Bovine binder-of-sperm protein BSP1 promotes protrusion and nanotube formation from liposomes

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

Lafleur, Michel, E-mail: michel.lafleur@umontreal.ca; Courtemanche, Lesley; Karlsson, Goeran

Research highlights: {yields} Binder-of-sperm protein 1 (BSP1) modifies the morphology of lipidic vesicles inducing bead necklace-like and thread-like structures. {yields} In the presence of multilamellar liposomes, BSP1 leads to the formation of long nanotubes. {yields} The insertion of BSP1 in the external lipid leaflet of membranes induces local changes in bilayer curvature. -- Abstract: Binder-of-sperm (BSP) proteins interact with sperm membranes and are proposed to extract selectively phosphatidylcholine and cholesterol from these. This change in lipid composition is a key step in sperm capacitation. The present work demonstrates that the interactions between the protein BSP1 and model membranes composed withmore » phosphatidylcholine lead to drastic changes in the morphology of the lipidic self-assemblies. Using cryo-electron microscopy and fluorescence microscopy, we show that, in the presence of the protein, the lipid vesicles elongate, and form bead necklace-like structures that evolve toward small vesicles or thread-like structures. In the presence of multilamellar vesicles, where a large reservoir of lipid is available, the presence of BSP proteins lead to the formation of long nanotubes. Long spiral-like threads, associated with lipid/protein complexes, are also observed. The local curvature of lipid membranes induced by the BSP proteins may be involved in lipid domain formation and the extraction of some lipids during the sperm maturation process.« less

Thread-Like CMOS Logic Circuits Enabled by Reel-Processed Single-Walled Carbon Nanotube Transistors via Selective Doping.

PubMed

Heo, Jae Sang; Kim, Taehoon; Ban, Seok-Gyu; Kim, Daesik; Lee, Jun Ho; Jur, Jesse S; Kim, Myung-Gil; Kim, Yong-Hoon; Hong, Yongtaek; Park, Sung Kyu

2017-08-01

The realization of large-area electronics with full integration of 1D thread-like devices may open up a new era for ultraflexible and human adaptable electronic systems because of their potential advantages in demonstrating scalable complex circuitry by a simply integrated weaving technology. More importantly, the thread-like fiber electronic devices can be achieved using a simple reel-to-reel process, which is strongly required for low-cost and scalable manufacturing technology. Here, high-performance reel-processed complementary metal-oxide-semiconductor (CMOS) integrated circuits are reported on 1D fiber substrates by using selectively chemical-doped single-walled carbon nanotube (SWCNT) transistors. With the introduction of selective n-type doping and a nonrelief photochemical patterning process, p- and n-type SWCNT transistors are successfully implemented on cylindrical fiber substrates under air ambient, enabling high-performance and reliable thread-like CMOS inverter circuits. In addition, it is noteworthy that the optimized reel-coating process can facilitate improvement in the arrangement of SWCNTs, building uniformly well-aligned SWCNT channels, and enhancement of the electrical performance of the devices. The p- and n-type SWCNT transistors exhibit field-effect mobility of 4.03 and 2.15 cm 2 V -1 s -1 , respectively, with relatively narrow distribution. Moreover, the SWCNT CMOS inverter circuits demonstrate a gain of 6.76 and relatively good dynamic operation at a supply voltage of 5.0 V. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electrical potentials between stent-grafts made from different metals induce negligible corrosion.

PubMed

Kazimierczak, A; Podraza, W; Lenart, S; Wiernicki, I; Gutowski, P

2013-10-01

Evaluation of the risk of galvanic corrosion in various stent-grafts in current practice, when devices with unmatched alloy compositions are deployed together. Five nitinol (NT) and two steel (SS) stent-grafts produced by different companies were used in different combinations to create 21 samples (NT:NT, n = 10; NT:SS, n = 10; SS:SS, n = 1). Electric potential was measured between the metal couplings after immersion in 0.9% NaCl at a temperature of 37 °C. Subsequently, the same samples were incubated for 24 months in 0.9% NaCl at 37-39 °C under hermetic conditions and examined under a scanning electron microscope in order to search for any evidence of corrosion. Electric potentials between different metals alloys were found (means: NT:SS, 181 μV; NT:NT, 101 μV; SS:SS, 160 μV). The mean electrical potential between stainless steel and nitinol samples was significantly higher than between NT:NT couplings (p < .001). During the final scanning electron microscope examination, only one spot of pitting corrosion (>10 μm) on a nitinol surface was found (associated with previous mechanical damage) in an NT:SS sample after 24 months of incubation in vitro and no sign of mechanical failure of the wires was found. Direct contact between the stainless steel and the nitinol alloys does indeed create electrical potential but with a minimal risk of galvanic corrosion. No evidence was found for significant galvanic corrosion when two endovascular implants (stent-grafts) made from different metal composition were used in the same procedure. Copyright © 2013 European Society for Vascular Surgery. Published by Elsevier Ltd. All rights reserved.

National Telerehabilitation Service System: Helping Rural Under-Served Communities and Individuals with Disabilities

ERIC Educational Resources Information Center

Exceptional Parent, 2006

2006-01-01

The National Telerehabilitation Service System (NTSS) was created to provide access to quality rehabilitation services by researching new or existing telecommunications (communicating information, including data, text, pictures, voice, and video, over long distances) and computing technologies and modifying them to meet the needs of people with…

75 FR 32935 - Combined Notice of Filings

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-10

.... Take notice that the Commission has received the following Natural Gas Pipeline Rate and Refund Report..., LLC Description: Columbia Gas Transmission, LLC submits tariff filing per 154.204: NTS-S Conversion to... Services negotiated rate for contract 781744 to be effective 6/1/2010. Filed Date: 05/28/2010 Accession...

Toward a Generation Free of Tuberculosis: TB Disease and Infection in Individuals of College Age in the United States

ERIC Educational Resources Information Center

Shah, N. S.; Flood-Bryzman, A.; Jeffries, C.; Scott, J.

2018-01-01

Objectives: To assess the magnitude of active TB disease and latent TB infection (LTBI) in young adults of college age. Participants: Individuals who were aged 18-24 years in 2011 were used as a proxy for college students. Methods: Active TB cases reported to the 2011 US National TB Surveillance System (NTSS) were included. LTBI prevalence was…

Trends in Mortality of Tuberculosis Patients in the United States: The Long-term Perspective

PubMed Central

Barnes, Richard F.W.; Moore, Maria Luisa; Garfein, Richard S.; Brodine, Stephanie; Strathdee, Steffanie A.; Rodwell, Timothy C.

2011-01-01

PURPOSE To describe long-term trends in TB mortality and to compare trends estimated from two different sources of public health surveillance data. METHODS Trends and changes in trend were estimated by joinpoint regression. Comparisons between datasets were made by fitting a Poisson regression model. RESULTS Since 1900, TB mortality rates estimated from death certificates have declined steeply, except for a period of no change in the 1980s. This decade had long-term consequences resulting in more TB deaths in later years than would have occurred had there been no flattening of the trend. Recent trends in TB mortality estimated from National Tuberculosis Surveillance System (NTSS) data, which record all-cause mortality, differed from trends based on death certificates. In particular, NTSS data showed TB mortality rates flattening since 2002. CONCLUSIONS Estimates of trends in TB mortality vary by data source, and therefore interpretation of the success of control efforts will depend upon the surveillance dataset used. The datasets may be subject to different biases that vary with time. One dataset showed a sustained improvement in the control of TB since the early 1990s while the other indicated that the rate of TB mortality was no longer declining. PMID:21820320

Pili and flagella biology, structure, and biotechnological applications.

PubMed

Van Gerven, Nani; Waksman, Gabriel; Remaut, Han

2011-01-01

Bacteria and Archaea expose on their outer surfaces a variety of thread-like proteinaceous organelles with which they interact with their environments. These structures are repetitive assemblies of covalently or non-covalently linked protein subunits, organized into filamentous polymers known as pili ("hair"), flagella ("whips") or injectisomes ("needles"). They serve different roles in cell motility, adhesion and host invasion, protein and DNA secretion and uptake, conductance, or cellular encapsulation. Here we describe the functional, morphological and genetic diversity of these bacterial filamentous protein structures. The organized, multi-copy build-up and/or the natural function of pili and flagella have lead to their biotechnological application as display and secretion tools, as therapeutic targets or as molecular motors. We review the documented and potential technological exploitation of bacterial surface filaments in light of their structural and functional traits. Copyright © 2011 Elsevier Inc. All rights reserved.

Hydrovolcanic and Hydrothermal Biomediated Mineral Growth in Basaltic Tuff, Surtsey Volcano, Iceland

NASA Astrophysics Data System (ADS)

Jackson, M. D.; Couper, S.; Ivarsson, M.; Stan, C. V.; Tamura, N.; Miyagi, L. M.; Moore, J. G.

2017-12-01

Fine-scale analyses of hydroclasts in 1979 Surtsey basaltic tuff drill core provide new methods for examining hydrovolcanic and hydrothermal magma-rock influences on biomediated alteration in palagonitized submarine tephra. Synchrotron source X-ray microdiffraction and microfluorescence studies from Advanced Light Source beamline 12.3.2, epifluorescent UVA illumination microscopy, S/TEM EDX compositional analyses, and Raman spectroscopy define diverse nanocrystalline clay mineral structures at 137.9 m depth (93.8 °C (1980)) and 102.6 m depth (141.3 °C (1980)). At 137.9 m, olivine contains endolithic microborings; vermicular microstructures in altered glass contain nontronite exhibiting crystallographic preferred orientation; and 75-150 µm sub-circular microstructures in altered glass contain Al-tobermorite, a calcium-silicate-hydrate with 11.3 Å interlayer spacing, zeolite, and epifluorescent, thread-like structures. At 102.6 m depth, concentrically-layered microstructures occur in altered glass and altered olivine. These have nontronite crystallographic preferred orientations that rotate around a longitudinal axis commonly occupied by a 10-80 µm long, epifluorescent thread-like structure. Pronounced carbon concentrations detected by S/TEM EDX trace layer boundaries. First-order Raman bands at 1370 cm-1 (disorder-related) and at 1580 cm-1 (order-related), and second-order bands at 2500-3300 cm-1 (overtone scattering) detect degraded organic carbonaceous matter, a strong indication of biological origin. Sub-circular nanostructures in altered glass at 137.9 m depth show similar spectra. Borehole fluid temperatures at 102.6 m, 141.3 °C in 1980, exceeded 130 °C, the assumed limit for growth of microorganisms, however. Previous analyses suggest an early low temperature episode in submarine deposits, prior to development of a hydrothermal system driven by 1964-1967 magmatic intrusions. The abundant traces of biomediated nanocrystalline clay mineral growth validate this hypothesis. Hydrovolcanic fragmentation apparently increased ingress of seawater from the marine biosphere. Both eruptive and hydrothermal water-rock interactions influenced palagonitic alteration at the submillimeter scale during diverse temperature chronologies in the very young volcano.

Vitamin B12 deficiency in metformin-treated type-2 diabetes patients, prevalence and association with peripheral neuropathy.

PubMed

Ahmed, Marwan A; Muntingh, George; Rheeder, Paul

2016-10-07

The association between long-term metformin use and low vitamin B12 levels has been proven. However, the prevalence estimates of metformin-induced vitamin B12 deficiency showed considerable variation among the studies. The potential of the deficiency to cause or worsen peripheral neuropathy in type-2 diabetes mellitus (T2DM) patients has been investigated with conflicting results. The aim of the study was to investigate: 1) the prevalence of vitamin B12 deficiency in T2DM patients on metformin; 2) the association between vitamin B12 and peripheral neuropathy; 3) and the risk factors for vitamin B12 deficiency in these patients. In this cross-sectional study, consecutive metformin-treated T2DM patients attending diabetes clinics of two public hospitals in South Africa were approached for participation. Participation included measuring vitamin B12 levels and assessing peripheral neuropathy using Neuropathy Total Symptom Score-6 (NTSS-6) questionnaire. The prevalence of vitamin B12 deficiency (defined by concentrations <150 pmol/L) was determined. Those with NTSS-6 scores >6 were considered to have peripheral neuropathy. The relationship between vitamin B12 and peripheral neuropathy was investigated when the two variables were in the binary and continuous forms. Multiple logistic regression was used to determine risk factors for vitamin B12 deficiency. Among 121 participants, the prevalence of vitamin B12 deficiency was 28.1 %. There was no difference in presence of neuropathy between those with normal and deficient vitamin levels (36.8 % vs. 32.3 %, P = 0.209). Vitamin B12 levels and NTSS-6 scores were not correlated (Spearman's rho =0.056, P = 0.54). HbA1c (mmol/mol) (OR = 0.97, 95 % CI: 0.95 to 0.99, P = 0.003) and black race (OR = 0.34, 95 % CI: 0.13 to 0.92, P = 0.033) were risk factors significantly associated with vitamin B12 deficiency. Metformin daily dose (gram) showed borderline significance (OR = 1.96, 95 % CI: 0.99 to 3.88, P = 0.053). Close to third of metformin-treated T2DM patients had vitamin B12 deficiency. The deficiency was not associated with peripheral neuropathy. Black race was a protective factor for vitamin B12 deficiency.

Ion-exchange synthesis and superconductivity at 8.6 K of Na2Cr3As3 with quasi-one-dimensional crystal structure

NASA Astrophysics Data System (ADS)

Mu, Qing-Ge; Ruan, Bin-Bin; Pan, Bo-Jin; Liu, Tong; Yu, Jia; Zhao, Kang; Chen, Gen-Fu; Ren, Zhi-An

2018-03-01

A Cr-based quasi-one-dimensional superconductor N a2 Cr3As3 was synthesized by an ion-exchange method in a sodium naphthalenide solution. The crystals are threadlike and the structure was analyzed by x-ray diffraction with a noncentrosymmetric hexagonal space group P -6 m 2 (No. 187), in which the (Cr3As3 )2 - linear chains are separated by N a+ ions, and the refined lattice parameters are a =9.239 (2 )Å and c =4.209 (6 )Å . The measurements for electrical resistivity, magnetic susceptibility, and heat capacity reveal a superconducting transition with unconventional characteristic at 8.6 K, which exceeds that of all previously reported Cr-based superconductors.

Acupuncture Treatment of Diabetic Peripheral Neuropathy in an American Indian Community.

PubMed

Bailey, Anne; Wingard, Deborah; Allison, Matthew; Summers, Priscilla; Calac, Daniel

2017-04-01

Diabetic peripheral neuropathy (DPN) develops in 30% of type 2 diabetes patients, increases the risk for foot ulcers and amputation, and is a significant source of disability and medical costs. Treatment remains challenging, propelling research to focus on therapeutic methods that aim to improve blood circulation or ameliorate oxidative stress that drives development of DPN. The aim of this study was to assess the effectiveness of acupuncture treatment for DPN symptoms and lower extremity arterial circulation in people with type 2 diabetes. Twenty-five patients seen at a Southern California Tribal Health Center who reported a threshold level of diabetic neuropathy symptoms in the lower extremities during the previous 4 weeks received acupuncture treatment once per week over a 10-week period between 2011 and 2013. The Neuropathy Total Symptom Scale (NTSS-6), Neuropathy Disability Score (NDS), and laser Doppler fluxmetry (LDF) were used for assessment at baseline and 10 weeks. A total of 19 of 25 study participants completed the study and reported a significant reduction in the NTSS symptoms of aching pain, burning pain, prickling sensation, numbness, and allodynia. Lancinating pain did not decrease significantly. LDF measures improved but not significantly. Acupuncture may effectively ameliorate selected DPN symptoms in these American Indian patients. Copyright © 2017 Medical Association of Pharmacopuncture Institute. Published by Elsevier B.V. All rights reserved.

A cosmic double helix in the archetypical quasar 3C273.

PubMed

Lobanov, A P; Zensus, J A

2001-10-05

Finding direct evidence for plasma instability in extragalactic jets is crucial for understanding the nature of relativistic outflows from active galactic nuclei. Our radio interferometric observations of the quasar 3C273 made with the orbiting radio telescope, HALCA, and an array of ground telescopes have yielded an image in which the emission across the jet is resolved, revealing two threadlike patterns that form a double helix inside the jet. This double helical structure is consistent with a Kelvin-Helmholtz instability, and at least five different instability modes can be identified and modeled by a light jet with a Lorentz factor of 2 and Mach number of 3.5. The model reproduces in detail the internal structure of the jet on scales of up to 30 milli-arc seconds ( approximately 300 parsecs) and is consistent with the general morphology of the jet on scales of up to 1 kiloparsec.

Assembly of one-dimensional supramolecular objects: From monomers to networks

NASA Astrophysics Data System (ADS)

Sayar, Mehmet; Stupp, Samuel I.

2005-07-01

One-dimensional supramolecular aggregates can form networks at exceedingly low concentrations. Recent experiments in several laboratories, including our own, have demonstrated the formation of gels by these systems at concentrations well under 1% by weight. The systems of interest in our laboratory form either cylindrical nanofibers or ribbons as a result of strong noncovalent interactions among monomers. The stiffness and interaction energies among these thread-like objects can vary significantly depending on the chemical structure of the monomers used. We have used Monte Carlo simulations to study the structure of the threads and their ability to form networks through bundle formation. The persistence length of the threads was found to be strongly affected not only by stiffness, but also by the strength of attractive two-body interactions among thread segments. The relative values of stiffness and attractive two-body interaction strength determine if threads collapse or create bundles. Only in the presence of sufficiently long threads and bundle formation can these systems assemble into networks of high connectivity.

Tornado-like Evolution of a Kink-unstable Solar Prominence

NASA Astrophysics Data System (ADS)

Wang, Wensi; Liu, Rui; Wang, Yuming

2017-01-01

We report on the tornado-like evolution of a quiescent prominence on 2014 November 1. The eastern section of the prominence first rose slowly, transforming into an arch-shaped structure as high as ˜150 Mm above the limb; the arch then writhed moderately in a left-handed sense, while the original dark prominence material emitted in the Fe ix 171 Å passband, and a braided structure appeared at the eastern edge of the warped arch. The unraveling of the braided structure was associated with a transient brightening in the EUV and apparently contributed to the formation of a curtain-like structure (CLS). The CLS consisted of myriad thread-like loops rotating counterclockwise about the vertical if viewed from above. Heated prominence material was observed to slide along these loops and land outside the filament channel. The tornado eventually disintegrated and the remaining material flew along a left-handed helical path constituting approximately a full turn, as corroborated through stereoscopic reconstruction, into the cavity of the stable, western section of the prominence. We suggest that the tornado-like evolution of the prominence was governed by the helical kink instability, and that the CLS formed through magnetic reconnections between the prominence field and the overlying coronal field.

Evidence for novel age-dependent network structures as a putative primo vascular network in the dura mater of the rat brain

PubMed Central

Lee, Ho-Sung; Kang, Dai-In; Yoon, Seung Zhoo; Ryu, Yeon Hee; Lee, Inhyung; Kim, Hoon-Gi; Lee, Byung-Cheon; Lee, Ki Bog

2015-01-01

With chromium-hematoxylin staining, we found evidence for the existence of novel age-dependent network structures in the dura mater of rat brains. Under stereomicroscopy, we noticed that chromium-hematoxylin-stained threadlike structures, which were barely observable in 1-week-old rats, were networked in specific areas of the brain, for example, the lateral lobes and the cerebella, in 4-week-old rats. In 7-week-old rats, those structures were found to have become larger and better networked. With phase contrast microscopy, we found that in 1-week-old rats, chromium-hematoxylin-stained granules were scattered in the same areas of the brain in which the network structures would later be observed in the 4- and 7-week-old rats. Such age-dependent network structures were examined by using optical and transmission electron microscopy, and the following results were obtained. The scattered granules fused into networks with increasing age. Cross-sections of the age-dependent network structures demonstrated heavily-stained basophilic substructures. Transmission electron microscopy revealed the basophilic substructures to be clusters with high electron densities consisting of nanosized particles. We report these data as evidence for the existence of age-dependent network structures in the dura mater, we discuss their putative functions of age-dependent network structures beyond the general concept of the dura mater as a supporting matrix. PMID:26330833

Principles for Protecting Wood Buildings from Decay. Revision

DTIC Science & Technology

1979-01-01

masked by the stain. growing stage are threadlike, and the individual Stained wood is more permeable to rainwater; strands, called hyphae , are...invisible to the naked thus wood in exterior service is more subject eye except in mass. These hyphae penetrate and to decay infection. ramify within wood...of cooling towers, for example, areMold hyphae , however, penetrate wood deeply subject to so•fl rot. Some of the molds and the and increaae

Ultrastructural characterization of the tau-immunoreactive tubules in the oligodendroglial perikarya and their inner loop processes in progressive supranuclear palsy.

PubMed

Arima, K; Nakamura, M; Sunohara, N; Ogawa, M; Anno, M; Izumiyama, Y; Hirai, S; Ikeda, K

1997-06-01

Coiled bodies and interfascicular threads are conspicuous white matter abnormalities of brains of patients with progressive supranuclear palsy (PSP). Both structures are argyrophilic and immunoreactive for the microtubule-binding protein tau. This report concerns the ultrastructural localization of interfascicular threads and their relationship to coiled bodies in five PSP patients. We showed for the first time that abnormal tubules with a 13- to 15-nm diameter and fuzzy outer contours were the common structures of coiled bodies in the oligodendroglial perikarya and of interfascicular threads. Moreover, the tubules were immunolabeled by anti-tau antibodies. The abnormal tau-positive tubules of interfascicular threads were located in the inner loop of the myelin sheath. Our study further indicated that the thread-like structures in the white matter comprised, at least in part, oligodendroglial processes, and that they were also present in gray matter. We consider that the formation of coiled bodies in the perikarya and of interfascicular threads represents a common cytoskeletal abnormality of the oligodendroglia of PSP patients. Moreover, even though the white matter alterations of PSP resemble those of corticobasal degeneration, there are certain ultrastructural differences in the abnormal oligodendroglial tubules of the two diseases.

Tornado-Like Evolution of A Kink-Unstable Solar Prominence

NASA Astrophysics Data System (ADS)

Wang, W.; Liu, R.; Wang, Y.

2016-12-01

We report on the tornado-like evolution of a quiescent prominence on 2014 November 1. The evolution started with a slow rise of the eastern section of the prominence into an arch-shaped structure as high as 150 Mm above the limb, and then the arch experienced a moderate, left-handed writhing. Following the writhing, the originally dark prominence material became in emission in the Fe IX 171 °A passband, and a braiding structure appeared at the eastern edge of the writhing prominence body, whose unraveling process was associated with a transient brightening in EUV and apparently contributed to the formation of a curtain-like structure (CLS), which consisted of myriads of thread-like loops rotating counterclockwise about the vertical if viewed from above. Material sliding along these loops landed outside of the prominence channel. The tornado was eventually disintegrated and the remaining material flew along a lefthanded helical path of approximately a full turn, as confirmed through stereoscopic reconstruction, into the cavity of the stable, western section of the prominence. We suggest that the tornado-like evolution of the prominence was regulated by the helical kink instability, and that the CLS forms through magnetic reconnections between the flux-rope flux and the overlying flux.

Dense white trichome production by plants as possible mimicry of arthropod silk or fungal hyphae that deter herbivory.

PubMed

Yamazaki, Kazuo; Lev-Yadun, Simcha

2015-01-07

Some spiders are well-known to mimic flowers or other plant surfaces in order to be cryptic to both their prey and their predators. We propose that dense, thread-like white trichomes of some plants from Estonia, Greece, Israel and Japan visually mimic spider webs, lepidopteran and spider-mite web nests and plant-pathogenic fungi, and that it may result in reduced herbivory, since various herbivores avoid spider- or other arthropod webs to circumvent predation or toxic attacks, or refrain from colonizing plants that have already been occupied by other herbivores and pathogens. Spiders and other web-forming arthropods are also the prey of certain vertebrate predators and wasps, and therefore such predators may be attracted to these web-like plant structures and prey on the invertebrate herbivores occupying them. We do not dismiss the possibility that these web-like structures may also have other defensive or physiological functions or that they are not classic mimics but rather exploit the herbivore׳s perceptual state concerning the avoidance of potentially risky objects. Copyright © 2014 Elsevier Ltd. All rights reserved.

von Willebrand factor, Jedi knight of the bloodstream.

PubMed

Springer, Timothy A

2014-08-28

When blood vessels are cut, the forces in the bloodstream increase and change character. The dark side of these forces causes hemorrhage and death. However, von Willebrand factor (VWF), with help from our circulatory system and platelets, harnesses the same forces to form a hemostatic plug. Force and VWF function are so closely intertwined that, like members of the Jedi Order in the movie Star Wars who learn to use "the Force" to do good, VWF may be considered the Jedi knight of the bloodstream. The long length of VWF enables responsiveness to flow. The shape of VWF is predicted to alter from irregularly coiled to extended thread-like in the transition from shear to elongational flow at sites of hemostasis and thrombosis. Elongational force propagated through the length of VWF in its thread-like shape exposes its monomers for multimeric binding to platelets and subendothelium and likely also increases affinity of the A1 domain for platelets. Specialized domains concatenate and compact VWF during biosynthesis. A2 domain unfolding by hydrodynamic force enables postsecretion regulation of VWF length. Mutations in VWF in von Willebrand disease contribute to and are illuminated by VWF biology. I attempt to integrate classic studies on the physiology of hemostatic plug formation into modern molecular understanding, and point out what remains to be learned. © 2014 by The American Society of Hematology.

Insights into bunyavirus architecture from electron cryotomography of Uukuniemi virus

PubMed Central

Överby, A. K.; Pettersson, R. F.; Grünewald, K.; Huiskonen, J. T.

2008-01-01

Bunyaviridae is a large family of viruses that have gained attention as “emerging viruses” because many members cause serious disease in humans, with an increasing number of outbreaks. These negative-strand RNA viruses possess a membrane envelope covered by glycoproteins. The virions are pleiomorphic and thus have not been amenable to structural characterization using common techniques that involve averaging of electron microscopic images. Here, we determined the three-dimensional structure of a member of the Bunyaviridae family by using electron cryotomography. The genome, incorporated as a complex with the nucleoprotein inside the virions, was seen as a thread-like structure partially interacting with the viral membrane. Although no ordered nucleocapsid was observed, lateral interactions between the two membrane glycoproteins determine the structure of the viral particles. In the most regular particles, the glycoprotein protrusions, or “spikes,” were seen to be arranged on an icosahedral lattice, with T = 12 triangulation. This arrangement has not yet been proven for a virus. Two distinctly different spike conformations were observed, which were shown to depend on pH. This finding is reminiscent of the fusion proteins of alpha-, flavi-, and influenza viruses, in which conformational changes occur in the low pH of the endosome to facilitate fusion of the viral and host membrane during viral entry. PMID:18272496

TORNADO-LIKE EVOLUTION OF A KINK-UNSTABLE SOLAR PROMINENCE

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

Wang, Wensi; Liu, Rui; Wang, Yuming, E-mail: rliu@ustc.edu.cn

We report on the tornado-like evolution of a quiescent prominence on 2014 November 1. The eastern section of the prominence first rose slowly, transforming into an arch-shaped structure as high as ∼150 Mm above the limb; the arch then writhed moderately in a left-handed sense, while the original dark prominence material emitted in the Fe ix 171 Å passband, and a braided structure appeared at the eastern edge of the warped arch. The unraveling of the braided structure was associated with a transient brightening in the EUV and apparently contributed to the formation of a curtain-like structure (CLS). The CLSmore » consisted of myriad thread-like loops rotating counterclockwise about the vertical if viewed from above. Heated prominence material was observed to slide along these loops and land outside the filament channel. The tornado eventually disintegrated and the remaining material flew along a left-handed helical path constituting approximately a full turn, as corroborated through stereoscopic reconstruction, into the cavity of the stable, western section of the prominence. We suggest that the tornado-like evolution of the prominence was governed by the helical kink instability, and that the CLS formed through magnetic reconnections between the prominence field and the overlying coronal field.« less

Unexpected decline in tuberculosis cases coincident with economic recession -- United States, 2009

PubMed Central

2011-01-01

Background Since 1953, through the cooperation of state and local health departments, the U.S. Centers for Disease Control and Prevention (CDC) has collected information on incident cases of tuberculosis (TB) disease in the United States. In 2009, TB case rates declined -11.4%, compared to an average annual -3.8% decline since 2000. The unexpectedly large decline raised concerns that TB cases may have gone unreported. To address the unexpected decline, we examined trends from multiple sources on TB treatment initiation, medication sales, and laboratory and genotyping data on culture-positive TB. Methods We analyzed 142,174 incident TB cases reported to the U. S. National Tuberculosis Surveillance System (NTSS) during January 1, 2000-December 31, 2009; TB control program data from 59 public health reporting areas; self-reported data from 50 CDC-funded public health laboratories; monthly electronic prescription claims for new TB therapy prescriptions; and complete genotyping results available for NTSS cases. Accounting for prior trends using regression and time-series analyses, we calculated the deviation between observed and expected TB cases in 2009 according to patient and clinical characteristics, and assessed at what point in time the deviation occurred. Results The overall deviation in TB cases in 2009 was -7.9%, with -994 fewer cases reported than expected (P < .001). We ruled out evidence of surveillance underreporting since declines were seen in states that used new software for case reporting in 2009 as well as states that did not, and we found no cases unreported to CDC in our examination of over 5400 individual line-listed reports in 11 areas. TB cases decreased substantially among both foreign-born and U.S.-born persons. The unexpected decline began in late 2008 or early 2009, and may have begun to reverse in late 2009. The decline was greater in terms of case counts among foreign-born than U.S.-born persons; among the foreign-born, the declines were greatest in terms of percentage deviation from expected among persons who had been in the United States less than 2 years. Among U.S.-born persons, the declines in percentage deviation from expected were greatest among homeless persons and substance users. Independent information systems (NTSS, TB prescription claims, and public health laboratories) reported similar patterns of declines. Genotyping data did not suggest sudden decreases in recent transmission. Conclusions Our assessments show that the decline in reported TB was not an artifact of changes in surveillance methods; rather, similar declines were found through multiple data sources. While the steady decline of TB cases before 2009 suggests ongoing improvement in TB control, we were not able to identify any substantial change in TB control activities or TB transmission that would account for the abrupt decline in 2009. It is possible that other multiple causes coincident with economic recession in the United States, including decreased immigration and delayed access to medical care, could be related to TB declines. Our findings underscore important needs in addressing health disparities as we move towards TB elimination in the United States. PMID:22059421

A novel two-step sintering for nano-hydroxyapatite scaffolds for bone tissue engineering

PubMed Central

Feng, Pei; Niu, Man; Gao, Chengde; Peng, Shuping; Shuai, Cijun

2014-01-01

In this study, nano-hydroxyapatite scaffolds with high mechanical strength and an interconnected porous structure were prepared using NTSS for the first time. The first step was performed using a laser characterized by the rapid heating to skip the surface diffusion and to obtain the driving force for grain boundary diffusion. Additionally, the interconnected porous structure was achieved by SLS. The second step consisted of isothermal heating in a furnace at a lower temperature (T2) than that of the laser beam to further increase the density and to suppress grain growth by exploiting the difference in kinetics between grain-boundary diffusion and grain-boundary migration. The results indicated that the mechanical properties first increased and then decreased as T2 was increased from 1050 to 1250°C. The optimal fracture toughness, compressive strength and stiffness were 1.69 MPam1/2, 18.68 MPa and 245.79 MPa, respectively. At the optimal point, the T2 was 1100°C, the grain size was 60 nm and the relative density was 97.6%. The decrease in mechanical properties was due to the growth of grains and the decomposition of HAP. The cytocompatibility test results indicated that cells adhered and spread well on the scaffolds. A bone-like apatite layer formed, indicating good bioactivity. PMID:24998362

Human Tau Isoforms Assemble into Ribbon-like Fibrils That Display Polymorphic Structure and Stability*

PubMed Central

Wegmann, Susanne; Jung, Yu Jin; Chinnathambi, Subashchandrabose; Mandelkow, Eva-Maria; Mandelkow, Eckhard; Muller, Daniel J.

2010-01-01

Fibrous aggregates of Tau protein are characteristic features of Alzheimer disease. We applied high resolution atomic force and EM microscopy to study fibrils assembled from different human Tau isoforms and domains. All fibrils reveal structural polymorphism; the “thin twisted” and “thin smooth” fibrils resemble flat ribbons (cross-section ∼10 × 15 nm) with diverse twist periodicities. “Thick fibrils” show periodicities of ∼65–70 nm and thicknesses of ∼9–18 nm such as routinely reported for “paired helical filaments” but structurally resemble heavily twisted ribbons. Therefore, thin and thick fibrils assembled from different human Tau isoforms challenge current structural models of paired helical filaments. Furthermore, all Tau fibrils reveal axial subperiodicities of ∼17–19 nm and, upon exposure to mechanical stress or hydrophobic surfaces, disassemble into uniform fragments that remain connected by thin thread-like structures (∼2 nm). This hydrophobically induced disassembly is inhibited at enhanced electrolyte concentrations, indicating that the fragments resemble structural building blocks and the fibril integrity depends largely on hydrophobic and electrostatic interactions. Because full-length Tau and repeat domain constructs assemble into fibrils of similar thickness, the “fuzzy coat” of Tau protein termini surrounding the fibril axis is nearly invisible for atomic force microscopy and EM, presumably because of its high flexibility. PMID:20566652

Translations on USSR Science and Technology. Physical Sciences and Technology, Number 4

DTIC Science & Technology

1976-11-23

collaboration with the Krivorozhkiy Ore-enrichment Combine and the "Artemugol’" Union, with the L’vov "Kineskop" and with the Black Sea Maritime Steamship... sea and oceans, the development of methods for preventing water pollution by petroleum and petroleum products, maximal use of the maritime fleet and... Microplastic deformation of threadlike crystals of silicon in the elastic phase of deformation in the temperature range of 20-500°C 187 Agalakova, T

High-performance two-ply yarn supercapacitors based on carbon nanotubes and polyaniline nanowire arrays.

PubMed

Wang, Kai; Meng, Qinghai; Zhang, Yajie; Wei, Zhixiang; Miao, Menghe

2013-03-13

Fine count two-ply yarn supercapacitors are constructed from carbon nanotube yarns and polyaniline nanowires. The thread-like supercapacitor possess excellent electrochemical capacity and are very strong and flexible. When being woven or knitted into wearable electronic devices, alone or in combination with conventional textile yarns, the two-ply yarn supercapacitors can be flexed and stretched repeatedly without significant loss of capacitance. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The functional role for condensin in the regulation of chromosomal organization during the cell cycle.

PubMed

Kagami, Yuya; Yoshida, Kiyotsugu

2016-12-01

In all organisms, the control of cell cycle progression is a fundamental process that is essential for cell growth, development, and survival. Through each cell cycle phase, the regulation of chromatin organization is essential for natural cell proliferation and maintaining cellular homeostasis. During mitosis, the chromatin morphology is dramatically changed to have a "thread-like" shape and the condensed chromosomes are segregated equally into two daughter cells. Disruption of the mitotic chromosome architecture physically impedes chromosomal behaviors, such as chromosome alignment and chromosome segregation; therefore, the proper mitotic chromosome structure is required to maintain chromosomal stability. Accumulating evidence has demonstrated that mitotic chromosome condensation is induced by condensin complexes. Moreover, recent studies have shown that condensin also modulates interphase chromatin and regulates gene expression. This review mainly focuses on the molecular mechanisms that condensin uses to exert its functions during the cell cycle progression. Moreover, we discuss the condensin-mediated chromosomal organization in cancer cells.

Ultrastructural morphogenesis of a virus associated with lymphocystis-like lesions in parore Girella tricuspidata (Kyphosidae: Perciformes).

PubMed

Hine, P M; Wakefield, St J; Mackereth, G; Morrison, R

2016-09-26

The morphogenesis of large icosahedral viruses associated with lymphocystis-like lesions in the skin of parore Girella tricuspidata is described. The electron-lucent perinuclear viromatrix comprised putative DNA with open capsids at the periphery, very large arrays of smooth endoplasmic reticulum (sER), much of it with a reticulated appearance (rsER) or occurring as rows of vesicles. Lysosomes, degenerating mitochondria and virions in various stages of assembly, and paracrystalline arrays were also present. Long electron-dense inclusions (EDIs) with 15 nm repeating units split terminally and curled to form tubular structures internalising the 15 nm repeating structures. These tubular structures appeared to form the virion capsids. Large parallel arrays of sER sometimes alternated with aligned arrays of crinkled cisternae along which passed a uniformly wide (20 nm) thread-like structure. Strings of small vesicles near open capsids may also have been involved in formation of an inner lipid layer. Granules with a fine fibrillar appearance also occurred in the viromatrix, and from the presence of a halo around mature virions it appeared that the fibrils may form a layer around the capsid. The general features of virogenesis of large icosahedral dsDNA viruses, the large amount of ER, particularly rsER and the EDIs, are features of nucleo-cytoplasmic large DNA viruses, rather than features of 1 genus or family.

ARE GIANT TORNADOES THE LEGS OF SOLAR PROMINENCES?

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

Wedemeyer, Sven; Scullion, Eamon; Rouppe van der Voort, Luc

Observations in the 171 A channel of the Atmospheric Imaging Assembly of the space-borne Solar Dynamics Observatory show tornado-like features in the atmosphere of the Sun. These giant tornadoes appear as dark, elongated, and apparently rotating structures in front of a brighter background. This phenomenon is thought to be produced by rotating magnetic field structures that extend throughout the atmosphere. We characterize giant tornadoes through a statistical analysis of properties such as spatial distribution, lifetimes, and sizes. A total number of 201 giant tornadoes are detected in a period of 25 days, suggesting that, on average, about 30 events aremore » present across the whole Sun at a time close to solar maximum. Most tornadoes appear in groups and seem to form the legs of prominences, thus serving as plasma sources/sinks. Additional H{alpha} observations with the Swedish 1 m Solar Telescope imply that giant tornadoes rotate as a structure, although they clearly exhibit a thread-like structure. We observe tornado groups that grow prior to the eruption of the connected prominence. The rotation of the tornadoes may progressively twist the magnetic structure of the prominence until it becomes unstable and erupts. Finally, we investigate the potential relation of giant tornadoes to other phenomena, which may also be produced by rotating magnetic field structures. A comparison to cyclones, magnetic tornadoes, and spicules implies that such events are more abundant and short-lived the smaller they are. This comparison might help to construct a power law for the effective atmospheric heating contribution as a function of spatial scale.« less

Are Giant Tornadoes the Legs of Solar Prominences?

NASA Astrophysics Data System (ADS)

Wedemeyer, Sven; Scullion, Eamon; Rouppe van der Voort, Luc; Bosnjak, Antonija; Antolin, Patrick

2013-09-01

Observations in the 171 Å channel of the Atmospheric Imaging Assembly of the space-borne Solar Dynamics Observatory show tornado-like features in the atmosphere of the Sun. These giant tornadoes appear as dark, elongated, and apparently rotating structures in front of a brighter background. This phenomenon is thought to be produced by rotating magnetic field structures that extend throughout the atmosphere. We characterize giant tornadoes through a statistical analysis of properties such as spatial distribution, lifetimes, and sizes. A total number of 201 giant tornadoes are detected in a period of 25 days, suggesting that, on average, about 30 events are present across the whole Sun at a time close to solar maximum. Most tornadoes appear in groups and seem to form the legs of prominences, thus serving as plasma sources/sinks. Additional Hα observations with the Swedish 1 m Solar Telescope imply that giant tornadoes rotate as a structure, although they clearly exhibit a thread-like structure. We observe tornado groups that grow prior to the eruption of the connected prominence. The rotation of the tornadoes may progressively twist the magnetic structure of the prominence until it becomes unstable and erupts. Finally, we investigate the potential relation of giant tornadoes to other phenomena, which may also be produced by rotating magnetic field structures. A comparison to cyclones, magnetic tornadoes, and spicules implies that such events are more abundant and short-lived the smaller they are. This comparison might help to construct a power law for the effective atmospheric heating contribution as a function of spatial scale.

Coulomb scatter of diamagnetic dust particles in a cusp magnetic trap under microgravity conditions

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

Myasnikov, M. I., E-mail: miasnikovmi@mail.ru; D’yachkov, L. G.; Petrov, O. F.

2017-02-15

The effect of a dc electric field on strongly nonideal Coulomb systems consisting of a large number (~10{sup 4}) of charged diamagnetic dust particles in a cusp magnetic trap are carried out aboard the Russian segment of the International Space Station (ISS) within the Coulomb Crystal experiment. Graphite particles of 100–400 μm in size are used in the experiments. Coulomb scatter of a dust cluster and the formation of threadlike chains of dust particles are observed experimentally. The processes observed are simulated by the molecular dynamics (MD) method.

α-Synuclein Amyloid Fibrils with Two Entwined, Asymmetrically Associated Protofibrils*

PubMed Central

Dearborn, Altaira D.; Wall, Joseph S.; Cheng, Naiqian; Heymann, J. Bernard; Kajava, Andrey V.; Varkey, Jobin; Langen, Ralf; Steven, Alasdair C.

2016-01-01

Parkinson disease and other progressive neurodegenerative conditions are characterized by the intracerebral presence of Lewy bodies, containing amyloid fibrils of α-synuclein. We used cryo-electron microscopy and scanning transmission electron microscopy (STEM) to study in vitro-assembled fibrils. These fibrils are highly polymorphic. Focusing on twisting fibrils with an inter-crossover spacing of 77 nm, our reconstructions showed them to consist of paired protofibrils. STEM mass per length data gave one subunit per 0.47 nm axial rise per protofibril, consistent with a superpleated β-structure. The STEM images show two thread-like densities running along each of these fibrils, which we interpret as ladders of metal ions. These threads confirmed the two-protofibril architecture of the 77-nm twisting fibrils and allowed us to identify this morphotype in STEM micrographs. Some other, but not all, fibril morphotypes also exhibit dense threads, implying that they also present a putative metal binding site. We propose a molecular model for the protofibril and suggest that polymorphic variant fibrils have different numbers of protofibrils that are associated differently. PMID:26644467

Solvent-Tuned Self-Assembled Nanostructures of Chiral l/d-Phenylalanine Derivatives of Protoporphyrin IX

PubMed Central

Bobe, Mr Sharad R; Al Kobaisi, Mohammad; Bhosale, Sheshanath V; Bhosale, Sidhanath V

2015-01-01

Protoporphyrin IX is a naturally occurring amphiphilic porphyrin with a rigid hydrophobic nonpolar core and two polar propionic acid substitutions on the porphyrin ring. This molecule can be modified on the hydrophilic group, which can lead to strengthened π–π-stacking and spontaneous self-assembly into novel nanostructures. Herein, we use l- phenylalanine and d-phenylalanine to modify protoporphyrin IX, and use the two derivatives for solvophobic-controlled self-assembly. Both derivatives possess two important features: 1) the aromatic core of the porphyrin for dispersive interactions and 2) a chiral amino acid to maximize the influence of chirality on selfassembly. These derivatives lead to the formation of a variety of nanostructure morphologies, such as spheres, nanofibers, lamellar structures, and thread-like and spherical shells. Solution-based self-assembly was determined by UV/Vis, fluorescence, and circular dichroism spectroscopy, and the formed nanostructures were characterized by scanning electron microscopy (SEM). Such engineered porphyrin derivatives could have potential applications in energy transport and storage, supramolecular chemistry, materials science, and medicine. PMID:26478848

Solvent-Tuned Self-Assembled Nanostructures of Chiral l/d-Phenylalanine Derivatives of Protoporphyrin IX.

PubMed

Bobe, Mr Sharad R; Al Kobaisi, Mohammad; Bhosale, Sheshanath V; Bhosale, Sidhanath V

2015-08-01

Protoporphyrin IX is a naturally occurring amphiphilic porphyrin with a rigid hydrophobic nonpolar core and two polar propionic acid substitutions on the porphyrin ring. This molecule can be modified on the hydrophilic group, which can lead to strengthened π-π-stacking and spontaneous self-assembly into novel nanostructures. Herein, we use l- phenylalanine and d-phenylalanine to modify protoporphyrin IX, and use the two derivatives for solvophobic-controlled self-assembly. Both derivatives possess two important features: 1) the aromatic core of the porphyrin for dispersive interactions and 2) a chiral amino acid to maximize the influence of chirality on selfassembly. These derivatives lead to the formation of a variety of nanostructure morphologies, such as spheres, nanofibers, lamellar structures, and thread-like and spherical shells. Solution-based self-assembly was determined by UV/Vis, fluorescence, and circular dichroism spectroscopy, and the formed nanostructures were characterized by scanning electron microscopy (SEM). Such engineered porphyrin derivatives could have potential applications in energy transport and storage, supramolecular chemistry, materials science, and medicine.

Conducting polymer nanowire arrays for high performance supercapacitors.

PubMed

Wang, Kai; Wu, Haiping; Meng, Yuena; Wei, Zhixiang

2014-01-15

This Review provides a brief summary of the most recent research developments in the fabrication and application of one-dimensional ordered conducting polymers nanostructure (especially nanowire arrays) and their composites as electrodes for supercapacitors. By controlling the nucleation and growth process of polymerization, aligned conducting polymer nanowire arrays and their composites with nano-carbon materials can be prepared by employing in situ chemical polymerization or electrochemical polymerization without a template. This kind of nanostructure (such as polypyrrole and polyaniline nanowire arrays) possesses high capacitance, superior rate capability ascribed to large electrochemical surface, and an optimal ion diffusion path in the ordered nanowire structure, which is proved to be an ideal electrode material for high performance supercapacitors. Furthermore, flexible, micro-scale, threadlike, and multifunctional supercapacitors are introduced based on conducting polyaniline nanowire arrays and their composites. These prototypes of supercapacitors utilize the high flexibility, good processability, and large capacitance of conducting polymers, which efficiently extend the usage of supercapacitors in various situations, and even for a complicated integration system of different electronic devices. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Dearborn, Altaira D.; Wall, Joseph S.; Cheng, Naiqian

Parkinson disease and other progressive neurodegenerative conditions are characterized by the intracerebral presence of Lewy bodies, containing amyloid fibrils of α-synuclein. We used cryo-electron microscopy and scanning transmission electron microscopy (STEM) to study in vitro-assembled fibrils. These fibrils are highly polymorphic. Focusing on twisting fibrils with an inter-crossover spacing of 77 nm, our reconstructions showed them to consist of paired protofibrils. STEM mass per length data gave one subunit per 0.47 nm axial rise per protofibril, consistent with a superpleated β-structure. The STEM images show two thread-like densities running along each of these fibrils, which we interpret as ladders ofmore » metal ions. These threads confirmed the two-protofibril architecture of the 77-nm twisting fibrils and allowed us to identify this morphotype in STEM micrographs. Some other, but not all, fibril morphotypes also exhibit dense threads, implying that they also present a putative metal binding site. As a result, we propose a molecular model for the protofibril and suggest that polymorphic variant fibrils have different numbers of protofibrils that are associated differently.« less

Implications of chronic daily anti-oxidant administration on the inflammatory response to intracortical microelectrodes

NASA Astrophysics Data System (ADS)

Potter-Baker, Kelsey A.; Stewart, Wade G.; Tomaszewski, William H.; Wong, Chun T.; Meador, William D.; Ziats, Nicholas P.; Capadona, Jeffrey R.

2015-08-01

Objective. Oxidative stress events have been implicated to occur and facilitate multiple failure modes of intracortical microelectrodes. The goal of the present study was to evaluate the ability of a sustained concentration of an anti-oxidant and to reduce oxidative stress-mediated neurodegeneration for the application of intracortical microelectrodes. Approach. Non-functional microelectrodes were implanted into the cortex of male Sprague Dawley rats for up to sixteen weeks. Half of the animals received a daily intraperitoneal injection of the natural anti-oxidant resveratrol, at 30 mg kg-1. The study was designed to investigate the biodistribution of the resveratrol, and the effects on neuroinflammation/neuroprotection following device implantation. Main results. Daily maintenance of a sustained range of resveratrol throughout the implantation period resulted in fewer degenerating neurons in comparison to control animals at both two and sixteen weeks post implantation. Initial and chronic improvements in neuronal viability in resveratrol-dosed animals were correlated with significant reductions in local superoxide anion accumulation around the implanted device at two weeks after implantation. Controls, receiving only saline injections, were also found to have reduced amounts of accumulated superoxide anion locally and less neurodegeneration than controls at sixteen weeks post-implantation. Despite observed benefits, thread-like adhesions were found between the liver and diaphragm in resveratrol-dosed animals. Significance. Overall, our chronic daily anti-oxidant dosing scheme resulted in improvements in neuronal viability surrounding implanted microelectrodes, which could result in improved device performance. However, due to the discovery of thread-like adhesions, further work is still required to optimize a chronic anti-oxidant dosing regime for the application of intracortical microelectrodes.

MazEF toxin-antitoxin proteins alter Escherichia coli cell morphology and infrastructure during persister formation and regrowth.

PubMed

Cho, Junho; Carr, Anita Nicole; Whitworth, Lisa; Johnson, Brent; Wilson, Kevin Scott

2017-03-01

When exposed to antibiotics, many bacteria respond by activating intracellular 'toxin' proteins, which arrest cell growth and induce formation of persister cells that survive antibiotics. After antibiotics are removed, persisters can regrow by synthesizing 'antitoxin' proteins that sequester toxin proteins. In Escherichia coli, MazE antitoxin sequesters the activity of MazF toxin, which extensively cleaves cellular RNAs. Although the functions of MazEF proteins are well characterized, there is surprisingly little known about their effects on cell structure. Here, using a combination of microscopy techniques, we visualized the effects of MazEF and three bactericidal antibiotics on E. coli cell morphology and infrastructure. When ectopically expressed in E. coli, MazF temporarily stalled cell growth and induced persister formation, but only mildly elevated DNA mutagenesis. Viewed by electron microscopy, MazF-expressing persister cells were arrested in cell growth and division. Their chromosomal DNAs were compacted into thread-like structures. Their ribosomes were excluded from their nucleoids. After exposure to ciprofloxacin, persister regrowth was activated by MazE. Cell division remained inhibited while cells became extraordinarily elongated, then divided multiple times during stationary growth phase. This extreme filamentation during persister regrowth was unique to ciprofloxacin-treated persisters, likely caused by inhibition of cell division during regrowth, and was not observed with kanamycin-treated persisters.

Plasma Brightenings in a Failed Solar Filament Eruption

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

Li, Y.; Ding, M. D., E-mail: yingli@nju.edu.cn

Failed filament eruptions are solar eruptions that are not associated with coronal mass ejections. In a failed filament eruption, the filament materials usually show some ascending and falling motions as well as generating bright EUV emissions. Here we report a failed filament eruption (SOL2016-07-22) that occurred in a quiet-Sun region observed by the Atmospheric Imaging Assembly on board the Solar Dynamics Observatory . In this event, the filament spreads out but gets confined by the surrounding magnetic field. When interacting with the ambient magnetic field, the filament material brightens up and flows along the magnetic field lines through the coronamore » to the chromosphere. We find that some materials slide down along the lifting magnetic structure containing the filament and impact the chromosphere, and through kinetic energy dissipation, cause two ribbon-like brightenings in a wide temperature range. There is evidence suggesting that magnetic reconnection occurs between the filament magnetic structure and the surrounding magnetic fields where filament plasma is heated to coronal temperatures. In addition, thread-like brightenings show up on top of the erupting magnetic fields at low temperatures, which might be produced by an energy imbalance from a fast drop of radiative cooling due to plasma rarefaction. Thus, this single event of a failed filament eruption shows the existence of a variety of plasma brightenings that may be caused by completely different heating mechanisms.« less

[An electron microscopy study of the structure of polyelectrolyte microcapsules containing protein and containing no protein].

PubMed

Kazakova, L I; Dubrovskiĭ, A V; Moshkov, D A; Shabarchina, L I; Sukhorukov, B I

2007-01-01

Electron micrographs of ultrathin sections of polyelectrolyte microparticles containing protein and free from protein for the formation of which CaCO3 spherulites served as a core basis have been obtained and analyzed. Polyelectrolyte microparticles with the number of alternately layered polyelectrolyte layers of polystyrene sulfonate and polyallylamine from 6 to 11 have been studied. It follows from the data obtained that protein-free polyelectrolyte particles having the dimensions 4.5-5 mm are formations of an intricate internal organization, which consist of a set of threadlike and closed nanoelements of polyelectrolyte nature with a thickness of 20-30 nm. The particles containing six to eight polyelectrolyte layers lack the external envelope; therefore, they were called polyelectrolyte microspherulites. With the number of layers nine and more, when a polyelectrolyte envelope appears on the surface, they transfer into polyelectrolyte microcapsules. It was found that, in a protein-containing polyelectrolyte microcapsule, as distinct from protein-free polyelectrolyte microspherulite and microcapsule, polyelectrolytes are located only in the nearsurface layer, and the external spatially organized envelope restricts the internal volume filled with protein solution. As the number of polyelectrolyte layers increases, the thickness of the envelope increases. The reasons for such substantial differences in the structures of polyelectrolyte microcapsules formed on protein-containing and protein-free CaCO3 spherulite are discussed.

A filament of dark matter between two clusters of galaxies.

PubMed

Dietrich, Jörg P; Werner, Norbert; Clowe, Douglas; Finoguenov, Alexis; Kitching, Tom; Miller, Lance; Simionescu, Aurora

2012-07-12

It is a firm prediction of the concordance cold-dark-matter cosmological model that galaxy clusters occur at the intersection of large-scale structure filaments. The thread-like structure of this 'cosmic web' has been traced by galaxy redshift surveys for decades. More recently, the warm–hot intergalactic medium (a sparse plasma with temperatures of 10(5) kelvin to 10(7) kelvin) residing in low-redshift filaments has been observed in emission and absorption. However, a reliable direct detection of the underlying dark-matter skeleton, which should contain more than half of all matter, has remained elusive, because earlier candidates for such detections were either falsified or suffered from low signal-to-noise ratios and unphysical misalignments of dark and luminous matter. Here we report the detection of a dark-matter filament connecting the two main components of the Abell 222/223 supercluster system from its weak gravitational lensing signal, both in a non-parametric mass reconstruction and in parametric model fits. This filament is coincident with an overdensity of galaxies and diffuse, soft-X-ray emission, and contributes a mass comparable to that of an additional galaxy cluster to the total mass of the supercluster. By combining this result with X-ray observations, we can place an upper limit of 0.09 on the hot gas fraction (the mass of X-ray-emitting gas divided by the total mass) in the filament.

α-Synuclein amyloid fibrils with two entwined, asymmetrically associated protofibrils [α-Synuclein amyloid fibrils with two entwined, asymmetrically associated, protofibrils and axially stacked metal binding sites

DOE PAGES

Dearborn, Altaira D.; Wall, Joseph S.; Cheng, Naiqian; ...

2015-12-07

Parkinson disease and other progressive neurodegenerative conditions are characterized by the intracerebral presence of Lewy bodies, containing amyloid fibrils of α-synuclein. We used cryo-electron microscopy and scanning transmission electron microscopy (STEM) to study in vitro-assembled fibrils. These fibrils are highly polymorphic. Focusing on twisting fibrils with an inter-crossover spacing of 77 nm, our reconstructions showed them to consist of paired protofibrils. STEM mass per length data gave one subunit per 0.47 nm axial rise per protofibril, consistent with a superpleated β-structure. The STEM images show two thread-like densities running along each of these fibrils, which we interpret as ladders ofmore » metal ions. These threads confirmed the two-protofibril architecture of the 77-nm twisting fibrils and allowed us to identify this morphotype in STEM micrographs. Some other, but not all, fibril morphotypes also exhibit dense threads, implying that they also present a putative metal binding site. As a result, we propose a molecular model for the protofibril and suggest that polymorphic variant fibrils have different numbers of protofibrils that are associated differently.« less

Three-dimensional morphological and textural complexity of Archean putative microfossils from the Northeastern Pilbara Craton: indications of biogenicity of large (>15 microm) spheroidal and spindle-like structures.

PubMed

Sugitani, Kenichiro; Grey, Kathleen; Nagaoka, Tsutomu; Mimura, Koichi

2009-09-01

We recently reported a diverse assemblage of carbonaceous structures (thread-like, film-like, spheroidal, and spindle-like) from chert in the ca. 3.0 Ga Farrel Quartzite of the Gorge Creek Group in the Pilbara Craton, Western Australia. Results from a rigorous examination of occurrence, composition, morphological complexity, size distributions, and taphonomy provided presumptive evidence for biogenicity. In this study, we present new data of morphological and textural complexity of large (>15 microm) spheroidal and spindle-like structures, using an in-focus, 3-D image reconstruction system, which further raises the scale of credibility that these structures are microfossils. While many of the large spheroids are single-walled, and the wall is irregularly folded, a few specimens are partially blistered, double walled, or have a dimpled wall. The wall-surface texture varies from smooth and homogeneous (hyaline) to patchy, granular or reticulate. Such variation is best explained as resulting from taphonomic processes. Additionally, an inner solitary body, present in some large spheroids, is hollow and partially broken, which indicates a primary origin for this substructure. Spindle-like structures have two types of flange-like appendage; one is attached at the equatorial plane of the body, whereas the other appears to be attached peripherally. In both cases, the appendage tends to have a flat geometry, a tapering thickness, and constancy in shape, proportions, and dimensions. Spindle-wall surfaces are variously textured and heterogeneous. These morphological and textural complexities and heterogeneity refute potential abiogenic formation models for these structures, such as crystals coated with organic matter, fenestrae, and the diagenetic redistribution of carbonaceous matter. When coupled with other data from Raman spectroscopy, NanoSIMS analysis, and palynology, the evidence that these large carbonaceous structures are biogenic appears compelling, though it is still equivocal as to whether they are cells or outer envelopes of colonies of smaller cells.

A new approach for high performance fiber manufacturing via simultaneous fiber spinning and UV initiated polymerization

NASA Astrophysics Data System (ADS)

Ellison, Chris

Synthetic fibers have been manufactured for decades using solvents or heat to reduce the viscosity of pre-formed polymers and promote drawing. However, nature has engineered spiders and silkworms with benign ways of making silk fibers with high strength and toughness. Conceptually, their approach of chemically linking small functional units (i.e., proteins) into long chain molecules and solid fibrillar structures ``on-demand'' is fundamentally different from current synthetic fiber manufacturing methods. Drawing inspiration from nature, a method will be described that uses light to trigger a thiol-ene photopolymerization to rapidly transform reactive liquid mixtures into solid thread-like structures as they are forced out of a capillary at high speeds. Besides being manufactured without using solvents/volatile components or heat, these fibers are mechanically robust and have excellent chemical and thermal stability due to their crosslinked nature. During processing, the balance between curing kinetics, fiber flight time, and monomer mixture viscoelasticity is essential for the formation of defect free fibers. This work focuses on developing a universal operating diagram to show how the intricate interplay of gel time, flight time, and fluid relaxation time leads to the formation of uniform fibers and other undesirable fiber morphologies such as beads-on-string, fused fibers, non-uniform fibers, and droplets. This predictive capability enables adaptation of this spinning concept to all existing fiber spinning platforms, and customization of monomer formulations to target desired properties.

Gizzard worms

USGS Publications Warehouse

Tuggle, B.N.; Friend, M.

1999-01-01

Gizzard worms are comprised of several species of parasitic nematodes or roundworms of birds. Severe infections can result in birds becoming unthrifty and debilitated to the extent that they are more susceptible to predation and to infection by other disease agents. The two gizzard worms that are emphasized here are trichostrongylid nematodes that belong to the genera Amidostomum sp. and Epomidiostomum sp. These long (10–35 millimeter), sometimes coiled, threadlike roundworms are found just beneath the surface lining and the grinding pads of the gizzard, and they are most frequently found in waterfowl. Other species of gizzard worms are found in upland gamebirds such as grouse, in psitticine birds such as parakeets, and in passerine or perching birds such as robins in various parts of the world.

Phylogenetic placement of an unusual coral mushroom challenges the classic hypothesis of strict coevolution in the apterostigma pilosum group ant-fungus mutualism.

PubMed

Dentinger, Bryn T M; Lodge, D Jean; Munkacsi, Andrew B; Desjardin, Dennis E; McLaughlin, David J

2009-08-01

The approximately 50 million-year-old fungus-farming ant mutualism is a classic example of coevolution, involving ants that subsist on asexual, fungal biomass, in turn propagating the fungus clonally through nest-to-nest transmission. Most mutualistic ants cultivate two closely related groups of gilled mushrooms, whereas one small group of ants in the genus Apterostigma cultivates a distantly related lineage comprised of the G2 and G4 groups. The G2 and G4 fungi were previously shown to form a monophyletic group sister to the thread-like coral mushroom family Pterulaceae. Here, we identify an enigmatic coral mushroom that produces both fertile and sterile fruiting structures as the closest free-living relative of the G4 fungi, challenging the monophyly of the Apterostigma-cultivated fungi for the first time. Both nonparametric bootstrap and Bayesian posterior probability support the node leading to the G4 cultivars and a free-living Pterula mushroom. These data suggest three scenarios that contradict the hypothesis of strict coevolution: (1) multiple domestications, (2) escape from domestication, (3) selection of single cultivar lineages from an ancestral mixed-fungus garden. These results illustrate how incomplete phylogenies for coevolved symbionts impede our understanding of the patterns and processes of coevolution.

