enduring gaps in P4P literature as it relates to Medicare's plans for Value-Based Purchasing and discuss important issues in the future of these implementations in Medicare. Copyright © 2013 Elsevier Inc. All rights reserved.

Fine-tuning structural RNA alignments in the twilight zone

PubMed Central

2010-01-01

Background A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score based on thermodynamics and covariance. This method works best around 75% sequence similarity. However, in a "twilight zone" below 55% similarity, the sequence alignment tends to obscure the covariance signal used in the second phase. Therefore, while the overall shape of the consensus structure may still be found, the degree of conservation cannot be estimated reliably. Results Based on a combination of available methods, we present a method named planACstar for improving structure conservation in structural alignments in the twilight zone. After constructing a consensus structure by alignment folding, planACstar abandons the original sequence alignment, refolds the sequences individually, but consistent with the consensus, aligns the structures, irrespective of sequence, by a pure structure alignment method, and derives an improved sequence alignment from the alignment of structures, to be re-submitted to alignment folding, etc.. This circle may be iterated as long as structural conservation improves, but normally, one step suffices. Conclusions Employing the tools ClustalW, RNAalifold, and RNAforester, we find that for sequences with 30-55% sequence identity, structural conservation can be improved by 10% on average, with a large variation, measured in terms of RNAalifold's own criterion, the structure conservation index. PMID:20433706

On-command on/off switching of progenitor cell and cancer cell polarized motility and aligned morphology via a cytocompatible shape memory polymer scaffold.

PubMed

Wang, Jing; Quach, Andy; Brasch, Megan E; Turner, Christopher E; Henderson, James H

2017-09-01

In vitro biomaterial models have enabled advances in understanding the role of extracellular matrix (ECM) architecture in the control of cell motility and polarity. Most models are, however, static and cannot mimic dynamic aspects of in vivo ECM remodeling and function. To address this limitation, we present an electrospun shape memory polymer scaffold that can change fiber alignment on command under cytocompatible conditions. Cellular response was studied using the human fibrosarcoma cell line HT-1080 and the murine mesenchymal stem cell line C3H/10T1/2. The results demonstrate successful on-command on/off switching of cell polarized motility and alignment. Decrease in fiber alignment causes a change from polarized motility along the direction of fiber alignment to non-polarized motility and from aligned to unaligned morphology, while increase in fiber alignment causes a change from non-polarized to polarized motility along the direction of fiber alignment and from unaligned to aligned morphology. In addition, the findings are consistent with the hypothesis that increased fiber alignment causes increased cell velocity, while decreased fiber alignment causes decreased cell velocity. On-command on/off switching of cell polarized motility and alignment is anticipated to enable new study of directed cell motility in tumor metastasis, in cell homing, and in tissue engineering. Copyright © 2017 Elsevier Ltd. All rights reserved.

Self-Alignment MEMS IMU Method Based on the Rotation Modulation Technique on a Swing Base

PubMed Central

Chen, Zhiyong; Yang, Haotian; Wang, Chengbin; Lin, Zhihui; Guo, Meifeng

2018-01-01

The micro-electro-mechanical-system (MEMS) inertial measurement unit (IMU) has been widely used in the field of inertial navigation due to its small size, low cost, and light weight, but aligning MEMS IMUs remains a challenge for researchers. MEMS IMUs have been conventionally aligned on a static base, requiring other sensors, such as magnetometers or satellites, to provide auxiliary information, which limits its application range to some extent. Therefore, improving the alignment accuracy of MEMS IMU as much as possible under swing conditions is of considerable value. This paper proposes an alignment method based on the rotation modulation technique (RMT), which is completely self-aligned, unlike the existing alignment techniques. The effect of the inertial sensor errors is mitigated by rotating the IMU. Then, inertial frame-based alignment using the rotation modulation technique (RMT-IFBA) achieved coarse alignment on the swing base. The strong tracking filter (STF) further improved the alignment accuracy. The performance of the proposed method was validated with a physical experiment, and the results of the alignment showed that the standard deviations of pitch, roll, and heading angle were 0.0140°, 0.0097°, and 0.91°, respectively, which verified the practicality and efficacy of the proposed method for the self-alignment of the MEMS IMU on a swing base. PMID:29649150

Score distributions of gapped multiple sequence alignments down to the low-probability tail

NASA Astrophysics Data System (ADS)

Fieth, Pascal; Hartmann, Alexander K.

2016-08-01

Assessing the significance of alignment scores of optimally aligned DNA or amino acid sequences can be achieved via the knowledge of the score distribution of random sequences. But this requires obtaining the distribution in the biologically relevant high-scoring region, where the probabilities are exponentially small. For gapless local alignments of infinitely long sequences this distribution is known analytically to follow a Gumbel distribution. Distributions for gapped local alignments and global alignments of finite lengths can only be obtained numerically. To obtain result for the small-probability region, specific statistical mechanics-based rare-event algorithms can be applied. In previous studies, this was achieved for pairwise alignments. They showed that, contrary to results from previous simple sampling studies, strong deviations from the Gumbel distribution occur in case of finite sequence lengths. Here we extend the studies to multiple sequence alignments with gaps, which are much more relevant for practical applications in molecular biology. We study the distributions of scores over a large range of the support, reaching probabilities as small as 10-160, for global and local (sum-of-pair scores) multiple alignments. We find that even after suitable rescaling, eliminating the sequence-length dependence, the distributions for multiple alignment differ from the pairwise alignment case. Furthermore, we also show that the previously discussed Gaussian correction to the Gumbel distribution needs to be refined, also for the case of pairwise alignments.

Improving SPAWAR PEO C4I Organizational Alignment to Better Enable Enterprise Technical Risk Management

DTIC Science & Technology

2017-03-01

possible. The thesis also utilized organizational alignment literature to include organizational alignment principles in the evaluation. Key principles ...thesis also utilized organizational alignment literature to include organizational alignment principles in the evaluation. Key principles include 1...39 A. CORE PRINCIPLES ...............................................................................39 B. RELATIONSHIP OF CORE PRINCIPLES

Alignment of Standards and Assessments as an Accountability Criterion. ERIC Digest.

ERIC Educational Resources Information Center

La Marca, Paul M.

This digest provides an overview of the concept of alignment and the role it plays in assessment and accountability systems. It also discusses methodological issues affecting the study of alignment and explores the relationship between alignment and test score interpretation. Alignment refers to the degree of match between test content and subject…

Homeotropic alignment of multiple bent-core liquid crystal phases using a polydimethylsiloxane alignment layer

NASA Astrophysics Data System (ADS)

Carlson, Eric D.; Foley, Lee M.; Guzman, Edward; Korblova, Eva D.; Visvanathan, Rayshan; Ryu, SeongHo; Gim, Min-Jun; Tuchband, Michael R.; Yoon, Dong Ki; Clark, Noel A.; Walba, David M.

2017-08-01

The control of the molecular orientation of liquid crystals (LCs) is important in both understanding phase properties and the continuing development of new LC technologies including displays, organic transistors, and electro-optic devices. Many techniques have been developed for successfully inducing alignment of calamitic LCs, though these techniques typically do not translate to the alignment of bent-core liquid crystals (BCLCs). Some techniques have been utilized to align various phases of BCLCs, but these techniques are often unsuccessful for general alignment of multiple materials and/or multiple phases. Here, we demonstrate that glass cells treated with polydimethylsiloxane (PDMS) thin films induce high quality homeotropic alignment of multiple mesophases of four BCLCs. On cooling to the lowest temperature phase the homeotropic alignment is lost, and spherulitic growth is seen in crystal and crystal-like phases including the dark conglomerate (DC) and helical nanofilament (HNF) phases. Evidence of homeotropic alignment is observed using polarized optical microscopy. We speculate that the methyl groups on the surface of the PDMS films strongly interact with the aliphatic tails of each mesogens, resulting in homeotropic alignment.

Some aspects of SR beamline alignment

NASA Astrophysics Data System (ADS)

Gaponov, Yu. A.; Cerenius, Y.; Nygaard, J.; Ursby, T.; Larsson, K.

2011-09-01

Based on the Synchrotron Radiation (SR) beamline optical element-by-element alignment with analysis of the alignment results an optimized beamline alignment algorithm has been designed and developed. The alignment procedures have been designed and developed for the MAX-lab I911-4 fixed energy beamline. It has been shown that the intermediate information received during the monochromator alignment stage can be used for the correction of both monochromator and mirror without the next stages of alignment of mirror, slits, sample holder, etc. Such an optimization of the beamline alignment procedures decreases the time necessary for the alignment and becomes useful and helpful in the case of any instability of the beamline optical elements, storage ring electron orbit or the wiggler insertion device, which could result in the instability of angular and positional parameters of the SR beam. A general purpose software package for manual, semi-automatic and automatic SR beamline alignment has been designed and developed using the developed algorithm. The TANGO control system is used as the middle-ware between the stand-alone beamline control applications BLTools, BPMonitor and the beamline equipment.

SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees.

PubMed

Liu, Kevin; Warnow, Tandy J; Holder, Mark T; Nelesen, Serita M; Yu, Jiaye; Stamatakis, Alexandros P; Linder, C Randal

2012-01-01

Highly accurate estimation of phylogenetic trees for large data sets is difficult, in part because multiple sequence alignments must be accurate for phylogeny estimation methods to be accurate. Coestimation of alignments and trees has been attempted but currently only SATé estimates reasonably accurate trees and alignments for large data sets in practical time frames (Liu K., Raghavan S., Nelesen S., Linder C.R., Warnow T. 2009b. Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science. 324:1561-1564). Here, we present a modification to the original SATé algorithm that improves upon SATé (which we now call SATé-I) in terms of speed and of phylogenetic and alignment accuracy. SATé-II uses a different divide-and-conquer strategy than SATé-I and so produces smaller more closely related subsets than SATé-I; as a result, SATé-II produces more accurate alignments and trees, can analyze larger data sets, and runs more efficiently than SATé-I. Generally, SATé is a metamethod that takes an existing multiple sequence alignment method as an input parameter and boosts the quality of that alignment method. SATé-II-boosted alignment methods are significantly more accurate than their unboosted versions, and trees based upon these improved alignments are more accurate than trees based upon the original alignments. Because SATé-I used maximum likelihood (ML) methods that treat gaps as missing data to estimate trees and because we found a correlation between the quality of tree/alignment pairs and ML scores, we explored the degree to which SATé's performance depends on using ML with gaps treated as missing data to determine the best tree/alignment pair. We present two lines of evidence that using ML with gaps treated as missing data to optimize the alignment and tree produces very poor results. First, we show that the optimization problem where a set of unaligned DNA sequences is given and the output is the tree and alignment of those sequences that maximize likelihood under the Jukes-Cantor model is uninformative in the worst possible sense. For all inputs, all trees optimize the likelihood score. Second, we show that a greedy heuristic that uses GTR+Gamma ML to optimize the alignment and the tree can produce very poor alignments and trees. Therefore, the excellent performance of SATé-II and SATé-I is not because ML is used as an optimization criterion for choosing the best tree/alignment pair but rather due to the particular divide-and-conquer realignment techniques employed.

Initial angular momentum and flow in high energy nuclear collisions

NASA Astrophysics Data System (ADS)

Fries, Rainer J.; Chen, Guangyao; Somanathan, Sidharth

2018-03-01

We study the transfer of angular momentum in high energy nuclear collisions from the colliding nuclei to the region around midrapidity, using the classical approximation of the color glass condensate (CGC) picture. We find that the angular momentum shortly after the collision (up to times ˜1 /Qs , where Qs is the saturation scale) is carried by the "β -type" flow of the initial classical gluon field, introduced by some of us earlier. βi˜μ1∇iμ2-μ2∇iμ1 (i =1 ,2 ) describes the rapidity-odd transverse energy flow and emerges from Gauss's law for gluon fields. Here μ1 and μ2 are the averaged color charge fluctuation densities in the two nuclei, respectively. Interestingly, strong coupling calculations using anti-de Sitter/conformal field theory (AdS/CFT) techniques also find an energy flow term featuring this particular combination of nuclear densities. In classical CGC the order of magnitude of the initial angular momentum per rapidity in the reaction plane, at a time 1 /Qs , is |d L2/d η |≈ RAQs-3ɛ¯0/2 at midrapidity, where RA is the nuclear radius, and ɛ¯0 is the average initial energy density. This result emerges as a cancellation between a vortex of energy flow in the reaction plane aligned with the total angular momentum, and energy shear flow opposed to it. We discuss in detail the process of matching classical Yang-Mills results to fluid dynamics. We will argue that dissipative corrections should not be discarded to ensure that macroscopic conservation laws, e.g., for angular momentum, hold. Viscous fluid dynamics tends to dissipate the shear flow contribution that carries angular momentum in boost-invariant fluid systems. This leads to small residual angular momentum around midrapidity at late times for collisions at high energies.

Matefin/SUN-1 Phosphorylation Is Part of a Surveillance Mechanism to Coordinate Chromosome Synapsis and Recombination with Meiotic Progression and Chromosome Movement

PubMed Central

Woglar, Alexander; Daryabeigi, Anahita; Adamo, Adele; Habacher, Cornelia; Machacek, Thomas; La Volpe, Adriana; Jantsch, Verena

2013-01-01

Faithful chromosome segregation during meiosis I depends on the establishment of a crossover between homologous chromosomes. This requires induction of DNA double-strand breaks (DSBs), alignment of homologs, homolog association by synapsis, and repair of DSBs via homologous recombination. The success of these events requires coordination between chromosomal events and meiotic progression. The conserved SUN/KASH nuclear envelope bridge establishes transient linkages between chromosome ends and cytoskeletal forces during meiosis. In Caenorhabditis elegans, this bridge is essential for bringing homologs together and preventing nonhomologous synapsis. Chromosome movement takes place during synapsis and recombination. Concomitant with the onset of chromosome movement, SUN-1 clusters at chromosome ends associated with the nuclear envelope, and it is phosphorylated in a chk-2- and plk-2-dependent manner. Identification of all SUN-1 phosphomodifications at its nuclear N terminus allowed us to address their role in prophase I. Failures in recombination and synapsis led to persistent phosphorylations, which are required to elicit a delay in progression. Unfinished meiotic tasks elicited sustained recruitment of PLK-2 to chromosome ends in a SUN-1 phosphorylation–dependent manner that is required for continued chromosome movement and characteristic of a zygotene arrest. Furthermore, SUN-1 phosphorylation supported efficient synapsis. We propose that signals emanating from a failure to successfully finish meiotic tasks are integrated at the nuclear periphery to regulate chromosome end–led movement and meiotic progression. The single unsynapsed X chromosome in male meiosis is precluded from inducing a progression delay, and we found it was devoid of a population of phosphorylated SUN-1. This suggests that SUN-1 phosphorylation is critical to delaying meiosis in response to perturbed synapsis. SUN-1 may be an integral part of a checkpoint system to monitor establishment of the obligate crossover, inducible only in leptotene/zygotene. Unrepaired DSBs and unsynapsed chromosomes maintain this checkpoint, but a crossover intermediate is necessary to shut it down. PMID:23505384

Assessing Flood Risk at Nuclear Power Plants with an Uncertain Climate

NASA Astrophysics Data System (ADS)

Wigmosta, M. S.; Vail, L. W.

2011-12-01

In 2010 a tsunami severely damaged the Fukushima Dai-ichi Nuclear Power Plant in Japan. As a result, the U.S. Nuclear Regulatory Commission directed that a systematic and methodical review of Commission processes and regulations be performed to determine whether the agency should make additional improvements to its regulatory system and to make recommendations to the Commission. Two of the recommendations of the Task Force created to inform the Commission were: establish a logical, systematic, and coherent regulatory framework for adequate protection that appropriately balances defense-in-depth and risk considerations and that the NRC require licensees to reevaluate and upgrade as necessary the design-basis flooding protection of structures, systems, and components for each operating reactor. These recommendations came at the same time as technical discussions about updating approaches to evaluate flood hazard were underway. These discussions included: consideration of climate nonstationarity in flood assessments; transitioning from PMP/PMF assessments to probabilistic flood analyses to better align with risk-informed decision making; and systematic consideration of combined events in flood risk analysis. There is no scientific basis to assume that shifts in long-term mean precipitation and temperature (such as is commonly derived from climate models) relate to flood probability. Flood mechanisms are often more complex and reflect climate pattern anomalies more than mean annual shifts. Instead of discounting historical data due to climatic nonstationarity, it is important to better understand the climate patterns that have triggered floods in the past and to look to climate forecasts to understand the likely changes in the frequency of those historical climate patterns with climate change. It is equally important to have a better understanding of whether climate change will result in flood-generating climate systems heretofore unknown in the particular locale. This presentation will provide a roadmap to ensuring that the flood hazards of existing and future nuclear power plants are well defined.

Amplicon Sequencing Reveals Microbiological Signatures in Spent Nuclear Fuel Storage Basins

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

Bagwell, Christopher E.; Noble, Peter A.; Milliken, Charles E.

Water quality is an important determinant for the structural integrity of alloy cladded fuels and assemblies during long-term wet storage. Detailed characterization of a water filled storage basin for spent nuclear reactor fuel was performed following the formation and proliferation of an amorphous white flocculent. White precipitant was sampled throughout the storage basin for chemical and spectroscopic characterization, and eDNA was extracted for pyrosequencing of bacterial rRNA gene diversity. Accordingly, spectroscopic analyses indicated the precipitant to be primarily amorphous to crystalline aluminum (oxy) hydroxides with minor associated elemental components including Fe, Si, Ti, and U. High levels of dissolved carbonmore » were co-localized with the precipitant relative to bulk water. Bacterial densities were highly variable between sampling locations and with depth; cell numbers (log scale) ranged from 5.6 to 4.89 cells / mL. Bacterial diversity that was physically associated with the aluminum (oxy) hydroxide complexes exceeded an estimated 4,000 OTUs / amplicon library (3% cutoff) and the greatest percent majority of sequences were aligned to the families Burkholderiales (23%), Nitrospiraceae (23%), Hyphomicrobiaceae (17%), and Comamonadaceae (6%). We surmise that episodic changes in the physical and chemical properties of the basin contribute to the polymerization of aluminum (oxy) hydroxides, which in turn can chemisorb nutrients, carbon ligands and bacterial cells from the surrounding bulk aqueous phase. As such, these precipitants should establish favorable microhabitats for bacterial colonization and growth. Comparative analyses of 16S rRNA gene amplicon libraries across diverse environmental landscapes were performed and microbiological signatures unique to the spent nuclear fuel storage basin environment were revealed. These insights could spur the development of tractable bioindicators that are specific of and diagnostic for water quality at discrete locations and finer scales of resolution, marking an important contribution for improved water quality and management of spent nuclear fuel storage facilities.« less

Evolutionary gradient of predicted nuclear localization signals (NLS)-bearing proteins in genomes of family Planctomycetaceae.

PubMed

Guo, Min; Yang, Ruifu; Huang, Chen; Liao, Qiwen; Fan, Guangyi; Sun, Chenghang; Lee, Simon Ming-Yuen

2017-04-04

The nuclear envelope is considered a key classification marker that distinguishes prokaryotes from eukaryotes. However, this marker does not apply to the family Planctomycetaceae, which has intracellular spaces divided by lipidic intracytoplasmic membranes (ICMs). Nuclear localization signal (NLS), a short stretch of amino acid sequence, destines to transport proteins from cytoplasm into nucleus, and is also associated with the development of nuclear envelope. We attempted to investigate the NLS motifs in Planctomycetaceae genomes to demonstrate the potential molecular transition in the development of intracellular membrane system. In this study, we identified NLS-like motifs that have the same amino acid compositions as experimentally identified NLSs in genomes of 11 representative species of family Planctomycetaceae. A total of 15 NLS types and 170 NLS-bearing proteins were detected in the 11 strains. To determine the molecular transformation, we compared NLS-bearing protein abundances in the 11 representative Planctomycetaceae genomes with them in genomes of 16 taxonomically varied microorganisms: nine bacteria, two archaea and five fungi. In the 27 strains, 29 NLS types and 1101 NLS-bearing proteins were identified, principal component analysis showed a significant transitional gradient from bacteria to Planctomycetaceae to fungi on their NLS-bearing protein abundance profiles. Then, we clustered the 993 non-redundant NLS-bearing proteins into 181 families and annotated their involved metabolic pathways. Afterwards, we aligned the ten types of NLS motifs from the 13 families containing NLS-bearing proteins among bacteria, Planctomycetaceae or fungi, considering their diversity, length and origin. A transition towards increased complexity from non-planctomycete bacteria to Planctomycetaceae to archaea and fungi was detected based on the complexity of the 10 types of NLS-like motifs in the 13 NLS-bearing proteins families. The results of this study reveal that Planctomycetaceae separates slightly from the members of non-planctomycete bacteria but still has substantial differences from fungi, based on the NLS-like motifs and NLS-bearing protein analysis.

VHF and UHF radar observations of equatorial F region ionospheric irregularities and background densities

NASA Astrophysics Data System (ADS)

Towle, D. M.

1980-02-01

A series of measurements of the properties of equatorial ionospheric irregularities were made at Kwajalein, Marshall Islands (M.I.) in August 1977 and July-August 1978. These measurements, sponsored by the Defense Nuclear Agency (DNA), involved coordinated ground-based and in situ sensors. The ARPA Long-Range Tracking and Instrumentation Radar (ALTAIR), operated by Lincoln Laboratory, obtained backscatter and transmission data during five nights in August 1977 and eight nights in July-August 1978. This report describes the ALTAIR data from the night of August 11, 1978, which yield direct quantitative measurements of 1-m and 3/8-m irregularities and of plasma depleted regions. These plasma depleted regions, previously predicted on the basis of theoretical analysis and in situ data, were observed during the decay phase and not the generative phase of the field-aligned irregularities.

Recoil distance lifetime measurements in82Kr

NASA Astrophysics Data System (ADS)

Brüssermann, S.; Keinonen, J.; Hellmeister, H. P.; Lieb, K. P.

1982-12-01

The lifetimes τ=124±12, 6{-2/+4} and 380±100 ps of the E x ( I π )=3.46(8+), 2.92(6+) and 3.04(6-) MeV states, respectively, populated by the reaction76Ge(12C, α2 n) were measured with the recoil distance method. In addition upper lifetime limits were obtained for nine states. The measured lifetimes and energies indicate a band crossing at about I π =8+, probably arising from the alignment of two g 9/2 neutrons. For the 3.04 MeV 6- state as a second member of a band built on the 2.65 MeV 4- state the measured lifetime points to a two-quasiparticle configuration. The positive-parity states have been discussed in the frame of the interacting boson approximation, nuclear field theory and the cranked shell model.

Intracellular distribution and stability of a luminescent rhenium(I) tricarbonyl tetrazolato complex using epifluorescence microscopy in conjunction with X-ray fluorescence imaging

DOE PAGES

Wedding, Jason L.; Harris, Hugh H.; Bader, Christie A.; ...

2016-11-23

Optical fluorescence microscopy was used in conjunction with X-ray fluorescence microscopy to monitor the stability and intracellular distribution of the luminescent rhenium(I) complex fac-[Re(CO) 3(phen)L], where phen = 1,10-phenathroline and L = 5-(4-iodophenyl)tetrazolato, in 22Rv1 cells. The rhenium complex showed no signs of ancillary ligand dissociation, a conclusion based on data obtained via X-ray fluorescence imaging aligning iodine and rhenium distributions. A diffuse reticular localisation was detected for the complex, in the nuclear/perinuclear region of cells, by either optical or X-ray fluorescence techniques. Furthermore, X-ray fluorescence also showed that the Re-I complex disrupted the homeostasis of some biologically relevant elements,more » such as chlorine, potassium and zinc.« less

Alignment method for solar collector arrays

DOEpatents

Driver, Jr., Richard B

2012-10-23

The present invention is directed to an improved method for establishing camera fixture location for aligning mirrors on a solar collector array (SCA) comprising multiple mirror modules. The method aligns the mirrors on a module by comparing the location of the receiver image in photographs with the predicted theoretical receiver image location. To accurately align an entire SCA, a common reference is used for all of the individual module images within the SCA. The improved method can use relative pixel location information in digital photographs along with alignment fixture inclinometer data to calculate relative locations of the fixture between modules. The absolute locations are determined by minimizing alignment asymmetry for the SCA. The method inherently aligns all of the mirrors in an SCA to the receiver, even with receiver position and module-to-module alignment errors.

NO2 sensing at room temperature using vertically aligned MoS2 flakes network

NASA Astrophysics Data System (ADS)

Kumar, Rahul; Goel, Neeraj; Kumar, Mahesh

2018-04-01

To exploit the role of alignment of MoS2 flake in chemical sensing, here, we have synthesized the horizontally and vertically aligned MoS2 flake network using conventional chemical vapor deposition technique. The morphology and number of layers were confirmed by SEM and Raman spectroscopy, respectively. The sensing performance of horizontally aligned and vertically aligned flake network was investigated to NO2 at room temperature. Vertically aligned MoS2 based sensor showed higher sensitivity 51.54 % and 63.2 % compared to horizontally aligned MoS2 sensor' sensitivity of 35.32 % and 45.2 % to 50 ppm and 100 ppm NO2, respectively. This high sensitivity attributed to the high aspect ratio and high adsorption energy on the edge site of vertically aligned MoS2.

Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees.

PubMed

Kück, Patrick; Meusemann, Karen; Dambach, Johannes; Thormann, Birthe; von Reumont, Björn M; Wägele, Johann W; Misof, Bernhard

2010-03-31

Methods of alignment masking, which refers to the technique of excluding alignment blocks prior to tree reconstructions, have been successful in improving the signal-to-noise ratio in sequence alignments. However, the lack of formally well defined methods to identify randomness in sequence alignments has prevented a routine application of alignment masking. In this study, we compared the effects on tree reconstructions of the most commonly used profiling method (GBLOCKS) which uses a predefined set of rules in combination with alignment masking, with a new profiling approach (ALISCORE) based on Monte Carlo resampling within a sliding window, using different data sets and alignment methods. While the GBLOCKS approach excludes variable sections above a certain threshold which choice is left arbitrary, the ALISCORE algorithm is free of a priori rating of parameter space and therefore more objective. ALISCORE was successfully extended to amino acids using a proportional model and empirical substitution matrices to score randomness in multiple sequence alignments. A complex bootstrap resampling leads to an even distribution of scores of randomly similar sequences to assess randomness of the observed sequence similarity. Testing performance on real data, both masking methods, GBLOCKS and ALISCORE, helped to improve tree resolution. The sliding window approach was less sensitive to different alignments of identical data sets and performed equally well on all data sets. Concurrently, ALISCORE is capable of dealing with different substitution patterns and heterogeneous base composition. ALISCORE and the most relaxed GBLOCKS gap parameter setting performed best on all data sets. Correspondingly, Neighbor-Net analyses showed the most decrease in conflict. Alignment masking improves signal-to-noise ratio in multiple sequence alignments prior to phylogenetic reconstruction. Given the robust performance of alignment profiling, alignment masking should routinely be used to improve tree reconstructions. Parametric methods of alignment profiling can be easily extended to more complex likelihood based models of sequence evolution which opens the possibility of further improvements.

