Strand displacement synthesis by yeast DNA polymerase ε

PubMed Central

Ganai, Rais A.; Zhang, Xiao-Ping; Heyer, Wolf-Dietrich; Johansson, Erik

2016-01-01

DNA polymerase ε (Pol ε) is a replicative DNA polymerase with an associated 3′–5′ exonuclease activity. Here, we explored the capacity of Pol ε to perform strand displacement synthesis, a process that influences many DNA transactions in vivo. We found that Pol ε is unable to carry out extended strand displacement synthesis unless its 3′–5′ exonuclease activity is removed. However, the wild-type Pol ε holoenzyme efficiently displaced one nucleotide when encountering double-stranded DNA after filling a gap or nicked DNA. A flap, mimicking a D-loop or a hairpin structure, on the 5′ end of the blocking primer inhibited Pol ε from synthesizing DNA up to the fork junction. This inhibition was observed for Pol ε but not with Pol δ, RB69 gp43 or Pol η. Neither was Pol ε able to extend a D-loop in reconstitution experiments. Finally, we show that the observed strand displacement synthesis by exonuclease-deficient Pol ε is distributive. Our results suggest that Pol ε is unable to extend the invading strand in D-loops during homologous recombination or to add more than two nucleotides during long-patch base excision repair. Our results support the hypothesis that Pol ε participates in short-patch base excision repair and ribonucleotide excision repair. PMID:27325747

Biomechanical comparison of fixation methods in transverse patella fractures.

PubMed

Scilaris, T A; Grantham, J L; Prayson, M J; Marshall, M P; Hamilton, J J; Williams, J L

1998-01-01

To compare monofilament wire versus braided cable for stabilizing transverse patella fractures using the modified AO tension band technique. A randomized blocked (paired) study comparing two fixation methods. Statistical analysis was performed using a nested repeated measures analysis, followed by Bonferroni post hoc testing. Seven paired embalmed knees (mean age 71.8 years, SD 14.6 years) were dissected, and transverse fractures were simulated. The knees were reduced and randomly fixed by either two parallel 0.062-inch Kirschner wires with a 1.0-millimeter-diameter 316L stainless steel monofilament wire tension loop or two Kirschner wires with a 1.0-millimeter-diameter 316L stainless steel braided cable tension loop. Knees were tested by applying a cyclic load through the suprapatellar tendon between twenty and 300 newtons for thirty cycles. The maximum fracture displacement increased with each cycle of loading for both the braided cable and monofilament wire tension loop configurations (p = 0.0001). The average peak displacement at the thirtieth cycle was 2.25 millimeters for monofilament wire and 0.73 millimeters for the cable. When comparing both methods for all cycles, the braided cable allowed less fracture displacement than did the monofilament wire (p = 0.002), and the rate of increase per cycle of maximum fracture displacement was less for the cable than for the wire (p = 0.0001). In transverse, noncomminuted patella fractures, fixation with two Kirschner wires and a 1.0-millimeter braided cable tension loop was superior to the monofilament wire tension loop. Most importantly, the braided cable afforded more predictable results during cyclic loading.

Simultaneous quantitation of nicotinamide riboside, nicotinamide mononucleotide and nicotinamide adenine dinucleotide in milk by a novel enzyme-coupled assay.

PubMed

Ummarino, Simone; Mozzon, Massimo; Zamporlini, Federica; Amici, Adolfo; Mazzola, Francesca; Orsomando, Giuseppe; Ruggieri, Silverio; Raffaelli, Nadia

2017-04-15

Nicotinamide riboside, the most recently discovered form of vitamin B3, and its phosphorylated form nicotinamide mononucleotide, have been shown to be potent supplements boosting intracellular nicotinamide adenine dinucleotide (NAD) levels, thus preventing or ameliorating metabolic and mitochondrial diseases in mouse models. Here we report for the first time on the simultaneous quantitation of nicotinamide riboside, nicotinamide mononucleotide and NAD in milk by means of a fluorometric, enzyme-coupled assay. Application of this assay to milk from different species revealed that the three vitamers were present in human and donkey milk, while being selectively distributed in the other milks. Human milk was the richest source of nicotinamide mononucleotide. Overall, the three vitamers accounted for a significant fraction of total vitamin B3 content. Pasteurization did not affect the bovine milk content of nicotinamide riboside, whereas UHT processing fully destroyed the vitamin. In human milk, NAD levels were significantly affected by the lactation time. Copyright © 2016 Elsevier Ltd. All rights reserved.

Conformational energy landscape of the acyl pocket loop in acetylcholinesterase: a Monte Carlo-generalized Born model study.

PubMed

Carlacci, Louis; Millard, Charles B; Olson, Mark A

2004-10-01

The X-ray crystal structure of the reaction product of acetylcholinesterase (AChE) with the inhibitor diisopropylphosphorofluoridate (DFP) showed significant structural displacement in a loop segment of residues 287-290. To understand this conformational selection, a Monte Carlo (MC) simulation study was performed of the energy landscape for the loop segment. A computational strategy was applied by using a combined simulated annealing and room temperature Metropolis sampling approach with solvent polarization modeled by a generalized Born (GB) approximation. Results from thermal annealing reveal a landscape topology of broader basin opening and greater distribution of energies for the displaced loop conformation, while the ensemble average of conformations at 298 K favored a shift in populations toward the native by a free-energy difference in good agreement with the estimated experimental value. Residue motions along a reaction profile of loop conformational reorganization are proposed where Arg-289 is critical in determining electrostatic effects of solvent interaction versus Coulombic charging.

Dynamics of a multi-thermal loop in the solar corona

NASA Astrophysics Data System (ADS)

Nisticò, G.; Anfinogentov, S.; Nakariakov, V. M.