Demonstration of a Real Time Capability to Produce Tidal Heights and Currents for Naval Operational Use: A Cast Study for the West Coast of Africa (Liberia)

NASA Technical Reports Server (NTRS)

Mehra, Avichal; Anantharaj, Valentine; Payne, Steve; Kantha, Lakshmi

1996-01-01

This report documents an existing capability to produce operationally relevant products on sea level and currents from a tides/storm surge model for any coastal region around the world within 48 hours from the time of the request. The model is ready for transition to the Naval Oceanographic Office (NAVOCEANO) for potential contingency use anywhere around the world. A recent application to naval operations offshore Liberia illustrates this. Mississippi State University, in collaboration with the University of Colorado and NAVOCEANO, successfully deployed the Colorado University Rapidly Relocatable Nestable Tides and Storm Surge (CURReNTSS) model that predicts sea surface height, tidal currents and storm surge, and provided operational products on tidal sea level and currents in the littoral region off south-western coast of Africa. This report summarizes the results of this collaborative effort in an actual contingency use of the relocatable model, summarizes the lessons learned, and provides recommendations for further evaluation and transition of this modeling capability to operational use.

Toward a generation free of tuberculosis: TB disease and infection in individuals of college age in the United States.

PubMed

Shah, N S; Flood-Bryzman, A; Jeffries, C; Scott, J

2018-01-01

To assess the magnitude of active TB disease and latent TB infection (LTBI) in young adults of college age. Individuals who were aged 18-24 years in 2011 were used as a proxy for college students. Active TB cases reported to the 2011 US National TB Surveillance System (NTSS) were included. LTBI prevalence was calculated from the 2011-2012 National Health and Nutrition Examination Survey. The 2011 American Community Survey was used to calculate population denominators. Analyses were stratified by nativity. Active TB disease incidence among persons aged 18-24 years was 2.82/100,000, 18.8/100,000 among foreign-born individuals and 0.9/100,000 among US-born individuals. In 2011, 878 TB cases were reported; 629 (71.6%) were foreign-born. LTBI prevalence among persons of 18-24 years was 2.5%: 8.7% and 1.3% among foreign-born and US-born, respectively. Active screening and treatment programs for foreign-born young adults could identify TB cases earlier and provide an opportunity for prevention efforts.

Deficiency of renal dopaminergic-dependent natriuretic response to acute sodium load in black salt-sensitive subjects in contrast to salt-resistant subjects.

PubMed

Damasceno, A; Santos, A; Serrão, P; Caupers, P; Soares-da-Silva, P; Polónia, J

1999-12-01

To evaluate the involvement of the renal dopaminergic system in the natriuretic responses to acute saline load in salt-resistant (SR) and salt-sensitive (SS) black normotensive (NT) and hypertensive (HT) subjects. We studied the relationship between the urinary excretion of dopa, dopamine (DA) and its metabolite DOPAC and the natriuretic responses to acute volume expansion (2 l NaCl 0.9% over 2 h) in 20 black NT subjects (12 SR and 8 SS) and 19 black HT subjects (10 SS and 9 SR). Subjects received a low salt (LS) diet (40 mmol sodium/day) for 1 week and a high salt (HS) diet (300 mmol sodium/day) for 1 week; the sequence of the dietary regimens was randomized. Comparisons were made between the results before the saline infusion (baseline) and the results 2 h after the infusion. In all the groups saline infusion induced significant increases in urinary volume (ml/4 h) of two- to three-fold and in urinary sodium excretion (mmol/4 h) of three- to ten-fold; these increases were significantly greater during the HS diet than during the LS diet. Saline infusion significantly increased the mean arterial pressure (MAP) by 5 mmHg in HT-SS subjects and by 4-5 mmHg in NT-SS subjects, but the MAP did not changed in the NT-SR and HT-SR groups. Under the LS diet, saline infusion changed the DA excretion (in nmol/4 h) by -49+/-89 in HT-SS subjects, by 17+/-52 in NT-SS subjects, by 235+/-72 in HT-SR subjects and by 220+/-86 in NT-SR subjects (P < 0.05 between SR and SS subjects). The saline infusion-induced changes in DA excretion correlated significantly with the increases in urinary sodium excretion (r = 0.71, P < 0.01) in the NT-SR and HT-SR subjects under the LS diet, but not in the SR groups on the HS diet nor in the SS groups (HT and NT) on either diet. Saline infusion significantly reduced the DA/dopa ratio in SS (NT and HT) but not SR (NT and HT) subjects, whereas the DA/DOPAC (dihydroxyphenylacetic acid) ratios were similar in all the groups. The urinary dopaminergic system may participate in the natriuretic responses to acute sodium load only in SR subjects (NT and HT) and only under LS diets, but not in SS subjects (NT and HT). This strongly suggests that black NT- and HT-SS subjects have an underlying impairment in the activity of the renal dopaminergic system which may be associated with a reduced decarboxylation of dopa into DA.

Microplastics in the benthic invertebrates from the coastal waters of Kochi, Southeastern Arabian Sea.

PubMed

Naidu, S A; Ranga Rao, V; Ramu, K

2018-01-05

This study examined microplastic particles present in the benthic invertebrates Sternaspis scutata, Magelona cinta (deposit feeders) and Tellina sp. (suspension feeder) from the surface sediments of off-Kochi, southwest coast of India. The microplastic particles and thread-like fibres detected in these organisms were identified to be polystyrene by using DXR Raman microscope. Examination of the microplastic particle in Sternaspis scutata by epifluorescent microscopy showed fragmentation marks on the surface suggesting that the microplastic particle was degraded/weathered in nature. The study provides preliminary evidence of the presence of microplastics in benthic fauna from the coastal waters of India. However, further studies are required to understand the sources, distribution, fate and toxicity of the different types of microplastics in benthic invertebrates in order to identify any potential threats to higher trophic level organisms.

DNA Knots: Theory and Experiments

NASA Astrophysics Data System (ADS)

Sumners, D. W.

Cellular DNA is a long, thread-like molecule with remarkably complex topology. Enzymes that manipulate the geometry and topology of cellular DNA perform many vital cellular processes (including segregation of daughter chromosomes, gene regulation, DNA repair, and generation of antibody diversity). Some enzymes pass DNA through itself via enzyme-bridged transient breaks in the DNA; other enzymes break the DNA apart and reconnect it to different ends. In the topological approach to enzymology, circular DNA is incubated with an enzyme, producing an enzyme signature in the form of DNA knots and links. By observing the changes in DNA geometry (supercoiling) and topology (knotting and linking) due to enzyme action, the enzyme binding and mechanism can often be characterized. This paper will discuss some personal research history, and the tangle model for the analysis of site-specific recombination experiments on circular DNA.

Sparganosis of liver: a rare entity and review of literature.

PubMed

Khurana, Sumeeta; Appannanavar, Suma; Bhatti, Harinder Singh; Verma, Sanjay

2012-12-06

Humans are known to serve as the secondary intermediate host for some larval forms of canine or feline tapeworms. Sparganosis is caused by plerocercoid larva of Spirometra of which there are three main species; Spirometra mansoni (or Spirometra erinaceieuropaei), Spirometra mansonoides and Spirometra proliferum. A one-and-half-year-old patient presenting with febrile illness was diagnosed radiologically as a case of liver abscess. The aspirate from the abscess cavity had a thin thread-like worm which was identified as a larval stage of Pseudophyllidea that was further confirmed as belonging to genus Spirometra. Aspiration of the worm and antiparasitic therapy with metronidazole led to complete recovery. Reports of sparganosis from Indian subcontinent are scanty and these cases had involvement of brain, kidney and eye. To the best of our knowledge this is the first case of hepatic sparganosis from India.

Reconstruction of a helical prominence in 3D from IRIS spectra and images

NASA Astrophysics Data System (ADS)

Schmieder, B.; Zapiór, M.; López Ariste, A.; Levens, P.; Labrosse, N.; Gravet, R.

2017-10-01

Context. Movies of prominences obtained by space instruments e.g. the Solar Optical Telescope (SOT) aboard the Hinode satellite and the Interface Region Imaging Spectrograph (IRIS) with high temporal and spatial resolution revealed the tremendous dynamical nature of prominences. Knots of plasma belonging to prominences appear to travel along both vertical and horizontal thread-like loops, with highly dynamical nature. Aims: The aim of the paper is to reconstruct the 3D shape of a helical prominence observed over two and a half hours by IRIS. Methods: From the IRIS Mg II k spectra we compute Doppler shifts of the plasma inside the prominence and from the slit-jaw images (SJI) we derive the transverse field in the plane of the sky. Finally we obtain the velocity vector field of the knots in 3D. Results.We reconstruct the real trajectories of nine knots travelling along ellipses. Conclusions: The spiral-like structure of the prominence observed in the plane of the sky is mainly due to the projection effect of long arches of threads (up to 8 × 104 km). Knots run along more or less horizontal threads with velocities reaching 65 km s-1. The dominant driving force is the gas pressure. Movies associated to Figs. 1, 9, 10, and 13 are available at http://www.aanda.org

corona Is Required for Higher-Order Assembly of Transverse Filaments into Full-Length Synaptonemal Complex in Drosophila Oocytes

PubMed Central

Page, Scott L.; Khetani, Radhika S.; Lake, Cathleen M.; Nielsen, Rachel J.; Jeffress, Jennifer K.; Warren, William D.; Bickel, Sharon E.; Hawley, R. Scott

2008-01-01

The synaptonemal complex (SC) is an intricate structure that forms between homologous chromosomes early during the meiotic prophase, where it mediates homolog pairing interactions and promotes the formation of genetic exchanges. In Drosophila melanogaster, C(3)G protein forms the transverse filaments (TFs) of the SC. The N termini of C(3)G homodimers localize to the Central Element (CE) of the SC, while the C-termini of C(3)G connect the TFs to the chromosomes via associations with the axial elements/lateral elements (AEs/LEs) of the SC. Here, we show that the Drosophila protein Corona (CONA) co-localizes with C(3)G in a mutually dependent fashion and is required for the polymerization of C(3)G into mature thread-like structures, in the context both of paired homologous chromosomes and of C(3)G polycomplexes that lack AEs/LEs. Although AEs assemble in cona oocytes, they exhibit defects that are characteristic of c(3)G mutant oocytes, including failure of AE alignment and synapsis. These results demonstrate that CONA, which does not contain a coiled coil domain, is required for the stable ‘zippering’ of TFs to form the central region of the Drosophila SC. We speculate that CONA's role in SC formation may be similar to that of the mammalian CE proteins SYCE2 and TEX12. However, the observation that AE alignment and pairing occurs in Tex12 and Syce2 mutant meiocytes but not in cona oocytes suggests that the SC plays a more critical role in the stable association of homologs in Drosophila than it does in mammalian cells. PMID:18802461

Two New Species of the Simulium (Simulium) variegatum Species-Group of Black Flies (Diptera: Simuliidae) From Thailand.

PubMed

Takaoka, Hiroyuki; Srisuka, Wichai; Saeung, Atiporn

2017-09-01

Two new species of black flies, Simulium (Simulium) srisukai and S. (S.) kiewmaepanense, are described from specimens collected in Thailand. Both species are assigned to the Simulium variegatum species-group of the subgenus Simulium (Simulium) Latreille. They are characterized by the darkened female femora and tibiae and six inflated pupal gill filaments, and the darkened female tibiae and six ordinary thread-like pupal gill filaments, respectively. Taxonomic notes are given to separate these new species from 10 related species among the group. These new species represent the third and fourth species of the S. variegatum species-group from Thailand. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com Version of Record, first published online May 15, 2017 with fixed content and layout in compliance with Art. 8.1.3.2 ICZN.

Sparganosis of liver: a rare entity and review of literature

PubMed Central

Khurana, Sumeeta; Appannanavar, Suma; Bhatti, Harinder Singh; Verma, Sanjay

2012-01-01

Humans are known to serve as the secondary intermediate host for some larval forms of canine or feline tapeworms. Sparganosis is caused by plerocercoid larva of Spirometra of which there are three main species; Spirometra mansoni (or Spirometra erinaceieuropaei), Spirometra mansonoides and Spirometra proliferum. A one-and-half-year-old patient presenting with febrile illness was diagnosed radiologically as a case of liver abscess. The aspirate from the abscess cavity had a thin thread-like worm which was identified as a larval stage of Pseudophyllidea that was further confirmed as belonging to genus Spirometra. Aspiration of the worm and antiparasitic therapy with metronidazole led to complete recovery. Reports of sparganosis from Indian subcontinent are scanty and these cases had involvement of brain, kidney and eye. To the best of our knowledge this is the first case of hepatic sparganosis from India. PMID:23220827

Opposable spines facilitate fine and gross object manipulation in fire ants

NASA Astrophysics Data System (ADS)

Cassill, Deby; Greco, Anthony; Silwal, Rajesh; Wang, Xuefeng

2007-04-01

Ants inhabit diverse terrestrial biomes from the Sahara Desert to the Arctic tundra. One factor contributing to the ants’ successful colonization of diverse geographical regions is their ability to manipulate objects when excavating nests, capturing, transporting and rendering prey or grooming, feeding and transporting helpless brood. This paper is the first to report the form and function of opposable spines on the foretarsi of queens and workers used during fine motor and gross motor object manipulation in the fire ant, Solenopsis invicta. In conjunction with their mandibles, queens and workers used their foretarsi to grasp and rotate eggs, push or pull thread-like objects out of their way or push excavated soil pellets behind them for disposal by other workers. Opposable spines were found on the foretarsi of workers from seven of eight other ant species suggesting that they might be a common feature in the Formicidae.

Characterization of adhesive from oysters: A structural and compositional study

NASA Astrophysics Data System (ADS)

Alberts, Erik

The inability for man-made adhesives to set in wet or humid environments is an ongoing challenging the design of biomedical and marine adhesive materials. However, we see that nature has already overcome this challenge. Mussels, barnacles, oysters and sandcastle worms all have unique mechanisms by which they attach themselves to surfaces. By understanding what evolution has already spent millions of years perfecting, we can design novel adhesive materials inspired by nature's elegant designs. The well-studied mussel is currently the standard for design of marine inspired biomimetic polymers. In the work presented here, we aim to provide new insights into the adhesive produced by the eastern oyster, Crassostrea virginica. Unlike the mussel, which produces thread-like plaques comprised of DOPA containing-protein, the oyster secretes an organic-inorganic hybrid adhesive as it settles and grows onto a surface. This form of adhesion renders the oyster to be permanently fixed in place. Over time, hundreds of thousands of oyster grow and agglomerate to form extensive reef structures. These reefs are not only essential to survival of the oyster, but are also vital to intertidal ecosystems. While the shell of the oyster has been extensively studied, curiously, only a few conflicting insights have been made into the nature of the adhesive and contact zone between shell and substrate, and even lesfs information has been ascertained on organic and inorganic composition. In this work, we provide microscopy and histochemical studies to characterize the structure and composition of the adhesive, using oyster in the adult and juvenile stages of life. Preliminary work on extracting and characterizing organic components through collaborative help with solid-state NMR (SSNMR) and proteomics are also detailed here. We aim to provide a full, comprehensive characterization of oyster adhesive so that in the future, we may apply what we learn to the design of new materials.

Insights into Clostridium phytofermentans biofilm formation: aggregation, microcolony development and the role of extracellular DNA.

PubMed

Zuroff, Trevor R; Gu, Weimin; Fore, Rachel L; Leschine, Susan B; Curtis, Wayne R

2014-06-01

Biofilm formation is a critical component to the lifestyle of many naturally occurring cellulose-degrading microbes. In this work, cellular aggregation and biofilm formation of Clostridium phytofermentans, a cellulolytic anaerobic bacterium, was investigated using a combination of microscopy and analytical techniques. Aggregates included thread-like linkages and a DNA/protein-rich extracellular matrix when grown on soluble cellobiose. Similar dense biofilms formed on the surface of the model cellulosic substrate Whatman no. 1 filter paper. Following initially dispersed attachment, microcolonies of ~500 µm diameter formed on the filter paper after 6 days. Enzymic treatment of both the biofilm and cellular aggregates with DNase and proteinase resulted in significant loss of rigidity, pointing to the key role of extracellular DNA and proteins in the biofilm structure. A high-throughput biofilm assay was adapted for studying potential regulators of biofilm formation. Various media manipulations were shown to greatly impact biofilm formation, including repression in the presence of glucose but not the β(1→4)-linked disaccharide cellobiose, implicating a balance of hydrolytic activity and assimilation to maintain biofilm integrity. Using the microtitre plate biofilm assay, DNase and proteinase dispersed ~60 and 30 % of mature biofilms, respectively, whilst RNase had no impact. This work suggests that Clostridium phytofermentans has evolved a DNA/protein-rich biofilm matrix complementing its cellulolytic nature. These insights add to our current understanding of natural ecosystems as well as strategies for efficient bioprocess design. © 2014 The Authors.

Quantification of VOC emissions from paint spraying on a construction site using solid phase microextraction devices.

PubMed

Cheng, Wen-Hsi; Huang, Hsiao-Lin; Chen, Kang-Shin; Chang, Yu-Jen

2017-10-15

The objective of this study was to measure the emission of, and personal exposure to workers, volatile organic compound (VOC) during paint spraying on a construction site. Needle trap samplers (NTSs), which are a green solid phase microextraction sampling technology, were used to obtain air samples at a large music exhibition center. The standard active sampling method using charcoal tubes and a personal air pump, Method 1501, was simultaneously utilized at the sampling sites to assess the workers' VOC exposures. Analysis of the data thus obtained showed that benzene, toluene, ethylenebenzene, and xylenes (BTEXs) were the main emission compounds. Acetone and isobutyl alcohol, which are used as thinning solvents, were detected as minor emission compounds. The emitted concentrations of most compounds were lower than the legal emission limits in Taiwan except that of benzene, for which the 2-ppm time weighted average short-term exposure limit was exceeded. The packed divinylbenzene (DVB) in the NTS was observed under an environmental scanning electron microscope, and many fine aerosols were found to be deposited on the surface of the DVB adsorbents, causing VOC extraction efficiencies after the fifth sampling in the field to decline. Workers on construction sites should be protected from emissions of VOC and fine particulates to preserve their occupational health.

A new species of Illacme Cook & Loomis, 1928 from Sequoia National Park, California, with a world catalog of the Siphonorhinidae (Diplopoda, Siphonophorida).

PubMed

Marek, Paul E; Krejca, Jean K; Shear, William A

2016-01-01

Members of the family Siphonorhinidae Cook, 1895 are thread-like eyeless millipedes that possess an astounding number of legs, including one individual with 750. Due to their cryptic lifestyle, rarity in natural history collections, and sporadic study over the last century, the family has an unclear phylogenetic placement, and intrafamilial relationships remain unknown. Here we report the discovery of a second species of Illacme , a millipede genus notable for possessing the greatest number of legs of any known animal on the planet. Illacme tobini sp. n. is described from a single male collected in a cave in Sequoia National Park, California, USA. After 90 years since the description of Illacme , the species represents a second of the genus in California. Siphonorhinidae now includes Illacme Cook & Loomis, 1928 (two species, USA), Kleruchus Attems, 1938 (one species, Vietnam), Nematozonium Verhoeff, 1939 (one species, South Africa) and Siphonorhinus Pocock, 1894 (eight species, India, Indonesia, Madagascar, Vietnam).

A new species of Illacme Cook & Loomis, 1928 from Sequoia National Park, California, with a world catalog of the Siphonorhinidae (Diplopoda, Siphonophorida)

PubMed Central

Marek, Paul E.; Krejca, Jean K.; Shear, William A.

2016-01-01

Abstract Members of the family Siphonorhinidae Cook, 1895 are thread-like eyeless millipedes that possess an astounding number of legs, including one individual with 750. Due to their cryptic lifestyle, rarity in natural history collections, and sporadic study over the last century, the family has an unclear phylogenetic placement, and intrafamilial relationships remain unknown. Here we report the discovery of a second species of Illacme, a millipede genus notable for possessing the greatest number of legs of any known animal on the planet. Illacme tobini sp. n. is described from a single male collected in a cave in Sequoia National Park, California, USA. After 90 years since the description of Illacme, the species represents a second of the genus in California. Siphonorhinidae now includes Illacme Cook & Loomis, 1928 (two species, USA), Kleruchus Attems, 1938 (one species, Vietnam), Nematozonium Verhoeff, 1939 (one species, South Africa) and Siphonorhinus Pocock, 1894 (eight species, India, Indonesia, Madagascar, Vietnam). PMID:27833431

A detailed observation of the ejection and retraction of defense tissue acontia in sea anemone (Exaiptasia pallida).

PubMed

Lam, Julie; Cheng, Ya-Wen; Chen, Wan-Nan U; Li, Hsing-Hui; Chen, Chii-Shiarng; Peng, Shao-En

2017-01-01

Acontia, located in the gastrovascular cavity of anemone, are thread-like tissue containing numerous stinging cells which serve as a unique defense tissue against predators of the immobile acontiarian sea anemone. Although its morphology and biological functions, such as defense and digestion, have been studied, the defense behavior and the specific events of acontia ejection and retraction are unclear. The aim of this study is to observe and record the detailed process of acontia control in anemones. Observations reveal that the anemone, Exaiptasia pallida , possibly controls a network of body muscles and manipulates water pressure in the gastrovascular cavity to eject and retract acontia. Instead of resynthesizing acontia after each ejection, the retraction and reuse of acontia enables the anemone to respond quickly at any given time, thus increasing its overall survivability. Since the Exaiptasia anemone is an emerging model for coral biology, this study provides a foundation to further investigate the biophysics, neuroscience, and defense biology of this marine model organism.

A detailed observation of the ejection and retraction of defense tissue acontia in sea anemone (Exaiptasia pallida)

PubMed Central

Lam, Julie; Cheng, Ya-Wen; Chen, Wan-Nan U.; Li, Hsing-Hui; Chen, Chii-Shiarng

2017-01-01

Acontia, located in the gastrovascular cavity of anemone, are thread-like tissue containing numerous stinging cells which serve as a unique defense tissue against predators of the immobile acontiarian sea anemone. Although its morphology and biological functions, such as defense and digestion, have been studied, the defense behavior and the specific events of acontia ejection and retraction are unclear. The aim of this study is to observe and record the detailed process of acontia control in anemones. Observations reveal that the anemone, Exaiptasia pallida, possibly controls a network of body muscles and manipulates water pressure in the gastrovascular cavity to eject and retract acontia. Instead of resynthesizing acontia after each ejection, the retraction and reuse of acontia enables the anemone to respond quickly at any given time, thus increasing its overall survivability. Since the Exaiptasia anemone is an emerging model for coral biology, this study provides a foundation to further investigate the biophysics, neuroscience, and defense biology of this marine model organism. PMID:28243530

Vitreous changes after intravitreal bevacizumab monotherapy for retinopathy of prematurity: a case series.

PubMed

Shoeibi, Nasser; Hosseini, Seyedeh Maryam; Banaee, Touka; Ansari-Astaneh, Mohammad-Reza; Abrishami, Majid; Ahmadieh, Hamid

2018-01-01

Reporting a special clinical finding after intravitreal bevacizumab monotherapy for retinopathy of prematurity. In a retrospective case series, the clinical courses of five premature infants with similar vitreous changes after a single dose of intravitreal bevacizumab (IVB) injection without additional laser therapy were reported. The mean post-conceptional age at IVB injection was 39.8 ± 2.2 (range 37-43) weeks. Localized vitreous syneresis and linear fibrotic vitreous condensation occurred 8.2 ± 2.3 weeks after IVB monotherapy in our patients (15.5% of injections). The mean last post injection visit was 61.6 ± 5.3 weeks (post-conceptional age). Further regression and complete retinal vascularization occurred in all patients. Thread-like vitreous condensation with localized vitreous liquefaction may be related to involutional ROP disease itself, combined to anti VEGF therapy and may be a predictor factor for further regression and retinal vascularization. The case series describes a successful response to anti-VEGF monotherapy with no further complications.

An easily fabricated three-dimensional threaded lemniscate-shaped micromixer for a wide range of flow rates

PubMed Central

Rafeie, Mehdi; Welleweerd, Marcel; Hassanzadeh-Barforoushi, Amin; Asadnia, Mohsen; Olthuis, Wouter; Ebrahimi Warkiani, Majid

2017-01-01

Mixing fluid samples or reactants is a paramount function in the fields of micro total analysis system (μTAS) and microchemical processing. However, rapid and efficient fluid mixing is difficult to achieve inside microchannels because of the difficulty of diffusive mass transfer in the laminar regime of the typical microfluidic flows. It has been well recorded that the mixing efficiency can be boosted by migrating from two-dimensional (2D) to three-dimensional (3D) geometries. Although several 3D chaotic mixers have been designed, most of them offer a high mixing efficiency only in a very limited range of Reynolds numbers (Re). In this work, we developed a 3D fine-threaded lemniscate-shaped micromixer whose maximum numerical and empirical efficiency is around 97% and 93%, respectively, and maintains its high performance (i.e., >90%) over a wide range of 1 < Re < 1000 which meets the requirements of both the μTAS and microchemical process applications. The 3D micromixer was designed based on two distinct mixing strategies, namely, the inducing of chaotic advection by the presence of Dean flow and diffusive mixing through thread-like grooves around the curved body of the mixers. First, a set of numerical simulations was performed to study the physics of the flow and to determine the essential geometrical parameters of the mixers. Second, a simple and cost-effective method was exploited to fabricate the convoluted structure of the micromixers through the removal of a 3D-printed wax structure from a block of cured polydimethylsiloxane. Finally, the fabricated mixers with different threads were tested using a fluorescent microscope demonstrating a good agreement with the results of the numerical simulation. We envisage that the strategy used in this work would expand the scope of the micromixer technology by broadening the range of efficient working flow rate and providing an easy way to the fabrication of 3D convoluted microstructures. PMID:28798843

An easily fabricated three-dimensional threaded lemniscate-shaped micromixer for a wide range of flow rates.

PubMed

Rafeie, Mehdi; Welleweerd, Marcel; Hassanzadeh-Barforoushi, Amin; Asadnia, Mohsen; Olthuis, Wouter; Ebrahimi Warkiani, Majid

2017-01-01

Mixing fluid samples or reactants is a paramount function in the fields of micro total analysis system (μTAS) and microchemical processing. However, rapid and efficient fluid mixing is difficult to achieve inside microchannels because of the difficulty of diffusive mass transfer in the laminar regime of the typical microfluidic flows. It has been well recorded that the mixing efficiency can be boosted by migrating from two-dimensional (2D) to three-dimensional (3D) geometries. Although several 3D chaotic mixers have been designed, most of them offer a high mixing efficiency only in a very limited range of Reynolds numbers ( Re ). In this work, we developed a 3D fine-threaded lemniscate-shaped micromixer whose maximum numerical and empirical efficiency is around 97% and 93%, respectively, and maintains its high performance (i.e., >90%) over a wide range of 1 <  Re  < 1000 which meets the requirements of both the μTAS and microchemical process applications. The 3D micromixer was designed based on two distinct mixing strategies, namely, the inducing of chaotic advection by the presence of Dean flow and diffusive mixing through thread-like grooves around the curved body of the mixers. First, a set of numerical simulations was performed to study the physics of the flow and to determine the essential geometrical parameters of the mixers. Second, a simple and cost-effective method was exploited to fabricate the convoluted structure of the micromixers through the removal of a 3D-printed wax structure from a block of cured polydimethylsiloxane. Finally, the fabricated mixers with different threads were tested using a fluorescent microscope demonstrating a good agreement with the results of the numerical simulation. We envisage that the strategy used in this work would expand the scope of the micromixer technology by broadening the range of efficient working flow rate and providing an easy way to the fabrication of 3D convoluted microstructures.

Facies implications of Trichichnus and Chondrites in turbidites and hemipelagites, Marnoso-arenacea Formation (Miocene), northern Apennines, Italy

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

McBride, E.F.; Picard, M.D.

Trichichnus, a thread-like burrow possibly the work of sipunculan worms, is widespread in Bouma E (turbidite claystone) and H (hemipelagic claystone) layers and some thin turbidite sandstone beds in basin-plain and outer fan-lobe deposits of the Marnoso-arenacea Formation. Trichichnus closely resembles that described elsewhere in chalk and marlstone, although the burrows are smaller (mean diameter=0.13 mm) and burrow curvature is tighter. Trichichnus fills are darker than the host claystone because of high organic content and disseminated pyrite. Any distinctive internal structure of the burrow wall or fill was destroyed by pyrite growth. Trichichnus is most abundant in Bouma E layers,more » where burrow spacing ranges from 0.4 to 50 cm and burrows extend to depths of 160 cm. The Trichichnus maker commonly burrowed vertically down through E and D layers (clay and silt) and then horizontally on top of C layers (sand). The burrows also vertically penetrate Bouma C sandstone layers up to 6 cm thick, but they are rare in beds thicker than 3 cm. They are less abundant or not well displayed in H layers where Chondrites predominates. Trichichnus overprints Chondrites. Following deposition of the Contessa megaturbidite, which exceeds 9 m in thickness, the sediment surface was repopulated chiefly by Trichichnus and Chondrites producers. Trichichnus extends 160 cm below the top of the Contessa, whereas Chondrites extend only to 64 cm. This suggests a greater tolerance of Trichichnus makers to low in situ oxygen levels. The near absence of laminations in the E division of the Contessa megabed may be the result of Trichichnus burrows that were not pyritized and which lack textural identity.« less

Activated actin-depolymerizing factor/cofilin sequesters phosphorylated microtubule-associated protein during the assembly of alzheimer-like neuritic cytoskeletal striations.

PubMed

Whiteman, Ineka T; Gervasio, Othon L; Cullen, Karen M; Guillemin, Gilles J; Jeong, Erica V; Witting, Paul K; Antao, Shane T; Minamide, Laurie S; Bamburg, James R; Goldsbury, Claire

2009-10-14

In Alzheimer's disease (AD), rod-like cofilin aggregates (cofilin-actin rods) and thread-like inclusions containing phosphorylated microtubule-associated protein (pMAP) tau form in the brain (neuropil threads), and the extent of their presence correlates with cognitive decline and disease progression. The assembly mechanism of these respective pathological lesions and the relationship between them is poorly understood, yet vital to understanding the causes of sporadic AD. We demonstrate that, during mitochondrial inhibition, activated actin-depolymerizing factor (ADF)/cofilin assemble into rods along processes of cultured primary neurons that recruit pMAP/tau and mimic neuropil threads. Fluorescence resonance energy transfer analysis revealed colocalization of cofilin-GFP (green fluorescent protein) and pMAP in rods, suggesting their close proximity within a cytoskeletal inclusion complex. The relationship between pMAP and cofilin-actin rods was further investigated using actin-modifying drugs and small interfering RNA knockdown of ADF/cofilin in primary neurons. The results suggest that activation of ADF/cofilin and generation of cofilin-actin rods is required for the subsequent recruitment of pMAP into the inclusions. Additionally, we were able to induce the formation of pMAP-positive ADF/cofilin rods by exposing cells to exogenous amyloid-beta (Abeta) peptides. These results reveal a common pathway for pMAP and cofilin accumulation in neuronal processes. The requirement of activated ADF/cofilin for the sequestration of pMAP suggests that neuropil thread structures in the AD brain may be initiated by elevated cofilin activation and F-actin bundling that can be caused by oxidative stress, mitochondrial dysfunction, or Abeta peptides, all suspected initiators of synaptic loss and neurodegeneration in AD.

Noncovalent Polymerization of Mesogens Crystallizes Lysozyme: Correlation between Nonamphiphilic Lyotropic Liquid Crystal Phase and Protein Crystal Formation

PubMed Central

Simon, Karen A.; Shetye, Gauri S.; Englich, Ulrich; Wu, Lei; Luk, Yan-Yeung

2011-01-01

Crystallization of proteins is important for fundamental studies and biopharmaceutical development but remains largely an empirical science. Here, we report the use of organic salts that can form a class of unusual non-amphiphilic lyotropic liquid crystals to crystallize the protein lysozyme. Certain non-amphiphilic organic molecules with fused aromatic rings and two charges can assemble into stable thread-like noncovalent polymers that may further form liquid crystal phases in water, traditionally termed chromonic liquid crystals. Using five of these mesogenic molecules as additives to induce protein crystallization, we discover that molecules that can form liquid crystal phases in water are highly effective at inducing the crystal formation of lysozyme, even at concentrations significantly lower than that required for forming liquid crystal phases. This result reveals an example of inducing protein crystallization by the molecular assembly of the additives, and is consistent with a new mechanism by which the strong hydration of an assembly process provides a gradual means to compete for the water molecules to enable solvated proteins to form crystals. PMID:21786812

Morphological and molecular identification of Sarcocystis arctica sarcocysts in three red foxes (Vulpes vulpes) from the Czech Republic.

PubMed

Pavlásek, Ivan; Máca, Ondřej

2017-10-01

Muscular sarcocystosis by Sarcocystis arctica was found for the first time in the Czech Republic, in different muscles of red fox (Vulpes vulpes). Cysts were slim, elongated, thread-like, whitish, 1-7mm long, and 206-270μm wide; bradyzoites were 7.9×2.7μm in unstained wet mounts and 9.2×2.9μm in cyst Giemsa-stained smears. The cyst wall was thin, with short villi-like protrusions, and no host response was observed in the histological sections. Examination of the distribution and intensity of sarcocysts in 17 different muscle groups revealed that the highest intensity was in the cranial tibial muscle (>15 cysts in compressoria), followed by the diaphragm, forearm, and other groups (with intensities of 3-15 cysts in compressoria). Sarcocysts were detected in 3 out of 86 foxes. Genetic characterization at 18S rRNA, 28S rRNA, ITS1 and cox1, consistently showed that the species was identical with S. arctica. Interestingly, this protozoan was also detected as a co-infection in 3 foxes with the nematode Trichinella spp. for the first time. Copyright © 2017 Elsevier B.V. All rights reserved.

Freezing behavior of adherent neuron-like cells and morphological change and viability of post-thaw cells.

PubMed

Uemura, Makoto; Ishiguro, Hiroshi

2015-04-01

Freezing of nerve cells forming a neuronal network has largely been neglected, despite the fact that the cryopreservation of nerve cells benefits the study of cells in the areas of medicine and poison screening. Freezing of nerve cells is also attractive for studying cell morphology because of the characteristic long, thread-like neurites extending from the cell body. In the present study, freezing of neuron-like cells adhering to the substrate (differentiated PC12 cells), in physiological saline, was investigated in order to understand the fundamental freezing and thawing characteristics of nerve cells with neurites. The microscopic freezing behavior of cells under different cooling rates was observed. Next, the post-thaw morphological changes in the cells, including the cytoskeleton, were investigated and post-thaw cell viability was evaluated by dye exclusion using propidium iodide. Two categories of morphological changes, beading and shortening of the neurites, were found and quantified. Also, the morphological changes of neurites due to osmotic stress from sodium chloride were studied to gain a better understanding of causation. The results showed that morphological changes and cell death were promoted with a decrease in end temperature during freezing. Copyright © 2015 Elsevier Inc. All rights reserved.

In vivo three-dimensional imaging of human corneal nerves using Fourier-domain optical coherence tomography

NASA Astrophysics Data System (ADS)

Shin, Jun Geun; Hwang, Ho Sik; Eom, Tae Joong; Lee, Byeong Ha

2017-01-01

We have employed Fourier-domain optical coherence tomography (FD-OCT) to achieve corneal nerve imaging, which could be useful in surgical planning and refractive surgery. Because the three-dimensional (3-D) images of the corneal nerves were acquired in vivo, unintentional movement of the subject during the measurement led to imaging artifacts. These artifacts were compensated for with a series of signal processing techniques, namely realigning A-scan images to flatten the boundary and cross-correlating adjacent B-scan images. To overcome the undesirably large signal from scattering at the corneal surface and iris, volume rendering and maximum intensity projections were performed with only the data taken in the stromal region of the cornea, which is located between 200 and 500 μm from the corneal surface. The 3-D volume imaging of a 10×10 mm2 area took 9.8 s, which is slightly shorter than the normal tear breakup time. This allowed us to image the branched and threadlike corneal nerve bundles within the human eye. The experimental results show that FD-OCT systems have the potential to be useful in clinical investigations of corneal nerves and by minimizing nerve injury during clinical or surgical procedures.

Chronic Traumatic Encephalopathy in Athletes: Progressive Tauopathy following Repetitive Head Injury

PubMed Central

McKee, Ann C.; Cantu, Robert C.; Nowinski, Christopher J.; Hedley-Whyte, E. Tessa; Gavett, Brandon E.; Budson, Andrew E.; Santini, Veronica E.; Lee, Hyo-Soon; Kubilus, Caroline A.; Stern, Robert A.

2009-01-01

Since the 1920s, it has been known that the repetitive brain trauma associated with boxing may produce a progressive neurological deterioration, originally termed “dementia pugilistica” and more recently, chronic traumatic encephalopathy (CTE). We review the 47 cases of neuropathologically verified CTE recorded in the literature and document the detailed findings of CTE in 3 professional athletes: one football player and 2 boxers. Clinically, CTE is associated with memory disturbances, behavioral and personality changes, Parkinsonism, and speech and gait abnormalities. Neuropathologically, CTE is characterized by atrophy of the cerebral hemispheres, medial temporal lobe, thalamus, mammillary bodies, and brainstem, with ventricular dilatation and a fenestrated cavum septum pellucidum. Microscopically, there are extensive tau-immunoreactive neurofibrillary tangles, astrocytic tangles, and spindle-shaped and threadlike neurites throughout the brain. The neurofibrillary degeneration of CTE is distinguished from other tauopathies by preferential involvement of the superficial cortical layers, irregular, patchy distribution in the frontal and temporal cortices, propensity for sulcal depths, prominent perivascular, periventricular and subpial distribution, and marked accumulation of tau-immunoreactive astrocytes. Deposition of beta amyloid, most commonly as diffuse plaques, occurs in fewer than half the cases. CTE is a neuropathologically distinct, slowly progressive tauopathy with a clear environmental etiology. PMID:19535999

Conidiogenesis-related DNA photolyase gene in Beauveria bassiana.

PubMed

Lee, Se Jin; Lee, Mi Rong; Kim, Sihyeon; Kim, Jong Cheol; Park, So Eun; Shin, Tae Young; Kim, Jae Su

2018-03-01

Beauveria bassiana is an entomopathogenic fungi used in environmentally mindful pest management. Its main active ingredient, conidia, is commercially available as a fungal biopesticide. Many studies of conidia production have focused on how to optimize culture conditions for maximum productivity and stability against unfavorable abiotic factors. However, understanding of how conidiogenesis-related genes provide improved conidial production remains unclear. In this study, we focus on identifying conidiogenesis-related genes in B. bassiana ERL1170 using a random mutagenesis technique. Transformation of ERL1170 using restriction enzyme-mediated integration generated one morphologically different transformant, ERL1170-pABeG #163. The transformant was confirmed to represent B. bassiana, and the binary vector was successfully integrated into the genome of ERL1170. Compared to the wild type, transformant #163 showed very slow hyphal growth and within 6 days only produced <1 × 10 6  conidia/0.28 cm 2 agar block (wild type: 6.2 × 10 7  conidia/agar block). Transformant #163 also exhibited different morphology than the wild type, including thicker hyphae with some club-shaped parts. In contrast, the typical morphology of wild type B. bassiana exhibits thread-like hyphae and conidiophore structures and circular conidia. To determine the location of the randomly inserted DNA, we conducted thermal asymmetric interlaced (TAIL) PCR and Escherichia coli cloning to clearly sequence the disrupted region. We identified one colony (colony No. 7) with an insertion site identified as DNA photolyase. This was confirmed through a gene knock-out study. It is possible the gene that encodes for DNA photolyase was disrupted during the insertion process and might be involved in fungal conidiogenesis. This work serves as a platform for exploring the function of a variety of B. bassiana genes involved in pest management and their downstream processing. Copyright © 2018 Elsevier Inc. All rights reserved.

High Performance Carbon Nanotube Yarn Supercapacitors with a Surface-Oxidized Copper Current Collector.

PubMed

Zhang, Daohong; Wu, Yunlong; Li, Ting; Huang, Yin; Zhang, Aiqing; Miao, Menghe

2015-11-25

Threadlike linear supercapacitors have demonstrated high potential for constructing fabrics to power electronic textiles (eTextiles). To improve the cyclic electrochemical performance and to produce power fabrics large enough for practical applications, a current collector has been introduced into the linear supercapcitors to transport charges produced by active materials along the length of the supercapacitor with high efficiency. Here, we first screened six candidate metal filaments (Pt, Au, Ag, AuAg, PtCu, and Cu) as current collectors for carbon nanotube (CNT) yarn-based linear supercapacitors. Although all of the metal filaments significantly improved the electrochemical performance of the linear supercapacitor, two supercapacitors constructed from Cu and PtCu filaments, respectively, demonstrate far better electrochemical performance than the other four supercapacitors. Further investigation shows that the surfaces of the two Cu-containing filaments are oxidized by the surrounding polymer electrolyte in the electrode. While the unoxidized core of the Cu-containing filaments remains highly conductive and functions as a current collector, the resulting CuO on the surface is an electrochemically active material. The linear supercapacitor architecture incorporating dual active materials CNT + Cu extends the potential window from 1.0 to 1.4 V, leading to significant improvement to the energy density and power density.

Plasma vitrification of asbestos fibers

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

Camacho, S.L.

Asbestos is a mineral in the form of long, thread-like fibers. Asbestos fibers have been among the best insulators of pipes, boilers, ducts, tanks, etc., in buildings, ships, and industrial furnaces. Over 150,000 metric tons of asbestos were consumed in the United States in 1984. The Environmental Protection Agency has declared asbestos fibers a known human carcinogen. And today, asbestos insulators are being replaced by manmade non-hazardous fibers. Millions of tons of replaced asbestos fiber insulators are in storage, awaiting the demonstration of effective alternative disposal technologies. Plasma vitrification has been demonstrated during May, June and July 1995 as amore » viable, cost-effective, safe technology for asbestos fiber disposal. A low-mass plasma arc heater is submerged under the waste asbestos insulating materials, and the intense heat of the plasma flame heats and melts the fibers. The by-product is dark, non-hazardous glass pellets. The vitrification process renders the asbestos waste safe for use as road construction aggregates or other fill materials. This paper will describe the results of start-up of a 1 ton-per-hour Plasma Mobile Asbestos Vitrification (MAV) Plant at a DOD Site in Port Clinton, Ohio. The Plasma MAV Plant is being demonstrated for the on-site disposal of 1.5 million pounds of Amosite asbestos fibers.« less

Actinomycetes benefaction role in soil and plant health.

PubMed

Bhatti, Asma Absar; Haq, Shamsul; Bhat, Rouf Ahmad

2017-10-01

Actinomycetes are aerobic, spore forming gram-positive bacteria, belonging to the order actinomycetales characterized with substrate and aerial mycelium growth. They are the most abundant organisms that form thread-like filaments in the soil and are responsible for characteristically "earthy" smell of freshly turned healthy soil. They play major roles in the cycling of organic matter; inhibit the growth of several plant pathogens in the rhizosphere and decompose complex mixtures of polymer in dead plant, animal and fungal material results in production of many extracellular enzymes which are conductive to crop production. The major contribution in biological buffering of soils, biological control of soil environments by nitrogen fixation and degradation of high molecular weight compounds like hydrocarbons in the polluted soils are remarkable characteristics of actinomycetes. Besides this, they are known to improve the availability of nutrients, minerals, enhance the production of metabolites and promote plant growth regulators. Furthermore, actinobacteria do not contaminate the environment instead, they help sustainably in improving soil health by formation and stabilization of compost piles, formation of stable humus and combine with other soil microorganisms in breaking down the tough plant residues such as cellulose and animal residues to maintain the biotic equilibrium of soil by cooperating with nutrient cycling. Copyright © 2017 Elsevier Ltd. All rights reserved.

Multiscale Modeling of the Effects of Salt and Perfume Raw Materials on the Rheological Properties of Commercial Threadlike Micellar Solutions.

PubMed

Tang, Xueming; Zou, Weizhong; Koenig, Peter H; McConaughy, Shawn D; Weaver, Mike R; Eike, David M; Schmidt, Michael J; Larson, Ronald G

2017-03-23

We link micellar structures to their rheological properties for two surfactant body-wash formulations at various concentrations of salts and perfume raw materials (PRMs) using molecular simulations and micellar-scale modeling, as well as traditional surfactant packing arguments. The two body washes, namely, BW-1EO and BW-3EO, are composed of sodium lauryl ethylene glycol ether sulfate (SLEnS, where n is the average number of ethylene glycol repeat units), cocamidopropyl betaine (CAPB), ACCORD (which is a mixture of six PRMs), and NaCl salt. BW-3EO is an SLE3S-based body wash, whereas BW-1EO is an SLE1S-based body wash. Additional PRMs are also added into the body washes. The effects of temperature, salt, and added PRMs on micellar lengths, breakage times, end-cap free energies, and other properties are obtained from fits of the rheological data to predictions of the "Pointer Algorithm" [ Zou , W. ; Larson , R.G. J. Rheol. 2014 , 58 , 1 - 41 ], which is a simulation method based on the Cates model of micellar dynamics. Changes in these micellar properties are interpreted using the Israelachvili surfactant packing argument. From coarse-grained molecular simulations, we infer how salt modifies the micellar properties by changing the packing between the surfactant head groups, with the micellar radius remaining nearly constant. PRMs do so by partitioning to different locations within the micelles according to their octanol/water partition coefficient P OW and chemical structures, adjusting the packing of the head and/or tail groups, and by changing the micelle radius, in the case of a large hydrophobic PRM. We find that relatively hydrophilic PRMs with log P OW < 2 partition primarily to the head group region and shrink micellar length, decreasing viscosity substantially, whereas more hydrophobic PRMs, with log P OW between 2 and 4, mix with the hydrophobic surfactant tails within the micellar core and slightly enhance the viscosity and micelle length, which is consistent with the packing argument. Large and very hydrophobic PRMs, with log P OW > 4, are isolated deep inside the micelle, separating from the tails and swelling the radius of the micelle, leading to shorter micelles and much lower viscosities, leading eventually to swollen-droplet micelles.

Clonal Differences between Non-Typhoidal Salmonella (NTS) Recovered from Children and Animals Living in Close Contact in The Gambia

PubMed Central

Dione, Michel M.; Ikumapayi, Usman N.; Saha, Debasish; Mohammed, Nuredin I.; Geerts, Stanny; Ieven, Margareta; Adegbola, Richard A.; Antonio, Martin

2011-01-01

Background Non-Typhoidal Salmonella (NTS) is an important cause of invasive bacterial disease and associated with mortality in Africa. However, little is known about the environmental reservoirs and predominant modes of transmission. Our study aimed to study the role of domestic animals in the transmission of NTS to humans in rural area of The Gambia. Methodology Human NTS isolates were obtained through an active population-based case-control surveillance study designated to determine the aetiology and epidemiology of enteric infections covering 27,567 Gambian children less than five years of age in the surveillance area. Fourteen children infected with NTS were traced back to their family compounds and anal swabs collected from 210 domestic animals present in their households. Identified NTSs were serotyped and genotyped by multi-locus sequencing typing. Principal Findings NTS was identified from 21/210 animal sources in the households of the 14 infected children. Chickens carried NTS more frequently than sheep and goats; 66.6%, 28.6% and 4.8% respectively. The most common NTS serovars were S. Colindale in humans (21.42%) and S. Poona in animals (14.28%). MLST on the 35 NTS revealed four new alleles and 24 sequence types (ST) of which 18 (75%) STs were novel. There was no overlap in serovars or genotypes of NTS recovered from humans or animal sources in the same household. Conclusion Our results do not support the hypothesis that humans and animals in close contact in the same household carry genotypically similar Salmonella serovars. These findings form an important baseline for future studies of transmission of NTS in humans and animals in Africa. PMID:21655353

Aggregation behavior of sodium lauryl ether sulfate with a positively bicharged organic salt and effects of the mixture on fluorescent properties of conjugated polyelectrolytes.

PubMed

Tang, Yongqiang; Liu, Zhang; Zhu, Linyi; Han, Yuchun; Wang, Yilin

2015-02-24

The aggregation behavior of anionic single-chain surfactant sodium lauryl ether sulfate containing three ether groups (SLE3S) with positively bicharged organic salt 1,2-bis(2-benzylammoniumethoxy)ethane dichloride (BEO) has been investigated in aqueous solution, and the effects of the BEO/SLE3S aggregate transitions on the fluorescent properties of anionic conjugated polyelectrolyte MPS-PPV with a larger molecular weight and cationic conjugated oligoelectrolyte DAB have been evaluated. Without BEO, SLE3S does not affect the fluorescent properties of MPS-PPV and only affects the fluorescent properties of DAB at a higher SLE3S concentration. With the addition of BEO, SLE3S and BEO form gemini-like surfactant (SLE3S)2-BEO. When the BEO/SLE3S molar ratio is fixed at 0.25, with increasing the BEO/SLE3S concentration, the BEO/SLE3S mixture forms large, loosely arranged aggregates and then transforms to closely packed spherical aggregates and finally to long thread-like micelles. The photoluminescence (PL) intensity of MPS-PPV varies with the morphologies of the BEO/SLE3S aggregates, while the PL intensity of DAB is almost independent of the aggregate morphologies. The results demonstrate that gemini-like surfactants formed through intermolecular interactions can effectively adjust the fluorescent properties of conjugated polyelectrolytes.

Eulimdana clava (Nematoda: Filarioidea) infection in domestic pigeons (Columba livia domestica): Molecular characterization and pathological changes.

PubMed

Šupić, Jovana; Alić, Alma Šeho; Hasanić, Melida; Goletić, Šejla; Duscher, Georg G; Hodžić, Adnan; Alić, Amer

2018-02-15

Filarial nematodes of the Eulimdana genus inhabit subcutaneous tissue of various avian species, mostly Charadriiforme birds. In domestic pigeons, E. clava is the only species recorded in the subcutaneous tissue in a number of isolated cases. In the present study, we discuss the morphology and histopathology of filarial nematodes recovered from subcutaneous tissue of domestic pigeons in Bosnia and Herzegovina. In total 110 pigeons were submitted to necropsy at the Department of Pathology of the Faculty of Veterinary Medicine in Sarajevo. At necropsy, in four pigeons (3.6%) numerous thread-like 0.9-2.1 cm long nematode parasites were observed in the subcutaneous tissue, peritracheal and periesophageal connective tissue. In one pigeon, the parasites were also found free in the body cavity around the heart and lungs. In addition, several 80-90 μm long microfilariae were noted in the tissue cross-sections. No significant lesions were observed associated with adult parasites or microfilariae. Based on morphology, host species and localization detected parasites were identified as E. clava. Molecular analyses of the cox1 and 12S rRNA nucleotide sequences herein generated revealed the close genetic relationship to other filarioid nematodes. The importance of the nematodes in pigeons and the lack of sequences in genetic databases for comparison of avian filarial parasites are emphasized. Copyright © 2018 Elsevier B.V. All rights reserved.

Laccase Production from a Temperature and pH Tolerant Fungal Strain of Trametes hirsuta (MTCC 11397).

PubMed

Dhakar, Kusum; Pandey, Anita

2013-01-01

Laccase production by a temperature and pH tolerant fungal strain (GBPI-CDF-03) isolated from a glacial site in Indian Himalayan Region (IHR) has been investigated. The fungus developed white cottony mass on potato dextrose agar and revealed thread-like mycelium under microscope. ITS region analysis of fungus showed its 100% similarity with Trametes hirsuta. The fungus tolerated temperature from 4 to 48°C ± 2 (25°C opt.) and pH 3-13 (5-7 opt.). Molecular weight of laccase was determined approximately 45 kDa by native PAGE. Amplification of laccase gene fragment (corresponding to the copper-binding conserved domain) contained 200 bp. The optimum pH for laccase production, at optimum growth temperature, was determined between 5.5 and 7.5. In optimization experiments, fructose and ammonium sulfate were found to be the best carbon and nitrogen sources, respectively, for enhancing the laccase production. Production of laccase was favored by high carbon/nitrogen ratio. Addition of CuSO4 (up to 1.0 mM) induced laccase production up to 2-fold, in case of 0.4 mM concentration. Addition of organic solvents also induced the production of laccase; acetone showed the highest (2-fold) induction. The study has implications in bioprospecting of ecologically resilient microbial strains.

Occurrence of Colombian datura virus in Brugmansia hybrids, Physalis peruviana L. and Solanum muricatum Ait. in Hungary.

PubMed

Salamon, P; Palkovics, L

2005-01-01

Colombian datura virus (CDV) has been found to infect angel trumpets (Brugmansia spp.) frequently and cape gooseberry (Physalis peruviana) and pepino (Solanum muricatum) sporadically in Hungary. A CDV BRG/H isolate was characterized. It had flexuous thread-like virions of about 750 x 12 nm in size. Host range and symptomathological studies revealed its great similarity to authentic CDV isolates. Nicotiana tabacum cultivars and lines resistant to Potato virus Y (PVYN) either genically or transgenically proved highly susceptible to the BRG/H isolate. Tomato (L. esculentum cvs.) was systemically susceptible to this isolate, but some lines of Lycopersicon hirsutum and L. peruvianum turned out to be resistant. Browallia demissa, Ipomoea purpurea, N. megalosiphon and S. scabrum were demonstrated as new experimental hosts of CDV. The BRG/ H isolate proved to be transmissible by the aphid Myzus persicae Sulz. in a non-persistent manner. Potyvirus-specific coat protein (CP) gene sequences of about 1700 bp from angel trumpet, cape gooseberry and pepino plants were amplified by RT-PCR. The cloned BRG/H CP gene showed a 99.12-99.31% identity with other CDV isolates. CDV has been found for the first time to infect naturally cape gooseberry and pepino. Since the botanical genus name of original hosts of CDV has changed from Datura to Brugmansia, we propose to change the virus name from CDV to Angel trumpet mosaic virus (ATMV).

MOLECULAR SYSTEMATICS OF THE AVIAN SCHISTOSOME GENUS TRICHOBILHARZIA (TREMATODA: SCHISTOSOMATIDAE) IN NORTH AMERICA

PubMed Central

Brant, Sara V.; Loker, Eric S.

2010-01-01

Trichobilharzia is a genus of thread-like schistosomes with a cosmopolitan distribution in birds. Species of Trichobilharzia achieve notoriety as major etiological agents of cercarial dermatitis, or swimmer’s itch. There are 40 species described in the literature, for which the majority lacks molecular sequence information. To better understand the phylogenetic relationships, diversity, species boundaries, host use, and geographic distribution of this genus, we surveyed 378 birds and over 10,000 snails from North America. The phylogenetic analysis was based on nuclear 18S, 28S rDNA, internal transcribed spacer region and mitochondrial cytochrome oxidase I sequence data. Specimens were recovered that could be related to 6 of the 14 described species of Trichobilharzia from North America (T. physellae, T. querquedulae, T. szidati, T. stagnicolae, T. franki, and T. brantae). An additional 5 lineages were found that could not be related directly to previously described species. Trichobilharzia brantae, transmitted by Gyraulus parvus, grouped outside the clade containing the recognized species of Trichobilharzia. A subgroup of the Trichobilharzia clade designated Clade Q was comprised of closely related species whose adults and eggs are similar, yet the European species use lymnaeids whereas the North American species use physids as snail hosts. This molecular phylogeny provides a useful framework to: 1) facilitate identification of worms, including those involved in dermatitis outbreaks; 2) test hypotheses about the evolution, diversification, host-parasite interactions and character evolution of Trichobilharzia; and 3) guide future taxonomic revision of Trichobilharzia. PMID:20049999

Biomimetic porous high-density polyethylene/polyethylene- grafted-maleic anhydride scaffold with improved in vitro cytocompatibility.

PubMed

Sharma, Swati; Bhaskar, Nitu; Bose, Surjasarathi; Basu, Bikaramjit

2018-05-01

A major challenge for tissue engineering is to design and to develop a porous biocompatible scaffold, which can mimic the properties of natural tissue. As a first step towards this endeavour, we here demonstrate a distinct methodology in biomimetically synthesized porous high-density polyethylene scaffolds. Co-extrusion approach was adopted, whereby high-density polyethylene was melt mixed with polyethylene oxide to form an immiscible binary blend. Selective dissolution of polyethylene oxide from the biphasic system revealed droplet-matrix-type morphology. An attempt to stabilize such morphology against thermal and shear effects was made by the addition of polyethylene- grafted-maleic anhydride as a compatibilizer. A maximum ultimate tensile strength of 7 MPa and elastic modulus of 370 MPa were displayed by the high-density polyethylene/polyethylene oxide binary blend with 5% maleated polyethylene during uniaxial tensile loading. The cell culture experiments with murine myoblast C2C12 cell line indicated that compared to neat high-density polyethylene and high-density polyethylene/polyethylene oxide, the high-density polyethylene/polyethylene oxide with 5% polyethylene- grafted-maleic anhydride scaffold significantly increased muscle cell attachment and proliferation with distinct elongated threadlike appearance and highly stained nuclei, in vitro. This has been partly attributed to the change in surface wettability property with a reduced contact angle (∼72°) for 5% PE- g-MA blends. These findings suggest that the high-density polyethylene/polyethylene oxide with 5% polyethylene- grafted-maleic anhydride can be treated as a cell growth substrate in bioengineering applications.

Subaqueous non-vesicular to poorly-vesicular shards: hydroclastic fragmentation on seamounts and summit calderas

NASA Astrophysics Data System (ADS)

Mueller, W. U.; Dingwell, D. B.; Downey, W. S.; Mastin, L. G.

2008-12-01

Recognizing pyroclastic deposits that originate directly from magmatic and phreatomagmatic explosions in a subaqueous setting is based upon sedimentary structures, such as massive, stratified, and graded beds as well as (pyro)clast size. Ideally such deposits form ordered fining-and thinning-upward sequences. Pumice, scoria, glass shards, euhedral and broken crystals, and lithic fragments are constituents that support an explosive heritage. Recent deep-sea ROV and submersible dives have retrieved non-vesicular to vesicle- poor, mm-scale, mafic shards in 5-15 cm-thick massive and/or graded (stratified) deposits, for which a subaqueous explosive origin has been inferred. These sheet hyaloclastites with variable shard shapes were first documented on Seamount 6 as deep-sea Limu O Pele at water depths > 1000 m. We identified in Seamount 6 samples equant to blocky shards with angular to subrounded terminations, but also subordinate hair-like and contorted glassy filaments, warped shards and irregular shards. Shards display internal laminations (flow-banding?) and have local perlitic fractures. Bubble wall shards derived from scoria burst were rare. In combination with all the above and a poor shard vesicularity (< 2%), a magmatic explosive origin seems improbable. Such small-volume deposits have been reported from seamounts and summit calderas associated with subaqueous drainage tubes and ponded magma in depths > 1000 m. We envision that hydrostatic pressure commensurate with water depth played a significant role. The deposits can be readily explained by a hydroclastic process whereby fragmentation occurred at the milli-second (Limu) to second scale (hyaloclastite). Hence, hyperquenched glass shards or thread-like glass filaments need not require magmatic explosivity. Constant surface interaction between aphyric, low-viscosity, high temperature, magma-lava at depth with seawater causes fragmentation (granulation) that can generate such delicate shards. The transfer of heat to the ambient medium, seawater, favours turbulent convection causing strong water movement that strips glassy rinds and lofts the fine-grained shards and Limu O Pele into the water column. Once entrained, shards are deposited after water turbulence abates. Congestion of the water column causes deposition from low-density turbidity currents and subaqueous fallout. In this manner delicate textures would remain intact even if removed from the site of hydroclastic fragmentation.

[Identification of varieties of cashmere by Vis/NIR spectroscopy technology based on PCA-SVM].

PubMed

Wu, Gui-Fang; He, Yong

2009-06-01

One mixed algorithm was presented to discriminate cashmere varieties with principal component analysis (PCA) and support vector machine (SVM). Cashmere fiber has such characteristics as threadlike, softness, glossiness and high tensile strength. The quality characters and economic value of each breed of cashmere are very different. In order to safeguard the consumer's rights and guarantee the quality of cashmere product, quickly, efficiently and correctly identifying cashmere has significant meaning to the production and transaction of cashmere material. The present research adopts Vis/NIRS spectroscopy diffuse techniques to collect the spectral data of cashmere. The near infrared fingerprint of cashmere was acquired by principal component analysis (PCA), and support vector machine (SVM) methods were used to further identify the cashmere material. The result of PCA indicated that the score map made by the scores of PC1, PC2 and PC3 was used, and 10 principal components (PCs) were selected as the input of support vector machine (SVM) based on the reliabilities of PCs of 99.99%. One hundred cashmere samples were used for calibration and the remaining 75 cashmere samples were used for validation. A one-against-all multi-class SVM model was built, the capabilities of SVM with different kernel function were comparatively analyzed, and the result showed that SVM possessing with the Gaussian kernel function has the best identification capabilities with the accuracy of 100%. This research indicated that the data mining method of PCA-SVM has a good identification effect, and can work as a new method for rapid identification of cashmere material varieties.

Generation of Esr1-Knockout Rats Using Zinc Finger Nuclease-Mediated Genome Editing

PubMed Central

Dhakal, Pramod; Kubota, Kaiyu; Chakraborty, Damayanti; Lei, Tianhua; Larson, Melissa A.; Wolfe, Michael W.; Roby, Katherine F.; Vivian, Jay L.

2014-01-01

Estrogens play pivotal roles in development and function of many organ systems, including the reproductive system. We have generated estrogen receptor 1 (Esr1)-knockout rats using zinc finger nuclease (ZFN) genome targeting. mRNAs encoding ZFNs targeted to exon 3 of Esr1 were microinjected into single-cell rat embryos and transferred to pseudopregnant recipients. Of 17 live births, 5 had biallelic and 1 had monoallelic Esr1 mutations. A founder with monoallelic mutations was backcrossed to a wild-type rat. Offspring possessed only wild-type Esr1 alleles or wild-type alleles and Esr1 alleles containing either 482 bp (Δ482) or 223 bp (Δ223) deletions, indicating mosaicism in the founder. These heterozygous mutants were bred for colony expansion, generation of homozygous mutants, and phenotypic characterization. The Δ482 Esr1 allele yielded altered transcript processing, including the absence of exon 3, aberrant splicing of exon 2 and 4, and a frameshift that generated premature stop codons located immediately after the codon for Thr157. ESR1 protein was not detected in homozygous Δ482 mutant uteri. ESR1 disruption affected sexually dimorphic postnatal growth patterns and serum levels of gonadotropins and sex steroid hormones. Both male and female Esr1-null rats were infertile. Esr1-null males had small testes with distended and dysplastic seminiferous tubules, whereas Esr1-null females possessed large polycystic ovaries, thread-like uteri, and poorly developed mammary glands. In addition, uteri of Esr1-null rats did not effectively respond to 17β-estradiol treatment, further demonstrating that the Δ482 Esr1 mutation created a null allele. This rat model provides a new experimental tool for investigating the pathophysiology of estrogen action. PMID:24506075

Generation of Esr1-knockout rats using zinc finger nuclease-mediated genome editing.