Colour stabilities of three types of orthodontic clear aligners exposed to staining agents

PubMed Central

Liu, Chen-Lu; Sun, Wen-Tian; Liao, Wen; Lu, Wen-Xin; Li, Qi-Wen; Jeong, Yunho; Liu, Jun; Zhao, Zhi-He

2016-01-01

The aim of this study was to evaluate and compare the colour stabilities of three types of orthodontic clear aligners exposed to staining agents in vitro. Sixty clear orthodontic aligners produced by three manufacturers (Invisalign, Angelalign, and Smartee) were immersed in three staining solutions (coffee, black tea, and red wine) and one control solution (distilled water). After 12-h and 7-day immersions, the aligners were washed in an ultrasonic cleaner and measured with a colourimeter. The colour changes (ΔE*) were calculated on the basis of the Commission Internationale de I'Eclairage L*a*b* colour system (CIE L*a*b*), and the results were then converted into National Bureau of Standards (NBS) units. Fourier transformation infrared (FT-IR) spectroscopy and scanning electron microscopy (SEM) were conducted to observe the molecular and morphologic alterations to the aligner surfaces, respectively. The three types of aligners exhibited slight colour changes after 12 h of staining, with the exception of the Invisalign aligners stained with coffee. The Invisalign aligners exhibited significantly higher ΔE* values (ranging from 0.30 to 27.81) than those of the Angelalign and Smartee aligners (ΔE* values ranging from 0.33 to 1.89 and 0.32 to 1.61, respectively, P<0.05). FT-IR analysis confirmed that the polymer-based structure of aligners did not exhibit significant chemical differences before and after the immersions. The SEM results revealed different surface alterations to the three types of aligner materials after the 7-day staining. The three types of aesthetic orthodontic appliances exhibited colour stability after the 12-h immersion, with the exception of the Invisalign aligners stained by coffee. The Invisalign aligners were more prone than the Angelalign and Smartee aligners to pigmentation. Aligner materials may be improved by considering aesthetic colour stability properties. PMID:27660048

LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening.

PubMed

Hu, Jun; Liu, Zi; Yu, Dong-Jun; Zhang, Yang

2018-02-15

Sequence-order independent structural comparison, also called structural alignment, of small ligand molecules is often needed for computer-aided virtual drug screening. Although many ligand structure alignment programs are proposed, most of them build the alignments based on rigid-body shape comparison which cannot provide atom-specific alignment information nor allow structural variation; both abilities are critical to efficient high-throughput virtual screening. We propose a novel ligand comparison algorithm, LS-align, to generate fast and accurate atom-level structural alignments of ligand molecules, through an iterative heuristic search of the target function that combines inter-atom distance with mass and chemical bond comparisons. LS-align contains two modules of Rigid-LS-align and Flexi-LS-align, designed for rigid-body and flexible alignments, respectively, where a ligand-size independent, statistics-based scoring function is developed to evaluate the similarity of ligand molecules relative to random ligand pairs. Large-scale benchmark tests are performed on prioritizing chemical ligands of 102 protein targets involving 1,415,871 candidate compounds from the DUD-E (Database of Useful Decoys: Enhanced) database, where LS-align achieves an average enrichment factor (EF) of 22.0 at the 1% cutoff and the AUC score of 0.75, which are significantly higher than other state-of-the-art methods. Detailed data analyses show that the advanced performance is mainly attributed to the design of the target function that combines structural and chemical information to enhance the sensitivity of recognizing subtle difference of ligand molecules and the introduces of structural flexibility that help capture the conformational changes induced by the ligand-receptor binding interactions. These data demonstrate a new avenue to improve the virtual screening efficiency through the development of sensitive ligand structural alignments. http://zhanglab.ccmb.med.umich.edu/LS-align/. njyudj@njust.edu.cn or zhng@umich.edu. Supplementary data are available at Bioinformatics online.

Colour stabilities of three types of orthodontic clear aligners exposed to staining agents.

PubMed

Liu, Chen-Lu; Sun, Wen-Tian; Liao, Wen; Lu, Wen-Xin; Li, Qi-Wen; Jeong, Yunho; Liu, Jun; Zhao, Zhi-He

2016-12-16

The aim of this study was to evaluate and compare the colour stabilities of three types of orthodontic clear aligners exposed to staining agents in vitro. Sixty clear orthodontic aligners produced by three manufacturers (Invisalign, Angelalign, and Smartee) were immersed in three staining solutions (coffee, black tea, and red wine) and one control solution (distilled water). After 12-h and 7-day immersions, the aligners were washed in an ultrasonic cleaner and measured with a colourimeter. The colour changes (ΔE*) were calculated on the basis of the Commission Internationale de I'Eclairage L*a*b* colour system (CIE L*a*b*), and the results were then converted into National Bureau of Standards (NBS) units. Fourier transformation infrared (FT-IR) spectroscopy and scanning electron microscopy (SEM) were conducted to observe the molecular and morphologic alterations to the aligner surfaces, respectively. The three types of aligners exhibited slight colour changes after 12 h of staining, with the exception of the Invisalign aligners stained with coffee. The Invisalign aligners exhibited significantly higher ΔE* values (ranging from 0.30 to 27.81) than those of the Angelalign and Smartee aligners (ΔE* values ranging from 0.33 to 1.89 and 0.32 to 1.61, respectively, P<0.05). FT-IR analysis confirmed that the polymer-based structure of aligners did not exhibit significant chemical differences before and after the immersions. The SEM results revealed different surface alterations to the three types of aligner materials after the 7-day staining. The three types of aesthetic orthodontic appliances exhibited colour stability after the 12-h immersion, with the exception of the Invisalign aligners stained by coffee. The Invisalign aligners were more prone than the Angelalign and Smartee aligners to pigmentation. Aligner materials may be improved by considering aesthetic colour stability properties.

StructAlign, a Program for Alignment of Structures of DNA-Protein Complexes.

PubMed

Popov, Ya V; Galitsyna, A A; Alexeevski, A V; Karyagina, A S; Spirin, S A

2015-11-01

Comparative analysis of structures of complexes of homologous proteins with DNA is important in the analysis of DNA-protein recognition. Alignment is a necessary stage of the analysis. An alignment is a matching of amino acid residues and nucleotides of one complex to residues and nucleotides of the other. Currently, there are no programs available for aligning structures of DNA-protein complexes. We present the program StructAlign, which should fill this gap. The program inputs a pair of complexes of DNA double helix with proteins and outputs an alignment of DNA chains corresponding to the best spatial fit of the protein chains.

SANA NetGO: a combinatorial approach to using Gene Ontology (GO) terms to score network alignments.

PubMed

Hayes, Wayne B; Mamano, Nil

2018-04-15

Gene Ontology (GO) terms are frequently used to score alignments between protein-protein interaction (PPI) networks. Methods exist to measure GO similarity between proteins in isolation, but proteins in a network alignment are not isolated: each pairing is dependent on every other via the alignment itself. Existing measures fail to take into account the frequency of GO terms across networks, instead imposing arbitrary rules on when to allow GO terms. Here we develop NetGO, a new measure that naturally weighs infrequent, informative GO terms more heavily than frequent, less informative GO terms, without arbitrary cutoffs, instead downweighting GO terms according to their frequency in the networks being aligned. This is a global measure applicable only to alignments, independent of pairwise GO measures, in the same sense that the edge-based EC or S3 scores are global measures of topological similarity independent of pairwise topological similarities. We demonstrate the superiority of NetGO in alignments of predetermined quality and show that NetGO correlates with alignment quality better than any existing GO-based alignment measures. We also demonstrate that NetGO provides a measure of taxonomic similarity between species, consistent with existing taxonomic measuresa feature not shared with existing GObased network alignment measures. Finally, we re-score alignments produced by almost a dozen aligners from a previous study and show that NetGO does a better job at separating good alignments from bad ones. Available as part of SANA. whayes@uci.edu. Supplementary data are available at Bioinformatics online.

Precision alignment and mounting apparatus

NASA Technical Reports Server (NTRS)

Preston, Dennis R. (Inventor)

1993-01-01

An alignment and mounting apparatus for mounting two modules (10,12) includes a first portion having a cylindrical alignment pin (16) projecting normal to a module surface, a second portion having a three-stage alignment guide (18) including a shoehorn flange (34), a Y-slot (42) and a V-block (22) which sequentially guide the alignment pin (16) with successively finer precision and a third portion in the form of a spring-loaded captive fastener (20) for connecting the two modules after alignment is achieved.

Mobile and replicated alignment of arrays in data-parallel programs

NASA Technical Reports Server (NTRS)

Chatterjee, Siddhartha; Gilbert, John R.; Schreiber, Robert

1993-01-01

When a data-parallel language like FORTRAN 90 is compiled for a distributed-memory machine, aggregate data objects (such as arrays) are distributed across the processor memories. The mapping determines the amount of residual communication needed to bring operands of parallel operations into alignment with each other. A common approach is to break the mapping into two stages: first, an alignment that maps all the objects to an abstract template, and then a distribution that maps the template to the processors. We solve two facets of the problem of finding alignments that reduce residual communication: we determine alignments that vary in loops, and objects that should have replicated alignments. We show that loop-dependent mobile alignment is sometimes necessary for optimum performance, and we provide algorithms with which a compiler can determine good mobile alignments for objects within do loops. We also identify situations in which replicated alignment is either required by the program itself (via spread operations) or can be used to improve performance. We propose an algorithm based on network flow that determines which objects to replicate so as to minimize the total amount of broadcast communication in replication. This work on mobile and replicated alignment extends our earlier work on determining static alignment.

Theory of grain alignment in molecular clouds

NASA Technical Reports Server (NTRS)

Roberge, Wayne G.

1993-01-01

Research accomplishments are presented and include the following: (1) mathematical theory of grain alignment; (2) super-paramagnetic alignment of molecular cloud grains; and (3) theory of grain alignment by ambipolar diffusion.

Attenuation-emission alignment in cardiac PET∕CT based on consistency conditions

PubMed Central

Alessio, Adam M.; Kinahan, Paul E.; Champley, Kyle M.; Caldwell, James H.

2010-01-01

Purpose: In cardiac PET and PET∕CT imaging, misaligned transmission and emission images are a common problem due to respiratory and cardiac motion. This misalignment leads to erroneous attenuation correction and can cause errors in perfusion mapping and quantification. This study develops and tests a method for automated alignment of attenuation and emission data. Methods: The CT-based attenuation map is iteratively transformed until the attenuation corrected emission data minimize an objective function based on the Radon consistency conditions. The alignment process is derived from previous work by Welch et al. [“Attenuation correction in PET using consistency information,” IEEE Trans. Nucl. Sci. 45, 3134–3141 (1998)] for stand-alone PET imaging. The process was evaluated with the simulated data and measured patient data from multiple cardiac ammonia PET∕CT exams. The alignment procedure was applied to simulations of five different noise levels with three different initial attenuation maps. For the measured patient data, the alignment procedure was applied to eight attenuation-emission combinations with initially acceptable alignment and eight combinations with unacceptable alignment. The initially acceptable alignment studies were forced out of alignment a known amount and quantitatively evaluated for alignment and perfusion accuracy. The initially unacceptable studies were compared to the proposed aligned images in a blinded side-by-side review. Results: The proposed automatic alignment procedure reduced errors in the simulated data and iteratively approaches global minimum solutions with the patient data. In simulations, the alignment procedure reduced the root mean square error to less than 5 mm and reduces the axial translation error to less than 1 mm. In patient studies, the procedure reduced the translation error by >50% and resolved perfusion artifacts after a known misalignment for the eight initially acceptable patient combinations. The side-by-side review of the proposed aligned attenuation-emission maps and initially misaligned attenuation-emission maps revealed that reviewers preferred the proposed aligned maps in all cases, except one inconclusive case. Conclusions: The proposed alignment procedure offers an automatic method to reduce attenuation correction artifacts in cardiac PET∕CT and provides a viable supplement to subjective manual realignment tools. PMID:20384256

SU-G-JeP3-02: Comparison of Magnitude and Frequency of Patient Positioning Errors in Breast Irradiation Using AlignRT 3D Optical Surface Imaging and Skin Mark Techniques

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

Yao, R; Chisela, W; Dorbu, G

2016-06-15

Purpose: To evaluate clinical usefulness of AlignRT (Vision RT Ltd., London, UK) in reducing patient positioning errors in breast irradiation. Methods: 60 patients undergoing whole breast irradiation were selected for this study. Patients were treated to the left or right breast lying on Qfix Access breast board (Qfix, Avondale, PA) in supine position for 28 fractions using tangential fields. 30 patients were aligned using AlignRT by aligning a breast surface region of interest (ROI) to the same area from a reference surface image extracted from planning CT. When the patient’s surface image deviated from the reference by more than 3mmmore » on one or more translational and rotational directions, a new reference was acquired using AlignRT in-room cameras. The other 30 patients were aligned to the skin marks with room lasers. On-Board MV portal images of medial field were taken daily and matched to the DRRs. The magnitude and frequency of positioning errors were determined from measured translational shifts. Kolmogorov-Smirnov test was used to evaluate statistical differences of positional accuracy and precision between AlignRT and non-AlignRT patients. Results: The percentage of port images with no shift required was 46.5% and 27.0% in vertical, 49.8% and 25.8% in longitudinal, 47.6% and 28.5% in lateral for AlignRT and non-AlignRT patients, respectively. The percentage of port images requiring more than 3mm shifts was 18.1% and 35.1% in vertical, 28.6% and 50.8% in longitudinal, 11.3% and 24.2% in lateral for AlignRT and non-AlignRT patients, respectively. Kolmogorov-Smirnov test showed that there were significant differences between the frequency distributions of AlignRT and non-AlignRT in vertical, longitudinal, and lateral shifts. Conclusion: As confirmed by port images, AlignRT-assisted patient positioning can significantly reduce the frequency and magnitude of patient setup errors in breast irradiation compared to the use of lasers and skin marks.« less

Optical Device for Converting a Laser Beam into Two Co-aligned but Oppositely Directed Beams

NASA Technical Reports Server (NTRS)

Jennings, Donald

2013-01-01

Optical systems consisting of a series of optical elements require alignment from the input end to the output end. The optical elements can be mirrors, lenses, sources, detectors, or other devices. Complex optical systems are often difficult to align from end-to-end because the alignment beam must be inserted at one end in order for the beam to traverse the entire optical path to the other end. The ends of the optical train may not be easily accessible to the alignment beam. Typically, when a series of optical elements is to be aligned, an alignment laser beam is inserted into the optical path with a pick-off mirror at one end of the series of elements. But it may be impossible to insert the beam at an end-point. It can be difficult to locate the pick-off mirror at the desired position because there is not enough space, there is no mounting surface, or the location is occupied by a source, detector, or other component. Alternatively, the laser beam might be inserted at an intermediate location (not at an end-point) and sent, first in one direction and then the other, to the opposite ends of the optical system for alignment. However, in this case, alignment must be performed in two directions and extra effort is required to co-align the two beams to make them parallel and coincident, i.e., to follow the same path as an end-to-end beam. An optical device has been developed that accepts a laser beam as input and produces two co-aligned, but counter-propagating beams. In contrast to a conventional alignment laser placed at one end of the optical path, this invention can be placed at a convenient position within the optical train and aligned to send its two beams simultaneously along precisely opposite paths that, taken together, trace out exactly the same path as the conventional alignment laser. This invention allows the user the freedom to choose locations within the optical train for placement of the alignment beam. It is also self-aligned by design and requires almost no adjustment.

Survey of local and global biological network alignment: the need to reconcile the two sides of the same coin.

PubMed

Guzzi, Pietro Hiram; Milenkovic, Tijana

2018-05-01

Analogous to genomic sequence alignment that allows for across-species transfer of biological knowledge between conserved sequence regions, biological network alignment can be used to guide the knowledge transfer between conserved regions of molecular networks of different species. Hence, biological network alignment can be used to redefine the traditional notion of a sequence-based homology to a new notion of network-based homology. Analogous to genomic sequence alignment, there exist local and global biological network alignments. Here, we survey prominent and recent computational approaches of each network alignment type and discuss their (dis)advantages. Then, as it was recently shown that the two approach types are complementary, in the sense that they capture different slices of cellular functioning, we discuss the need to reconcile the two network alignment types and present a recent first step in this direction. We conclude with some open research problems on this topic and comment on the usefulness of network alignment in other domains besides computational biology.

Four-quadrant gratings moiré fringe alignment measurement in proximity lithography.

PubMed

Zhu, Jiangping; Hu, Song; Yu, Junsheng; Zhou, Shaolin; Tang, Yan; Zhong, Min; Zhao, Lixin; Chen, Minyong; Li, Lanlan; He, Yu; Jiang, Wei

2013-02-11

This paper aims to deal with a four-quadrant gratings alignment method benefiting from phase demodulation for proximity lithography, which combines the advantages of interferometry with image processing. Both the mask alignment mark and the wafer alignment mark consist of four sets of gratings, which bring the convenience and simplification of realization for coarse alignment and fine alignment. Four sets of moiré fringes created by superposing the mask alignment mark and the wafer alignment mark are highly sensitive to the misalignment between them. And the misalignment can be easily determined through demodulating the phase of moiré fringe without any external reference. Especially, the period and phase distribution of moiré fringes are unaffected by the gap between the mask and the wafer, not excepting the wavelength of alignment illumination. Disturbance from the illumination can also be negligible, which enhances the technological adaptability. The experimental results bear out the feasibility and rationality of our designed approach.

A generalized global alignment algorithm.

PubMed

Huang, Xiaoqiu; Chao, Kun-Mao

2003-01-22

Homologous sequences are sometimes similar over some regions but different over other regions. Homologous sequences have a much lower global similarity if the different regions are much longer than the similar regions. We present a generalized global alignment algorithm for comparing sequences with intermittent similarities, an ordered list of similar regions separated by different regions. A generalized global alignment model is defined to handle sequences with intermittent similarities. A dynamic programming algorithm is designed to compute an optimal general alignment in time proportional to the product of sequence lengths and in space proportional to the sum of sequence lengths. The algorithm is implemented as a computer program named GAP3 (Global Alignment Program Version 3). The generalized global alignment model is validated by experimental results produced with GAP3 on both DNA and protein sequences. The GAP3 program extends the ability of standard global alignment programs to recognize homologous sequences of lower similarity. The GAP3 program is freely available for academic use at http://bioinformatics.iastate.edu/aat/align/align.html.

Fast Response and Spontaneous Alignment in Liquid Crystals Doped with 12-Hydroxystearic Acid Gelators.

PubMed

Lin, Hui-Chi; Wang, Chih-Hung; Wang, Jyun-Kai; Tsai, Sheng-Feng

2018-05-07

The spontaneous vertical alignment of liquid crystals (LCs) in gelator (12-hydroxystearic acid)-doped LC cells was studied. Gelator-induced alignment can be used in both positive and negative LC cells. The electro-optical characteristics of the gelator-doped negative LC cell were similar to those of an LC cell that contained a vertically aligned (VA) host. The rise time of the gelator-doped LC cell was two orders of magnitude shorter than that of the VA host LC cell. The experimental results indicate that the gelator-induced vertical alignment of LC molecules occurred not only on the surface of the indium tin oxide (ITO) but also on the homogeneous alignment layer. Various LC alignments (planar, hybrid, multistable hybrid, and vertical alignments) were achieved by modulating the doped gelator concentrations. The multistable characteristic of LCs doped with the gelator is also presented. The alignment by doping with a gelator reduces the manufacturing costs and provides a means of fabricating fast-responding, flexible LC displays using a low-temperature process.

A fast cross-validation method for alignment of electron tomography images based on Beer-Lambert law.

PubMed

Yan, Rui; Edwards, Thomas J; Pankratz, Logan M; Kuhn, Richard J; Lanman, Jason K; Liu, Jun; Jiang, Wen

2015-11-01

In electron tomography, accurate alignment of tilt series is an essential step in attaining high-resolution 3D reconstructions. Nevertheless, quantitative assessment of alignment quality has remained a challenging issue, even though many alignment methods have been reported. Here, we report a fast and accurate method, tomoAlignEval, based on the Beer-Lambert law, for the evaluation of alignment quality. Our method is able to globally estimate the alignment accuracy by measuring the goodness of log-linear relationship of the beam intensity attenuations at different tilt angles. Extensive tests with experimental data demonstrated its robust performance with stained and cryo samples. Our method is not only significantly faster but also more sensitive than measurements of tomogram resolution using Fourier shell correlation method (FSCe/o). From these tests, we also conclude that while current alignment methods are sufficiently accurate for stained samples, inaccurate alignments remain a major limitation for high resolution cryo-electron tomography. Copyright © 2015 Elsevier Inc. All rights reserved.

A fast cross-validation method for alignment of electron tomography images based on Beer-Lambert law

PubMed Central

Yan, Rui; Edwards, Thomas J.; Pankratz, Logan M.; Kuhn, Richard J.; Lanman, Jason K.; Liu, Jun; Jiang, Wen

2015-01-01

In electron tomography, accurate alignment of tilt series is an essential step in attaining high-resolution 3D reconstructions. Nevertheless, quantitative assessment of alignment quality has remained a challenging issue, even though many alignment methods have been reported. Here, we report a fast and accurate method, tomoAlignEval, based on the Beer-Lambert law, for the evaluation of alignment quality. Our method is able to globally estimate the alignment accuracy by measuring the goodness of log-linear relationship of the beam intensity attenuations at different tilt angles. Extensive tests with experimental data demonstrated its robust performance with stained and cryo samples. Our method is not only significantly faster but also more sensitive than measurements of tomogram resolution using Fourier shell correlation method (FSCe/o). From these tests, we also conclude that while current alignment methods are sufficiently accurate for stained samples, inaccurate alignments remain a major limitation for high resolution cryo-electron tomography. PMID:26455556

Slider--maximum use of probability information for alignment of short sequence reads and SNP detection.

PubMed

Malhis, Nawar; Butterfield, Yaron S N; Ester, Martin; Jones, Steven J M

2009-01-01

A plethora of alignment tools have been created that are designed to best fit different types of alignment conditions. While some of these are made for aligning Illumina Sequence Analyzer reads, none of these are fully utilizing its probability (prb) output. In this article, we will introduce a new alignment approach (Slider) that reduces the alignment problem space by utilizing each read base's probabilities given in the prb files. Compared with other aligners, Slider has higher alignment accuracy and efficiency. In addition, given that Slider matches bases with probabilities other than the most probable, it significantly reduces the percentage of base mismatches. The result is that its SNP predictions are more accurate than other SNP prediction approaches used today that start from the most probable sequence, including those using base quality.

Genome alignment with graph data structures: a comparison

PubMed Central

2014-01-01

Background Recent advances in rapid, low-cost sequencing have opened up the opportunity to study complete genome sequences. The computational approach of multiple genome alignment allows investigation of evolutionarily related genomes in an integrated fashion, providing a basis for downstream analyses such as rearrangement studies and phylogenetic inference. Graphs have proven to be a powerful tool for coping with the complexity of genome-scale sequence alignments. The potential of graphs to intuitively represent all aspects of genome alignments led to the development of graph-based approaches for genome alignment. These approaches construct a graph from a set of local alignments, and derive a genome alignment through identification and removal of graph substructures that indicate errors in the alignment. Results We compare the structures of commonly used graphs in terms of their abilities to represent alignment information. We describe how the graphs can be transformed into each other, and identify and classify graph substructures common to one or more graphs. Based on previous approaches, we compile a list of modifications that remove these substructures. Conclusion We show that crucial pieces of alignment information, associated with inversions and duplications, are not visible in the structure of all graphs. If we neglect vertex or edge labels, the graphs differ in their information content. Still, many ideas are shared among all graph-based approaches. Based on these findings, we outline a conceptual framework for graph-based genome alignment that can assist in the development of future genome alignment tools. PMID:24712884

A statistically harmonized alignment-classification in image space enables accurate and robust alignment of noisy images in single particle analysis.

PubMed

Kawata, Masaaki; Sato, Chikara

2007-06-01

In determining the three-dimensional (3D) structure of macromolecular assemblies in single particle analysis, a large representative dataset of two-dimensional (2D) average images from huge number of raw images is a key for high resolution. Because alignments prior to averaging are computationally intensive, currently available multireference alignment (MRA) software does not survey every possible alignment. This leads to misaligned images, creating blurred averages and reducing the quality of the final 3D reconstruction. We present a new method, in which multireference alignment is harmonized with classification (multireference multiple alignment: MRMA). This method enables a statistical comparison of multiple alignment peaks, reflecting the similarities between each raw image and a set of reference images. Among the selected alignment candidates for each raw image, misaligned images are statistically excluded, based on the principle that aligned raw images of similar projections have a dense distribution around the correctly aligned coordinates in image space. This newly developed method was examined for accuracy and speed using model image sets with various signal-to-noise ratios, and with electron microscope images of the Transient Receptor Potential C3 and the sodium channel. In every data set, the newly developed method outperformed conventional methods in robustness against noise and in speed, creating 2D average images of higher quality. This statistically harmonized alignment-classification combination should greatly improve the quality of single particle analysis.

Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search

NASA Technical Reports Server (NTRS)

Wheeler, Ward C.

2003-01-01

A method to align sequence data based on parsimonious synapomorphy schemes generated by direct optimization (DO; earlier termed optimization alignment) is proposed. DO directly diagnoses sequence data on cladograms without an intervening multiple-alignment step, thereby creating topology-specific, dynamic homology statements. Hence, no multiple-alignment is required to generate cladograms. Unlike general and globally optimal multiple-alignment procedures, the method described here, implied alignment (IA), takes these dynamic homologies and traces them back through a single cladogram, linking the unaligned sequence positions in the terminal taxa via DO transformation series. These "lines of correspondence" link ancestor-descendent states and, when displayed as linearly arrayed columns without hypothetical ancestors, are largely indistinguishable from standard multiple alignment. Since this method is based on synapomorphy, the treatment of certain classes of insertion-deletion (indel) events may be different from that of other alignment procedures. As with all alignment methods, results are dependent on parameter assumptions such as indel cost and transversion:transition ratios. Such an IA could be used as a basis for phylogenetic search, but this would be questionable since the homologies derived from the implied alignment depend on its natal cladogram and any variance, between DO and IA + Search, due to heuristic approach. The utility of this procedure in heuristic cladogram searches using DO and the improvement of heuristic cladogram cost calculations are discussed. c2003 The Willi Hennig Society. Published by Elsevier Science (USA). All rights reserved.

Using confidence intervals to evaluate the focus alignment of spectrograph detector arrays.