PubMed

Rumi, M A Karim; Dhakal, Pramod; Kubota, Kaiyu; Chakraborty, Damayanti; Lei, Tianhua; Larson, Melissa A; Wolfe, Michael W; Roby, Katherine F; Vivian, Jay L; Soares, Michael J

2014-05-01

Estrogens play pivotal roles in development and function of many organ systems, including the reproductive system. We have generated estrogen receptor 1 (Esr1)-knockout rats using zinc finger nuclease (ZFN) genome targeting. mRNAs encoding ZFNs targeted to exon 3 of Esr1 were microinjected into single-cell rat embryos and transferred to pseudopregnant recipients. Of 17 live births, 5 had biallelic and 1 had monoallelic Esr1 mutations. A founder with monoallelic mutations was backcrossed to a wild-type rat. Offspring possessed only wild-type Esr1 alleles or wild-type alleles and Esr1 alleles containing either 482 bp (Δ482) or 223 bp (Δ223) deletions, indicating mosaicism in the founder. These heterozygous mutants were bred for colony expansion, generation of homozygous mutants, and phenotypic characterization. The Δ482 Esr1 allele yielded altered transcript processing, including the absence of exon 3, aberrant splicing of exon 2 and 4, and a frameshift that generated premature stop codons located immediately after the codon for Thr157. ESR1 protein was not detected in homozygous Δ482 mutant uteri. ESR1 disruption affected sexually dimorphic postnatal growth patterns and serum levels of gonadotropins and sex steroid hormones. Both male and female Esr1-null rats were infertile. Esr1-null males had small testes with distended and dysplastic seminiferous tubules, whereas Esr1-null females possessed large polycystic ovaries, thread-like uteri, and poorly developed mammary glands. In addition, uteri of Esr1-null rats did not effectively respond to 17β-estradiol treatment, further demonstrating that the Δ482 Esr1 mutation created a null allele. This rat model provides a new experimental tool for investigating the pathophysiology of estrogen action.

Morgellons disease: Analysis of a population with clinically confirmed microscopic subcutaneous fibers of unknown etiology.

PubMed

Savely, Virginia R; Stricker, Raphael B

2010-05-13

Morgellons disease is a controversial illness in which patients complain of stinging, burning, and biting sensations under the skin. Unusual subcutaneous fibers are the unique objective finding. The etiology of Morgellons disease is unknown, and diagnostic criteria have yet to be established. Our goal was to identify prevalent symptoms in patients with clinically confirmed subcutaneous fibers in order to develop a case definition for Morgellons disease. Patients with subcutaneous fibers observed on physical examination (designated as the fiber group) were evaluated using a data extraction tool that measured clinical and demographic characteristics. The prevalence of symptoms common to the fiber group was then compared with the prevalence of these symptoms in patients with Lyme disease and no complaints of skin fibers. The fiber group consisted of 122 patients. Significant findings in this group were an association with tick-borne diseases and hypothyroidism, high numbers from two states (Texas and California), high prevalence in middle-aged Caucasian women, and an increased prevalence of smoking and substance abuse. Although depression was noted in 29% of the fiber patients, pre-existing delusional disease was not reported. After adjusting for nonspecific symptoms, the most common symptoms reported in the fiber group were: crawling sensations under the skin; spontaneously appearing, slow-healing lesions; hyperpigmented scars when lesions heal; intense pruritus; seed-like objects, black specks, or "fuzz balls" in lesions or on intact skin; fine, thread-like fibers of varying colors in lesions and intact skin; lesions containing thick, tough, translucent fibers that are highly resistant to extraction; and a sensation of something trying to penetrate the skin from the inside out. This study of the largest clinical cohort reported to date provides the basis for an accurate and clinically useful case definition for Morgellons disease.

Congenital portosystemic shunts in children: a new anatomical classification correlated with surgical strategy.

PubMed

Blanc, Thomas; Guerin, Florent; Franchi-Abella, Stéphanie; Jacquemin, Emmanuel; Pariente, Danièle; Soubrane, Olivier; Branchereau, Sophie; Gauthier, Frédéric

2014-07-01

To propose an anatomical classification of congenital portosystemic shunts (CPSs) correlating with conservative surgery. CPSs entail a risk of life-threatening complications because of poor portal inflow, which may be prevented or cured by their closure. Current classifications based on portal origin of the shunt are not helpful for planning conservative surgery. Twenty-three patients who underwent at least 1 surgical procedure to close the CPSs were included in this retrospective study (1997-2012). We designed a classification according to the ending of the shunt in the caval system. We analyzed the results and outcomes of surgery according to this classification. Two patients had an extrahepatic portosystemic shunt, 17 had a portacaval shunt [subdivided in 5 end-to-side-like portal-caval, 7 side-to-side-like portal-caval, and 5 H-shaped (H-type portal-caval)], 2 had portal-to-hepatic vein shunts (portohepatic), and 2 had a persistent ductus venosus. All extrahepatic portosystemic shunts, H-type portal-caval, portohepatic, and patent ductus venosus patients had a successful 1-stage ligation. All 5 end-to-side-like portal-caval patients had a threadlike intrahepatic portal venous system; a 2-stage complete closure was successfully achieved for 4 and a partial closure for 1. The first 2 side-to-side-like portal-caval patients had a successful 2-stage closure whereas the 5 others had a 1-stage longitudinal caval partition. All patients are alive and none needed a liver transplantation. Our classification correlates the anatomy of CPSs and the surgical strategy: outcomes are good provided end-to-side-like portal-caval shunts patients have a 2-stage closure, side-to-side portal-caval shunts patients have a 1-stage caval partition, and the others have a 1-stage ligation.

Transgene delivery to endothelial cultures derived from porcine carotid artery ex vivo.

PubMed

Andoh, J; Sawyer, B; Szewczyk, K; Nortley, M; Rossetti, T; Loftus, I M; Yáñez-Muñoz, R J; Hainsworth, A H

2013-10-01

Carotid artery disease is a widespread cause of morbidity and mortality. Porcine models of vascular disease are well established in vivo, but existing endothelial systems in vitro (e.g. human umbilical vein endothelial cells, rat aortic endothelial cultures) poorly reflect carotid endothelium. A reliable in vitro assay would improve design of in vivo experiments and allow reduction and refinement of animal use. This study aimed (1) to develop ex vivo endothelial cultures from porcine carotid and (2) to test whether these were suitable for lentivector-mediated transgene delivery. Surplus carotid arteries were harvested from young adult female Large White pigs within 10 min post-mortem. Small sectors of carotid artery wall (approximately 4 mm×4 mm squares) were immobilised in a stable gel matrix. Cultures were exposed to HIV-derived lentivector (LV) encoding a reporter transgene or the equivalent integration-deficient vector (IDLV). After 7-14 days in vitro, cultures were fixed and labelled histochemically. Thread-like multicellular outgrowths were observed that were positive for endothelial cell markers (CD31, VEGFR2, von Willebrand factor). A minority of cells co-labelled for smooth muscle markers. Sensitivity to cytotoxic agents (paclitaxel, cycloheximide, staurosporine) was comparable to that in cell cultures, indicating that the gel matrix permits diffusive access of small pharmacological molecules. Transgene-expressing cells were more abundant following exposure to LV than IDLV (4.7, 0.1% of cells, respectively). In conclusion, ex vivo adult porcine carotid artery produced endothelial cell outgrowths that were effectively transduced by LV. This system will facilitate translation of novel therapies to clinical trials, with reduction and refinement of in vivo experiments.

Winter cover crops on processing tomato yield, quality, pest pressure, nitrogen availability, and profit margins.

PubMed

Belfry, Kimberly D; Trueman, Cheryl; Vyn, Richard J; Loewen, Steven A; Van Eerd, Laura L

2017-01-01

Much of cover crop research to date focuses on key indicators of impact without considering the implications over multiple years, in the absence of a systems-based approach. To evaluate the effect of three years of autumn cover crops on subsequent processing tomato (Solanum lycopersicum L.) production in 2010 and 2011, a field split-split-plot factorial design trial with effects of cover crop type, urea ammonium nitrate fertilizer rate (0 or 140 kg N ha-1 preplant broadcast incorporated) and tomato cultivar (early vs. late) was conducted. The main plot factor, cover crop, included a no cover crop control, oat (Avena sativa L.), winter cereal rye (hereafter referred to as rye) (Secale cereale L.), oilseed radish (OSR) (Raphanus sativus L. var. oleiferus Metzg Stokes), and mix of OSR and rye (OSR + rye) treatments. Cover crop biomass of 0.5 to 2.8 and 1.7 to 3.1 Mg ha-1 was attained in early Oct. and the following early May, respectively. In general, OSR increased soil mineral N during cover crop growth and into the succeeding summer tomato growing season, while the remaining cover crops did not differ from the no cover crop control. The lack of a cover crop by N rate interaction in soil and plant N analyses at harvest suggests that growers may not need to modify N fertilizer rates to tomatoes based on cover crop type. Processing tomato fruit quality at harvest (rots, insect or disease damage, Agtron colour, pH, or natural tomato soluble solids (NTSS)) was not affected by cover crop type. In both years, marketable yield in the no cover crop treatment was lower or not statistically different than all planted cover crops. Partial profit margins over both years were 1320 $ ha-1 higher with OSR and $960 higher with oat compared to the no cover crop control. Thus, results from a systems-based approach suggest that the cover crops tested had no observed negative impact on processing tomato production and have the potential to increase marketable yield and profit margins.

Winter cover crops on processing tomato yield, quality, pest pressure, nitrogen availability, and profit margins

PubMed Central

Belfry, Kimberly D.; Trueman, Cheryl; Vyn, Richard J.; Loewen, Steven A.; Van Eerd, Laura L.

2017-01-01

Much of cover crop research to date focuses on key indicators of impact without considering the implications over multiple years, in the absence of a systems-based approach. To evaluate the effect of three years of autumn cover crops on subsequent processing tomato (Solanum lycopersicum L.) production in 2010 and 2011, a field split-split-plot factorial design trial with effects of cover crop type, urea ammonium nitrate fertilizer rate (0 or 140 kg N ha-1 preplant broadcast incorporated) and tomato cultivar (early vs. late) was conducted. The main plot factor, cover crop, included a no cover crop control, oat (Avena sativa L.), winter cereal rye (hereafter referred to as rye) (Secale cereale L.), oilseed radish (OSR) (Raphanus sativus L. var. oleiferus Metzg Stokes), and mix of OSR and rye (OSR + rye) treatments. Cover crop biomass of 0.5 to 2.8 and 1.7 to 3.1 Mg ha-1 was attained in early Oct. and the following early May, respectively. In general, OSR increased soil mineral N during cover crop growth and into the succeeding summer tomato growing season, while the remaining cover crops did not differ from the no cover crop control. The lack of a cover crop by N rate interaction in soil and plant N analyses at harvest suggests that growers may not need to modify N fertilizer rates to tomatoes based on cover crop type. Processing tomato fruit quality at harvest (rots, insect or disease damage, Agtron colour, pH, or natural tomato soluble solids (NTSS)) was not affected by cover crop type. In both years, marketable yield in the no cover crop treatment was lower or not statistically different than all planted cover crops. Partial profit margins over both years were 1320 $ ha-1 higher with OSR and $960 higher with oat compared to the no cover crop control. Thus, results from a systems-based approach suggest that the cover crops tested had no observed negative impact on processing tomato production and have the potential to increase marketable yield and profit margins. PMID:28683080

Occurrence and distribution of microplastics at selected coastal sites along the southeastern United States.

PubMed

Yu, Xubiao; Ladewig, Samantha; Bao, Shaowu; Toline, Catherine A; Whitmire, Stefanie; Chow, Alex T

2018-02-01

To investigate the occurrence and distribution of microplastics in the southeastern coastal region of the United States, we quantified the amount of microplastics in sand samples from multiple coastal sites and developed a predictive model to understand the drift of plastics via ocean currents. Sand samples from eighteen National Park Service (NPS) beaches in the Southeastern Region were collected and microplastics were isolated from each sample. Microplastic counts were compared among sites and local geography was used to make inferences about sources and modes of distribution. Samples were analyzed to identify the composition of particles using Fourier transform infrared spectroscopy (FTIR). To predict the spatiotemporal distribution and movements of particles via coastal currents, a Regional Ocean Modeling System (ROMS) was applied. Microplastics were detected in each of the sampled sites although abundance among sites was highly variable. Approximately half of the samples were dominated by thread-like and fibrous materials as opposed to beads and particles. Results of FTIR suggested that 24% consisted of polyethylene terephthalate (PET), while about 68% of the fibers tested were composed of man-made cellulosic materials such as rayon. Based on published studies examining sources of microplastics, the shape of the particles found here (mostly fibers) and the presence of PET, we infer the source of microplastics in coastal areas is mainly from urban areas, such as wastewater discharge, rather than breakdown of larger marine debris drifting in the ocean. Local geographic features, e.g., the nearness of sites to large rivers and urbanized areas, explain variance in amount of microplastics among sites. Additionally, the distribution of simulated particles is explained by ocean current patterns; computer simulations were correlated with field observations, reinforcing the idea that ocean currents can be a good predictor of the fate and distribution of microplastics at the sites sampled here. Copyright © 2017 Elsevier B.V. All rights reserved.

Prediction of Brugia malayi antigenic peptides: candidates for synthetic vaccine design against lymphatic filariasis.

PubMed

Gomase, Virendra S; Chitlange, Nikhilkumar R; Changbhale, Smruti S; Kale, Karbhari V

2013-08-01

Brugia malayi is a threadlike nematode cause's swelling of lymphatic organs, condition well known as lymphatic filariasis; till date no invention made to effectively address lymphatic filariasis. In this analysis we a have predicted suitable antigenic peptides from Brugia malayi antigen protein for peptide vaccine design against lymphatic filariasis based on cross protection phenomenon as, an ample immune response can be generated with a single protein subunit. We found MHC class II binding peptides of Brugia malayi antigen protein are important determinant against the diseased condition. The analysis shows Brugia malayi antigen protein having 505 amino acids, which shows 497 nonamers. In this assay, we have predicted MHC-I binding peptides for 8mer_H2_Db (optimal score- 15.966), 9mer_H2_Db (optimal score- 15.595), 10mer_H2_Db (optimal score- 19.405), 11mer_H2_Dballeles (optimal score- 23.801). We also predicted the SVM based MHCII-IAb nonamers, 51-FQQIDPLDA, 442-FAAIACLVH, 206-YLNPFGHQF, 167-WYVIMAACY, 367-YAMIVIRLL, 434- LVITTAANF, 176-LDSYCLWKP, 435-VITTAANFA, 364-WPGYAMIVI (optimal score- 13.963); MHCII-IAd nonamers, 52-QQIDPLDAE, 171-MAACYLDSY, 239-QWRSVILCN, 168-YVIMAACYL, 3-QYLSVHSLS, 322-EILLHAKVV, 417- LGIIASFVS, 396-KAIFLAHFG, 167-WYVIMAACY, 269-LALHCINVI, 93-FINKAAPKQ, 259-NCIIVLKAF, 79- QGVLLIIPR, 22-TILQRSQAI, 63-RGFVYGNVS, 109-NISSLAFET,(optimal score- 16.748); and MHCII-IAg7 nonamers 171-MAACYLDSY, 73-KIVNGAQGV, 259-NCIIVLKAF, 209-PFGHQFSFE, 102-SCDTLLKNI, 25-QRSQAIRIV, 444- AIACLVHLF, 88-SLVNGFINK, 252-FPRHQLLNC, 471-RFVLANDNE, 52-QQIDPLDAE, 469-HRRFVLAND, 457- SNRHYFLAD, 362-KSWPGYAMI, 476-NDNEGEDFE, 370-IVIRLLQAL (optimal score- 19.847) which represents potential binders from Brugia malayi antigen protein. The method integrates prediction of MHC class I binding proteasomal C-terminal cleavage peptides and Eighteen potential antigenic peptides at average propensity 1.063 having highest local hydrophilicity. Thus a small antigen fragment can induce immune response against whole antigen. This approach can be applied for designing subunit and synthetic peptide vaccines.

The Greatest Saturn Portrait ...Yet

NASA Image and Video Library

2005-02-24

While cruising around Saturn in early October 2004, Cassini captured a series of images that have been composed into the largest, most detailed, global natural color view of Saturn and its rings ever made. This grand mosaic consists of 126 images acquired in a tile-like fashion, covering one end of Saturn's rings to the other and the entire planet in between. The images were taken over the course of two hours on Oct. 6, 2004, while Cassini was approximately 6.3 million kilometers (3.9 million miles) from Saturn. Since the view seen by Cassini during this time changed very little, no re-projection or alteration of any of the images was necessary. Three images (red, green and blue) were taken of each of 42 locations, or "footprints," across the planet. The full color footprints were put together to produce a mosaic that is 8,888 pixels across and 4,544 pixels tall. The smallest features seen here are 38 kilometers (24 miles) across. Many of Saturn's splendid features noted previously in single frames taken by Cassini are visible in this one detailed, all-encompassing view: subtle color variations across the rings, the thread-like F ring, ring shadows cast against the blue northern hemisphere, the planet's shadow making its way across the rings to the left, and blue-grey storms in Saturn's southern hemisphere to the right. Tiny Mimas and even smaller Janus are both faintly visible at the lower left. The Sun-Saturn-Cassini, or phase, angle at the time was 72 degrees; hence, the partial illumination of Saturn in this portrait. Later in the mission, when the spacecraft's trajectory takes it far from Saturn and also into the direction of the Sun, Cassini will be able to look back and view Saturn and its rings in a more fully-illuminated geometry. http://photojournal.jpl.nasa.gov/catalog/PIA06193

Morgellons disease: Analysis of a population with clinically confirmed microscopic subcutaneous fibers of unknown etiology

PubMed Central

Savely, Virginia R; Stricker, Raphael B

2010-01-01

Background: Morgellons disease is a controversial illness in which patients complain of stinging, burning, and biting sensations under the skin. Unusual subcutaneous fibers are the unique objective finding. The etiology of Morgellons disease is unknown, and diagnostic criteria have yet to be established. Our goal was to identify prevalent symptoms in patients with clinically confirmed subcutaneous fibers in order to develop a case definition for Morgellons disease. Methods: Patients with subcutaneous fibers observed on physical examination (designated as the fiber group) were evaluated using a data extraction tool that measured clinical and demographic characteristics. The prevalence of symptoms common to the fiber group was then compared with the prevalence of these symptoms in patients with Lyme disease and no complaints of skin fibers. Results: The fiber group consisted of 122 patients. Significant findings in this group were an association with tick-borne diseases and hypothyroidism, high numbers from two states (Texas and California), high prevalence in middle-aged Caucasian women, and an increased prevalence of smoking and substance abuse. Although depression was noted in 29% of the fiber patients, pre-existing delusional disease was not reported. After adjusting for nonspecific symptoms, the most common symptoms reported in the fiber group were: crawling sensations under the skin; spontaneously appearing, slow-healing lesions; hyperpigmented scars when lesions heal; intense pruritus; seed-like objects, black specks, or “fuzz balls” in lesions or on intact skin; fine, thread-like fibers of varying colors in lesions and intact skin; lesions containing thick, tough, translucent fibers that are highly resistant to extraction; and a sensation of something trying to penetrate the skin from the inside out. Conclusions: This study of the largest clinical cohort reported to date provides the basis for an accurate and clinically useful case definition for Morgellons disease. PMID:21437061

In vivo demonstration of injectable microstimulators based on charge-balanced rectification of epidermically applied currents

NASA Astrophysics Data System (ADS)

Ivorra, Antoni; Becerra-Fajardo, Laura; Castellví, Quim

2015-12-01

Objective. It is possible to develop implantable microstimulators whose actuation principle is based on rectification of high-frequency (HF) current bursts supplied through skin electrodes. This has been demonstrated previously by means of devices consisting of a single diode. However, previous single diode devices caused dc currents which made them impractical for clinical applications. Here flexible thread-like stimulation implants which perform charge balance are demonstrated in vivo. Approach. The implants weigh 40.5 mg and they consist of a 3 cm long tubular silicone body with a diameter of 1 mm, two electrodes at opposite ends, and, within the central section of the body, an electronic circuit made up of a diode, two capacitors, and a resistor. In the present study, each implant was percutaneously introduced through a 14 G catheter into either the gastrocnemius muscle or the cranial tibial muscle of a rabbit hindlimb. Then stimulation was performed by delivering HF bursts (amplitude <60 V, frequency 1 MHz, burst repetition frequency from 10 Hz to 200 Hz, duration = 200 μs) through a pair of textile electrodes strapped around the hindlimb and either isometric plantarflexion or dorsiflexion forces were recorded. Stimulation was also assayed 1, 2 and 4 weeks after implantation. Main results. The implants produced bursts of rectified current whose mean value was of a few mA and were capable of causing local neuromuscular stimulation. The implants were well-tolerated during the 4 weeks. Significance. Existing power supply methods, and, in particular inductive links, comprise stiff and bulky parts. This hinders the development of minimally invasive implantable devices for neuroprostheses based on electrical stimulation. The proposed methodology is intended to relieving such bottleneck. In terms of mass, thinness, and flexibility, the demonstrated implants appear to be unprecedented among the intramuscular stimulation implants ever assayed in vertebrates.

New Genus of Blood Fluke (Digenea: Schistosomatoidea) from Malaysian Freshwater Turtles (Geoemydidae) and its Phylogenetic Position Within Schistosomatoidea.

PubMed

Roberts, Jackson R; Platt, Thomas R; Orélis-Ribeiro, Raphael; Bullard, Stephen A

2016-08-01

:  Baracktrema obamai n. gen., n. sp. infects the lung of geoemydid turtles (black marsh turtle, Siebenrockiella crassicollis [type host] and southeast Asian box turtle, Cuora amboinensis ) in the Malaysian states of Perak, Perlis, and Selangor. Baracktrema and Unicaecum Stunkard, 1925 are the only accepted turtle blood fluke genera having the combination of a single cecum, single testis, oviducal seminal receptacle, and uterine pouch. Baracktrema differs from Unicaecum by having a thread-like body approximately 30-50× longer than wide and post-cecal terminal genitalia. Unicaecum has a body approximately 8-12× longer than wide and terminal genitalia that are anterior to the distal end of the cecum. The new genus further differs from all other accepted turtle blood fluke genera by having a cecum that is highly convoluted for its entire length, a spindle-shaped ovary between the cirrus sac and testis, a uterine pouch that loops around the primary vitelline collecting duct, a Laurer's canal, and a dorsal common genital pore. Phylogenetic analysis of the D1-D3 domains of the nuclear large subunit ribosomal DNA (28S) revealed, with high nodal support and as predicted by morphology, that Baracktrema and Unicaecum share a recent common ancestor and form a clade sister to the freshwater turtle blood flukes of Spirorchis, paraphyletic Spirhapalum, and Vasotrema and that, collectively, these flukes were sister to all other tetrapod blood flukes (Hapalorhynchus + Griphobilharzia plus the marine turtle blood flukes and schistosomes). Pending a forthcoming emended morphological diagnosis of the family, the clade including Spirorchis spp., paraphyletic Spirhapalum, Vasotrema, Baracktrema, and Unicaecum is a likely placeholder for "Spirorchiidae Stunkard, 1921 " (type genus Spirorchis MacCallum, 1918 ; type species Spirorchis innominatus Ward, 1921 ). The present study comprises the 17th blood fluke known to infect geoemydid turtles and the first proposal of a new genus of turtle blood fluke in 21 yr.

Multigene phylogeny and cell evolution of chromist infrakingdom Rhizaria: contrasting cell organisation of sister phyla Cercozoa and Retaria.

PubMed

Cavalier-Smith, Thomas; Chao, Ema E; Lewis, Rhodri

2018-04-17

Infrakingdom Rhizaria is one of four major subgroups with distinct cell body plans that comprise eukaryotic kingdom Chromista. Unlike other chromists, Rhizaria are mostly heterotrophic flagellates, amoebae or amoeboflagellates, commonly with reticulose (net-like) or filose (thread-like) feeding pseudopodia; uniquely for eukaryotes, cilia have proximal ciliary transition-zone hub-lattices. They comprise predominantly flagellate phylum Cercozoa and reticulopodial phylum Retaria, whose exact phylogenetic relationship has been uncertain. Given even less clear relationships amongst cercozoan classes, we sequenced partial transcriptomes of seven Cercozoa representing five classes and endomyxan retarian Filoreta marina to establish 187-gene multiprotein phylogenies. Ectoreta (retarian infraphyla Foraminifera, Radiozoa) branch within classical Cercozoa as sister to reticulose Endomyxa. This supports recent transfer of subphylum Endomyxa from Cercozoa to Retaria alongside subphylum Ectoreta which embraces classical retarians where capsules or tests subdivide cells into organelle-containing endoplasm and anastomosing pseudopodial net-like ectoplasm. Cercozoa are more homogeneously filose, often with filose pseudopodia and/or posterior ciliary gliding motility: zooflagellate Helkesimastix and amoeboid Guttulinopsis form a strongly supported clade, order Helkesida. Cercomonads are polyphyletic (Cercomonadida sister to glissomonads; Paracercomonadida deeper). Thecofilosea are a clade, whereas Imbricatea may not be; Sarcomonadea may be paraphyletic. Helkesea and Metromonadea are successively deeper outgroups within cercozoan subphylum Monadofilosa; subphylum Reticulofilosa (paraphyletic on site-heterogeneous trees) branches earliest, Granofilosea before Chlorarachnea. Our multiprotein trees confirm that Rhizaria are sisters of infrakingdom Halvaria (Alveolata, Heterokonta) within chromist subkingdom Harosa (= SAR); they further support holophyly of chromist subkingdom Hacrobia, and are consistent with holophyly of Chromista as sister of kingdom Plantae. Site-heterogeneous rDNA trees group Kraken with environmental DNA clade 'eSarcomonad', not Paracercomonadida. Ectoretan fossil dates evidence ultrarapid episodic stem sequence evolution. We discuss early rhizarian cell evolution and multigene tree coevolutionary patterns, gene-paralogue evidence for chromist monophyly, and integrate this with fossil evidence for the age of Rhizaria and eukaryote cells, and revise rhizarian classification.

In Vivo Demonstration of Addressable Microstimulators Powered by Rectification of Epidermically Applied Currents for Miniaturized Neuroprostheses

PubMed Central

2015-01-01

Electrical stimulation is used in order to restore nerve mediated functions in patients with neurological disorders, but its applicability is constrained by the invasiveness of the systems required to perform it. As an alternative to implantable systems consisting of central stimulation units wired to the stimulation electrodes, networks of wireless microstimulators have been devised for fine movement restoration. Miniaturization of these microstimulators is currently hampered by the available methods for powering them. Previously, we have proposed and demonstrated a heterodox electrical stimulation method based on electronic rectification of high frequency current bursts. These bursts can be delivered through textile electrodes on the skin. This approach has the potential to result in an unprecedented level of miniaturization as no bulky parts such as coils or batteries are included in the implant. We envision microstimulators designs based on application-specific integrated circuits (ASICs) that will be flexible, thread-like (diameters < 0.5 mm) and not only with controlled stimulation capabilities but also with sensing capabilities for artificial proprioception. We in vivo demonstrate that neuroprostheses composed of addressable microstimulators based on this electrical stimulation method are feasible and can perform controlled charge-balanced electrical stimulation of muscles. We developed miniature external circuit prototypes connected to two bipolar probes that were percutaneously implanted in agonist and antagonist muscles of the hindlimb of an anesthetized rabbit. The electronic implant architecture was able to decode commands that were amplitude modulated on the high frequency (1 MHz) auxiliary current bursts. The devices were capable of independently stimulating the target tissues, accomplishing controlled dorsiflexion and plantarflexion joint movements. In addition, we numerically show that the high frequency current bursts comply with safety standards both in terms of tissue heating and unwanted electro-stimulation. We demonstrate that addressable microstimulators powered by rectification of epidermically applied currents are feasible. PMID:26147771

In Vivo Demonstration of Addressable Microstimulators Powered by Rectification of Epidermically Applied Currents for Miniaturized Neuroprostheses.

PubMed

Becerra-Fajardo, Laura; Ivorra, Antoni

2015-01-01

Electrical stimulation is used in order to restore nerve mediated functions in patients with neurological disorders, but its applicability is constrained by the invasiveness of the systems required to perform it. As an alternative to implantable systems consisting of central stimulation units wired to the stimulation electrodes, networks of wireless microstimulators have been devised for fine movement restoration. Miniaturization of these microstimulators is currently hampered by the available methods for powering them. Previously, we have proposed and demonstrated a heterodox electrical stimulation method based on electronic rectification of high frequency current bursts. These bursts can be delivered through textile electrodes on the skin. This approach has the potential to result in an unprecedented level of miniaturization as no bulky parts such as coils or batteries are included in the implant. We envision microstimulators designs based on application-specific integrated circuits (ASICs) that will be flexible, thread-like (diameters < 0.5 mm) and not only with controlled stimulation capabilities but also with sensing capabilities for artificial proprioception. We in vivo demonstrate that neuroprostheses composed of addressable microstimulators based on this electrical stimulation method are feasible and can perform controlled charge-balanced electrical stimulation of muscles. We developed miniature external circuit prototypes connected to two bipolar probes that were percutaneously implanted in agonist and antagonist muscles of the hindlimb of an anesthetized rabbit. The electronic implant architecture was able to decode commands that were amplitude modulated on the high frequency (1 MHz) auxiliary current bursts. The devices were capable of independently stimulating the target tissues, accomplishing controlled dorsiflexion and plantarflexion joint movements. In addition, we numerically show that the high frequency current bursts comply with safety standards both in terms of tissue heating and unwanted electro-stimulation. We demonstrate that addressable microstimulators powered by rectification of epidermically applied currents are feasible.

SOME NEW DATA ON SELF-COMPRESSED DISCHARGES (in Russian)

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

Kvartskhava, I.F.; Kervalidze, K.N.; Gvaladze, Yu.C.

1962-01-01

The theory of self-constricted discharges, which predicts the possibiiity of the appearance of various types of instabilities, does not reflect fully the multiple phenoniena which are experimentally observed. The models used in the theory evidentiy do not consider the presence of some processes in self- constricted discharges which materially determine the real behavior of the plasma. The experiments showed a number of such processes. Basically, they consist of an unequal heating of the discharge near the walls of the chamber. Thereby the discharge currents fiow along distorted threadlike channels which, in theta - pinches mostly follow either the z-direction ormore » the theta -direction, and in z- pinches they basically follow the theta -direction. In the process of plasma compression the above mentioned thread formations experience unequal accelerations. Having a high conductivity, these formations facilitate the capture of magnetic fieids which obstructs the thermaiization of the kinetic energy of the plasma's radial motion. As a result of this process the plasma is far from thermial equilibrium when in the stage of maximum compression. It is encompassed by a motion of turbulent character. After the maximum compression of the plasma, various kinds of plasma formation are ejected from the surface of the pinch. The magnetic field is more effectively trapped than in zpinches. Consequently, a greater variety of types of instability is observed in theta - pinches than in z-pinches. Highspeed photography of the discharge turned out to be the most practical and fruitful method of studying the processes of formation and the subsequent motion of the plasma. Photographs of the discharges obtained by streak photography and by framing camera are discussed. The results of probe measurements of magnetic and electric fields as well as the results of measurements of currents by means of Rogovsky belts are given. (auth)« less

Preliminary Results of the Permafrost Carbon Study in the Lower Kolyma Lowland (Eastern Siberia) Based on Drilling Record

NASA Astrophysics Data System (ADS)

Spektor, V. V.; Kholodov, A. L.; Bulygina, E. B.; Andreeva, V.; Broderick, D.; Spawn, S.; Natali, S.; Davydova, A.

2012-12-01

In 2012, the Polaris Project (thepolarisproject.org, Director R.M. Holmes) has conducted the permafrost drilling on the Kolyma Lowland for a complex study of permafrost carbon as a potential source for microbial decomposition. In July 2012, the first two boreholes, 15.1 and 13.4 m in depth, were drilled. The first borehole (BH 12/1) was drilled in the stratum of ice complex (yedoma) on the local watershed near the Schuch'e lake in the vicinity of the town Chersky (N68°44.7' E161°23'). The depth of active layer is 45 cm. The permafrost to the depth of 15.1 m represents grey and brown silts with predominant homogeneous structure. Silts contain numerous thread-like roots, scarce plant macrofossils, and in places are colored with unclear spots of ferrugination. Cryostructure is mainly pore ice or thin lense-like ice layers. Wedge ice is observed in the interval 12.5-12.9 m. The moisture volumetric percentage of silts varies along the stratum, mainly, between 40-50%. The organic content, defined in every 20 cm of the core as a loss on ignition, varies between 2-4%. The second borehole (BH 12/2), located in the Pleistocene Park (N68°30.8' E161°30') was drilled through modern floodplain sediments (0-0.6 m) of the Kolyma River with polygonal network at the surface, underlain by peat (0.6-1.3 m), silt deposits of thermokarst lake (1.3-12.0 m), and river grey sands (12.0-13.4 m). The active layer thickness is 65 cm. The cryostructure is predominantly lattice-like. Silts contain modern wedge ice at the depth of 2.5-2.7 m. Mollusk shells and large amount of plant macrofossils are observed in the interval 5.7-8.0 m. The organic content in the thermokarst deposits varies in average within 2-3 %, but is about 1% in the underlying river sands. To investigate permafrost carbon, samples for microbial and enzyme activities, as well as samples of trapped gases were collected from different horizons of frozen cores. Samples for palynological, diatom, and lithological analyses, as well as for absolute age AMS 14C and isotopes O16/O18, and D were collected for reconstructing paleoclimate and paleogeographic conditions of organic matter accumulation and preservation. As a part of the TSP Program (Thermal State Permafrost), both boreholes were equipped with loggers for temperature measurements at 3,5,10, and 15 m and 3,4,10, and 13 m for the BH 12/1 and 12/2 correspondingly. To evaluate the role of landscape conditions on the thermal regime of permafrost and active layer dynamics terrestrial survey near the boreholes was conducted.

Imaging complex nutrient dynamics in mycelial networks.

PubMed

Fricker, M D; Lee, J A; Bebber, D P; Tlalka, M; Hynes, J; Darrah, P R; Watkinson, S C; Boddy, L

2008-08-01

Transport networks are vital components of multi-cellular organisms, distributing nutrients and removing waste products. Animal cardiovascular and respiratory systems, and plant vasculature, are branching trees whose architecture is thought to determine universal scaling laws in these organisms. In contrast, the transport systems of many multi-cellular fungi do not fit into this conceptual framework, as they have evolved to explore a patchy environment in search of new resources, rather than ramify through a three-dimensional organism. These fungi grow as a foraging mycelium, formed by the branching and fusion of threadlike hyphae, that gives rise to a complex network. To function efficiently, the mycelial network must both transport nutrients between spatially separated source and sink regions and also maintain its integrity in the face of continuous attack by mycophagous insects or random damage. Here we review the development of novel imaging approaches and software tools that we have used to characterise nutrient transport and network formation in foraging mycelia over a range of spatial scales. On a millimetre scale, we have used a combination of time-lapse confocal imaging and fluorescence recovery after photobleaching to quantify the rate of diffusive transport through the unique vacuole system in individual hyphae. These data then form the basis of a simulation model to predict the impact of such diffusion-based movement on a scale of several millimetres. On a centimetre scale, we have used novel photon-counting scintillation imaging techniques to visualize radiolabel movement in small microcosms. This approach has revealed novel N-transport phenomena, including rapid, preferential N-resource allocation to C-rich sinks, induction of simultaneous bi-directional transport, abrupt switching between different pre-existing transport routes, and a strong pulsatile component to transport in some species. Analysis of the pulsatile transport component using Fourier techniques shows that as the colony forms, it self-organizes into well demarcated domains that are identifiable by differences in the phase relationship of the pulses. On the centimetre to metre scale, we have begun to use techniques borrowed from graph theory to characterize the development and dynamics of the network, and used these abstracted network models to predict the transport characteristics, resilience, and cost of the network.

Flight-vehicle materials, structures, and dynamics - Assessment and future directions. Vol. 5 - Structural dynamics and aeroelasticity

NASA Technical Reports Server (NTRS)

Noor, Ahmed K. (Editor); Venneri, Samuel L. (Editor)

1993-01-01

Various papers on flight vehicle materials, structures, and dynamics are presented. Individual topics addressed include: general modeling methods, component modeling techniques, time-domain computational techniques, dynamics of articulated structures, structural dynamics in rotating systems, structural dynamics in rotorcraft, damping in structures, structural acoustics, structural design for control, structural modeling for control, control strategies for structures, system identification, overall assessment of needs and benefits in structural dynamics and controlled structures. Also discussed are: experimental aeroelasticity in wind tunnels, aeroservoelasticity, nonlinear aeroelasticity, aeroelasticity problems in turbomachines, rotary-wing aeroelasticity with application to VTOL vehicles, computational aeroelasticity, structural dynamic testing and instrumentation.

Hypermedia 1990 structured Hypertext tutorial

NASA Technical Reports Server (NTRS)

Johnson, J. Scott

1990-01-01

Hypermedia 1990 structured Hypertext tutorial is presented in the form of view-graphs. The following subject areas are covered: structured hypertext; analyzing hypertext documents for structure; designing structured hypertext documents; creating structured hypertext applications; structuring service and repair documents; maintaining structured hypertext documents; and structured hypertext conclusion.

Conservative secondary structure motifs already present in early-stage folding (in silico) as found in serpines family.

PubMed

Brylinski, Michal; Konieczny, Leszek; Kononowicz, Andrzej; Roterman, Irena

2008-03-21

The well-known procedure implemented in ClustalW oriented on the sequence comparison was applied to structure comparison. The consensus sequence as well as consensus structure has been defined for proteins belonging to serpine family. The structure of early stage intermediate was the object for similarity search. The high values of W(sequence) appeared to be accordant with high values of W(structure) making possible structure comparison using common criteria for sequence and structure comparison. Since the early stage structural form has been created according to limited conformational sub-space which does not include the beta-structure (this structure is mediated by C7eq structural form), is particularly important to see, that the C7eq structural form may be treated as the seed for beta-structure present in the final native structure of protein. The applicability of ClustalW procedure to structure comparison makes these two comparisons unified.

Classification of Structural Coal-Controlling Styles and Analysis on Structural Coal-Controlling Actions

NASA Astrophysics Data System (ADS)

Zhan, Wen-feng

2017-11-01

Tectonism was the primary geologic factors for controlling the formation, deformation, and occurrence of coal measures. As the core of a new round of prediction and evaluation on the coalfield resource potential, the effect of coal-controlling structure was further strengthened and deepened in related researches. By systematically combing the tectonic coal-controlling effect and structure, this study determined the geodynamical classification basis for coal-controlling structures. According to the systematic analysis and summary on the related research results, the coal-controlling structure was categorized into extensional structure, compressive structure, shearing and rotational structure, inverted structure, as well as the sliding structure, syndepositional structure with coalfield structure characteristics. In accordance with the structure combination and distribution characteristics, the six major classes were further classified into 32 subclasses. Moreover, corresponding mode maps were drawn to discuss the basic characteristics and effect of the coal-controlling structures.

Coupled structural/thermal/electromagnetic analysis/tailoring of graded composite structures

NASA Technical Reports Server (NTRS)

Mcknight, R. L.; Huang, H.; Hartle, M.

1992-01-01

Accomplishments are described for the third years effort of a 5-year program to develop a methodology for coupled structural/thermal/electromagnetic analysis/tailoring of graded composite structures. These accomplishments include: (1) structural analysis capability specialized for graded composite structures including large deformation and deformation position eigenanalysis technologies; (2) a thermal analyzer specialized for graded composite structures; (3) absorption of electromagnetic waves by graded composite structures; and (4) coupled structural thermal/electromagnetic analysis of graded composite structures.

The Quality and Validation of Structures from Structural Genomics

PubMed Central

Domagalski, Marcin J.; Zheng, Heping; Zimmerman, Matthew D.; Dauter, Zbigniew; Wlodawer, Alexander; Minor, Wladek

2014-01-01

Quality control of three-dimensional structures of macromolecules is a critical step to ensure the integrity of structural biology data, especially those produced by structural genomics centers. Whereas the Protein Data Bank (PDB) has proven to be a remarkable success overall, the inconsistent quality of structures reveals a lack of universal standards for structure/deposit validation. Here, we review the state-of-the-art methods used in macromolecular structure validation, focusing on validation of structures determined by X-ray crystallography. We describe some general protocols used in the rebuilding and re-refinement of problematic structural models. We also briefly discuss some frontier areas of structure validation, including refinement of protein–ligand complexes, automation of structure redetermination, and the use of NMR structures and computational models to solve X-ray crystal structures by molecular replacement. PMID:24203341

A structural design decomposition method utilizing substructuring

NASA Technical Reports Server (NTRS)

Scotti, Stephen J.

1994-01-01

A new method of design decomposition for structural analysis and optimization is described. For this method, the structure is divided into substructures where each substructure has its structural response described by a structural-response subproblem, and its structural sizing determined from a structural-sizing subproblem. The structural responses of substructures that have rigid body modes when separated from the remainder of the structure are further decomposed into displacements that have no rigid body components, and a set of rigid body modes. The structural-response subproblems are linked together through forces determined within a structural-sizing coordination subproblem which also determines the magnitude of any rigid body displacements. Structural-sizing subproblems having constraints local to the substructures are linked together through penalty terms that are determined by a structural-sizing coordination subproblem. All the substructure structural-response subproblems are totally decoupled from each other, as are all the substructure structural-sizing subproblems, thus there is significant potential for use of parallel solution methods for these subproblems.

On topological RNA interaction structures.

PubMed

Qin, Jing; Reidys, Christian M

2013-07-01

Recently a folding algorithm of topological RNA pseudoknot structures was presented in Reidys et al. (2011). This algorithm folds single-stranded γ-structures, that is, RNA structures composed by distinct motifs of bounded topological genus. In this article, we set the theoretical foundations for the folding of the two backbone analogues of γ structures: the RNA γ-interaction structures. These are RNA-RNA interaction structures that are constructed by a finite number of building blocks over two backbones having genus at most γ. Combinatorial properties of γ-interaction structures are of practical interest since they have direct implications for the folding of topological interaction structures. We compute the generating function of γ-interaction structures and show that it is algebraic, which implies that the numbers of interaction structures can be computed recursively. We obtain simple asymptotic formulas for 0- and 1-interaction structures. The simplest class of interaction structures are the 0-interaction structures, which represent the two backbone analogues of secondary structures.

Efficient near-field wireless energy transfer using adiabatic system variations

DOEpatents

Hamam, Rafif E.; Karalis, Aristeidis; Joannopoulos, John D.; Soljacic, Marin

2013-01-29

Disclosed is a method for transferring energy wirelessly including transferring energy wirelessly from a first resonator structure to an intermediate resonator structure, wherein the coupling rate between the first resonator structure and the intermediate resonator structure is .kappa..sub.1B, transferring energy wirelessly from the intermediate resonator structure to a second resonator structure, wherein the coupling rate between the intermediate resonator structure and the second resonator structure is .kappa..sub.B2, and during the wireless energy transfers, adjusting at least one of the coupling rates .kappa..sub.1B and .kappa..sub.B2 to reduce energy accumulation in the intermediate resonator structure and improve wireless energy transfer from the first resonator structure to the second resonator structure through the intermediate resonator structure.

Efficient near-field wireless energy transfer using adiabatic system variations

DOEpatents

Hamam, Rafif E; Karalis, Aristeidis; Joannopoulos, John D; Soljacic, Marin

2014-09-16

Disclosed is a method for transferring energy wirelessly including transferring energy wirelessly from a first resonator structure to an intermediate resonator structure, wherein the coupling rate between the first resonator structure and the intermediate resonator structure is .kappa..sub.1B, transferring energy wirelessly from the intermediate resonator structure to a second resonator structure, wherein the coupling rate between the intermediate resonator structure and the second resonator structure is .kappa..sub.B2, and during the wireless energy transfers, adjusting at least one of the coupling rates .kappa..sub.1B and .kappa..sub.B2 to reduce energy accumulation in the intermediate resonator structure and improve wireless energy transfer from the first resonator structure to the second resonator structure through the intermediate resonator structure.

The non-independence discussion about cycle structure in the computer language: the final simplification of computer language in the structural design

NASA Astrophysics Data System (ADS)

Yang, Peilu

2013-03-01

In the first place, the article discusses the theory, content, development, and questions about structured programming design. The further extension on this basement provides the cycle structure in computer language is the sequence structure, branch structure, and the cycle structure with independence. Through the deeply research by the writer, we find the non-independence and reach the final simplification about the computer language design. In the first, the writer provides the language structure of linear structure (I structure) and curvilinear structure (Y structure). This makes the computer language has high proficiency with simplification during the program exploration. The research in this article is corresponding with the widely used dualistic structure in the computer field. Moreover, it is greatly promote the evolution of computer language.

Taking advantage of local structure descriptors to analyze interresidue contacts in protein structures and protein complexes.

PubMed

Martin, Juliette; Regad, Leslie; Etchebest, Catherine; Camproux, Anne-Claude

2008-11-15

Interresidue protein contacts in proteins structures and at protein-protein interface are classically described by the amino acid types of interacting residues and the local structural context of the contact, if any, is described using secondary structures. In this study, we present an alternate analysis of interresidue contact using local structures defined by the structural alphabet introduced by Camproux et al. This structural alphabet allows to describe a 3D structure as a sequence of prototype fragments called structural letters, of 27 different types. Each residue can then be assigned to a particular local structure, even in loop regions. The analysis of interresidue contacts within protein structures defined using Voronoï tessellations reveals that pairwise contact specificity is greater in terms of structural letters than amino acids. Using a simple heuristic based on specificity score comparison, we find that 74% of the long-range contacts within protein structures are better described using structural letters than amino acid types. The investigation is extended to a set of protein-protein complexes, showing that the similar global rules apply as for intraprotein contacts, with 64% of the interprotein contacts best described by local structures. We then present an evaluation of pairing functions integrating structural letters to decoy scoring and show that some complexes could benefit from the use of structural letter-based pairing functions.

Dali server update.

PubMed

Holm, Liisa; Laakso, Laura M

2016-07-08

The Dali server (http://ekhidna2.biocenter.helsinki.fi/dali) is a network service for comparing protein structures in 3D. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. The Dali server has been running in various places for over 20 years and is used routinely by crystallographers on newly solved structures. The latest update of the server provides enhanced analytics for the study of sequence and structure conservation. The server performs three types of structure comparisons: (i) Protein Data Bank (PDB) search compares one query structure against those in the PDB and returns a list of similar structures; (ii) pairwise comparison compares one query structure against a list of structures specified by the user; and (iii) all against all structure comparison returns a structural similarity matrix, a dendrogram and a multidimensional scaling projection of a set of structures specified by the user. Structural superimpositions are visualized using the Java-free WebGL viewer PV. The structural alignment view is enhanced by sequence similarity searches against Uniprot. The combined structure-sequence alignment information is compressed to a stack of aligned sequence logos. In the stack, each structure is structurally aligned to the query protein and represented by a sequence logo. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Construction of crystal structure prototype database: methods and applications.

PubMed

Su, Chuanxun; Lv, Jian; Li, Quan; Wang, Hui; Zhang, Lijun; Wang, Yanchao; Ma, Yanming

2017-04-26

Crystal structure prototype data have become a useful source of information for materials discovery in the fields of crystallography, chemistry, physics, and materials science. This work reports the development of a robust and efficient method for assessing the similarity of structures on the basis of their interatomic distances. Using this method, we proposed a simple and unambiguous definition of crystal structure prototype based on hierarchical clustering theory, and constructed the crystal structure prototype database (CSPD) by filtering the known crystallographic structures in a database. With similar method, a program structure prototype analysis package (SPAP) was developed to remove similar structures in CALYPSO prediction results and extract predicted low energy structures for a separate theoretical structure database. A series of statistics describing the distribution of crystal structure prototypes in the CSPD was compiled to provide an important insight for structure prediction and high-throughput calculations. Illustrative examples of the application of the proposed database are given, including the generation of initial structures for structure prediction and determination of the prototype structure in databases. These examples demonstrate the CSPD to be a generally applicable and useful tool for materials discovery.

Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement

PubMed Central

Xu, Dong; Zhang, Jian; Roy, Ambrish; Zhang, Yang

2011-01-01

I-TASSER is an automated pipeline for protein tertiary structure prediction using multiple threading alignments and iterative structure assembly simulations. In CASP9 experiments, two new algorithms, QUARK and FG-MD, were added to the I-TASSER pipeline for improving the structural modeling accuracy. QUARK is a de novo structure prediction algorithm used for structure modeling of proteins that lack detectable template structures. For distantly homologous targets, QUARK models are found useful as a reference structure for selecting good threading alignments and guiding the I-TASSER structure assembly simulations. FG-MD is an atomic-level structural refinement program that uses structural fragments collected from the PDB structures to guide molecular dynamics simulation and improve the local structure of predicted model, including hydrogen-bonding networks, torsion angles and steric clashes. Despite considerable progress in both the template-based and template-free structure modeling, significant improvements on protein target classification, domain parsing, model selection, and ab initio folding of beta-proteins are still needed to further improve the I-TASSER pipeline. PMID:22069036

Construction of crystal structure prototype database: methods and applications

NASA Astrophysics Data System (ADS)

Su, Chuanxun; Lv, Jian; Li, Quan; Wang, Hui; Zhang, Lijun; Wang, Yanchao; Ma, Yanming

2017-04-01

Crystal structure prototype data have become a useful source of information for materials discovery in the fields of crystallography, chemistry, physics, and materials science. This work reports the development of a robust and efficient method for assessing the similarity of structures on the basis of their interatomic distances. Using this method, we proposed a simple and unambiguous definition of crystal structure prototype based on hierarchical clustering theory, and constructed the crystal structure prototype database (CSPD) by filtering the known crystallographic structures in a database. With similar method, a program structure prototype analysis package (SPAP) was developed to remove similar structures in CALYPSO prediction results and extract predicted low energy structures for a separate theoretical structure database. A series of statistics describing the distribution of crystal structure prototypes in the CSPD was compiled to provide an important insight for structure prediction and high-throughput calculations. Illustrative examples of the application of the proposed database are given, including the generation of initial structures for structure prediction and determination of the prototype structure in databases. These examples demonstrate the CSPD to be a generally applicable and useful tool for materials discovery.

A Review of Influence of Various Types of Structural Bracing to the Structural Performance of Buildings

NASA Astrophysics Data System (ADS)

Razak, S. M.; Kong, T. C.; Zainol, N. Z.; Adnan, A.; Azimi, M.

2018-03-01

Excessive lateral drift can contribute significantly towards crack formation, leading to structural damage. The structural damage will in turn reduce the capacity of the structure and weaken it from the intended design capacity. Generally, lateral drift is more pronounced in higher and longer structure, such as high rise buildings and bridges. A typical method employed to control lateral drift is structural bracing, which works by increasing stiffness and stability of structure. This paper reviews the influence of various types of structural bracing to structural performance of buildings. The history of structural bracing is visited and the differences between numerous structural bracing in term of suitability to different types of buildings and loading, mechanisms, technical details, advantages and limitations, and the overall effect on the structural behaviour and performance are dissected. Proper and efficient structural bracing is pertinent for each high rise building as this will lead towards safer, sustainable and more economical buildings, which are cheaper to maintain throughout the life of the buildings in the future.

Efficient near-field wireless energy transfer using adiabatic system variations

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

Hamam, Rafif E.; Karalis, Aristeidis; Joannopoulos, John D.

Disclosed is a method for transferring energy wirelessly including transferring energy wirelessly from a first resonator structure to an intermediate resonator structure, wherein the coupling rate between the first resonator structure and the intermediate resonator structure is .kappa..sub.1B, transferring energy wirelessly from the intermediate resonator structure to a second resonator structure, wherein the coupling rate between the intermediate resonator structure and the second resonator structure is .kappa..sub.B2, and during the wireless energy transfers, adjusting at least one of the coupling rates .kappa..sub.1B and .kappa..sub.B2 to reduce energy accumulation in the intermediate resonator structure and improve wireless energy transfer from themore » first resonator structure to the second resonator structure through the intermediate resonator structure.« less

Prosodic Structure as a Parallel to Musical Structure

PubMed Central

Heffner, Christopher C.; Slevc, L. Robert

2015-01-01

What structural properties do language and music share? Although early speculation identified a wide variety of possibilities, the literature has largely focused on the parallels between musical structure and syntactic structure. Here, we argue that parallels between musical structure and prosodic structure deserve more attention. We review the evidence for a link between musical and prosodic structure and find it to be strong. In fact, certain elements of prosodic structure may provide a parsimonious comparison with musical structure without sacrificing empirical findings related to the parallels between language and music. We then develop several predictions related to such a hypothesis. PMID:26733930

Security system

DOEpatents

Baumann, Mark J.; Kuca, Michal; Aragon, Mona L.

2016-02-02

A security system includes a structure having a structural surface. The structure is sized to contain an asset therein and configured to provide a forceful breaching delay. The structure has an opening formed therein to permit predetermined access to the asset contained within the structure. The structure includes intrusion detection features within or associated with the structure that are activated in response to at least a partial breach of the structure.

In Search of Structures: How Does the Mind Explore Infinity?

ERIC Educational Resources Information Center

Singer, Florence Mihaela; Voica, Cristian

2010-01-01

When reasoning about infinite sets, children seem to activate four categories of conceptual structures: geometric (g-structures), arithmetic (a-structures), fractal-type (f-structures), and density-type (d-structures). Students select different problem-solving strategies depending on the structure they recognize within the problem domain. They…

47 CFR 27.56 - Antenna structures; air navigation safety.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 47 Telecommunication 2 2012-10-01 2012-10-01 false Antenna structures; air navigation safety. 27... SERVICES MISCELLANEOUS WIRELESS COMMUNICATIONS SERVICES Technical Standards § 27.56 Antenna structures; air navigation safety. A licensee that owns its antenna structure(s) must not allow such antenna structure(s) to...

47 CFR 27.56 - Antenna structures; air navigation safety.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 47 Telecommunication 2 2013-10-01 2013-10-01 false Antenna structures; air navigation safety. 27... SERVICES MISCELLANEOUS WIRELESS COMMUNICATIONS SERVICES Technical Standards § 27.56 Antenna structures; air navigation safety. A licensee that owns its antenna structure(s) must not allow such antenna structure(s) to...

47 CFR 27.56 - Antenna structures; air navigation safety.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 47 Telecommunication 2 2011-10-01 2011-10-01 false Antenna structures; air navigation safety. 27... SERVICES MISCELLANEOUS WIRELESS COMMUNICATIONS SERVICES Technical Standards § 27.56 Antenna structures; air navigation safety. A licensee that owns its antenna structure(s) must not allow such antenna structure(s) to...

47 CFR 27.56 - Antenna structures; air navigation safety.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 47 Telecommunication 2 2014-10-01 2014-10-01 false Antenna structures; air navigation safety. 27... SERVICES MISCELLANEOUS WIRELESS COMMUNICATIONS SERVICES Technical Standards § 27.56 Antenna structures; air navigation safety. A licensee that owns its antenna structure(s) must not allow such antenna structure(s) to...

Vertical structure use by the Stout Iguana (Cyclura pinguis) on Guana Island, BVI

USGS Publications Warehouse

Cheek, Christopher A.; Hlavaty, Shay; Perkins, Rebecca N.; Peyton, Mark A.; Ryan, Caitlin N.; Zavaleta, Jennifer C.; Boal, Clint W.; Perry, Gad

2013-01-01

The Stout Iguana (Cyclura pinguis) is a critically endangered species endemic to the Puerto Rico Bank and currently restricted to the British Virgin Islands (BVI). Our study on Guana Island, BVI, focused on vertical structure use. Based on previous incidental observations, we hypothesized that Stout Iguanas use vertical structures and that adults and juveniles use such structures differently. In October 2011, we documented movement and vertical structure use by adult (n = 4) and juvenile (n = 11) iguanas with tracking bobbins. We recorded structure types used, heights attained on structures, distances between structures, and structure sizes. We found that Stout Iguanas used vertical structure more than previously documented. Trees comprised a significantly greater (P < 0.001) proportion of structures used by juveniles than by adults, whereas rocks comprised the greatest proportion of structures used by adults. In addition to differential structure use, juveniles climbed significantly higher (2.4 vs. 0.9 m on average; P < 0.001) than adults. We found no difference in the diameter or distance between structures used by adults and juveniles. Our results suggest that vertical structure use may be an important habitat element for free-ranging juvenile Stout Iguanas. Habitat management that provides vertical structure may be advantageous for the conservation of this species.

Magnetic multilayer structure

DOEpatents

Herget, Philipp; O'Sullivan, Eugene J.; Romankiw, Lubomyr T.; Wang, Naigang; Webb, Bucknell C.

2016-07-05

A mechanism is provided for an integrated laminated magnetic device. A substrate and a multilayer stack structure form the device. The multilayer stack structure includes alternating magnetic layers and diode structures formed on the substrate. Each magnetic layer in the multilayer stack structure is separated from another magnetic layer in the multilayer stack structure by a diode structure.

Magnetic multilayer structure

DOEpatents

Herget, Philipp; O'Sullivan, Eugene J.; Romankiw, Lubomyr T.; Wang, Naigang; Webb, Bucknell C.

2017-03-21

A mechanism is provided for an integrated laminated magnetic device. A substrate and a multilayer stack structure form the device. The multilayer stack structure includes alternating magnetic layers and diode structures formed on the substrate. Each magnetic layer in the multilayer stack structure is separated from another magnetic layer in the multilayer stack structure by a diode structure.

The Structure of Ill-Structured (and Well-Structured) Problems Revisited

ERIC Educational Resources Information Center

Reed, Stephen K.

2016-01-01

In his 1973 article "The Structure of ill structured problems", Herbert Simon proposed that solving ill-structured problems could be modeled within the same information-processing framework developed for solving well-structured problems. This claim is reexamined within the context of over 40 years of subsequent research and theoretical…

Effect of Initial Microstructure on Impact Toughness of 1200 MPa-Class High Strength Steel with Ultrafine Elongated Grain Structure

NASA Astrophysics Data System (ADS)

Jafari, Meysam; Garrison, Warren M.; Tsuzaki, Kaneaki

2014-02-01

A medium-carbon low-alloy steel was prepared with initial structures of either martensite or bainite. For both initial structures, warm caliber-rolling was conducted at 773 K (500 °C) to obtain ultrafine elongated grain (UFEG) structures with strong <110>//rolling direction (RD) fiber deformation textures. The UFEG structures consisted of spheroidal cementite particles distributed uniformly in a ferrite matrix of a transverse grain size of about 331 and 311 nm in samples with initial martensite and bainite structures, respectively. For both initial structures, the UFEG materials had similar tensile properties, upper shelf energy (145 J), and ductile-to-brittle transition temperatures 98 K (500 °C). Obtaining the martensitic structure requires more rapid cooling than is needed to obtain the bainitic structure and this more rapid cooling promote cracking. As the UFEG structures obtained from initial martensitic and bainitic structures have almost identical properties, but obtaining the bainitic structure does not require a rapid cooling which promotes cracking suggests the use of a bainitic structure in obtaining UFEG structures should be examined further.

Computational structural mechanics for engine structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

1988-01-01

The computational structural mechanics (CSM) program at Lewis encompasses the formulation and solution of structural mechanics problems and the development of integrated software systems to computationally simulate the performance, durability, and life of engine structures. It is structured to supplement, complement, and, whenever possible, replace costly experimental efforts. Specific objectives are to investigate unique advantages of parallel and multiprocessing for reformulating and solving structural mechanics and formulating and solving multidisciplinary mechanics and to develop integrated structural system computational simulators for predicting structural performance, evaluating newly developed methods, and identifying and prioritizing improved or missing methods.

Computational structural mechanics for engine structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

1989-01-01

The computational structural mechanics (CSM) program at Lewis encompasses the formulation and solution of structural mechanics problems and the development of integrated software systems to computationally simulate the performance, durability, and life of engine structures. It is structured to supplement, complement, and, whenever possible, replace costly experimental efforts. Specific objectives are to investigate unique advantages of parallel and multiprocessing for reformulating and solving structural mechanics and formulating and solving multidisciplinary mechanics and to develop integrated structural system computational simulators for predicting structural performance, evaluating newly developed methods, and identifying and prioritizing improved or missing methods.

Computing the Partition Function for Kinetically Trapped RNA Secondary Structures

PubMed Central

Lorenz, William A.; Clote, Peter

2011-01-01

An RNA secondary structure is locally optimal if there is no lower energy structure that can be obtained by the addition or removal of a single base pair, where energy is defined according to the widely accepted Turner nearest neighbor model. Locally optimal structures form kinetic traps, since any evolution away from a locally optimal structure must involve energetically unfavorable folding steps. Here, we present a novel, efficient algorithm to compute the partition function over all locally optimal secondary structures of a given RNA sequence. Our software, RNAlocopt runs in time and space. Additionally, RNAlocopt samples a user-specified number of structures from the Boltzmann subensemble of all locally optimal structures. We apply RNAlocopt to show that (1) the number of locally optimal structures is far fewer than the total number of structures – indeed, the number of locally optimal structures approximately equal to the square root of the number of all structures, (2) the structural diversity of this subensemble may be either similar to or quite different from the structural diversity of the entire Boltzmann ensemble, a situation that depends on the type of input RNA, (3) the (modified) maximum expected accuracy structure, computed by taking into account base pairing frequencies of locally optimal structures, is a more accurate prediction of the native structure than other current thermodynamics-based methods. The software RNAlocopt constitutes a technical breakthrough in our study of the folding landscape for RNA secondary structures. For the first time, locally optimal structures (kinetic traps in the Turner energy model) can be rapidly generated for long RNA sequences, previously impossible with methods that involved exhaustive enumeration. Use of locally optimal structure leads to state-of-the-art secondary structure prediction, as benchmarked against methods involving the computation of minimum free energy and of maximum expected accuracy. Web server and source code available at http://bioinformatics.bc.edu/clotelab/RNAlocopt/. PMID:21297972

Improving consensus structure by eliminating averaging artifacts

PubMed Central

KC, Dukka B

2009-01-01

Background Common structural biology methods (i.e., NMR and molecular dynamics) often produce ensembles of molecular structures. Consequently, averaging of 3D coordinates of molecular structures (proteins and RNA) is a frequent approach to obtain a consensus structure that is representative of the ensemble. However, when the structures are averaged, artifacts can result in unrealistic local geometries, including unphysical bond lengths and angles. Results Herein, we describe a method to derive representative structures while limiting the number of artifacts. Our approach is based on a Monte Carlo simulation technique that drives a starting structure (an extended or a 'close-by' structure) towards the 'averaged structure' using a harmonic pseudo energy function. To assess the performance of the algorithm, we applied our approach to Cα models of 1364 proteins generated by the TASSER structure prediction algorithm. The average RMSD of the refined model from the native structure for the set becomes worse by a mere 0.08 Å compared to the average RMSD of the averaged structures from the native structure (3.28 Å for refined structures and 3.36 A for the averaged structures). However, the percentage of atoms involved in clashes is greatly reduced (from 63% to 1%); in fact, the majority of the refined proteins had zero clashes. Moreover, a small number (38) of refined structures resulted in lower RMSD to the native protein versus the averaged structure. Finally, compared to PULCHRA [1], our approach produces representative structure of similar RMSD quality, but with much fewer clashes. Conclusion The benchmarking results demonstrate that our approach for removing averaging artifacts can be very beneficial for the structural biology community. Furthermore, the same approach can be applied to almost any problem where averaging of 3D coordinates is performed. Namely, structure averaging is also commonly performed in RNA secondary prediction [2], which could also benefit from our approach. PMID:19267905

Micro/nano-mechanical test system employing tensile test holder with push-to-pull transformer

DOEpatents

Oh, Yunje; Cyrankowski, Edward; Shan, Zhiwei; Asif, Syed Amanula Syed

2013-05-07

A micromachined or microelectromechanical system (MEMS) based push-to-pull mechanical transformer for tensile testing of micro-to-nanometer scale material samples including a first structure and a second structure. The second structure is coupled to the first structure by at least one flexible element that enables the second structure to be moveable relative to the first structure, wherein the second structure is disposed relative to the first structure so as to form a pulling gap between the first and second structures such that when an external pushing force is applied to and pushes the second structure in a tensile extension direction a width of the pulling gap increases so as to apply a tensile force to a test sample mounted across the pulling gap between a first sample mounting area on the first structure and a second sample mounting area on the second structure.

Micro/nano-mechanical test system employing tensile test holder with push-to-pull transformer

DOEpatents

Oh, Yunje; Cyrankowski, Edward; Shan, Zhiwei; Syed Asif, Syed Amanula

2014-07-29

A micromachined or microelectromechanical system (MEMS) based push-to-pull mechanical transformer for tensile testing of micro-to-nanometer scale material samples including a first structure and a second structure. The second structure is coupled to the first structure by at least one flexible element that enables the second structure to be moveable relative to the first structure, wherein the second structure is disposed relative to the first structure so as to form a pulling gap between the first and second structures such that when an external pushing force is applied to and pushes the second structure in a tensile extension direction a width of the pulling gap increases so as to apply a tensile force to a test sample mounted across the pulling gap between a first sample mounting area on the first structure and a second sample mounting area on the second structure.

Electro-dynamic machine, system and method

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

Ouyang, Wen; Ramanan, Varagur

One embodiment is a unique Vernier machine comprising a rotor and a stator. The rotor comprises a back portion and a plurality of permanent magnets. The stator comprises a plurality of ferromagnetic arm structures, a plurality of ferromagnetic pole structures extending from each of the ferromagnetic arm structures in a direction toward the permanent magnets, and a plurality of conductive windings disposed about respective ones of the plurality of ferromagnetic arm structures. The ferromagnetic pole structures are structured to collect magnetic flux from the permanent magnets. The ferromagnetic pole structures of each of said ferromagnetic arm structures are spaced apartmore » from one another according to a non-uniform pattern such that the ferromagnetic pole structures of a given ferromagnetic arm structure have substantially the same angular position relative to the permanent magnets radially opposite from the ferromagnetic pole structures of the given ferromagnetic arm structure.« less

In silico local structure approach: a case study on outer membrane proteins.

PubMed

Martin, Juliette; de Brevern, Alexandre G; Camproux, Anne-Claude

2008-04-01

The detection of Outer Membrane Proteins (OMP) in whole genomes is an actual question, their sequence characteristics have thus been intensively studied. This class of protein displays a common beta-barrel architecture, formed by adjacent antiparallel strands. However, due to the lack of available structures, few structural studies have been made on this class of proteins. Here we propose a novel OMP local structure investigation, based on a structural alphabet approach, i.e., the decomposition of 3D structures using a library of four-residue protein fragments. The optimal decomposition of structures using hidden Markov model results in a specific structural alphabet of 20 fragments, six of them dedicated to the decomposition of beta-strands. This optimal alphabet, called SA20-OMP, is analyzed in details, in terms of local structures and transitions between fragments. It highlights a particular and strong organization of beta-strands as series of regular canonical structural fragments. The comparison with alphabets learned on globular structures indicates that the internal organization of OMP structures is more constrained than in globular structures. The analysis of OMP structures using SA20-OMP reveals some recurrent structural patterns. The preferred location of fragments in the distinct regions of the membrane is investigated. The study of pairwise specificity of fragments reveals that some contacts between structural fragments in beta-sheets are clearly favored whereas others are avoided. This contact specificity is stronger in OMP than in globular structures. Moreover, SA20-OMP also captured sequential information. This can be integrated in a scoring function for structural model ranking with very promising results. (c) 2007 Wiley-Liss, Inc.

Structure based alignment and clustering of proteins (STRALCP)

DOEpatents

Zemla, Adam T.; Zhou, Carol E.; Smith, Jason R.; Lam, Marisa W.

2013-06-18

Disclosed are computational methods of clustering a set of protein structures based on local and pair-wise global similarity values. Pair-wise local and global similarity values are generated based on pair-wise structural alignments for each protein in the set of protein structures. Initially, the protein structures are clustered based on pair-wise local similarity values. The protein structures are then clustered based on pair-wise global similarity values. For each given cluster both a representative structure and spans of conserved residues are identified. The representative protein structure is used to assign newly-solved protein structures to a group. The spans are used to characterize conservation and assign a "structural footprint" to the cluster.

Equivalent refractive-index structure constant of non-Kolmogorov turbulence.

PubMed

Li, Yujie; Zhu, Wenyue; Wu, Xiaoqing; Rao, Ruizhong

2015-09-07

The relationship between the non-Kolmogorov refractive-index structure constant and the Kolmogorov refractive-index structure constant is derived by using the refractive-index structure function and the variance of refractive-index fluctuations. It shows that the non-Kolmogorov structure constant is proportional to the Kolmogorov structure constant and the scaling factor depends on the outer scale and the spectral power law. For a fixed Kolmogorov structure constant, the non-Kolmogorov structure constant increases with a increasing outer scale for the power law less than 11/3, the trend is opposite for the power law greater than 11/3. This equivalent relation provides a way of obtaining the non-Kolmogorov structure constant by using the Kolmogorov structure constant.

Utilization of protein intrinsic disorder knowledge in structural proteomics

PubMed Central

Oldfield, Christopher J.; Xue, Bin; Van, Ya-Yue; Ulrich, Eldon L.; Markley, John L.; Dunker, A. Keith; Uversky, Vladimir N.

2014-01-01

Intrinsically disordered proteins (IDPs) and proteins with long disordered regions are highly abundant in various proteomes. Despite their lack of well-defined ordered structure, these proteins and regions are frequently involved in crucial biological processes. Although in recent years these proteins have attracted the attention of many researchers, IDPs represent a significant challenge for structural characterization since these proteins can impact many of the processes in the structure determination pipeline. Here we investigate the effects of IDPs on the structure determination process and the utility of disorder prediction in selecting and improving proteins for structural characterization. Examination of the extent of intrinsic disorder in existing crystal structures found that relatively few protein crystal structures contain extensive regions of intrinsic disorder. Although intrinsic disorder is not the only cause of crystallization failures and many structured proteins cannot be crystallized, filtering out highly disordered proteins from structure-determination target lists is still likely to be cost effective. Therefore it is desirable to avoid highly disordered proteins from structure-determination target lists and we show that disorder prediction can be applied effectively to enrich structure determination pipelines with proteins more likely to yield crystal structures. For structural investigation of specific proteins, disorder prediction can be used to improve targets for structure determination. Finally, a framework for considering intrinsic disorder in the structure determination pipeline is proposed. PMID:23232152

Gaia: automated quality assessment of protein structure models.

PubMed

Kota, Pradeep; Ding, Feng; Ramachandran, Srinivas; Dokholyan, Nikolay V

2011-08-15

Increasing use of structural modeling for understanding structure-function relationships in proteins has led to the need to ensure that the protein models being used are of acceptable quality. Quality of a given protein structure can be assessed by comparing various intrinsic structural properties of the protein to those observed in high-resolution protein structures. In this study, we present tools to compare a given structure to high-resolution crystal structures. We assess packing by calculating the total void volume, the percentage of unsatisfied hydrogen bonds, the number of steric clashes and the scaling of the accessible surface area. We assess covalent geometry by determining bond lengths, angles, dihedrals and rotamers. The statistical parameters for the above measures, obtained from high-resolution crystal structures enable us to provide a quality-score that points to specific areas where a given protein structural model needs improvement. We provide these tools that appraise protein structures in the form of a web server Gaia (http://chiron.dokhlab.org). Gaia evaluates the packing and covalent geometry of a given protein structure and provides quantitative comparison of the given structure to high-resolution crystal structures. dokh@unc.edu Supplementary data are available at Bioinformatics online.

NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores.

PubMed

Ryu, Hyojung; Lim, GyuTae; Sung, Bong Hyun; Lee, Jinhyuk

2016-02-15

Protein structure refinement is a necessary step for the study of protein function. In particular, some nuclear magnetic resonance (NMR) structures are of lower quality than X-ray crystallographic structures. Here, we present NMRe, a web-based server for NMR structure refinement. The previously developed knowledge-based energy function STAP (Statistical Torsion Angle Potential) was used for NMRe refinement. With STAP, NMRe provides two refinement protocols using two types of distance restraints. If a user provides NOE (Nuclear Overhauser Effect) data, the refinement is performed with the NOE distance restraints as a conventional NMR structure refinement. Additionally, NMRe generates NOE-like distance restraints based on the inter-hydrogen distances derived from the input structure. The efficiency of NMRe refinement was validated on 20 NMR structures. Most of the quality assessment scores of the refined NMR structures were better than those of the original structures. The refinement results are provided as a three-dimensional structure view, a secondary structure scheme, and numerical and graphical structure validation scores. NMRe is available at http://psb.kobic.re.kr/nmre/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Molecular Dynamic Simulation of Space and Earth-Grown Crystal Structures of Thermostable T1 Lipase Geobacillus zalihae Revealed a Better Structure.

PubMed

Ishak, Siti Nor Hasmah; Aris, Sayangku Nor Ariati Mohamad; Halim, Khairul Bariyyah Abd; Ali, Mohd Shukuri Mohamad; Leow, Thean Chor; Kamarudin, Nor Hafizah Ahmad; Masomian, Malihe; Rahman, Raja Noor Zaliha Raja Abd

2017-09-25

Less sedimentation and convection in a microgravity environment has become a well-suited condition for growing high quality protein crystals. Thermostable T1 lipase derived from bacterium Geobacillus zalihae has been crystallized using the counter diffusion method under space and earth conditions. Preliminary study using YASARA molecular modeling structure program for both structures showed differences in number of hydrogen bond, ionic interaction, and conformation. The space-grown crystal structure contains more hydrogen bonds as compared with the earth-grown crystal structure. A molecular dynamics simulation study was used to provide insight on the fluctuations and conformational changes of both T1 lipase structures. The analysis of root mean square deviation (RMSD), radius of gyration, and root mean square fluctuation (RMSF) showed that space-grown structure is more stable than the earth-grown structure. Space-structure also showed more hydrogen bonds and ion interactions compared to the earth-grown structure. Further analysis also revealed that the space-grown structure has long-lived interactions, hence it is considered as the more stable structure. This study provides the conformational dynamics of T1 lipase crystal structure grown in space and earth condition.

Visualization of RNA structure models within the Integrative Genomics Viewer.

PubMed

Busan, Steven; Weeks, Kevin M

2017-07-01

Analyses of the interrelationships between RNA structure and function are increasingly important components of genomic studies. The SHAPE-MaP strategy enables accurate RNA structure probing and realistic structure modeling of kilobase-length noncoding RNAs and mRNAs. Existing tools for visualizing RNA structure models are not suitable for efficient analysis of long, structurally heterogeneous RNAs. In addition, structure models are often advantageously interpreted in the context of other experimental data and gene annotation information, for which few tools currently exist. We have developed a module within the widely used and well supported open-source Integrative Genomics Viewer (IGV) that allows visualization of SHAPE and other chemical probing data, including raw reactivities, data-driven structural entropies, and data-constrained base-pair secondary structure models, in context with linear genomic data tracks. We illustrate the usefulness of visualizing RNA structure in the IGV by exploring structure models for a large viral RNA genome, comparing bacterial mRNA structure in cells with its structure under cell- and protein-free conditions, and comparing a noncoding RNA structure modeled using SHAPE data with a base-pairing model inferred through sequence covariation analysis. © 2017 Busan and Weeks; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

A semi-supervised learning approach for RNA secondary structure prediction.

PubMed

Yonemoto, Haruka; Asai, Kiyoshi; Hamada, Michiaki

2015-08-01

RNA secondary structure prediction is a key technology in RNA bioinformatics. Most algorithms for RNA secondary structure prediction use probabilistic models, in which the model parameters are trained with reliable RNA secondary structures. Because of the difficulty of determining RNA secondary structures by experimental procedures, such as NMR or X-ray crystal structural analyses, there are still many RNA sequences that could be useful for training whose secondary structures have not been experimentally determined. In this paper, we introduce a novel semi-supervised learning approach for training parameters in a probabilistic model of RNA secondary structures in which we employ not only RNA sequences with annotated secondary structures but also ones with unknown secondary structures. Our model is based on a hybrid of generative (stochastic context-free grammars) and discriminative models (conditional random fields) that has been successfully applied to natural language processing. Computational experiments indicate that the accuracy of secondary structure prediction is improved by incorporating RNA sequences with unknown secondary structures into training. To our knowledge, this is the first study of a semi-supervised learning approach for RNA secondary structure prediction. This technique will be useful when the number of reliable structures is limited. Copyright © 2015 Elsevier Ltd. All rights reserved.

Convergence of an iterative procedure for large-scale static analysis of structural components

NASA Technical Reports Server (NTRS)

Austin, F.; Ojalvo, I. U.

1976-01-01

The paper proves convergence of an iterative procedure for calculating the deflections of built-up component structures which can be represented as consisting of a dominant, relatively stiff primary structure and a less stiff secondary structure, which may be composed of one or more substructures that are not connected to one another but are all connected to the primary structure. The iteration consists in estimating the deformation of the primary structure in the absence of the secondary structure on the assumption that all mechanical loads are applied directly to the primary structure. The j-th iterate primary structure deflections at the interface are imposed on the secondary structure, and the boundary loads required to produce these deflections are computed. The cycle is completed by applying the interface reaction to the primary structure and computing its updated deflections. It is shown that the mathematical condition for convergence of this procedure is that the maximum eigenvalue of the equation relating primary-structure deflection to imposed secondary-structure deflection be less than unity, which is shown to correspond with the physical requirement that the secondary structure be more flexible at the interface boundary.

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

Manikandan, M.; Santhosh, M.; Rajeswarapalanichamy, R., E-mail: rrpalanichamy@gmail.com

Ab initio calculations are performed to investigate the structural stability, electronic structure and mechanical properties of actinide carbides AnC (An=U, Np) for three different crystal structures, namely NaCl, CsCl and ZnS. Among the considered structures, NaCl structure is found to be the most stable structure for these carbides at normal pressure. A pressure induced structural phase transition from NaCl to ZnS is observed. The electronic structure reveals that these carbides are metals. The calculated elastic constants indicate that these carbides are mechanically stable at normal pressure.

Separation system

DOEpatents

Rubin, Leslie S.

1986-01-01

A separation system for dewatering radioactive waste materials includes a disposal container, drive structure for receiving the container, and means for releasably attaching the container to the drive structure. Separation structure disposed in the container adjacent the inner surface of the side wall structure retains solids while allowing passage of liquids. Inlet port structure in the container top wall is normally closed by first valve structure that is centrifugally actuated to open the inlet port and discharge port structure at the container periphery receives liquid that passes through the separation structure and is normally closed by second valve structure that is centrifugally actuated to open the discharge ports. The container also includes coupling structure for releasable engagement with the centrifugal drive structure. Centrifugal force produced when the container is driven in rotation by the drive structure opens the valve structures, and radioactive waste material introduced into the container through the open inlet port is dewatered, and the waste is compacted. The ports are automatically closed by the valves when the container drum is not subjected to centrifugal force such that containment effectiveness is enhanced and exposure of personnel to radioactive materials is minimized.

Probabilistic structural analysis methods of hot engine structures

NASA Technical Reports Server (NTRS)

Chamis, C. C.; Hopkins, D. A.

1989-01-01

Development of probabilistic structural analysis methods for hot engine structures at Lewis Research Center is presented. Three elements of the research program are: (1) composite load spectra methodology; (2) probabilistic structural analysis methodology; and (3) probabilistic structural analysis application. Recent progress includes: (1) quantification of the effects of uncertainties for several variables on high pressure fuel turbopump (HPFT) turbine blade temperature, pressure, and torque of the space shuttle main engine (SSME); (2) the evaluation of the cumulative distribution function for various structural response variables based on assumed uncertainties in primitive structural variables; and (3) evaluation of the failure probability. Collectively, the results demonstrate that the structural durability of hot engine structural components can be effectively evaluated in a formal probabilistic/reliability framework.

Lewis Structures Technology, 1988. Volume 3: Structural Integrity Fatigue and Fracture Wind Turbines HOST

NASA Technical Reports Server (NTRS)

1988-01-01

The charter of the Structures Division is to perform and disseminate results of research conducted in support of aerospace engine structures. These results have a wide range of applicability to practioners of structural engineering mechanics beyond the aerospace arena. The specific purpose of the symposium was to familiarize the engineering structures community with the depth and range of research performed by the division and its academic and industrial partners. Sessions covered vibration control, fracture mechanics, ceramic component reliability, parallel computing, nondestructive evaluation, constitutive models and experimental capabilities, dynamic systems, fatigue and damage, wind turbines, hot section technology (HOST), aeroelasticity, structural mechanics codes, computational methods for dynamics, structural optimization, and applications of structural dynamics, and structural mechanics computer codes.

Likelihood-based modification of experimental crystal structure electron density maps

DOEpatents

Terwilliger, Thomas C [Sante Fe, NM

2005-04-16

A maximum-likelihood method for improves an electron density map of an experimental crystal structure. A likelihood of a set of structure factors {F.sub.h } is formed for the experimental crystal structure as (1) the likelihood of having obtained an observed set of structure factors {F.sub.h.sup.OBS } if structure factor set {F.sub.h } was correct, and (2) the likelihood that an electron density map resulting from {F.sub.h } is consistent with selected prior knowledge about the experimental crystal structure. The set of structure factors {F.sub.h } is then adjusted to maximize the likelihood of {F.sub.h } for the experimental crystal structure. An improved electron density map is constructed with the maximized structure factors.

Computational structural mechanics for engine structures

NASA Technical Reports Server (NTRS)

Chamis, C. C.

1989-01-01

The computational structural mechanics (CSM) program at Lewis encompasses: (1) fundamental aspects for formulating and solving structural mechanics problems, and (2) development of integrated software systems to computationally simulate the performance/durability/life of engine structures. It is structured to mainly supplement, complement, and whenever possible replace, costly experimental efforts which are unavoidable during engineering research and development programs. Specific objectives include: investigate unique advantages of parallel and multiprocesses for: reformulating/solving structural mechanics and formulating/solving multidisciplinary mechanics and develop integrated structural system computational simulators for: predicting structural performances, evaluating newly developed methods, and for identifying and prioritizing improved/missing methods needed. Herein the CSM program is summarized with emphasis on the Engine Structures Computational Simulator (ESCS). Typical results obtained using ESCS are described to illustrate its versatility.

Deciphering the shape and deformation of secondary structures through local conformation analysis

PubMed Central

2011-01-01

Background Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. Results Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface) reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations. Conclusion The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons. PMID:21284872

Three Types of Flower Structures in a Divergent-Wrench Fault Zone

NASA Astrophysics Data System (ADS)

Huang, Lei; Liu, Chi-yang

2017-12-01

Flower structures are typical features of wrench fault zones. In conventional studies, two distinct kinds of flower structures have been identified based on differences in their internal structural architecture: (1) negative flower structures characterized by synforms and normal separations and (2) positive flower structures characterized by antiforms and reverse separations. In addition to negative and positive flower structures, in this study, a third kind of flower structure was identified in a divergent-wrench fault zone, a hybrid characterized by both antiforms and normal separations. Negative flower structures widely occur in divergent-wrench fault zones, and their presence indicates the combined effects of extensional and strike-slip motion. In contrast, positive and hybrid flower structures occur only in fault restraining bends and step overs. A hybrid flower structure can be considered as product of a kind of structural deformation typical of divergent-wrench zones; it is the result of the combined effects of extensional, compressional, and strike-slip strains under a locally appropriate compressional environment. The strain situation in it represents the transition stage that in between positive and negative flower structures. Kinematic and dynamic characteristics of the hybrid flower structures indicate the salient features of structural deformation in restraining bends and step overs along divergent-wrench faults, including the coexistence of three kinds of strains (i.e., compression, extension, and strike-slip) and synchronous presence of compressional (i.e., typical fault-bend fold) and extensional (normal faults) deformation in the same place. Hybrid flower structures are also favorable for the accumulation of hydrocarbons because of their special structural configuration in divergent-wrench fault zones.

Deciphering the shape and deformation of secondary structures through local conformation analysis.

PubMed

Baussand, Julie; Camproux, Anne-Claude

2011-02-01

Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface) reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations. The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons.

40 CFR 165.87 - Design and capacity requirements for existing structures.

Code of Federal Regulations, 2013 CFR

2013-07-01

... existing containment structure: (1) The containment structure must be constructed of steel, reinforced... existing structures. 165.87 Section 165.87 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Structures § 165.87 Design and capacity requirements for existing structures. (a) For all existing...

40 CFR 165.87 - Design and capacity requirements for existing structures.

Code of Federal Regulations, 2011 CFR

2011-07-01

... existing containment structure: (1) The containment structure must be constructed of steel, reinforced... existing structures. 165.87 Section 165.87 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Structures § 165.87 Design and capacity requirements for existing structures. (a) For all existing...

40 CFR 165.87 - Design and capacity requirements for existing structures.

Code of Federal Regulations, 2012 CFR

2012-07-01

... existing containment structure: (1) The containment structure must be constructed of steel, reinforced... existing structures. 165.87 Section 165.87 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Structures § 165.87 Design and capacity requirements for existing structures. (a) For all existing...

40 CFR 165.87 - Design and capacity requirements for existing structures.

Code of Federal Regulations, 2014 CFR

2014-07-01

... existing containment structure: (1) The containment structure must be constructed of steel, reinforced... existing structures. 165.87 Section 165.87 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Structures § 165.87 Design and capacity requirements for existing structures. (a) For all existing...

Distributed multifunctional sensor network for composite structural state sensing

NASA Astrophysics Data System (ADS)

Qing, Xinlin P.; Wang, Yishou; Gao, Limin; Kumar, Amrita

2012-04-01

Advanced fiber reinforced composite materials are becoming the main structural materials of next generation of aircraft because of their high strength and stiffness to weight ratios, and strong designability. In order to take full advantages of composite materials, there is a need to develop an embeddable multifunctional sensing system to allow a structure to "feel" and "think" its structural state. In this paper, the concept of multifunctional sensor network integrated with a structure, similar to the human nervous system, has been developed. Different types of network sensors are permanently integrated within a composite structure to sense structural strain, temperature, moisture, aerodynamic pressure; monitor external impact on the structure; and detect structural damages. Utilizing this revolutionary concept, future composite structures can be designed and manufactured to provide multiple modes of information, so that the structures have the capabilities for intelligent sensing, environmental adaptation and multi-functionality. The challenges for building such a structural state sensing system and some solutions to address the challenges are also discussed in the paper.

New Era of Studying RNA Secondary Structure and Its Influence on Gene Regulation in Plants.

PubMed

Yang, Xiaofei; Yang, Minglei; Deng, Hongjing; Ding, Yiliang

2018-01-01

The dynamic structure of RNA plays a central role in post-transcriptional regulation of gene expression such as RNA maturation, degradation, and translation. With the rise of next-generation sequencing, the study of RNA structure has been transformed from in vitro low-throughput RNA structure probing methods to in vivo high-throughput RNA structure profiling. The development of these methods enables incremental studies on the function of RNA structure to be performed, revealing new insights of novel regulatory mechanisms of RNA structure in plants. Genome-wide scale RNA structure profiling allows us to investigate general RNA structural features over 10s of 1000s of mRNAs and to compare RNA structuromes between plant species. Here, we provide a comprehensive and up-to-date overview of: (i) RNA structure probing methods; (ii) the biological functions of RNA structure; (iii) genome-wide RNA structural features corresponding to their regulatory mechanisms; and (iv) RNA structurome evolution in plants.

Structural health monitoring system/method using electroactive polymer fibers

NASA Technical Reports Server (NTRS)

Scott-Carnell, Lisa A. (Inventor); Siochi, Emilie J. (Inventor)

2013-01-01

A method for monitoring the structural health of a structure of interest by coupling one or more electroactive polymer fibers to the structure and monitoring the electroactive responses of the polymer fiber(s). Load changes that are experienced by the structure cause changes in the baseline responses of the polymer fiber(s). A system for monitoring the structural health of the structure is also provided.

Taking structure searches to the next dimension.

PubMed

Schafferhans, Andrea; Rost, Burkhard

2014-07-08

Structure comparisons are now the first step when a new experimental high-resolution protein structure has been determined. In this issue of Structure, Wiederstein and colleagues describe their latest tool for comparing structures, which gives us the unprecedented power to discover crucial structural connections between whole complexes of proteins in the full structural database in real time. Copyright © 2014 Elsevier Ltd. All rights reserved.

Crossing Phenomena in Overhead Line Equipment (OHLE) Structure in 3D Space Considering Soil-Structure Interaction

NASA Astrophysics Data System (ADS)

Ngamkhanong, Chayut; Kaewunruen, Sakdirat; Baniotopoulos, Charalampos; Papaelias, Mayorkinos

2017-10-01

Nowadays, the electric train becomes one of the efficient railway systems that are lighter, cleaner, quieter, cheaper and faster than a conventional train. Overhead line equipment (OHLE), which supplies electric power to the trains, is designed on the principle of overhead wires placed over the railway track. The OHLE is supported by mast structure which located at the lineside along the track. Normally, mast structure is a steel column or truss structure which supports the overhead wire carrying the power. Due to the running train and severe periodic force, such as an earthquake, in surrounding area may cause damage to the OHLE structure especially mast structure which leads to the failure of the electrical system. The mast structure needs to be discussed in order to resist the random forces. Due to the vibration effect, the natural frequencies of the structure are necessary. This is because when the external applied force occurs within a range of frequency of the structure, resonance effect can be expected which lead to the large oscillations and deflections. The natural frequency of a system is dependent only on the stiffness of the structure and the mass which participates with the structure, including self-weight. The modal analysis is used in order to calculate the mode shapes and natural frequencies of the mast structure during free vibration. A mast structure with varying rotational soil stiffness is used to observe the influence of soil-structure action. It is common to use finite element analysis to perform a modal analysis. This paper presents the fundamental mode shapes, natural frequencies and crossing phenomena of three-dimensional mast structure considering soil-structure interaction. The sensitivity of mode shapes to the variation of soil-structure interaction is discussed. The outcome of this study will improve the understanding of the fundamental dynamic behaviour of the mast structure which supports the OHLE. Moreover, this study will be a recommendation for the structural engineer to associate with the behaviour of mast structure during vibration.

Lewis Structures Technology, 1988. Volume 2: Structural Mechanics

NASA Technical Reports Server (NTRS)

1988-01-01

Lewis Structures Div. performs and disseminates results of research conducted in support of aerospace engine structures. These results have a wide range of applicability to practitioners of structural engineering mechanics beyond the aerospace arena. The engineering community was familiarized with the depth and range of research performed by the division and its academic and industrial partners. Sessions covered vibration control, fracture mechanics, ceramic component reliability, parallel computing, nondestructive evaluation, constitutive models and experimental capabilities, dynamic systems, fatigue and damage, wind turbines, hot section technology (HOST), aeroelasticity, structural mechanics codes, computational methods for dynamics, structural optimization, and applications of structural dynamics, and structural mechanics computer codes.

16th International Conference on Nuclear Structure: NS2016

DOE PAGES

Galindo-Uribarri, Alfredo

2016-10-28

Every two years the Nuclear Structure (NS) conference series brings together researchers from an international community of experimental and theoretical nuclear physicists to present and discuss their latest results in nuclear structure. This biennial conference covered the latest results on experimental and theoretical research into the structure of nuclei at the extremes of isospin, excitation energy, mass, and angular momentum. Topics included many of the most exciting areas of modern nuclear structure research such as transitional behavior, nuclear structure and its evolution across the nuclear landscape, shell structure, collectivity, nuclear structure with radioactive beams, and macroscopic and microscopic approaches tomore » nuclear structure.« less

16th International Conference on Nuclear Structure: NS2016

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

Galindo-Uribarri, Alfredo

Every two years the Nuclear Structure (NS) conference series brings together researchers from an international community of experimental and theoretical nuclear physicists to present and discuss their latest results in nuclear structure. This biennial conference covered the latest results on experimental and theoretical research into the structure of nuclei at the extremes of isospin, excitation energy, mass, and angular momentum. Topics included many of the most exciting areas of modern nuclear structure research such as transitional behavior, nuclear structure and its evolution across the nuclear landscape, shell structure, collectivity, nuclear structure with radioactive beams, and macroscopic and microscopic approaches tomore » nuclear structure.« less

Deformation behavior of dragonfly-inspired nodus structured wing in gliding flight through experimental visualization approach.

PubMed

Zhang, Sheng; Sunami, Yuta; Hashimoto, Hiromu

2018-04-10

Dragonfly has excellent flight performance and maneuverability due to the complex vein structure of wing. In this research, nodus as an important structural element of the dragonfly wing is investigated through an experimental visualization approach. Three vein structures were fabricated as, open-nodus structure, closed-nodus structure (with a flex-limiter) and rigid wing. The samples were conducted in a wind tunnel with a high speed camera to visualize the deformation of wing structure in order to study the function of nodus structured wing in gliding flight. According to the experimental results, nodus has a great influence on the flexibility of the wing structure. Moreover, the closed-nodus wing (with a flex-limiter) enables the vein structure to be flexible without losing the strength and rigidity of the joint. These findings enhance the knowledge of insect-inspired nodus structured wing and facilitate the application of Micro Air Vehicle (MAV) in gliding flight.

Speckle lithography for fabricating Gaussian, quasi-random 2D structures and black silicon structures.

PubMed

Bingi, Jayachandra; Murukeshan, Vadakke Matham

2015-12-18

Laser speckle pattern is a granular structure formed due to random coherent wavelet interference and generally considered as noise in optical systems including photolithography. Contrary to this, in this paper, we use the speckle pattern to generate predictable and controlled Gaussian random structures and quasi-random structures photo-lithographically. The random structures made using this proposed speckle lithography technique are quantified based on speckle statistics, radial distribution function (RDF) and fast Fourier transform (FFT). The control over the speckle size, density and speckle clustering facilitates the successful fabrication of black silicon with different surface structures. The controllability and tunability of randomness makes this technique a robust method for fabricating predictable 2D Gaussian random structures and black silicon structures. These structures can enhance the light trapping significantly in solar cells and hence enable improved energy harvesting. Further, this technique can enable efficient fabrication of disordered photonic structures and random media based devices.

User's guide to computer program CIVM-JET 4B to calculate the transient structural responses of partial and/or complete structural rings to engine-rotor-fragment impact

NASA Technical Reports Server (NTRS)

Stagliano, T. R.; Spilker, R. L.; Witmer, E. A.

1976-01-01

A user-oriented computer program CIVM-JET 4B is described to predict the large-deflection elastic-plastic structural responses of fragment impacted single-layer: (a) partial-ring fragment containment or deflector structure or (b) complete-ring fragment containment structure. These two types of structures may be either free or supported in various ways. Supports accommodated include: (1) point supports such as pinned-fixed, ideally-clamped, or supported by a structural branch simulating mounting-bracket structure and (2) elastic foundation support distributed over selected regions of the structure. The initial geometry of each partial or complete ring may be circular or arbitrarily curved; uniform or variable thicknesses of the structure are accommodated. The structural material is assumed to be initially isotropic; strain hardening and strain rate effects are taken into account.

Reduction of the Radiating Sound of a Submerged Finite Cylindrical Shell Structure by Active Vibration Control

PubMed Central

Kim, Heung Soo; Sohn, Jung Woo; Jeon, Juncheol; Choi, Seung-Bok

2013-01-01

In this work, active vibration control of an underwater cylindrical shell structure was investigated, to suppress structural vibration and structure-borne noise in water. Finite element modeling of the submerged cylindrical shell structure was developed, and experimentally evaluated. Modal reduction was conducted to obtain the reduced system equation for the active feedback control algorithm. Three Macro Fiber Composites (MFCs) were used as actuators and sensors. One MFC was used as an exciter. The optimum control algorithm was designed based on the reduced system equations. The active control performance was then evaluated using the lab scale underwater cylindrical shell structure. Structural vibration and structure-borne noise of the underwater cylindrical shell structure were reduced significantly by activating the optimal controller associated with the MFC actuators. The results provide that active vibration control of the underwater structure is a useful means to reduce structure-borne noise in water. PMID:23389344

Reduction of the radiating sound of a submerged finite cylindrical shell structure by active vibration control.

PubMed

Kim, Heung Soo; Sohn, Jung Woo; Jeon, Juncheol; Choi, Seung-Bok

2013-02-06

In this work, active vibration control of an underwater cylindrical shell structure was investigated, to suppress structural vibration and structure-borne noise in water. Finite element modeling of the submerged cylindrical shell structure was developed, and experimentally evaluated. Modal reduction was conducted to obtain the reduced system equation for the active feedback control algorithm. Three Macro Fiber Composites (MFCs) were used as actuators and sensors. One MFC was used as an exciter. The optimum control algorithm was designed based on the reduced system equations. The active control performance was then evaluated using the lab scale underwater cylindrical shell structure. Structural vibration and structure-borne noise of the underwater cylindrical shell structure were reduced significantly by activating the optimal controller associated with the MFC actuators. The results provide that active vibration control of the underwater structure is a useful means to reduce structure-borne noise in water.

PDBFlex: exploring flexibility in protein structures

PubMed Central

Hrabe, Thomas; Li, Zhanwen; Sedova, Mayya; Rotkiewicz, Piotr; Jaroszewski, Lukasz; Godzik, Adam

2016-01-01

The PDBFlex database, available freely and with no login requirements at http://pdbflex.org, provides information on flexibility of protein structures as revealed by the analysis of variations between depositions of different structural models of the same protein in the Protein Data Bank (PDB). PDBFlex collects information on all instances of such depositions, identifying them by a 95% sequence identity threshold, performs analysis of their structural differences and clusters them according to their structural similarities for easy analysis. The PDBFlex contains tools and viewers enabling in-depth examination of structural variability including: 2D-scaling visualization of RMSD distances between structures of the same protein, graphs of average local RMSD in the aligned structures of protein chains, graphical presentation of differences in secondary structure and observed structural disorder (unresolved residues), difference distance maps between all sets of coordinates and 3D views of individual structures and simulated transitions between different conformations, the latter displayed using JSMol visualization software. PMID:26615193

47 CFR 22.365 - Antenna structures; air navigation safety.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 47 Telecommunication 2 2014-10-01 2014-10-01 false Antenna structures; air navigation safety. 22... Antenna structures; air navigation safety. Licensees that own their antenna structures must not allow these antenna structures to become a hazard to air navigation. In general, antenna structure owners are...

47 CFR 22.365 - Antenna structures; air navigation safety.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 47 Telecommunication 2 2012-10-01 2012-10-01 false Antenna structures; air navigation safety. 22... Antenna structures; air navigation safety. Licensees that own their antenna structures must not allow these antenna structures to become a hazard to air navigation. In general, antenna structure owners are...

47 CFR 22.365 - Antenna structures; air navigation safety.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 47 Telecommunication 2 2013-10-01 2013-10-01 false Antenna structures; air navigation safety. 22... Antenna structures; air navigation safety. Licensees that own their antenna structures must not allow these antenna structures to become a hazard to air navigation. In general, antenna structure owners are...

47 CFR 22.365 - Antenna structures; air navigation safety.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 47 Telecommunication 2 2011-10-01 2011-10-01 false Antenna structures; air navigation safety. 22... Antenna structures; air navigation safety. Licensees that own their antenna structures must not allow these antenna structures to become a hazard to air navigation. In general, antenna structure owners are...

47 CFR 22.365 - Antenna structures; air navigation safety.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 2 2010-10-01 2010-10-01 false Antenna structures; air navigation safety. 22... Antenna structures; air navigation safety. Licensees that own their antenna structures must not allow these antenna structures to become a hazard to air navigation. In general, antenna structure owners are...

Structuralism, Post-Structuralism, and Neo-Liberalism: Assessing Foucault's Legacy.

ERIC Educational Resources Information Center

Olssen, Mark

2003-01-01

Traces Foucault's distinctive commitment to "post-structuralism." Argues that under the influence of Nietzsche, Foucault's approach marks a distinct break with structuralism in several crucial aspects. What results is a materialist post-structuralism that is also distinctively different from the post-structuralism of Derrida, Lyotard,…

Structurally compliant microbearing devices and methods thereof

NASA Technical Reports Server (NTRS)

Boedo, Stephen (Inventor); Grande, William (Inventor)

2011-01-01

A microbearing device includes at least one inner bearing structure, at least one outer bearing structure, and one or more fasteners. Each of the one or more fasteners is connected between the inner bearing structure and the outer bearing structure and the inner bearing structure is substantially elastic.

Inferences from structural comparison: flexibility, secondary structure wobble and sequence alignment optimization.

PubMed

Zhang, Gaihua; Su, Zhen

2012-01-01

Work on protein structure prediction is very useful in biological research. To evaluate their accuracy, experimental protein structures or their derived data are used as the 'gold standard'. However, as proteins are dynamic molecular machines with structural flexibility such a standard may be unreliable. To investigate the influence of the structure flexibility, we analysed 3,652 protein structures of 137 unique sequences from 24 protein families. The results showed that (1) the three-dimensional (3D) protein structures were not rigid: the root-mean-square deviation (RMSD) of the backbone Cα of structures with identical sequences was relatively large, with the average of the maximum RMSD from each of the 137 sequences being 1.06 Å; (2) the derived data of the 3D structure was not constant, e.g. the highest ratio of the secondary structure wobble site was 60.69%, with the sequence alignments from structural comparisons of two proteins in the same family sometimes being completely different. Proteins may have several stable conformations and the data derived from resolved structures as a 'gold standard' should be optimized before being utilized as criteria to evaluate the prediction methods, e.g. sequence alignment from structural comparison. Helix/β-sheet transition exists in normal free proteins. The coil ratio of the 3D structure could affect its resolution as determined by X-ray crystallography.

Sequence-similar, structure-dissimilar protein pairs in the PDB.

PubMed

Kosloff, Mickey; Kolodny, Rachel

2008-05-01

It is often assumed that in the Protein Data Bank (PDB), two proteins with similar sequences will also have similar structures. Accordingly, it has proved useful to develop subsets of the PDB from which "redundant" structures have been removed, based on a sequence-based criterion for similarity. Similarly, when predicting protein structure using homology modeling, if a template structure for modeling a target sequence is selected by sequence alone, this implicitly assumes that all sequence-similar templates are equivalent. Here, we show that this assumption is often not correct and that standard approaches to create subsets of the PDB can lead to the loss of structurally and functionally important information. We have carried out sequence-based structural superpositions and geometry-based structural alignments of a large number of protein pairs to determine the extent to which sequence similarity ensures structural similarity. We find many examples where two proteins that are similar in sequence have structures that differ significantly from one another. The source of the structural differences usually has a functional basis. The number of such proteins pairs that are identified and the magnitude of the dissimilarity depend on the approach that is used to calculate the differences; in particular sequence-based structure superpositioning will identify a larger number of structurally dissimilar pairs than geometry-based structural alignments. When two sequences can be aligned in a statistically meaningful way, sequence-based structural superpositioning provides a meaningful measure of structural differences. This approach and geometry-based structure alignments reveal somewhat different information and one or the other might be preferable in a given application. Our results suggest that in some cases, notably homology modeling, the common use of nonredundant datasets, culled from the PDB based on sequence, may mask important structural and functional information. We have established a data base of sequence-similar, structurally dissimilar protein pairs that will help address this problem (http://luna.bioc.columbia.edu/rachel/seqsimstrdiff.htm).

Modeling, Analysis, and Optimization Issues for Large Space Structures

NASA Technical Reports Server (NTRS)

Pinson, L. D. (Compiler); Amos, A. K. (Compiler); Venkayya, V. B. (Compiler)

1983-01-01

Topics concerning the modeling, analysis, and optimization of large space structures are discussed including structure-control interaction, structural and structural dynamics modeling, thermal analysis, testing, and design.

Advances in engineering science, volume 2

NASA Technical Reports Server (NTRS)

1976-01-01

Papers are presented dealing with structural dynamics; structural synthesis; and the nonlinear analysis of structures, structural members, and composite structures and materials. Applications of mathematics and computer science are included.

77 FR 45518 - Airworthiness Directives; The Boeing Company Airplanes

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-01

... structure not supporting the limit load condition, which could lead to loss of structural integrity of the... wing structure not supporting the limit load condition, which could lead to loss of the structural... wing structure not supporting the limit load condition, which could lead to loss of structural...

First principles and experimental study of the electronic structure and phase stability of bulk thallium bromide

NASA Astrophysics Data System (ADS)

Smith, Holland M.; Zhou, Yuzhi; Ciampi, Guido; Kim, Hadong; Cirignano, Leonard J.; Shah, Kanai S.; Haller, E. E.; Chrzan, D. C.

2013-08-01

We apply state-of-art first principle calculations to study the polymorphism and electronic structure of three previously reported phases of TlBr. The calculated band structures of NaCl-structure phase and orthorhombic-structure phase have different features than that of commonly observed CsCl-structure phase. We further interpret photoluminescence spectra based on our calculations. Several peaks close to calculated band gap values of the NaCl-structure phase and the orthorhombic-structure phase are found in unpolished TlBr samples.

Design and Manufacturing of Composite Tower Structure for Wind Turbine Equipment

NASA Astrophysics Data System (ADS)

Park, Hyunbum

2018-02-01

This study proposes the composite tower design process for large wind turbine equipment. In this work, structural design of tower and analysis using finite element method was performed. After structural design, prototype blade manufacturing and test was performed. The used material is a glass fiber and epoxy resin composite. And also, sand was used in the middle part. The optimized structural design and analysis was performed. The parameter for optimized structural design is weight reduction and safety of structure. Finally, structure of tower will be confirmed by structural test.

Thermostructural analysis of three structural concepts for reusable space vehicles

NASA Technical Reports Server (NTRS)

Taylor, A. H.; Jackson, L. R.

1979-01-01

Three structural concepts are studied: (1) a state-of-the-art insulated aluminum skin-stringer structure; (2) a near-art insulated evacuated aluminum-alloy honeycomb structure; and (3) an advanced evacuated Rene 41 honeycomb hot structure. Each is evaluated for its thermostructural performance for each of the flight profiles (ascent, entry, and a recall or abort). Results indicate that (1) the state-of-the-art structure encounters negligible thermal stress; (2) the near-art structure has acceptable thermal stresses; and (3) the advanced structure will have thermal stress levels above the material allowables.

In Silico Analysis for the Study of Botulinum Toxin Structure

NASA Astrophysics Data System (ADS)

Suzuki, Tomonori; Miyazaki, Satoru

2010-01-01

Protein-protein interactions play many important roles in biological function. Knowledge of protein-protein complex structure is required for understanding the function. The determination of protein-protein complex structure by experimental studies remains difficult, therefore computational prediction of protein structures by structure modeling and docking studies is valuable method. In addition, MD simulation is also one of the most popular methods for protein structure modeling and characteristics. Here, we attempt to predict protein-protein complex structure and property using some of bioinformatic methods, and we focus botulinum toxin complex as target structure.

Structural reliability methods: Code development status

NASA Astrophysics Data System (ADS)

Millwater, Harry R.; Thacker, Ben H.; Wu, Y.-T.; Cruse, T. A.

1991-05-01

The Probabilistic Structures Analysis Method (PSAM) program integrates state of the art probabilistic algorithms with structural analysis methods in order to quantify the behavior of Space Shuttle Main Engine structures subject to uncertain loadings, boundary conditions, material parameters, and geometric conditions. An advanced, efficient probabilistic structural analysis software program, NESSUS (Numerical Evaluation of Stochastic Structures Under Stress) was developed as a deliverable. NESSUS contains a number of integrated software components to perform probabilistic analysis of complex structures. A nonlinear finite element module NESSUS/FEM is used to model the structure and obtain structural sensitivities. Some of the capabilities of NESSUS/FEM are shown. A Fast Probability Integration module NESSUS/FPI estimates the probability given the structural sensitivities. A driver module, PFEM, couples the FEM and FPI. NESSUS, version 5.0, addresses component reliability, resistance, and risk.

Reliability and risk assessment of structures

NASA Technical Reports Server (NTRS)

Chamis, C. C.

1991-01-01

Development of reliability and risk assessment of structural components and structures is a major activity at Lewis Research Center. It consists of five program elements: (1) probabilistic loads; (2) probabilistic finite element analysis; (3) probabilistic material behavior; (4) assessment of reliability and risk; and (5) probabilistic structural performance evaluation. Recent progress includes: (1) the evaluation of the various uncertainties in terms of cumulative distribution functions for various structural response variables based on known or assumed uncertainties in primitive structural variables; (2) evaluation of the failure probability; (3) reliability and risk-cost assessment; and (4) an outline of an emerging approach for eventual certification of man-rated structures by computational methods. Collectively, the results demonstrate that the structural durability/reliability of man-rated structural components and structures can be effectively evaluated by using formal probabilistic methods.

Structural reliability methods: Code development status

NASA Technical Reports Server (NTRS)

Millwater, Harry R.; Thacker, Ben H.; Wu, Y.-T.; Cruse, T. A.

1991-01-01

The Probabilistic Structures Analysis Method (PSAM) program integrates state of the art probabilistic algorithms with structural analysis methods in order to quantify the behavior of Space Shuttle Main Engine structures subject to uncertain loadings, boundary conditions, material parameters, and geometric conditions. An advanced, efficient probabilistic structural analysis software program, NESSUS (Numerical Evaluation of Stochastic Structures Under Stress) was developed as a deliverable. NESSUS contains a number of integrated software components to perform probabilistic analysis of complex structures. A nonlinear finite element module NESSUS/FEM is used to model the structure and obtain structural sensitivities. Some of the capabilities of NESSUS/FEM are shown. A Fast Probability Integration module NESSUS/FPI estimates the probability given the structural sensitivities. A driver module, PFEM, couples the FEM and FPI. NESSUS, version 5.0, addresses component reliability, resistance, and risk.

Plated lamination structures for integrated magnetic devices

DOEpatents

Webb, Bucknell C.

2014-06-17

Semiconductor integrated magnetic devices such as inductors, transformers, etc., having laminated magnetic-insulator stack structures are provided, wherein the laminated magnetic-insulator stack structures are formed using electroplating techniques. For example, an integrated laminated magnetic device includes a multilayer stack structure having alternating magnetic and insulating layers formed on a substrate, wherein each magnetic layer in the multilayer stack structure is separated from another magnetic layer in the multilayer stack structure by an insulating layer, and a local shorting structure to electrically connect each magnetic layer in the multilayer stack structure to an underlying magnetic layer in the multilayer stack structure to facilitate electroplating of the magnetic layers using an underlying conductive layer (magnetic or seed layer) in the stack as an electrical cathode/anode for each electroplated magnetic layer in the stack structure.

A PDE-based methodology for modeling, parameter estimation and feedback control in structural and structural acoustic systems

NASA Technical Reports Server (NTRS)

Banks, H. T.; Brown, D. E.; Metcalf, Vern L.; Silcox, R. J.; Smith, Ralph C.; Wang, Yun

1994-01-01

A problem of continued interest concerns the control of vibrations in a flexible structure and the related problem of reducing structure-borne noise in structural acoustic systems. In both cases, piezoceramic patches bonded to the structures have been successfully used as control actuators. Through the application of a controlling voltage, the patches can be used to reduce structural vibrations which in turn lead to methods for reducing structure-borne noise. A PDE-based methodology for modeling, estimating physical parameters, and implementing a feedback control scheme for problems of this type is discussed. While the illustrating example is a circular plate, the methodology is sufficiently general so as to be applicable in a variety of structural and structural acoustic systems.

Recent developments in structural proteomics for protein structure determination.

PubMed

Liu, Hsuan-Liang; Hsu, Jyh-Ping

2005-05-01

The major challenges in structural proteomics include identifying all the proteins on the genome-wide scale, determining their structure-function relationships, and outlining the precise three-dimensional structures of the proteins. Protein structures are typically determined by experimental approaches such as X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. However, the knowledge of three-dimensional space by these techniques is still limited. Thus, computational methods such as comparative and de novo approaches and molecular dynamic simulations are intensively used as alternative tools to predict the three-dimensional structures and dynamic behavior of proteins. This review summarizes recent developments in structural proteomics for protein structure determination; including instrumental methods such as X-ray crystallography and NMR spectroscopy, and computational methods such as comparative and de novo structure prediction and molecular dynamics simulations.

Accurate Structural Correlations from Maximum Likelihood Superpositions

PubMed Central

Theobald, Douglas L; Wuttke, Deborah S

2008-01-01

The cores of globular proteins are densely packed, resulting in complicated networks of structural interactions. These interactions in turn give rise to dynamic structural correlations over a wide range of time scales. Accurate analysis of these complex correlations is crucial for understanding biomolecular mechanisms and for relating structure to function. Here we report a highly accurate technique for inferring the major modes of structural correlation in macromolecules using likelihood-based statistical analysis of sets of structures. This method is generally applicable to any ensemble of related molecules, including families of nuclear magnetic resonance (NMR) models, different crystal forms of a protein, and structural alignments of homologous proteins, as well as molecular dynamics trajectories. Dominant modes of structural correlation are determined using principal components analysis (PCA) of the maximum likelihood estimate of the correlation matrix. The correlations we identify are inherently independent of the statistical uncertainty and dynamic heterogeneity associated with the structural coordinates. We additionally present an easily interpretable method (“PCA plots”) for displaying these positional correlations by color-coding them onto a macromolecular structure. Maximum likelihood PCA of structural superpositions, and the structural PCA plots that illustrate the results, will facilitate the accurate determination of dynamic structural correlations analyzed in diverse fields of structural biology. PMID:18282091

An efficient algorithm for planar drawing of RNA structures with pseudoknots of any type.

PubMed

Byun, Yanga; Han, Kyungsook

2016-06-01

An RNA pseudoknot is a tertiary structural element in which bases of a loop pair with complementary bases are outside the loop. A drawing of RNA secondary structures is a tree, but a drawing of RNA pseudoknots is a graph that has an inner cycle within a pseudoknot and possibly outer cycles formed between the pseudoknot and other structural elements. Visualizing a large-scale RNA structure with pseudoknots as a planar drawing is challenging because a planar drawing of an RNA structure requires both pseudoknots and an entire structure enclosing the pseudoknots to be embedded into a plane without overlapping or crossing. This paper presents an efficient heuristic algorithm for visualizing a pseudoknotted RNA structure as a planar drawing. The algorithm consists of several parts for finding crossing stems and page mapping the stems, for the layout of stem-loops and pseudoknots, and for overlap detection between structural elements and resolving it. Unlike previous algorithms, our algorithm generates a planar drawing for a large RNA structure with pseudoknots of any type and provides a bracket view of the structure. It generates a compact and aesthetic structure graph for a large pseudoknotted RNA structure in O([Formula: see text]) time, where n is the number of stems of the RNA structure.

R-chie: a web server and R package for visualizing RNA secondary structures

PubMed Central

Lai, Daniel; Proctor, Jeff R.; Zhu, Jing Yun A.; Meyer, Irmtraud M.

2012-01-01

Visually examining RNA structures can greatly aid in understanding their potential functional roles and in evaluating the performance of structure prediction algorithms. As many functional roles of RNA structures can already be studied given the secondary structure of the RNA, various methods have been devised for visualizing RNA secondary structures. Most of these methods depict a given RNA secondary structure as a planar graph consisting of base-paired stems interconnected by roundish loops. In this article, we present an alternative method of depicting RNA secondary structure as arc diagrams. This is well suited for structures that are difficult or impossible to represent as planar stem-loop diagrams. Arc diagrams can intuitively display pseudo-knotted structures, as well as transient and alternative structural features. In addition, they facilitate the comparison of known and predicted RNA secondary structures. An added benefit is that structure information can be displayed in conjunction with a corresponding multiple sequence alignments, thereby highlighting structure and primary sequence conservation and variation. We have implemented the visualization algorithm as a web server R-chie as well as a corresponding R package called R4RNA, which allows users to run the software locally and across a range of common operating systems. PMID:22434875

Development of structural health monitoring techniques using dynamics testing

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

James, G.H. III

Today`s society depends upon many structures (such as aircraft, bridges, wind turbines, offshore platforms, buildings, and nuclear weapons) which are nearing the end of their design lifetime. Since these structures cannot be economically replaced, techniques for structural health monitoring must be developed and implemented. Modal and structural dynamics measurements hold promise for the global non-destructive inspection of a variety of structures since surface measurements of a vibrating structure can provide information about the health of the internal members without costly (or impossible) dismantling of the structure. In order to develop structural health monitoring for application to operational structures, developments inmore » four areas have been undertaken within this project: operational evaluation, diagnostic measurements, information condensation, and damage identification. The developments in each of these four aspects of structural health monitoring have been exercised on a broad range of experimental data. This experimental data has been extracted from structures from several application areas which include aging aircraft, wind energy, aging bridges, offshore structures, structural supports, and mechanical parts. As a result of these advances, Sandia National Laboratories is in a position to perform further advanced development, operational implementation, and technical consulting for a broad class of the nation`s aging infrastructure problems.« less

MMDB: Entrez’s 3D-structure database

PubMed Central

Wang, Yanli; Anderson, John B.; Chen, Jie; Geer, Lewis Y.; He, Siqian; Hurwitz, David I.; Liebert, Cynthia A.; Madej, Thomas; Marchler, Gabriele H.; Marchler-Bauer, Aron; Panchenko, Anna R.; Shoemaker, Benjamin A.; Song, James S.; Thiessen, Paul A.; Yamashita, Roxanne A.; Bryant, Stephen H.

2002-01-01

Three-dimensional structures are now known within many protein families and it is quite likely, in searching a sequence database, that one will encounter a homolog with known structure. The goal of Entrez’s 3D-structure database is to make this information, and the functional annotation it can provide, easily accessible to molecular biologists. To this end Entrez’s search engine provides three powerful features. (i) Sequence and structure neighbors; one may select all sequences similar to one of interest, for example, and link to any known 3D structures. (ii) Links between databases; one may search by term matching in MEDLINE, for example, and link to 3D structures reported in these articles. (iii) Sequence and structure visualization; identifying a homolog with known structure, one may view molecular-graphic and alignment displays, to infer approximate 3D structure. In this article we focus on two features of Entrez’s Molecular Modeling Database (MMDB) not described previously: links from individual biopolymer chains within 3D structures to a systematic taxonomy of organisms represented in molecular databases, and links from individual chains (and compact 3D domains within them) to structure neighbors, other chains (and 3D domains) with similar 3D structure. MMDB may be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Structure. PMID:11752307

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/.

Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments.

PubMed

Park, Hahnbeom; Lee, Gyu Rie; Heo, Lim; Seok, Chaok

2014-01-01

Protein loop modeling is a tool for predicting protein local structures of particular interest, providing opportunities for applications involving protein structure prediction and de novo protein design. Until recently, the majority of loop modeling methods have been developed and tested by reconstructing loops in frameworks of experimentally resolved structures. In many practical applications, however, the protein loops to be modeled are located in inaccurate structural environments. These include loops in model structures, low-resolution experimental structures, or experimental structures of different functional forms. Accordingly, discrepancies in the accuracy of the structural environment assumed in development of the method and that in practical applications present additional challenges to modern loop modeling methods. This study demonstrates a new strategy for employing a hybrid energy function combining physics-based and knowledge-based components to help tackle this challenge. The hybrid energy function is designed to combine the strengths of each energy component, simultaneously maintaining accurate loop structure prediction in a high-resolution framework structure and tolerating minor environmental errors in low-resolution structures. A loop modeling method based on global optimization of this new energy function is tested on loop targets situated in different levels of environmental errors, ranging from experimental structures to structures perturbed in backbone as well as side chains and template-based model structures. The new method performs comparably to force field-based approaches in loop reconstruction in crystal structures and better in loop prediction in inaccurate framework structures. This result suggests that higher-accuracy predictions would be possible for a broader range of applications. The web server for this method is available at http://galaxy.seoklab.org/loop with the PS2 option for the scoring function.

Protein structure similarity from Principle Component Correlation analysis.

PubMed

Zhou, Xiaobo; Chou, James; Wong, Stephen T C

2006-01-25

Owing to rapid expansion of protein structure databases in recent years, methods of structure comparison are becoming increasingly effective and important in revealing novel information on functional properties of proteins and their roles in the grand scheme of evolutionary biology. Currently, the structural similarity between two proteins is measured by the root-mean-square-deviation (RMSD) in their best-superimposed atomic coordinates. RMSD is the golden rule of measuring structural similarity when the structures are nearly identical; it, however, fails to detect the higher order topological similarities in proteins evolved into different shapes. We propose new algorithms for extracting geometrical invariants of proteins that can be effectively used to identify homologous protein structures or topologies in order to quantify both close and remote structural similarities. We measure structural similarity between proteins by correlating the principle components of their secondary structure interaction matrix. In our approach, the Principle Component Correlation (PCC) analysis, a symmetric interaction matrix for a protein structure is constructed with relationship parameters between secondary elements that can take the form of distance, orientation, or other relevant structural invariants. When using a distance-based construction in the presence or absence of encoded N to C terminal sense, there are strong correlations between the principle components of interaction matrices of structurally or topologically similar proteins. The PCC method is extensively tested for protein structures that belong to the same topological class but are significantly different by RMSD measure. The PCC analysis can also differentiate proteins having similar shapes but different topological arrangements. Additionally, we demonstrate that when using two independently defined interaction matrices, comparison of their maximum eigenvalues can be highly effective in clustering structurally or topologically similar proteins. We believe that the PCC analysis of interaction matrix is highly flexible in adopting various structural parameters for protein structure comparison.

Functional structural motifs for protein-ligand, protein-protein, and protein-nucleic acid interactions and their connection to supersecondary structures.

PubMed

Kinjo, Akira R; Nakamura, Haruki

2013-01-01

Protein functions are mediated by interactions between proteins and other molecules. One useful approach to analyze protein functions is to compare and classify the structures of interaction interfaces of proteins. Here, we describe the procedures for compiling a database of interface structures and efficiently comparing the interface structures. To do so requires a good understanding of the data structures of the Protein Data Bank (PDB). Therefore, we also provide a detailed account of the PDB exchange dictionary necessary for extracting data that are relevant for analyzing interaction interfaces and secondary structures. We identify recurring structural motifs by classifying similar interface structures, and we define a coarse-grained representation of supersecondary structures (SSS) which represents a sequence of two or three secondary structure elements including their relative orientations as a string of four to seven letters. By examining the correspondence between structural motifs and SSS strings, we show that no SSS string has particularly high propensity to be found interaction interfaces in general, indicating any SSS can be used as a binding interface. When individual structural motifs are examined, there are some SSS strings that have high propensity for particular groups of structural motifs. In addition, it is shown that while the SSS strings found in particular structural motifs for nonpolymer and protein interfaces are as abundant as in other structural motifs that belong to the same subunit, structural motifs for nucleic acid interfaces exhibit somewhat stronger preference for SSS strings. In regard to protein folds, many motif-specific SSS strings were found across many folds, suggesting that SSS may be a useful description to investigate the universality of ligand binding modes.