PubMed

Sawyer, Travis W; Hawkins, Kyle S; Damento, Michael

2017-06-20

High-resolution spectrographs extract detailed spectral information of a sample and are frequently used in astronomy, laser-induced breakdown spectroscopy, and Raman spectroscopy. These instruments employ dispersive elements such as prisms and diffraction gratings to spatially separate different wavelengths of light, which are then detected by a charge-coupled device (CCD) or complementary metal-oxide-semiconductor (CMOS) detector array. Precise alignment along the optical axis (focus position) of the detector array is critical to maximize the instrumental resolution; however, traditional approaches of scanning the detector through focus lack a quantitative measure of precision, limiting the repeatability and relying on one's experience. Here we propose a method to evaluate the focus alignment of spectrograph detector arrays by establishing confidence intervals to measure the alignment precision. We show that propagation of uncertainty can be used to estimate the variance in an alignment, thus providing a quantitative and repeatable means to evaluate the precision and confidence of an alignment. We test the approach by aligning the detector array of a prototype miniature echelle spectrograph. The results indicate that the procedure effectively quantifies alignment precision, enabling one to objectively determine when an alignment has reached an acceptable level. This quantitative approach also provides a foundation for further optimization, including automated alignment. Furthermore, the procedure introduced here can be extended to other alignment techniques that rely on numerically fitting data to a model, providing a general framework for evaluating the precision of alignment methods.

Onorbit IMU alignment error budget

NASA Technical Reports Server (NTRS)

Corson, R. W.

1980-01-01

The Star Tracker, Crew Optical Alignment Sight (COAS), and Inertial Measurement Unit (IMU) from a complex navigation system with a multitude of error sources were combined. A complete list of the system errors is presented. The errors were combined in a rational way to yield an estimate of the IMU alignment accuracy for STS-1. The expected standard deviation in the IMU alignment error for STS-1 type alignments was determined to be 72 arc seconds per axis for star tracker alignments and 188 arc seconds per axis for COAS alignments. These estimates are based on current knowledge of the star tracker, COAS, IMU, and navigation base error specifications, and were partially verified by preliminary Monte Carlo analysis.

Grasping Beer Mugs: On the Dynamics of Alignment Effects Induced by Handled Objects

ERIC Educational Resources Information Center

Bub, Daniel N.; Masson, Michael E. J.

2010-01-01

We examined automatic spatial alignment effects evoked by handled objects. Using color as the relevant cue carried by an irrelevant handled object aligned or misaligned with the response hand, responses to color were faster when the handle aligned with the response hand. Alignment effects were observed only when the task was to make a reach and…

Jig Aligns Shadow Mask On CCD

NASA Technical Reports Server (NTRS)

Matus, Carlos V.

1989-01-01

Alignment viewed through microscope. Alignment jig positions shadow mask on charge-coupled device (CCD) so metal film deposited on it precisely. Allows CCD package to be inserted and removed without disturbing alignment of mask. Holds CCD packages securely and isolates it electrostatically while providing electrical contact to each of its pins. When alignment jig assembled with CCD, used to move mask under micrometer control.

Information Technology Governance Maturity: Examining the Moderating Effect on the Relationship between Strategic Alignment Maturity and Information Technology Effectiveness

ERIC Educational Resources Information Center

Kouakou, Claude N.

2013-01-01

The positive contribution of information technology (IT) in an organization is undeniable. Most organizations take advantage of that contributive benefit by aligning their business strategy with their IT strategy. This alignment is known as IT-business strategic alignment. Strategic alignment involves making the best possible use of corporate IT…

Global Network Alignment in the Context of Aging.

PubMed

Faisal, Fazle Elahi; Zhao, Han; Milenkovic, Tijana

2015-01-01

Analogous to sequence alignment, network alignment (NA) can be used to transfer biological knowledge across species between conserved network regions. NA faces two algorithmic challenges: 1) Which cost function to use to capture "similarities" between nodes in different networks? 2) Which alignment strategy to use to rapidly identify "high-scoring" alignments from all possible alignments? We "break down" existing state-of-the-art methods that use both different cost functions and different alignment strategies to evaluate each combination of their cost functions and alignment strategies. We find that a combination of the cost function of one method and the alignment strategy of another method beats the existing methods. Hence, we propose this combination as a novel superior NA method. Then, since human aging is hard to study experimentally due to long lifespan, we use NA to transfer aging-related knowledge from well annotated model species to poorly annotated human. By doing so, we produce novel human aging-related knowledge, which complements currently available knowledge about aging that has been obtained mainly by sequence alignment. We demonstrate significant similarity between topological and functional properties of our novel predictions and those of known aging-related genes. We are the first to use NA to learn more about aging.

The twilight zone of cis element alignments.

PubMed

Sebastian, Alvaro; Contreras-Moreira, Bruno

2013-02-01

Sequence alignment of proteins and nucleic acids is a routine task in bioinformatics. Although the comparison of complete peptides, genes or genomes can be undertaken with a great variety of tools, the alignment of short DNA sequences and motifs entails pitfalls that have not been fully addressed yet. Here we confront the structural superposition of transcription factors with the sequence alignment of their recognized cis elements. Our goals are (i) to test TFcompare (http://floresta.eead.csic.es/tfcompare), a structural alignment method for protein-DNA complexes; (ii) to benchmark the pairwise alignment of regulatory elements; (iii) to define the confidence limits and the twilight zone of such alignments and (iv) to evaluate the relevance of these thresholds with elements obtained experimentally. We find that the structure of cis elements and protein-DNA interfaces is significantly more conserved than their sequence and measures how this correlates with alignment errors when only sequence information is considered. Our results confirm that DNA motifs in the form of matrices produce better alignments than individual sequences. Finally, we report that empirical and theoretically derived twilight thresholds are useful for estimating the natural plasticity of regulatory sequences, and hence for filtering out unreliable alignments.

The twilight zone of cis element alignments

PubMed Central

Sebastian, Alvaro; Contreras-Moreira, Bruno

2013-01-01

Sequence alignment of proteins and nucleic acids is a routine task in bioinformatics. Although the comparison of complete peptides, genes or genomes can be undertaken with a great variety of tools, the alignment of short DNA sequences and motifs entails pitfalls that have not been fully addressed yet. Here we confront the structural superposition of transcription factors with the sequence alignment of their recognized cis elements. Our goals are (i) to test TFcompare (http://floresta.eead.csic.es/tfcompare), a structural alignment method for protein–DNA complexes; (ii) to benchmark the pairwise alignment of regulatory elements; (iii) to define the confidence limits and the twilight zone of such alignments and (iv) to evaluate the relevance of these thresholds with elements obtained experimentally. We find that the structure of cis elements and protein–DNA interfaces is significantly more conserved than their sequence and measures how this correlates with alignment errors when only sequence information is considered. Our results confirm that DNA motifs in the form of matrices produce better alignments than individual sequences. Finally, we report that empirical and theoretically derived twilight thresholds are useful for estimating the natural plasticity of regulatory sequences, and hence for filtering out unreliable alignments. PMID:23268451

Nurses' Satisfaction With Using Nursing Information Systems From Technology Acceptance Model and Information Systems Success Model Perspectives: A Reductionist Approach.

PubMed

Lin, Hsien-Cheng

2017-02-01

Nursing information systems can enhance nursing practice and the efficiency and quality of administrative affairs within the nursing department and thus have been widely considered for implementation. Close alignment of human-computer interaction can advance optimal clinical performance with the use of information systems. However, a lack of introduction of the concept of alignment between users' perceptions and technological functionality has caused dissatisfaction, as shown in the existing literature. This study provides insight into the alignment between nurses' perceptions and how technological functionality affects their satisfaction with Nursing Information System use through a reductionist perspective of alignment. This cross-sectional study collected data from 531 registered nurses in Taiwan. The results indicated that "perceived usefulness in system quality alignment," "perceived usefulness in information quality alignment," "perceived ease of use in system quality alignment," "perceived ease of use in information quality alignment," and "perceived ease of use in service quality alignment" have significantly affected nurses' satisfaction with Nursing Information System use. However, "perceived usefulness in service quality alignment" had no significant effect on nurses' satisfaction. This study also provides some meaningful implications for theoretical and practical aspects of design.

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

Wilbur, Jeffrey D.; Gomez, Enrique D.; Ellsworth, Mark W.

A procedure for creating samples that can be repeatedly cycled between weakly aligned and strongly aligned states is described. Poly(styrene-b-isoprene) block copolymer samples were first shear-aligned and then cross-linked using a high energy electron beam. Samples with more than 1.0 cross-links per chain on average showed almost complete recovery of their initial alignment state even after 20 cycles of heating above the order–disorder transition temperature of the un-cross-linked block copolymer. Samples with 1.1 cross-links per chain, which showed over 90% loss of alignment on heating and almost 100% recovery of alignment on cooling, provided the best example of a reversiblemore » aligned-to-unaligned transition. Samples with lower cross-linking densities exhibited irreversible loss of alignment upon heating, while those with higher cross-linking densities exhibited less than 90% loss of alignment upon heating. Alignment was quantified by a technique that we call two color depolarized light scattering (TCDLS), an extension of the traditional depolarized light scattering experiment used to determine the state of order in block copolymers. Qualitative confirmation of our interpretation of TCDLS data was obtained by small-angle X-ray scattering and transmission electron microscopy.« less

Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic.

PubMed

Brown, Peter; Pullan, Wayne; Yang, Yuedong; Zhou, Yaoqi

2016-02-01

The three dimensional tertiary structure of a protein at near atomic level resolution provides insight alluding to its function and evolution. As protein structure decides its functionality, similarity in structure usually implies similarity in function. As such, structure alignment techniques are often useful in the classifications of protein function. Given the rapidly growing rate of new, experimentally determined structures being made available from repositories such as the Protein Data Bank, fast and accurate computational structure comparison tools are required. This paper presents SPalignNS, a non-sequential protein structure alignment tool using a novel asymmetrical greedy search technique. The performance of SPalignNS was evaluated against existing sequential and non-sequential structure alignment methods by performing trials with commonly used datasets. These benchmark datasets used to gauge alignment accuracy include (i) 9538 pairwise alignments implied by the HOMSTRAD database of homologous proteins; (ii) a subset of 64 difficult alignments from set (i) that have low structure similarity; (iii) 199 pairwise alignments of proteins with similar structure but different topology; and (iv) a subset of 20 pairwise alignments from the RIPC set. SPalignNS is shown to achieve greater alignment accuracy (lower or comparable root-mean squared distance with increased structure overlap coverage) for all datasets, and the highest agreement with reference alignments from the challenging dataset (iv) above, when compared with both sequentially constrained alignments and other non-sequential alignments. SPalignNS was implemented in C++. The source code, binary executable, and a web server version is freely available at: http://sparks-lab.org yaoqi.zhou@griffith.edu.au. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A new statistical framework to assess structural alignment quality using information compression

PubMed Central

Collier, James H.; Allison, Lloyd; Lesk, Arthur M.; Garcia de la Banda, Maria; Konagurthu, Arun S.

2014-01-01

Motivation: Progress in protein biology depends on the reliability of results from a handful of computational techniques, structural alignments being one. Recent reviews have highlighted substantial inconsistencies and differences between alignment results generated by the ever-growing stock of structural alignment programs. The lack of consensus on how the quality of structural alignments must be assessed has been identified as the main cause for the observed differences. Current methods assess structural alignment quality by constructing a scoring function that attempts to balance conflicting criteria, mainly alignment coverage and fidelity of structures under superposition. This traditional approach to measuring alignment quality, the subject of considerable literature, has failed to solve the problem. Further development along the same lines is unlikely to rectify the current deficiencies in the field. Results: This paper proposes a new statistical framework to assess structural alignment quality and significance based on lossless information compression. This is a radical departure from the traditional approach of formulating scoring functions. It links the structural alignment problem to the general class of statistical inductive inference problems, solved using the information-theoretic criterion of minimum message length. Based on this, we developed an efficient and reliable measure of structural alignment quality, I-value. The performance of I-value is demonstrated in comparison with a number of popular scoring functions, on a large collection of competing alignments. Our analysis shows that I-value provides a rigorous and reliable quantification of structural alignment quality, addressing a major gap in the field. Availability: http://lcb.infotech.monash.edu.au/I-value Contact: arun.konagurthu@monash.edu Supplementary information: Online supplementary data are available at http://lcb.infotech.monash.edu.au/I-value/suppl.html PMID:25161241

Using Quasi-Horizontal Alignment in the absence of the actual alignment.

PubMed

Banihashemi, Mohamadreza

2016-10-01

Horizontal alignment is a major roadway characteristic used in safety and operational evaluations of many facility types. The Highway Safety Manual (HSM) uses this characteristic in crash prediction models for rural two-lane highways, freeway segments, and freeway ramps/C-D roads. Traffic simulation models use this characteristic in their processes on almost all types of facilities. However, a good portion of roadway databases do not include horizontal alignment data; instead, many contain point coordinate data along the roadways. SHRP 2 Roadway Information Database (RID) is a good example of this type of data. Only about 5% of this geodatabase contains alignment information and for the rest, point data can easily be produced. Even though the point data can be used to extract actual horizontal alignment data but, extracting horizontal alignment is a cumbersome and costly process, especially for a database of miles and miles of highways. This research introduces a so called "Quasi-Horizontal Alignment" that can be produced easily and automatically from point coordinate data and can be used in the safety and operational evaluations of highways. SHRP 2 RID for rural two-lane highways in Washington State is used in this study. This paper presents a process through which Quasi-Horizontal Alignments are produced from point coordinates along highways by using spreadsheet software such as MS EXCEL. It is shown that the safety and operational evaluations of the highways with Quasi-Horizontal Alignments are almost identical to the ones with the actual alignments. In the absence of actual alignment the Quasi-Horizontal Alignment can easily be produced from any type of databases that contain highway coordinates such geodatabases and digital maps. Copyright © 2016 Elsevier Ltd. All rights reserved.

The development and progress of XeCl Excimer laser system

NASA Astrophysics Data System (ADS)

Zhang, Yongsheng; Ma, Lianying; Wang, Dahui; Zhao, Xueqing; Zhu, Yongxiang; Hu, Yun; Qian, Hang; Shao, Bibo; Yi, Aiping; Liu, Jingru

2015-05-01

A large angularly multiplexed XeCl Excimer laser system is under development at the Northwest Institute of Nuclear Technology (NINT). It is designed to explore the technical issues of uniform and controllable target illumination. Short wavelength, uniform and controllable target illumination is the fundamental requirement of high energy density physics research using large laser facility. With broadband, extended light source and multi-beam overlapping techniques, rare gas halide Excimer laser facility will provide uniform target illumination theoretically. Angular multiplexing and image relay techniques are briefly reviewed and some of the limitations are examined to put it more practical. The system consists of a commercial oscillator front end, three gas discharge amplifiers, two electron beam pumped amplifiers and the optics required to relay, encode and decode the laser beam. An 18 lens array targeting optics direct and focus the laser in the vacuum target chamber. The system is operational and currently undergoing tests. The total 18 beams output energy is more than 100J and the pulse width is 7ns (FWHM), the intensities on the target will exceed 1013W/cm2. The aberration of off-axis imaging optics at main amplifier should be minimized to improve the final image quality at the target. Automatic computer controlled alignment of the whole system is vital to efficiency and stability of the laser system, an array of automatic alignment model is under test and will be incorporated in the system soon.

The role of interstitial binding in radiation induced segregation in W-Re alloys

NASA Astrophysics Data System (ADS)

Gharaee, Leili; Marian, Jaime; Erhart, Paul

2016-07-01

Due to their high strength and advantageous high-temperature properties, tungsten-based alloys are being considered as plasma-facing candidate materials in fusion devices. Under neutron irradiation, rhenium, which is produced by nuclear transmutation, has been found to precipitate in elongated precipitates forming thermodynamic intermetallic phases at concentrations well below the solubility limit. Recent measurements have shown that Re precipitation can lead to substantial hardening, which may have a detrimental effect on the fracture toughness of W alloys. This puzzle of sub-solubility precipitation points to the role played by irradiation induced defects, specifically mixed solute-W interstitials. Here, using first-principles calculations based on density functional theory, we study the energetics of mixed interstitial defects in W-Re, W-V, and W-Ti alloys, as well as the heat of mixing for each substitutional solute. We find that mixed interstitials in all systems are strongly attracted to each other with binding energies of -2.4 to -3.2 eV and form interstitial pairs that are aligned along parallel first-neighbor <111 > strings. Low barriers for defect translation and rotation enable defect agglomeration and alignment even at moderate temperatures. We propose that these elongated agglomerates of mixed-interstitials may act as precursors for the formation of needle-shaped intermetallic precipitates. This interstitial-based mechanism is not limited to radiation induced segregation and precipitation in W-Re alloys but is also applicable to other body-centered cubic alloys.

Evolution of Binary Supermassive Black Holes in Rotating Nuclei

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

Rasskazov, Alexander; Merritt, David

The interaction of a binary supermassive black hole with stars in a galactic nucleus can result in changes to all the elements of the binary’s orbit, including the angles that define its orientation. If the nucleus is rotating, the orientation changes can be large, causing large changes in the binary’s orbital eccentricity as well. We present a general treatment of this problem based on the Fokker–Planck equation for f , defined as the probability distribution for the binary’s orbital elements. First- and second-order diffusion coefficients are derived for the orbital elements of the binary using numerical scattering experiments, and analyticmore » approximations are presented for some of these coefficients. Solutions of the Fokker–Planck equation are then derived under various assumptions about the initial rotational state of the nucleus and the binary hardening rate. We find that the evolution of the orbital elements can become qualitatively different when we introduce nuclear rotation: (1) the orientation of the binary’s orbit evolves toward alignment with the plane of rotation of the nucleus and (2) binary orbital eccentricity decreases for aligned binaries and increases for counteraligned ones. We find that the diffusive (random-walk) component of a binary’s evolution is small in nuclei with non-negligible rotation, and we derive the time-evolution equations for the semimajor axis, eccentricity, and inclination in that approximation. The aforementioned effects could influence gravitational wave production as well as the relative orientation of host galaxies and radio jets.« less

The floral transcriptomes of four bamboo species (Bambusoideae; Poaceae): support for common ancestry among woody bamboos.

PubMed

Wysocki, William P; Ruiz-Sanchez, Eduardo; Yin, Yanbin; Duvall, Melvin R

2016-05-20

Next-generation sequencing now allows for total RNA extracts to be sequenced in non-model organisms such as bamboos, an economically and ecologically important group of grasses. Bamboos are divided into three lineages, two of which are woody perennials with bisexual flowers, which undergo gregarious monocarpy. The third lineage, which are herbaceous perennials, possesses unisexual flowers that undergo annual flowering events. Transcriptomes were assembled using both reference-based and de novo methods. These two methods were tested by characterizing transcriptome content using sequence alignment to previously characterized reference proteomes and by identifying Pfam domains. Because of the striking differences in floral morphology and phenology between the herbaceous and woody bamboo lineages, MADS-box genes, transcription factors that control floral development and timing, were characterized and analyzed in this study. Transcripts were identified using phylogenetic methods and categorized as A, B, C, D or E-class genes, which control floral development, or SOC or SVP-like genes, which control the timing of flowering events. Putative nuclear orthologues were also identified in bamboos to use as phylogenetic markers. Instances of gene copies exhibiting topological patterns that correspond to shared phenotypes were observed in several gene families including floral development and timing genes. Alignments and phylogenetic trees were generated for 3,878 genes and for all genes in a concatenated analysis. Both the concatenated analysis and those of 2,412 separate gene trees supported monophyly among the woody bamboos, which is incongruent with previous phylogenetic studies using plastid markers.

Laser beam alignment apparatus and method

DOEpatents

Gruhn, C.R.; Hammond, R.B.

The disclosure related to an apparatus and method for laser beam alignment. Thermoelectric properties of a disc in a laser beam path are used to provide an indication of beam alignment and/or automatic laser alignment.

Laser beam alignment apparatus and method

DOEpatents

Gruhn, Charles R.; Hammond, Robert B.

1981-01-01

The disclosure relates to an apparatus and method for laser beam alignment. Thermoelectric properties of a disc in a laser beam path are used to provide an indication of beam alignment and/or automatic laser alignment.

ARYANA: Aligning Reads by Yet Another Approach

PubMed Central

2014-01-01

Motivation Although there are many different algorithms and software tools for aligning sequencing reads, fast gapped sequence search is far from solved. Strong interest in fast alignment is best reflected in the $106 prize for the Innocentive competition on aligning a collection of reads to a given database of reference genomes. In addition, de novo assembly of next-generation sequencing long reads requires fast overlap-layout-concensus algorithms which depend on fast and accurate alignment. Contribution We introduce ARYANA, a fast gapped read aligner, developed on the base of BWA indexing infrastructure with a completely new alignment engine that makes it significantly faster than three other aligners: Bowtie2, BWA and SeqAlto, with comparable generality and accuracy. Instead of the time-consuming backtracking procedures for handling mismatches, ARYANA comes with the seed-and-extend algorithmic framework and a significantly improved efficiency by integrating novel algorithmic techniques including dynamic seed selection, bidirectional seed extension, reset-free hash tables, and gap-filling dynamic programming. As the read length increases ARYANA's superiority in terms of speed and alignment rate becomes more evident. This is in perfect harmony with the read length trend as the sequencing technologies evolve. The algorithmic platform of ARYANA makes it easy to develop mission-specific aligners for other applications using ARYANA engine. Availability ARYANA with complete source code can be obtained from http://github.com/aryana-aligner PMID:25252881

The ties that bind: an integrative framework of physician-hospital alignment

PubMed Central

2011-01-01

Background Alignment between physicians and hospitals is of major importance to the health care sector. Two distinct approaches to align the medical staff with the hospital have characterized previous research. The first approach, economic integration, is rooted in the economic literature, in which alignment is realized by financial means. The second approach, noneconomic integration, represents a sociological perspective emphasizing the cooperative nature of their relationship. Discussion Empirical studies and management theory (agency theory and social exchange theory) are used to increase holistic understanding of physician hospital alignment. On the one hand, noneconomic integration is identified as a means to realize a cooperative relationship. On the other hand, economic integration is studied as a way to align financial incentives. The framework is developed around two key antecedent factors which play an important role in aligning the medical staff. First, provider financial risk bearing is identified as a driving force towards closer integration. Second, organizational trust is believed to be important in explaining the causal relation between noneconomic and economic integration. Summary Hospital financial risk bearing creates a greater need for closer cooperation with the medical staff and alignment of financial incentives. Noneconomic integration lies at the very basis of alignment. It contributes directly to alignment through the norm of reciprocity and indirectly by building trust with the medical staff, laying the foundation for alignment of financial incentives. PMID:21324128

The ties that bind: an integrative framework of physician-hospital alignment.

PubMed

Trybou, Jeroen; Gemmel, Paul; Annemans, Lieven

2011-02-15

Alignment between physicians and hospitals is of major importance to the health care sector. Two distinct approaches to align the medical staff with the hospital have characterized previous research. The first approach, economic integration, is rooted in the economic literature, in which alignment is realized by financial means. The second approach, noneconomic integration, represents a sociological perspective emphasizing the cooperative nature of their relationship. Empirical studies and management theory (agency theory and social exchange theory) are used to increase holistic understanding of physician hospital alignment. On the one hand, noneconomic integration is identified as a means to realize a cooperative relationship. On the other hand, economic integration is studied as a way to align financial incentives. The framework is developed around two key antecedent factors which play an important role in aligning the medical staff. First, provider financial risk bearing is identified as a driving force towards closer integration. Second, organizational trust is believed to be important in explaining the causal relation between noneconomic and economic integration. Hospital financial risk bearing creates a greater need for closer cooperation with the medical staff and alignment of financial incentives. Noneconomic integration lies at the very basis of alignment. It contributes directly to alignment through the norm of reciprocity and indirectly by building trust with the medical staff, laying the foundation for alignment of financial incentives.

A greedy, graph-based algorithm for the alignment of multiple homologous gene lists.

PubMed

Fostier, Jan; Proost, Sebastian; Dhoedt, Bart; Saeys, Yvan; Demeester, Piet; Van de Peer, Yves; Vandepoele, Klaas

2011-03-15

Many comparative genomics studies rely on the correct identification of homologous genomic regions using accurate alignment tools. In such case, the alphabet of the input sequences consists of complete genes, rather than nucleotides or amino acids. As optimal multiple sequence alignment is computationally impractical, a progressive alignment strategy is often employed. However, such an approach is susceptible to the propagation of alignment errors in early pairwise alignment steps, especially when dealing with strongly diverged genomic regions. In this article, we present a novel accurate and efficient greedy, graph-based algorithm for the alignment of multiple homologous genomic segments, represented as ordered gene lists. Based on provable properties of the graph structure, several heuristics are developed to resolve local alignment conflicts that occur due to gene duplication and/or rearrangement events on the different genomic segments. The performance of the algorithm is assessed by comparing the alignment results of homologous genomic segments in Arabidopsis thaliana to those obtained by using both a progressive alignment method and an earlier graph-based implementation. Especially for datasets that contain strongly diverged segments, the proposed method achieves a substantially higher alignment accuracy, and proves to be sufficiently fast for large datasets including a few dozens of eukaryotic genomes. http://bioinformatics.psb.ugent.be/software. The algorithm is implemented as a part of the i-ADHoRe 3.0 package.

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC

PubMed Central

Satija, Rahul; Novák, Ádám; Miklós, István; Lyngsø, Rune; Hein, Jotun

2009-01-01

Background We have previously combined statistical alignment and phylogenetic footprinting to detect conserved functional elements without assuming a fixed alignment. Considering a probability-weighted distribution of alignments removes sensitivity to alignment errors, properly accommodates regions of alignment uncertainty, and increases the accuracy of functional element prediction. Our method utilized standard dynamic programming hidden markov model algorithms to analyze up to four sequences. Results We present a novel approach, implemented in the software package BigFoot, for performing phylogenetic footprinting on greater numbers of sequences. We have developed a Markov chain Monte Carlo (MCMC) approach which samples both sequence alignments and locations of slowly evolving regions. We implement our method as an extension of the existing StatAlign software package and test it on well-annotated regions controlling the expression of the even-skipped gene in Drosophila and the α-globin gene in vertebrates. The results exhibit how adding additional sequences to the analysis has the potential to improve the accuracy of functional predictions, and demonstrate how BigFoot outperforms existing alignment-based phylogenetic footprinting techniques. Conclusion BigFoot extends a combined alignment and phylogenetic footprinting approach to analyze larger amounts of sequence data using MCMC. Our approach is robust to alignment error and uncertainty and can be applied to a variety of biological datasets. The source code and documentation are publicly available for download from PMID:19715598

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC.

PubMed

Satija, Rahul; Novák, Adám; Miklós, István; Lyngsø, Rune; Hein, Jotun

2009-08-28

We have previously combined statistical alignment and phylogenetic footprinting to detect conserved functional elements without assuming a fixed alignment. Considering a probability-weighted distribution of alignments removes sensitivity to alignment errors, properly accommodates regions of alignment uncertainty, and increases the accuracy of functional element prediction. Our method utilized standard dynamic programming hidden markov model algorithms to analyze up to four sequences. We present a novel approach, implemented in the software package BigFoot, for performing phylogenetic footprinting on greater numbers of sequences. We have developed a Markov chain Monte Carlo (MCMC) approach which samples both sequence alignments and locations of slowly evolving regions. We implement our method as an extension of the existing StatAlign software package and test it on well-annotated regions controlling the expression of the even-skipped gene in Drosophila and the alpha-globin gene in vertebrates. The results exhibit how adding additional sequences to the analysis has the potential to improve the accuracy of functional predictions, and demonstrate how BigFoot outperforms existing alignment-based phylogenetic footprinting techniques. BigFoot extends a combined alignment and phylogenetic footprinting approach to analyze larger amounts of sequence data using MCMC. Our approach is robust to alignment error and uncertainty and can be applied to a variety of biological datasets. The source code and documentation are publicly available for download from http://www.stats.ox.ac.uk/~satija/BigFoot/

ARYANA: Aligning Reads by Yet Another Approach.

PubMed

Gholami, Milad; Arbabi, Aryan; Sharifi-Zarchi, Ali; Chitsaz, Hamidreza; Sadeghi, Mehdi

2014-01-01

Although there are many different algorithms and software tools for aligning sequencing reads, fast gapped sequence search is far from solved. Strong interest in fast alignment is best reflected in the $10(6) prize for the Innocentive competition on aligning a collection of reads to a given database of reference genomes. In addition, de novo assembly of next-generation sequencing long reads requires fast overlap-layout-concensus algorithms which depend on fast and accurate alignment. We introduce ARYANA, a fast gapped read aligner, developed on the base of BWA indexing infrastructure with a completely new alignment engine that makes it significantly faster than three other aligners: Bowtie2, BWA and SeqAlto, with comparable generality and accuracy. Instead of the time-consuming backtracking procedures for handling mismatches, ARYANA comes with the seed-and-extend algorithmic framework and a significantly improved efficiency by integrating novel algorithmic techniques including dynamic seed selection, bidirectional seed extension, reset-free hash tables, and gap-filling dynamic programming. As the read length increases ARYANA's superiority in terms of speed and alignment rate becomes more evident. This is in perfect harmony with the read length trend as the sequencing technologies evolve. The algorithmic platform of ARYANA makes it easy to develop mission-specific aligners for other applications using ARYANA engine. ARYANA with complete source code can be obtained from http://github.com/aryana-aligner.

AlexSys: a knowledge-based expert system for multiple sequence alignment construction and analysis

PubMed Central

Aniba, Mohamed Radhouene; Poch, Olivier; Marchler-Bauer, Aron; Thompson, Julie Dawn

2010-01-01

Multiple sequence alignment (MSA) is a cornerstone of modern molecular biology and represents a unique means of investigating the patterns of conservation and diversity in complex biological systems. Many different algorithms have been developed to construct MSAs, but previous studies have shown that no single aligner consistently outperforms the rest. This has led to the development of a number of ‘meta-methods’ that systematically run several aligners and merge the output into one single solution. Although these methods generally produce more accurate alignments, they are inefficient because all the aligners need to be run first and the choice of the best solution is made a posteriori. Here, we describe the development of a new expert system, AlexSys, for the multiple alignment of protein sequences. AlexSys incorporates an intelligent inference engine to automatically select an appropriate aligner a priori, depending only on the nature of the input sequences. The inference engine was trained on a large set of reference multiple alignments, using a novel machine learning approach. Applying AlexSys to a test set of 178 alignments, we show that the expert system represents a good compromise between alignment quality and running time, making it suitable for high throughput projects. AlexSys is freely available from http://alnitak.u-strasbg.fr/∼aniba/alexsys. PMID:20530533

Design of practical alignment device in KSTAR Thomson diagnostic

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

Lee, J. H., E-mail: jhlee@nfri.re.kr; University of Science and Technology; Lee, S. H.

2016-11-15

The precise alignment of the laser path and collection optics in Thomson scattering measurements is essential for accurately determining electron temperature and density in tokamak experiments. For the last five years, during the development stage, the KSTAR tokamak’s Thomson diagnostic system has had alignment fibers installed in its optical collection modules, but these lacked a proper alignment detection system. In order to address these difficulties, an alignment verifying detection device between lasers and an object field of collection optics is developed. The alignment detection device utilizes two types of filters: a narrow laser band wavelength for laser, and a broadmore » wavelength filter for Thomson scattering signal. Four such alignment detection devices have been successfully developed for the KSTAR Thomson scattering system in this year, and these will be tested in KSTAR experiments in 2016. In this paper, we present the newly developed alignment detection device for KSTAR’s Thomson scattering diagnostics.« less

Design of practical alignment device in KSTAR Thomson diagnostic.

PubMed

Lee, J H; Lee, S H; Yamada, I

2016-11-01

The precise alignment of the laser path and collection optics in Thomson scattering measurements is essential for accurately determining electron temperature and density in tokamak experiments. For the last five years, during the development stage, the KSTAR tokamak's Thomson diagnostic system has had alignment fibers installed in its optical collection modules, but these lacked a proper alignment detection system. In order to address these difficulties, an alignment verifying detection device between lasers and an object field of collection optics is developed. The alignment detection device utilizes two types of filters: a narrow laser band wavelength for laser, and a broad wavelength filter for Thomson scattering signal. Four such alignment detection devices have been successfully developed for the KSTAR Thomson scattering system in this year, and these will be tested in KSTAR experiments in 2016. In this paper, we present the newly developed alignment detection device for KSTAR's Thomson scattering diagnostics.

Studies on in situ magnetic alignment of bonded anisotropic Nd-Fe-B alloy powders

DOE PAGES

Nlebedim, I. C.; Ucar, Huseyin; Hatter, Christine B.; ...

2016-08-30

We presented some considerations for achieving high degree of alignment in polymer bonded permanent magnets via the results of a study on in situ magnetic alignment of anisotropic Nd-Fe-B magnet powders. Contributions from effect of the alignment temperature, alignment magnetic field and the properties of the polymer on the hard magnetic properties of the bonded magnet were considered. Moreover, the thermo-rheological properties of the polymer and the response of the magnet powders to the applied magnetic field indicate that hard magnetic properties were optimized at an alignment temperature just above the melting temperature of the EVA co-polymer. This agrees withmore » an observed correlation between the change in magnetization due to improved magnetic alignment of the anisotropic powders and the change in viscosity of the binder. Finally, manufacturing cost can be minimized by identifying optimum alignment temperatures and magnetic field strengths.« less

Unaligned instruction relocation

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

Bertolli, Carlo; O'Brien, John K.; Sallenave, Olivier H.

In one embodiment, a computer-implemented method includes receiving source code to be compiled into an executable file for an unaligned instruction set architecture (ISA). Aligned assembled code is generated, by a computer processor. The aligned assembled code complies with an aligned ISA and includes aligned processor code for a processor and aligned accelerator code for an accelerator. A first linking pass is performed on the aligned assembled code, including relocating a first relocation target in the aligned accelerator code that refers to a first object outside the aligned accelerator code. Unaligned assembled code is generated in accordance with the unalignedmore » ISA and includes unaligned accelerator code for the accelerator and unaligned processor code for the processor. A second linking pass is performed on the unaligned assembled code, including relocating a second relocation target outside the unaligned accelerator code that refers to an object in the unaligned accelerator code.« less

Mechanical design of multiple zone plates precision alignment apparatus for hard X-ray focusing in twenty-nanometer scale

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

Shu, Deming; Liu, Jie; Gleber, Sophie C.

An enhanced mechanical design of multiple zone plates precision alignment apparatus for hard x-ray focusing in a twenty-nanometer scale is provided. The precision alignment apparatus includes a zone plate alignment base frame; a plurality of zone plates; and a plurality of zone plate holders, each said zone plate holder for mounting and aligning a respective zone plate for hard x-ray focusing. At least one respective positioning stage drives and positions each respective zone plate holder. Each respective positioning stage is mounted on the zone plate alignment base frame. A respective linkage component connects each respective positioning stage and the respectivemore » zone plate holder. The zone plate alignment base frame, each zone plate holder and each linkage component is formed of a selected material for providing thermal expansion stability and positioning stability for the precision alignment apparatus.« less

ChromA: signal-based retention time alignment for chromatography-mass spectrometry data.

PubMed

Hoffmann, Nils; Stoye, Jens

2009-08-15

We describe ChromA, a web-based alignment tool for chromatography-mass spectrometry data from the metabolomics and proteomics domains. Users can supply their data in open and standardized file formats for retention time alignment using dynamic time warping with different configurable local distance and similarity functions. Additionally, user-defined anchors can be used to constrain and speedup the alignment. A neighborhood around each anchor can be added to increase the flexibility of the constrained alignment. ChromA offers different visualizations of the alignment for easier qualitative interpretation and comparison of the data. For the multiple alignment of more than two data files, the center-star approximation is applied to select a reference among input files to align to. ChromA is available at http://bibiserv.techfak.uni-bielefeld.de/chroma. Executables and source code under the L-GPL v3 license are provided for download at the same location.

QUASAR--scoring and ranking of sequence-structure alignments.

PubMed

Birzele, Fabian; Gewehr, Jan E; Zimmer, Ralf

2005-12-15

Sequence-structure alignments are a common means for protein structure prediction in the fields of fold recognition and homology modeling, and there is a broad variety of programs that provide such alignments based on sequence similarity, secondary structure or contact potentials. Nevertheless, finding the best sequence-structure alignment in a pool of alignments remains a difficult problem. QUASAR (quality of sequence-structure alignments ranking) provides a unifying framework for scoring sequence-structure alignments that aids finding well-performing combinations of well-known and custom-made scoring schemes. Those scoring functions can be benchmarked against widely accepted quality scores like MaxSub, TMScore, Touch and APDB, thus enabling users to test their own alignment scores against 'standard-of-truth' structure-based scores. Furthermore, individual score combinations can be optimized with respect to benchmark sets based on known structural relationships using QUASAR's in-built optimization routines.

Spatio-temporal alignment of multiple sensors

NASA Astrophysics Data System (ADS)

Zhang, Tinghua; Ni, Guoqiang; Fan, Guihua; Sun, Huayan; Yang, Biao

2018-01-01

Aiming to achieve the spatio-temporal alignment of multi sensor on the same platform for space target observation, a joint spatio-temporal alignment method is proposed. To calibrate the parameters and measure the attitude of cameras, an astronomical calibration method is proposed based on star chart simulation and collinear invariant features of quadrilateral diagonal between the observed star chart. In order to satisfy a temporal correspondence and spatial alignment similarity simultaneously, the method based on the astronomical calibration and attitude measurement in this paper formulates the video alignment to fold the spatial and temporal alignment into a joint alignment framework. The advantage of this method is reinforced by exploiting the similarities and prior knowledge of velocity vector field between adjacent frames, which is calculated by the SIFT Flow algorithm. The proposed method provides the highest spatio-temporal alignment accuracy compared to the state-of-the-art methods on sequences recorded from multi sensor at different times.

Unaligned instruction relocation

DOEpatents

Bertolli, Carlo; O'Brien, John K.; Sallenave, Olivier H.; Sura, Zehra N.

2018-01-23

In one embodiment, a computer-implemented method includes receiving source code to be compiled into an executable file for an unaligned instruction set architecture (ISA). Aligned assembled code is generated, by a computer processor. The aligned assembled code complies with an aligned ISA and includes aligned processor code for a processor and aligned accelerator code for an accelerator. A first linking pass is performed on the aligned assembled code, including relocating a first relocation target in the aligned accelerator code that refers to a first object outside the aligned accelerator code. Unaligned assembled code is generated in accordance with the unaligned ISA and includes unaligned accelerator code for the accelerator and unaligned processor code for the processor. A second linking pass is performed on the unaligned assembled code, including relocating a second relocation target outside the unaligned accelerator code that refers to an object in the unaligned accelerator code.

Projected power iteration for network alignment

NASA Astrophysics Data System (ADS)

Onaran, Efe; Villar, Soledad

2017-08-01

The network alignment problem asks for the best correspondence between two given graphs, so that the largest possible number of edges are matched. This problem appears in many scientific problems (like the study of protein-protein interactions) and it is very closely related to the quadratic assignment problem which has graph isomorphism, traveling salesman and minimum bisection problems as particular cases. The graph matching problem is NP-hard in general. However, under some restrictive models for the graphs, algorithms can approximate the alignment efficiently. In that spirit the recent work by Feizi and collaborators introduce EigenAlign, a fast spectral method with convergence guarantees for Erd-s-Renyí graphs. In this work we propose the algorithm Projected Power Alignment, which is a projected power iteration version of EigenAlign. We numerically show it improves the recovery rates of EigenAlign and we describe the theory that may be used to provide performance guarantees for Projected Power Alignment.

Studies on in situ magnetic alignment of bonded anisotropic Nd-Fe-B alloy powders

NASA Astrophysics Data System (ADS)

Nlebedim, I. C.; Ucar, Huseyin; Hatter, Christine B.; McCallum, R. W.; McCall, Scott K.; Kramer, M. J.; Paranthaman, M. Parans

2017-01-01

Considerations for achieving high degree of alignment in polymer bonded permanent magnets are presented via the results of a study on in situ magnetic alignment of anisotropic Nd-Fe-B magnet powders. Contributions from effect of the alignment temperature, alignment magnetic field and the properties of the polymer on the hard magnetic properties of the bonded magnet were considered. The thermo-rheological properties of the polymer and the response of the magnet powders to the applied magnetic field indicate that hard magnetic properties were optimized at an alignment temperature just above the melting temperature of the EVA co-polymer. This agrees with an observed correlation between the change in magnetization due to improved magnetic alignment of the anisotropic powders and the change in viscosity of the binder. Manufacturing cost can be minimized by identifying optimum alignment temperatures and magnetic field strengths.

Validation of Splicing Events in Transcriptome Sequencing Data

PubMed Central

Kaisers, Wolfgang; Ptok, Johannes; Schwender, Holger; Schaal, Heiner

2017-01-01

Genomic alignments of sequenced cellular messenger RNA contain gapped alignments which are interpreted as consequence of intron removal. The resulting gap-sites, genomic locations of alignment gaps, are landmarks representing potential splice-sites. As alignment algorithms report gap-sites with a considerable false discovery rate, validations are required. We describe two quality scores, gap quality score (gqs) and weighted gap information score (wgis), developed for validation of putative splicing events: While gqs solely relies on alignment data wgis additionally considers information from the genomic sequence. FASTQ files obtained from 54 human dermal fibroblast samples were aligned against the human genome (GRCh38) using TopHat and STAR aligner. Statistical properties of gap-sites validated by gqs and wgis were evaluated by their sequence similarity to known exon-intron borders. Within the 54 samples, TopHat identifies 1,000,380 and STAR reports 6,487,577 gap-sites. Due to the lack of strand information, however, the percentage of identified GT-AG gap-sites is rather low. While gap-sites from TopHat contain ≈89% GT-AG, gap-sites from STAR only contain ≈42% GT-AG dinucleotide pairs in merged data from 54 fibroblast samples. Validation with gqs yields 156,251 gap-sites from TopHat alignments and 166,294 from STAR alignments. Validation with wgis yields 770,327 gap-sites from TopHat alignments and 1,065,596 from STAR alignments. Both alignment algorithms, TopHat and STAR, report gap-sites with considerable false discovery rate, which can drastically be reduced by validation with gqs and wgis. PMID:28545234

X-ray verification of an optically aligned off-plane grating module

NASA Astrophysics Data System (ADS)

Donovan, Benjamin D.; McEntaffer, Randall L.; Tutt, James H.; DeRoo, Casey T.; Allured, Ryan; Gaskin, Jessica A.; Kolodziejczak, Jeffery J.

2018-01-01

Off-plane x-ray reflection gratings are theoretically capable of achieving high resolution and high diffraction efficiencies over the soft x-ray bandpass, making them an ideal technology to implement on upcoming x-ray spectroscopy missions. To achieve high effective area, these gratings must be aligned into grating modules. X-ray testing was performed on an aligned grating module to assess the current optical alignment methods. Results indicate that the grating module achieved the desired alignment for an upcoming x-ray spectroscopy suborbital rocket payload with modest effective area and resolving power. These tests have also outlined a pathway towards achieving the stricter alignment tolerances of future x-ray spectrometer payloads, which require improvements in alignment metrology, grating fabrication, and testing techniques.

Optical alignment of the JWST ISIM to the OTE simulator (OSIM): current concept and design studies

NASA Astrophysics Data System (ADS)

Frey, Bradley J.; Davila, Pamela S.; Hagopian, John G.; Marsh, James M.; Ohl, Raymond G.; Wilson, Mark E.; Young, Philip J.

2007-09-01

The James Webb Space Telescope's (JWST) Integrated Science Instrument Module (ISIM) contains the observatory's four science instruments and their support subsystems. During alignment and test of the integrated ISIM at NASA's Goddard Space Flight Center (GSFC), the Optical telescope element SIMulator (OSIM) will be used to optically stimulate the science instruments to verify their operation and performance. In this paper we present the design of two cryogenic alignment fixtures that will be used to align the OSIM to the ISIM during testing at GSFC. These fixtures, the Master Alignment Target Fixture (MATF) and the ISIM Alignment Target Fixture (IATF), will provide continuous, six degree of freedom feedback to OSIM during initial ambient alignment as well as during cryogenic vacuum testing. These fixtures will allow us to position the OSIM and detect OSIM-ISIM absolute alignment to better than 180 microns in translation and 540 micro-radians in rotation. We will provide a brief overview of the OSIM system and we will also discuss the relevance of these fixtures in the context of the overall ISIM alignment and test plan.

Node fingerprinting: an efficient heuristic for aligning biological networks.

PubMed

Radu, Alex; Charleston, Michael

2014-10-01

With the continuing increase in availability of biological data and improvements to biological models, biological network analysis has become a promising area of research. An emerging technique for the analysis of biological networks is through network alignment. Network alignment has been used to calculate genetic distance, similarities between regulatory structures, and the effect of external forces on gene expression, and to depict conditional activity of expression modules in cancer. Network alignment is algorithmically complex, and therefore we must rely on heuristics, ideally as efficient and accurate as possible. The majority of current techniques for network alignment rely on precomputed information, such as with protein sequence alignment, or on tunable network alignment parameters, which may introduce an increased computational overhead. Our presented algorithm, which we call Node Fingerprinting (NF), is appropriate for performing global pairwise network alignment without precomputation or tuning, can be fully parallelized, and is able to quickly compute an accurate alignment between two biological networks. It has performed as well as or better than existing algorithms on biological and simulated data, and with fewer computational resources. The algorithmic validation performed demonstrates the low computational resource requirements of NF.

BatMis: a fast algorithm for k-mismatch mapping.

PubMed

Tennakoon, Chandana; Purbojati, Rikky W; Sung, Wing-Kin

2012-08-15

Second-generation sequencing (SGS) generates millions of reads that need to be aligned to a reference genome allowing errors. Although current aligners can efficiently map reads allowing a small number of mismatches, they are not well suited for handling a large number of mismatches. The efficiency of aligners can be improved using various heuristics, but the sensitivity and accuracy of the alignments are sacrificed. In this article, we introduce Basic Alignment tool for Mismatches (BatMis)--an efficient method to align short reads to a reference allowing k mismatches. BatMis is a Burrows-Wheeler transformation based aligner that uses a seed and extend approach, and it is an exact method. Benchmark tests show that BatMis performs better than competing aligners in solving the k-mismatch problem. Furthermore, it can compete favorably even when compared with the heuristic modes of the other aligners. BatMis is a useful alternative for applications where fast k-mismatch mappings, unique mappings or multiple mappings of SGS data are required. BatMis is written in C/C++ and is freely available from http://code.google.com/p/batmis/

Efficient and robust model-to-image alignment using 3D scale-invariant features.

PubMed

Toews, Matthew; Wells, William M

2013-04-01

This paper presents feature-based alignment (FBA), a general method for efficient and robust model-to-image alignment. Volumetric images, e.g. CT scans of the human body, are modeled probabilistically as a collage of 3D scale-invariant image features within a normalized reference space. Features are incorporated as a latent random variable and marginalized out in computing a maximum a posteriori alignment solution. The model is learned from features extracted in pre-aligned training images, then fit to features extracted from a new image to identify a globally optimal locally linear alignment solution. Novel techniques are presented for determining local feature orientation and efficiently encoding feature intensity in 3D. Experiments involving difficult magnetic resonance (MR) images of the human brain demonstrate FBA achieves alignment accuracy similar to widely-used registration methods, while requiring a fraction of the memory and computation resources and offering a more robust, globally optimal solution. Experiments on CT human body scans demonstrate FBA as an effective system for automatic human body alignment where other alignment methods break down. Copyright © 2012 Elsevier B.V. All rights reserved.

Fast Response and Spontaneous Alignment in Liquid Crystals Doped with 12-Hydroxystearic Acid Gelators

PubMed Central

Lin, Hui-Chi; Wang, Chih-Hung; Wang, Jyun-Kai; Tsai, Sheng-Feng

2018-01-01

The spontaneous vertical alignment of liquid crystals (LCs) in gelator (12-hydroxystearic acid)-doped LC cells was studied. Gelator-induced alignment can be used in both positive and negative LC cells. The electro-optical characteristics of the gelator-doped negative LC cell were similar to those of an LC cell that contained a vertically aligned (VA) host. The rise time of the gelator-doped LC cell was two orders of magnitude shorter than that of the VA host LC cell. The experimental results indicate that the gelator-induced vertical alignment of LC molecules occurred not only on the surface of the indium tin oxide (ITO) but also on the homogeneous alignment layer. Various LC alignments (planar, hybrid, multistable hybrid, and vertical alignments) were achieved by modulating the doped gelator concentrations. The multistable characteristic of LCs doped with the gelator is also presented. The alignment by doping with a gelator reduces the manufacturing costs and provides a means of fabricating fast-responding, flexible LC displays using a low-temperature process. PMID:29735937

Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space

PubMed Central

Budavari, Tamas; Langmead, Ben; Wheelan, Sarah J.; Salzberg, Steven L.; Szalay, Alexander S.

2015-01-01

When computing alignments of DNA sequences to a large genome, a key element in achieving high processing throughput is to prioritize locations in the genome where high-scoring mappings might be expected. We formulated this task as a series of list-processing operations that can be efficiently performed on graphics processing unit (GPU) hardware.We followed this approach in implementing a read aligner called Arioc that uses GPU-based parallel sort and reduction techniques to identify high-priority locations where potential alignments may be found. We then carried out a read-by-read comparison of Arioc’s reported alignments with the alignments found by several leading read aligners. With simulated reads, Arioc has comparable or better accuracy than the other read aligners we tested. With human sequencing reads, Arioc demonstrates significantly greater throughput than the other aligners we evaluated across a wide range of sensitivity settings. The Arioc software is available at https://github.com/RWilton/Arioc. It is released under a BSD open-source license. PMID:25780763

Efficient and Robust Model-to-Image Alignment using 3D Scale-Invariant Features

PubMed Central

Toews, Matthew; Wells, William M.

2013-01-01

This paper presents feature-based alignment (FBA), a general method for efficient and robust model-to-image alignment. Volumetric images, e.g. CT scans of the human body, are modeled probabilistically as a collage of 3D scale-invariant image features within a normalized reference space. Features are incorporated as a latent random variable and marginalized out in computing a maximum a-posteriori alignment solution. The model is learned from features extracted in pre-aligned training images, then fit to features extracted from a new image to identify a globally optimal locally linear alignment solution. Novel techniques are presented for determining local feature orientation and efficiently encoding feature intensity in 3D. Experiments involving difficult magnetic resonance (MR) images of the human brain demonstrate FBA achieves alignment accuracy similar to widely-used registration methods, while requiring a fraction of the memory and computation resources and offering a more robust, globally optimal solution. Experiments on CT human body scans demonstrate FBA as an effective system for automatic human body alignment where other alignment methods break down. PMID:23265799

Optical tools and techniques for aligning solar payloads with the SPARCS control system. [Solar Pointing Aerobee Rocket Control System

NASA Technical Reports Server (NTRS)

Thomas, N. L.; Chisel, D. M.

1976-01-01

The success of a rocket-borne experiment depends not only on the pointing of the attitude control system, but on the alignment of the attitude control system to the payload. To ensure proper alignment, special optical tools and alignment techniques are required. Those that were used in the SPARCS program are described and discussed herein. These tools include theodolites, autocollimators, a 38-cm diameter solar simulator, a high-performance 1-m heliostat to provide a stable solar source during the integration of the rocket payload, a portable 75-cm sun tracker for use at the launch site, and an innovation called the Solar Alignment Prism. Using the real sun as the primary reference under field conditions, the Solar Alignment Prism facilitates the coalignment of the attitude sun sensor with the payload. The alignment techniques were developed to ensure the precise alignment of the solar payloads to the SPARCS attitude sensors during payload integration and to verify the required alignment under field conditions just prior to launch.

Alignment displacements of the solar optical telescope primary mirror

NASA Technical Reports Server (NTRS)

Medenica, W. V.

1978-01-01

Solar optical telescope is a space shuttle payload which is at the present time (1978) being planned. The selected alignment method for the telescope's primary mirror is such that the six inclined legs supporting the mirror are at the same time motorized alignment actuators, changing their own length according to the alignment requirement and command. The alignment displacements were described, including circumvention of some apparent NASTRAN limitations.

Automatic target alignment of the Helios laser system

NASA Astrophysics Data System (ADS)

Liberman, I.; Viswanathan, V. K.; Klein, M.; Seery, B. D.

1980-05-01

An automatic target-alignment technique for the Helios laser facility is reported and verified experimentally. The desired alignment condition is completely described by an autocollimation test. A computer program examines the autocollimated return pattern from the surrogate target and correctly describes any changes required in mirror orientation to yield optimum target alignment with either aberrated or misaligned beams. Automated on-line target alignment is thus shown to be feasible.

Development of a method of alignment between various SOLAR MAXIMUM MISSION experiments

NASA Technical Reports Server (NTRS)

1977-01-01

Results of an engineering study of the methods of alignment between various experiments for the solar maximum mission are described. The configuration studied consists of the instruments, mounts and instrument support platform located within the experiment module. Hardware design, fabrication methods and alignment techniques were studied with regard to optimizing the coalignment between the experiments and the fine sun sensor. The proposed hardware design was reviewed with regard to loads, stress, thermal distortion, alignment error budgets, fabrication techniques, alignment techniques and producibility. Methods of achieving comparable alignment accuracies on previous projects were also reviewed.

Electric-Field-Induced Alignment of Block Copolymer/Nanoparticle Blends

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

Liedel, Clemens; Schindler, Kerstin; Pavan, Mariela J.

External electric fi elds readily align birefringent block-copolymer mesophases. In this study the effect of gold nanoparticles on the electric-fi eld-induced alignment of a lamellae-forming polystyrene- block -poly(2-vinylpyridine) copolymer is assessed. Nanoparticles are homogeneously dispersed in the styrenic phase and promote the quantitative alignment of lamellar domains by substantially lowering the critical field strength above which alignment proceeds. The results suggest that the electric-fi eldassisted alignment of nanostructured block copolymer/nanoparticle composites may offer a simple way to greatly mitigate structural and orientational defects of such fi lms under benign experimental conditions.