RNA-SSPT: RNA Secondary Structure Prediction Tools.

PubMed

Ahmad, Freed; Mahboob, Shahid; Gulzar, Tahsin; Din, Salah U; Hanif, Tanzeela; Ahmad, Hifza; Afzal, Muhammad

2013-01-01

The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challenging. RNA-SSPT is a tool that computationally predicts secondary structure of a single RNA sequence. Most of the RNA secondary structure prediction tools do not allow pseudoknots in the structure or are unable to locate them. Nussinov dynamic programming algorithm has been implemented in RNA-SSPT. The current studies shows only energetically most favorable secondary structure is required and the algorithm modification is also available that produces base pairs to lower the total free energy of the secondary structure. For visualization of RNA secondary structure, NAVIEW in C language is used and modified in C# for tool requirement. RNA-SSPT is built in C# using Dot Net 2.0 in Microsoft Visual Studio 2005 Professional edition. The accuracy of RNA-SSPT is tested in terms of Sensitivity and Positive Predicted Value. It is a tool which serves both secondary structure prediction and secondary structure visualization purposes.

RNA-SSPT: RNA Secondary Structure Prediction Tools

PubMed Central

Ahmad, Freed; Mahboob, Shahid; Gulzar, Tahsin; din, Salah U; Hanif, Tanzeela; Ahmad, Hifza; Afzal, Muhammad

2013-01-01

The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challenging. RNA-SSPT is a tool that computationally predicts secondary structure of a single RNA sequence. Most of the RNA secondary structure prediction tools do not allow pseudoknots in the structure or are unable to locate them. Nussinov dynamic programming algorithm has been implemented in RNA-SSPT. The current studies shows only energetically most favorable secondary structure is required and the algorithm modification is also available that produces base pairs to lower the total free energy of the secondary structure. For visualization of RNA secondary structure, NAVIEW in C language is used and modified in C# for tool requirement. RNA-SSPT is built in C# using Dot Net 2.0 in Microsoft Visual Studio 2005 Professional edition. The accuracy of RNA-SSPT is tested in terms of Sensitivity and Positive Predicted Value. It is a tool which serves both secondary structure prediction and secondary structure visualization purposes. PMID:24250115

Automated 3D structure composition for large RNAs

PubMed Central

Popenda, Mariusz; Szachniuk, Marta; Antczak, Maciej; Purzycka, Katarzyna J.; Lukasiak, Piotr; Bartol, Natalia; Blazewicz, Jacek; Adamiak, Ryszard W.

2012-01-01

Understanding the numerous functions that RNAs play in living cells depends critically on knowledge of their three-dimensional structure. Due to the difficulties in experimentally assessing structures of large RNAs, there is currently great demand for new high-resolution structure prediction methods. We present the novel method for the fully automated prediction of RNA 3D structures from a user-defined secondary structure. The concept is founded on the machine translation system. The translation engine operates on the RNA FRABASE database tailored to the dictionary relating the RNA secondary structure and tertiary structure elements. The translation algorithm is very fast. Initial 3D structure is composed in a range of seconds on a single processor. The method assures the prediction of large RNA 3D structures of high quality. Our approach needs neither structural templates nor RNA sequence alignment, required for comparative methods. This enables the building of unresolved yet native and artificial RNA structures. The method is implemented in a publicly available, user-friendly server RNAComposer. It works in an interactive mode and a batch mode. The batch mode is designed for large-scale modelling and accepts atomic distance restraints. Presently, the server is set to build RNA structures of up to 500 residues. PMID:22539264

ProTSAV: A protein tertiary structure analysis and validation server.

PubMed

Singh, Ankita; Kaushik, Rahul; Mishra, Avinash; Shanker, Asheesh; Jayaram, B

2016-01-01

Quality assessment of predicted model structures of proteins is as important as the protein tertiary structure prediction. A highly efficient quality assessment of predicted model structures directs further research on function. Here we present a new server ProTSAV, capable of evaluating predicted model structures based on some popular online servers and standalone tools. ProTSAV furnishes the user with a single quality score in case of individual protein structure along with a graphical representation and ranking in case of multiple protein structure assessment. The server is validated on ~64,446 protein structures including experimental structures from RCSB and predicted model structures for CASP targets and from public decoy sets. ProTSAV succeeds in predicting quality of protein structures with a specificity of 100% and a sensitivity of 98% on experimentally solved structures and achieves a specificity of 88%and a sensitivity of 91% on predicted protein structures of CASP11 targets under 2Å.The server overcomes the limitations of any single server/method and is seen to be robust in helping in quality assessment. ProTSAV is freely available at http://www.scfbio-iitd.res.in/software/proteomics/protsav.jsp. Copyright © 2015 Elsevier B.V. All rights reserved.

Decoupling feedforward and feedback structures in hybrid active noise control systems for uncorrelated narrowband disturbances

NASA Astrophysics Data System (ADS)

Wu, Lifu; Qiu, Xiaojun; Burnett, Ian S.; Guo, Yecai

2015-08-01

Hybrid feedforward and feedback structures are useful for active noise control (ANC) applications where the noise can only be partially obtained with reference sensors. The traditional method uses the secondary signals of both the feedforward and feedback structures to synthesize a reference signal for the feedback structure in the hybrid structure. However, this approach introduces coupling between the feedforward and feedback structures and parameter changes in one structure affect the other during adaptation such that the feedforward and feedback structures must be optimized simultaneously in practical ANC system design. Two methods are investigated in this paper to remove such coupling effects. One is a simplified method, which uses the error signal directly as the reference signal in the feedback structure, and the second method generates the reference signal for the feedback structure by using only the secondary signal from the feedback structure and utilizes the generated reference signal as the error signal of the feedforward structure. Because the two decoupling methods can optimize the feedforward and feedback structures separately, they provide more flexibility in the design and optimization of the adaptive filters in practical ANC applications.

Pressure profiles in detonation cells with rectangular and diagonal structures

NASA Astrophysics Data System (ADS)

Hanana, M.; Lefebvre, M. H.

Experimental results presented in this work enable us to classify the three-dimensional structure of the detonation into two fundamental types: a rectangular structure and a diagonal structure. The rectangular structure is well documented in the literature and consists of orthogonal waves travelling independently from each another. The soot record in this case shows the classical diamond detonation cell exhibiting `slapping waves'. The experiments indicate that the diagonal structure is a structure with the triple point intersections moving along the diagonal line of the tube cross section. The axes of the transverse waves are canted at 45 degrees to the wall, accounting for the lack of slapping waves. It is possible to reproduce these diagonal structures by appropriately controlling the experimental ignition procedure. The characteristics of the diagonal structure show some similarities with detonation structure in round tube. Pressure measurements recorded along the central axis of the cellular structure show a series of pressure peaks, depending on the type of structure and the position inside the detonation cell. Pressure profiles measured for the whole length of the two types of detonation cells show that the intensity of the shock front is higher and the length of the detonation cell is shorter for the diagonal structures.

The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods.

PubMed

Gabanyi, Margaret J; Adams, Paul D; Arnold, Konstantin; Bordoli, Lorenza; Carter, Lester G; Flippen-Andersen, Judith; Gifford, Lida; Haas, Juergen; Kouranov, Andrei; McLaughlin, William A; Micallef, David I; Minor, Wladek; Shah, Raship; Schwede, Torsten; Tao, Yi-Ping; Westbrook, John D; Zimmerman, Matthew; Berman, Helen M

2011-07-01

The Protein Structure Initiative's Structural Biology Knowledgebase (SBKB, URL: http://sbkb.org ) is an open web resource designed to turn the products of the structural genomics and structural biology efforts into knowledge that can be used by the biological community to understand living systems and disease. Here we will present examples on how to use the SBKB to enable biological research. For example, a protein sequence or Protein Data Bank (PDB) structure ID search will provide a list of related protein structures in the PDB, associated biological descriptions (annotations), homology models, structural genomics protein target status, experimental protocols, and the ability to order available DNA clones from the PSI:Biology-Materials Repository. A text search will find publication and technology reports resulting from the PSI's high-throughput research efforts. Web tools that aid in research, including a system that accepts protein structure requests from the community, will also be described. Created in collaboration with the Nature Publishing Group, the Structural Biology Knowledgebase monthly update also provides a research library, editorials about new research advances, news, and an events calendar to present a broader view of structural genomics and structural biology.

Crystal structure of a c-kit promoter quadruplex reveals the structural role of metal ions and water molecules in maintaining loop conformation.

PubMed

Wei, Dengguo; Parkinson, Gary N; Reszka, Anthony P; Neidle, Stephen

2012-05-01

We report here the 1.62 Å crystal structure of an intramolecular quadruplex DNA formed from a sequence in the promoter region of the c-kit gene. This is the first reported crystal structure of a promoter quadruplex and the first observation of localized magnesium ions in a quadruplex structure. The structure reveals that potassium and magnesium ions have an unexpected yet significant structural role in stabilizing particular quadruplex loops and grooves that is distinct from but in addition to the role of potassium ions in the ion channel at the centre of all quadruplex structures. The analysis also shows how ions cluster together with structured water molecules to stabilize the quadruplex arrangement. This particular quadruplex has been previously studied by NMR methods, and the present X-ray structure is in accord with the earlier topology assignment. However, as well as the observations of potassium and magnesium ions, the crystal structure has revealed a highly significant difference in the dimensions of the large cleft in the structure, which is a plausible target for small molecules. This difference can be understood by the stabilizing role of structured water networks.

Reversed structures and bounce structures: are they recognizable? Are they real?

NASA Astrophysics Data System (ADS)

Means, W. D.

1999-08-01

This note poses two related questions about structural evolution in rocks. How easy is it to recognize structural features that have reversed their sense of development over time? Are there circumstances in rock deformation where early intensification of structure sows the seeds for a later, more or less inevitable, diminution of intensity? It is suggested, as a partial answer to the first question, that there is an irreversibility principle inherent to most structural development, such that even if bulk strain is reversed, the structural changes that accompanied `forward' structural development will not be completely reversed when the strain is reversed. Where this principle applies, it should always be possible to recognize structural reversals, by sufficiently close observation of the final state. It is suggested, as a partial answer to the second question, that where energy is stored by forward structural changes, this energy can often be expected to drive further structural changes, and these further changes may sometimes cause the original structure to `bounce' back to a less intense state. These questions may have some bearing on developing a firmer basis for kinematic analysis, and for understanding overprinting structures in orogens.

Space Structure Development

NASA Technical Reports Server (NTRS)

Smith, Thomas

2015-01-01

The duration of my Summer 2015 Internship Tour at NASA's Johnson Space Center was spent working in the Structural Engineering Division's Structures Branch. One of the two main roles of the Structures Branch, ES2, is to ensure the structural integrity of spacecraft vehicles and the structural subsystems needed to support those vehicles. The other main objective of this branch is to develop the lightweight structures that are necessary to take humans beyond Low-Earth Orbit. Within ES2, my four projects involved inflatable space structure air bladder material testing; thermal and impact material testing for spacecraft windows; structural analysis on a joint used in the Boeing CST-100 airbag system; and an additive manufacturing design project.

Weight optimization of ultra large space structures

NASA Technical Reports Server (NTRS)

Reinert, R. P.

1979-01-01

The paper describes the optimization of a solar power satellite structure for minimum mass and system cost. The solar power satellite is an ultra large low frequency and lightly damped space structure; derivation of its structural design requirements required accommodation of gravity gradient torques which impose primary loads, life up to 100 years in the rigorous geosynchronous orbit radiation environment, and prevention of continuous wave motion in a solar array blanket suspended from a huge, lightly damped structure subject to periodic excitations. The satellite structural design required a parametric study of structural configurations and consideration of the fabrication and assembly techniques, which resulted in a final structure which met all requirements at a structural mass fraction of 10%.

Structure-Based Characterization of Multiprotein Complexes

PubMed Central

Wiederstein, Markus; Gruber, Markus; Frank, Karl; Melo, Francisco; Sippl, Manfred J.

2014-01-01

Summary Multiprotein complexes govern virtually all cellular processes. Their 3D structures provide important clues to their biological roles, especially through structural correlations among protein molecules and complexes. The detection of such correlations generally requires comprehensive searches in databases of known protein structures by means of appropriate structure-matching techniques. Here, we present a high-speed structure search engine capable of instantly matching large protein oligomers against the complete and up-to-date database of biologically functional assemblies of protein molecules. We use this tool to reveal unseen structural correlations on the level of protein quaternary structure and demonstrate its general usefulness for efficiently exploring complex structural relationships among known protein assemblies. PMID:24954616

The use of small-molecule structures to complement protein–ligand crystal structures in drug discovery

PubMed Central

Cole, Jason C.

2017-01-01

Many ligand-discovery stories tell of the use of structures of protein–ligand complexes, but the contribution of structural chemistry is such a core part of finding and improving ligands that it is often overlooked. More than 800 000 crystal structures are available to the community through the Cambridge Structural Database (CSD). Individually, these structures can be of tremendous value and the collection of crystal structures is even more helpful. This article provides examples of how small-molecule crystal structures have been used to complement those of protein–ligand complexes to address challenges ranging from affinity, selectivity and bioavailability though to solubility. PMID:28291759

GOSSIP: a method for fast and accurate global alignment of protein structures.

PubMed

Kifer, I; Nussinov, R; Wolfson, H J

2011-04-01

The database of known protein structures (PDB) is increasing rapidly. This results in a growing need for methods that can cope with the vast amount of structural data. To analyze the accumulating data, it is important to have a fast tool for identifying similar structures and clustering them by structural resemblance. Several excellent tools have been developed for the comparison of protein structures. These usually address the task of local structure alignment, an important yet computationally intensive problem due to its complexity. It is difficult to use such tools for comparing a large number of structures to each other at a reasonable time. Here we present GOSSIP, a novel method for a global all-against-all alignment of any set of protein structures. The method detects similarities between structures down to a certain cutoff (a parameter of the program), hence allowing it to detect similar structures at a much higher speed than local structure alignment methods. GOSSIP compares many structures in times which are several orders of magnitude faster than well-known available structure alignment servers, and it is also faster than a database scanning method. We evaluate GOSSIP both on a dataset of short structural fragments and on two large sequence-diverse structural benchmarks. Our conclusions are that for a threshold of 0.6 and above, the speed of GOSSIP is obtained with no compromise of the accuracy of the alignments or of the number of detected global similarities. A server, as well as an executable for download, are available at http://bioinfo3d.cs.tau.ac.il/gossip/.

Lewis Structures Technology, 1988. Volume 1: Structural Dynamics

NASA Technical Reports Server (NTRS)

1988-01-01

The specific purpose of the symposium was to familiarize the engineering structures community with the depth and range of research performed by the Structures Division of the Lewis Research Center and its academic and industrial partners. Sessions covered vibration control, fracture mechanics, ceramic component reliability, parallel computing, nondestructive testing, dynamical systems, fatigue and damage, wind turbines, hot section technology, structural mechanics codes, computational methods for dynamics, structural optimization, and applications of structural dynamics.

Mixed-mu superconducting bearings

DOEpatents

Hull, John R.; Mulcahy, Thomas M.

1998-01-01

A mixed-mu superconducting bearing including a ferrite structure disposed for rotation adjacent a stationary superconductor material structure and a stationary permanent magnet structure. The ferrite structure is levitated by said stationary permanent magnet structure.

Thermal-Mechanical Testing of Hypersonic Vehicle Structures

NASA Technical Reports Server (NTRS)

Hudson, Larry; Stephens, Craig

2007-01-01

A viewgraph presentation describing thermal-mechanical tests on the structures of hypersonic vehicles is shown. The topics include: 1) U.S. Laboratories for Hot Structures Testing; 2) NASA Dryden Flight Loads Laboratory; 3) Hot Structures Test Programs; 4) Typical Sequence for Hot Structures Testing; 5) Current Hot Structures Testing; and 6) Concluding Remarks.

Method of using triaxial magnetic fields for making particle structures

DOEpatents

Martin, James E.; Anderson, Robert A.; Williamson, Rodney L.

2005-01-18

A method of producing three-dimensional particle structures with enhanced magnetic susceptibility in three dimensions by applying a triaxial energetic field to a magnetic particle suspension and subsequently stabilizing said particle structure. Combinations of direct current and alternating current fields in three dimensions produce particle gel structures, honeycomb structures, and foam-like structures.

Differently Structured Advance Organizers Lead to Different Initial Schemata and Learning Outcomes

ERIC Educational Resources Information Center

Gurlitt, Johannes; Dummel, Sebastian; Schuster, Silvia; Nuckles, Matthias

2012-01-01

Does the specific structure of advance organizers influence learning outcomes? In the first experiment, 48 psychology students were randomly assigned to three differently structured advance organizers: a well-structured, a well-structured and key-concept emphasizing, and a less structured advance organizer. These were followed by a sorting task, a…

Structures to Resist the Effects of Accidental Explosions

DTIC Science & Technology

1969-06-01

theorems, are generally used. il to Ce e same structure. reactions of the foundatio4 must also be equal to zero . e. For the analysis of structures...3. BASIS FOR STRUCTURAL D)ESIGN Section 1. Structural Response General ----------------------------------- -c--- -13- Pressure design ranges...4-11 4-.i9 V. External Blast Loads on Structures General

Aviation Maintenance Technology. Airframe. A201. Airframe Structures and Non-Metallic Structural Repairs. Instructor Material.

ERIC Educational Resources Information Center

Oklahoma State Board of Vocational and Technical Education, Stillwater. Curriculum and Instructional Materials Center.

This teacher's guide is designed to aid teachers in leading students through a module on airframe structures and nonmetallic structural repairs. The module contains four units that cover the following topics: (1) identifying aerodynamic and construction characteristics of aircraft structures; (2) inspecting wooden structures; (3) inspecting and…

A finite element analysis of a 3D auxetic textile structure for composite reinforcement

NASA Astrophysics Data System (ADS)

Ge, Zhaoyang; Hu, Hong; Liu, Yanping

2013-08-01

This paper reports the finite element analysis of an innovative 3D auxetic textile structure consisting of three yarn systems (weft, warp and stitch yarns). Different from conventional 3D textile structures, the proposed structure exhibits an auxetic behaviour under compression and can be used as a reinforcement to manufacture auxetic composites. The geometry of the structure is first described. Then a 3D finite element model is established using ANSYS software and validated by the experimental results. The deformation process of the structure at different compression strains is demonstrated, and the validated finite element model is finally used to simulate the auxetic behaviour of the structure with different structural parameters and yarn properties. The results show that the auxetic behaviour of the proposed structure increases with increasing compression strain, and all the structural parameters and yarn properties have significant effects on the auxetic behaviour of the structure. It is expected that the study could provide a better understanding of 3D auxetic textile structures and could promote their application in auxetic composites.

Structural competency: Theorizing a new medical engagement with stigma and inequality

PubMed Central

Metzl, Jonathan M.; Hansen, Helena

2014-01-01

This paper describes a shift in medical education away from pedagogic approaches to stigma and inequalities that emphasize cross-cultural understandings of individual patients, toward attention to forces that influence health outcomes at levels above individual interactions. It reviews existing structural approaches to stigma and health inequalities developed outside of medicine, and proposes changes to U.S. medical education that will infuse clinical training with a structural focus. The approach, termed “structural competency,” consists of training in five core competencies: 1) recognizing the structures that shape clinical interactions; 2) developing an extra-clinical language of structure; 3) rearticulating “cultural” formulations in structural terms; 4) observing and imagining structural interventions; and 5) developing structural humility. Examples are provided of structural health scholarship that should be adopted into medical didactic curricula, and of structural interventions that can provide participant-observation opportunities for clinical trainees. The paper ultimately argues that increasing recognition of the ways in which social and economic forces produce symptoms or methylate genes then needs to be better coupled with medical models for structural change. PMID:24507917

Composite isogrid structures for parabolic surfaces

NASA Technical Reports Server (NTRS)

Silverman, Edward M. (Inventor); Boyd, Jr., William E. (Inventor); Rhodes, Marvin D. (Inventor); Dyer, Jack E. (Inventor)

2000-01-01

The invention relates to high stiffness parabolic structures utilizing integral reinforced grids. The parabolic structures implement the use of isogrid structures which incorporate unique and efficient orthotropic patterns for efficient stiffness and structural stability.

Titanium and advanced composite structures for a supersonic cruise arrow wing configuration

NASA Technical Reports Server (NTRS)

Turner, M. J.; Hoy, J. M.

1976-01-01

Structural design studies were made, based on current technology and on an estimate of technology to be available in the mid 1980's, to assess the relative merits of structural concepts and materials for an advanced arrow wing configuration cruising at Mach 2.7. Preliminary studies were made to insure compliance of the configuration with general design criteria, integrate the propulsion system with the airframe, and define an efficient structural arrangement. Material and concept selection, detailed structural analysis, structural design and airplane mass analysis were completed based on current technology. Based on estimated future technology, structural sizing for strength and a preliminary assessment of the flutter of a strength designed composite structure were completed. An advanced computerized structural design system was used, in conjunction with a relatively complex finite element model, for detailed analysis and sizing of structural members.

A Review of Structure Construction of Silk Fibroin Biomaterials from Single Structures to Multi-Level Structures.

PubMed

Qi, Yu; Wang, Hui; Wei, Kai; Yang, Ya; Zheng, Ru-Yue; Kim, Ick Soo; Zhang, Ke-Qin

2017-03-03

The biological performance of artificial biomaterials is closely related to their structure characteristics. Cell adhesion, migration, proliferation, and differentiation are all strongly affected by the different scale structures of biomaterials. Silk fibroin (SF), extracted mainly from silkworms, has become a popular biomaterial due to its excellent biocompatibility, exceptional mechanical properties, tunable degradation, ease of processing, and sufficient supply. As a material with excellent processability, SF can be processed into various forms with different structures, including particulate, fiber, film, and three-dimensional (3D) porous scaffolds. This review discusses and summarizes the various constructions of SF-based materials, from single structures to multi-level structures, and their applications. In combination with single structures, new techniques for creating special multi-level structures of SF-based materials, such as micropatterning and 3D-printing, are also briefly addressed.

Correlating Structural Order with Structural Rearrangement in Dusty Plasma Liquids: Can Structural Rearrangement be Predicted by Static Structural Information?

NASA Astrophysics Data System (ADS)

Su, Yen-Shuo; Liu, Yu-Hsuan; I, Lin

2012-11-01

Whether the static microstructural order information is strongly correlated with the subsequent structural rearrangement (SR) and their predicting power for SR are investigated experimentally in the quenched dusty plasma liquid with microheterogeneities. The poor local structural order is found to be a good alarm to identify the soft spot and predict the short term SR. For the site with good structural order, the persistent time for sustaining the structural memory until SR has a large mean value but a broad distribution. The deviation of the local structural order from that averaged over nearest neighbors serves as a good second alarm to further sort out the short time SR sites. It has the similar sorting power to that using the temporal fluctuation of the local structural order over a small time interval.

Rebelling for a Reason: Protein Structural “Outliers”

PubMed Central

Arumugam, Gandhimathi; Nair, Anu G.; Hariharaputran, Sridhar; Ramanathan, Sowdhamini

2013-01-01

Analysis of structural variation in domain superfamilies can reveal constraints in protein evolution which aids protein structure prediction and classification. Structure-based sequence alignment of distantly related proteins, organized in PASS2 database, provides clues about structurally conserved regions among different functional families. Some superfamily members show large structural differences which are functionally relevant. This paper analyses the impact of structural divergence on function for multi-member superfamilies, selected from the PASS2 superfamily alignment database. Functional annotations within superfamilies, with structural outliers or ‘rebels’, are discussed in the context of structural variations. Overall, these data reinforce the idea that functional similarities cannot be extrapolated from mere structural conservation. The implication for fold-function prediction is that the functional annotations can only be inherited with very careful consideration, especially at low sequence identities. PMID:24073209

Exploration of tetrahedral structures in silicate cathodes using a motif-network scheme

PubMed Central

Zhao, Xin; Wu, Shunqing; Lv, Xiaobao; Nguyen, Manh Cuong; Wang, Cai-Zhuang; Lin, Zijing; Zhu, Zi-Zhong; Ho, Kai-Ming

2015-01-01

Using a motif-network search scheme, we studied the tetrahedral structures of the dilithium/disodium transition metal orthosilicates A2MSiO4 with A = Li or Na and M = Mn, Fe or Co. In addition to finding all previously reported structures, we discovered many other different tetrahedral-network-based crystal structures which are highly degenerate in energy. These structures can be classified into structures with 1D, 2D and 3D M-Si-O frameworks. A clear trend of the structural preference in different systems was revealed and possible indicators that affect the structure stabilities were introduced. For the case of Na systems which have been much less investigated in the literature relative to the Li systems, we predicted their ground state structures and found evidence for the existence of new structural motifs. PMID:26497381

Coherent structures: Comments on mechanisms

NASA Technical Reports Server (NTRS)

Hunt, J. C. R.

1987-01-01

There is now overwhelming evidence that in most turbulent flows there exist regions moving with the flow where the velocity and vorticity have a characteristic structure. These regions are called coherent structures because within them the large-scale distributions of velocity and/or vorticity remain coherent even as these structures move through the flow and interact with other structures. Since the flow enters and leaves the bounding surfaces of these structures, a useful definition for coherent structures is that they are open volumes with distinctive large-scale vorticity distributions. Possible fruitful directions for the study of the dynamics of coherent structures are suggested. Most coherent structures research to data was concentrated on measurement and kinematical analysis; there is now a welcome move to examine the dynamics of coherent structures, by a variety of different methods. A few of them will be described.

Improving substructure identification accuracy of shear structures using virtual control system

NASA Astrophysics Data System (ADS)

Zhang, Dongyu; Yang, Yang; Wang, Tingqiang; Li, Hui

2018-02-01

Substructure identification is a powerful tool to identify the parameters of a complex structure. Previously, the authors developed an inductive substructure identification method for shear structures. The identification error analysis showed that the identification accuracy of this method is significantly influenced by the magnitudes of two key structural responses near a certain frequency; if these responses are unfavorable, the method cannot provide accurate estimation results. In this paper, a novel method is proposed to improve the substructure identification accuracy by introducing a virtual control system (VCS) into the structure. A virtual control system is a self-balanced system, which consists of some control devices and a set of self-balanced forces. The self-balanced forces counterbalance the forces that the control devices apply on the structure. The control devices are combined with the structure to form a controlled structure used to replace the original structure in the substructure identification; and the self-balance forces are treated as known external excitations to the controlled structure. By optimally tuning the VCS’s parameters, the dynamic characteristics of the controlled structure can be changed such that the original structural responses become more favorable for the substructure identification and, thus, the identification accuracy is improved. A numerical example of 6-story shear structure is utilized to verify the effectiveness of the VCS based controlled substructure identification method. Finally, shake table tests are conducted on a 3-story structural model to verify the efficacy of the VCS to enhance the identification accuracy of the structural parameters.

[Network structures in biological systems].

PubMed

Oleskin, A V

2013-01-01

Network structures (networks) that have been extensively studied in the humanities are characterized by cohesion, a lack of a central control unit, and predominantly fractal properties. They are contrasted with structures that contain a single centre (hierarchies) as well as with those whose elements predominantly compete with one another (market-type structures). As far as biological systems are concerned, their network structures can be subdivided into a number of types involving different organizational mechanisms. Network organization is characteristic of various structural levels of biological systems ranging from single cells to integrated societies. These networks can be classified into two main subgroups: (i) flat (leaderless) network structures typical of systems that are composed of uniform elements and represent modular organisms or at least possess manifest integral properties and (ii) three-dimensional, partly hierarchical structures characterized by significant individual and/or intergroup (intercaste) differences between their elements. All network structures include an element that performs structural, protective, and communication-promoting functions. By analogy to cell structures, this element is denoted as the matrix of a network structure. The matrix includes a material and an immaterial component. The material component comprises various structures that belong to the whole structure and not to any of its elements per se. The immaterial (ideal) component of the matrix includes social norms and rules regulating network elements' behavior. These behavioral rules can be described in terms of algorithms. Algorithmization enables modeling the behavior of various network structures, particularly of neuron networks and their artificial analogs.

NMR in structural genomics to increase structural coverage of the protein universe: Delivered by Prof. Kurt Wüthrich on 7 July 2013 at the 38th FEBS Congress in St. Petersburg, Russia.

PubMed

Serrano, Pedro; Dutta, Samit K; Proudfoot, Andrew; Mohanty, Biswaranjan; Susac, Lukas; Martin, Bryan; Geralt, Michael; Jaroszewski, Lukasz; Godzik, Adam; Elsliger, Marc; Wilson, Ian A; Wüthrich, Kurt

2016-11-01

For more than a decade, the Joint Center for Structural Genomics (JCSG; www.jcsg.org) worked toward increased three-dimensional structure coverage of the protein universe. This coordinated quest was one of the main goals of the four high-throughput (HT) structure determination centers of the Protein Structure Initiative (PSI; www.nigms.nih.gov/Research/specificareas/PSI). To achieve the goals of the PSI, the JCSG made use of the complementarity of structure determination by X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy to increase and diversify the range of targets entering the HT structure determination pipeline. The overall strategy, for both techniques, was to determine atomic resolution structures for representatives of large protein families, as defined by the Pfam database, which had no structural coverage and could make significant contributions to biological and biomedical research. Furthermore, the experimental structures could be leveraged by homology modeling to further expand the structural coverage of the protein universe and increase biological insights. Here, we describe what could be achieved by this structural genomics approach, using as an illustration the contributions from 20 NMR structure determinations out of a total of 98 JCSG NMR structures, which were selected because they are the first three-dimensional structure representations of the respective Pfam protein families. The information from this small sample is representative for the overall results from crystal and NMR structure determination in the JCSG. There are five new folds, which were classified as domains of unknown functions (DUF), three of the proteins could be functionally annotated based on three-dimensional structure similarity with previously characterized proteins, and 12 proteins showed only limited similarity with previous deposits in the Protein Data Bank (PDB) and were classified as DUFs. © 2016 Federation of European Biochemical Societies.

Two Decades of Structure Building

PubMed Central

Gernsbacher, Morton Ann

2014-01-01

During the past decade I have been developing a very simple framework for describing the cognitive processes and mechanisms involved in discourse comprehension. I call this framework the Structure Building Framework, and it is based on evidence provided during the first decade of discourse processing research. According to the Structure Building Framework, the goal of comprehension is to build coherent mental representations or structures. Comprehenders build each structure by first laying a foundation. Comprehenders develop mental structures by mapping on new information when that information coheres or relates to previous information. However, when the incoming information is less related, comprehenders shift and attach a new substructure. The building blocks of mental structures are memory nodes, which are activated by incoming stimuli and controlled by two cognitive mechanisms: suppression and enhancement. In this article, first I review the seminal work on which the Structure Building Framework is based (the first decade of structure building research); then I recount the research I have conducted to test the Structure Building Framework (the second decade of structure building research). PMID:25484476

Materials and structures technology insertion into spacecraft systems: Successes and challenges

NASA Astrophysics Data System (ADS)

Rawal, Suraj

2018-05-01

Over the last 30 years, significant advancements have led to the use of multifunctional materials and structures technologies in spacecraft systems. This includes the integration of adaptive structures, advanced composites, nanotechnology, and additive manufacturing technologies. Development of multifunctional structures has been directly influenced by the implementation of processes and tools for adaptive structures pioneered by Prof. Paolo Santini. Multifunctional materials and structures incorporating non-structural engineering functions such as thermal, electrical, radiation shielding, power, and sensors have been investigated. The result has been an integrated structure that offers reduced mass, packaging volume, and ease of integration for spacecraft systems. Current technology development efforts are being conducted to develop innovative multifunctional materials and structures designs incorporating advanced composites, nanotechnology, and additive manufacturing. However, these efforts offer significant challenges in the qualification and acceptance into spacecraft systems. This paper presents a brief overview of the technology development and successful insertion of advanced material technologies into spacecraft structures. Finally, opportunities and challenges to develop and mature next generation advanced materials and structures are presented.

RNApdbee 2.0: multifunctional tool for RNA structure annotation.

PubMed

Zok, Tomasz; Antczak, Maciej; Zurkowski, Michal; Popenda, Mariusz; Blazewicz, Jacek; Adamiak, Ryszard W; Szachniuk, Marta

2018-04-30

In the field of RNA structural biology and bioinformatics, an access to correctly annotated RNA structure is of crucial importance, especially in the secondary and 3D structure predictions. RNApdbee webserver, introduced in 2014, primarily aimed to address the problem of RNA secondary structure extraction from the PDB files. Its new version, RNApdbee 2.0, is a highly advanced multifunctional tool for RNA structure annotation, revealing the relationship between RNA secondary and 3D structure given in the PDB or PDBx/mmCIF format. The upgraded version incorporates new algorithms for recognition and classification of high-ordered pseudoknots in large RNA structures. It allows analysis of isolated base pairs impact on RNA structure. It can visualize RNA secondary structures-including that of quadruplexes-with depiction of non-canonical interactions. It also annotates motifs to ease identification of stems, loops and single-stranded fragments in the input RNA structure. RNApdbee 2.0 is implemented as a publicly available webserver with an intuitive interface and can be freely accessed at http://rnapdbee.cs.put.poznan.pl/.

Speckle lithography for fabricating Gaussian, quasi-random 2D structures and black silicon structures

PubMed Central

Bingi, Jayachandra; Murukeshan, Vadakke Matham

2015-01-01

Laser speckle pattern is a granular structure formed due to random coherent wavelet interference and generally considered as noise in optical systems including photolithography. Contrary to this, in this paper, we use the speckle pattern to generate predictable and controlled Gaussian random structures and quasi-random structures photo-lithographically. The random structures made using this proposed speckle lithography technique are quantified based on speckle statistics, radial distribution function (RDF) and fast Fourier transform (FFT). The control over the speckle size, density and speckle clustering facilitates the successful fabrication of black silicon with different surface structures. The controllability and tunability of randomness makes this technique a robust method for fabricating predictable 2D Gaussian random structures and black silicon structures. These structures can enhance the light trapping significantly in solar cells and hence enable improved energy harvesting. Further, this technique can enable efficient fabrication of disordered photonic structures and random media based devices. PMID:26679513

Increased reliability of nuclear magnetic resonance protein structures by consensus structure bundles.

PubMed

Buchner, Lena; Güntert, Peter

2015-02-03

Nuclear magnetic resonance (NMR) structures are represented by bundles of conformers calculated from different randomized initial structures using identical experimental input data. The spread among these conformers indicates the precision of the atomic coordinates. However, there is as yet no reliable measure of structural accuracy, i.e., how close NMR conformers are to the "true" structure. Instead, the precision of structure bundles is widely (mis)interpreted as a measure of structural quality. Attempts to increase precision often overestimate accuracy by tight bundles of high precision but much lower accuracy. To overcome this problem, we introduce a protocol for NMR structure determination with the software package CYANA, which produces, like the traditional method, bundles of conformers in agreement with a common set of conformational restraints but with a realistic precision that is, throughout a variety of proteins and NMR data sets, a much better estimate of structural accuracy than the precision of conventional structure bundles. Copyright © 2015 Elsevier Ltd. All rights reserved.

Autonomous System for Monitoring the Integrity of Composite Fan Housings

NASA Technical Reports Server (NTRS)

Qing, Xinlin P.; Aquino, Christopher; Kumar, Amrita

2010-01-01

A low-cost and reliable system assesses the integrity of composite fan-containment structures. The system utilizes a network of miniature sensors integrated with the structure to scan the entire structural area for any impact events and resulting structural damage, and to monitor degradation due to usage. This system can be used to monitor all types of composite structures on aircraft and spacecraft, as well as automatically monitor in real time the location and extent of damage in the containment structures. This diagnostic information is passed to prognostic modeling that is being developed to utilize the information and provide input on the residual strength of the structure, and maintain a history of structural degradation during usage. The structural health-monitoring system would consist of three major components: (1) sensors and a sensor network, which is permanently bonded onto the structure being monitored; (2) integrated hardware; and (3) software to monitor in-situ the health condition of in-service structures.

Representing and comparing protein structures as paths in three-dimensional space

PubMed Central

Zhi, Degui; Krishna, S Sri; Cao, Haibo; Pevzner, Pavel; Godzik, Adam

2006-01-01

Background Most existing formulations of protein structure comparison are based on detailed atomic level descriptions of protein structures and bypass potential insights that arise from a higher-level abstraction. Results We propose a structure comparison approach based on a simplified representation of proteins that describes its three-dimensional path by local curvature along the generalized backbone of the polypeptide. We have implemented a dynamic programming procedure that aligns curvatures of proteins by optimizing a defined sum turning angle deviation measure. Conclusion Although our procedure does not directly optimize global structural similarity as measured by RMSD, our benchmarking results indicate that it can surprisingly well recover the structural similarity defined by structure classification databases and traditional structure alignment programs. In addition, our program can recognize similarities between structures with extensive conformation changes that are beyond the ability of traditional structure alignment programs. We demonstrate the applications of procedure to several contexts of structure comparison. An implementation of our procedure, CURVE, is available as a public webserver. PMID:17052359

Integrative interactive visualization of crystal structure, band structure, and Brillouin zone

NASA Astrophysics Data System (ADS)

Hanson, Robert; Hinke, Ben; van Koevering, Matthew; Oses, Corey; Toher, Cormac; Hicks, David; Gossett, Eric; Plata Ramos, Jose; Curtarolo, Stefano; Aflow Collaboration

The AFLOW library is an open-access database for high throughput ab-initio calculations that serves as a resource for the dissemination of computational results in the area of materials science. Our project aims to create an interactive web-based visualization of any structure in the AFLOW database that has associate band structure data in a way that allows novel simultaneous exploration of the crystal structure, band structure, and Brillouin zone. Interactivity is obtained using two synchronized JSmol implementations, one for the crystal structure and one for the Brillouin zone, along with a D3-based band-structure diagram produced on the fly from data obtained from the AFLOW database. The current website portal (http://aflowlib.mems.duke.edu/users/jmolers/matt/website) allows interactive access and visualization of crystal structure, Brillouin zone and band structure for more than 55,000 inorganic crystal structures. This work was supported by the US Navy Office of Naval Research through a Broad Area Announcement administered by Duke University.

A quantification model for the structure of clay materials.

PubMed

Tang, Liansheng; Sang, Haitao; Chen, Haokun; Sun, Yinlei; Zhang, Longjian

2016-07-04

In this paper, the quantification for clay structure is explicitly explained, and the approach and goals of quantification are also discussed. The authors consider that the purpose of the quantification for clay structure is to determine some parameters that can be used to quantitatively characterize the impact of clay structure on the macro-mechanical behaviour. According to the system theory and the law of energy conservation, a quantification model for the structure characteristics of clay materials is established and three quantitative parameters (i.e., deformation structure potential, strength structure potential and comprehensive structure potential) are proposed. And the corresponding tests are conducted. The experimental results show that these quantitative parameters can accurately reflect the influence of clay structure on the deformation behaviour, strength behaviour and the relative magnitude of structural influence on the above two quantitative parameters, respectively. These quantitative parameters have explicit mechanical meanings, and can be used to characterize the structural influences of clay on its mechanical behaviour.

Capillary Structures for Exploration Life Support (Capillary Structures)

NASA Image and Video Library

2017-07-10

iss052e013146 (July 10, 2017) --- Astronaut Jack Fischer is photographed during setup of hardware for the Capillary Structures for Exploration Life Support (Capillary Structures) two sorbent demonstrations. The Capillary Structures for Exploration Life Support (Capillary Structures) investigation studies a new method using structures of specific shapes to manage fluid and gas mixtures. The investigation studies water recycling and carbon dioxide removal, benefiting future efforts to design lightweight, more reliable life support systems for future space missions.

Structural pounding of concrete frame structure with masonry infill wall under seismic loading

NASA Astrophysics Data System (ADS)

Ismail, Rozaina; Hasnan, Mohd Hafizudin; Shamsudin, Nurhanis

2017-10-01

Structural pounding is additional problem than the other harmful damage that may occurs due to the earthquake vibrations. A lot of study has been made by past researcher but most of them did not include the walls. The infill masonry walls are rarely involved analysis of structural systems but it does contribute to earthquake response of the structures. In this research, a comparison between adjacent building of 10-storey and 7-storey concrete frame structure without of masonry infill walls and the same dynamic properties of buildings. The diagonal strut approach is adopted for modeling masonry infill walls. This research also focused on finding critical building separation in order to prevent the adjacent structures from pounding. LUSAS FEA v14.03 software has been used for modeling analyzing the behavior of structures due to seismic loading and the displacement each floor of the building has been taken in order to determine the critical separation distance between the buildings. From the analysis that has been done, it is found that masonry infill walls do affect the structures behavior under seismic load. Structures without masonry infill walls needs more distance between the structures to prevent structural pounding due to higher displacement of the buildings when it sways under seismic load compared to structures with masonry infill walls. This shows that contribution of masonry infill walls to the analysis of structures cannot be neglected.

Restricted N-glycan conformational space in the PDB and its implication in glycan structure modeling.

PubMed

Jo, Sunhwan; Lee, Hui Sun; Skolnick, Jeffrey; Im, Wonpil

2013-01-01

Understanding glycan structure and dynamics is central to understanding protein-carbohydrate recognition and its role in protein-protein interactions. Given the difficulties in obtaining the glycan's crystal structure in glycoconjugates due to its flexibility and heterogeneity, computational modeling could play an important role in providing glycosylated protein structure models. To address if glycan structures available in the PDB can be used as templates or fragments for glycan modeling, we present a survey of the N-glycan structures of 35 different sequences in the PDB. Our statistical analysis shows that the N-glycan structures found on homologous glycoproteins are significantly conserved compared to the random background, suggesting that N-glycan chains can be confidently modeled with template glycan structures whose parent glycoproteins share sequence similarity. On the other hand, N-glycan structures found on non-homologous glycoproteins do not show significant global structural similarity. Nonetheless, the internal substructures of these N-glycans, particularly, the substructures that are closer to the protein, show significantly similar structures, suggesting that such substructures can be used as fragments in glycan modeling. Increased interactions with protein might be responsible for the restricted conformational space of N-glycan chains. Our results suggest that structure prediction/modeling of N-glycans of glycoconjugates using structure database could be effective and different modeling approaches would be needed depending on the availability of template structures.

Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling

PubMed Central

Jo, Sunhwan; Lee, Hui Sun; Skolnick, Jeffrey; Im, Wonpil

2013-01-01

Understanding glycan structure and dynamics is central to understanding protein-carbohydrate recognition and its role in protein-protein interactions. Given the difficulties in obtaining the glycan's crystal structure in glycoconjugates due to its flexibility and heterogeneity, computational modeling could play an important role in providing glycosylated protein structure models. To address if glycan structures available in the PDB can be used as templates or fragments for glycan modeling, we present a survey of the N-glycan structures of 35 different sequences in the PDB. Our statistical analysis shows that the N-glycan structures found on homologous glycoproteins are significantly conserved compared to the random background, suggesting that N-glycan chains can be confidently modeled with template glycan structures whose parent glycoproteins share sequence similarity. On the other hand, N-glycan structures found on non-homologous glycoproteins do not show significant global structural similarity. Nonetheless, the internal substructures of these N-glycans, particularly, the substructures that are closer to the protein, show significantly similar structures, suggesting that such substructures can be used as fragments in glycan modeling. Increased interactions with protein might be responsible for the restricted conformational space of N-glycan chains. Our results suggest that structure prediction/modeling of N-glycans of glycoconjugates using structure database could be effective and different modeling approaches would be needed depending on the availability of template structures. PMID:23516343

Method of fabricating free-form, high-aspect ratio components for high-current, high-speed microelectrics

DOEpatents

Maxwell, James L; Rose, Chris R; Black, Marcie R; Springer, Robert W

2014-03-11

Microelectronic structures and devices, and method of fabricating a three-dimensional microelectronic structure is provided, comprising passing a first precursor material for a selected three-dimensional microelectronic structure into a reaction chamber at temperatures sufficient to maintain said precursor material in a predominantly gaseous state; maintaining said reaction chamber under sufficient pressures to enhance formation of a first portion of said three-dimensional microelectronic structure; applying an electric field between an electrode and said microelectronic structure at a desired point under conditions whereat said first portion of a selected three-dimensional microelectronic structure is formed from said first precursor material; positionally adjusting either said formed three-dimensional microelectronic structure or said electrode whereby further controlled growth of said three-dimensional microelectronic structure occurs; passing a second precursor material for a selected three-dimensional microelectronic structure into a reaction chamber at temperatures sufficient to maintain said precursor material in a predominantly gaseous state; maintaining said reaction chamber under sufficient pressures whereby a second portion of said three-dimensional microelectronic structure formation is enhanced; applying an electric field between an electrode and said microelectronic structure at a desired point under conditions whereat said second portion of a selected three-dimensional microelectronic structure is formed from said second precursor material; and, positionally adjusting either said formed three-dimensional microelectronic structure or said electrode whereby further controlled growth of said three-dimensional microelectronic structure occurs.

PRINCEPS: A computer-based approach to the structural description and recognition of trends within structural databases, and its application to the Ce-Ni-Si System

DOE PAGES

Guo, Yiming; Fredrickson, Daniel C.

2016-04-01

Intermetallic crystal structures offer an enormous structural diversity, with an endless array of structural motifs whose connection to stability and physical properties are often mysterious. Making sense of the often complex crystal structures that arise here, developing a clear structural description, and identifying connections to other phases can be laborious and require an encyclopedic knowledge of structure types. In this Article, we present PRINCEPS, an algorithm based on a new coordination environment projection scheme that facilitates the structural analysis and comparison of such crystal structures. We demonstrate the potential of this approach by applying it to the complex Ce-Ni-Si ternarymore » system, whose 17 binary and 21 ternary phases would present a daunting challenge to one seeking to understand the system by manual inspection (but has nonetheless been well-described through the heroic efforts of previous researchers). With the help of PRINCEPS, most of the ternary phases in this system can be rationalized as intergrowths of simple structural fragments, and grouped into a handful of structural series (with some outliers). Lastly, these results illustrate how the PRINCEPS approach can be used to organize a vast collection of crystal structures into structurally meaningful families, and guide the description of complex atomic arrangements.« less

Review of beetle forewing structures and their biomimetic applications in China: (I) On the structural colors and the vertical and horizontal cross-sectional structures.

PubMed

Chen, Jinxiang; Xie, Juan; Wu, Zhishen; Elbashiry, Elsafi Mohamed Adam; Lu, Yun

2015-10-01

This paper discusses the progress made in China in terms of the structural colors, microstructure and mechanical properties of the beetle forewing. 1) The forewing microstructures can be classified into six phases, the first three of which are characterized by sandwich, multilayer and fiber layer structures, respectively. The fracture behaviors resulting from these three phases suggest that different scale microstructures or coupled adjacent scale microstructures can determine the macroscopic mechanical behavior of the forewing. 2) The forewing colors are derived from three features: regulation of the structural parameters of the internal optical structures, i.e., a sculpted multilayer composite two-dimensional nanopillar structure grating system; scattering on the three-dimensional surface of the bowl-shaped structure; and reversible color changes due to changes in the physical microstructure of fluffs. Their formation mechanisms were clarified, and fibers with ecological biomimetic structural colors have been developed. 3) Beetles exhibit a lightweight sectional frame structure with a trabecular core structure. Both of the joints on the left and right are concave-convex butt-joint structures with burrs, which provide an efficient docking mechanism with high intensity. The forewing of dichotoma exhibits a non-equiangular layered structure, which results in anisotropy in its tensile strength. Finally, the authors propose potential new research directions for the next 20 years. Copyright © 2015 Elsevier B.V. All rights reserved.

Structural analysis of a set of proteins resulting from a bacterial genomics project.

PubMed

Badger, J; Sauder, J M; Adams, J M; Antonysamy, S; Bain, K; Bergseid, M G; Buchanan, S G; Buchanan, M D; Batiyenko, Y; Christopher, J A; Emtage, S; Eroshkina, A; Feil, I; Furlong, E B; Gajiwala, K S; Gao, X; He, D; Hendle, J; Huber, A; Hoda, K; Kearins, P; Kissinger, C; Laubert, B; Lewis, H A; Lin, J; Loomis, K; Lorimer, D; Louie, G; Maletic, M; Marsh, C D; Miller, I; Molinari, J; Muller-Dieckmann, H J; Newman, J M; Noland, B W; Pagarigan, B; Park, F; Peat, T S; Post, K W; Radojicic, S; Ramos, A; Romero, R; Rutter, M E; Sanderson, W E; Schwinn, K D; Tresser, J; Winhoven, J; Wright, T A; Wu, L; Xu, J; Harris, T J R

2005-09-01

The targets of the Structural GenomiX (SGX) bacterial genomics project were proteins conserved in multiple prokaryotic organisms with no obvious sequence homolog in the Protein Data Bank of known structures. The outcome of this work was 80 structures, covering 60 unique sequences and 49 different genes. Experimental phase determination from proteins incorporating Se-Met was carried out for 45 structures with most of the remainder solved by molecular replacement using members of the experimentally phased set as search models. An automated tool was developed to deposit these structures in the Protein Data Bank, along with the associated X-ray diffraction data (including refined experimental phases) and experimentally confirmed sequences. BLAST comparisons of the SGX structures with structures that had appeared in the Protein Data Bank over the intervening 3.5 years since the SGX target list had been compiled identified homologs for 49 of the 60 unique sequences represented by the SGX structures. This result indicates that, for bacterial structures that are relatively easy to express, purify, and crystallize, the structural coverage of gene space is proceeding rapidly. More distant sequence-structure relationships between the SGX and PDB structures were investigated using PDB-BLAST and Combinatorial Extension (CE). Only one structure, SufD, has a truly unique topology compared to all folds in the PDB. Copyright 2005 Wiley-Liss, Inc.

Extraction of membrane structure in eyeball from MR volumes

NASA Astrophysics Data System (ADS)

Oda, Masahiro; Kin, Taichi; Mori, Kensaku

2017-03-01

This paper presents an accurate extraction method of spherical shaped membrane structures in the eyeball from MR volumes. In ophthalmic surgery, operation field is limited to a small region. Patient specific surgical simulation is useful to reduce complications. Understanding of tissue structure in the eyeball of a patient is required to achieve patient specific surgical simulations. Previous extraction methods of tissue structure in the eyeball use optical coherence tomography (OCT) images. Although OCT images have high resolution, imaging regions are limited to very small. Global structure extraction of the eyeball is difficult from OCT images. We propose an extraction method of spherical shaped membrane structures including the sclerotic coat, choroid, and retina. This method is applied to a T2 weighted MR volume of the head region. MR volume can capture tissue structure of whole eyeball. Because we use MR volumes, out method extracts whole membrane structures in the eyeball. We roughly extract membrane structures by applying a sheet structure enhancement filter. The rough extraction result includes parts of the membrane structures. Then, we apply the Hough transform to extract a sphere structure from the voxels set of the rough extraction result. The Hough transform finds a sphere structure from the rough extraction result. An experimental result using a T2 weighted MR volume of the head region showed that the proposed method can extract spherical shaped membrane structures accurately.

Vfold: a web server for RNA structure and folding thermodynamics prediction.

PubMed

Xu, Xiaojun; Zhao, Peinan; Chen, Shi-Jie

2014-01-01

The ever increasing discovery of non-coding RNAs leads to unprecedented demand for the accurate modeling of RNA folding, including the predictions of two-dimensional (base pair) and three-dimensional all-atom structures and folding stabilities. Accurate modeling of RNA structure and stability has far-reaching impact on our understanding of RNA functions in human health and our ability to design RNA-based therapeutic strategies. The Vfold server offers a web interface to predict (a) RNA two-dimensional structure from the nucleotide sequence, (b) three-dimensional structure from the two-dimensional structure and the sequence, and (c) folding thermodynamics (heat capacity melting curve) from the sequence. To predict the two-dimensional structure (base pairs), the server generates an ensemble of structures, including loop structures with the different intra-loop mismatches, and evaluates the free energies using the experimental parameters for the base stacks and the loop entropy parameters given by a coarse-grained RNA folding model (the Vfold model) for the loops. To predict the three-dimensional structure, the server assembles the motif scaffolds using structure templates extracted from the known PDB structures and refines the structure using all-atom energy minimization. The Vfold-based web server provides a user friendly tool for the prediction of RNA structure and stability. The web server and the source codes are freely accessible for public use at "http://rna.physics.missouri.edu".

Microbial shaping of wrinkle structures in siliciclastic deposits

NASA Astrophysics Data System (ADS)

Bosak, T.; Mariotti, G.; Pruss, S. B.; Perron, J.; O'Grady, M.

2013-12-01

Wrinkle structures are millimeter- to centimeter-scale elongated or reticulate sedimentary structures that resemble symmetric ripples. Sharp-crested and flat-topped wrinkle structures up to 1 cm wide occur on numerous bedding planes in the Neoproterozoic and Cambrian, as well as in some Archean and Phanerozoic siliciclastic deposits. Because similar, but unlithified structures occur in some modern, microbially-colonized sands, wrinkle structures are typically interpreted as microbially induced sedimentary structures. However, it is unclear if physical processes, such as the motion of suspended sand grains, can produce similar features in sand even before microbial colonization. We introduced mat fragments to the surface of silica sand in wave tanks and generated sharp-crested, flat-topped and pitted wrinkle structures. The abrasion of the sandy surface by rolling, low density, millimeter-size fragments of microbial mats produces wrinkle structures at extremely weak orbital velocities that cannot move sand grains in the absence of light particles. Wrinkle structures form in a few hours and can become colonized by microbial mats within weeks. Thus, wrinkle structures are patterns formed by microbially mediated sand motion at low orbital velocities in the absence of bioturbation. Once formed, wrinkle structures can be colonized and stabilized by microbial mats, but the shape of these mats does not dictate the shape of wrinkle structures. These experiments bolster the interpretation of wrinkle structures as morphological signatures of organic particles and early life in Archean and Proterozoic siliciclastic deposits.

Computational structural mechanics engine structures computational simulator

NASA Technical Reports Server (NTRS)

Chamis, C. C.

1989-01-01

The Computational Structural Mechanics (CSM) program at Lewis encompasses: (1) fundamental aspects for formulating and solving structural mechanics problems, and (2) development of integrated software systems to computationally simulate the performance/durability/life of engine structures.

Mixed-mu superconducting bearings

DOEpatents

Hull, J.R.; Mulcahy, T.M.

1998-03-03

A mixed-mu superconducting bearing is disclosed including a ferrite structure disposed for rotation adjacent a stationary superconductor material structure and a stationary permanent magnet structure. The ferrite structure is levitated by said stationary permanent magnet structure. 9 figs.

30 CFR 75.1708-1 - Surface structures; fireproof construction.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Surface structures; fireproof construction. 75... Surface structures; fireproof construction. Structures of fireproof construction is interpreted to mean structures with fireproof exterior surfaces. ...

Some Lower Valence Vanadium Fluorides: Their Crystal Distortions, Domain Structures, Modulated Structures, Ferrimagnetism, and Composition Dependence.

ERIC Educational Resources Information Center

Hong, Y. S.; And Others

1980-01-01

Describes some contemporary concepts unique to the structure of advanced solids, i.e., their crystal distortions, domain structures, modulated structures, ferrimagnetism, and composition dependence. (Author/CS)

Structural Performance of the Second Oldest Glued-Laminated Structure in the United States

Treesearch

Douglas R. Rammer; Jorge de Melo Moura; Robert J. Ross

2014-01-01

The second glued-laminated structure built in the United States was constructed at the USDA Forest Products Laboratory (FPL) in 1934 to demonstrate the performance of wooden arch buildings. After 75 years of use the structure was decommissioned in 2010. Shortly after construction, researchers structurally evaluated the glued-laminated arch structure for uniform loading...

Structural Evaluation of the Second Oldest Glued-Laminated Structure in the United States

Treesearch

Douglas R. Rammer; Jorge de Melo Moura

2013-01-01

The second glued-laminated structure built in the United States was constructed at the USDA Forest Products Laboratory (FPL) in 1934 to demonstrate the performance of wooden arch buildings. After decades of use the structure was decommissioned in 2010. Shortly after construction, researchers structurally evaluated the glued-laminated arch structure for uniform loading...

Hydrophilic structures for condensation management in appliances

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

Kuehl, Steven John; Vonderhaar, John J.; Wu, Guolian

2016-02-02

An appliance that includes a cabinet having an exterior surface; a refrigeration compartment located within the cabinet; and a hydrophilic structure disposed on the exterior surface. The hydrophilic structure is configured to spread condensation. The appliance further includes a wicking structure located in proximity to the hydrophilic structure, and the wicking structure is configured to receive the condensation.

33 CFR 67.25-1 - Class “B” structures.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Class âBâ structures. 67.25-1... NAVIGATION AIDS TO NAVIGATION ON ARTIFICIAL ISLANDS AND FIXED STRUCTURES Class âBâ Requirements § 67.25-1 Class “B” structures. Class “B” structures shall be the structures erected in an area where Class “B...

Recent Advances in Structures for Hypersonic Flight, part 2

NASA Technical Reports Server (NTRS)

1978-01-01

The papers at this symposium were presented by 24 speakers representing airframe, missile, and engine manufacturers, the U.S. Air Force, and two NASA Research Centers. The papers cover a variety of topics including engine structures, cooled airframe structures, hot structures, thermal protection systems, cryogenic tankage structures, cryogenic insulations, and analysis methods for thermal/structures.

Structure-based characterization of multiprotein complexes.

PubMed

Wiederstein, Markus; Gruber, Markus; Frank, Karl; Melo, Francisco; Sippl, Manfred J

2014-07-08

Multiprotein complexes govern virtually all cellular processes. Their 3D structures provide important clues to their biological roles, especially through structural correlations among protein molecules and complexes. The detection of such correlations generally requires comprehensive searches in databases of known protein structures by means of appropriate structure-matching techniques. Here, we present a high-speed structure search engine capable of instantly matching large protein oligomers against the complete and up-to-date database of biologically functional assemblies of protein molecules. We use this tool to reveal unseen structural correlations on the level of protein quaternary structure and demonstrate its general usefulness for efficiently exploring complex structural relationships among known protein assemblies. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

DNA secondary structures: stability and function of G-quadruplex structures

PubMed Central

Bochman, Matthew L.; Paeschke, Katrin; Zakian, Virginia A.

2013-01-01

In addition to the canonical double helix, DNA can fold into various other inter- and intramolecular secondary structures. Although many such structures were long thought to be in vitro artefacts, bioinformatics demonstrates that DNA sequences capable of forming these structures are conserved throughout evolution, suggesting the existence of non-B-form DNA in vivo. In addition, genes whose products promote formation or resolution of these structures are found in diverse organisms, and a growing body of work suggests that the resolution of DNA secondary structures is critical for genome integrity. This Review focuses on emerging evidence relating to the characteristics of G-quadruplex structures and the possible influence of such structures on genomic stability and cellular processes, such as transcription. PMID:23032257

Mining protein loops using a structural alphabet and statistical exceptionality

PubMed Central

2010-01-01

Background Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. Results We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times). Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words). These structural words have low structural variability (mean RMSd of 0.85 Å). As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues) and long loops. Moreover, half of recurrent motifs exhibit a significant level of amino-acid conservation with at least four significant positions and 87% of long loops contain at least one such word. We complement our analysis with the detection of statistically over-represented patterns of structural letters as in conventional DNA sequence analysis. About 30% (930) of structural words are over-represented, and cover about 40% of loop lengths. Interestingly, these words exhibit lower structural variability and higher sequential specificity, suggesting structural or functional constraints. Conclusions We developed a method to systematically decompose and study protein loops using recurrent structural motifs. This method is based on the structural alphabet HMM-SA and not on structural alignment and geometrical parameters. We extracted meaningful structural motifs that are found in both short and long loops. To our knowledge, it is the first time that pattern mining helps to increase the signal-to-noise ratio in protein loops. This finding helps to better describe protein loops and might permit to decrease the complexity of long-loop analysis. Detailed results are available at http://www.mti.univ-paris-diderot.fr/publication/supplementary/2009/ACCLoop/. PMID:20132552

Mining protein loops using a structural alphabet and statistical exceptionality.

PubMed

Regad, Leslie; Martin, Juliette; Nuel, Gregory; Camproux, Anne-Claude

2010-02-04

Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times). Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words). These structural words have low structural variability (mean RMSd of 0.85 A). As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues) and long loops. Moreover, half of recurrent motifs exhibit a significant level of amino-acid conservation with at least four significant positions and 87% of long loops contain at least one such word. We complement our analysis with the detection of statistically over-represented patterns of structural letters as in conventional DNA sequence analysis. About 30% (930) of structural words are over-represented, and cover about 40% of loop lengths. Interestingly, these words exhibit lower structural variability and higher sequential specificity, suggesting structural or functional constraints. We developed a method to systematically decompose and study protein loops using recurrent structural motifs. This method is based on the structural alphabet HMM-SA and not on structural alignment and geometrical parameters. We extracted meaningful structural motifs that are found in both short and long loops. To our knowledge, it is the first time that pattern mining helps to increase the signal-to-noise ratio in protein loops. This finding helps to better describe protein loops and might permit to decrease the complexity of long-loop analysis. Detailed results are available at http://www.mti.univ-paris-diderot.fr/publication/supplementary/2009/ACCLoop/.

The Aerodynamic and Dynamic Loading of a Slender Structure by an Impacting Tornado-Like Vortex: The Influence of Relative Vortex-to-Structure Size on Structural Loading

NASA Astrophysics Data System (ADS)

Strasser, Matthew N.