Alignments of Dark Matter Halos with Large-scale Tidal Fields: Mass and Redshift Dependence

NASA Astrophysics Data System (ADS)

Chen, Sijie; Wang, Huiyuan; Mo, H. J.; Shi, Jingjing

2016-07-01

Large-scale tidal fields estimated directly from the distribution of dark matter halos are used to investigate how halo shapes and spin vectors are aligned with the cosmic web. The major, intermediate, and minor axes of halos are aligned with the corresponding tidal axes, and halo spin axes tend to be parallel with the intermediate axes and perpendicular to the major axes of the tidal field. The strengths of these alignments generally increase with halo mass and redshift, but the dependence is only on the peak height, ν \\equiv {δ }{{c}}/σ ({M}{{h}},z). The scaling relations of the alignment strengths with the value of ν indicate that the alignment strengths remain roughly constant when the structures within which the halos reside are still in a quasi-linear regime, but decreases as nonlinear evolution becomes more important. We also calculate the alignments in projection so that our results can be compared directly with observations. Finally, we investigate the alignments of tidal tensors on large scales, and use the results to understand alignments of halo pairs separated at various distances. Our results suggest that the coherent structure of the tidal field is the underlying reason for the alignments of halos and galaxies seen in numerical simulations and in observations.

Halo Intrinsic Alignment: Dependence on Mass, Formation Time, and Environment

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

Xia, Qianli; Kang, Xi; Wang, Peng

In this paper we use high-resolution cosmological simulations to study halo intrinsic alignment and its dependence on mass, formation time, and large-scale environment. In agreement with previous studies using N -body simulations, it is found that massive halos have stronger alignment. For the first time, we find that for a given halo mass older halos have stronger alignment and halos in cluster regions also have stronger alignment than those in filaments. To model these dependencies, we extend the linear alignment model with inclusion of halo bias and find that the halo alignment with its mass and formation time dependence canmore » be explained by halo bias. However, the model cannot account for the environment dependence, as it is found that halo bias is lower in clusters and higher in filaments. Our results suggest that halo bias and environment are independent factors in determining halo alignment. We also study the halo alignment correlation function and find that halos are strongly clustered along their major axes and less clustered along the minor axes. The correlated halo alignment can extend to scales as large as 100 h {sup −1} Mpc, where its feature is mainly driven by the baryon acoustic oscillation effect.« less

Enhanced critical-current in P-doped BaFe2As2 thin films on metal substrates arising from poorly aligned grain boundaries.

PubMed

Sato, Hikaru; Hiramatsu, Hidenori; Kamiya, Toshio; Hosono, Hideo

2016-11-11

Thin films of the iron-based superconductor BaFe 2 (As 1-x P x ) 2 (Ba122:P) were fabricated on polycrystalline metal-tape substrates with two kinds of in-plane grain boundary alignments (well aligned (4°) and poorly aligned (8°)) by pulsed laser deposition. The poorly aligned substrate is not applicable to cuprate-coated conductors because the in-plane alignment >4° results in exponential decay of the critical current density (J c ). The Ba122:P film exhibited higher J c at 4 K when grown on the poorly aligned substrate than on the well-aligned substrate even though the crystallinity was poorer. It was revealed that the misorientation angles of the poorly aligned samples were less than 6°, which are less than the critical angle of an iron-based superconductor, cobalt-doped BaFe 2 As 2 (~9°), and the observed strong pinning in the Ba122:P is attributed to the high-density grain boundaries with the misorientation angles smaller than the critical angle. This result reveals a distinct advantage over cuprate-coated conductors because well-aligned metal-tape substrates are not necessary for practical applications of the iron-based superconductors.

Effect of alignment perturbations in a trans-tibial prosthesis user: A pilot study.

PubMed

Courtney, Anna; Orendurff, Michael S; Buis, Arjan

2016-04-01

A recurring complication in trans-tibial prosthetic limb users is "poor socket fit" with painful residuum-socket interfaces, a consequence of excess pressure. This is due to both poor socket fit and poor socket alignment; however, the interaction of these factors has not been quantified. Through evaluation of kinetic data this study aimed to articulate an interaction uniting socket design, alignment and interface pressures. The results will help to refine future studies and will hopefully help determine whether sockets can be designed, fitted and aligned to maximize mobility whilst minimizing injurious forces. Interface pressures were recorded throughout ambulation in one user with "optimal (reference) alignment" followed by 5 malalignments in a patellar tendon-bearing and a hydrocast socket. Marked differences in pressure distribution were discovered when equating the patellar tendon-bearing against the hydrocast socket and when comparing interface pressures from reference with offset alignment. Patellar tendon-bearing sockets were found to be more sensitive to alignment perturbations than hydrocast sockets. A complex interaction was found, with the most prominent finding demonstrating the requisite for attainment of optimal alignment: a translational alignment error of 10 mm can increase maximum peak pressures by 227% (mean 17.5%). Refinements for future trials are described and the necessity for future research into socket design, alignment and interface pressures has been estabilished.

Engineering survey planning for the alignment of a particle accelerator: part I. Proposition of an assessment method

NASA Astrophysics Data System (ADS)

Junqueira Leão, Rodrigo; Raffaelo Baldo, Crhistian; Collucci da Costa Reis, Maria Luisa; Alves Trabanco, Jorge Luiz

2018-03-01

The performance of particle accelerators depends highly on the relative alignment between their components. The position and orientation of the magnetic lenses that form the trajectory of the charged beam is kept to micrometric tolerances in a range of hundreds of meters of the length of the machines. Therefore, the alignment problem is fundamentally of a dimensional metrology nature. There is no common way of expressing these tolerances in terms of terminology and alignment concept. The alignment needs for a certain machine is normally given in terms of deviations between the position of any magnet in the accelerator and the fitted line that relates the actual position of the magnets’ assembly. Root mean square errors and standard deviations are normally used interchangeably and measurement uncertainty is often neglected. Although some solutions have been employed successfully in several accelerators, there is no off-the-shelf solution to perform the alignment. Also, each alignment campaign makes use of different measuring instruments to achieve the desired results, which makes the alignment process a complex measurement chain. This paper explores these issues by reviewing the tolerances specified for the alignment of particle accelerators, and proposes a metric to assess the quality of the alignment. The metric has the advantage of fully integrating the measurement uncertainty in the process.

Ontology Alignment Repair through Modularization and Confidence-Based Heuristics

PubMed Central

Santos, Emanuel; Faria, Daniel; Pesquita, Catia; Couto, Francisco M.

2015-01-01

Ontology Matching aims at identifying a set of semantic correspondences, called an alignment, between related ontologies. In recent years, there has been a growing interest in efficient and effective matching methods for large ontologies. However, alignments produced for large ontologies are often logically incoherent. It was only recently that the use of repair techniques to improve the coherence of ontology alignments began to be explored. This paper presents a novel modularization technique for ontology alignment repair which extracts fragments of the input ontologies that only contain the necessary classes and relations to resolve all detectable incoherences. The paper presents also an alignment repair algorithm that uses a global repair strategy to minimize both the degree of incoherence and the number of mappings removed from the alignment, while overcoming the scalability problem by employing the proposed modularization technique. Our evaluation shows that our modularization technique produces significantly small fragments of the ontologies and that our repair algorithm produces more complete alignments than other current alignment repair systems, while obtaining an equivalent degree of incoherence. Additionally, we also present a variant of our repair algorithm that makes use of the confidence values of the mappings to improve alignment repair. Our repair algorithm was implemented as part of AgreementMakerLight, a free and open-source ontology matching system. PMID:26710335

Ontology Alignment Repair through Modularization and Confidence-Based Heuristics.

PubMed

Santos, Emanuel; Faria, Daniel; Pesquita, Catia; Couto, Francisco M

2015-01-01

Ontology Matching aims at identifying a set of semantic correspondences, called an alignment, between related ontologies. In recent years, there has been a growing interest in efficient and effective matching methods for large ontologies. However, alignments produced for large ontologies are often logically incoherent. It was only recently that the use of repair techniques to improve the coherence of ontology alignments began to be explored. This paper presents a novel modularization technique for ontology alignment repair which extracts fragments of the input ontologies that only contain the necessary classes and relations to resolve all detectable incoherences. The paper presents also an alignment repair algorithm that uses a global repair strategy to minimize both the degree of incoherence and the number of mappings removed from the alignment, while overcoming the scalability problem by employing the proposed modularization technique. Our evaluation shows that our modularization technique produces significantly small fragments of the ontologies and that our repair algorithm produces more complete alignments than other current alignment repair systems, while obtaining an equivalent degree of incoherence. Additionally, we also present a variant of our repair algorithm that makes use of the confidence values of the mappings to improve alignment repair. Our repair algorithm was implemented as part of AgreementMakerLight, a free and open-source ontology matching system.

mTM-align: a server for fast protein structure database search and multiple protein structure alignment.

PubMed

Dong, Runze; Pan, Shuo; Peng, Zhenling; Zhang, Yang; Yang, Jianyi

2018-05-21

With the rapid increase of the number of protein structures in the Protein Data Bank, it becomes urgent to develop algorithms for efficient protein structure comparisons. In this article, we present the mTM-align server, which consists of two closely related modules: one for structure database search and the other for multiple structure alignment. The database search is speeded up based on a heuristic algorithm and a hierarchical organization of the structures in the database. The multiple structure alignment is performed using the recently developed algorithm mTM-align. Benchmark tests demonstrate that our algorithms outperform other peering methods for both modules, in terms of speed and accuracy. One of the unique features for the server is the interplay between database search and multiple structure alignment. The server provides service not only for performing fast database search, but also for making accurate multiple structure alignment with the structures found by the search. For the database search, it takes about 2-5 min for a structure of a medium size (∼300 residues). For the multiple structure alignment, it takes a few seconds for ∼10 structures of medium sizes. The server is freely available at: http://yanglab.nankai.edu.cn/mTM-align/.

Electron tomography of the microtubule cytoskeleton in multinucleated hyphae of Ashbya gossypii.

PubMed

Gibeaux, Romain; Lang, Claudia; Politi, Antonio Z; Jaspersen, Sue L; Philippsen, Peter; Antony, Claude

2012-12-01

We report the mechanistic basis guiding the migration pattern of multiple nuclei in hyphae of Ashbya gossypii. Using electron tomography, we reconstructed the cytoplasmic microtubule (cMT) cytoskeleton in three tip regions with a total of 13 nuclei and also the spindle microtubules of four mitotic nuclei. Each spindle pole body (SPB) nucleates three cMTs and most cMTs above a certain length grow according to their plus-end structure. Long cMTs closely align for several microns along the cortex, presumably marking regions where dynein generates pulling forces on nuclei. Close proximity between cMTs emanating from adjacent nuclei was not observed. The majority of nuclei carry duplicated side-by-side SPBs, which together emanate an average of six cMTs, in most cases in opposite orientation with respect to the hyphal growth axis. Such cMT arrays explain why many nuclei undergo short-range back and forth movements. Only occasionally do all six cMTs orient in one direction, a precondition for long-range nuclear bypassing. Following mitosis, daughter nuclei carry a single SPB with three cMTs. The increased probability that all three cMTs orient in one direction explains the high rate of nuclear bypassing observed in these nuclei. The A. gossypii mitotic spindle was found to be structurally similar to that of Saccharomyces cerevisiae in terms of nuclear microtubule (nMT) number, length distribution and three-dimensional organization even though the two organisms differ significantly in chromosome number. Our results suggest that two nMTs attach to each kinetochore in A. gossypii and not only one nMT like in S. cerevisiae.

Preliminary Neutronics Analysis of the ITER Toroidal Interferometer and Polarimeter Diagnostic Corner Cube Retroreflectors

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

Tresemer, K. R.

2015-07-01

ITER is an international project under construction in France that will demonstrate nuclear fusion at a power plant-relevant scale. The Toroidal Interferometer and Polarimeter (TIP) Diagnostic will be used to measure the plasma electron line density along 5 laser-beam chords. This line-averaged density measurement will be input to the ITER feedback-control system. The TIP is considered the primary diagnostic for these measurements, which are needed for basic ITER machine control. Therefore, system reliability & accuracy is a critical element in TIP’s design. There are two major challenges to the reliability of the TIP system. First is the survivability and performancemore » of in-vessel optics and second is maintaining optical alignment over long optical paths and large vessel movements. Both of these issues greatly depend on minimizing the overall distortion due to neutron & gamma heating of the Corner Cube Retroreflectors (CCRs). These are small optical mirrors embedded in five first wall locations around the vacuum vessel, corresponding to certain plasma tangency radii. During the development of the design and location of these CCRs, several iterations of neutronics analyses were performed to determine and minimize the total distortion due to nuclear heating of the CCRs. The CCR corresponding to TIP Channel 2 was chosen for analysis as a good middle-road case, being an average distance from the plasma (of the five channels) and having moderate neutron shielding from its blanket shield housing. Results show that Channel 2 meets the requirements of the TIP Diagnostic, but barely. These results suggest other CCRs might be at risk of exceeding thermal deformation due to nuclear heating.« less

Lack of sex-biased dispersal promotes fine-scale genetic structure in alpine ungulates

USGS Publications Warehouse

Roffler, Gretchen H.; Talbot, Sandra L.; Luikart, Gordon; Sage, George K.; Pilgrim, Kristy L.; Adams, Layne G.; Schwartz, Michael K.

2014-01-01

Identifying patterns of fine-scale genetic structure in natural populations can advance understanding of critical ecological processes such as dispersal and gene flow across heterogeneous landscapes. Alpine ungulates generally exhibit high levels of genetic structure due to female philopatry and patchy configuration of mountain habitats. We assessed the spatial scale of genetic structure and the amount of gene flow in 301 Dall’s sheep (Ovis dalli dalli) at the landscape level using 15 nuclear microsatellites and 473 base pairs of the mitochondrial (mtDNA) control region. Dall’s sheep exhibited significant genetic structure within contiguous mountain ranges, but mtDNA structure occurred at a broader geographic scale than nuclear DNA within the study area, and mtDNA structure for other North American mountain sheep populations. No evidence of male-mediated gene flow or greater philopatry of females was observed; there was little difference between markers with different modes of inheritance (pairwise nuclear DNA F ST = 0.004–0.325; mtDNA F ST = 0.009–0.544), and males were no more likely than females to be recent immigrants. Historical patterns based on mtDNA indicate separate northern and southern lineages and a pattern of expansion following regional glacial retreat. Boundaries of genetic clusters aligned geographically with prominent mountain ranges, icefields, and major river valleys based on Bayesian and hierarchical modeling of microsatellite and mtDNA data. Our results suggest that fine-scale genetic structure in Dall’s sheep is influenced by limited dispersal, and structure may be weaker in populations occurring near ancestral levels of density and distribution in continuous habitats compared to other alpine ungulates that have experienced declines and marked habitat fragmentation.

Office of the Assistant Secretary for Preparedness and Response; HHS Public Health Emergency Medical Countermeasures Enterprise implementation plan for chemical, biological, radiological and nuclear threats. Notice.

PubMed

2007-04-23

The United States faces serious public health threats from the deliberate use of weapons of mass destruction (WMD)--chemical, biological, radiological, or nuclear (CBRN)--by hostile States or terrorists, and from naturally emerging infectious diseases that have a potential to cause illness on a scale that could adversely impact national security. Effective strategies to prevent, mitigate, and treat the consequences of CBRN threats is an integral component of our national security strategy. To that end, the United States must be able to rapidly develop, stockpile, and deploy effective medical countermeasures to protect the American people. The HHS Public Health Emergency Medical Countermeasures Enterprise (PHEMCE) has taken a holistic, end-to-end approach that considers multiple aspects of the medical countermeasures mission including research, development, acquisition, storage, maintenance, deployment, and guidance for utilization. Phase one of this approach established the HHS PHEMCE Strategy for Chemical, Biological, Radiological, and Nuclear Threats (HHS PHEMCE Strategy). The HHS PHEMCE Strategy, published in the Federal Register on March 20, 2007, described a framework of strategic policy goals and objectives for identifying medical countermeasure requirements and establishing priorities for medical countermeasure evaluation, development and acquisition. These strategic policy goals and objectives were used to establish the Four Pillars upon which this HHS Public Health Emergency Medical Countermeasures Enterprise Implementation Plan (HHS PHEMCE Implementation Plan) is based. The HHS PHEMCE Implementation Plan considers the full spectrum of medical countermeasures-related activities, including research, development, acquisition, storage/maintenance, deployment, and utilization. The HHS PHEMCE Implementation Plan is consistent with the President's Biodefense for the 21st Century and is aligned with the National Strategy for Medical Countermeasures against Weapons of Mass Destruction.

Anisotropic piezoresistivity characteristics of aligned carbon nanotube-polymer nanocomposites

NASA Astrophysics Data System (ADS)

Sengezer, Engin C.; Seidel, Gary D.; Bodnar, Robert J.

2017-09-01

Dielectrophoresis under the application of AC electric fields is one of the primary fabrication techniques for obtaining aligned carbon nanotube (CNT)-polymer nanocomposites, and is used here to generate long range alignment of CNTs at the structural level. The degree of alignment of CNTs within this long range architecture is observed via polarized Raman spectroscopy so that its influence on the electrical conductivity and piezoresistive response in both the alignment and transverse to alignment directions can be assessed. Nanocomposite samples consisting of randomly oriented, well dispersed single-wall carbon nanotubes (SWCNTs) and of long range electric field aligned SWCNTs in a photopolymerizable monomer blend (urethane dimethacrylate and 1,6-hexanediol dimethacrylate) are quantitatively and qualitatively evaluated. Piezoresistive sensitivities in form of gauge factors were measured for randomly oriented, well dispersed specimens with 0.03, 0.1 and 0.5 wt% SWCNTs and compared with gauge factors in both the axial and transverse to SWCNT alignment directions for electric field aligned 0.03 wt% specimens under both quasi-static monotonic and cyclic tensile loading. Gauge factors in the axial direction were observed to be on the order of 2, while gauge factors in the transverse direction demonstrated a 5 fold increase with values on the order of 10 for aligned specimens. Based on Raman analysis, it is believed the higher sensitivity of the transverse direction is related to architectural evolution of misaligned bridging structures which connect alignment structures under load due to Poisson’s contraction.

Alignment as a Teacher Variable

ERIC Educational Resources Information Center

Porter, Andrew C.; Smithson, John; Blank, Rolf; Zeidner, Timothy

2007-01-01

With the exception of the procedures developed by Porter and colleagues (Porter, 2002), other methods of defining and measuring alignment are essentially limited to alignment between tests and standards. Porter's procedures have been generalized to investigating the alignment between content standards, tests, textbooks, and even classroom…

The number of reduced alignments between two DNA sequences

PubMed Central

2014-01-01

Background In this study we consider DNA sequences as mathematical strings. Total and reduced alignments between two DNA sequences have been considered in the literature to measure their similarity. Results for explicit representations of some alignments have been already obtained. Results We present exact, explicit and computable formulas for the number of different possible alignments between two DNA sequences and a new formula for a class of reduced alignments. Conclusions A unified approach for a wide class of alignments between two DNA sequences has been provided. The formula is computable and, if complemented by software development, will provide a deeper insight into the theory of sequence alignment and give rise to new comparison methods. AMS Subject Classification Primary 92B05, 33C20, secondary 39A14, 65Q30 PMID:24684679

Beam alignment based on two-dimensional power spectral density of a near-field image.

PubMed

Wang, Shenzhen; Yuan, Qiang; Zeng, Fa; Zhang, Xin; Zhao, Junpu; Li, Kehong; Zhang, Xiaolu; Xue, Qiao; Yang, Ying; Dai, Wanjun; Zhou, Wei; Wang, Yuanchen; Zheng, Kuixing; Su, Jingqin; Hu, Dongxia; Zhu, Qihua

2017-10-30

Beam alignment is crucial to high-power laser facilities and is used to adjust the laser beams quickly and accurately to meet stringent requirements of pointing and centering. In this paper, a novel alignment method is presented, which employs data processing of the two-dimensional power spectral density (2D-PSD) for a near-field image and resolves the beam pointing error relative to the spatial filter pinhole directly. Combining this with a near-field fiducial mark, the operation of beam alignment is achieved. It is experimentally demonstrated that this scheme realizes a far-field alignment precision of approximately 3% of the pinhole size. This scheme adopts only one near-field camera to construct the alignment system, which provides a simple, efficient, and low-cost way to align lasers.

Functional Alignment of Metabolic Networks.

PubMed

Mazza, Arnon; Wagner, Allon; Ruppin, Eytan; Sharan, Roded

2016-05-01

Network alignment has become a standard tool in comparative biology, allowing the inference of protein function, interaction, and orthology. However, current alignment techniques are based on topological properties of networks and do not take into account their functional implications. Here we propose, for the first time, an algorithm to align two metabolic networks by taking advantage of their coupled metabolic models. These models allow us to assess the functional implications of genes or reactions, captured by the metabolic fluxes that are altered following their deletion from the network. Such implications may spread far beyond the region of the network where the gene or reaction lies. We apply our algorithm to align metabolic networks from various organisms, ranging from bacteria to humans, showing that our alignment can reveal functional orthology relations that are missed by conventional topological alignments.

Integrative network alignment reveals large regions of global network similarity in yeast and human.

PubMed

Kuchaiev, Oleksii; Przulj, Natasa

2011-05-15

High-throughput methods for detecting molecular interactions have produced large sets of biological network data with much more yet to come. Analogous to sequence alignment, efficient and reliable network alignment methods are expected to improve our understanding of biological systems. Unlike sequence alignment, network alignment is computationally intractable. Hence, devising efficient network alignment heuristics is currently a foremost challenge in computational biology. We introduce a novel network alignment algorithm, called Matching-based Integrative GRAph ALigner (MI-GRAAL), which can integrate any number and type of similarity measures between network nodes (e.g. proteins), including, but not limited to, any topological network similarity measure, sequence similarity, functional similarity and structural similarity. Hence, we resolve the ties in similarity measures and find a combination of similarity measures yielding the largest contiguous (i.e. connected) and biologically sound alignments. MI-GRAAL exposes the largest functional, connected regions of protein-protein interaction (PPI) network similarity to date: surprisingly, it reveals that 77.7% of proteins in the baker's yeast high-confidence PPI network participate in such a subnetwork that is fully contained in the human high-confidence PPI network. This is the first demonstration that species as diverse as yeast and human contain so large, continuous regions of global network similarity. We apply MI-GRAAL's alignments to predict functions of un-annotated proteins in yeast, human and bacteria validating our predictions in the literature. Furthermore, using network alignment scores for PPI networks of different herpes viruses, we reconstruct their phylogenetic relationship. This is the first time that phylogeny is exactly reconstructed from purely topological alignments of PPI networks. Supplementary files and MI-GRAAL executables: http://bio-nets.doc.ic.ac.uk/MI-GRAAL/.

Rapid detection, classification and accurate alignment of up to a million or more related protein sequences.

PubMed

Neuwald, Andrew F

2009-08-01

The patterns of sequence similarity and divergence present within functionally diverse, evolutionarily related proteins contain implicit information about corresponding biochemical similarities and differences. A first step toward accessing such information is to statistically analyze these patterns, which, in turn, requires that one first identify and accurately align a very large set of protein sequences. Ideally, the set should include many distantly related, functionally divergent subgroups. Because it is extremely difficult, if not impossible for fully automated methods to align such sequences correctly, researchers often resort to manual curation based on detailed structural and biochemical information. However, multiply-aligning vast numbers of sequences in this way is clearly impractical. This problem is addressed using Multiply-Aligned Profiles for Global Alignment of Protein Sequences (MAPGAPS). The MAPGAPS program uses a set of multiply-aligned profiles both as a query to detect and classify related sequences and as a template to multiply-align the sequences. It relies on Karlin-Altschul statistics for sensitivity and on PSI-BLAST (and other) heuristics for speed. Using as input a carefully curated multiple-profile alignment for P-loop GTPases, MAPGAPS correctly aligned weakly conserved sequence motifs within 33 distantly related GTPases of known structure. By comparison, the sequence- and structurally based alignment methods hmmalign and PROMALS3D misaligned at least 11 and 23 of these regions, respectively. When applied to a dataset of 65 million protein sequences, MAPGAPS identified, classified and aligned (with comparable accuracy) nearly half a million putative P-loop GTPase sequences. A C++ implementation of MAPGAPS is available at http://mapgaps.igs.umaryland.edu. Supplementary data are available at Bioinformatics online.

Effect of alignment changes on sagittal and coronal socket reaction moment interactions in transtibial prostheses.

PubMed

Kobayashi, Toshiki; Orendurff, Michael S; Zhang, Ming; Boone, David A

2013-04-26

Alignment is important for comfortable and stable gait of lower-limb prosthesis users. The magnitude of socket reaction moments in the multiple planes acting simultaneously upon the residual limb may be related to perception of comfort in individuals using prostheses through socket interface pressures. The aim of this study was to investigate the effect of prosthetic alignment changes on sagittal and coronal socket reaction moment interactions (moment-moment curves) and to characterize the curves in 11 individuals with transtibial amputation using novel moment-moment interaction parameters measured by plotting sagittal socket reaction moments versus coronal ones under various alignment conditions. A custom instrumented prosthesis alignment component was used to measure socket reaction moments during walking. Prosthetic alignment was tuned to a nominally aligned condition by a prosthetist, and from this position, angular (3° and 6° of flexion, extension, abduction or adduction of the socket) and translational (5mm and 10mm of anterior, posterior, medial or lateral translation of the socket) alignment changes were performed in either the sagittal or the coronal plane in a randomized manner. A total of 17 alignment conditions were tested. Coronal angulation and translation alignment changes demonstrated similar consistent changes in the moment-moment curves. Sagittal alignment changes demonstrated more complex changes compared to the coronal alignment changes. Effect of sagittal angulations and translations on the moment-moment curves was different during 2nd rocker (mid-stance) with extension malalignment appearing to cause medio-lateral instability. Presentation of coronal and sagittal socket reaction moment interactions may provide useful visual information for prosthetists to understand the biomechanical effects of malalignment of transtibial prostheses. Copyright © 2013 Elsevier Ltd. All rights reserved.

Enhanced spatio-temporal alignment of plantar pressure image sequences using B-splines.

PubMed

Oliveira, Francisco P M; Tavares, João Manuel R S

2013-03-01

This article presents an enhanced methodology to align plantar pressure image sequences simultaneously in time and space. The temporal alignment of the sequences is accomplished using B-splines in the time modeling, and the spatial alignment can be attained using several geometric transformation models. The methodology was tested on a dataset of 156 real plantar pressure image sequences (3 sequences for each foot of the 26 subjects) that was acquired using a common commercial plate during barefoot walking. In the alignment of image sequences that were synthetically deformed both in time and space, an outstanding accuracy was achieved with the cubic B-splines. This accuracy was significantly better (p < 0.001) than the one obtained using the best solution proposed in our previous work. When applied to align real image sequences with unknown transformation involved, the alignment based on cubic B-splines also achieved superior results than our previous methodology (p < 0.001). The consequences of the temporal alignment on the dynamic center of pressure (COP) displacement was also assessed by computing the intraclass correlation coefficients (ICC) before and after the temporal alignment of the three image sequence trials of each foot of the associated subject at six time instants. The results showed that, generally, the ICCs related to the medio-lateral COP displacement were greater when the sequences were temporally aligned than the ICCs of the original sequences. Based on the experimental findings, one can conclude that the cubic B-splines are a remarkable solution for the temporal alignment of plantar pressure image sequences. These findings also show that the temporal alignment can increase the consistency of the COP displacement on related acquired plantar pressure image sequences.

Solving the problem of Trans-Genomic Query with alignment tables.

PubMed

Parker, Douglass Stott; Hsiao, Ruey-Lung; Xing, Yi; Resch, Alissa M; Lee, Christopher J

2008-01-01

The trans-genomic query (TGQ) problem--enabling the free query of biological information, even across genomes--is a central challenge facing bioinformatics. Solutions to this problem can alter the nature of the field, moving it beyond the jungle of data integration and expanding the number and scope of questions that can be answered. An alignment table is a binary relationship on locations (sequence segments). An important special case of alignment tables are hit tables ? tables of pairs of highly similar segments produced by alignment tools like BLAST. However, alignment tables also include general binary relationships, and can represent any useful connection between sequence locations. They can be curated, and provide a high-quality queryable backbone of connections between biological information. Alignment tables thus can be a natural foundation for TGQ, as they permit a central part of the TGQ problem to be reduced to purely technical problems involving tables of locations.Key challenges in implementing alignment tables include efficient representation and indexing of sequence locations. We define a location datatype that can be incorporated naturally into common off-the-shelf database systems. We also describe an implementation of alignment tables in BLASTGRES, an extension of the open-source POSTGRESQL database system that provides indexing and operators on locations required for querying alignment tables. This paper also reviews several successful large-scale applications of alignment tables for Trans-Genomic Query. Tables with millions of alignments have been used in queries about alternative splicing, an area of genomic analysis concerning the way in which a single gene can yield multiple transcripts. Comparative genomics is a large potential application area for TGQ and alignment tables.

Standard versus physiologic bone preparation in total knee arthroplasty and the effect on joint space opening.

PubMed

Burkhart, Timothy A; Herman, Benjamin V; Perry, Kevin; Vandekerckhove, Pieter-Jan; Howard, James; Lanting, Brent

2017-11-01

Total knee arthroplasty is an effective treatment for osteoarthritis. Restoration of physiologic varus alignment may restore the native soft tissue tension and improve outcomes. Six paired fresh-frozen knee specimens were used to perform total knee arthroplastys. The left and right sides of were randomly assigned to have either a physiologic alignment cut or a standard of care neutral alignment bony cut prior to the implantation. Loads of 100 and 200N were applied at 0, 30, 60, and 90° of flexion and the magnitude of the medial and lateral compartment distraction was measured. The loads were applied with the knee specimen intact and post arthroplasty. The physiologic alignment had no difference between medial and lateral gaps at either load. With 100N of load the physiologic alignment had a greater gap at 90° than at full extension while the standard alignment had significantly more gap at 60° of flexion than full extension. The physiologic alignment had a significantly greater gap with the implant compared to the intact condition at both loads. The standard alignment had no significant difference in overall gap between the implant and intact condition with any load. Although performing a physiologic aligned TKA resulted in medial-lateral soft tissue balance, the flexion gap was found to have greater magnitude than the intact knee. Notably, a neutral aligned TKA was found to be balanced, but also was found to recreate the intact knee flexion gaps. These results suggest that coronal plane stability can be achieved with physiologic alignment objectives, but the clinician needs to be aware of the potential to have greater laxity than the intact and neutral alignment surgical objectives. Copyright © 2017 Elsevier Ltd. All rights reserved.

Automatic alignment of double optical paths in excimer laser amplifier

NASA Astrophysics Data System (ADS)

Wang, Dahui; Zhao, Xueqing; Hua, Hengqi; Zhang, Yongsheng; Hu, Yun; Yi, Aiping; Zhao, Jun

2013-05-01

A kind of beam automatic alignment method used for double paths amplification in the electron pumped excimer laser system is demonstrated. In this way, the beams from the amplifiers can be transferred along the designated direction and accordingly irradiate on the target with high stabilization and accuracy. However, owing to nonexistence of natural alignment references in excimer laser amplifiers, two cross-hairs structure is used to align the beams. Here, one crosshair put into the input beam is regarded as the near-field reference while the other put into output beam is regarded as the far-field reference. The two cross-hairs are transmitted onto Charge Coupled Devices (CCD) by image-relaying structures separately. The errors between intersection points of two cross-talk images and centroid coordinates of actual beam are recorded automatically and sent to closed loop feedback control mechanism. Negative feedback keeps running until preset accuracy is reached. On the basis of above-mentioned design, the alignment optical path is built and the software is compiled, whereafter the experiment of double paths automatic alignment in electron pumped excimer laser amplifier is carried through. Meanwhile, the related influencing factors and the alignment precision are analyzed. Experimental results indicate that the alignment system can achieve the aiming direction of automatic aligning beams in short time. The analysis shows that the accuracy of alignment system is 0.63μrad and the beam maximum restoration error is 13.75μm. Furthermore, the bigger distance between the two cross-hairs, the higher precision of the system is. Therefore, the automatic alignment system has been used in angular multiplexing excimer Main Oscillation Power Amplification (MOPA) system and can satisfy the requirement of beam alignment precision on the whole.

Rotation of intramedullary alignment rods affects distal femoral cutting plane in total knee arthroplasty.

PubMed

Maderbacher, Günther; Matussek, Jan; Keshmiri, Armin; Greimel, Felix; Baier, Clemens; Grifka, Joachim; Maderbacher, Hermann

2018-02-17

Intramedullary rods are widely used to align the distal femoral cut in total knee arthroplasty. We hypothesised that both coronal (varus/valgus) and sagittal (extension/flexion) cutting plane are affected by rotational changes of intramedullary femoral alignment guides. Distal femoral cuts using intramedullary alignment rods were simulated by means of a computer-aided engineering software in 4°, 6°, 8°, 10°, and 12° of valgus in relation to the femoral anatomical axis and 4° extension, neutral, as well as 4°, 8°, and 12° of flexion in relation to the femoral mechanical axis. This reflects the different angles between anatomical and mechanical axis in coronal and sagittal planes. To assess the influence of rotation of the alignment guide on the effective distal femoral cutting plane, all combinations were simulated with the rod gradually aligned from 40° of external to 40° of internal rotation. Rotational changes of the distal femoral alignment guides affect both the coronal and sagittal cutting planes. When alignment rods are intruded neutrally with regards to sagittal alignment, external rotation causes flexion, while internal rotation causes extension of the sagittal cutting plane. Simultaneously the coronal effect (valgus) decreases resulting in an increased varus of the cutting plane. However, when alignment rods are intruded in extension or flexion partly contradictory effects are observed. Generally the effect increases with the degree of valgus preset, rotation and flexion. As incorrect rotation of intramedullary alignment guides for distal femoral cuts causes significant cutting errors, exact rotational alignment is crucial. Coronal cutting errors in the distal femoral plane might result in overall leg malalignment, asymmetric extension gaps and subsequent sagittal cutting errors.

Generic accelerated sequence alignment in SeqAn using vectorization and multi-threading.

PubMed

Rahn, René; Budach, Stefan; Costanza, Pascal; Ehrhardt, Marcel; Hancox, Jonny; Reinert, Knut

2018-05-03

Pairwise sequence alignment is undoubtedly a central tool in many bioinformatics analyses. In this paper, we present a generically accelerated module for pairwise sequence alignments applicable for a broad range of applications. In our module, we unified the standard dynamic programming kernel used for pairwise sequence alignments and extended it with a generalized inter-sequence vectorization layout, such that many alignments can be computed simultaneously by exploiting SIMD (Single Instruction Multiple Data) instructions of modern processors. We then extended the module by adding two layers of thread-level parallelization, where we a) distribute many independent alignments on multiple threads and b) inherently parallelize a single alignment computation using a work stealing approach producing a dynamic wavefront progressing along the minor diagonal. We evaluated our alignment vectorization and parallelization on different processors, including the newest Intel® Xeon® (Skylake) and Intel® Xeon Phi™ (KNL) processors, and use cases. The instruction set AVX512-BW (Byte and Word), available on Skylake processors, can genuinely improve the performance of vectorized alignments. We could run single alignments 1600 times faster on the Xeon Phi™ and 1400 times faster on the Xeon® than executing them with our previous sequential alignment module. The module is programmed in C++ using the SeqAn (Reinert et al., 2017) library and distributed with version 2.4. under the BSD license. We support SSE4, AVX2, AVX512 instructions and included UME::SIMD, a SIMD-instruction wrapper library, to extend our module for further instruction sets. We thoroughly test all alignment components with all major C++ compilers on various platforms. rene.rahn@fu-berlin.de.

On the alignment of cellulose microfibrils by cortical microtubules: a review and a model.

PubMed

Baskin, T I

2001-01-01

The hypothesis that microtubules align microfibrils, termed the alignment hypothesis, states that there is a causal link between the orientation of cortical microtubules and the orientation of nascent microfibrils. I have assessed the generality of this hypothesis by reviewing what is known about the relation between microtubules and microfibrils in a wide group of examples: in algae of the family Characeae, Closterium acerosum, Oocystis solitaria, and certain genera of green coenocytes and in land plant tip-growing cells, xylem, diffusely growing cells, and protoplasts. The salient features about microfibril alignment to emerge are as follows. Cellulose microfibrils can be aligned by cortical microtubules, thus supporting the alignment hypothesis. Alignment of microfibrils can occur independently of microtubules, showing that an alternative to the alignment hypothesis must exist. Microfibril organization is often random, suggesting that self-assembly is insufficient. Microfibril organization differs on different faces of the same cell, suggesting that microfibrils are aligned locally, not with respect to the entire cell. Nascent microfibrils appear to associate tightly with the plasma membrane. To account for these observations, I present a model that posits alignment to be mediated through binding the nascent microfibril. The model, termed templated incorporation, postulates that the nascent microfibril is incorporated into the cell wall by binding to a scaffold that is oriented; further, the scaffold is built and oriented around either already incorporated microfibrils or plasma membrane proteins, or both. The role of cortical microtubules is to bind and orient components of the scaffold at the plasma membrane. In this way, spatial information to align the microfibrils may come from either the cell wall or the cell interior, and microfibril alignment with and without microtubules are subsets of a single mechanism.

A UNIFIED MODEL OF GRAIN ALIGNMENT: RADIATIVE ALIGNMENT OF INTERSTELLAR GRAINS WITH MAGNETIC INCLUSIONS

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

Hoang, Thiem; Lazarian, A.

The radiative torque (RAT) alignment of interstellar grains with ordinary paramagnetic susceptibilities has been supported by earlier studies. The alignment of such grains depends on the so-called RAT parameter q {sup max}, which is determined by the grain shape. In this paper, we elaborate on our model of RAT alignment for grains with enhanced magnetic susceptibility due to iron inclusions, such that RAT alignment is magnetically enhanced, which we term the MRAT mechanism. Such grains can be aligned with high angular momentum at the so-called high- J attractor points, achieving a high degree of alignment. Using our analytical model ofmore » RATs, we derive the critical value of the magnetic relaxation parameter δ {sub m} to produce high- J attractor points as functions of q {sup max} and the anisotropic radiation angle relative to the magnetic field ψ . We find that if about 10% of the total iron abundance present in silicate grains is forming iron clusters, this is sufficient to produce high- J attractor points for all reasonable values of q {sup max}. To calculate the degree of grain alignment, we carry out numerical simulations of MRAT alignment by including stochastic excitations from gas collisions and magnetic fluctuations. We show that large grains can achieve perfect alignment when the high- J attractor point is present, regardless of the values of q {sup max}. Our obtained results pave the way for the physical modeling of polarized thermal dust emission as well as magnetic dipole emission. We also find that millimeter-sized grains in accretion disks may be aligned with the magnetic field if they are incorporated with iron nanoparticles.« less

PARTS: Probabilistic Alignment for RNA joinT Secondary structure prediction

PubMed Central

Harmanci, Arif Ozgun; Sharma, Gaurav; Mathews, David H.

2008-01-01

A novel method is presented for joint prediction of alignment and common secondary structures of two RNA sequences. The joint consideration of common secondary structures and alignment is accomplished by structural alignment over a search space defined by the newly introduced motif called matched helical regions. The matched helical region formulation generalizes previously employed constraints for structural alignment and thereby better accommodates the structural variability within RNA families. A probabilistic model based on pseudo free energies obtained from precomputed base pairing and alignment probabilities is utilized for scoring structural alignments. Maximum a posteriori (MAP) common secondary structures, sequence alignment and joint posterior probabilities of base pairing are obtained from the model via a dynamic programming algorithm called PARTS. The advantage of the more general structural alignment of PARTS is seen in secondary structure predictions for the RNase P family. For this family, the PARTS MAP predictions of secondary structures and alignment perform significantly better than prior methods that utilize a more restrictive structural alignment model. For the tRNA and 5S rRNA families, the richer structural alignment model of PARTS does not offer a benefit and the method therefore performs comparably with existing alternatives. For all RNA families studied, the posterior probability estimates obtained from PARTS offer an improvement over posterior probability estimates from a single sequence prediction. When considering the base pairings predicted over a threshold value of confidence, the combination of sensitivity and positive predictive value is superior for PARTS than for the single sequence prediction. PARTS source code is available for download under the GNU public license at http://rna.urmc.rochester.edu. PMID:18304945

ChromAlign: A two-step algorithmic procedure for time alignment of three-dimensional LC-MS chromatographic surfaces.

PubMed

Sadygov, Rovshan G; Maroto, Fernando Martin; Hühmer, Andreas F R

2006-12-15

We present an algorithmic approach to align three-dimensional chromatographic surfaces of LC-MS data of complex mixture samples. The approach consists of two steps. In the first step, we prealign chromatographic profiles: two-dimensional projections of chromatographic surfaces. This is accomplished by correlation analysis using fast Fourier transforms. In this step, a temporal offset that maximizes the overlap and dot product between two chromatographic profiles is determined. In the second step, the algorithm generates correlation matrix elements between full mass scans of the reference and sample chromatographic surfaces. The temporal offset from the first step indicates a range of the mass scans that are possibly correlated, then the correlation matrix is calculated only for these mass scans. The correlation matrix carries information on highly correlated scans, but it does not itself determine the scan or time alignment. Alignment is determined as a path in the correlation matrix that maximizes the sum of the correlation matrix elements. The computational complexity of the optimal path generation problem is reduced by the use of dynamic programming. The program produces time-aligned surfaces. The use of the temporal offset from the first step in the second step reduces the computation time for generating the correlation matrix and speeds up the process. The algorithm has been implemented in a program, ChromAlign, developed in C++ language for the .NET2 environment in WINDOWS XP. In this work, we demonstrate the applications of ChromAlign to alignment of LC-MS surfaces of several datasets: a mixture of known proteins, samples from digests of surface proteins of T-cells, and samples prepared from digests of cerebrospinal fluid. ChromAlign accurately aligns the LC-MS surfaces we studied. In these examples, we discuss various aspects of the alignment by ChromAlign, such as constant time axis shifts and warping of chromatographic surfaces.

Alternative alignments development and evaluation for the US 220 project in Maryland.

DOT National Transportation Integrated Search

2011-06-01

This project aims to find the preferred alternative alignments for the Maryland section of existing US 220, using the highway : alignment optimization (HAO) model. The model was used to explore alternative alignments within a 4,000 foot-wide buffer o...

Alignment of gold nanorods by angular photothermal depletion

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

Taylor, Adam B.; Chow, Timothy T. Y.; Chon, James W. M., E-mail: jchon@swin.edu.au

2014-02-24

In this paper, we demonstrate that a high degree of alignment can be imposed upon randomly oriented gold nanorod films by angular photothermal depletion with linearly polarized laser irradiation. The photothermal reshaping of gold nanorods is observed to follow quadratic melting model rather than the threshold melting model, which distorts the angular and spectral hole created on 2D distribution map of nanorods to be an open crater shape. We have accounted these observations to the alignment procedures and demonstrated good agreement between experiment and simulations. The use of multiple laser depletion wavelengths allowed alignment criteria over a large range ofmore » aspect ratios, achieving 80% of the rods in the target angular range. We extend the technique to demonstrate post-alignment in a multilayer of randomly oriented gold nanorod films, with arbitrary control of alignment shown across the layers. Photothermal angular depletion alignment of gold nanorods is a simple, promising post-alignment method for creating future 3D or multilayer plasmonic nanorod based devices and structures.« less

Galaxy Alignments: Theory, Modelling & Simulations

NASA Astrophysics Data System (ADS)

Kiessling, Alina; Cacciato, Marcello; Joachimi, Benjamin; Kirk, Donnacha; Kitching, Thomas D.; Leonard, Adrienne; Mandelbaum, Rachel; Schäfer, Björn Malte; Sifón, Cristóbal; Brown, Michael L.; Rassat, Anais

2015-11-01

The shapes of galaxies are not randomly oriented on the sky. During the galaxy formation and evolution process, environment has a strong influence, as tidal gravitational fields in the large-scale structure tend to align nearby galaxies. Additionally, events such as galaxy mergers affect the relative alignments of both the shapes and angular momenta of galaxies throughout their history. These "intrinsic galaxy alignments" are known to exist, but are still poorly understood. This review will offer a pedagogical introduction to the current theories that describe intrinsic galaxy alignments, including the apparent difference in intrinsic alignment between early- and late-type galaxies and the latest efforts to model them analytically. It will then describe the ongoing efforts to simulate intrinsic alignments using both N-body and hydrodynamic simulations. Due to the relative youth of this field, there is still much to be done to understand intrinsic galaxy alignments and this review summarises the current state of the field, providing a solid basis for future work.

Comparison of two on-orbit attitude sensor alignment methods

NASA Technical Reports Server (NTRS)

Krack, Kenneth; Lambertson, Michael; Markley, F. Landis

1990-01-01

Compared here are two methods of on-orbit alignment of vector attitude sensors. The first method uses the angular difference between simultaneous measurements from two or more sensors. These angles are compared to the angular differences between the respective reference positions of the sensed objects. The alignments of the sensors are adjusted to minimize the difference between the two sets of angles. In the second method, the sensor alignment is part of a state vector that includes the attitude. The alignments are adjusted along with the attitude to minimize all observation residuals. It is shown that the latter method can result in much less alignment uncertainty when gyroscopes are used for attitude propagation during the alignment estimation. The additional information for this increased accuracy comes from knowledge of relative attitude obtained from the spacecraft gyroscopes. The theoretical calculations of this difference in accuracy are presented. Also presented are numerical estimates of the alignment uncertainties of the fixed-head star trackers on the Extreme Ultraviolet Explorer spacecraft using both methods.

Optimizing Mechanical Alignment With Modular Stems in Revision TKA.

PubMed

Fleischman, Andrew N; Azboy, Ibrahim; Restrepo, Camilo; Maltenfort, Mitchell G; Parvizi, Javad

2017-09-01

Although mechanical alignment is critical for optimal function and long-term implant durability, the role of modular stems in achieving ideal alignment is unclear. We identified 319 revision total knee arthroplasty from 2003-2013, for which stem length, stem diameter, and stem fixation method were recorded prospectively. Three-dimensional canal-filling ratio, the product of canal-filling ratio at the stem tip in both the anteroposterior and lateral planes, and alignment were measured radiographically. Ideal alignment of the femur was considered to be 95° in the anteroposterior (AP) plane and from 1° of extension to 4° of flexion in the lateral plane, and ideal tibial alignment was considered to be 90° in the AP plane. Even after accounting for difference in stem size and canal-fill, ideal AP alignment was more reliably achieved with press-fit stems. Furthermore, increased engagement of the diaphysis and its anatomical axis with canal-filling stems facilitates accurate alignment. Copyright © 2017 Elsevier Inc. All rights reserved.

Dissipation dynamics of field-free molecular alignment for symmetric-top molecules: Ethane (C2H6)

NASA Astrophysics Data System (ADS)

Zhang, H.; Billard, F.; Yu, X.; Faucher, O.; Lavorel, B.

2018-03-01

The field-free molecular alignment of symmetric-top molecules, ethane, induced by intense non-resonant linearly polarized femtosecond laser pulses is investigated experimentally in the presence of collisional relaxation. The dissipation dynamics of field-free molecular alignment are measured by the balanced detection of ultrafast molecular birefringence of ethane gas samples at high pressures. By separating the molecular alignment into the permanent alignment and the transient alignment, the decay time-constants of both components are quantified at the same pressure. It is observed that the permanent alignment always decays slower compared to the transient alignment within the measured pressure range. This demonstrates that the propensity of molecules to conserve the orientation of angular momentum during collisions, previously observed for linear species, is also applicable to symmetric-top molecules. The results of this work provide valuable information for further theoretical understanding of collisional relaxation within nonlinear polyatomic molecules, which are expected to present interesting and nontrivial features due to an extra rotational degree of freedom.

Concurrent and Accurate Short Read Mapping on Multicore Processors.

PubMed

Martínez, Héctor; Tárraga, Joaquín; Medina, Ignacio; Barrachina, Sergio; Castillo, Maribel; Dopazo, Joaquín; Quintana-Ortí, Enrique S

2015-01-01

We introduce a parallel aligner with a work-flow organization for fast and accurate mapping of RNA sequences on servers equipped with multicore processors. Our software, HPG Aligner SA (HPG Aligner SA is an open-source application. The software is available at http://www.opencb.org, exploits a suffix array to rapidly map a large fraction of the RNA fragments (reads), as well as leverages the accuracy of the Smith-Waterman algorithm to deal with conflictive reads. The aligner is enhanced with a careful strategy to detect splice junctions based on an adaptive division of RNA reads into small segments (or seeds), which are then mapped onto a number of candidate alignment locations, providing crucial information for the successful alignment of the complete reads. The experimental results on a platform with Intel multicore technology report the parallel performance of HPG Aligner SA, on RNA reads of 100-400 nucleotides, which excels in execution time/sensitivity to state-of-the-art aligners such as TopHat 2+Bowtie 2, MapSplice, and STAR.

Comparative Analysis of Mass Spectral Similarity Measures on Peak Alignment for Comprehensive Two-Dimensional Gas Chromatography Mass Spectrometry

PubMed Central

2013-01-01

Peak alignment is a critical procedure in mass spectrometry-based biomarker discovery in metabolomics. One of peak alignment approaches to comprehensive two-dimensional gas chromatography mass spectrometry (GC×GC-MS) data is peak matching-based alignment. A key to the peak matching-based alignment is the calculation of mass spectral similarity scores. Various mass spectral similarity measures have been developed mainly for compound identification, but the effect of these spectral similarity measures on the performance of peak matching-based alignment still remains unknown. Therefore, we selected five mass spectral similarity measures, cosine correlation, Pearson's correlation, Spearman's correlation, partial correlation, and part correlation, and examined their effects on peak alignment using two sets of experimental GC×GC-MS data. The results show that the spectral similarity measure does not affect the alignment accuracy significantly in analysis of data from less complex samples, while the partial correlation performs much better than other spectral similarity measures when analyzing experimental data acquired from complex biological samples. PMID:24151524

Implant alignment in total elbow arthroplasty: conventional vs. navigated techniques

NASA Astrophysics Data System (ADS)

McDonald, Colin P.; Johnson, James A.; King, Graham J. W.; Peters, Terry M.

2009-02-01

Incorrect selection of the native flexion-extension axis during implant alignment in elbow replacement surgery is likely a significant contributor to failure of the prosthesis. Computer and image-assisted surgery is emerging as a useful surgical tool in terms of improving the accuracy of orthopaedic procedures. This study evaluated the accuracy of implant alignment using an image-based navigation technique compared against a conventional non-navigated approach. Implant alignment error was 0.8 +/- 0.3 mm in translation and 1.1 +/- 0.4° in rotation for the navigated alignment, compared with 3.1 +/- 1.3 mm and 5.0 +/- 3.8° for the non-navigated alignment. Five (5) of the 11 non-navigated alignments were malaligned greater than 5° while none of the navigated alignments were placed with an error of greater than 2.0°. It is likely that improved implant positioning will lead to reduced implant loading and wear, resulting in fewer implantrelated complications and revision surgeries.

ChromA: signal-based retention time alignment for chromatography–mass spectrometry data

PubMed Central

Hoffmann, Nils; Stoye, Jens

2009-01-01

Summary: We describe ChromA, a web-based alignment tool for chromatography–mass spectrometry data from the metabolomics and proteomics domains. Users can supply their data in open and standardized file formats for retention time alignment using dynamic time warping with different configurable local distance and similarity functions. Additionally, user-defined anchors can be used to constrain and speedup the alignment. A neighborhood around each anchor can be added to increase the flexibility of the constrained alignment. ChromA offers different visualizations of the alignment for easier qualitative interpretation and comparison of the data. For the multiple alignment of more than two data files, the center-star approximation is applied to select a reference among input files to align to. Availability: ChromA is available at http://bibiserv.techfak.uni-bielefeld.de/chroma. Executables and source code under the L-GPL v3 license are provided for download at the same location. Contact: stoye@techfak.uni-bielefeld.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19505941

ProfileGrids: a sequence alignment visualization paradigm that avoids the limitations of Sequence Logos.

PubMed

Roca, Alberto I

2014-01-01

The 2013 BioVis Contest provided an opportunity to evaluate different paradigms for visualizing protein multiple sequence alignments. Such data sets are becoming extremely large and thus taxing current visualization paradigms. Sequence Logos represent consensus sequences but have limitations for protein alignments. As an alternative, ProfileGrids are a new protein sequence alignment visualization paradigm that represents an alignment as a color-coded matrix of the residue frequency occurring at every homologous position in the aligned protein family. The JProfileGrid software program was used to analyze the BioVis contest data sets to generate figures for comparison with the Sequence Logo reference images. The ProfileGrid representation allows for the clear and effective analysis of protein multiple sequence alignments. This includes both a general overview of the conservation and diversity sequence patterns as well as the interactive ability to query the details of the protein residue distributions in the alignment. The JProfileGrid software is free and available from http://www.ProfileGrid.org.

Improving scanner wafer alignment performance by target optimization

NASA Astrophysics Data System (ADS)

Leray, Philippe; Jehoul, Christiane; Socha, Robert; Menchtchikov, Boris; Raghunathan, Sudhar; Kent, Eric; Schoonewelle, Hielke; Tinnemans, Patrick; Tuffy, Paul; Belen, Jun; Wise, Rich

2016-03-01

In the process nodes of 10nm and below, the patterning complexity along with the processing and materials required has resulted in a need to optimize alignment targets in order to achieve the required precision, accuracy and throughput performance. Recent industry publications on the metrology target optimization process have shown a move from the expensive and time consuming empirical methodologies, towards a faster computational approach. ASML's Design for Control (D4C) application, which is currently used to optimize YieldStar diffraction based overlay (DBO) metrology targets, has been extended to support the optimization of scanner wafer alignment targets. This allows the necessary process information and design methodology, used for DBO target designs, to be leveraged for the optimization of alignment targets. In this paper, we show how we applied this computational approach to wafer alignment target design. We verify the correlation between predictions and measurements for the key alignment performance metrics and finally show the potential alignment and overlay performance improvements that an optimized alignment target could achieve.