Structural loading produced by an impacting vortex is a hazardous phenomenon that is encountered in numerous applications ranging from the destruction of residences by tornados to the chopping of tip vortices by rotors. Adequate design of structures to resist vortex-induced structural loading necessitates study of the phenomenon that control the structural loading produced by an impacting vortex. This body of work extends the current knowledge base of vortex-structure interaction by evaluating the influence of the relative vortex-to-structure size on the structural loading that the vortex produces. A computer model is utilized to directly simulate the two-dimensional impact of an impinging vortex with a slender, cylindrical structure. The vortex's tangential velocity profile (TVP) is defined by a normalization of the Vatistas analytical (TVP) which realistically replicates the documented spectrum of measured vortex TVPs. The impinging vortex's maximum tangential velocity is fixed, and the vortex's critical radius is incremented from one to one-hundred times the structure's diameter. When the impinging vortex is small, it interacts with vortices produced on the structure by the free stream, and maximum force coefficient amplitudes vary by more than 400% when the impinging vortex impacts the structure at different times. Maximum drag and lift force coefficient amplitudes reach asymptotic values as the impinging vortex's size increases that are respectively 94.77% and 10.66% less than maximum force coefficients produced by an equivalent maximum velocity free stream. The vortex produces maximum structural loading when its path is shifted above the structure's centerline, and maximum drag and lift force coefficients are respectively up to 4.80% and 34.07% greater than maximum force coefficients produced by an equivalent-velocity free stream. Finally, the dynamic load factor (DLF) concept is used to develop a generalized methodology to assess the dynamic amplification of a structure's response to vortex loading and to assess the dynamic loading threat that tornados pose. Typical civil and residential structures will not experience significant response amplification, but responses of very flexible structures may be amplified by up to 2.88 times.

Effects of non-structural components and soil-structure interaction on the seismic response of framed structures

NASA Astrophysics Data System (ADS)

Ditommaso, Rocco; Auletta, Gianluca; Iacovino, Chiara; Nigro, Antonella; Carlo Ponzo, Felice

2017-04-01

In this paper, several nonlinear numerical models of reinforced concrete framed structures have been defined in order to evaluate the effects of non-structural elements and soil-structure interaction on the elastic dynamic behaviour of buildings. In the last few years, many and various studies have highlighted the significant effects derived from the interaction between structural and non-structural components on the main dynamic characteristics of a building. Usually, structural and non-structural elements act together, adding both masses and stiffness. The presence of infill panels is generally neglected in the design process of structural elements, although these elements can significantly increase the lateral stiffness of a structure leading to a modification in the dynamic properties. Particularly, at the Damage Limit State (where an elastic behaviour is expected), soil-structure interaction effects and non-structural elements may further affect the elastic natural period of buildings, changing the spectral accelerations compared with those provided by seismic codes in case of static analyses. In this work, a parametric study has been performed in order to evaluate the elastic fundamental period of vibration of buildings as a function of structural morphology (height, plan area, ratio between plan dimensions), infills presence and distribution and soil characteristics. Acknowledgements This study was partially funded by the Italian Department of Civil Protection within the project DPC-RELUIS 2016 - RS4 ''Seismic observatory of structures and health monitoring'' and by the "Centre of Integrated Geomorphology for the Mediterranean Area - CGIAM" within the Framework Agreement with the University of Basilicata "Study, Research and Experimentation in the Field of Analysis and Monitoring of Seismic Vulnerability of Strategic and Relevant Buildings for the purposes of Civil Protection and Development of Innovative Strategies of Seismic Reinforcement".

Nondestructive Structural Damage Detection in Flexible Space Structures Using Vibration Characterization

NASA Technical Reports Server (NTRS)

Ricles, James M.

1991-01-01

Spacecraft are susceptible to structural damage over their operating life from impact, environmental loads, and fatigue. Structural damage that is not detected and not corrected may potentially cause more damage and eventually catastrophic structural failure. NASA's current fleet of reusable spacecraft, namely the Space Shuttle, has been flown on several missions. In addition, configurations of future NASA space structures, e.g. Space Station Freedom, are larger and more complex than current structures, making them more susceptible to damage as well as being more difficult to inspect. Consequently, a reliable structural damage detection capability is essential to maintain the flight safety of these structures. Visual inspections alone can not locate impending material failure (fatigue cracks, yielding); it can only observe post-failure situations. An alternative approach is to develop an inspection and monitoring system based on vibration characterization that assesses the integrity of structural and mechanical components. A methodology for detecting structural damage is presented. This methodology is based on utilizing modal test data in conjunction with a correlated analytical model of the structure to: (1) identify the structural dynamic characteristics (resonant frequencies and mode shapes) from measurements of ambient motions and/or force excitation; (2) calculate modal residual force vectors to identify the location of structural damage; and (3) conduct a weighted sensitivity analysis in order to assess the extent of mass and stiffness variations, where structural damage is characterized by stiffness reductions. The approach is unique from other existing approaches in that varying system mass and stiffness, mass center locations, the perturbation of both the natural frequencies and mode shapes, and statistical confidence factors for structural parameters and experimental instrumentation are all accounted for directly.

Structural changes and fluctuations of proteins. I. A statistical thermodynamic model.

PubMed

Ikegami, A

1977-01-01

A general theory of the structural changes and fluctuations of proteins has been proposed based on statistical thermodynamic considerations at the chain level. The "structure" of protein was assumed to be characterized by the state of secondary bonds between unique pairs of specific sites on peptide chains. Every secondary bond changes between the bonded and unbonded states by thermal agitation and the "structure" is continuously fluctuating. The free energy of the "structural state" that is defined by the fraction of secondary bonds in the bonded state has been expressed by the bond energy, the cooperative interaction between bonds, the mixing entropy of bonds, and the entropy of polypeptide chains. The most probable "structural state" can be simply determined by graphical analysis and the effect of temperature or solvent composition on it is discussed. The temperature dependence of the free energy, the probability distribution of structural states and the specific heat have been calculted for two examples of structural change. The theory predicts two different types of structural changes from the ordered to disorderd state, a "structured transition" and a "gradual structural change" with rising temperature. In the "structural transition", the probability distribution has two maxima in the temperature range of transition. In the "gradual structural change", the probabilty distribution has only one maximum during the change. A considerable fraction of secondary bonds is in the unbounded state and is always fluctuating even in the ordered state at room temperature. Such structural flucutations in a single protein molecule have been discussed quantitatively. The theory is extended to include small molecules which bind to the protein molecule and affect the structural state. The changes of structural state caused by specific and non-specific binding and allosteric effects are explained in a unified manner.

Structural diversity of domain superfamilies in the CATH database.

PubMed

Reeves, Gabrielle A; Dallman, Timothy J; Redfern, Oliver C; Akpor, Adrian; Orengo, Christine A

2006-07-14

The CATH database of domain structures has been used to explore the structural variation of homologous domains in 294 well populated domain structure superfamilies, each containing at least three sequence diverse relatives. Our analyses confirm some previously detected trends relating sequence divergence to structural variation but for a much larger dataset and in some superfamilies the new data reveal exceptional structural variation. Use of a new algorithm (2DSEC) to analyse variability in secondary structure compositions across a superfamily sheds new light on how structures evolve. 2DSEC detects inserted secondary structures that embellish the core of conserved secondary structures found throughout the superfamily. Analysis showed that for 56% of highly populated superfamilies (>9 sequence diverse relatives), there are twofold or more increases in the numbers of secondary structures in some relatives. In some families fivefold increases occur, sometimes modifying the fold of the domain. Manual inspection of secondary structure insertions or embellishments in 48 particularly variable superfamilies revealed that although these insertions were usually discontiguous in the sequence they were often co-located in 3D resulting in a larger structural motif that often modified the geometry of the active site or the surface conformation promoting diverse domain partnerships and protein interactions. These observations, supported by automatic analysis of all well populated CATH families, suggest that accretion of small secondary structure insertions may provide a simple mechanism for evolving new functions in diverse relatives. Some layered domain architectures (e.g. mainly-beta and alpha-beta sandwiches) that recur highly in the genomes more frequently exploit these types of embellishments to modify function. In these architectures, aggregation occurs most often at the edges, top or bottom of the beta-sheets. Information on structural variability across domain superfamilies has been made available through the CATH Dictionary of Homologous Structures (DHS).

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features.

PubMed

Ding, Yiliang; Tang, Yin; Kwok, Chun Kit; Zhang, Yu; Bevilacqua, Philip C; Assmann, Sarah M

2014-01-30

RNA structure has critical roles in processes ranging from ligand sensing to the regulation of translation, polyadenylation and splicing. However, a lack of genome-wide in vivo RNA structural data has limited our understanding of how RNA structure regulates gene expression in living cells. Here we present a high-throughput, genome-wide in vivo RNA structure probing method, structure-seq, in which dimethyl sulphate methylation of unprotected adenines and cytosines is identified by next-generation sequencing. Application of this method to Arabidopsis thaliana seedlings yielded the first in vivo genome-wide RNA structure map at nucleotide resolution for any organism, with quantitative structural information across more than 10,000 transcripts. Our analysis reveals a three-nucleotide periodic repeat pattern in the structure of coding regions, as well as a less-structured region immediately upstream of the start codon, and shows that these features are strongly correlated with translation efficiency. We also find patterns of strong and weak secondary structure at sites of alternative polyadenylation, as well as strong secondary structure at 5' splice sites that correlates with unspliced events. Notably, in vivo structures of messenger RNAs annotated for stress responses are poorly predicted in silico, whereas mRNA structures of genes related to cell function maintenance are well predicted. Global comparison of several structural features between these two categories shows that the mRNAs associated with stress responses tend to have more single-strandedness, longer maximal loop length and higher free energy per nucleotide, features that may allow these RNAs to undergo conformational changes in response to environmental conditions. Structure-seq allows the RNA structurome and its biological roles to be interrogated on a genome-wide scale and should be applicable to any organism.

The dynamics of interacting salt structures and associated fluid flow in the western Norwegian-Danish Basin

NASA Astrophysics Data System (ADS)

Olsen, Mikkel S.; Clausen, Ole R.; Andresen, Katrine J.; Korstgård, John A.

2015-04-01

Minor secondary structures observed along the flanks of major salt structures in the Norwegian-Danish Basin appear to be generated mainly during the early stages of halokinesis. Seismic anomalies in the cover sediments at the flanks of the major salt structures and in relation to one of the secondary structures show several circular patterns. The circular patterns are generally interpreted as faults related to collapsing salt, indicating a subtle and dynamic cannibalization relationship between the secondary structure and the main diapir. High-amplitude reflections interpreted as either entrapped gas along the circular faults or diagenetic changes induced by the fluids originating from the salt-sediment interface generally enhances the seismic appearance of the circular faults, but potentially also disturb the seismic imaging of the faults. Other secondary salt structures, with a similar geometry, do not show sign of collapse, apparently due to a greater distance from the main salt structures and therefore not within the reach of being cannibalized by these. The observations furthermore suggest a trend showing a more advanced development of the main salt structures when the secondary structures are cannibalized. The lateral distribution of the main salt structures thus appears to be controlled not only by the initial thickness of the Zechstein salt, and possible underlying structures, but also by subtle variations in the location and evolution of secondary structures. The secondary structures have a major impact on the drainage of the deep Mesozoic succession as indicated by the fluid flow pattern also observed in the study, which emphasizes that a detailed mapping of salt structures including secondary structures at the flanks is of major importance during evaluation of petroleum systems in areas dominated by halokinesis.

Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D).

PubMed

van de Streek, Jacco; Neumann, Marcus A

2014-12-01

In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom.

Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D)

PubMed Central

van de Streek, Jacco; Neumann, Marcus A.

2014-01-01

In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom. PMID:25449625

Harnessing data structure for recovery of randomly missing structural vibration responses time history: Sparse representation versus low-rank structure

NASA Astrophysics Data System (ADS)

Yang, Yongchao; Nagarajaiah, Satish

2016-06-01

Randomly missing data of structural vibration responses time history often occurs in structural dynamics and health monitoring. For example, structural vibration responses are often corrupted by outliers or erroneous measurements due to sensor malfunction; in wireless sensing platforms, data loss during wireless communication is a common issue. Besides, to alleviate the wireless data sampling or communication burden, certain accounts of data are often discarded during sampling or before transmission. In these and other applications, recovery of the randomly missing structural vibration responses from the available, incomplete data, is essential for system identification and structural health monitoring; it is an ill-posed inverse problem, however. This paper explicitly harnesses the data structure itself-of the structural vibration responses-to address this (inverse) problem. What is relevant is an empirical, but often practically true, observation, that is, typically there are only few modes active in the structural vibration responses; hence a sparse representation (in frequency domain) of the single-channel data vector, or, a low-rank structure (by singular value decomposition) of the multi-channel data matrix. Exploiting such prior knowledge of data structure (intra-channel sparse or inter-channel low-rank), the new theories of ℓ1-minimization sparse recovery and nuclear-norm-minimization low-rank matrix completion enable recovery of the randomly missing or corrupted structural vibration response data. The performance of these two alternatives, in terms of recovery accuracy and computational time under different data missing rates, is investigated on a few structural vibration response data sets-the seismic responses of the super high-rise Canton Tower and the structural health monitoring accelerations of a real large-scale cable-stayed bridge. Encouraging results are obtained and the applicability and limitation of the presented methods are discussed.

RNA secondary structure prediction with pseudoknots: Contribution of algorithm versus energy model.

PubMed

Jabbari, Hosna; Wark, Ian; Montemagno, Carlo

2018-01-01

RNA is a biopolymer with various applications inside the cell and in biotechnology. Structure of an RNA molecule mainly determines its function and is essential to guide nanostructure design. Since experimental structure determination is time-consuming and expensive, accurate computational prediction of RNA structure is of great importance. Prediction of RNA secondary structure is relatively simpler than its tertiary structure and provides information about its tertiary structure, therefore, RNA secondary structure prediction has received attention in the past decades. Numerous methods with different folding approaches have been developed for RNA secondary structure prediction. While methods for prediction of RNA pseudoknot-free structure (structures with no crossing base pairs) have greatly improved in terms of their accuracy, methods for prediction of RNA pseudoknotted secondary structure (structures with crossing base pairs) still have room for improvement. A long-standing question for improving the prediction accuracy of RNA pseudoknotted secondary structure is whether to focus on the prediction algorithm or the underlying energy model, as there is a trade-off on computational cost of the prediction algorithm versus the generality of the method. The aim of this work is to argue when comparing different methods for RNA pseudoknotted structure prediction, the combination of algorithm and energy model should be considered and a method should not be considered superior or inferior to others if they do not use the same scoring model. We demonstrate that while the folding approach is important in structure prediction, it is not the only important factor in prediction accuracy of a given method as the underlying energy model is also as of great value. Therefore we encourage researchers to pay particular attention in comparing methods with different energy models.

Simulation Analysis and Performance Study of CoCrMo Porous Structure Manufactured by Selective Laser Melting

NASA Astrophysics Data System (ADS)

Guoqing, Zhang; Junxin, Li; Jin, Li; Chengguang, Zhang; Zefeng, Xiao

2018-04-01

To fabricate porous implants with improved biocompatibility and mechanical properties that are matched to their application using selective laser melting (SLM), flow within the mold and compressive properties and performance of the porous structures must be comprehensively studied. Parametric modeling was used to build 3D models of octahedron and hexahedron structures. Finite element analysis was used to evaluate the mold flow and compressive properties of the parametric porous structures. A DiMetal-100 SLM molding apparatus was used to manufacture the porous structures and the results evaluated by light microscopy. The results showed that parametric modeling can produce robust models. Square structures caused higher blood cell adhesion than cylindrical structures. "Vortex" flow in square structures resulted in chaotic distribution of blood elements, whereas they were mostly distributed around the connecting parts in the cylindrical structures. No significant difference in elastic moduli or compressive strength was observed in square and cylindrical porous structures of identical characteristics. Hexahedron, square and cylindrical porous structures had the same stress-strain properties. For octahedron porous structures, cylindrical structures had higher stress-strain properties. Using these modeling and molding results, an important basis for designing and the direct manufacture of fixed biological implants is provided.

The importance of building construction materials relative to other factors affecting structure survival during wildfire

USGS Publications Warehouse

Syphard, Alexandra D.; Brennan, Teresa J.; Keeley, Jon E.

2017-01-01

Structure loss to wildfire is a serious problem in wildland-urban interface areas across the world. Laboratory experiments suggest that fire-resistant building construction and design could be important for reducing structure destruction, but these need to be evaluated under real wildfire conditions, especially relative to other factors. Using empirical data from destroyed and surviving structures from large wildfires in southern California, we evaluated the relative importance of building construction and structure age compared to other local and landscape-scale variables associated with structure survival. The local-scale analysis showed that window preparation was especially important but, in general, creating defensible space adjacent to the home was as important as building construction. At the landscape scale, structure density and structure age were the two most important factors affecting structure survival, but there was a significant interaction between them. That is, young structure age was most important in higher-density areas where structure survival overall was more likely. On the other hand, newer-construction structures were less likely to survive wildfires at lower density. Here, appropriate defensible space near the structure and accessibility to major roads were important factors. In conclusion, community safety is a multivariate problem that will require a comprehensive solution involving land use planning, fire-safe construction, and property maintenance.

VK-phantom male with 583 structures and female with 459 structures, based on the sectioned images of a male and a female, for computational dosimetry

PubMed Central

Park, Jin Seo; Jung, Yong Wook; Choi, Hyung-Do; Lee, Ae-Kyoung

2018-01-01

Abstract The anatomical structures in most phantoms are classified according to tissue properties rather than according to their detailed structures, because the tissue properties, not the detailed structures, are what is considered important. However, if a phantom does not have detailed structures, the phantom will be unreliable because different tissues can be regarded as the same. Thus, we produced the Visible Korean (VK) -phantoms with detailed structures (male, 583 structures; female, 459 structures) based on segmented images of the whole male body (interval, 1.0 mm; pixel size, 1.0 mm2) and the whole female body (interval, 1.0 mm; pixel size, 1.0 mm2), using house-developed software to analyze the text string and voxel information for each of the structures. The density of each structure in the VK-phantom was calculated based on Virtual Population and a publication of the International Commission on Radiological Protection. In the future, we will standardize the size of each structure in the VK-phantoms. If the VK-phantoms are standardized and the mass density of each structure is precisely known, researchers will be able to measure the exact absorption rate of electromagnetic radiation in specific organs and tissues of the whole body. PMID:29659988

VK-phantom male with 583 structures and female with 459 structures, based on the sectioned images of a male and a female, for computational dosimetry.

PubMed

Park, Jin Seo; Jung, Yong Wook; Choi, Hyung-Do; Lee, Ae-Kyoung

2018-05-01

The anatomical structures in most phantoms are classified according to tissue properties rather than according to their detailed structures, because the tissue properties, not the detailed structures, are what is considered important. However, if a phantom does not have detailed structures, the phantom will be unreliable because different tissues can be regarded as the same. Thus, we produced the Visible Korean (VK) -phantoms with detailed structures (male, 583 structures; female, 459 structures) based on segmented images of the whole male body (interval, 1.0 mm; pixel size, 1.0 mm2) and the whole female body (interval, 1.0 mm; pixel size, 1.0 mm2), using house-developed software to analyze the text string and voxel information for each of the structures. The density of each structure in the VK-phantom was calculated based on Virtual Population and a publication of the International Commission on Radiological Protection. In the future, we will standardize the size of each structure in the VK-phantoms. If the VK-phantoms are standardized and the mass density of each structure is precisely known, researchers will be able to measure the exact absorption rate of electromagnetic radiation in specific organs and tissues of the whole body.

Simulation Analysis and Performance Study of CoCrMo Porous Structure Manufactured by Selective Laser Melting

NASA Astrophysics Data System (ADS)

Guoqing, Zhang; Junxin, Li; Jin, Li; Chengguang, Zhang; Zefeng, Xiao

2018-05-01

To fabricate porous implants with improved biocompatibility and mechanical properties that are matched to their application using selective laser melting (SLM), flow within the mold and compressive properties and performance of the porous structures must be comprehensively studied. Parametric modeling was used to build 3D models of octahedron and hexahedron structures. Finite element analysis was used to evaluate the mold flow and compressive properties of the parametric porous structures. A DiMetal-100 SLM molding apparatus was used to manufacture the porous structures and the results evaluated by light microscopy. The results showed that parametric modeling can produce robust models. Square structures caused higher blood cell adhesion than cylindrical structures. "Vortex" flow in square structures resulted in chaotic distribution of blood elements, whereas they were mostly distributed around the connecting parts in the cylindrical structures. No significant difference in elastic moduli or compressive strength was observed in square and cylindrical porous structures of identical characteristics. Hexahedron, square and cylindrical porous structures had the same stress-strain properties. For octahedron porous structures, cylindrical structures had higher stress-strain properties. Using these modeling and molding results, an important basis for designing and the direct manufacture of fixed biological implants is provided.

Sequence-structure mapping errors in the PDB: OB-fold domains

PubMed Central

Venclovas, Česlovas; Ginalski, Krzysztof; Kang, Chulhee

2004-01-01

The Protein Data Bank (PDB) is the single most important repository of structural data for proteins and other biologically relevant molecules. Therefore, it is critically important to keep the PDB data, as much as possible, error-free. In this study, we have analyzed PDB crystal structures possessing oligonucleotide/oligosaccharide binding (OB)-fold, one of the highly populated folds, for the presence of sequence-structure mapping errors. Using energy-based structure quality assessment coupled with sequence analyses, we have found that there are at least five OB-structures in the PDB that have regions where sequences have been incorrectly mapped onto the structure. We have demonstrated that the combination of these computation techniques is effective not only in detecting sequence-structure mapping errors, but also in providing guidance to correct them. Namely, we have used results of computational analysis to direct a revision of X-ray data for one of the PDB entries containing a fairly inconspicuous sequence-structure mapping error. The revised structure has been deposited with the PDB. We suggest use of computational energy assessment and sequence analysis techniques to facilitate structure determination when homologs having known structure are available to use as a reference. Such computational analysis may be useful in either guiding the sequence-structure assignment process or verifying the sequence mapping within poorly defined regions. PMID:15133161

JNSViewer—A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures

PubMed Central

Dong, Min; Graham, Mitchell; Yadav, Nehul

2017-01-01

Many tools are available for visualizing RNA or DNA secondary structures, but there is scarce implementation in JavaScript that provides seamless integration with the increasingly popular web computational platforms. We have developed JNSViewer, a highly interactive web service, which is bundled with several popular tools for DNA/RNA secondary structure prediction and can provide precise and interactive correspondence among nucleotides, dot-bracket data, secondary structure graphs, and genic annotations. In JNSViewer, users can perform RNA secondary structure predictions with different programs and settings, add customized genic annotations in GFF format to structure graphs, search for specific linear motifs, and extract relevant structure graphs of sub-sequences. JNSViewer also allows users to choose a transcript or specific segment of Arabidopsis thaliana genome sequences and predict the corresponding secondary structure. Popular genome browsers (i.e., JBrowse and BrowserGenome) were integrated into JNSViewer to provide powerful visualizations of chromosomal locations, genic annotations, and secondary structures. In addition, we used StructureFold with default settings to predict some RNA structures for Arabidopsis by incorporating in vivo high-throughput RNA structure profiling data and stored the results in our web server, which might be a useful resource for RNA secondary structure studies in plants. JNSViewer is available at http://bioinfolab.miamioh.edu/jnsviewer/index.html. PMID:28582416

Ability of Impedance-Based Health Monitoring To Detect Structural Damage of Propulsion System Components Assessed

NASA Technical Reports Server (NTRS)

Martin, Richard E.; Gyekenyesi, Andrew L.; Sawicki, Jerzy T.; Baaklini, George Y.

2005-01-01

Impedance-based structural-health-monitoring uses piezoelectric (PZT) patches that are bonded onto or embedded in a structure. Each individual patch behaves as both an actuator of the surrounding structural area as well as a sensor of the structural response. The size of the excited area varies with the geometry and material composition of the structure, and an active patch is driven by a sinusoidal voltage sweep. When a PZT patch is subjected to an electric field, it produces a mechanical strain; and when it is stressed, it produces an electric charge. Since the patch is bonded to the structure, driving a patch deforms and vibrates the structure. The structure then produces a localized dynamic response. This structural system response is transferred back to the PZT patch, which in turn produces an electrical response. The electromechanical impedance method is based on the principle of electromechanical coupling between the active sensor and the structure, which allows researchers to assess local structural dynamics directly by interrogating a distributed sensor array. Because of mechanical coupling between the sensor and the host structure, this mechanical effect is picked up by the sensor and, through electromechanical coupling inside the active element, is reflected in electrical impedance measured at the sensor s terminals.

Secondary structure prediction and structure-specific sequence analysis of single-stranded DNA.

PubMed

Dong, F; Allawi, H T; Anderson, T; Neri, B P; Lyamichev, V I

2001-08-01

DNA sequence analysis by oligonucleotide binding is often affected by interference with the secondary structure of the target DNA. Here we describe an approach that improves DNA secondary structure prediction by combining enzymatic probing of DNA by structure-specific 5'-nucleases with an energy minimization algorithm that utilizes the 5'-nuclease cleavage sites as constraints. The method can identify structural differences between two DNA molecules caused by minor sequence variations such as a single nucleotide mutation. It also demonstrates the existence of long-range interactions between DNA regions separated by >300 nt and the formation of multiple alternative structures by a 244 nt DNA molecule. The differences in the secondary structure of DNA molecules revealed by 5'-nuclease probing were used to design structure-specific probes for mutation discrimination that target the regions of structural, rather than sequence, differences. We also demonstrate the performance of structure-specific 'bridge' probes complementary to non-contiguous regions of the target molecule. The structure-specific probes do not require the high stringency binding conditions necessary for methods based on mismatch formation and permit mutation detection at temperatures from 4 to 37 degrees C. Structure-specific sequence analysis is applied for mutation detection in the Mycobacterium tuberculosis katG gene and for genotyping of the hepatitis C virus.

Advanced Structural Analyses by Third Generation Synchrotron Radiation Powder Diffraction

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

Sakata, M.; Aoyagi, S.; Ogura, T.

2007-01-19

Since the advent of the 3rd generation Synchrotron Radiation (SR) sources, such as SPring-8, the capabilities of SR powder diffraction increased greatly not only in an accurate structure refinement but also ab initio structure determination. In this study, advanced structural analyses by 3rd generation SR powder diffraction based on the Large Debye-Scherrer camera installed at BL02B2, SPring-8 is described. Because of high angular resolution and high counting statistics powder data collected at BL02B2, SPring-8, ab initio structure determination can cope with a molecular crystals with 65 atoms including H atoms. For the structure refinements, it is found that a kindmore » of Maximum Entropy Method in which several atoms are omitted in phase calculation become very important to refine structural details of fairy large molecule in a crystal. It should be emphasized that until the unknown structure is refined very precisely, the obtained structure by Genetic Algorithm (GA) or some other ab initio structure determination method using real space structural knowledge, it is not possible to tell whether the structure obtained by the method is correct or not. In order to determine and/or refine crystal structure of rather complicated molecules, we cannot overemphasize the importance of the 3rd generation SR sources.« less

Protein domain assignment from the recurrence of locally similar structures

PubMed Central

Tai, Chin-Hsien; Sam, Vichetra; Gibrat, Jean-Francois; Garnier, Jean; Munson, Peter J.

2010-01-01

Domains are basic units of protein structure and essential for exploring protein fold space and structure evolution. With the structural genomics initiative, the number of protein structures in the Protein Databank (PDB) is increasing dramatically and domain assignments need to be done automatically. Most existing structural domain assignment programs define domains using the compactness of the domains and/or the number and strength of intra-domain versus inter-domain contacts. Here we present a different approach based on the recurrence of locally similar structural pieces (LSSPs) found by one-against-all structure comparisons with a dataset of 6,373 protein chains from the PDB. Residues of the query protein are clustered using LSSPs via three different procedures to define domains. This approach gives results that are comparable to several existing programs that use geometrical and other structural information explicitly. Remarkably, most of the proteins that contribute the LSSPs defining a domain do not themselves contain the domain of interest. This study shows that domains can be defined by a collection of relatively small locally similar structural pieces containing, on average, four secondary structure elements. In addition, it indicates that domains are indeed made of recurrent small structural pieces that are used to build protein structures of many different folds as suggested by recent studies. PMID:21287617

Revisiting the blind tests in crystal structure prediction: accurate energy ranking of molecular crystals.

PubMed

Asmadi, Aldi; Neumann, Marcus A; Kendrick, John; Girard, Pascale; Perrin, Marc-Antoine; Leusen, Frank J J

2009-12-24

In the 2007 blind test of crystal structure prediction hosted by the Cambridge Crystallographic Data Centre (CCDC), a hybrid DFT/MM method correctly ranked each of the four experimental structures as having the lowest lattice energy of all the crystal structures predicted for each molecule. The work presented here further validates this hybrid method by optimizing the crystal structures (experimental and submitted) of the first three CCDC blind tests held in 1999, 2001, and 2004. Except for the crystal structures of compound IX, all structures were reminimized and ranked according to their lattice energies. The hybrid method computes the lattice energy of a crystal structure as the sum of the DFT total energy and a van der Waals (dispersion) energy correction. Considering all four blind tests, the crystal structure with the lowest lattice energy corresponds to the experimentally observed structure for 12 out of 14 molecules. Moreover, good geometrical agreement is observed between the structures determined by the hybrid method and those measured experimentally. In comparison with the correct submissions made by the blind test participants, all hybrid optimized crystal structures (apart from compound II) have the smallest calculated root mean squared deviations from the experimentally observed structures. It is predicted that a new polymorph of compound V exists under pressure.

Multi-functional composite structures

DOEpatents

Mulligan, Anthony C.; Halloran, John; Popovich, Dragan; Rigali, Mark J.; Sutaria, Manish P.; Vaidyanathan, K. Ranji; Fulcher, Michael L.; Knittel, Kenneth L.

2004-10-19

Fibrous monolith processing techniques to fabricate multifunctional structures capable of performing more than one discrete function such as structures capable of bearing structural loads and mechanical stresses in service and also capable of performing at least one additional non-structural function.

Multi-functional composite structures

DOEpatents

Mulligan, Anthony C.; Halloran, John; Popovich, Dragan; Rigali, Mark J.; Sutaria, Manish P.; Vaidyanathan, K. Ranji; Fulcher, Michael L.; Knittel, Kenneth L.

2010-04-27

Fibrous monolith processing techniques to fabricate multifunctional structures capable of performing more than one discrete function such as structures capable of bearing structural loads and mechanical stresses in service and also capable of performing at least one additional non-structural function.

EVALUATIONS ON ASR DAMAGE OF CONCRETE STRUCTURE AND ITS STRUCTURAL PERFORMANCE

NASA Astrophysics Data System (ADS)

Ueda, Naoshi; Nakamura, Hikaru; Kunieda, Minoru; Maeno, Hirofumi; Morishit, Noriaki; Asai, Hiroshi

In this paper, experiments and finite element analyses were conducted in order to evaluate effects of ASR on structural performance of RC and PC structures. From the experimental results, it was confirmed that the ASR expansion was affected by the restraint of reinforcement and the magnitude of prestress. The material properties of concrete damaged by ASR had anisotropic characteristics depending on the degree of ASR expansion. Therefore, when the structural performance of RC and PC structures were evaluated by using the material properties of core concrete, the direction and place where cylinder specimens were cored should be considered. On the other hand, by means of proposed analytical method, ASR expansion behaviors of RC and PC beams and changing of their structural performance were evaluated. As the results, it was confirmed that PC structure had much advantage comparing with RC structure regarding the structural performance under ASR damage because of restraint by prestress against the ASR.

A Review of Structure Construction of Silk Fibroin Biomaterials from Single Structures to Multi-Level Structures

PubMed Central

Qi, Yu; Wang, Hui; Wei, Kai; Yang, Ya; Zheng, Ru-Yue; Kim, Ick Soo; Zhang, Ke-Qin

2017-01-01

The biological performance of artificial biomaterials is closely related to their structure characteristics. Cell adhesion, migration, proliferation, and differentiation are all strongly affected by the different scale structures of biomaterials. Silk fibroin (SF), extracted mainly from silkworms, has become a popular biomaterial due to its excellent biocompatibility, exceptional mechanical properties, tunable degradation, ease of processing, and sufficient supply. As a material with excellent processability, SF can be processed into various forms with different structures, including particulate, fiber, film, and three-dimensional (3D) porous scaffolds. This review discusses and summarizes the various constructions of SF-based materials, from single structures to multi-level structures, and their applications. In combination with single structures, new techniques for creating special multi-level structures of SF-based materials, such as micropatterning and 3D-printing, are also briefly addressed. PMID:28273799

Ordering structured populations in multiplayer cooperation games

PubMed Central

Peña, Jorge; Wu, Bin; Traulsen, Arne

2016-01-01

Spatial structure greatly affects the evolution of cooperation. While in two-player games the condition for cooperation to evolve depends on a single structure coefficient, in multiplayer games the condition might depend on several structure coefficients, making it difficult to compare different population structures. We propose a solution to this issue by introducing two simple ways of ordering population structures: the containment order and the volume order. If population structure is greater than population structure in the containment or the volume order, then can be considered a stronger promoter of cooperation. We provide conditions for establishing the containment order, give general results on the volume order, and illustrate our theory by comparing different models of spatial games and associated update rules. Our results hold for a large class of population structures and can be easily applied to specific cases once the structure coefficients have been calculated or estimated. PMID:26819335

Sensitivity analysis for axis rotation diagrid structural systems according to brace angle changes

NASA Astrophysics Data System (ADS)

Yang, Jae-Kwang; Li, Long-Yang; Park, Sung-Soo

2017-10-01

General regular shaped diagrid structures can express diverse shapes because braces are installed along the exterior faces of the structures and the structures have no columns. However, since irregular shaped structures have diverse variables, studies to assess behaviors resulting from various variables are continuously required to supplement the imperfections related to such variables. In the present study, materials elastic modulus and yield strength were selected as variables for strength that would be applied to diagrid structural systems in the form of Twisters among the irregular shaped buildings classified by Vollers and that affect the structural design of these structural systems. The purpose of this study is to conduct sensitivity analysis for axial rotation diagrid structural systems according to changes in brace angles in order to identify the design variables that have relatively larger effects and the tendencies of the sensitivity of the structures according to changes in brace angles and axial rotation angles.

Nonlinear Analysis and Scaling Laws for Noncircular Composite Structures Subjected to Combined Loads

NASA Technical Reports Server (NTRS)

Hilburger, Mark W.; Rose, Cheryl A.; Starnes, James H., Jr.

2001-01-01

Results from an analytical study of the response of a built-up, multi-cell noncircular composite structure subjected to combined internal pressure and mechanical loads are presented. Nondimensional parameters and scaling laws based on a first-order shear-deformation plate theory are derived for this noncircular composite structure. The scaling laws are used to design sub-scale structural models for predicting the structural response of a full-scale structure representative of a portion of a blended-wing-body transport aircraft. Because of the complexity of the full-scale structure, some of the similitude conditions are relaxed for the sub-scale structural models. Results from a systematic parametric study are used to determine the effects of relaxing selected similitude conditions on the sensitivity of the effectiveness of using the sub-scale structural model response characteristics for predicting the full-scale structure response characteristics.

Experimental Validation of an Integrated Controls-Structures Design Methodology

NASA Technical Reports Server (NTRS)

Maghami, Peiman G.; Gupta, Sandeep; Elliot, Kenny B.; Walz, Joseph E.

1996-01-01

The first experimental validation of an integrated controls-structures design methodology for a class of large order, flexible space structures is described. Integrated redesign of the controls-structures-interaction evolutionary model, a laboratory testbed at NASA Langley, was described earlier. The redesigned structure was fabricated, assembled in the laboratory, and experimentally tested against the original structure. Experimental results indicate that the structure redesigned using the integrated design methodology requires significantly less average control power than the nominal structure with control-optimized designs, while maintaining the required line-of-sight pointing performance. Thus, the superiority of the integrated design methodology over the conventional design approach is experimentally demonstrated. Furthermore, amenability of the integrated design structure to other control strategies is evaluated, both analytically and experimentally. Using Linear-Quadratic-Guassian optimal dissipative controllers, it is observed that the redesigned structure leads to significantly improved performance with alternate controllers as well.

ERP Evidence for the Activation of Syntactic Structure During Comprehension of Lexical Idiom.

PubMed

Zhang, Meichao; Lu, Aitao; Song, Pingfang

2017-10-01

The present study used event-related potentials to investigate whether the syntactic structure was activated in the comprehension of lexical idioms, and if so, whether it varied as a function of familiarity and semantic transparency. Participants were asked to passively read the "1+2" structural Chinese lexical idioms with each being presented following 3-5 contextual "1+2" (congruent-structure condition) or "2+1" structural Chinese phrases (incongruent-structure condition). The N400 ERP responses showed more positivity in congruent-structure condition relative to incongruent-structure condition in idioms with high familiarity and high semantic transparency, but less positivity in congruent-structure condition in idioms with high familiarity but low semantic transparency, idioms with low familiarity but high semantic transparency, and idioms with low familiarity and low semantic transparency. Our results suggest that syntactic structure, as the unnecessarity of lexical idiomatic words, was nevertheless activated, independent of familiarity and semantic transparency.

A key heterogeneous structure of fractal networks based on inverse renormalization scheme

NASA Astrophysics Data System (ADS)

Bai, Yanan; Huang, Ning; Sun, Lina

2018-06-01

Self-similarity property of complex networks was found by the application of renormalization group theory. Based on this theory, network topologies can be classified into universality classes in the space of configurations. In return, through inverse renormalization scheme, a given primitive structure can grow into a pure fractal network, then adding different types of shortcuts, it exhibits different characteristics of complex networks. However, the effect of primitive structure on networks structural property has received less attention. In this paper, we introduce a degree variance index to measure the dispersion of nodes degree in the primitive structure, and investigate the effect of the primitive structure on network structural property quantified by network efficiency. Numerical simulations and theoretical analysis show a primitive structure is a key heterogeneous structure of generated networks based on inverse renormalization scheme, whether or not adding shortcuts, and the network efficiency is positively correlated with degree variance of the primitive structure.

Troublesome Crystal Structures: Prevention, Detection, and Resolution

PubMed Central

Harlow, Richard L.

1996-01-01

A large number of incorrect crystal structures is being published today. These structures are proving to be a particular problem to those of us who are interested in comparing structural moieties found in the databases in order to develop structure-property relationships. Problems can reside in the input data, e.g., wrong unit cell or low quality intensity data, or in the structural model, e.g., wrong space group or atom types. Many of the common mistakes are, however, relatively easy to detect and thus should be preventable; at the very least, suspicious structures can be flagged, if not by the authors then by the referees and, ultimately, the crystallographic databases. This article describes some of the more common mistakes and their effects on the resulting structures, lists a series of tests that can be used to detect incorrect structures, and makes a strong plea for the publication of higher quality structures. PMID:27805169

Variability of Protein Structure Models from Electron Microscopy.

PubMed

Monroe, Lyman; Terashi, Genki; Kihara, Daisuke

2017-04-04

An increasing number of biomolecular structures are solved by electron microscopy (EM). However, the quality of structure models determined from EM maps vary substantially. To understand to what extent structure models are supported by information embedded in EM maps, we used two computational structure refinement methods to examine how much structures can be refined using a dataset of 49 maps with accompanying structure models. The extent of structure modification as well as the disagreement between refinement models produced by the two computational methods scaled inversely with the global and the local map resolutions. A general quantitative estimation of deviations of structures for particular map resolutions are provided. Our results indicate that the observed discrepancy between the deposited map and the refined models is due to the lack of structural information present in EM maps and thus these annotations must be used with caution for further applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

Structural verification for GAS experiments

NASA Technical Reports Server (NTRS)

Peden, Mark Daniel

1992-01-01

The purpose of this paper is to assist the Get Away Special (GAS) experimenter in conducting a thorough structural verification of its experiment structural configuration, thus expediting the structural review/approval process and the safety process in general. Material selection for structural subsystems will be covered with an emphasis on fasteners (GSFC fastener integrity requirements) and primary support structures (Stress Corrosion Cracking requirements and National Space Transportation System (NSTS) requirements). Different approaches to structural verifications (tests and analyses) will be outlined especially those stemming from lessons learned on load and fundamental frequency verification. In addition, fracture control will be covered for those payloads that utilize a door assembly or modify the containment provided by the standard GAS Experiment Mounting Plate (EMP). Structural hazard assessment and the preparation of structural hazard reports will be reviewed to form a summation of structural safety issues for inclusion in the safety data package.

Application of Composite Mechanics to Composites Enhanced Concrete Structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.; Gotsis, Pascal K.

2006-01-01

A new and effective method is described to design composites to repair damage or enhance the overload strength of concrete infrastructures. The method is based on composite mechanics which is available in computer codes. It is used to simulate structural sections made from reinforced concrete which are typical in infrastructure as well as select reinforced concrete structures. The structural sections are represented by a number of layers through the thickness where different layers are used in concrete, and for the composite. The reinforced concrete structures are represented with finite elements where the element stiffness parameters are from the structural sections which are represented by composite mechanics. The load carrying capability of the structure is determined by progressive structural fracture. Results show up to 40 percent improvements for damage and for overload enhancement with relatively small laminate thickness for the structural sections and up to three times for the composite enhanced select structures (arches and domes).

Exploration of tetrahedral structures in silicate cathodes using a motif-network scheme

DOE PAGES

Zhao, Xin; Wu, Shunqing; Lv, Xiaobao; ...

2015-10-26

Using a motif-network search scheme, we studied the tetrahedral structures of the dilithium/disodium transition metal orthosilicates A 2MSiO 4 with A = Li or Na and M = Mn, Fe or Co. In addition to finding all previously reported structures, we discovered many other different tetrahedral-network-based crystal structures which are highly degenerate in energy. In addition, these structures can be classified into structures with 1D, 2D and 3D M-Si-O frameworks. A clear trend of the structural preference in different systems was revealed and possible indicators that affect the structure stabilities were introduced. For the case of Na systems which havemore » been much less investigated in the literature relative to the Li systems, we predicted their ground state structures and found evidence for the existence of new structural motifs.« less

Interdisciplinary optimum design. [of aerospace structures

NASA Technical Reports Server (NTRS)

Sobieszczanski-Sobieski, Jaroslaw; Haftka, Raphael T.

1986-01-01

Problems related to interdisciplinary interactions in the design of a complex engineering systems are examined with reference to aerospace applications. The interdisciplinary optimization problems examined include those dealing with controls and structures, materials and structures, control and stability, structure and aerodynamics, and structure and thermodynamics. The discussion is illustrated by the following specific applications: integrated aerodynamic/structural optimization of glider wing; optimization of an antenna parabolic dish structure for minimum weight and prescribed emitted signal gain; and a multilevel optimization study of a transport aircraft.

Conformable pressure vessel for high pressure gas storage

DOEpatents

Simmons, Kevin L.; Johnson, Kenneth I.; Lavender, Curt A.; Newhouse, Norman L.; Yeggy, Brian C.

2016-01-12

A non-cylindrical pressure vessel storage tank is disclosed. The storage tank includes an internal structure. The internal structure is coupled to at least one wall of the storage tank. The internal structure shapes and internally supports the storage tank. The pressure vessel storage tank has a conformability of about 0.8 to about 1.0. The internal structure can be, but is not limited to, a Schwarz-P structure, an egg-crate shaped structure, or carbon fiber ligament structure.

Control of resonant frequencies in adaptive structures by prestressing

NASA Technical Reports Server (NTRS)

Baycan, Can M.; Utku, Senol; Wada, Ben K.

1992-01-01

The natural vibration frequencies of a structure can be affected by inducing stress in the structure. The success of this kind of control of the resonant frequencies of a truss structure depends on the geometry of the structure. It is shown that in adaptive truss structures the method is effective for vibrations in less stiff directions, such as the normal direction of the plane containing all of the bars of a node, suggesting its applicability for cable, membrane, and thin plate and shell structures.

Deployable telescope having a thin-film mirror and metering structure

DOEpatents

Krumel, Leslie J [Cedar Crest, NM; Martin, Jeffrey W [Albuquerque, NM

2010-08-24

A deployable thin-film mirror telescope comprises a base structure and a metering structure. The base structure houses a thin-film mirror, which can be rolled for stowage and unrolled for deployment. The metering structure is coupled to the base structure and can be folded for stowage and unfolded for deployment. In the deployed state, the unrolled thin-film mirror forms a primary minor for the telescope and the unfolded metering structure positions a secondary minor for the telescope.

Structures Technology for Future Aerospace Systems

NASA Technical Reports Server (NTRS)

Noor, Ahmed K.; Venneri, Samuel L.; Paul, Donald B.; Hopkins, Mark A.

2000-01-01

An overview of structures technology for future aerospace systems is given. Discussion focuses on developments in component technologies that will improve the vehicle performance, advance the technology exploitation process, and reduce system life-cycle costs. The component technologies described are smart materials and structures, multifunctional materials and structures, affordable composite structures, extreme environment structures, flexible load bearing structures, and computational methods and simulation-based design. The trends in each of the component technologies are discussed and the applicability of these technologies to future aerospace vehicles is described.

K-Partite RNA Secondary Structures

NASA Astrophysics Data System (ADS)

Jiang, Minghui; Tejada, Pedro J.; Lasisi, Ramoni O.; Cheng, Shanhong; Fechser, D. Scott

RNA secondary structure prediction is a fundamental problem in structural bioinformatics. The prediction problem is difficult because RNA secondary structures may contain pseudoknots formed by crossing base pairs. We introduce k-partite secondary structures as a simple classification of RNA secondary structures with pseudoknots. An RNA secondary structure is k-partite if it is the union of k pseudoknot-free sub-structures. Most known RNA secondary structures are either bipartite or tripartite. We show that there exists a constant number k such that any secondary structure can be modified into a k-partite secondary structure with approximately the same free energy. This offers a partial explanation of the prevalence of k-partite secondary structures with small k. We give a complete characterization of the computational complexities of recognizing k-partite secondary structures for all k ≥ 2, and show that this recognition problem is essentially the same as the k-colorability problem on circle graphs. We present two simple heuristics, iterated peeling and first-fit packing, for finding k-partite RNA secondary structures. For maximizing the number of base pair stackings, our iterated peeling heuristic achieves a constant approximation ratio of at most k for 2 ≤ k ≤ 5, and at most frac6{1-(1-6/k)^k} le frac6{1-e^{-6}} < 6.01491 for k ≥ 6. Experiment on sequences from PseudoBase shows that our first-fit packing heuristic outperforms the leading method HotKnots in predicting RNA secondary structures with pseudoknots. Source code, data set, and experimental results are available at http://www.cs.usu.edu/ mjiang/rna/kpartite/.

FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately.

PubMed

Budowski-Tal, Inbal; Nov, Yuval; Kolodny, Rachel

2010-02-23

Fast identification of protein structures that are similar to a specified query structure in the entire Protein Data Bank (PDB) is fundamental in structure and function prediction. We present FragBag: An ultrafast and accurate method for comparing protein structures. We describe a protein structure by the collection of its overlapping short contiguous backbone segments, and discretize this set using a library of fragments. Then, we succinctly represent the protein as a "bags-of-fragments"-a vector that counts the number of occurrences of each fragment-and measure the similarity between two structures by the similarity between their vectors. Our representation has two additional benefits: (i) it can be used to construct an inverted index, for implementing a fast structural search engine of the entire PDB, and (ii) one can specify a structure as a collection of substructures, without combining them into a single structure; this is valuable for structure prediction, when there are reliable predictions only of parts of the protein. We use receiver operating characteristic curve analysis to quantify the success of FragBag in identifying neighbor candidate sets in a dataset of over 2,900 structures. The gold standard is the set of neighbors found by six state of the art structural aligners. Our best FragBag library finds more accurate candidate sets than the three other filter methods: The SGM, PRIDE, and a method by Zotenko et al. More interestingly, FragBag performs on a par with the computationally expensive, yet highly trusted structural aligners STRUCTAL and CE.

Readers generalize adaptation to newly-encountered dialectal structures to other unfamiliar structures

PubMed Central

Fraundorf, Scott H.; Jaeger, T. Florian

2016-01-01

Growing evidence suggests that syntactic processing may be guided in part by expectations about the statistics of the input that comprehenders have encountered; however, these statistics and even the syntactic structures themselves vary from situation to situation. Some recent work suggests that readers can adapt to variability in the frequencies of known, but infrequent syntactic structures. But, the relation between adaptation to altered frequencies of familiar structures and learning to process unfamiliar, never-before-seen structures is under-explored. In two self-paced reading experiments, we investigated readers’ adaptation to an unfamiliar structure used in some regional dialects of American English: the needs+past participle structure, such as using The car needs washed to mean The car needs to be washed. Study 1 used a novel Web-based recruitment method to target regions where participants were likely to be familiar (Ohio, western Pennsylvania) or unfamiliar (Colorado) with the needs+past participle structure. Participants unfamiliar with the structure initially read the structure more slowly, but over the course of the experiment came to read it more like the familiar participants. Study 2 further demonstrated that participants who have adapted to needs+past participle generalize this adaptation to a different, but related structure. These results suggest (a) that readers adapt to unfamiliar syntactic structures, (b) that, in doing so, they become more like existing users of those structures, and (c) that they can generalize this other structures that they may also be more likely to encounter. We discuss these results in the context of implicit learning accounts of exposure effects on syntactic processing. PMID:28377640

Semiconductor wire array structures, and solar cells and photodetectors based on such structures

DOEpatents

Kelzenberg, Michael D.; Atwater, Harry A.; Briggs, Ryan M.; Boettcher, Shannon W.; Lewis, Nathan S.; Petykiewicz, Jan A.

2014-08-19

A structure comprising an array of semiconductor structures, an infill material between the semiconductor materials, and one or more light-trapping elements is described. Photoconverters and photoelectrochemical devices based on such structure also described.

GENERAL VIEW OF DEHYDRATER (STRUCTURE 12), SHED (STRUCTURE 18), FRUIT ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

GENERAL VIEW OF DEHYDRATER (STRUCTURE 12), SHED (STRUCTURE 18), FRUIT TRAY STORAGE ROOM (STRUCTURE 11), WITH FRUIT DRYING AREA AND TRAM TRACKS IN FOREGROUND, FROM NORTHWEST - Stevens Ranch Complex, State Route 101, Coyote, Santa Clara County, CA

Structural Dynamics and Control Interaction of Flexible Structures

NASA Technical Reports Server (NTRS)

Ryan, Robert S. (Editor); Scofield, Harold N. (Editor)

1987-01-01

A workshop on structural dynamics and control interaction of flexible structures was held to promote technical exchange between the structural dynamics and control disciplines, foster joint technology, and provide a forum for discussing and focusing critical issues in the separate and combined areas. Issues and areas of emphasis were identified in structure-control interaction for the next generation of flexible systems.

Distributed Structure Searchable Toxicity

EPA Pesticide Factsheets

The Distributed Structure Searchable Toxicity (DSSTox) online resource provides high quality chemical structures and annotations in association with toxicity data. It helps to build a data foundation for improved structure-activity relationships and predictive toxicology. DSSTox publishes summarized chemical activity representations for structure-activity modeling and provides a structure browser. This tool also houses the chemical inventories for the ToxCast and Tox21 projects.

Structural reliability assessment capability in NESSUS

NASA Technical Reports Server (NTRS)

Millwater, H.; Wu, Y.-T.

1992-01-01

The principal capabilities of NESSUS (Numerical Evaluation of Stochastic Structures Under Stress), an advanced computer code developed for probabilistic structural response analysis, are reviewed, and its structural reliability assessed. The code combines flexible structural modeling tools with advanced probabilistic algorithms in order to compute probabilistic structural response and resistance, component reliability and risk, and system reliability and risk. An illustrative numerical example is presented.

Structural reliability assessment capability in NESSUS

NASA Astrophysics Data System (ADS)

Millwater, H.; Wu, Y.-T.

1992-07-01

The principal capabilities of NESSUS (Numerical Evaluation of Stochastic Structures Under Stress), an advanced computer code developed for probabilistic structural response analysis, are reviewed, and its structural reliability assessed. The code combines flexible structural modeling tools with advanced probabilistic algorithms in order to compute probabilistic structural response and resistance, component reliability and risk, and system reliability and risk. An illustrative numerical example is presented.

Integrating spatial and numerical structure in mathematical patterning

NASA Astrophysics Data System (ADS)

Ni’mah, K.; Purwanto; Irawan, E. B.; Hidayanto, E.

2018-03-01

This paper reports a study monitoring the integrating spatial and numerical structure in mathematical patterning skills of 30 students grade 7th of junior high school. The purpose of this research is to clarify the processes by which learners construct new knowledge in mathematical patterning. Findings indicate that: (1) students are unable to organize the structure of spatial and numerical, (2) students were only able to organize the spatial structure, but the numerical structure is still incorrect, (3) students were only able to organize numerical structure, but its spatial structure is still incorrect, (4) students were able to organize both of the spatial and numerical structure.

Arrow-wing supersonic cruise aircraft structural design concepts evaluation. Volume 4: Sections 15 through 21

NASA Technical Reports Server (NTRS)

Sakata, I. F.; Davis, G. W.

1975-01-01

The analyses performed to provide structural mass estimates for the arrow wing supersonic cruise aircraft are presented. To realize the full potential for structural mass reduction, a spectrum of approaches for the wing and fuselage primary structure design were investigated. The objective was: (1) to assess the relative merits of various structural arrangements, concepts, and materials; (2) to select the structural approach best suited for the Mach 2.7 environment; and (3) to provide construction details and structural mass estimates based on in-depth structural design studies. Production costs, propulsion-airframe integration, and advanced technology assessment are included.

Interdependence of spin structure, anion height and electronic structure of BaFe{sub 2}As{sub 2}

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

Sen, Smritijit, E-mail: smritijit.sen@gmail.com; Ghosh, Haranath, E-mail: hng@rrcat.gov.in; Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094

2016-05-06

Superconducting as well as other electronic properties of Fe-based superconductors are quite sensitive to the structural parameters specially, on anion height which is intimately related to z{sub As}, the fractional z co-ordinate of As atom. Due to presence of strong magnetic fluctuation in these Fe-based superconductors, optimized structural parameters (lattice parameters a, b, c) including z{sub As} using density functional theory (DFT) under generalized gradient approximation (GGA) does not match experimental values accurately. In this work, we show that the optimized value of z{sub As} is strongly influenced by the spin structures in the orthorhombic phase of BaFe{sub 2}As{sub 2}more » system. We take all possible spin structures for the orthorhombic BaFe{sub 2}As{sub 2} system and then optimize z{sub As}. Using these optimized structures we calculate electronic structures like density of states, band structures etc., for each spin configurations. From these studies we show that the electronic structure, orbital order which is responsible for structural as well as related to nematic transition, are significantly influenced by the spin structures.« less

Challenges in NMR-based structural genomics

NASA Astrophysics Data System (ADS)

Sue, Shih-Che; Chang, Chi-Fon; Huang, Yao-Te; Chou, Ching-Yu; Huang, Tai-huang

2005-05-01

Understanding the functions of the vast number of proteins encoded in many genomes that have been completely sequenced recently is the main challenge for biologists in the post-genomics era. Since the function of a protein is determined by its exact three-dimensional structure it is paramount to determine the 3D structures of all proteins. This need has driven structural biologists to undertake the structural genomics project aimed at determining the structures of all known proteins. Several centers for structural genomics studies have been established throughout the world. Nuclear magnetic resonance (NMR) spectroscopy has played a major role in determining protein structures in atomic details and in a physiologically relevant solution state. Since the number of new genes being discovered daily far exceeds the number of structures determined by both NMR and X-ray crystallography, a high-throughput method for speeding up the process of protein structure determination is essential for the success of the structural genomics effort. In this article we will describe NMR methods currently being employed for protein structure determination. We will also describe methods under development which may drastically increase the throughput, as well as point out areas where opportunities exist for biophysicists to make significant contribution in this important field.

The interplay of hydrogen bonding and dispersion in phenol dimer and trimer: structures from broadband rotational spectroscopy.

PubMed

Seifert, Nathan A; Steber, Amanda L; Neill, Justin L; Pérez, Cristóbal; Zaleski, Daniel P; Pate, Brooks H; Lesarri, Alberto

2013-07-21

The structures of the phenol dimer and phenol trimer complexes in the gas phase have been determined using chirped-pulse Fourier transform microwave spectroscopy in the 2-8 GHz band. All fourteen (13)C and (18)O phenol dimer isotopologues were assigned in natural abundance. A full heavy atom experimental substitution structure was determined, and a least-squares fit ground state r0 structure was determined by proper constraint of the M06-2X/6-311++g(d,p) ab initio structure. The structure of phenol dimer features a water dimer-like hydrogen bond, as well as a cooperative contribution from inter-ring dispersion. Comparisons between the experimental structure and previously determined experimental structures, as well as ab initio structures from various levels of theory, are discussed. For phenol trimer, a C3 symmetric barrel-like structure is found, and an experimental substitution structure was determined via measurement of the six unique (13)C isotopologues. The least-squares fit rm((1)) structure reveals a similar interplay between hydrogen bonding and dispersion in the trimer, with water trimer-like hydrogen bonding and C-H···π interactions.

Damage Detection and Self-Repair in Inflatable/Deployable Structures

NASA Technical Reports Server (NTRS)

Brandon, Erik; Studor, George; Banks, DAvid; Curry, Mark; Broccato, Robert; Jackson, Tom; Champaigne, Kevin; Sottos, Nancy

2009-01-01

Inflatable/deployable structures are under consideration for applications as varied as expansion modules for the International Space Station to destinations for space tourism to habitats for the lunar surface. Monitoring and maintaining the integrity of the physical structure is critical, particularly since these structures rely on non-traditional engineering materials such as fabrics, foams, and elastomeric polymers to provide the primary protection for the human crew. The closely related prior concept of monitoring structural integrity by use of built-in or permanently attached sensors has been applied to structures made of such standard engineering materials as metals, alloys, and rigid composites. To effect monitoring of flexible structures comprised mainly of soft goods, however, it will be necessary to solve a different set of problems - especially those of integrating power and data-transfer cabling that can withstand, and not unduly interfere with, stowage and subsequent deployment of the structures. By incorporating capabilities for self-repair along with capabilities for structural health monitoring, successful implementation of these technologies would be a significant step toward semi-autonomous structures, which need little human intervention to maintain. This would not only increase the safety of these structures, but also reduce the inspection and maintenance costs associated with more conventional structures.

Protein structure database search and evolutionary classification.

PubMed

Yang, Jinn-Moon; Tung, Chi-Hua

2006-01-01

As more protein structures become available and structural genomics efforts provide structural models in a genome-wide strategy, there is a growing need for fast and accurate methods for discovering homologous proteins and evolutionary classifications of newly determined structures. We have developed 3D-BLAST, in part, to address these issues. 3D-BLAST is as fast as BLAST and calculates the statistical significance (E-value) of an alignment to indicate the reliability of the prediction. Using this method, we first identified 23 states of the structural alphabet that represent pattern profiles of the backbone fragments and then used them to represent protein structure databases as structural alphabet sequence databases (SADB). Our method enhanced BLAST as a search method, using a new structural alphabet substitution matrix (SASM) to find the longest common substructures with high-scoring structured segment pairs from an SADB database. Using personal computers with Intel Pentium4 (2.8 GHz) processors, our method searched more than 10 000 protein structures in 1.3 s and achieved a good agreement with search results from detailed structure alignment methods. [3D-BLAST is available at http://3d-blast.life.nctu.edu.tw].

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

Guo, Yiming; Fredrickson, Daniel C.

Intermetallic crystal structures offer an enormous structural diversity, with an endless array of structural motifs whose connection to stability and physical properties are often mysterious. Making sense of the often complex crystal structures that arise here, developing a clear structural description, and identifying connections to other phases can be laborious and require an encyclopedic knowledge of structure types. In this Article, we present PRINCEPS, an algorithm based on a new coordination environment projection scheme that facilitates the structural analysis and comparison of such crystal structures. We demonstrate the potential of this approach by applying it to the complex Ce-Ni-Si ternarymore » system, whose 17 binary and 21 ternary phases would present a daunting challenge to one seeking to understand the system by manual inspection (but has nonetheless been well-described through the heroic efforts of previous researchers). With the help of PRINCEPS, most of the ternary phases in this system can be rationalized as intergrowths of simple structural fragments, and grouped into a handful of structural series (with some outliers). Lastly, these results illustrate how the PRINCEPS approach can be used to organize a vast collection of crystal structures into structurally meaningful families, and guide the description of complex atomic arrangements.« less

Structure to self-structuring: infrastructures and processes in neurobehavioural rehabilitation.

PubMed

Jackson, Howard F; Hague, Gemma; Daniels, Leanne; Aguilar, Ralph; Carr, Darren; Kenyon, William

2014-01-01

The importance of structure in post-acute brain injury rehabilitation is repeatedly mentioned in clinical practice. However, there has been little exploration of the key elements of structure that promote greater levels of functioning and emotional/behavioural stability and how these elements are optimally integrated within the infrastructure of a rehabilitation service. The nature of structure and why it is helpful is explored initially. Thereafter, the processes involved in transition from externally supported structure to the client 'self-structuring' are described. The infrastructure for facilitating these transitional processes are considered in terms of the design of services for systemic neurorehabilitation encompassing environmental factors (e.g. living environments, vocational and recreational options, step-up services and social milieus), therapeutic alliances (rehabilitation professionals, family, friends), organisational structures (service delivery, rehabilitation coaching, transdisciplinary teams) and rehabilitation philosophies and practice. It is concluded that the process of supporting individuals to transition from the 'structure' of the environment and other people towards self-structuring skills is a critical process in rehabilitation. This is reliant upon a comprehensive and robust organisational infrastructure that can successfully and flexibly integrate the core elements of structure across a transitional pathway towards increased independence and self-structuring.

Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative

PubMed Central

Khafizov, Kamil; Madrid-Aliste, Carlos; Almo, Steven C.; Fiser, Andras

2014-01-01

The exponential growth of protein sequence data provides an ever-expanding body of unannotated and misannotated proteins. The National Institutes of Health-supported Protein Structure Initiative and related worldwide structural genomics efforts facilitate functional annotation of proteins through structural characterization. Recently there have been profound changes in the taxonomic composition of sequence databases, which are effectively redefining the scope and contribution of these large-scale structure-based efforts. The faster-growing bacterial genomic entries have overtaken the eukaryotic entries over the last 5 y, but also have become more redundant. Despite the enormous increase in the number of sequences, the overall structural coverage of proteins—including proteins for which reliable homology models can be generated—on the residue level has increased from 30% to 40% over the last 10 y. Structural genomics efforts contributed ∼50% of this new structural coverage, despite determining only ∼10% of all new structures. Based on current trends, it is expected that ∼55% structural coverage (the level required for significant functional insight) will be achieved within 15 y, whereas without structural genomics efforts, realizing this goal will take approximately twice as long. PMID:24567391

The macro-structural variability of the human neocortex.

PubMed

Kruggel, Frithjof

2018-05-15

The human neocortex shows a considerable individual structural variability. While primary gyri and sulci are found in all normally developed brains and bear clear-cut gross structural descriptions, secondary structures are highly variable and not present in all brains. The blend of common and individual structures poses challenges when comparing structural and functional results from quantitative neuroimaging studies across individuals, and sets limits on the precision of location information much above the spatial resolution of current neuroimaging methods. This work aimed at quantifying structural variability on the neocortex, and at assessing the spatial relationship between regions common to all brains and their individual structural variants. Based on structural MRI data provided as the "900 Subjects Release" of the Human Connectome Project, a data-driven analytic approach was employed here from which the definition of seven cortical "communities" emerged. Apparently, these communities comprise common regions of structural features, while the individual variability is confined within a community. Similarities between the community structure and the state of the brain development at gestation week 32 lead suggest that communities are segregated early. Subdividing the neocortex into communities is suggested as anatomically more meaningful than the traditional lobar structure. Copyright © 2018 Elsevier Inc. All rights reserved.

Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative.

PubMed

Khafizov, Kamil; Madrid-Aliste, Carlos; Almo, Steven C; Fiser, Andras

2014-03-11

The exponential growth of protein sequence data provides an ever-expanding body of unannotated and misannotated proteins. The National Institutes of Health-supported Protein Structure Initiative and related worldwide structural genomics efforts facilitate functional annotation of proteins through structural characterization. Recently there have been profound changes in the taxonomic composition of sequence databases, which are effectively redefining the scope and contribution of these large-scale structure-based efforts. The faster-growing bacterial genomic entries have overtaken the eukaryotic entries over the last 5 y, but also have become more redundant. Despite the enormous increase in the number of sequences, the overall structural coverage of proteins--including proteins for which reliable homology models can be generated--on the residue level has increased from 30% to 40% over the last 10 y. Structural genomics efforts contributed ∼50% of this new structural coverage, despite determining only ∼10% of all new structures. Based on current trends, it is expected that ∼55% structural coverage (the level required for significant functional insight) will be achieved within 15 y, whereas without structural genomics efforts, realizing this goal will take approximately twice as long.

Novel interpretation of the mean structure of feroxyhyte

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

Sestu, Matteo, E-mail: msestu@unica.it; Carta, Daniela; Casula, Maria F.

2015-05-15

The structure of the iron oxyhydroxide called feroxyhyte (δ-FeOOH), which shows an elusive X-ray powder diffraction pattern, has been represented so far using models describing a mean structure based on the crystalline network of the iron(III) oxide hematite (α-Fe{sub 2}O{sub 3}). In this paper, a novel description of the mean structure of feroxyhyte is presented, which is based on the structure of the thermodynamically stable iron oxyhydroxide goethite. Starting from different local arrangements present in the goethite network, a mean structural model is determined which shows an X-ray powder diffraction pattern almost coincident with previous studies. This outcome enables tomore » integrate the structure of feroxyhyte among those of other well characterized iron oxyhydroxides. - Graphical abstract: The structure of the iron oxy-hydroxide feroxyhyte can be described by local arrangements present in the goethite network. - Highlights: • The structure of feroxyhyte (δ-FeOOH) proposed in literature is discussed. • The structure of goethite (α-FeOOH) is analyzed. • A structural relationship between feroxyhyte and goethite is found. • New interpretation of the mean structure of δ-FeOOH is given.« less

Towards Long-Range RNA Structure Prediction in Eukaryotic Genes.

PubMed

Pervouchine, Dmitri D

2018-06-15

The ability to form an intramolecular structure plays a fundamental role in eukaryotic RNA biogenesis. Proximate regions in the primary transcripts fold into a local secondary structure, which is then hierarchically assembled into a tertiary structure that is stabilized by RNA-binding proteins and long-range intramolecular base pairings. While the local RNA structure can be predicted reasonably well for short sequences, long-range structure at the scale of eukaryotic genes remains problematic from the computational standpoint. The aim of this review is to list functional examples of long-range RNA structures, to summarize current comparative methods of structure prediction, and to highlight their advances and limitations in the context of long-range RNA structures. Most comparative methods implement the “first-align-then-fold” principle, i.e., they operate on multiple sequence alignments, while functional RNA structures often reside in non-conserved parts of the primary transcripts. The opposite “first-fold-then-align” approach is currently explored to a much lesser extent. Developing novel methods in both directions will improve the performance of comparative RNA structure analysis and help discover novel long-range structures, their higher-order organization, and RNA⁻RNA interactions across the transcriptome.

Structural and Machine Design Using Piezoceramic Materials: A Guide for Structural Design Engineers

NASA Technical Reports Server (NTRS)

Inman, Daniel J.; Cudney, Harley H.

2000-01-01

Using piezoceramic materials is one way the design engineer can create structures which have an ability to both sense and respond to their environment. Piezoceramic materials can be used to create structural sensors and structural actuators. Because piezoceramic materials have transduction as a material property, their sensing or actuation functions are a result of what happens to the material. This is different than discrete devices we might attach to the structure. For example, attaching an accelerometer to a structure will yield an electrical signal proportional to the acceleration at the attachment point on the structure. Using a electromagnetic shaker as an actuator will create an applied force at the attachment point. Active material elements in a structural design are not easily modeled as providing transduction at a point, but rather they change the physics of the structure in the areas where they are used. Hence, a designer must not think of adding discrete devices to a structure to obtain an effect, but rather must design a structural system which accounts for the physical principles of all the elements in the structure. The purpose of this manual is to provide practicing engineers the information necessary to incorporate piezoelectric materials in structural design and machine design. First, we will review the solid-state physics of piezoelectric materials. Then we will discuss the physical characteristics of the electrical-active material-structural system. We will present the elements of this system which must be considered as part of the design task for a structural engineer. We will cover simple modeling techniques and review the features and capabilities of commercial design tools that are available. We will then cover practical how-to elements of working with piezoceramic materials. We will review sources of piezoceramic materials and built-up devices, and their characteristics. Finally, we will provide two design examples using piezoceramic materials, first as discrete actuators for vibration isolation, and second as structurally-distributed sensor/actuators for active acoustic control.

Algorithms for Determining Physical Responses of Structures Under Load

NASA Technical Reports Server (NTRS)

Richards, W. Lance; Ko, William L.

2012-01-01

Ultra-efficient real-time structural monitoring algorithms have been developed to provide extensive information about the physical response of structures under load. These algorithms are driven by actual strain data to measure accurately local strains at multiple locations on the surface of a structure. Through a single point load calibration test, these structural strains are then used to calculate key physical properties of the structure at each measurement location. Such properties include the structure s flexural rigidity (the product of the structure's modulus of elasticity, and its moment of inertia) and the section modulus (the moment of inertia divided by the structure s half-depth). The resulting structural properties at each location can be used to determine the structure s bending moment, shear, and structural loads in real time while the structure is in service. The amount of structural information can be maximized through the use of highly multiplexed fiber Bragg grating technology using optical time domain reflectometry and optical frequency domain reflectometry, which can provide a local strain measurement every 10 mm on a single hair-sized optical fiber. Since local strain is used as input to the algorithms, this system serves multiple purposes of measuring strains and displacements, as well as determining structural bending moment, shear, and loads for assessing real-time structural health. The first step is to install a series of strain sensors on the structure s surface in such a way as to measure bending strains at desired locations. The next step is to perform a simple ground test calibration. For a beam of length l (see example), discretized into n sections and subjected to a tip load of P that places the beam in bending, the flexural rigidity of the beam can be experimentally determined at each measurement location x. The bending moment at each station can then be determined for any general set of loads applied during operation.

Coverage of whole proteome by structural genomics observed through protein homology modeling database

PubMed Central

Yamaguchi, Akihiro; Go, Mitiko

2006-01-01

We have been developing FAMSBASE, a protein homology-modeling database of whole ORFs predicted from genome sequences. The latest update of FAMSBASE (http://daisy.nagahama-i-bio.ac.jp/Famsbase/), which is based on the protein three-dimensional (3D) structures released by November 2003, contains modeled 3D structures for 368,724 open reading frames (ORFs) derived from genomes of 276 species, namely 17 archaebacterial, 130 eubacterial, 18 eukaryotic and 111 phage genomes. Those 276 genomes are predicted to have 734,193 ORFs in total and the current FAMSBASE contains protein 3D structure of approximately 50% of the ORF products. However, cases that a modeled 3D structure covers the whole part of an ORF product are rare. When portion of an ORF with 3D structure is compared in three kingdoms of life, in archaebacteria and eubacteria, approximately 60% of the ORFs have modeled 3D structures covering almost the entire amino acid sequences, however, the percentage falls to about 30% in eukaryotes. When annual differences in the number of ORFs with modeled 3D structure are calculated, the fraction of modeled 3D structures of soluble protein for archaebacteria is increased by 5%, and that for eubacteria by 7% in the last 3 years. Assuming that this rate would be maintained and that determination of 3D structures for predicted disordered regions is unattainable, whole soluble protein model structures of prokaryotes without the putative disordered regions will be in hand within 15 years. For eukaryotic proteins, they will be in hand within 25 years. The 3D structures we will have at those times are not the 3D structure of the entire proteins encoded in single ORFs, but the 3D structures of separate structural domains. Measuring or predicting spatial arrangements of structural domains in an ORF will then be a coming issue of structural genomics. PMID:17146617

Carbon nanotube heat-exchange systems

DOEpatents

Hendricks, Terry Joseph; Heben, Michael J.

2008-11-11

A carbon nanotube heat-exchange system (10) and method for producing the same. One embodiment of the carbon nanotube heat-exchange system (10) comprises a microchannel structure (24) having an inlet end (30) and an outlet end (32), the inlet end (30) providing a cooling fluid into the microchannel structure (24) and the outlet end (32) discharging the cooling fluid from the microchannel structure (24). At least one flow path (28) is defined in the microchannel structure (24), fluidically connecting the inlet end (30) to the outlet end (32) of the microchannel structure (24). A carbon nanotube structure (26) is provided in thermal contact with the microchannel structure (24), the carbon nanotube structure (26) receiving heat from the cooling fluid in the microchannel structure (24) and dissipating the heat into an external medium (19).

Prospects of joining multi-material structures

NASA Astrophysics Data System (ADS)

Sankaranarayanan, R.; Hynes, N. Rajesh Jesudoss

2018-05-01

Spring up trends and necessities make the pipelines for the brand new Technologies. The same way, Multimaterial structures emerging as fruitful alternatives for the conventional structures in the manufacturing sector. Especially manufacturing of transport vehicles is placing a perfect platform for these new structures. Bonding or joining technology plays a crucial role in the field of manufacturing for sustainability. These latest structures are purely depending on such joining technologies so that multi-material structuring can be possible practically. The real challenge lies on joining dissimilar materials of different properties and nature. Escalation of thermoplastic usage in large structural components also faces similar ambiguity for joining multi-material structures. Adhesive bonding, mechanical fastening and are the answering technologies for multi-material structures. This current paper analysis the prospects of these bonding technologies to meet the challenges of tomorrow.

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

Arendt, Paul N.; DePaula, Ramond F.; Zhu, Yuntian T.

An array of carbon nanotubes is prepared by exposing a catalyst structure to a carbon nanotube precursor. Embodiment catalyst structures include one or more trenches, channels, or a combination of trenches and channels. A system for preparing the array includes a heated surface for heating the catalyst structure and a cooling portion that cools gas above the catalyst structure. The system heats the catalyst structure so that the interaction between the precursor and the catalyst structure results in the formation of an array of carbon nanotubes on the catalyst structure, and cools the gas near the catalyst structure and alsomore » cools any carbon nanotubes that form on the catalyst structure to prevent or at least minimize the formation of amorphous carbon. Arrays thus formed may be used for spinning fibers of carbon nanotubes.« less

Dynamic Structural Health Monitoring of slender structures using optical sensors.

PubMed

Antunes, Paulo; Travanca, Rui; Rodrigues, Hugo; Melo, José; Jara, José; Varum, Humberto; André, Paulo

2012-01-01

In this paper we summarize the research activities at the Instituto de Telecomunicações--Pólo de Aveiro and University of Aveiro, in the field of fiber Bragg grating based sensors and their applications in dynamic measurements for Structural Health Monitoring of slender structures such as towers. In this work we describe the implementation of an optical biaxial accelerometer based on fiber Bragg gratings inscribed on optical fibers. The proof-of-concept was done with the dynamic monitoring of a reinforced concrete structure and a slender metallic telecommunication tower. Those structures were found to be suitable to demonstrate the feasibility of FBG accelerometers to obtain the structures' natural frequencies, which are the key parameters in Structural Health Monitoring and in the calibration of numerical models used to simulate the structure behavior.

Efficient reanalysis of structures by a direct modification method. [local stiffness modifications of large structures

NASA Technical Reports Server (NTRS)

Raibstein, A. I.; Kalev, I.; Pipano, A.

1976-01-01

A procedure for the local stiffness modifications of large structures is described. It enables structural modifications without an a priori definition of the changes in the original structure and without loss of efficiency due to multiple loading conditions. The solution procedure, implemented in NASTRAN, involved the decomposed stiffness matrix and the displacement vectors of the original structure. It solves the modified structure exactly, irrespective of the magnitude of the stiffness changes. In order to investigate the efficiency of the present procedure and to test its applicability within a design environment, several real and large structures were solved. The results of the efficiency studies indicate that the break-even point of the procedure varies between 8% and 60% stiffness modifications, depending upon the structure's characteristics and the options employed.

Ab Initio Study of Structural and Electronic Properties of (ZnO) n "Magical" Nanoclusters n = (34, 60)

NASA Astrophysics Data System (ADS)

Bovhyra, Rostyslav; Popovych, Dmytro; Bovgyra, Oleg; Serednytski, Andrew

2017-01-01

Density functional theory studies of the structural and electronic properties of nanoclusters (ZnO) n ( n = 34, 60) in different geometric configurations were conducted. For each cluster, an optimization (relaxation) of structure geometry was performed, and the basic properties of the band structure were investigated. It was established that for the (ZnO)34 nanoclusters, the most stable are fullerene-like hollow structures that satisfy the rule of six isolated quadrangles. For the (ZnO)60 nanoclusters, different types of isomers, including hollow structures and sodalite-like structures composed from (ZnO)12 nanoclusters, were investigated. It was determined that the most energetically favorable structure was sodalite-type structure composed of seven (ZnO)12 clusters with common quadrangle edges.

Rapid and reliable protein structure determination via chemical shift threading.

PubMed

Hafsa, Noor E; Berjanskii, Mark V; Arndt, David; Wishart, David S

2018-01-01

Protein structure determination using nuclear magnetic resonance (NMR) spectroscopy can be both time-consuming and labor intensive. Here we demonstrate how chemical shift threading can permit rapid, robust, and accurate protein structure determination using only chemical shift data. Threading is a relatively old bioinformatics technique that uses a combination of sequence information and predicted (or experimentally acquired) low-resolution structural data to generate high-resolution 3D protein structures. The key motivations behind using NMR chemical shifts for protein threading lie in the fact that they are easy to measure, they are available prior to 3D structure determination, and they contain vital structural information. The method we have developed uses not only sequence and chemical shift similarity but also chemical shift-derived secondary structure, shift-derived super-secondary structure, and shift-derived accessible surface area to generate a high quality protein structure regardless of the sequence similarity (or lack thereof) to a known structure already in the PDB. The method (called E-Thrifty) was found to be very fast (often < 10 min/structure) and to significantly outperform other shift-based or threading-based structure determination methods (in terms of top template model accuracy)-with an average TM-score performance of 0.68 (vs. 0.50-0.62 for other methods). Coupled with recent developments in chemical shift refinement, these results suggest that protein structure determination, using only NMR chemical shifts, is becoming increasingly practical and reliable. E-Thrifty is available as a web server at http://ethrifty.ca .

Accurate protein structure modeling using sparse NMR data and homologous structure information.

PubMed

Thompson, James M; Sgourakis, Nikolaos G; Liu, Gaohua; Rossi, Paolo; Tang, Yuefeng; Mills, Jeffrey L; Szyperski, Thomas; Montelione, Gaetano T; Baker, David

2012-06-19

While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that allows robust modeling of protein structures of up to 225 residues by combining (1)H(N), (13)C, and (15)N backbone and (13)Cβ chemical shift data, distance restraints derived from homologous structures, and a physically realistic all-atom energy function. Accurate models are distinguished from inaccurate models generated using incorrect sequence alignments by requiring that (i) the all-atom energies of models generated using the restraints are lower than models generated in unrestrained calculations and (ii) the low-energy structures converge to within 2.0 Å backbone rmsd over 75% of the protein. Benchmark calculations on known structures and blind targets show that the method can accurately model protein structures, even with very remote homology information, to a backbone rmsd of 1.2-1.9 Å relative to the conventional determined NMR ensembles and of 0.9-1.6 Å relative to X-ray structures for well-defined regions of the protein structures. This approach facilitates the accurate modeling of protein structures using backbone chemical shift data without need for side-chain resonance assignments and extensive analysis of NOESY cross-peak assignments.

Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations

PubMed Central

Seeliger, Daniel; de Groot, Bert L.

2010-01-01

Biological function of proteins is frequently associated with the formation of complexes with small-molecule ligands. Experimental structure determination of such complexes at atomic resolution, however, can be time-consuming and costly. Computational methods for structure prediction of protein/ligand complexes, particularly docking, are as yet restricted by their limited consideration of receptor flexibility, rendering them not applicable for predicting protein/ligand complexes if large conformational changes of the receptor upon ligand binding are involved. Accurate receptor models in the ligand-bound state (holo structures), however, are a prerequisite for successful structure-based drug design. Hence, if only an unbound (apo) structure is available distinct from the ligand-bound conformation, structure-based drug design is severely limited. We present a method to predict the structure of protein/ligand complexes based solely on the apo structure, the ligand and the radius of gyration of the holo structure. The method is applied to ten cases in which proteins undergo structural rearrangements of up to 7.1 Å backbone RMSD upon ligand binding. In all cases, receptor models within 1.6 Å backbone RMSD to the target were predicted and close-to-native ligand binding poses were obtained for 8 of 10 cases in the top-ranked complex models. A protocol is presented that is expected to enable structure modeling of protein/ligand complexes and structure-based drug design for cases where crystal structures of ligand-bound conformations are not available. PMID:20066034

Deployable robotic woven wire structures and joints for space applications

NASA Technical Reports Server (NTRS)

Shahinpoor, MO; Smith, Bradford

1991-01-01

Deployable robotic structures are basically expandable and contractable structures that may be transported or launched to space in a compact form. These structures may then be intelligently deployed by suitable actuators. The deployment may also be done by means of either airbag or spring-loaded typed mechanisms. The actuators may be pneumatic, hydraulic, ball-screw type, or electromagnetic. The means to trigger actuation may be on-board EPROMS, programmable logic controllers (PLCs) that trigger actuation based on some input caused by the placement of the structure in the space environment. The actuation may also be performed remotely by suitable remote triggering devices. Several deployable woven wire structures are examined. These woven wire structures possess a unique form of joint, the woven wire joint, which is capable of moving and changing its position and orientation with respect to the structure itself. Due to the highly dynamic and articulate nature of these joints the 3-D structures built using them are uniquely and highly expandable, deployable, and dynamic. The 3-D structure naturally gives rise to a new generation of deployable three-dimensional spatial structures.

Advances in optical structure systems; Proceedings of the Meeting, Orlando, FL, Apr. 16-19, 1990

NASA Astrophysics Data System (ADS)

Breakwell, John; Genberg, Victor L.; Krumweide, Gary C.

Various papers on advances in optical structure systems are presented. Individual topics addressed include: beam pathlength optimization, thermal stress in glass/metal bond with PR 1578 adhesive, structural and optical properties for typical solid mirror shapes, parametric study of spinning polygon mirror deformations, simulation of small structures-optics-controls system, spatial PSDs of optical structures due to random vibration, mountings for a four-meter glass mirror, fast-steering mirrors in optical control systems, adaptive state estimation for control of flexible structures, surface control techniques for large segmented mirrors, two-time-scale control designs for large flexible structures, closed-loop dynamic shape control of a flexible beam. Also discussed are: inertially referenced pointing for body-fixed payloads, sensor blending line-of-sight stabilization, controls/optics/structures simulation development, transfer functions for piezoelectric control of a flexible beam, active control experiments for large-optics vibration alleviation, composite structures for a large-optical test bed, graphite/epoxy composite mirror for beam-steering applications, composite structures for optical-mirror applications, thin carbon-fiber prepregs for dimensionally critical structures.

Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations.

PubMed

Zhu, Tong; Zhang, John Z H; He, Xiao

2014-09-14

In this work, protein side chain (1)H chemical shifts are used as probes to detect and correct side-chain packing errors in protein's NMR structures through structural refinement. By applying the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method for ab initio calculation of chemical shifts, incorrect side chain packing was detected in the NMR structures of the Pin1 WW domain. The NMR structure is then refined by using molecular dynamics simulation and the polarized protein-specific charge (PPC) model. The computationally refined structure of the Pin1 WW domain is in excellent agreement with the corresponding X-ray structure. In particular, the use of the PPC model yields a more accurate structure than that using the standard (nonpolarizable) force field. For comparison, some of the widely used empirical models for chemical shift calculations are unable to correctly describe the relationship between the particular proton chemical shift and protein structures. The AF-QM/MM method can be used as a powerful tool for protein NMR structure validation and structural flaw detection.

Structure-driven turbulence in ``No man's Land''

NASA Astrophysics Data System (ADS)

Kosuga, Yusuke; Diamond, Patrick

2012-10-01

Structures are often observed in many physical systems. In tokamaks, for example, such structures are observed as density blobs and holes. Such density blobs and holes are generated at the tokamak edge, where strong gradient perturbations generate an outgoing blob and an incoming hole. Since density holes can propagate from the edge to the core, such structures may play an important role in understanding the phenomenology of the edge-core coupling region, so-called ``No Man's Land.'' In this work, we discuss the dynamics of such structures in real space. In particular, we consider the dynamics of density blobs and holes in the Hasegawa-Wakatani system. Specific questions addressed here include: i) how these structures extract free energy and enhance transport? how different is the relaxation driven by such structures from that driven by linear drift waves? ii) how these structures interact with shear flows? In particular, how these structures interact with a shear layer, which can absorb structures resonantly? iii) how can we calculate the coupled evolution of structures and shear flows? Implications for edge-core coupling problem are discussed as well.

Engineering nonspherical hollow structures with complex interiors by template-engaged redox etching.

PubMed

Wang, Zhiyu; Luan, Deyan; Li, Chang Ming; Su, Fabing; Madhavi, Srinivasan; Boey, Freddy Yin Chiang; Lou, Xiong Wen

2010-11-17

Despite the significant advancement in making hollow structures, one unsolved challenge in the field is how to engineer hollow structures with specific shapes, tunable compositions, and desirable interior structures. In particular, top-down engineering the interiors inside preformed hollow structures is still a daunting task. In this work, we demonstrate a facile approach for the preparation of a variety of uniform hollow structures, including Cu(2)O@Fe(OH)(x) nanorattles and Fe(OH)(x) cages with various shapes and dimensions by template-engaged redox etching of shape-controlled Cu(2)O crystals. The composition can be readily modulated at different structural levels to generate other interesting structures such as Cu(2)O@Fe(2)O(3) and Cu@Fe(3)O(4) rattles, as well as Fe(2)O(3) and Fe(3)O(4) cages. More remarkably, this strategy enables top-down engineering the interiors of hollow structures as demonstrated by the fabrication of double-walled nanorattles and nanoboxes, and even box-in-box structures. In addition, this approach is also applied to form Au and MnO(x) based hollow structures.

SETTER: web server for RNA structure comparison

PubMed Central

Čech, Petr; Svozil, Daniel; Hoksza, David

2012-01-01

The recent discoveries of regulatory non-coding RNAs changed our view of RNA as a simple information transfer molecule. Understanding the architecture and function of active RNA molecules requires methods for comparing and analyzing their 3D structures. While structural alignment of short RNAs is achievable in a reasonable amount of time, large structures represent much bigger challenge. Here, we present the SETTER web server for the RNA structure pairwise comparison utilizing the SETTER (SEcondary sTructure-based TERtiary Structure Similarity Algorithm) algorithm. The SETTER method divides an RNA structure into the set of non-overlapping structural elements called generalized secondary structure units (GSSUs). The SETTER algorithm scales as O(n2) with the size of a GSSUs and as O(n) with the number of GSSUs in the structure. This scaling gives SETTER its high speed as the average size of the GSSU remains constant irrespective of the size of the structure. However, the favorable speed of the algorithm does not compromise its accuracy. The SETTER web server together with the stand-alone implementation of the SETTER algorithm are freely accessible at http://siret.cz/setter. PMID:22693209

Dissecting the relationship between protein structure and sequence variation

NASA Astrophysics Data System (ADS)

Shahmoradi, Amir; Wilke, Claus; Wilke Lab Team

2015-03-01

Over the past decade several independent works have shown that some structural properties of proteins are capable of predicting protein evolution. The strength and significance of these structure-sequence relations, however, appear to vary widely among different proteins, with absolute correlation strengths ranging from 0 . 1 to 0 . 8 . Here we present the results from a comprehensive search for the potential biophysical and structural determinants of protein evolution by studying more than 200 structural and evolutionary properties in a dataset of 209 monomeric enzymes. We discuss the main protein characteristics responsible for the general patterns of protein evolution, and identify sequence divergence as the main determinant of the strengths of virtually all structure-evolution relationships, explaining ~ 10 - 30 % of observed variation in sequence-structure relations. In addition to sequence divergence, we identify several protein structural properties that are moderately but significantly coupled with the strength of sequence-structure relations. In particular, proteins with more homogeneous back-bone hydrogen bond energies, large fractions of helical secondary structures and low fraction of beta sheets tend to have the strongest sequence-structure relation. BEACON-NSF center for the study of evolution in action.

Functional materials discovery using energy-structure-function maps

NASA Astrophysics Data System (ADS)

Pulido, Angeles; Chen, Linjiang; Kaczorowski, Tomasz; Holden, Daniel; Little, Marc A.; Chong, Samantha Y.; Slater, Benjamin J.; McMahon, David P.; Bonillo, Baltasar; Stackhouse, Chloe J.; Stephenson, Andrew; Kane, Christopher M.; Clowes, Rob; Hasell, Tom; Cooper, Andrew I.; Day, Graeme M.

2017-03-01

Molecular crystals cannot be designed in the same manner as macroscopic objects, because they do not assemble according to simple, intuitive rules. Their structures result from the balance of many weak interactions, rather than from the strong and predictable bonding patterns found in metal-organic frameworks and covalent organic frameworks. Hence, design strategies that assume a topology or other structural blueprint will often fail. Here we combine computational crystal structure prediction and property prediction to build energy-structure-function maps that describe the possible structures and properties that are available to a candidate molecule. Using these maps, we identify a highly porous solid, which has the lowest density reported for a molecular crystal so far. Both the structure of the crystal and its physical properties, such as methane storage capacity and guest-molecule selectivity, are predicted using the molecular structure as the only input. More generally, energy-structure-function maps could be used to guide the experimental discovery of materials with any target function that can be calculated from predicted crystal structures, such as electronic structure or mechanical properties.

SA-Mot: a web server for the identification of motifs of interest extracted from protein loops

PubMed Central

Regad, Leslie; Saladin, Adrien; Maupetit, Julien; Geneix, Colette; Camproux, Anne-Claude

2011-01-01

The detection of functional motifs is an important step for the determination of protein functions. We present here a new web server SA-Mot (Structural Alphabet Motif) for the extraction and location of structural motifs of interest from protein loops. Contrary to other methods, SA-Mot does not focus only on functional motifs, but it extracts recurrent and conserved structural motifs involved in structural redundancy of loops. SA-Mot uses the structural word notion to extract all structural motifs from uni-dimensional sequences corresponding to loop structures. Then, SA-Mot provides a description of these structural motifs using statistics computed in the loop data set and in SCOP superfamily, sequence and structural parameters. SA-Mot results correspond to an interactive table listing all structural motifs extracted from a target structure and their associated descriptors. Using this information, the users can easily locate loop regions that are important for the protein folding and function. The SA-Mot web server is available at http://sa-mot.mti.univ-paris-diderot.fr. PMID:21665924

SA-Mot: a web server for the identification of motifs of interest extracted from protein loops.

PubMed

Regad, Leslie; Saladin, Adrien; Maupetit, Julien; Geneix, Colette; Camproux, Anne-Claude

2011-07-01

The detection of functional motifs is an important step for the determination of protein functions. We present here a new web server SA-Mot (Structural Alphabet Motif) for the extraction and location of structural motifs of interest from protein loops. Contrary to other methods, SA-Mot does not focus only on functional motifs, but it extracts recurrent and conserved structural motifs involved in structural redundancy of loops. SA-Mot uses the structural word notion to extract all structural motifs from uni-dimensional sequences corresponding to loop structures. Then, SA-Mot provides a description of these structural motifs using statistics computed in the loop data set and in SCOP superfamily, sequence and structural parameters. SA-Mot results correspond to an interactive table listing all structural motifs extracted from a target structure and their associated descriptors. Using this information, the users can easily locate loop regions that are important for the protein folding and function. The SA-Mot web server is available at http://sa-mot.mti.univ-paris-diderot.fr.

An Overview: NASA LeRC Structures Programs

NASA Technical Reports Server (NTRS)

Zaretsky, Erwin V.

1998-01-01

A workshop on National Structures Programs was held, jointly sponsored by the AIAA Structures Technical Committee, the University of Virginia's Center for Advanced Computational Technology and NASA. The Objectives of the Workshop were to: provide a forum for discussion of current Government-sponsored programs in the structures area; identify high potential research areas for future aerospace systems; and initiate suitable interaction mechanisms with the managers of structures programs. The presentations covered structures programs at NASA, DOD (AFOSR, ONR, ARO and DARPA), and DOE. This publication is the presentation of the Structures and Acoustics Division of the NASA Lewis Research Center. The Structures and Acoustics Division has its genesis dating back to 1943. It is responsible for NASA research related to rotating structures and structural hot sections of both airbreathing and rocket engines. The work of the division encompasses but is not limited to aeroelasticity, structural life prediction and reliability, fatigue and fracture, mechanical components such as bearings, gears, and seals, and aeroacoustics. These programs are discussed and the names of responsible individuals are provided for future reference.

Functional materials discovery using energy-structure-function maps.

PubMed

Pulido, Angeles; Chen, Linjiang; Kaczorowski, Tomasz; Holden, Daniel; Little, Marc A; Chong, Samantha Y; Slater, Benjamin J; McMahon, David P; Bonillo, Baltasar; Stackhouse, Chloe J; Stephenson, Andrew; Kane, Christopher M; Clowes, Rob; Hasell, Tom; Cooper, Andrew I; Day, Graeme M

2017-03-30

Molecular crystals cannot be designed in the same manner as macroscopic objects, because they do not assemble according to simple, intuitive rules. Their structures result from the balance of many weak interactions, rather than from the strong and predictable bonding patterns found in metal-organic frameworks and covalent organic frameworks. Hence, design strategies that assume a topology or other structural blueprint will often fail. Here we combine computational crystal structure prediction and property prediction to build energy-structure-function maps that describe the possible structures and properties that are available to a candidate molecule. Using these maps, we identify a highly porous solid, which has the lowest density reported for a molecular crystal so far. Both the structure of the crystal and its physical properties, such as methane storage capacity and guest-molecule selectivity, are predicted using the molecular structure as the only input. More generally, energy-structure-function maps could be used to guide the experimental discovery of materials with any target function that can be calculated from predicted crystal structures, such as electronic structure or mechanical properties.

Vibration attenuation of the NASA Langley evolutionary structure experiment using H(sub infinity) and structured singular value (micron) robust multivariable control techniques

NASA Technical Reports Server (NTRS)

Balas, Gary J.

1992-01-01

The use is studied of active control to attenuate structural vibrations of the NASA Langley Phase Zero Evolutionary Structure due to external disturbance excitations. H sub infinity and structured singular value (mu) based control techniques are used to analyze and synthesize control laws for the NASA Langley Controls Structures Interaction (CSI) Evolutionary Model (CEM). The CEM structure experiment provides an excellent test bed to address control design issues for large space structures. Specifically, control design for structures with numerous lightly damped, coupled flexible modes, collocated and noncollocated sensors and actuators and stringent performance specifications. The performance objectives are to attenuate the vibration of the structure due to external disturbances, and minimize the actuator control force. The control design problem formulation for the CEM Structure uses a mathematical model developed with finite element techniques. A reduced order state space model for the control design is formulated from the finite element model. It is noted that there are significant variations between the design model and the experimentally derived transfer function data.

Active member control of a precision structure with an H(infinity) performance objective

NASA Technical Reports Server (NTRS)

Fanson, J. L.; Chu, C.-C.; Smith, R. S.; Anderson, E. H.

1990-01-01

This paper addresses the noncollocated control of active structures using active structural elements. A top level architecture for active structures is presented, and issues pertaining to robust control of structures are discussed. Controllers optimized for an H sub inf performance specification are implemented on a test structure and the results are compared with analytical predictions. Directions for further research are identified.

Integrated transient thermal-structural finite element analysis

NASA Technical Reports Server (NTRS)

Thornton, E. A.; Dechaumphai, P.; Wieting, A. R.; Tamma, K. K.

1981-01-01

An integrated thermal structural finite element approach for efficient coupling of transient thermal and structural analysis is presented. Integrated thermal structural rod and one dimensional axisymmetric elements considering conduction and convection are developed and used in transient thermal structural applications. The improved accuracy of the integrated approach is illustrated by comparisons with exact transient heat conduction elasticity solutions and conventional finite element thermal finite element structural analyses.

RAG-3D: A search tool for RNA 3D substructures

DOE PAGES

Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; ...

2015-08-24

In this study, to address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally describedmore » in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.« less

RAG-3D: a search tool for RNA 3D substructures

PubMed Central

Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; Schlick, Tamar

2015-01-01

To address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally described in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding. PMID:26304547

Evaluating the quality of NMR structures by local density of protons.

PubMed

Ban, Yih-En Andrew; Rudolph, Johannes; Zhou, Pei; Edelsbrunner, Herbert

2006-03-01

Evaluating the quality of experimentally determined protein structural models is an essential step toward identifying potential errors and guiding further structural refinement. Herein, we report the use of proton local density as a sensitive measure to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256 high-resolution crystal structures with protons added and optimized, we show that the local density of different proton types display distinct distributions. These distributions can be characterized by statistical moments and are used to establish local density Z-scores for evaluating both global and local packing for individual protons. Analysis of 546 crystal structures at various resolutions shows that the local density Z-scores increase as the structural resolution decreases and correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711-1733) generated by all atom contact analysis. Local density Z-scores for NMR structures exhibit a significantly wider range of values than for X-ray structures and demonstrate a combination of potentially problematic inflation and compression. Water-refined NMR structures show improved packing quality. Our analysis of a high-quality structural ensemble of ubiquitin refined against order parameters shows proton density distributions that correlate nearly perfectly with our standards derived from crystal structures, further validating our approach. We present an automated analysis and visualization tool for proton packing to evaluate the quality of NMR structures. 2005 Wiley-Liss, Inc.

Railway vehicle body structures

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

Not Available

1985-01-01

The strength and durability of railway vehicle structures is a major topic of engineering research and design. To reflect this importance the Railway Division of the Institution of Mechanical Engineers organised a conference to discuss all matters relating to railway vehicle design. This book presents the papers discussed in that conference. The contents include: Vehicle body design and the UIC's international contribution; LUL prototype 1986 stock - body structure; vehicle structure for the intermediate capacity transmit system vehicles; car body technology of advanced light rapid transit vehicles; concepts, techniques and experience in the idealization of car body structures for finitemore » element analysis; Calcutta metropolitan railway; design for a lightweight diesel multiple unit body; the design of lightweight inter-city coal structures; the BREL international coach body shell structure; new concepts and design techniques versus material standards; structures of BR diesel electric freight locomotives; structural design philosophy for electric locomotives; suspension design for a locomotive with low structural frequencies; freight wagon structures; a finite element study of coal bodyside panels including the effects of joint flexibility; a fresh approach to the problem of car body design strength; energy absorption in automatic couplings and draw gear; passenger vehicle design loads and structural crashworthiness; design of the front part of railway vehicles (in case of frontal impact); the development of a theoretical technique for rail vehicle structural crashworthiness.« less

Validation of Molecular Dynamics Simulations for Prediction of Three-Dimensional Structures of Small Proteins.

PubMed

Kato, Koichi; Nakayoshi, Tomoki; Fukuyoshi, Shuichi; Kurimoto, Eiji; Oda, Akifumi

2017-10-12

Although various higher-order protein structure prediction methods have been developed, almost all of them were developed based on the three-dimensional (3D) structure information of known proteins. Here we predicted the short protein structures by molecular dynamics (MD) simulations in which only Newton's equations of motion were used and 3D structural information of known proteins was not required. To evaluate the ability of MD simulationto predict protein structures, we calculated seven short test protein (10-46 residues) in the denatured state and compared their predicted and experimental structures. The predicted structure for Trp-cage (20 residues) was close to the experimental structure by 200-ns MD simulation. For proteins shorter or longer than Trp-cage, root-mean square deviation values were larger than those for Trp-cage. However, secondary structures could be reproduced by MD simulations for proteins with 10-34 residues. Simulations by replica exchange MD were performed, but the results were similar to those from normal MD simulations. These results suggest that normal MD simulations can roughly predict short protein structures and 200-ns simulations are frequently sufficient for estimating the secondary structures of protein (approximately 20 residues). Structural prediction method using only fundamental physical laws are useful for investigating non-natural proteins, such as primitive proteins and artificial proteins for peptide-based drug delivery systems.

Structural deformation upon protein-protein interaction: A structural alphabet approach

PubMed Central

Martin, Juliette; Regad, Leslie; Lecornet, Hélène; Camproux, Anne-Claude

2008-01-01

Background In a number of protein-protein complexes, the 3D structures of bound and unbound partners significantly differ, supporting the induced fit hypothesis for protein-protein binding. Results In this study, we explore the induced fit modifications on a set of 124 proteins available in both bound and unbound forms, in terms of local structure. The local structure is described thanks to a structural alphabet of 27 structural letters that allows a detailed description of the backbone. Using a control set to distinguish induced fit from experimental error and natural protein flexibility, we show that the fraction of structural letters modified upon binding is significantly greater than in the control set (36% versus 28%). This proportion is even greater in the interface regions (41%). Interface regions preferentially involve coils. Our analysis further reveals that some structural letters in coil are not favored in the interface. We show that certain structural letters in coil are particularly subject to modifications at the interface, and that the severity of structural change also varies. These information are used to derive a structural letter substitution matrix that summarizes the local structural changes observed in our data set. We also illustrate the usefulness of our approach to identify common binding motifs in unrelated proteins. Conclusion Our study provides qualitative information about induced fit. These results could be of help for flexible docking. PMID:18307769

Structural deformation upon protein-protein interaction: a structural alphabet approach.

PubMed

Martin, Juliette; Regad, Leslie; Lecornet, Hélène; Camproux, Anne-Claude

2008-02-28

In a number of protein-protein complexes, the 3D structures of bound and unbound partners significantly differ, supporting the induced fit hypothesis for protein-protein binding. In this study, we explore the induced fit modifications on a set of 124 proteins available in both bound and unbound forms, in terms of local structure. The local structure is described thanks to a structural alphabet of 27 structural letters that allows a detailed description of the backbone. Using a control set to distinguish induced fit from experimental error and natural protein flexibility, we show that the fraction of structural letters modified upon binding is significantly greater than in the control set (36% versus 28%). This proportion is even greater in the interface regions (41%). Interface regions preferentially involve coils. Our analysis further reveals that some structural letters in coil are not favored in the interface. We show that certain structural letters in coil are particularly subject to modifications at the interface, and that the severity of structural change also varies. These information are used to derive a structural letter substitution matrix that summarizes the local structural changes observed in our data set. We also illustrate the usefulness of our approach to identify common binding motifs in unrelated proteins. Our study provides qualitative information about induced fit. These results could be of help for flexible docking.

Structural Priming and Frequency Effects Interact in Chinese Sentence Comprehension

PubMed Central

Wei, Hang; Dong, Yanping; Boland, Julie E.; Yuan, Fang

2016-01-01

Previous research in several European languages has shown that the language processing system is sensitive to both structural frequency and structural priming effects. However, it is currently not clear whether these two types of effects interact during online sentence comprehension, especially for languages that do not have morphological markings. To explore this issue, the present study investigated the possible interplay between structural priming and frequency effects for sentences containing the Chinese ambiguous construction V NP1 de NP2 in a self-paced reading experiment. The sentences were disambiguated to either the more frequent/preferred NP structure or the less frequent VP structure. Each target sentence was preceded by a prime sentence of three possible types: NP primes, VP primes, and neutral primes. When the ambiguous construction V NP1 de NP2 was disambiguated to the dispreferred VP structure, participants experienced more processing difficulty following an NP prime relative to following a VP prime or a neutral baseline. When the ambiguity was resolved to the preferred NP structure, prime type had no effect. These results suggest that structural priming in comprehension is modulated by the baseline frequency of alternative structures, with the less frequent structure being more subject to structural priming effects. These results are discussed in the context of the error-based, implicit learning account of structural priming. PMID:26869954

Argument structure hierarchy system and method for facilitating analysis and decision-making processes

DOEpatents

Janssen, Terry

2000-01-01

A system and method for facilitating decision-making comprising a computer program causing linkage of data representing a plurality of argument structure units into a hierarchical argument structure. Each argument structure unit comprises data corresponding to a hypothesis and its corresponding counter-hypothesis, data corresponding to grounds that provide a basis for inference of the hypothesis or its corresponding counter-hypothesis, data corresponding to a warrant linking the grounds to the hypothesis or its corresponding counter-hypothesis, and data corresponding to backing that certifies the warrant. The hierarchical argument structure comprises a top level argument structure unit and a plurality of subordinate level argument structure units. Each of the plurality of subordinate argument structure units comprises at least a portion of the grounds of the argument structure unit to which it is subordinate. Program code located on each of a plurality of remote computers accepts input from one of a plurality of contributors. Each input comprises data corresponding to an argument structure unit in the hierarchical argument structure and supports the hypothesis or its corresponding counter-hypothesis. A second programming code is adapted to combine the inputs into a single hierarchical argument structure. A third computer program code is responsive to the second computer program code and is adapted to represent a degree of support for the hypothesis and its corresponding counter-hypothesis in the single hierarchical argument structure.

RAG-3D: A search tool for RNA 3D substructures

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

Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef

In this study, to address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally describedmore » in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.« less

Structure-seq2: sensitive and accurate genome-wide profiling of RNA structure in vivo

PubMed Central

Ritchey, Laura E.; Su, Zhao; Tang, Yin; Tack, David C.

2017-01-01

Abstract RNA serves many functions in biology such as splicing, temperature sensing, and innate immunity. These functions are often determined by the structure of RNA. There is thus a pressing need to understand RNA structure and how it changes during diverse biological processes both in vivo and genome-wide. Here, we present Structure-seq2, which provides nucleotide-resolution RNA structural information in vivo and genome-wide. This optimized version of our original Structure-seq method increases sensitivity by at least 4-fold and improves data quality by minimizing formation of a deleterious by-product, reducing ligation bias, and improving read coverage. We also present a variation of Structure-seq2 in which a biotinylated nucleotide is incorporated during reverse transcription, which greatly facilitates the protocol by eliminating two PAGE purification steps. We benchmark Structure-seq2 on both mRNA and rRNA structure in rice (Oryza sativa). We demonstrate that Structure-seq2 can lead to new biological insights. Our Structure-seq2 datasets uncover hidden breaks in chloroplast rRNA and identify a previously unreported N1-methyladenosine (m1A) in a nuclear-encoded Oryza sativa rRNA. Overall, Structure-seq2 is a rapid, sensitive, and unbiased method to probe RNA in vivo and genome-wide that facilitates new insights into RNA biology. PMID:28637286

MultiSETTER: web server for multiple RNA structure comparison.

PubMed

Čech, Petr; Hoksza, David; Svozil, Daniel

2015-08-12

Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their tertiary and quaternary structures. While structural superposition of short RNAs is achievable in a reasonable time, large structures represent much bigger challenge. Therefore, we have developed a fast and accurate algorithm for RNA pairwise structure superposition called SETTER and implemented it in the SETTER web server. However, though biological relationships can be inferred by a pairwise structure alignment, key features preserved by evolution can be identified only from a multiple structure alignment. Thus, we extended the SETTER algorithm to the alignment of multiple RNA structures and developed the MultiSETTER algorithm. In this paper, we present the updated version of the SETTER web server that implements a user friendly interface to the MultiSETTER algorithm. The server accepts RNA structures either as the list of PDB IDs or as user-defined PDB files. After the superposition is computed, structures are visualized in 3D and several reports and statistics are generated. To the best of our knowledge, the MultiSETTER web server is the first publicly available tool for a multiple RNA structure alignment. The MultiSETTER server offers the visual inspection of an alignment in 3D space which may reveal structural and functional relationships not captured by other multiple alignment methods based either on a sequence or on secondary structure motifs.

Conveying, Assessing, and Learning (Strategies for) Structural Knowledge.

ERIC Educational Resources Information Center

Jonassen, David H.; And Others

Diagrams showing the components of structural knowledge and the theoretical basis for structural knowledge introduce four tables presenting information on: (1) implicit strategies for conveying cognitive structure, including content/structures signalling (Meyer), frames/slots (Armbruster and Anderson), and Elaboration Theory (Reigeluth and…

Structures for capturing CO.sub.2, methods of making the structures, and methods of capturing CO.sub.2

DOEpatents

Jones, Christopher W; Hicks, Jason C; Fauth, Daniel J; McMahan, Gray

2012-10-30

Briefly described, embodiments of this disclosure, among others, include carbon dioxide (CO.sub.2) sorption structures, methods of making CO.sub.2 sorption structures, and methods of using CO.sub.2 sorption structures.

Low-loss, high-speed, high-T.sub.c superconducting bearings

DOEpatents

Hull, John R.; Mulcahy, Thomas M.; Uherka, Kenneth L.

1997-01-01

A flywheel energy storage device including an iron structure disposed for rotation adjacent a stationary superconductor material structure and a stationary permanent magnet. The stationary permanent magnet levitates the iron structure while the superconductor structure can stabilize the rotating iron structure.

Structured wafer for device processing

DOEpatents

Okandan, Murat; Nielson, Gregory N

2014-05-20

A structured wafer that includes through passages is used for device processing. Each of the through passages extends from or along one surface of the structured wafer and forms a pattern on a top surface area of the structured wafer. The top surface of the structured wafer is bonded to a device layer via a release layer. Devices are processed on the device layer, and are released from the structured wafer using etchant. The through passages within the structured wafer allow the etchant to access the release layer to thereby remove the release layer.

Structured wafer for device processing

DOEpatents

Okandan, Murat; Nielson, Gregory N

2014-11-25

A structured wafer that includes through passages is used for device processing. Each of the through passages extends from or along one surface of the structured wafer and forms a pattern on a top surface area of the structured wafer. The top surface of the structured wafer is bonded to a device layer via a release layer. Devices are processed on the device layer, and are released from the structured wafer using etchant. The through passages within the structured wafer allow the etchant to access the release layer to thereby remove the release layer.

Chip connectivity verification program

NASA Technical Reports Server (NTRS)

Riley, Josh (Inventor); Patterson, George (Inventor)

1999-01-01

A method for testing electrical connectivity between conductive structures on a chip that is preferably layered with conductive and nonconductive layers. The method includes determining the layer on which each structure is located and defining the perimeter of each structure. Conductive layer connections between each of the layers are determined, and, for each structure, the points of intersection between the perimeter of that structure and the perimeter of each other structure on the chip are also determined. Finally, electrical connections between the structures are determined using the points of intersection and the conductive layer connections.

Monitoring Corrosion of Steel Bars in Reinforced Concrete Structures

PubMed Central

Verma, Sanjeev Kumar; Bhadauria, Sudhir Singh; Akhtar, Saleem

2014-01-01

Corrosion of steel bars embedded in reinforced concrete (RC) structures reduces the service life and durability of structures causing early failure of structure, which costs significantly for inspection and maintenance of deteriorating structures. Hence, monitoring of reinforcement corrosion is of significant importance for preventing premature failure of structures. This paper attempts to present the importance of monitoring reinforcement corrosion and describes the different methods for evaluating the corrosion state of RC structures, especially hal-cell potential (HCP) method. This paper also presents few techniques to protect concrete from corrosion. PMID:24558346

Analytical ultrasonics for structural materials

NASA Technical Reports Server (NTRS)

Kupperman, D. S.

1986-01-01

The application of ultrasonic velocity and attenuation measurements to characterize the microstructure of structural materials is discussed. Velocity measurements in cast stainless steel are correlated with microstructural variations ranging from equiaxed (elastically isotropic) to columnar (elastically anisotropic) grain structure. The effect of the anisotropic grain structure on the deviation of ultrasonic waves in cast stainless steel is also reported. Field-implementable techniques for distinguishing equiaxed from columnar grain structures in cast strainless steel structural members are presented. The application of ultrasonic velocity measurements to characterize structural ceramics in the green state is also discussed.

Nanoscale structure in AgSbTe2 determined by diffuse elastic neutron scattering

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

Specht, Eliot D; Ma, Jie; Delaire, Olivier A

2015-01-01

Diffuse elastic neutron scattering measurements confirm that AgSbTe2 has a hierarchical structure, with defects on length scales from nanometers to microns. While scattering from mesoscale structure is consistent with previously-proposed structures in which Ag and Sb order on a NaCl lattice, more diffuse scattering from nanoscale structure suggests a structural rearrangement in which hexagonal layers form a combination of (ABC), (ABA), and (AAB) stacking sequences. The AgCrSe2 structure is the best-fitting model for the local atomic arrangements.

Supramolecular structure of polymer binders and composites: targeted control based on the hierarchy

NASA Astrophysics Data System (ADS)

Matveeva, Larisa; Belentsov, Yuri

2017-10-01

The article discusses the problem of targeted control over properties by modifying the supramolecular structure of polymer binders and composites based on their hierarchy. Control over the structure formation of polymers and introduction of modifying additives should be tailored to the specific hierarchical structural levels. Characteristics of polymer materials are associated with structural defects, which also display a hierarchical pattern. Classification of structural defects in polymers is presented. The primary structural level (nano level) of supramolecular formations is of great importance to the reinforcement and regulation of strength characteristics.

Monitoring corrosion of steel bars in reinforced concrete structures.

PubMed

Verma, Sanjeev Kumar; Bhadauria, Sudhir Singh; Akhtar, Saleem

2014-01-01

Corrosion of steel bars embedded in reinforced concrete (RC) structures reduces the service life and durability of structures causing early failure of structure, which costs significantly for inspection and maintenance of deteriorating structures. Hence, monitoring of reinforcement corrosion is of significant importance for preventing premature failure of structures. This paper attempts to present the importance of monitoring reinforcement corrosion and describes the different methods for evaluating the corrosion state of RC structures, especially hal-cell potential (HCP) method. This paper also presents few techniques to protect concrete from corrosion.

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.

Density functional theory study of structural and electronic properties of trans and cis structures of thiothixene as a nano-drug.

PubMed

Noori Tahneh, Akram; Bagheri Novir, Samaneh; Balali, Ebrahim

2017-11-25

The geometrical structure, electronic and optical properties, electronic absorption spectra, vibrational frequencies, natural charge distribution, MEP analysis and thermodynamic properties of the trans and cis structures of the drug thiothixene were investigated using density functional theory (DFT) and time-dependent DFT (TDDFT) methods with the B3LYP hybrid functional and 6-311 + G(d,p) basis set. The results of the calculations demonstrate that the cis structure of thiothixene has appropriate quantum properties that can act as an active medicine. The relative energies of trans and cis structures of thiothixene shows that the cis structure is more stable than the trans structure, with a small energy difference. TDDFT calculations show that the cis structure of thiothixene has the best absorption properties. The calculated NLO properties show that the NLO properties of the cis structure of thiothixene are higher than the trans structure, and the fact that the chemical hardness of the cis structure is lower than that of the trans structure that indicates that the reactivity and charge transfer of the cis isomer of thiothixene is higher than that of trans thiothixene. The molecular electrostatic potential (MEP) maps of both structures of thiothixene demonstrate that the oxygen atoms of the molecule are appropriate areas for electrophilic reactions. The vibrational frequencies of the two conformations of thiothixene demonstrate that both structures of thiothixene have almost similar modes of vibrations. The calculated thermodynamic parameters show that these quantities increase with enhancing temperature due to the enhancement of molecular vibrational intensities with temperature. Graphical abstract Trans/Cis isomerization of thiothixene drug.

Defining and predicting structurally conserved regions in protein superfamilies

PubMed Central

Huang, Ivan K.; Grishin, Nick V.

2013-01-01

Motivation: The structures of homologous proteins are generally better conserved than their sequences. This phenomenon is demonstrated by the prevalence of structurally conserved regions (SCRs) even in highly divergent protein families. Defining SCRs requires the comparison of two or more homologous structures and is affected by their availability and divergence, and our ability to deduce structurally equivalent positions among them. In the absence of multiple homologous structures, it is necessary to predict SCRs of a protein using information from only a set of homologous sequences and (if available) a single structure. Accurate SCR predictions can benefit homology modelling and sequence alignment. Results: Using pairwise DaliLite alignments among a set of homologous structures, we devised a simple measure of structural conservation, termed structural conservation index (SCI). SCI was used to distinguish SCRs from non-SCRs. A database of SCRs was compiled from 386 SCOP superfamilies containing 6489 protein domains. Artificial neural networks were then trained to predict SCRs with various features deduced from a single structure and homologous sequences. Assessment of the predictions via a 5-fold cross-validation method revealed that predictions based on features derived from a single structure perform similarly to ones based on homologous sequences, while combining sequence and structural features was optimal in terms of accuracy (0.755) and Matthews correlation coefficient (0.476). These results suggest that even without information from multiple structures, it is still possible to effectively predict SCRs for a protein. Finally, inspection of the structures with the worst predictions pinpoints difficulties in SCR definitions. Availability: The SCR database and the prediction server can be found at http://prodata.swmed.edu/SCR. Contact: 91huangi@gmail.com or grishin@chop.swmed.edu Supplementary information: Supplementary data are available at Bioinformatics Online PMID:23193223

Template-based structure modeling of protein-protein interactions

PubMed Central

Szilagyi, Andras; Zhang, Yang

2014-01-01

The structure of protein-protein complexes can be constructed by using the known structure of other protein complexes as a template. The complex structure templates are generally detected either by homology-based sequence alignments or, given the structure of monomer components, by structure-based comparisons. Critical improvements have been made in recent years by utilizing interface recognition and by recombining monomer and complex template libraries. Encouraging progress has also been witnessed in genome-wide applications of template-based modeling, with modeling accuracy comparable to high-throughput experimental data. Nevertheless, bottlenecks exist due to the incompleteness of the proteinprotein complex structure library and the lack of methods for distant homologous template identification and full-length complex structure refinement. PMID:24721449

Interaction Between Syntactic Structure and Information Structure in the Processing of a Head-Final Language.

PubMed

Koizumi, Masatoshi; Imamura, Satoshi

2017-02-01

The effects of syntactic and information structures on sentence processing load were investigated using two reading comprehension experiments in Japanese, a head-final SOV language. In the first experiment, we discovered the main effects of syntactic and information structures, as well as their interaction, showing that interaction of these two factors is not restricted to head-initial languages. The second experiment revealed that the interaction between syntactic structure and information structure occurs at the second NP (O of SOV and S of OSV), which, crucially, is a pre-head position, suggesting the incremental nature of the processing of both syntactic structure and information structure in head-final languages.

STAGS Developments for Residual Strength Analysis Methods for Metallic Fuselage Structures

NASA Technical Reports Server (NTRS)

Young, Richard D.; Rose, Cheryl A.

2014-01-01

A summary of advances in the Structural Analysis of General Shells (STAGS) finite element code for the residual strength analysis of metallic fuselage structures, that were realized through collaboration between the structures group at NASA Langley, and Dr. Charles Rankin is presented. The majority of the advancements described were made in the 1990's under the NASA Airframe Structural Integrity Program (NASIP). Example results from studies that were conducted using the STAGS code to develop improved understanding of the nonlinear response of cracked fuselage structures subjected to combined loads are presented. An integrated residual strength analysis methodology for metallic structure that models crack growth to predict the effect of cracks on structural integrity is demonstrated

NMR in the SPINE Structural Proteomics project.

PubMed

Ab, E; Atkinson, A R; Banci, L; Bertini, I; Ciofi-Baffoni, S; Brunner, K; Diercks, T; Dötsch, V; Engelke, F; Folkers, G E; Griesinger, C; Gronwald, W; Günther, U; Habeck, M; de Jong, R N; Kalbitzer, H R; Kieffer, B; Leeflang, B R; Loss, S; Luchinat, C; Marquardsen, T; Moskau, D; Neidig, K P; Nilges, M; Piccioli, M; Pierattelli, R; Rieping, W; Schippmann, T; Schwalbe, H; Travé, G; Trenner, J; Wöhnert, J; Zweckstetter, M; Kaptein, R

2006-10-01

This paper describes the developments, role and contributions of the NMR spectroscopy groups in the Structural Proteomics In Europe (SPINE) consortium. Focusing on the development of high-throughput (HTP) pipelines for NMR structure determinations of proteins, all aspects from sample preparation, data acquisition, data processing, data analysis to structure determination have been improved with respect to sensitivity, automation, speed, robustness and validation. Specific highlights are protonless (13)C-direct detection methods and inferential structure determinations (ISD). In addition to technological improvements, these methods have been applied to deliver over 60 NMR structures of proteins, among which are five that failed to crystallize. The inclusion of NMR spectroscopy in structural proteomics pipelines improves the success rate for protein structure determinations.

Hatch Integration Testing of a NASA TransHab Derivative Woven Inflatable Module

NASA Technical Reports Server (NTRS)

Edgecombe, John; Valle, Gerald

2009-01-01

Current options for Lunar habitat architecture include inflatable habitats and airlocks. Inflatable structures can have mass and volume advantages over conventional structures. However, inflatable structures are also perceived to carry additional risk because they are at a lower Technical Readiness Level (TRL) than more conventional metallic structures. The use of inflatable structures for habitation will require large penetrations in the inflatable structure to accommodate hatches and/or windows The Hatch Integration Test is designed to study the structural integrity of an expandable structure with an integrated hatch, and to verify mathematical models of the structure. The TransHab project developed an experimental inflatable module at Johnson Space Center in the 1990's. The TransHab design was originally envisioned for use in Mars Transits but was also studied as a potential habitat for the International Space Station (ISS).

Dynamic Structural Health Monitoring of Slender Structures Using Optical Sensors

PubMed Central

Antunes, Paulo; Travanca, Rui; Rodrigues, Hugo; Melo, José; Jara, José; Varum, Humberto; André, Paulo

2012-01-01

In this paper we summarize the research activities at the Instituto de Telecomunicações—Pólo de Aveiro and University of Aveiro, in the field of fiber Bragg grating based sensors and their applications in dynamic measurements for Structural Health Monitoring of slender structures such as towers. In this work we describe the implementation of an optical biaxial accelerometer based on fiber Bragg gratings inscribed on optical fibers. The proof-of-concept was done with the dynamic monitoring of a reinforced concrete structure and a slender metallic telecommunication tower. Those structures were found to be suitable to demonstrate the feasibility of FBG accelerometers to obtain the structures' natural frequencies, which are the key parameters in Structural Health Monitoring and in the calibration of numerical models used to simulate the structure behavior. PMID:22778661

The Scottish Structural Proteomics Facility: targets, methods and outputs.

PubMed

Oke, Muse; Carter, Lester G; Johnson, Kenneth A; Liu, Huanting; McMahon, Stephen A; Yan, Xuan; Kerou, Melina; Weikart, Nadine D; Kadi, Nadia; Sheikh, Md Arif; Schmelz, Stefan; Dorward, Mark; Zawadzki, Michal; Cozens, Christopher; Falconer, Helen; Powers, Helen; Overton, Ian M; van Niekerk, C A Johannes; Peng, Xu; Patel, Prakash; Garrett, Roger A; Prangishvili, David; Botting, Catherine H; Coote, Peter J; Dryden, David T F; Barton, Geoffrey J; Schwarz-Linek, Ulrich; Challis, Gregory L; Taylor, Garry L; White, Malcolm F; Naismith, James H

2010-06-01

The Scottish Structural Proteomics Facility was funded to develop a laboratory scale approach to high throughput structure determination. The effort was successful in that over 40 structures were determined. These structures and the methods harnessed to obtain them are reported here. This report reflects on the value of automation but also on the continued requirement for a high degree of scientific and technical expertise. The efficiency of the process poses challenges to the current paradigm of structural analysis and publication. In the 5 year period we published ten peer-reviewed papers reporting structural data arising from the pipeline. Nevertheless, the number of structures solved exceeded our ability to analyse and publish each new finding. By reporting the experimental details and depositing the structures we hope to maximize the impact of the project by allowing others to follow up the relevant biology.