Amperometric Detection in Microchip Electrophoresis Devices: Effect of Electrode Material and Alignment on Analytical Performance

PubMed Central

Fischer, David J.; Hulvey, Matthew K.; Regel, Anne R.; Lunte, Susan M.

2012-01-01

The fabrication and evaluation of different electrode materials and electrode alignments for microchip electrophoresis with electrochemical (EC) detection is described. The influences of electrode material, both metal and carbon-based, on sensitivity and limits of detection (LOD) were examined. In addition, the effects of working electrode alignment on analytical performance (in terms of peak shape, resolution, sensitivity, and LOD) were directly compared. Using dopamine (DA), norepinephrine (NE), and catechol (CAT) as test analytes, it was found that pyrolyzed photoresist electrodes with end-channel alignment yielded the lowest limit of detection (35 nM for DA). In addition to being easier to implement, end-channel alignment also offered better analytical performance than off-channel alignment for the detection of all three analytes. In-channel electrode alignment resulted in a 3.6-fold reduction in peak skew and reduced peak tailing by a factor of 2.1 for catechol in comparison to end-channel alignment. PMID:19802847

Unsupervised parameter optimization for automated retention time alignment of severely shifted gas chromatographic data using the piecework alignment algorithm.

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

Pierce, Karisa M.; Wright, Bob W.; Synovec, Robert E.

2007-02-02

First, simulated chromatographic separations with declining retention time precision were used to study the performance of the piecewise retention time alignment algorithm and to demonstrate an unsupervised parameter optimization method. The average correlation coefficient between the first chromatogram and every other chromatogram in the data set was used to optimize the alignment parameters. This correlation method does not require a training set, so it is unsupervised and automated. This frees the user from needing to provide class information and makes the alignment algorithm more generally applicable to classifying completely unknown data sets. For a data set of simulated chromatograms wheremore » the average chromatographic peak was shifted past two neighboring peaks between runs, the average correlation coefficient of the raw data was 0.46 ± 0.25. After automated, optimized piecewise alignment, the average correlation coefficient was 0.93 ± 0.02. Additionally, a relative shift metric and principal component analysis (PCA) were used to independently quantify and categorize the alignment performance, respectively. The relative shift metric was defined as four times the standard deviation of a given peak’s retention time in all of the chromatograms, divided by the peak-width-at-base. The raw simulated data sets that were studied contained peaks with average relative shifts ranging between 0.3 and 3.0. Second, a “real” data set of gasoline separations was gathered using three different GC methods to induce severe retention time shifting. In these gasoline separations, retention time precision improved ~8 fold following alignment. Finally, piecewise alignment and the unsupervised correlation optimization method were applied to severely shifted GC separations of reformate distillation fractions. The effect of piecewise alignment on peak heights and peak areas is also reported. Piecewise alignment either did not change the peak height, or caused it to slightly decrease. The average relative difference in peak height after piecewise alignment was –0.20%. Piecewise alignment caused the peak areas to either stay the same, slightly increase, or slightly decrease. The average absolute relative difference in area after piecewise alignment was 0.15%.« less

Surveying alignment-free features for Ortholog detection in related yeast proteomes by using supervised big data classifiers.

PubMed

Galpert, Deborah; Fernández, Alberto; Herrera, Francisco; Antunes, Agostinho; Molina-Ruiz, Reinaldo; Agüero-Chapin, Guillermin

2018-05-03

The development of new ortholog detection algorithms and the improvement of existing ones are of major importance in functional genomics. We have previously introduced a successful supervised pairwise ortholog classification approach implemented in a big data platform that considered several pairwise protein features and the low ortholog pair ratios found between two annotated proteomes (Galpert, D et al., BioMed Research International, 2015). The supervised models were built and tested using a Saccharomycete yeast benchmark dataset proposed by Salichos and Rokas (2011). Despite several pairwise protein features being combined in a supervised big data approach; they all, to some extent were alignment-based features and the proposed algorithms were evaluated on a unique test set. Here, we aim to evaluate the impact of alignment-free features on the performance of supervised models implemented in the Spark big data platform for pairwise ortholog detection in several related yeast proteomes. The Spark Random Forest and Decision Trees with oversampling and undersampling techniques, and built with only alignment-based similarity measures or combined with several alignment-free pairwise protein features showed the highest classification performance for ortholog detection in three yeast proteome pairs. Although such supervised approaches outperformed traditional methods, there were no significant differences between the exclusive use of alignment-based similarity measures and their combination with alignment-free features, even within the twilight zone of the studied proteomes. Just when alignment-based and alignment-free features were combined in Spark Decision Trees with imbalance management, a higher success rate (98.71%) within the twilight zone could be achieved for a yeast proteome pair that underwent a whole genome duplication. The feature selection study showed that alignment-based features were top-ranked for the best classifiers while the runners-up were alignment-free features related to amino acid composition. The incorporation of alignment-free features in supervised big data models did not significantly improve ortholog detection in yeast proteomes regarding the classification qualities achieved with just alignment-based similarity measures. However, the similarity of their classification performance to that of traditional ortholog detection methods encourages the evaluation of other alignment-free protein pair descriptors in future research.

FASMA: a service to format and analyze sequences in multiple alignments.

PubMed

Costantini, Susan; Colonna, Giovanni; Facchiano, Angelo M

2007-12-01

Multiple sequence alignments are successfully applied in many studies for under- standing the structural and functional relations among single nucleic acids and protein sequences as well as whole families. Because of the rapid growth of sequence databases, multiple sequence alignments can often be very large and difficult to visualize and analyze. We offer a new service aimed to visualize and analyze the multiple alignments obtained with different external algorithms, with new features useful for the comparison of the aligned sequences as well as for the creation of a final image of the alignment. The service is named FASMA and is available at http://bioinformatica.isa.cnr.it/FASMA/.

PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences.

PubMed

Mirarab, Siavash; Nguyen, Nam; Guo, Sheng; Wang, Li-San; Kim, Junhyong; Warnow, Tandy

2015-05-01

We introduce PASTA, a new multiple sequence alignment algorithm. PASTA uses a new technique to produce an alignment given a guide tree that enables it to be both highly scalable and very accurate. We present a study on biological and simulated data with up to 200,000 sequences, showing that PASTA produces highly accurate alignments, improving on the accuracy and scalability of the leading alignment methods (including SATé). We also show that trees estimated on PASTA alignments are highly accurate--slightly better than SATé trees, but with substantial improvements relative to other methods. Finally, PASTA is faster than SATé, highly parallelizable, and requires relatively little memory.

Alignment and focus of mirrored facets of a heliosat

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

Yellowhair, Julius E; Ho, Clifford Kuofei; Diver, Richard B

2013-11-12

Various technologies pertaining to aligning and focusing mirrored facets of a heliostat are described herein. Updating alignment and/or focus of mirrored facets is undertaken through generation of a theoretical image, wherein the theoretical image is indicative of a reflection of the target via the mirrored facets when the mirrored facets are properly aligned. This theoretical image includes reference points that are overlaid on an image of the target as reflected by the mirrored facets of the heliostat. A technician adjusts alignment/focus of a mirrored facet by causing reflected reference markings to become aligned with the reference points in the theoreticalmore » image.« less

Business-IT Alignment in Trade Facilitation: A Case Study

NASA Astrophysics Data System (ADS)

Adaba, Godfried; Rusu, Lazar; El-Mekawy, Mohamed

In the information age, no organization can thrive without harnessing the power of IT. The effective deployment of IT to achieve business goals and gain competitive advantage requires the alignment of business and IT strategies of organizations. Using the Strategic Alignment Maturity model, this paper evaluates strategic alignment maturity of Customs Excise Preventive service, a frontline public organization charged with trade facilitation in Ghana. Strategic alignment maturity is at level 3; which implies the existence of an established process to leverage IT for efficiency and effectiveness. Efforts are required to strengthen alignment and fully harness the potential of IT to facilitate trade in Ghana.

Initial Alignment for SINS Based on Pseudo-Earth Frame in Polar Regions.

PubMed

Gao, Yanbin; Liu, Meng; Li, Guangchun; Guang, Xingxing

2017-06-16

An accurate initial alignment must be required for inertial navigation system (INS). The performance of initial alignment directly affects the following navigation accuracy. However, the rapid convergence of meridians and the small horizontalcomponent of rotation of Earth make the traditional alignment methods ineffective in polar regions. In this paper, from the perspective of global inertial navigation, a novel alignment algorithm based on pseudo-Earth frame and backward process is proposed to implement the initial alignment in polar regions. Considering that an accurate coarse alignment of azimuth is difficult to obtain in polar regions, the dynamic error modeling with large azimuth misalignment angle is designed. At the end of alignment phase, the strapdown attitude matrix relative to local geographic frame is obtained without influence of position errors and cumbersome computation. As a result, it would be more convenient to access the following polar navigation system. Then, it is also expected to unify the polar alignment algorithm as much as possible, thereby further unifying the form of external reference information. Finally, semi-physical static simulation and in-motion tests with large azimuth misalignment angle assisted by unscented Kalman filter (UKF) validate the effectiveness of the proposed method.

A method of alignment masking for refining the phylogenetic signal of multiple sequence alignments.

PubMed

Rajan, Vaibhav

2013-03-01

Inaccurate inference of positional homologies in multiple sequence alignments and systematic errors introduced by alignment heuristics obfuscate phylogenetic inference. Alignment masking, the elimination of phylogenetically uninformative or misleading sites from an alignment before phylogenetic analysis, is a common practice in phylogenetic analysis. Although masking is often done manually, automated methods are necessary to handle the much larger data sets being prepared today. In this study, we introduce the concept of subsplits and demonstrate their use in extracting phylogenetic signal from alignments. We design a clustering approach for alignment masking where each cluster contains similar columns-similarity being defined on the basis of compatible subsplits; our approach then identifies noisy clusters and eliminates them. Trees inferred from the columns in the retained clusters are found to be topologically closer to the reference trees. We test our method on numerous standard benchmarks (both synthetic and biological data sets) and compare its performance with other methods of alignment masking. We find that our method can eliminate sites more accurately than other methods, particularly on divergent data, and can improve the topologies of the inferred trees in likelihood-based analyses. Software available upon request from the author.

YAHA: fast and flexible long-read alignment with optimal breakpoint detection.

PubMed

Faust, Gregory G; Hall, Ira M

2012-10-01

With improved short-read assembly algorithms and the recent development of long-read sequencers, split mapping will soon be the preferred method for structural variant (SV) detection. Yet, current alignment tools are not well suited for this. We present YAHA, a fast and flexible hash-based aligner. YAHA is as fast and accurate as BWA-SW at finding the single best alignment per query and is dramatically faster and more sensitive than both SSAHA2 and MegaBLAST at finding all possible alignments. Unlike other aligners that report all, or one, alignment per query, or that use simple heuristics to select alignments, YAHA uses a directed acyclic graph to find the optimal set of alignments that cover a query using a biologically relevant breakpoint penalty. YAHA can also report multiple mappings per defined segment of the query. We show that YAHA detects more breakpoints in less time than BWA-SW across all SV classes, and especially excels at complex SVs comprising multiple breakpoints. YAHA is currently supported on 64-bit Linux systems. Binaries and sample data are freely available for download from http://faculty.virginia.edu/irahall/YAHA. imh4y@virginia.edu.

STELLAR: fast and exact local alignments

PubMed Central

2011-01-01

Background Large-scale comparison of genomic sequences requires reliable tools for the search of local alignments. Practical local aligners are in general fast, but heuristic, and hence sometimes miss significant matches. Results We present here the local pairwise aligner STELLAR that has full sensitivity for ε-alignments, i.e. guarantees to report all local alignments of a given minimal length and maximal error rate. The aligner is composed of two steps, filtering and verification. We apply the SWIFT algorithm for lossless filtering, and have developed a new verification strategy that we prove to be exact. Our results on simulated and real genomic data confirm and quantify the conjecture that heuristic tools like BLAST or BLAT miss a large percentage of significant local alignments. Conclusions STELLAR is very practical and fast on very long sequences which makes it a suitable new tool for finding local alignments between genomic sequences under the edit distance model. Binaries are freely available for Linux, Windows, and Mac OS X at http://www.seqan.de/projects/stellar. The source code is freely distributed with the SeqAn C++ library version 1.3 and later at http://www.seqan.de. PMID:22151882

Vector correlation between the alignment of reactant N2 (A 3Σu+) and the alignment of product NO (A 2Σ+) rotation in the energy transfer reaction of aligned N2 (A 3Σu+) + NO (X 2Π) → NO (A 2Σ+) + N2 (X 1Σg+).

PubMed

Ohoyama, H

2013-12-21

The vector correlation between the alignment of reactant N2 (A (3)Σu(+)) and the alignment of product NO (A (2)Σ(+)) rotation has been studied in the energy transfer reaction of aligned N2 (A (3)Σu(+)) + NO (X (2)Π) → NO (A (2)Σ(+)) + N2 (X (1)Σg(+)) under the crossed beam condition at a collision energy of ~0.07 eV. NO (A (2)Σ(+)) emission in the two linear polarization directions (i.e., parallel and perpendicular with respect to the relative velocity vector v(R)) has been measured as a function of the alignment of N2 (A (3)Σu(+)) along its molecular axis in the collision frame. The degree of polarization of NO (A (2)Σ(+)) emission is found to depend on the alignment angle (θ(v(R))) of N2 (A (3)Σu(+)) in the collision frame. The shape of the steric opacity function at the two polarization conditions turns out to be extremely different from each other: The steric opacity function at the parallel polarization condition is more favorable for the oblique configuration of N2 (A (3)Σu(+)) at an alignment angle of θ(v(R)) ~ 45° as compared with that at the perpendicular polarization condition. The alignment of N2 (A (3)Σu(+)) is found to give a significant effect on the alignment of NO (A (2)Σ(+)) rotation in the collision frame: The N2 (A (3)Σu(+)) configuration at an oblique alignment angle θ(v(R)) ~ 45° leads to a parallel alignment of NO (A (2)Σ(+)) rotation (J-vector) with respect to v(R), while the axial and sideways configurations of N2 (A (3)Σu(+)) lead to a perpendicular alignment of NO (A (2)Σ(+)) rotation with respect to vR. These stereocorrelated alignments of the product rotation have a good correlation with the stereocorrelated reactivity observed in the multi-dimensional steric opacity function [H. Ohoyama and S. Maruyama, J. Chem. Phys. 137, 064311 (2012)].

Quantifying NMR relaxation correlation and exchange in articular cartilage with time domain analysis

NASA Astrophysics Data System (ADS)

Mailhiot, Sarah E.; Zong, Fangrong; Maneval, James E.; June, Ronald K.; Galvosas, Petrik; Seymour, Joseph D.

2018-02-01

Measured nuclear magnetic resonance (NMR) transverse relaxation data in articular cartilage has been shown to be multi-exponential and correlated to the health of the tissue. The observed relaxation rates are dependent on experimental parameters such as solvent, data acquisition methods, data analysis methods, and alignment to the magnetic field. In this study, we show that diffusive exchange occurs in porcine articular cartilage and impacts the observed relaxation rates in T1-T2 correlation experiments. By using time domain analysis of T2-T2 exchange spectroscopy, the diffusive exchange time can be quantified by measurements that use a single mixing time. Measured characteristic times for exchange are commensurate with T1 in this material and so impacts the observed T1 behavior. The approach used here allows for reliable quantification of NMR relaxation behavior in cartilage in the presence of diffusive fluid exchange between two environments.

Simulation of concomitant magnetic fields on fast switched gradient coils used in advanced application of MRI

NASA Astrophysics Data System (ADS)

Salinas-Muciño, G.; Torres-García, E.; Hidalgo-Tobon, S.

2012-10-01

The process to produce an MR image includes nuclear alignment, RF excitation, spatial encoding, and image formation. To form an image, it is necessary to perform spatial localization of the MR signals, which is achieved using gradient coils. MRI requires the use of gradient coils that generate magnetic fields, which vary linearly with position over the imaging volume. Safety issues have been a motivation to study deeply the relation between the interaction of gradient magnetic field and the peripheral nerve stimulation. In this work is presented a numerical modeling between the concomitant magnetic fields produced by the gradient coils and the electric field induced in a cube with σ conductivity by the gradient field switching in pulse sequences as Eco planar Imaging (EPI), due to this kind of sequence is the most used in advance applications of magnetic resonance imaging as functional MRI, cardiac imaging or diffusion.

Position indicator

DOEpatents

Tanner, David E.

1981-01-01

A nuclear reactor system is described in which a position indicator is provided for detecting and indicating the position of a movable element inside a pressure vessel. The movable element may be a valve element or similar device which moves about an axis. Light from a light source is transmitted from a source outside the pressure vessel to a first region inside the pressure vessel in alignment with the axis of the movable element. The light is redirected by a reflector prism to a second region displaced radially from the first region. The reflector prism moves in response to movement of the movable element about its axis such that the second region moves arcuately with respect to the first region. Sensors are arrayed in an arc corresponding to the arc of movement of the second region and signals are transmitted from the sensors to the exterior of the reactor vessel to provide indication of the position of the movable element.

ELECTRON MICROSCOPY OF MITOSIS IN AMEBAE

PubMed Central

Roth, L. E.

1967-01-01

The mitotic apparatus (MA) of the giant ameba, Chaos carolinensis, has characteristic sequences of microtubule arrays and deployment of nuclear envelope fragments. If mitotic organisms are subjected to 2°C for 5 min, the MA microtubules are completely degraded, and the envelope fragments are released from the chromosomes which remain condensed but lose their metaphase-plate orientation. On warming, microtubules reform but show partial loss of their parallel alignment; displacement of the envelope fragments persists or is increased by microtubule reformation. This study demonstrates that cooling causes destruction of microtubules and intermicrotubular cross-bonds and further shows that such controlled dissolution and reformation can provide an in vivo test sequence for studies on the effects of inhibitor-compounds on microtubule subunit aggregation. Urea, at the comparatively low concentration of 0.8 M, inhibited reformation following cooling and rewarming but was ineffective in altering microtubules that had formed before treatment. PMID:6040537

Use of a hard mask for formation of gate and dielectric via nanofilament field emission devices

DOEpatents

Morse, Jeffrey D.; Contolini, Robert J.

2001-01-01

A process for fabricating a nanofilament field emission device in which a via in a dielectric layer is self-aligned to gate metal via structure located on top of the dielectric layer. By the use of a hard mask layer located on top of the gate metal layer, inert to the etch chemistry for the gate metal layer, and in which a via is formed by the pattern from etched nuclear tracks in a trackable material, a via is formed by the hard mask will eliminate any erosion of the gate metal layer during the dielectric via etch. Also, the hard mask layer will protect the gate metal layer while the gate structure is etched back from the edge of the dielectric via, if such is desired. This method provides more tolerance for the electroplating of a nanofilament in the dielectric via and sharpening of the nanofilament.

15N Hyperpolarization of Imidazole-15N2 for Magnetic Resonance pH Sensing via SABRE-SHEATH

PubMed Central

2016-01-01

15N nuclear spins of imidazole-15N2 were hyperpolarized using NMR signal amplification by reversible exchange in shield enables alignment transfer to heteronuclei (SABRE-SHEATH). A 15N NMR signal enhancement of ∼2000-fold at 9.4 T is reported using parahydrogen gas (∼50% para-) and ∼0.1 M imidazole-15N2 in methanol:aqueous buffer (∼1:1). Proton binding to a 15N site of imidazole occurs at physiological pH (pKa ∼ 7.0), and the binding event changes the 15N isotropic chemical shift by ∼30 ppm. These properties are ideal for in vivo pH sensing. Additionally, imidazoles have low toxicity and are readily incorporated into a wide range of biomolecules. 15N-Imidazole SABRE-SHEATH hyperpolarization potentially enables pH sensing on scales ranging from peptide and protein molecules to living organisms. PMID:27379344

15N Hyperpolarization of Imidazole-15N2 for Magnetic Resonance pH Sensing via SABRE-SHEATH.

PubMed

Shchepin, Roman V; Barskiy, Danila A; Coffey, Aaron M; Theis, Thomas; Shi, Fan; Warren, Warren S; Goodson, Boyd M; Chekmenev, Eduard Y

2016-06-24

15 N nuclear spins of imidazole- 15 N 2 were hyperpolarized using NMR signal amplification by reversible exchange in shield enables alignment transfer to heteronuclei (SABRE-SHEATH). A 15 N NMR signal enhancement of ∼2000-fold at 9.4 T is reported using parahydrogen gas (∼50% para-) and ∼0.1 M imidazole- 15 N 2 in methanol:aqueous buffer (∼1:1). Proton binding to a 15 N site of imidazole occurs at physiological pH (p K a ∼ 7.0), and the binding event changes the 15 N isotropic chemical shift by ∼30 ppm. These properties are ideal for in vivo pH sensing. Additionally, imidazoles have low toxicity and are readily incorporated into a wide range of biomolecules. 15 N-Imidazole SABRE-SHEATH hyperpolarization potentially enables pH sensing on scales ranging from peptide and protein molecules to living organisms.

Identical superdeformed bands in yrast 152Dy: a systematic description

NASA Astrophysics Data System (ADS)

Dadwal, Anshul; Mittal, H. M.

2018-06-01

The nuclear softness (NS) formula, semiclassical particle rotor model (PRM) and modified exponential model with pairing attenuation are used for the systematic study of the identical superdeformed bands in the A ∼ 150 mass region. These formulae/models are employed to study the identical superdeformed bands relative to the yrast SD band 152Dy(1), {152Dy(1), 151Tb(2)}, {152Dy(1), 151Dy(4)} (midpoint), {152Dy(1), 153Dy(2)} (quarter point), {152Dy(1), 153Dy(3)} (three-quarter point). The parameters, baseline moment of inertia ({{I}}0), alignment (i) and effective pairing parameter (Δ0) are calculated using the least-squares fitting of the γ-ray transitions energies in the NS formula, semiclassical-PRM and modified exponential model with pairing attenuation, respectively. The calculated parameters are found to depend sensitively on the proposed baseline spin (I 0).

Some Alignment Considerations for the Next Linear Collider

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

Ruland, R

Next Linear Collider type accelerators require a new level of alignment quality. The relative alignment of these machines is to be maintained in an error envelope dimensioned in micrometers and for certain parts in nanometers. In the nanometer domain our terra firma cannot be considered monolithic but compares closer to jelly. Since conventional optical alignment methods cannot deal with the dynamics and cannot approach the level of accuracy, special alignment and monitoring techniques must be pursued.

Aligning Plasma-Arc Welding Oscillations

NASA Technical Reports Server (NTRS)

Norris, Jeff; Fairley, Mike

1989-01-01

Tool aids in alignment of oscillator probe on variable-polarity plasma-arc welding torch. Probe magnetically pulls arc from side to side as it moves along joint. Tensile strength of joint depends on alignment of weld bead and on alignment of probe. Operator installs new tool on front of torch body, levels it with built-in bubble glass, inserts probe in slot on tool, and locks probe in place. Procedure faster and easier and resulting alignment more accurate and repeatable.

Optimal network alignment with graphlet degree vectors.

PubMed

Milenković, Tijana; Ng, Weng Leong; Hayes, Wayne; Przulj, Natasa

2010-06-30

Important biological information is encoded in the topology of biological networks. Comparative analyses of biological networks are proving to be valuable, as they can lead to transfer of knowledge between species and give deeper insights into biological function, disease, and evolution. We introduce a new method that uses the Hungarian algorithm to produce optimal global alignment between two networks using any cost function. We design a cost function based solely on network topology and use it in our network alignment. Our method can be applied to any two networks, not just biological ones, since it is based only on network topology. We use our new method to align protein-protein interaction networks of two eukaryotic species and demonstrate that our alignment exposes large and topologically complex regions of network similarity. At the same time, our alignment is biologically valid, since many of the aligned protein pairs perform the same biological function. From the alignment, we predict function of yet unannotated proteins, many of which we validate in the literature. Also, we apply our method to find topological similarities between metabolic networks of different species and build phylogenetic trees based on our network alignment score. The phylogenetic trees obtained in this way bear a striking resemblance to the ones obtained by sequence alignments. Our method detects topologically similar regions in large networks that are statistically significant. It does this independent of protein sequence or any other information external to network topology.

Retention time alignment of LC/MS data by a divide-and-conquer algorithm.

PubMed

Zhang, Zhongqi

2012-04-01

Liquid chromatography-mass spectrometry (LC/MS) has become the method of choice for characterizing complex mixtures. These analyses often involve quantitative comparison of components in multiple samples. To achieve automated sample comparison, the components of interest must be detected and identified, and their retention times aligned and peak areas calculated. This article describes a simple pairwise iterative retention time alignment algorithm, based on the divide-and-conquer approach, for alignment of ion features detected in LC/MS experiments. In this iterative algorithm, ion features in the sample run are first aligned with features in the reference run by applying a single constant shift of retention time. The sample chromatogram is then divided into two shorter chromatograms, which are aligned to the reference chromatogram the same way. Each shorter chromatogram is further divided into even shorter chromatograms. This process continues until each chromatogram is sufficiently narrow so that ion features within it have a similar retention time shift. In six pairwise LC/MS alignment examples containing a total of 6507 confirmed true corresponding feature pairs with retention time shifts up to five peak widths, the algorithm successfully aligned these features with an error rate of 0.2%. The alignment algorithm is demonstrated to be fast, robust, fully automatic, and superior to other algorithms. After alignment and gap-filling of detected ion features, their abundances can be tabulated for direct comparison between samples.

B-MIC: An Ultrafast Three-Level Parallel Sequence Aligner Using MIC.

PubMed

Cui, Yingbo; Liao, Xiangke; Zhu, Xiaoqian; Wang, Bingqiang; Peng, Shaoliang

2016-03-01

Sequence alignment is the central process for sequence analysis, where mapping raw sequencing data to reference genome. The large amount of data generated by NGS is far beyond the process capabilities of existing alignment tools. Consequently, sequence alignment becomes the bottleneck of sequence analysis. Intensive computing power is required to address this challenge. Intel recently announced the MIC coprocessor, which can provide massive computing power. The Tianhe-2 is the world's fastest supercomputer now equipped with three MIC coprocessors each compute node. A key feature of sequence alignment is that different reads are independent. Considering this property, we proposed a MIC-oriented three-level parallelization strategy to speed up BWA, a widely used sequence alignment tool, and developed our ultrafast parallel sequence aligner: B-MIC. B-MIC contains three levels of parallelization: firstly, parallelization of data IO and reads alignment by a three-stage parallel pipeline; secondly, parallelization enabled by MIC coprocessor technology; thirdly, inter-node parallelization implemented by MPI. In this paper, we demonstrate that B-MIC outperforms BWA by a combination of those techniques using Inspur NF5280M server and the Tianhe-2 supercomputer. To the best of our knowledge, B-MIC is the first sequence alignment tool to run on Intel MIC and it can achieve more than fivefold speedup over the original BWA while maintaining the alignment precision.

Galaxy-halo alignments in the Horizon-AGN cosmological hydrodynamical simulation

NASA Astrophysics Data System (ADS)

Chisari, N. E.; Koukoufilippas, N.; Jindal, A.; Peirani, S.; Beckmann, R. S.; Codis, S.; Devriendt, J.; Miller, L.; Dubois, Y.; Laigle, C.; Slyz, A.; Pichon, C.

2017-11-01

Intrinsic alignments of galaxies are a significant astrophysical systematic affecting cosmological constraints from weak gravitational lensing. Obtaining numerical predictions from hydrodynamical simulations of expected survey volumes is expensive, and a cheaper alternative relies on populating large dark matter-only simulations with accurate models of alignments calibrated on smaller hydrodynamical runs. This requires connecting the shapes and orientations of galaxies to those of dark matter haloes and to the large-scale structure. In this paper, we characterize galaxy-halo alignments in the Horizon-AGN cosmological hydrodynamical simulation. We compare the shapes and orientations of galaxies in the redshift range of 0 < z < 3 to those of their embedding dark matter haloes, and to the matching haloes of a twin dark-matter only run with identical initial conditions. We find that galaxy ellipticities, in general, cannot be predicted directly from halo ellipticities. The mean misalignment angle between the minor axis of a galaxy and its embedding halo is a function of halo mass, with residuals arising from the dependence of alignment on galaxy type, but not on environment. Haloes are much more strongly aligned among themselves than galaxies, and they decrease their alignment towards low redshift. Galaxy alignments compete with this effect, as galaxies tend to increase their alignment with haloes towards low redshift. We discuss the implications of these results for current halo models of intrinsic alignments and suggest several avenues for improvement.

Alignment of Irregular Grains by Mechanical Torques

NASA Astrophysics Data System (ADS)

Hoang, Thiem; Cho, Jungyeon; Lazarian, A.

2018-01-01

We study the alignment of irregular dust grains by mechanical torques due to the drift of grains through the ambient gas. We first calculate mechanical alignment torques (MATs) resulting from specular reflection of gas atoms for seven irregular shapes: one shape of mirror symmetry, three highly irregular shapes (HIS), and three weakly irregular shapes (WIS). We find that the grain with mirror symmetry experiences negligible MATs due to its mirror-symmetry geometry. Three HIS can produce strong MATs, which exhibit some generic properties as radiative torques (RATs), while three WIS produce less efficient MATs. We then study grain alignment by MATs for the different angles between the drift velocity and the ambient magnetic field, for paramagnetic and superparamagnetic grains assuming efficient internal relaxation. We find that for HIS grains, MATs can align subsonically drifting grains in the same way as RATs, with low-J and high-J attractors. For supersonic drift, MATs can align grains with low-J and high-J attractors, analogous to RAT alignment by anisotropic radiation. We also show that the joint action of MATs and magnetic torques in grains with iron inclusions can lead to perfect MAT alignment. Our results point out the potential importance of MAT alignment for HIS grains predicted by the analytical model of Lazarian & Hoang, although more theoretical and observational studies are required due to uncertainty in the shape of interstellar grains. We outline astrophysical environments where MAT alignment is potentially important.

Phylo-mLogo: an interactive and hierarchical multiple-logo visualization tool for alignment of many sequences

PubMed Central

Shih, Arthur Chun-Chieh; Lee, DT; Peng, Chin-Lin; Wu, Yu-Wei

2007-01-01

Background When aligning several hundreds or thousands of sequences, such as epidemic virus sequences or homologous/orthologous sequences of some big gene families, to reconstruct the epidemiological history or their phylogenies, how to analyze and visualize the alignment results of many sequences has become a new challenge for computational biologists. Although there are several tools available for visualization of very long sequence alignments, few of them are applicable to the alignments of many sequences. Results A multiple-logo alignment visualization tool, called Phylo-mLogo, is presented in this paper. Phylo-mLogo calculates the variabilities and homogeneities of alignment sequences by base frequencies or entropies. Different from the traditional representations of sequence logos, Phylo-mLogo not only displays the global logo patterns of the whole alignment of multiple sequences, but also demonstrates their local homologous logos for each clade hierarchically. In addition, Phylo-mLogo also allows the user to focus only on the analysis of some important, structurally or functionally constrained sites in the alignment selected by the user or by built-in automatic calculation. Conclusion With Phylo-mLogo, the user can symbolically and hierarchically visualize hundreds of aligned sequences simultaneously and easily check the changes of their amino acid sites when analyzing many homologous/orthologous or influenza virus sequences. More information of Phylo-mLogo can be found at URL . PMID:17319966

Optical Alignment of the JWST ISIM to the OTE Simulator (OSIM): Current Concept and Design Studies

NASA Technical Reports Server (NTRS)

Frey, Bradley J.; Davila, Pamela S.; Marsh, James M.; Ohl, Raymond G.; Sullivan, Joseph

2007-01-01

The James Webb Space Telescope's (JWST) Integrated Science Instrument Module (ISIM) is the scientific payload of the observatory and contai ns four science instruments. During alignment and test of the integrated ISIM (i.e. ISIM + science instruments) at NASA's Goddard Space Fli ght Center (GSFC), the Optical telescope element SIMulator (OSIM) wil l be used to optically stimulate the science instruments to verify their operation and performance. In this paper we present the design of two cryogenic alignment fixtures that will be used to determine and verify the proper alignment of OSIM to ISIM during testing at GSFC. The se fixtures, the Master Alignment Target Fixture (MATF) and the ISIM Alignment Target Fixture (IATF), will provide continuous, 6 degree of freedom feedback to OSIM during initial ambient alignment as well as during cryogenic vacuum testing.

Image Alignment for Multiple Camera High Dynamic Range Microscopy.

PubMed

Eastwood, Brian S; Childs, Elisabeth C

2012-01-09

This paper investigates the problem of image alignment for multiple camera high dynamic range (HDR) imaging. HDR imaging combines information from images taken with different exposure settings. Combining information from multiple cameras requires an alignment process that is robust to the intensity differences in the images. HDR applications that use a limited number of component images require an alignment technique that is robust to large exposure differences. We evaluate the suitability for HDR alignment of three exposure-robust techniques. We conclude that image alignment based on matching feature descriptors extracted from radiant power images from calibrated cameras yields the most accurate and robust solution. We demonstrate the use of this alignment technique in a high dynamic range video microscope that enables live specimen imaging with a greater level of detail than can be captured with a single camera.

Image Alignment for Multiple Camera High Dynamic Range Microscopy

PubMed Central

Eastwood, Brian S.; Childs, Elisabeth C.

2012-01-01

This paper investigates the problem of image alignment for multiple camera high dynamic range (HDR) imaging. HDR imaging combines information from images taken with different exposure settings. Combining information from multiple cameras requires an alignment process that is robust to the intensity differences in the images. HDR applications that use a limited number of component images require an alignment technique that is robust to large exposure differences. We evaluate the suitability for HDR alignment of three exposure-robust techniques. We conclude that image alignment based on matching feature descriptors extracted from radiant power images from calibrated cameras yields the most accurate and robust solution. We demonstrate the use of this alignment technique in a high dynamic range video microscope that enables live specimen imaging with a greater level of detail than can be captured with a single camera. PMID:22545028

Effect of alignment changes on socket reaction moments while walking in transtibial prostheses with energy storage and return feet

PubMed Central

Kobayashi, Toshiki; Arabian, Adam K.; Orendurff, Michael S.; Rosenbaum-Chou, Teri G.; Boone, David A.

2014-01-01

Background Energy storage and return feet are designed for active amputees. However, little is known about the socket reaction moments in transtibial prostheses with energy storage and return feet. The aim of this study was to investigate the effect of alignment changes on the socket reaction moments during gait while using the energy storage and return feet. Methods A Smart Pyramid™ was used to measure the socket reaction moments in 10 subjects with transtibial prostheses while walking under 25 alignment conditions, including a nominal alignment (as defined by conventional clinical methods), as well as angle malalignments of 2°, 4° and 6° (flexion, extension, abduction, and adduction) and translation malalignments of 5mm, 10mm and 15mm (anterior, posterior, lateral, and medial) referenced from the nominal alignment. The socket reaction moments of the nominal alignment were compared with each malalignment. Findings Both coronal and sagittal alignment changes demonstrated systematic effects on the socket reaction moments. In the sagittal plane, angle and translation alignment changes demonstrated significant differences (P<0.05) in the minimum moment, the moment at 45% of stance and the maximum moment for some comparisons. In the coronal plane, angle and translation alignment changes demonstrated significant differences (P<0.05) in the moment at 30% and 75% of stance for all comparisons. Interpretation The alignment may have systematic effects on the socket reaction moments in transtibial prostheses with energy storage and return feet. The socket reaction moments could potentially be a useful biomechanical parameter to evaluate the alignment of the transtibial prostheses. PMID:24315709

Effect of prosthetic alignment changes on socket reaction moment impulse during walking in transtibial amputees

PubMed Central

Kobayashi, Toshiki; Orendurff, Michael S.; Arabian, Adam K.; Rosenbaum-Chou, Teri G.; Boone, David A.

2014-01-01

The alignment of a lower limb prosthesis affects the way load is transferred to the residual limb through the socket, and this load is critically important for the comfort and function of the prosthesis. Both magnitude and duration of the moment are important factors that may affect the residual limb health. Moment impulse is a well-accepted measurement that incorporates both factors via moment–time integrals. The aim of this study was to investigate the effect of alignment changes on the socket reaction moment impulse in transtibial prostheses. Ten amputees with transtibial prostheses participated in this study. The socket reaction moment impulse was measured at a self-selected walking speed using a Smart Pyramid™ in 25 alignment conditions, including a nominal alignment (clinically aligned by a prosthetist), as well as angle malalignments of 2°, 4° and 6° (abduction, adduction, extension and flexion) and translation malalignments of 5 mm, 10 mm and 15 mm (lateral, medial, anterior and posterior). The socket reaction moment impulse of the nominal alignment was compared for each condition. The relationship between the alignment and the socket reaction moment impulse was clearly observed in the coronal angle, coronal translation and sagittal translation alignment changes. However, this relationship was not evident in the sagittal angle alignment changes. The results of this study suggested that the socket reaction moment impulse could potentially serve as a valuable parameter to assist the alignment tuning process for transtibial prostheses. Further study is needed to investigate the influence of the socket reaction moment impulse on the residual limb health. PMID:24612718

The Impact of Imaging Modality on the Measurement of Coronal Plane Alignment After Total Knee Arthroplasty.

PubMed

Nam, Denis; Vajapey, Sravya; Nunley, Ryan M; Barrack, Robert L

2016-10-01

The optimal coronal alignment after total knee arthroplasty (TKA) has become an area of increased debate. Sources of variability among investigations include the radiographic technique used for both preoperative surgical planning and postoperative alignment assessments. This study's purpose was to assess the impact of the imaging modality used on the measurement of coronal plane alignment after TKA. A consecutive series of patients undergoing TKA using the same cruciate-retaining prosthesis were included for analysis. Postoperatively, all patients received both a rotationally controlled, scout computed tomography scan and a hip-knee-ankle (HKA) image using the EOS Imaging system (EOS Inc., Paris, France). Two, independent observers measured the HKA angle, and femoral and tibial component alignment from each image. After classifying overall and component alignment as neutral, varus, or valgus, 40.6% (65 of 160) of knees had a discordant alignment classification for HKA, 28.1% (45 of 160) for femoral component alignment, and 26.9% (43 of 160) for tibial component alignment between their computed tomography and EOS images. Overall, 24.4% (39 of 160) of patients had a HKA difference of ≥3° between the 2 images, whereas 18.8% (30 of 160) and 20.0% (32 of 160) of patients had a femoral and tibial component alignment difference of ≥2°, respectively. Significant differences are present when comparing 2 measurement techniques of mechanical alignment after TKA. The impact of imaging modality on postoperative assessments must be accounted for and be consistent when comparing the results of different investigations. Copyright © 2016 Elsevier Inc. All rights reserved.

Algorithms for Automatic Alignment of Arrays

NASA Technical Reports Server (NTRS)

Chatterjee, Siddhartha; Gilbert, John R.; Oliker, Leonid; Schreiber, Robert; Sheffler, Thomas J.

1996-01-01

Aggregate data objects (such as arrays) are distributed across the processor memories when compiling a data-parallel language for a distributed-memory machine. The mapping determines the amount of communication needed to bring operands of parallel operations into alignment with each other. A common approach is to break the mapping into two stages: an alignment that maps all the objects to an abstract template, followed by a distribution that maps the template to the processors. This paper describes algorithms for solving the various facets of the alignment problem: axis and stride alignment, static and mobile offset alignment, and replication labeling. We show that optimal axis and stride alignment is NP-complete for general program graphs, and give a heuristic method that can explore the space of possible solutions in a number of ways. We show that some of these strategies can give better solutions than a simple greedy approach proposed earlier. We also show how local graph contractions can reduce the size of the problem significantly without changing the best solution. This allows more complex and effective heuristics to be used. We show how to model the static offset alignment problem using linear programming, and we show that loop-dependent mobile offset alignment is sometimes necessary for optimum performance. We describe an algorithm with for determining mobile alignments for objects within do loops. We also identify situations in which replicated alignment is either required by the program itself or can be used to improve performance. We describe an algorithm based on network flow that replicates objects so as to minimize the total amount of broadcast communication in replication.

Transition of vertically aligned liquid crystal driven by fan-shaped electric field

NASA Astrophysics Data System (ADS)

Tsung, J. W.; Ting, T. L.; Chen, C. Y.; Liang, W. L.; Lai, C. W.; Lin, T. H.; Hsu, W. H.

2017-09-01

Interdigital electrodes are implemented in many commercial and novel liquid crystal devices to align molecules. Although many empirical principles and patents apply to electrode design, only a few numerical simulations of alignment have been conducted. Why and how the molecules align in an ordered manner has never been adequately explained. Hence, this investigation addresses the Fréedericksz transition of vertically aligned liquid crystal that is driven by fishbone electrodes, and thereafter identifies the mechanism of liquid crystal alignment. Theoretical calculations suggest that the periodic deformation that is caused by the fan-shaped fringe field minimizes the free energy in the liquid crystal cell, and the optimal alignment can be obtained when the cell parameters satisfy the relation p /2 d =√{k11/k33 } , where p is the spatial period of the strips of the electrode; d denotes the cell gap; and k11 and k33 are the splay and bend elastic constants of the liquid crystal, respectively. Polymer-stabilized vertical alignment test cells with various p values and spacings between the electrodes were fabricated, and the process of liquid crystal alignment was observed under an optical microscope. The degree of alignment was evaluated by measuring the transmittance of the test cell. The experimental results were consistent with the theoretical predictions. The principle of design, p /2 d =√{k11/k33 } , greatly improves the uniformity and stability of the aligned liquid crystal. The methods that are presented here can be further applied to cholesteric liquid crystal and other self-assembled soft materials.

An Alignment/Transfer Experiment with Low Socioeconomic Level Students.

ERIC Educational Resources Information Center

Elia, June Isaacs

1994-01-01

This study examined the amount of variance explained by alignment of testing to instruction among low socioeconomic level fourth graders, proposing two instructional alignment hypotheses. Results indicated that alignment had an unusually high effect. Low performing low socioeconomic level students achieved high success levels when conditions of…

Vertically aligned nanostructure scanning probe microscope tips

DOEpatents

Guillorn, Michael A.; Ilic, Bojan; Melechko, Anatoli V.; Merkulov, Vladimir I.; Lowndes, Douglas H.; Simpson, Michael L.

2006-12-19

Methods and apparatus are described for cantilever structures that include a vertically aligned nanostructure, especially vertically aligned carbon nanofiber scanning probe microscope tips. An apparatus includes a cantilever structure including a substrate including a cantilever body, that optionally includes a doped layer, and a vertically aligned nanostructure coupled to the cantilever body.

Temporal Effects of Alignment in Text-Based, Task-Oriented Discourse

ERIC Educational Resources Information Center

Foltz, Anouschka; Gaspers, Judith; Meyer, Carolin; Thiele, Kristina; Cimiano, Philipp; Stenneken, Prisca

2015-01-01

Communicative alignment refers to adaptation to one's communication partner. Temporal aspects of such alignment have been little explored. This article examines temporal aspects of lexical and syntactic alignment (i.e., tendencies to use the interlocutor's lexical items and syntactic structures) in task-oriented discourse. In particular, we…

Opportunities to Align California's PreK-3 Education System

ERIC Educational Resources Information Center

Policy Analysis for California Education, PACE, 2016

2016-01-01

"PreK-3 Alignment in California's Education System: Obstacles and Opportunities" by Rachel Valentino and Deborah J. Stipek reviews the opportunities and challenges that must be addressed to better align PreK-3 education in California. The report describes policies and practices that districts have implemented to strengthen alignment, and…

Alignment of Iron Nanoparticles in a Magnetic Field Due to Shape Anisotropy

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

Radhakrishnan, Balasubramaniam; Nicholson, Don M; Eisenbach, Markus

2015-07-09

During high magnetic field processing there is evidence for alignment of non-spherical metallic particles above the Curie temperature in alloys with negligible magneto-crystalline anisotropy. The main driving force for alignment is the magnetic shape anisotropy. Current understanding of the phenomenon is not adequate to quantify the effect of particle size, aspect ratio, temperature and the magnetic field on particle alignment. We demonstrate a Monte Carlo approach coupled with size scaling to show the conditions under which alignment is possible.

Permanent bending and alignment of ZnO nanowires.

PubMed

Borschel, Christian; Spindler, Susann; Lerose, Damiana; Bochmann, Arne; Christiansen, Silke H; Nietzsche, Sandor; Oertel, Michael; Ronning, Carsten

2011-05-06

Ion beams can be used to permanently bend and re-align nanowires after growth. We have irradiated ZnO nanowires with energetic ions, achieving bending and alignment in different directions. Not only the bending of single nanowires is studied in detail, but also the simultaneous alignment of large ensembles of ZnO nanowires. Computer simulations reveal how the bending is initiated by ion beam induced damage. Detailed structural characterization identifies dislocations to relax stresses and make the bending and alignment permanent, even surviving annealing procedures.

Earle K. Plyler Prize Lecture: The Three Pillars of Ultrafast Molecular Science - Time, Phase, Intensity

NASA Astrophysics Data System (ADS)

Stolow, Albert

We discuss the probing and control of molecular wavepacket dynamics in the context of three main `pillars' of light-matter interaction: time, phase, intensity. Time: Using short, coherent laser pulses and perturbative matter-field interactions, we study molecular wavepackets with a focus on the ultrafast non-Born-Oppenheimer dynamics, that is, the coupling of electronic and nuclear motions. Time-Resolved Photoelectron Spectroscopy (TRPES) is a powerful ultrafast probe of these processes in polyatomic molecules because it is sensitive both electronic and vibrational dynamics. Ideally, one would like to observe these ultrafast processes from the molecule's point of view - the Molecular Frame - thereby avoiding loss of information due to orientational averaging. This can be achieved by Time-Resolved Coincidence Imaging Spectroscopy (TRCIS) which images 3D recoil vectors of both photofragments and photoelectrons, in coincidence and as a function of time, permitting direct Molecular Frame imaging of valence electronic dynamics during a molecular dynamics. Phase: Using intermediate strength non-perturbative interactions, we apply the second order (polarizability) Non-Resonant Dynamic Stark Effect (NRDSE) to control molecular dynamics without any net absorption of light. NRDSE is also the interaction underlying molecular alignment and applies to field-free 1D of linear molecules and field-free 3D alignment of general (asymmetric) molecules. Using laser alignment, we can transiently fix a molecule in space, yielding a more general approach to direct Molecular Frame imaging of valence electronic dynamics during a chemical reaction. Intensity: In strong (ionizing) laser fields, a new laser-matter physics emerges for polyatomic systems wherein both the single active electron picture and the adiabatic electron response, both implicit in the standard 3-step models, can fail dramatically. This has important consequences for all attosecond strong field spectroscopies of polyatomic molecules, including high harmonic generation (HHG). We discuss an experimental method, Channel-Resolved Above Threshold Ionization (CRATI), which directly unveils the electronic channels participating in the attosecond molecular strong field ionization response [10]. This work was supported by the National Research Council of Canada and the Natural Sciences & Engineering Research Council.

Epidemiological survey of idiopathic scoliosis and sequence alignment analysis of multiple candidate genes.

PubMed

Yang, Tao; Jia, Quanzhang; Guo, Hong; Xu, Jianzhong; Bai, Yun; Yang, Kai; Luo, Fei; Zhang, Zehua; Hou, Tianyong

2012-06-01

To investigate the effects of genetic factors on idiopathic scoliosis (IS) and genetic modes through genetic epidemiological survey on IS in Chongqing City, China, and to determine whether SH3GL1, GADD45B, and FGF22 in the chromosome 19p13.3 are the pathogenic genes of IS through genetic sequence analysis. 214 nuclear families were investigated to analyse the age incidence, familial aggregation, and heritability. SH3GL1, GADD45B, and FGF22 were chosen as candidate genes for mutation screening in 56 IS patients of 214 families. The sequence alignment analysis was performed to determine mutations and predict the protein structure. The average age of onset of 10.8 years suggests that IS is a early onset disease. Incidences of IS in first-, second-, third-degree relatives and the overall incidence in families (5.68%) were also significantly higher than that of the general population (1.04%). The U test indicated a significant difference, suggesting that IS has a familial aggregation. The heritability of first-degree relatives (77.68 ±10.39%), second-degree relatives (69.89 ±3.14%), and third-degree relatives (62.14 ±11.92%) illustrated that genetic factors play an important role in IS pathogenesis. The incidence of first-degree relatives (10.01%), second-degree relatives (2.55%) and third-degree relatives (1.76%) illustrated that IS is not in simple accord with monogenic Mendel's law but manifests as traits of multifactorial hereditary diseases. Sequence alignment of exons of SH3GL1, GADD45B, and FGF22 showed 17 base mutations, of which 16 mutations do not induce open reading frame (ORF) shift or amino acid changes whereas one mutation (C→T)occurred in SH3GL1 results in formation of the termination codon, which induces variation of protein reading frame. Prediction analysis of protein sequence showed that the SH3GL1 mutant encoded a truncated protein, thus affecting the protein structure. IS is a multifactorial genetic disease and SH3GL1 may be one of the pathogenic genes for IS.

A facile method to align carbon nanotubes on polymeric membrane substrate

PubMed Central

Zhao, Haiyang; Zhou, Zhijun; Dong, Hang; Zhang, Lin; Chen, Huanlin; Hou, Lian

2013-01-01

The alignment of carbon nanotubes (CNT) is the fundamental requirement to ensure their excellent functions but seems to be desolated in recent years. A facile method, hot-press combined with peel-off (HPPO), is introduced here, through which CNT can be successfully vertically aligned on the polymeric membrane substrate. Shear force and mechanical stretch are proposed to be the main forces to align the tubes perpendicular to the substrate surface during the peel-off process. The alignment of CNT keeps its orientation in a thin hybrid membrane by dip-coating cellulose acetate dope solution. It is expected that the stable alignment of CNT by HPPO would contribute to the realization of its potential applications. PMID:24326297

Chromaligner: a web server for chromatogram alignment.

PubMed

Wang, San-Yuan; Ho, Tsung-Jung; Kuo, Ching-Hua; Tseng, Yufeng J

2010-09-15

Chromaligner is a tool for chromatogram alignment to align retention time for chromatographic methods coupled to spectrophotometers such as high performance liquid chromatography and capillary electrophoresis for metabolomics works. Chromaligner resolves peak shifts by a constrained chromatogram alignment. For a collection of chromatograms and a set of defined peaks, Chromaligner aligns the chromatograms on defined peaks using correlation warping (COW). Chromaligner is faster than the original COW algorithm by k(2) times, where k is the number of defined peaks in a chromatogram. It also provides alignments based on known component peaks to reach the best results for further chemometric analysis. Chromaligner is freely accessible at http://cmdd.csie.ntu.edu.tw/~chromaligner.

PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences

PubMed Central

Mirarab, Siavash; Nguyen, Nam; Guo, Sheng; Wang, Li-San; Kim, Junhyong

2015-01-01

Abstract We introduce PASTA, a new multiple sequence alignment algorithm. PASTA uses a new technique to produce an alignment given a guide tree that enables it to be both highly scalable and very accurate. We present a study on biological and simulated data with up to 200,000 sequences, showing that PASTA produces highly accurate alignments, improving on the accuracy and scalability of the leading alignment methods (including SATé). We also show that trees estimated on PASTA alignments are highly accurate—slightly better than SATé trees, but with substantial improvements relative to other methods. Finally, PASTA is faster than SATé, highly parallelizable, and requires relatively little memory. PMID:25549288

In-flight alignment using H ∞ filter for strapdown INS on aircraft.

PubMed

Pei, Fu-Jun; Liu, Xuan; Zhu, Li

2014-01-01

In-flight alignment is an effective way to improve the accuracy and speed of initial alignment for strapdown inertial navigation system (INS). During the aircraft flight, strapdown INS alignment was disturbed by lineal and angular movements of the aircraft. To deal with the disturbances in dynamic initial alignment, a novel alignment method for SINS is investigated in this paper. In this method, an initial alignment error model of SINS in the inertial frame is established. The observability of the system is discussed by piece-wise constant system (PWCS) theory and observable degree is computed by the singular value decomposition (SVD) theory. It is demonstrated that the system is completely observable, and all the system state parameters can be estimated by optimal filter. Then a H ∞ filter was designed to resolve the uncertainty of measurement noise. The simulation results demonstrate that the proposed algorithm can reach a better accuracy under the dynamic disturbance condition.

A Method for the Alignment of Heterogeneous Macromolecules from Electron Microscopy

PubMed Central

Shatsky, Maxim; Hall, Richard J.; Brenner, Steven E.; Glaeser, Robert M.

2009-01-01

We propose a feature-based image alignment method for single-particle electron microscopy that is able to accommodate various similarity scoring functions while efficiently sampling the two-dimensional transformational space. We use this image alignment method to evaluate the performance of a scoring function that is based on the Mutual Information (MI) of two images rather than one that is based on the cross-correlation function. We show that alignment using MI for the scoring function has far less model-dependent bias than is found with cross-correlation based alignment. We also demonstrate that MI improves the alignment of some types of heterogeneous data, provided that the signal to noise ratio is relatively high. These results indicate, therefore, that use of MI as the scoring function is well suited for the alignment of class-averages computed from single particle images. Our method is tested on data from three model structures and one real dataset. PMID:19166941