Detection of core-periphery structure in networks based on 3-tuple motifs

NASA Astrophysics Data System (ADS)

Ma, Chuang; Xiang, Bing-Bing; Chen, Han-Shuang; Small, Michael; Zhang, Hai-Feng

2018-05-01

Detecting mesoscale structure, such as community structure, is of vital importance for analyzing complex networks. Recently, a new mesoscale structure, core-periphery (CP) structure, has been identified in many real-world systems. In this paper, we propose an effective algorithm for detecting CP structure based on a 3-tuple motif. In this algorithm, we first define a 3-tuple motif in terms of the patterns of edges as well as the property of nodes, and then a motif adjacency matrix is constructed based on the 3-tuple motif. Finally, the problem is converted to find a cluster that minimizes the smallest motif conductance. Our algorithm works well in different CP structures: including single or multiple CP structure, and local or global CP structures. Results on the synthetic and the empirical networks validate the high performance of our method.

Biomimetic superwettable materials with structural colours.

PubMed

Wang, Zelinlan; Guo, Zhiguang

2017-12-05

Structural colours and superwettability are of great interest due to their unique characteristics. However, the application of materials with either structural colours or superwettability is limited. Moreover, materials possessing both structural colours and superwettability are crucial for many practical applications. The combination of structural colours and superwettability can result in materials for use various applications, such as in sensors, detectors, bioassays, anti-counterfeiting, and liquid actuators, by controlling surfaces to repel or absorb liquids. Regarding superwettability and structural colours, surface texture and chemical composition are two factors for the construction of materials with superwettable structural colours. This review aims at offering a comprehensive elaboration of the mechanism, recent biomimetic research, and applications of biomimetic superwettable materials with structural colours. Furthermore, this review provides significant insight into the design, fabrication, and application of biomimetic superwettable materials with structural colours.

Identification of structural variation in mouse genomes.

PubMed

Keane, Thomas M; Wong, Kim; Adams, David J; Flint, Jonathan; Reymond, Alexandre; Yalcin, Binnaz

2014-01-01

Structural variation is variation in structure of DNA regions affecting DNA sequence length and/or orientation. It generally includes deletions, insertions, copy-number gains, inversions, and transposable elements. Traditionally, the identification of structural variation in genomes has been challenging. However, with the recent advances in high-throughput DNA sequencing and paired-end mapping (PEM) methods, the ability to identify structural variation and their respective association to human diseases has improved considerably. In this review, we describe our current knowledge of structural variation in the mouse, one of the prime model systems for studying human diseases and mammalian biology. We further present the evolutionary implications of structural variation on transposable elements. We conclude with future directions on the study of structural variation in mouse genomes that will increase our understanding of molecular architecture and functional consequences of structural variation.

On the structural context and identification of enzyme catalytic residues.

PubMed

Chien, Yu-Tung; Huang, Shao-Wei

2013-01-01

Enzymes play important roles in most of the biological processes. Although only a small fraction of residues are directly involved in catalytic reactions, these catalytic residues are the most crucial parts in enzymes. The study of the fundamental and unique features of catalytic residues benefits the understanding of enzyme functions and catalytic mechanisms. In this work, we analyze the structural context of catalytic residues based on theoretical and experimental structure flexibility. The results show that catalytic residues have distinct structural features and context. Their neighboring residues, whether sequence or structure neighbors within specific range, are usually structurally more rigid than those of noncatalytic residues. The structural context feature is combined with support vector machine to identify catalytic residues from enzyme structure. The prediction results are better or comparable to those of recent structure-based prediction methods.

Nanoscale array structures suitable for surface enhanced raman scattering and methods related thereto

DOEpatents

Bond, Tiziana C.; Miles, Robin; Davidson, James C.; Liu, Gang Logan

2014-07-22

Methods for fabricating nanoscale array structures suitable for surface enhanced Raman scattering, structures thus obtained, and methods to characterize the nanoscale array structures suitable for surface enhanced Raman scattering. Nanoscale array structures may comprise nanotrees, nanorecesses and tapered nanopillars.

Low-loss, high-speed, high-{Tc} superconducting bearings

DOEpatents

Hull, J.R.; Mulcahy, T.M.; Uherka, K.L.

1997-06-24

A flywheel energy storage device is disclosed including an iron structure disposed for rotation adjacent a stationary superconductor material structure and a stationary permanent magnet. The stationary permanent magnet levitates the iron structure while the superconductor structure can stabilize the rotating iron structure. 15 figs.

Low-loss, high-speed, high-T.sub.C superconducting bearings

DOEpatents

Hull, John R.; Mulcahy, Thomas M.; Uherka, Kenneth L.

1996-01-01

A flywheel energy storage device including an iron structure disposed for rotation adjacent a stationary superconductor material structure and a stationary permanent magnet. The stationary permanent magnet levitates the iron structure while the superconductor structure can stabilize and levitate the rotating iron structure.

Nanoscale array structures suitable for surface enhanced raman scattering and methods related thereto

DOEpatents

Bond, Tiziana C.; Miles, Robin; Davidson, James C.; Liu, Gang Logan

2015-07-14

Methods for fabricating nanoscale array structures suitable for surface enhanced Raman scattering, structures thus obtained, and methods to characterize the nanoscale array structures suitable for surface enhanced Raman scattering. Nanoscale array structures may comprise nanotrees, nanorecesses and tapered nanopillars.

Nanoscale array structures suitable for surface enhanced raman scattering and methods related thereto

DOEpatents

Bond, Tiziana C; Miles, Robin; Davidson, James; Liu, Gang Logan

2015-11-03

Methods for fabricating nanoscale array structures suitable for surface enhanced Raman scattering, structures thus obtained, and methods to characterize the nanoscale array structures suitable for surface enhanced Raman scattering. Nanoscale array structures may comprise nanotrees, nanorecesses and tapered nanopillars.

Institutional Structure: An Impediment to Professionalism.

ERIC Educational Resources Information Center

Palardy, J. Michael.

1988-01-01

Large schools have a tall organizational structure with long chains of command and limited control for "low-level" staff, including teachers and principals. To resolve this problem, two alternative structures are suggested: a dual structure involving spheres of administrative and professional responsibility and a flat structure featuring…

All-printed smart structures: a viable option?

NASA Astrophysics Data System (ADS)

O'Donnell, John; Ahmadkhanlou, Farzad; Yoon, Hwan-Sik; Washington, Gregory

2014-03-01

The last two decades have seen evolution of smart materials and structures technologies from theoretical concepts to physical realization in many engineering fields. These include smart sensors and actuators, active damping and vibration control, biomimetics, and structural health monitoring. Recently, additive manufacturing technologies such as 3D printing and printed electronics have received attention as methods to produce 3D objects or electronic components for prototyping or distributed manufacturing purposes. In this paper, the viability of manufacturing all-printed smart structures, with embedded sensors and actuators, will be investigated. To this end, the current 3D printing and printed electronics technologies will be reviewed first. Then, the plausibility of combining these two different additive manufacturing technologies to create all-printed smart structures will be discussed. Potential applications for this type of all-printed smart structures include most of the traditional smart structures where sensors and actuators are embedded or bonded to the structures to measure structural response and cause desired static and dynamic changes in the structure.

Structural optimization of large ocean-going structures

NASA Technical Reports Server (NTRS)

Hughes, O. F.

1984-01-01

Ocean-going vehicles and platforms are among the largest structures in the world and are subjected to relatively harsh conditions of motions and loads. Some of them, such as semi-submersible platforms, are a relatively new type of structure and hence there is no formal, well evolved and established structural design code as there is for more traditional structures. More recently, efforts have also been made to develop a design method of this type for ships and other ocean structures. One of the many advantages of a rationally based design method is versatility; it can be used for structures that have widely differing purposes, measures of merit, shapes and sizes. The purpose is to describe a rationally based design method that has been developed within the field of ocean structures, in order that persons dealing with other types of structure can judge whether and to what extent its various features may be useful for those other types. Also, even though some features may not be applicable they might stimulate some useful ideas.

Intricate Hollow Structures: Controlled Synthesis and Applications in Energy Storage and Conversion.

PubMed

Zhou, Liang; Zhuang, Zechao; Zhao, Huihui; Lin, Mengting; Zhao, Dongyuan; Mai, Liqiang

2017-05-01

Intricate hollow structures garner tremendous interest due to their aesthetic beauty, unique structural features, fascinating physicochemical properties, and widespread applications. Here, the recent advances in the controlled synthesis are discussed, as well as applications of intricate hollow structures with regard to energy storage and conversion. The synthetic strategies toward complex multishelled hollow structures are classified into six categories, including well-established hard- and soft-templating methods, as well as newly emerging approaches based on selective etching of "soft@hard" particles, Ostwald ripening, ion exchange, and thermally induced mass relocation. Strategies for constructing structures beyond multishelled hollow structures, such as bubble-within-bubble, tube-in-tube, and wire-in-tube structures, are also covered. Niche applications of intricate hollow structures in lithium-ion batteries, Li-S batteries, supercapacitors, Li-O 2 batteries, dye-sensitized solar cells, photocatalysis, and fuel cells are discussed in detail. Some perspectives on the future research and development of intricate hollow structures are also provided. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

CSM research: Methods and application studies

NASA Technical Reports Server (NTRS)

Knight, Norman F., Jr.

1989-01-01

Computational mechanics is that discipline of applied science and engineering devoted to the study of physical phenomena by means of computational methods based on mathematical modeling and simulation, utilizing digital computers. The discipline combines theoretical and applied mechanics, approximation theory, numerical analysis, and computer science. Computational mechanics has had a major impact on engineering analysis and design. When applied to structural mechanics, the discipline is referred to herein as computational structural mechanics. Complex structures being considered by NASA for the 1990's include composite primary aircraft structures and the space station. These structures will be much more difficult to analyze than today's structures and necessitate a major upgrade in computerized structural analysis technology. NASA has initiated a research activity in structural analysis called Computational Structural Mechanics (CSM). The broad objective of the CSM activity is to develop advanced structural analysis technology that will exploit modern and emerging computers, such as those with vector and/or parallel processing capabilities. Here, the current research directions for the Methods and Application Studies Team of the Langley CSM activity are described.

Probabilistic simulation of uncertainties in thermal structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.; Shiao, Michael

1990-01-01

Development of probabilistic structural analysis methods for hot structures is a major activity at Lewis Research Center. It consists of five program elements: (1) probabilistic loads; (2) probabilistic finite element analysis; (3) probabilistic material behavior; (4) assessment of reliability and risk; and (5) probabilistic structural performance evaluation. Recent progress includes: (1) quantification of the effects of uncertainties for several variables on high pressure fuel turbopump (HPFT) blade temperature, pressure, and torque of the Space Shuttle Main Engine (SSME); (2) the evaluation of the cumulative distribution function for various structural response variables based on assumed uncertainties in primitive structural variables; (3) evaluation of the failure probability; (4) reliability and risk-cost assessment, and (5) an outline of an emerging approach for eventual hot structures certification. Collectively, the results demonstrate that the structural durability/reliability of hot structural components can be effectively evaluated in a formal probabilistic framework. In addition, the approach can be readily extended to computationally simulate certification of hot structures for aerospace environments.

A symmetry measure for damage detection with mode shapes

NASA Astrophysics Data System (ADS)

Chen, Justin G.; Büyüköztürk, Oral

2017-11-01

This paper introduces a feature for detecting damage or changes in structures, the continuous symmetry measure, which can quantify the amount of a particular rotational, mirror, or translational symmetry in a mode shape of a structure. Many structures in the built environment have geometries that are either symmetric or almost symmetric, however damage typically occurs in a local manner causing asymmetric changes in the structure's geometry or material properties, and alters its mode shapes. The continuous symmetry measure can quantify these changes in symmetry as a novel indicator of damage for data-based structural health monitoring approaches. This paper describes the concept as a basis for detecting changes in mode shapes and detecting structural damage. Application of the method is demonstrated in various structures with different symmetrical properties: a pipe cross-section with a finite element model and experimental study, the NASA 8-bay truss model, and the simulated IASC-ASCE structural health monitoring benchmark structure. The applicability and limitations of the feature in applying it to structures of varying geometries is discussed.

Solid-State NMR Studies Reveal Native-like β-Sheet Structures in Transthyretin Amyloid

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

Lim, Kwang Hun; Dasari, Anvesh K. R.; Hung, Ivan

Structural characterization of amyloid rich in cross-β structures is crucial for unraveling the molecular basis of protein misfolding and amyloid formation associated with a wide range of human disorders. Elucidation of the β-sheet structure in noncrystalline amyloid has, however, remained an enormous challenge. Here we report structural analyses of the β-sheet structure in a full-length transthyretin amyloid using solid-state NMR spectroscopy. Magic-angle-spinning (MAS) solid-state NMR was employed to investigate native-like β-sheet structures in the amyloid state using selective labeling schemes for more efficient solid-state NMR studies. Analyses of extensive long-range 13 C- 13 C correlation MAS spectra obtained with selectivelymore » 13 CO- and 13 Cα-labeled TTR reveal that the two main β-structures in the native state, the CBEF and DAGH β-sheets, remain intact after amyloid formation. The tertiary structural information would be of great use for examining the quaternary structure of TTR amyloid.« less

Solid-State NMR Studies Reveal Native-like β-Sheet Structures in Transthyretin Amyloid

DOE PAGES

Lim, Kwang Hun; Dasari, Anvesh K. R.; Hung, Ivan; ...

2016-09-02

Structural characterization of amyloid rich in cross-β structures is crucial for unraveling the molecular basis of protein misfolding and amyloid formation associated with a wide range of human disorders. Elucidation of the β-sheet structure in noncrystalline amyloid has, however, remained an enormous challenge. Here we report structural analyses of the β-sheet structure in a full-length transthyretin amyloid using solid-state NMR spectroscopy. Magic-angle-spinning (MAS) solid-state NMR was employed to investigate native-like β-sheet structures in the amyloid state using selective labeling schemes for more efficient solid-state NMR studies. Analyses of extensive long-range 13 C- 13 C correlation MAS spectra obtained with selectivelymore » 13 CO- and 13 Cα-labeled TTR reveal that the two main β-structures in the native state, the CBEF and DAGH β-sheets, remain intact after amyloid formation. The tertiary structural information would be of great use for examining the quaternary structure of TTR amyloid.« less

Effect of microstructure on the impact toughness and temper embrittlement of SA508Gr.4N steel for advanced pressure vessel materials.

PubMed

Yang, Zhiqiang; Liu, Zhengdong; He, Xikou; Qiao, Shibin; Xie, Changsheng

2018-01-09

The effect of microstructure on the impact toughness and the temper embrittlement of a SA508Gr.4N steel was investigated. Martensitic and bainitic structures formed in this material were examined via scanning electron microscopy, electron backscatter diffraction, transmission electron microscopy, and Auger electron spectroscopy (AES) analysis. The martensitic structure had a positive effect on both the strength and toughness. Compared with the bainitic structure, this structure consisted of smaller blocks and more high-angle grain boundaries (HAGBs). Changes in the ultimate tensile strength and toughness of the martensitic structure were attributed to an increase in the crack propagation path. This increase resulted from an increased number of HAGBs and refinement of the sub-structure (block). The AES results revealed that sulfur segregation is higher in the martensitic structure than in the bainitic structure. Therefore, the martensitic structure is more susceptible to temper embrittlement than the bainitic structure.

Advances and trends in structures and dynamics; Proceedings of the Symposium, Washington, DC, October 22-25, 1984

NASA Technical Reports Server (NTRS)

Noor, A. K. (Editor); Hayduk, R. J. (Editor)

1985-01-01

Among the topics discussed are developments in structural engineering hardware and software, computation for fracture mechanics, trends in numerical analysis and parallel algorithms, mechanics of materials, advances in finite element methods, composite materials and structures, determinations of random motion and dynamic response, optimization theory, automotive tire modeling methods and contact problems, the damping and control of aircraft structures, and advanced structural applications. Specific topics covered include structural design expert systems, the evaluation of finite element system architectures, systolic arrays for finite element analyses, nonlinear finite element computations, hierarchical boundary elements, adaptive substructuring techniques in elastoplastic finite element analyses, automatic tracking of crack propagation, a theory of rate-dependent plasticity, the torsional stability of nonlinear eccentric structures, a computation method for fluid-structure interaction, the seismic analysis of three-dimensional soil-structure interaction, a stress analysis for a composite sandwich panel, toughness criterion identification for unidirectional composite laminates, the modeling of submerged cable dynamics, and damping synthesis for flexible spacecraft structures.

Structure of the Newcastle disease virus F protein in the post-fusion conformation

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

Swanson, Kurt; Wen, Xiaolin; Leser, George P.

2010-11-17

The paramyxovirus F protein is a class I viral membrane fusion protein which undergoes a significant refolding transition during virus entry. Previous studies of the Newcastle disease virus, human parainfluenza virus 3 and parainfluenza virus 5 F proteins revealed differences in the pre- and post-fusion structures. The NDV Queensland (Q) F structure lacked structural elements observed in the other two structures, which are key to the refolding and fusogenic activity of F. Here we present the NDV Australia-Victoria (AV) F protein post-fusion structure and provide EM evidence for its folding to a pre-fusion form. The NDV AV F structure containsmore » heptad repeat elements missing in the previous NDV Q F structure, forming a post-fusion six-helix bundle (6HB) similar to the post-fusion hPIV3 F structure. Electrostatic and temperature factor analysis of the F structures points to regions of these proteins that may be functionally important in their membrane fusion activity.« less

Age-related differences in the structural complexity of subcortical and ventricular structures.

PubMed

Madan, Christopher R; Kensinger, Elizabeth A

2017-02-01

It has been well established that the volume of several subcortical structures decreases in relation to age. Different metrics of cortical structure (e.g., volume, thickness, surface area, and gyrification) have been shown to index distinct characteristics of interindividual differences; thus, it is important to consider the relation of age to multiple structural measures. Here, we compare age-related differences in subcortical and ventricular volume to those differences revealed with a measure of structural complexity, quantified as fractal dimensionality. Across 3 large data sets, totaling nearly 900 individuals across the adult lifespan (aged 18-94 years), we found greater age-related differences in complexity than volume for the subcortical structures, particularly in the caudate and thalamus. The structural complexity of ventricular structures was not more strongly related to age than volume. These results demonstrate that considering shape-related characteristics improves sensitivity to detect age-related differences in subcortical structures. Copyright © 2016 Elsevier Inc. All rights reserved.

Clathrate Structure Determination by Combining Crystal Structure Prediction with Computational and Experimental 129Xe NMR Spectroscopy

PubMed Central

Selent, Marcin; Nyman, Jonas; Roukala, Juho; Ilczyszyn, Marek; Oilunkaniemi, Raija; Bygrave, Peter J.; Laitinen, Risto; Jokisaari, Jukka

2017-01-01

Abstract An approach is presented for the structure determination of clathrates using NMR spectroscopy of enclathrated xenon to select from a set of predicted crystal structures. Crystal structure prediction methods have been used to generate an ensemble of putative structures of o‐ and m‐fluorophenol, whose previously unknown clathrate structures have been studied by 129Xe NMR spectroscopy. The high sensitivity of the 129Xe chemical shift tensor to the chemical environment and shape of the crystalline cavity makes it ideal as a probe for porous materials. The experimental powder NMR spectra can be used to directly confirm or reject hypothetical crystal structures generated by computational prediction, whose chemical shift tensors have been simulated using density functional theory. For each fluorophenol isomer one predicted crystal structure was found, whose measured and computed chemical shift tensors agree within experimental and computational error margins and these are thus proposed as the true fluorophenol xenon clathrate structures. PMID:28111848

Investigating Molecular Structures of Bio-Fuel and Bio-Oil Seeds as Predictors To Estimate Protein Bioavailability for Ruminants by Advanced Nondestructive Vibrational Molecular Spectroscopy.

PubMed

Ban, Yajing; L Prates, Luciana; Yu, Peiqiang

2017-10-18

This study was conducted to (1) determine protein and carbohydrate molecular structure profiles and (2) quantify the relationship between structural features and protein bioavailability of newly developed carinata and canola seeds for dairy cows by using Fourier transform infrared molecular spectroscopy. Results showed similarity in protein structural makeup within the entire protein structural region between carinata and canola seeds. The highest area ratios related to structural CHO, total CHO, and cellulosic compounds were obtained for carinata seeds. Carinata and canola seeds showed similar carbohydrate and protein molecular structures by multivariate analyses. Carbohydrate molecular structure profiles were highly correlated to protein rumen degradation and intestinal digestion characteristics. In conclusion, the molecular spectroscopy can detect inherent structural characteristics in carinata and canola seeds in which carbohydrate-relative structural features are related to protein metabolism and utilization. Protein and carbohydrate spectral profiles could be used as predictors of rumen protein bioavailability in cows.

Tertiary structural propensities reveal fundamental sequence/structure relationships.

PubMed

Zheng, Fan; Zhang, Jian; Grigoryan, Gevorg

2015-05-05

Extracting useful generalizations from the continually growing Protein Data Bank (PDB) is of central importance. We hypothesize that the PDB contains valuable quantitative information on the level of local tertiary structural motifs (TERMs). We show that by breaking a protein structure into its constituent TERMs, and querying the PDB to characterize the natural ensemble matching each, we can estimate the compatibility of the structure with a given amino acid sequence through a metric we term "structure score." Considering submissions from recent Critical Assessment of Structure Prediction (CASP) experiments, we found a strong correlation (R = 0.69) between structure score and model accuracy, with poorly predicted regions readily identifiable. This performance exceeds that of leading atomistic statistical energy functions. Furthermore, TERM-based analysis of two prototypical multi-state proteins rapidly produced structural insights fully consistent with prior extensive experimental studies. We thus find that TERM-based analysis should have considerable utility for protein structural biology. Copyright © 2015 Elsevier Ltd. All rights reserved.

First-principles study of high-pressure structural phase transitions of magnesium

NASA Astrophysics Data System (ADS)

Liu, Qiuxiang; Fan, Changzeng; Zhang, Ruijun

2009-06-01

The structural phase transitions for the hcp, bcc, dhcp, and fcc of magnesium at hydrostatic pressures larger than about 200 GPa at zero temperature are studied by first-principles total energy calculations. The plane-wave basis pseudopotential method has been adopted, in which the generalized gradient approximation implanted in the CASTEP code is employed. By comparing the enthalpy differences of the hcp structure with other three structures under different pressures, it can be seen that when the pressure becomes higher than about 65, 130, and 190 GPa, the bcc, dhcp, and fcc structures become more stable relative to the hcp structure, respectively. Due to the lowest enthalpy value of the bcc structure above 65 GPa, it can be deduced that magnesium may transform to the bcc structure from the ground state hcp structure around 65 GPa, but no further phase transitions occur without additionally applying high temperature. In addition, the equation of state of magnesium is calculated, indicating that bcc structure is the softest phase.

Agriculturization in the Argentinean Northern Humid Pampas: the Impact on Soil Structure and Runoff

NASA Astrophysics Data System (ADS)

Sasal, M. C.; Léonard, J.; Andriulo, A.; Wilson, M. G.

2012-04-01

Argentina is among the countries with the largest cropped area under no-tillage (NT). No tillage was adopted in the northern Humid Pampas to reduce the widespread soil degradation by water erosion. With the advent of genetically modified soybean varieties, NT has developed exponentially. This evolution, combined with the influence of the international market trend, has resulted in large changes in crop sequence composition toward the disappearance of pastures and the expansion of soybean monoculture. The aim of this work was to evaluate the long-term consequences of these changes on the topsoil structure and the way in which the evolution of soil structure relates to the simplification of the crop sequence and to runoff at a regional scale. We analyzed the topsoil structure of 25 sites with Argiudolls having 4 to 29 consecutive years of NT using the cultural profile approach. An intensification sequence index (ISI) was calculated as the ratio between the length of the growth period and the length of the year. Fifteen natural-rainfall runoff plots (100 m2) with 3.5% slope were used to analyze the relationship between soil structural state, crop sequence and runoff for four years. Four types of soil structures were identified and a general pattern of vertical soil structure organization was revealed. The top centimeters of 72% of the sites were dominated by a granular structure. Platy soil structure development was omnipresent: all sites exhibited a horizontal platy structure (<10 cm thick) developing either directly from the soil surface or from below the granular structure. Below the platy structure layer, a gamma soil structure (with visible structural porosity) was observed in all sites (30-75% of the A horizon), while compacted delta soil structure was detected in localized zones. A significant parabolic relationship (R2=0.60) was found between the number of consecutive years under NT and the proportion of platy structure in the A horizon. The proportion of platy structure increased during the first 15 years of NT, and then the extension of platy structure tended to stabilize and even to decrease after 20 to 25 years. The development of platy soil structure was negatively related to the ISI (R2=0.57) and runoff increased as the proportion of platy structure increased and the proportion of granular structure decreased (R2=0.85). We concluded that high soybean frequency in cropping systems under NT favors the extension of platy soil structure and increases runoff. More than 70% of the agricultural area of the northern Humid Pampas region is currently covered by soybean cultivation, mostly as a single annual crop (ISI=0.38). Our results thus suggest that promoting management practices such as the expansion of wheat/soybean double crop (ISI=0.83) could limit soil structure degradation and reduce runoff and the associated environmental risks.

Study on Detailing Design of Precast Concrete Frame Structure

NASA Astrophysics Data System (ADS)

Lida, Tian; Liming, Li; Kang, Liu; Jiao, Geng; Ming, Li

2018-03-01

Taking a certain precast concrete frame structure as an example, this paper introduces the general procedures and key points in detailing design of emulative cast-in-place prefabricated structure from the aspects of structural scheme, precast element layout, shop drawing design and BIM 3D modelling. This paper gives a practical solution for the detailing design of precast concrete frame structure under structural design codes in China.

Structural dissipative solitons in passive mode-locked fiber lasers.

PubMed

Komarov, Andrey; Sanchez, François

2008-06-01

On the basis of numerical simulation of fiber laser passive mode locking with anomalous dispersion we have found the dissipative solitons with powerful pedestals having oscillating structure. The pedestal structure causes a complex structural spectrum. These solitons can be multistable: with the same laser parameters the pedestals can have different structures. For some nonlinear-dispersion parameters there exist solitons with asymmetric structural pedestals moving relatively solitons with symmetric ones.

The Paris-Sud yeast structural genomics pilot-project: from structure to function.

PubMed

Quevillon-Cheruel, Sophie; Liger, Dominique; Leulliot, Nicolas; Graille, Marc; Poupon, Anne; Li de La Sierra-Gallay, Inès; Zhou, Cong-Zhao; Collinet, Bruno; Janin, Joël; Van Tilbeurgh, Herman

2004-01-01

We present here the outlines and results from our yeast structural genomics (YSG) pilot-project. A lab-scale platform for the systematic production and structure determination is presented. In order to validate this approach, 250 non-membrane proteins of unknown structure were targeted. Strategies and final statistics are evaluated. We finally discuss the opportunity of structural genomics programs to contribute to functional biochemical annotation.

Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 2. Teaching Units that Utilize an Interactive Web-Accessible Subset of the Cambridge Structural Database

ERIC Educational Resources Information Center

Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.

2010-01-01

A series of online interactive teaching units have been developed that illustrate the use of experimentally measured three-dimensional (3D) structures to teach fundamental chemistry concepts. The units integrate a 500-structure subset of the Cambridge Structural Database specially chosen for their pedagogical value. The units span a number of key…

Study on Human-structure Dynamic Interaction in Civil Engineering

NASA Astrophysics Data System (ADS)

Gao, Feng; Cao, Li Lin; Li, Xing Hua

2018-06-01

The research of human-structure dynamic interaction are reviewed. Firstly, the influence of the crowd load on structural dynamic characteristics is introduced and the advantages and disadvantages of different crowd load models are analyzed. Then, discussing the influence of structural vibration on the human-induced load, especially the influence of different stiffness structures on the crowd load. Finally, questions about human-structure interaction that require further study are presented.

Structures and Dynamics Division: Research and technology plans for FY 1983 and accomplishments for FY 1982

NASA Technical Reports Server (NTRS)

Bales, K. S.

1983-01-01

The objectives, expected results, approach, and milestones for research projects of the IPAD Project Office and the impact dynamics, structural mechanics, and structural dynamics branches of the Structures and Dynamics Division are presented. Research facilities are described. Topics covered include computer aided design; general aviation/transport crash dynamics; aircraft ground performance; composite structures; failure analysis, space vehicle dynamics; and large space structures.

Integrated smart panel and support structure response

NASA Astrophysics Data System (ADS)

DeGiorgi, Virginia G.

1998-06-01

The performance of smart structures is a complex interaction between active and passive components. Active components, even when non-activated, can have an impact on structural performance and, conversely, structural characteristics of passive components can have a measurable impact on active component performance. The present work is an evaluation of the structural characteristics of an active panel designed for acoustic quieting. The support structure is included in the panel design as evaluated. Finite element methods are used to determine the active panel-support structure response. Two conditions are considered; a hollow unfilled support structure and the same structure filled with a polymer compound. Finite element models were defined so that stiffness values corresponding to the center of individual pistons could be determined. Superelement techniques were used to define mass and stiffness values representative of the combined active and support structure at the center of each piston. Results of interest obtained from the analysis include mode shapes, natural frequencies, and equivalent spring stuffiness for use in structural response models to represent the support structure. The effects on plate motion on piston performance cannot be obtained from this analysis, however mass and stiffness matrices for use in an integrated system model to determine piston head velocities can be obtained from this work.

Experimental validation of a structural damage detection method based on marginal Hilbert spectrum

NASA Astrophysics Data System (ADS)

Banerji, Srishti; Roy, Timir B.; Sabamehr, Ardalan; Bagchi, Ashutosh

2017-04-01

Structural Health Monitoring (SHM) using dynamic characteristics of structures is crucial for early damage detection. Damage detection can be performed by capturing and assessing structural responses. Instrumented structures are monitored by analyzing the responses recorded by deployed sensors in the form of signals. Signal processing is an important tool for the processing of the collected data to diagnose anomalies in structural behavior. The vibration signature of the structure varies with damage. In order to attain effective damage detection, preservation of non-linear and non-stationary features of real structural responses is important. Decomposition of the signals into Intrinsic Mode Functions (IMF) by Empirical Mode Decomposition (EMD) and application of Hilbert-Huang Transform (HHT) addresses the time-varying instantaneous properties of the structural response. The energy distribution among different vibration modes of the intact and damaged structure depicted by Marginal Hilbert Spectrum (MHS) detects location and severity of the damage. The present work investigates damage detection analytically and experimentally by employing MHS. The testing of this methodology for different damage scenarios of a frame structure resulted in its accurate damage identification. The sensitivity of Hilbert Spectral Analysis (HSA) is assessed with varying frequencies and damage locations by means of calculating Damage Indices (DI) from the Hilbert spectrum curves of the undamaged and damaged structures.

Cytoplasmic inheritance of parent-offspring cell structure in the clonal diatom Cyclotella meneghiniana.

PubMed

Shirokawa, Yuka; Shimada, Masakazu

2016-11-16

In cytoplasmic inheritance, structural states of a parent cell could be transmitted to offspring cells via two mechanisms. The first is referred to as the hangover of parent structure, where the structure itself remains and faithfully transmits within offspring cells; the second is structural inheritance, wherein the parent structure functions as a template for development of new offspring structure. We estimated to what extent the parent structure affects the development of offspring structure by structural inheritance, using a clone of the diatom Cyclotella meneghiniana The cell has two siliceous valves (a cell wall part at both cell poles): one is inherited from the parent and the other is newly formed. We estimated cytoplasmic heritability by comparing valve traits (central fultoportulae (CTFP), striae, central area, and cell diameter) of parent and new offspring valves, using single-cell isolation and valve labelling. Parent-offspring valve trait regressions showed that all traits, except CTFP, were significantly correlated. We formulated a quantitative genetic model considering the diatom inheritance system and revealed short-term rapid evolution compared with other inheritance systems. Diatom structural inheritance will have evolved to enable clonal populations to rapidly acquire and maintain suitable structures for temporal changes in environments and life-cycle stages. © 2016 The Author(s).

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.

Local and average structure of Mn- and La-substituted BiFeO3

NASA Astrophysics Data System (ADS)

Jiang, Bo; Selbach, Sverre M.

2017-06-01

The local and average structure of solid solutions of the multiferroic perovskite BiFeO3 is investigated by synchrotron X-ray diffraction (XRD) and electron density functional theory (DFT) calculations. The average experimental structure is determined by Rietveld refinement and the local structure by total scattering data analyzed in real space with the pair distribution function (PDF) method. With equal concentrations of La on the Bi site or Mn on the Fe site, La causes larger structural distortions than Mn. Structural models based on DFT relaxed geometry give an improved fit to experimental PDFs compared to models constrained by the space group symmetry. Berry phase calculations predict a higher ferroelectric polarization than the experimental literature values, reflecting that structural disorder is not captured in either average structure space group models or DFT calculations with artificial long range order imposed by periodic boundary conditions. Only by including point defects in a supercell, here Bi vacancies, can DFT calculations reproduce the literature results on the structure and ferroelectric polarization of Mn-substituted BiFeO3. The combination of local and average structure sensitive experimental methods with DFT calculations is useful for illuminating the structure-property-composition relationships in complex functional oxides with local structural distortions.

Review of Large Spacecraft Deployable Membrane Antenna Structures

NASA Astrophysics Data System (ADS)

Liu, Zhi-Quan; Qiu, Hui; Li, Xiao; Yang, Shu-Li

2017-11-01

The demand for large antennas in future space missions has increasingly stimulated the development of deployable membrane antenna structures owing to their light weight and small stowage volume. However, there is little literature providing a comprehensive review and comparison of different membrane antenna structures. Space-borne membrane antenna structures are mainly classified as either parabolic or planar membrane antenna structures. For parabolic membrane antenna structures, there are five deploying and forming methods, including inflation, inflation-rigidization, elastic ribs driven, Shape Memory Polymer (SMP)-inflation, and electrostatic forming. The development and detailed comparison of these five methods are presented. Then, properties of membrane materials (including polyester film and polyimide film) for parabolic membrane antennas are compared. Additionally, for planar membrane antenna structures, frame shapes have changed from circular to rectangular, and different tensioning systems have emerged successively, including single Miura-Natori, double, and multi-layer tensioning systems. Recent advances in structural configurations, tensioning system design, and dynamic analysis for planar membrane antenna structures are investigated. Finally, future trends for large space membrane antenna structures are pointed out and technical problems are proposed, including design and analysis of membrane structures, materials and processes, membrane packing, surface accuracy stability, and test and verification technology. Through a review of large deployable membrane antenna structures, guidance for space membrane-antenna research and applications is provided.

D2N: Distance to the native.

PubMed

Mishra, Avinash; Rana, Prashant Singh; Mittal, Aditya; Jayaram, B

2014-10-01

Root-mean-square-deviation (RMSD), of computationally-derived protein structures from experimentally determined structures, is a critical index to assessing protein-structure-prediction-algorithms (PSPAs). The development of PSPAs to obtain 0Å RMSD from native structures is considered central to computational biology. However, till date it has been quite challenging to measure how far a predicted protein structure is from its native - in the absence of a known experimental/native structure. In this work, we report the development of a metric "D2N" (distance to the native) - that predicts the "RMSD" of any structure without actually knowing the native structure. By combining physico-chemical properties and known universalities in spatial organization of soluble proteins to develop D2N, we demonstrate the ability to predict the distance of a proposed structure to within ±1.5Ǻ error with a remarkable average accuracy of 93.6% for structures below 5Ǻ from the native. We believe that this work opens up a completely new avenue towards assigning reliable structures to whole proteomes even in the absence of experimentally determined native structures. The D2N tool is freely available at http://www.scfbio-iitd.res.in/software/d2n.jsp. Copyright © 2014 Elsevier B.V. All rights reserved.

Structural Evolution of Nanoscale Zero-Valent Iron (nZVI) in Anoxic Co2+ Solution: Interactional Performance and Mechanism

PubMed Central

Zhang, Yalei; Chen, Wen; Dai, Chaomeng; Zhou, Chuanlong; Zhou, Xuefei

2015-01-01

The structures of nanoscale zero-valent iron (nZVI) particles evolving during reactions, and the reactions are influenced by the evolved structures. To understand the removal process in detail, it is important to investigate the relationships between the reactions and structural evolution. Using high resolution-transmission electron microscopy (HR-TEM), typical evolved structures (sheet coprecipitation and cavity corrosion) of nZVI in anoxic Co2+ solutions were revealed. The system pH (pH measured in mixture), which controls the stability of coprecipitation and the nZVI corrosion rate, were found to be the determining factors of structural evolutions. X-ray photoelectron spectroscopy (XPS) results indicated that the formation and dissolution of sheet structure impacts on the ratio of Fe(0) on the nZVI surface and the surface Co2+ reduction. The cavity structure provides the possibility of Co migration from the surface to the bulk of nZVI, leading to continuous removal. Subacidity conditions could accelerate the evolution and improve the removal; the results of structurally controlled reactions further indicated that the removal was suspended by the sheet structure and enhanced by cavity structure. The results and discussion in this paper revealed the “structural influence” crucial for the full and dynamical understanding of nZVI reactions. PMID:26355955

Structural Evolution of Nanoscale Zero-Valent Iron (nZVI) in Anoxic Co(2+) Solution: Interactional Performance and Mechanism.

PubMed

Zhang, Yalei; Chen, Wen; Dai, Chaomeng; Zhou, Chuanlong; Zhou, Xuefei

2015-09-10

The structures of nanoscale zero-valent iron (nZVI) particles evolving during reactions, and the reactions are influenced by the evolved structures. To understand the removal process in detail, it is important to investigate the relationships between the reactions and structural evolution. Using high resolution-transmission electron microscopy (HR-TEM), typical evolved structures (sheet coprecipitation and cavity corrosion) of nZVI in anoxic Co(2+) solutions were revealed. The system pH (pH measured in mixture), which controls the stability of coprecipitation and the nZVI corrosion rate, were found to be the determining factors of structural evolutions. X-ray photoelectron spectroscopy (XPS) results indicated that the formation and dissolution of sheet structure impacts on the ratio of Fe(0) on the nZVI surface and the surface Co(2+) reduction. The cavity structure provides the possibility of Co migration from the surface to the bulk of nZVI, leading to continuous removal. Subacidity conditions could accelerate the evolution and improve the removal; the results of structurally controlled reactions further indicated that the removal was suspended by the sheet structure and enhanced by cavity structure. The results and discussion in this paper revealed the "structural influence" crucial for the full and dynamical understanding of nZVI reactions.

Structural Evolution of Nanoscale Zero-Valent Iron (nZVI) in Anoxic Co2+ Solution: Interactional Performance and Mechanism

NASA Astrophysics Data System (ADS)

Zhang, Yalei; Chen, Wen; Dai, Chaomeng; Zhou, Chuanlong; Zhou, Xuefei

2015-09-01

The structures of nanoscale zero-valent iron (nZVI) particles evolving during reactions, and the reactions are influenced by the evolved structures. To understand the removal process in detail, it is important to investigate the relationships between the reactions and structural evolution. Using high resolution-transmission electron microscopy (HR-TEM), typical evolved structures (sheet coprecipitation and cavity corrosion) of nZVI in anoxic Co2+ solutions were revealed. The system pH (pH measured in mixture), which controls the stability of coprecipitation and the nZVI corrosion rate, were found to be the determining factors of structural evolutions. X-ray photoelectron spectroscopy (XPS) results indicated that the formation and dissolution of sheet structure impacts on the ratio of Fe(0) on the nZVI surface and the surface Co2+ reduction. The cavity structure provides the possibility of Co migration from the surface to the bulk of nZVI, leading to continuous removal. Subacidity conditions could accelerate the evolution and improve the removal; the results of structurally controlled reactions further indicated that the removal was suspended by the sheet structure and enhanced by cavity structure. The results and discussion in this paper revealed the “structural influence” crucial for the full and dynamical understanding of nZVI reactions.

Structural Configuration Systems Analysis for Advanced Aircraft Fuselage Concepts

NASA Technical Reports Server (NTRS)

Mukhopadhyay, Vivek; Welstead, Jason R.; Quinlan, Jesse R.; Guynn, Mark D.

2016-01-01

Structural configuration analysis of an advanced aircraft fuselage concept is investigated. This concept is characterized by a double-bubble section fuselage with rear mounted engines. Based on lessons learned from structural systems analysis of unconventional aircraft, high-fidelity finite-element models (FEM) are developed for evaluating structural performance of three double-bubble section configurations. Structural sizing and stress analysis are applied for design improvement and weight reduction. Among the three double-bubble configurations, the double-D cross-section fuselage design was found to have a relatively lower structural weight. The structural FEM weights of these three double-bubble fuselage section concepts are also compared with several cylindrical fuselage models. Since these fuselage concepts are different in size, shape and material, the fuselage structural FEM weights are normalized by the corresponding passenger floor area for a relative comparison. This structural systems analysis indicates that an advanced composite double-D section fuselage may have a relative structural weight ratio advantage over a conventional aluminum fuselage. Ten commercial and conceptual aircraft fuselage structural weight estimates, which are empirically derived from the corresponding maximum takeoff gross weight, are also presented and compared with the FEM- based estimates for possible correlation. A conceptual full vehicle FEM model with a double-D fuselage is also developed for preliminary structural analysis and weight estimation.

SMART Layer and SMART Suitcase for structural health monitoring applications

NASA Astrophysics Data System (ADS)

Lin, Mark; Qing, Xinlin; Kumar, Amrita; Beard, Shawn J.

2001-06-01

Knowledge of integrity of in-service structures can greatly enhance their safety and reliability and lower structural maintenance cost. Current practices limit the extent of real-time knowledge that can be obtained from structures during inspection, are labor-intensive and thereby increase life-cycle costs. Utilization of distributed sensors integrated with the structure is a viable and cost-effective means of monitoring the structure and reducing inspection costs. Acellent Technologies is developing a novel system for actively and passively interrogating the health of a structure through an integrated network of sensors and actuators. Acellent's system comprises of SMART Layers, SMART Suitcase and diagnostic software. The patented SMART Layer is a thin dielectric film with an embedded network of distributed piezoelectric actuators/sensors that can be surface-mounted on metallic structures or embedded inside composite structures. The SMART Suitcase is a portable diagnostic unit designed with multiple sensor/actuator channels to interface with the SMART Layer, generate diagnostic signals from actuators and record measurements from the embedded sensors. With appropriate diagnostic software, Acellent's system can be used for monitoring structural condition and for detecting damage while the structures are in service. This paper enumerates on the SMART Layer and SMART Suitcase and their applicability to composite and metal structures.

Template-based modeling and ab initio refinement of protein oligomer structures using GALAXY in CAPRI round 30.

PubMed

Lee, Hasup; Baek, Minkyung; Lee, Gyu Rie; Park, Sangwoo; Seok, Chaok

2017-03-01

Many proteins function as homo- or hetero-oligomers; therefore, attempts to understand and regulate protein functions require knowledge of protein oligomer structures. The number of available experimental protein structures is increasing, and oligomer structures can be predicted using the experimental structures of related proteins as templates. However, template-based models may have errors due to sequence differences between the target and template proteins, which can lead to functional differences. Such structural differences may be predicted by loop modeling of local regions or refinement of the overall structure. In CAPRI (Critical Assessment of PRotein Interactions) round 30, we used recently developed features of the GALAXY protein modeling package, including template-based structure prediction, loop modeling, model refinement, and protein-protein docking to predict protein complex structures from amino acid sequences. Out of the 25 CAPRI targets, medium and acceptable quality models were obtained for 14 and 1 target(s), respectively, for which proper oligomer or monomer templates could be detected. Symmetric interface loop modeling on oligomer model structures successfully improved model quality, while loop modeling on monomer model structures failed. Overall refinement of the predicted oligomer structures consistently improved the model quality, in particular in interface contacts. Proteins 2017; 85:399-407. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Fast protein tertiary structure retrieval based on global surface shape similarity.

PubMed

Sael, Lee; Li, Bin; La, David; Fang, Yi; Ramani, Karthik; Rustamov, Raif; Kihara, Daisuke

2008-09-01

Characterization and identification of similar tertiary structure of proteins provides rich information for investigating function and evolution. The importance of structure similarity searches is increasing as structure databases continue to expand, partly due to the structural genomics projects. A crucial drawback of conventional protein structure comparison methods, which compare structures by their main-chain orientation or the spatial arrangement of secondary structure, is that a database search is too slow to be done in real-time. Here we introduce a global surface shape representation by three-dimensional (3D) Zernike descriptors, which represent a protein structure compactly as a series expansion of 3D functions. With this simplified representation, the search speed against a few thousand structures takes less than a minute. To investigate the agreement between surface representation defined by 3D Zernike descriptor and conventional main-chain based representation, a benchmark was performed against a protein classification generated by the combinatorial extension algorithm. Despite the different representation, 3D Zernike descriptor retrieved proteins of the same conformation defined by combinatorial extension in 89.6% of the cases within the top five closest structures. The real-time protein structure search by 3D Zernike descriptor will open up new possibility of large-scale global and local protein surface shape comparison. 2008 Wiley-Liss, Inc.

Local and average structure of Mn- and La-substituted BiFeO 3

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

Jiang, Bo; Selbach, Sverre M.

2017-06-01

The local and average structure of solid solutions of the multiferroic perovskite BiFeO 3 is investigated by synchrotron X-ray diffraction (XRD) and electron density functional theory (DFT) calculations. The average experimental structure is determined by Rietveld refinement and the local structure by total scattering data analyzed in real space with the pair distribution function (PDF) method. With equal concentrations of La on the Bi site or Mn on the Fe site, La causes larger structural distortions than Mn. Structural models based on DFT relaxed geometry give an improved fit to experimental PDFs compared to models constrained by the space groupmore » symmetry. Berry phase calculations predict a higher ferroelectric polarization than the experimental literature values, reflecting that structural disorder is not captured in either average structure space group models or DFT calculations with artificial long range order imposed by periodic boundary conditions. Only by including point defects in a supercell, here Bi vacancies, can DFT calculations reproduce the literature results on the structure and ferroelectric polarization of Mn-substituted BiFeO 3. The combination of local and average structure sensitive experimental methods with DFT calculations is useful for illuminating the structure-property-composition relationships in complex functional oxides with local structural distortions.« less

The CAD-score web server: contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes.

PubMed

Olechnovič, Kliment; Venclovas, Ceslovas

2014-07-01

The Contact Area Difference score (CAD-score) web server provides a universal framework to compute and analyze discrepancies between different 3D structures of the same biological macromolecule or complex. The server accepts both single-subunit and multi-subunit structures and can handle all the major types of macromolecules (proteins, RNA, DNA and their complexes). It can perform numerical comparison of both structures and interfaces. In addition to entire structures and interfaces, the server can assess user-defined subsets. The CAD-score server performs both global and local numerical evaluations of structural differences between structures or interfaces. The results can be explored interactively using sortable tables of global scores, profiles of local errors, superimposed contact maps and 3D structure visualization. The web server could be used for tasks such as comparison of models with the native (reference) structure, comparison of X-ray structures of the same macromolecule obtained in different states (e.g. with and without a bound ligand), analysis of nuclear magnetic resonance (NMR) structural ensemble or structures obtained in the course of molecular dynamics simulation. The web server is freely accessible at: http://www.ibt.lt/bioinformatics/cad-score. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Mechanical properties and cell-culture characteristics of a polycaprolactone kagome-structure scaffold fabricated by a precision extruding deposition system.

PubMed

Lee, Se-Hwan; Cho, Yong Sang; Hong, Myoung Wha; Lee, Bu-Kyu; Park, Yongdoo; Park, Sang-Hyug; Kim, Young Yul; Cho, Young-Sam

2017-09-13

To enhance the mechanical properties of three-dimensional (3D) scaffolds used for bone regeneration in tissue engineering, many researchers have studied their structure and chemistry. In the structural engineering field, the kagome structure has been known to have an excellent relative strength. In this study, to enhance the mechanical properties of a synthetic polymer scaffold used for tissue engineering, we applied the 3D kagome structure to a porous scaffold for bone regeneration. Prior to fabricating the biocompatible-polymer scaffold, the ideal kagome structure, which was manufactured by a 3D printer of the digital light processing type, was compared with a grid-structure, which was used as the control group, using a compressive experiment. A polycaprolactone (PCL) kagome-structure scaffold was successfully fabricated by additive manufacturing using a 3D printer with a precision extruding deposition head. To assess the physical characteristics of the fabricated PCL-kagome-structure scaffold, we analyzed its porosity, pore size, morphological structure, surface roughness, compressive stiffness, and mechanical bending properties. The results showed that, the mechanical properties of proposed kagome-structure scaffold were superior to those of a grid-structure scaffold. Moreover, Sarcoma osteogenic (Saos-2) cells were used to evaluate the characteristics of in vitro cell proliferation. We carried out cell counting kit-8 (CCK-8) and DNA contents assays. Consequently, the cell proliferation of the kagome-structure scaffold was increased; this could be because the surface roughness of the kagome-structure scaffold enhances initial cell attachment.

Energetically Unfavorable Amide Conformations for N6-Acetyllysine Side Chains in Refined Protein Structures

PubMed Central

Genshaft, Alexander; Moser, Joe-Ann S.; D'Antonio, Edward L.; Bowman, Christine M.; Christianson, David W.

2013-01-01

The reversible acetylation of lysine to form N6-acetyllysine in the regulation of protein function is a hallmark of epigenetics. Acetylation of the positively charged amino group of the lysine side chain generates a neutral N-alkylacetamide moiety that serves as a molecular “switch” for the modulation of protein function and protein-protein interactions. We now report the analysis of 381 N6-acetyllysine side chain amide conformations as found in 79 protein crystal structures and 11 protein NMR structures deposited in the Protein Data Bank (PDB) of the Research Collaboratory for Structural Bioinformatics. We find that only 74.3% of N6-acetyllysine residues in protein crystal structures and 46.5% in protein NMR structures contain amide groups with energetically preferred trans or generously trans conformations. Surprisingly, 17.6% of N6-acetyllysine residues in protein crystal structures and 5.3% in protein NMR structures contain amide groups with energetically unfavorable cis or generously cis conformations. Even more surprisingly, 8.1% of N6-acetyllysine residues in protein crystal structures and 48.2% in NMR structures contain amide groups with energetically prohibitive twisted conformations that approach the transition state structure for cis-trans isomerization. In contrast, 109 unique N-alkylacetamide groups contained in 84 highly-accurate small molecule crystal structures retrieved from the Cambridge Structural Database exclusively adopt energetically preferred trans conformations. Therefore, we conclude that cis and twisted N6-acetyllysine amides in protein structures deposited in the PDB are erroneously modeled due to their energetically unfavorable or prohibitive conformations. PMID:23401043

Sound transmission through triple-panel structures lined with poroelastic materials

NASA Astrophysics Data System (ADS)

Liu, Yu

2015-03-01

In this paper, previous theories on the prediction of sound transmission loss for a double-panel structure lined with poroelastic materials are extended to address the problem of a triple-panel structure. Six typical configurations are considered for a triple-panel structure based on the method of coupling the porous layers to the facing panels which determines critically the sound insulation performance of the system. The transfer matrix method is employed to solve the system by applying appropriate types of boundary conditions for these configurations. The transmission loss of the triple-panel structures in a diffuse sound field is calculated as a function of frequency and compared with that of corresponding double-panel structures. Generally, the triple-panel structure with poroelastic linings has superior acoustic performance to the double-panel counterpart, remarkably in the mid-high frequency range and possibly at low frequencies, by selecting appropriate configurations in which those with two air gaps in the structure exhibit the best overall performance over the entire frequency range. The poroelastic lining significantly lowers the cut-on frequency above which the triple-panel structure exhibits noticeably higher transmission loss. Compared with a double-panel structure, the wider range of system parameters for a triple-panel structure due to the additional partition provides more design space for tuning the sound insulation performance. Despite the increased structural complexity, the triple-panel structure lined with poroelastic materials has the obvious advantages in sound transmission loss while without the penalties in weight and volume, and is hence a promising replacement for the widely used double-panel sandwich structure.

Local Structural Differences in Homologous Proteins: Specificities in Different SCOP Classes

PubMed Central

Joseph, Agnel Praveen; Valadié, Hélène; Srinivasan, Narayanaswamy; de Brevern, Alexandre G.

2012-01-01

The constant increase in the number of solved protein structures is of great help in understanding the basic principles behind protein folding and evolution. 3-D structural knowledge is valuable in designing and developing methods for comparison, modelling and prediction of protein structures. These approaches for structure analysis can be directly implicated in studying protein function and for drug design. The backbone of a protein structure favours certain local conformations which include α-helices, β-strands and turns. Libraries of limited number of local conformations (Structural Alphabets) were developed in the past to obtain a useful categorization of backbone conformation. Protein Block (PB) is one such Structural Alphabet that gave a reasonable structure approximation of 0.42 Å. In this study, we use PB description of local structures to analyse conformations that are preferred sites for structural variations and insertions, among group of related folds. This knowledge can be utilized in improving tools for structure comparison that work by analysing local structure similarities. Conformational differences between homologous proteins are known to occur often in the regions comprising turns and loops. Interestingly, these differences are found to have specific preferences depending upon the structural classes of proteins. Such class-specific preferences are mainly seen in the all-β class with changes involving short helical conformations and hairpin turns. A test carried out on a benchmark dataset also indicates that the use of knowledge on the class specific variations can improve the performance of a PB based structure comparison approach. The preference for the indel sites also seem to be confined to a few backbone conformations involving β-turns and helix C-caps. These are mainly associated with short loops joining the regular secondary structures that mediate a reversal in the chain direction. Rare β-turns of type I’ and II’ are also identified as preferred sites for insertions. PMID:22745680

NASA Workshop on Computational Structural Mechanics 1987, part 3

NASA Technical Reports Server (NTRS)

Sykes, Nancy P. (Editor)

1989-01-01

Computational Structural Mechanics (CSM) topics are explored. Algorithms and software for nonlinear structural dynamics, concurrent algorithms for transient finite element analysis, computational methods and software systems for dynamics and control of large space structures, and the use of multi-grid for structural analysis are discussed.

Embedded high-contrast distributed grating structures

DOEpatents

Zubrzycki, Walter J.; Vawter, Gregory A.; Allerman, Andrew A.

2002-01-01

A new class of fabrication methods for embedded distributed grating structures is claimed, together with optical devices which include such structures. These new methods are the only known approach to making defect-free high-dielectric contrast grating structures, which are smaller and more efficient than are conventional grating structures.

47 CFR 24.55 - Antenna structures; air navigation safety.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 47 Telecommunication 2 2013-10-01 2013-10-01 false Antenna structures; air navigation safety. 24... SERVICES PERSONAL COMMUNICATIONS SERVICES Technical Standards § 24.55 Antenna structures; air navigation safety. Licensees that own their antenna structures must not allow these antenna structures to become a...

47 CFR 17.4 - Antenna structure registration.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 1 2010-10-01 2010-10-01 false Antenna structure registration. 17.4 Section 17... ANTENNA STRUCTURES General Information § 17.4 Antenna structure registration. (a) Effective July 1, 1996, the owner of any proposed or existing antenna structure that requires notice of proposed construction...

47 CFR 17.4 - Antenna structure registration.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 47 Telecommunication 1 2011-10-01 2011-10-01 false Antenna structure registration. 17.4 Section 17... ANTENNA STRUCTURES General Information § 17.4 Antenna structure registration. (a) Effective July 1, 1996, the owner of any proposed or existing antenna structure that requires notice of proposed construction...

47 CFR 24.55 - Antenna structures; air navigation safety.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 47 Telecommunication 2 2011-10-01 2011-10-01 false Antenna structures; air navigation safety. 24... SERVICES PERSONAL COMMUNICATIONS SERVICES Technical Standards § 24.55 Antenna structures; air navigation safety. Licensees that own their antenna structures must not allow these antenna structures to become a...

47 CFR 73.1213 - Antenna structure, marking and lighting.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 47 Telecommunication 4 2013-10-01 2013-10-01 false Antenna structure, marking and lighting. 73... SERVICES RADIO BROADCAST SERVICES Rules Applicable to All Broadcast Stations § 73.1213 Antenna structure... of Antenna Structures), requires certain antenna structures to be painted and/or lighted in...

47 CFR 73.1213 - Antenna structure, marking and lighting.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 4 2010-10-01 2010-10-01 false Antenna structure, marking and lighting. 73... SERVICES RADIO BROADCAST SERVICES Rules Applicable to All Broadcast Stations § 73.1213 Antenna structure... of Antenna Structures), requires certain antenna structures to be painted and/or lighted in...

47 CFR 24.55 - Antenna structures; air navigation safety.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 47 Telecommunication 2 2012-10-01 2012-10-01 false Antenna structures; air navigation safety. 24... SERVICES PERSONAL COMMUNICATIONS SERVICES Technical Standards § 24.55 Antenna structures; air navigation safety. Licensees that own their antenna structures must not allow these antenna structures to become a...

47 CFR 73.1213 - Antenna structure, marking and lighting.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 47 Telecommunication 4 2012-10-01 2012-10-01 false Antenna structure, marking and lighting. 73... SERVICES RADIO BROADCAST SERVICES Rules Applicable to All Broadcast Stations § 73.1213 Antenna structure... of Antenna Structures), requires certain antenna structures to be painted and/or lighted in...

47 CFR 24.55 - Antenna structures; air navigation safety.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 2 2010-10-01 2010-10-01 false Antenna structures; air navigation safety. 24... SERVICES PERSONAL COMMUNICATIONS SERVICES Technical Standards § 24.55 Antenna structures; air navigation safety. Licensees that own their antenna structures must not allow these antenna structures to become a...

47 CFR 24.55 - Antenna structures; air navigation safety.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 47 Telecommunication 2 2014-10-01 2014-10-01 false Antenna structures; air navigation safety. 24... SERVICES PERSONAL COMMUNICATIONS SERVICES Technical Standards § 24.55 Antenna structures; air navigation safety. Licensees that own their antenna structures must not allow these antenna structures to become a...

47 CFR 73.1213 - Antenna structure, marking and lighting.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 47 Telecommunication 4 2011-10-01 2011-10-01 false Antenna structure, marking and lighting. 73... SERVICES RADIO BROADCAST SERVICES Rules Applicable to All Broadcast Stations § 73.1213 Antenna structure... of Antenna Structures), requires certain antenna structures to be painted and/or lighted in...

47 CFR 73.1213 - Antenna structure, marking and lighting.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 47 Telecommunication 4 2014-10-01 2014-10-01 false Antenna structure, marking and lighting. 73... SERVICES RADIO BROADCAST SERVICES Rules Applicable to All Broadcast Stations § 73.1213 Antenna structure... of Antenna Structures), requires certain antenna structures to be painted and/or lighted in...

46 CFR 154.176 - Longitudinal contiguous hull structure.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 5 2010-10-01 2010-10-01 false Longitudinal contiguous hull structure. 154.176 Section... Equipment Hull Structure § 154.176 Longitudinal contiguous hull structure. (a) The longitudinal contiguous hull structure of a vessel having cargo containment systems without secondary barriers must meet the...

Low-loss, high-speed, high-{Tc} superconducting bearings

DOEpatents

Hull, J.R.; Mulcahy, T.M.; Uherka, K.L.

1996-07-30

A flywheel energy storage device is disclosed including an iron structure disposed for rotation adjacent a stationary superconductor material structure and a stationary permanent magnet. The stationary permanent magnet levitates the iron structure while the superconductor structure can stabilize and levitate the rotating iron structure. 15 figs.

46 CFR 154.174 - Transverse contiguous hull structure.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 5 2010-10-01 2010-10-01 false Transverse contiguous hull structure. 154.174 Section... Equipment Hull Structure § 154.174 Transverse contiguous hull structure. (a) The transverse contiguous hull...) The transverse contiguous hull structure of a vessel having cargo containment systems with secondary...

14 CFR 29.571 - Fatigue Tolerance Evaluation of Metallic Structure.

Code of Federal Regulations, 2013 CFR

2013-01-01

... Structure. 29.571 Section 29.571 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF... Evaluation § 29.571 Fatigue Tolerance Evaluation of Metallic Structure. (a) A fatigue tolerance evaluation of... Administrator. (d) Considering all rotorcraft structure, structural elements, and assemblies, each PSE must be...

14 CFR 29.571 - Fatigue Tolerance Evaluation of Metallic Structure.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Structure. 29.571 Section 29.571 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF... Evaluation § 29.571 Fatigue Tolerance Evaluation of Metallic Structure. (a) A fatigue tolerance evaluation of... Administrator. (d) Considering all rotorcraft structure, structural elements, and assemblies, each PSE must be...

30 CFR 75.1708 - Surface structures, fireproofing.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Surface structures, fireproofing. 75.1708... structures, fireproofing. [Statutory Provisions] After March 30, 1970, all structures erected on the surface within 100 feet of any mine opening shall be of fireproof construction. Unless structures existing on or...

47 CFR 17.17 - Existing structures.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 1 2010-10-01 2010-10-01 false Existing structures. 17.17 Section 17.17... STRUCTURES Federal Aviation Administration Notification Criteria § 17.17 Existing structures. (a) The requirements found in § 17.23 relating to painting and lighting of antenna structures shall not apply to those...