2014-10-01

Context. We present an observation of a long-living multi-thermal coronal loop, visible in different extreme ultra-violet wavebands of SDO/AIA in a quiet-Sun region close to the western solar limb. Aims: Analysis of persistent kink displacements of the loop seen in different bandpasses that correspond to different temperatures of the plasma allows sub-resolution structuring of the loop to be revealed. Methods: A vertically oriented slit is taken at the loop top, and time-distance maps are made from it. Loop displacements in time-distance maps are automatically tracked with the Gaussian fitting technique and fitted with a sinusoidal function that is "guessed". Wavelet transforms are further used in order to quantify the periodicity variation in time of the kink oscillations. Results: The loop strands are found to oscillate with the periods ranging between 3 and 15 min. The oscillations are observed in intermittent regime with temporal changes in the period and amplitude. The oscillations are different at three analysed wavelengths. Conclusions: This finding suggests that the loop-like threads seen at different wavelengths are not co-spatial, hence that the loop consists of several multi-thermal strands. The detected irregularity of the oscillations can be associated with a stochastic driver acting at the footpoints of the loop. A movie associated to Fig. 1 is available in electronic form at http://www.aanda.org

Strand displacement synthesis by yeast DNA polymerase ε.

PubMed

Ganai, Rais A; Zhang, Xiao-Ping; Heyer, Wolf-Dietrich; Johansson, Erik

2016-09-30

DNA polymerase ε (Pol ε) is a replicative DNA polymerase with an associated 3'-5' exonuclease activity. Here, we explored the capacity of Pol ε to perform strand displacement synthesis, a process that influences many DNA transactions in vivo We found that Pol ε is unable to carry out extended strand displacement synthesis unless its 3'-5' exonuclease activity is removed. However, the wild-type Pol ε holoenzyme efficiently displaced one nucleotide when encountering double-stranded DNA after filling a gap or nicked DNA. A flap, mimicking a D-loop or a hairpin structure, on the 5' end of the blocking primer inhibited Pol ε from synthesizing DNA up to the fork junction. This inhibition was observed for Pol ε but not with Pol δ, RB69 gp43 or Pol η. Neither was Pol ε able to extend a D-loop in reconstitution experiments. Finally, we show that the observed strand displacement synthesis by exonuclease-deficient Pol ε is distributive. Our results suggest that Pol ε is unable to extend the invading strand in D-loops during homologous recombination or to add more than two nucleotides during long-patch base excision repair. Our results support the hypothesis that Pol ε participates in short-patch base excision repair and ribonucleotide excision repair. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Illusory spirals and loops in crystal growth

PubMed Central

Shtukenberg, Alexander G.; Zhu, Zina; Bhandari, Misha; Song, Pengcheng; Kahr, Bart; Ward, Michael D.

2013-01-01

The theory of dislocation-controlled crystal growth identifies a continuous spiral step with an emergent lattice displacement on a crystal surface; a mechanistic corollary is that closely spaced, oppositely winding spirals merge to form concentric loops. In situ atomic force microscopy of step propagation on pathological l-cystine crystals did indeed show spirals and islands with step heights of one lattice displacement. We show by analysis of the rates of growth of smaller steps only one molecule high that the major morphological spirals and loops are actually consequences of the bunching of the smaller steps. The morphology of the bunched steps actually inverts the predictions of the theory: Spirals arise from pairs of dislocations, loops from single dislocations. Only through numerical simulation of the growth is it revealed how normal growth of anisotropic layers of molecules within the highly symmetrical crystals can conspire to create features in apparent violation of the classic theory. PMID:24101507

Multi-mode ultrasonic welding control and optimization

DOEpatents

Tang, Jason C.H.; Cai, Wayne W

2013-05-28

A system and method for providing multi-mode control of an ultrasonic welding system. In one embodiment, the control modes include the energy of the weld, the time of the welding process and the compression displacement of the parts being welded during the welding process. The method includes providing thresholds for each of the modes, and terminating the welding process after the threshold for each mode has been reached, the threshold for more than one mode has been reached or the threshold for one of the modes has been reached. The welding control can be either open-loop or closed-loop, where the open-loop process provides the mode thresholds and once one or more of those thresholds is reached the welding process is terminated. The closed-loop control provides feedback of the weld energy and/or the compression displacement so that the weld power and/or weld pressure can be increased or decreased accordingly.

A displacement pump procedure to load extracts for automated gel permeation chromatography.

PubMed

Daft, J; Hopper, M; Hensley, D; Sisk, R

1990-01-01

Automated gel permeation chromatography (GPC) effectively separates lipids from pesticides in sample extracts that contain fat. Using a large syringe to load sample extracts manually onto GPC models having 5 mL holding loops is awkward, slow, and potentially hazardous. Loading with a small-volume displacement pump, however, is convenient and fast (ca 1 loop every 20 s). And more importantly, the analyst is not exposed to toxic organic vapors because the loading pump and its connecting lines do not leak in the way that a syringe does.

Reciprocating Magnetic Refrigerator

NASA Technical Reports Server (NTRS)

Johnson, D. L.

1985-01-01

Unit cools to 4 K by adiabatic demagnetization. Two porous matrices of paramagnetic material gadolinium/gallium/garnet held in long piston called displacer, machined out of Micarta (phenol formaldehyde polymer). Holes in side of displacer allow heat-exchange fluid to flow to and through matrices within. Piston seals on displacer prevent substantial mixing of fluid in two loops. Magnetic refrigerator provides continuous rather than "one-shot" cooling.

Different mutation patterns of mitochondrial DNA displacement-loop in hepatocellular carcinomas induced by N-nitrosodiethylamine and a choline-deficient l-amino acid-defined diet in rats.

PubMed

Onishi, Mariko; Sokuza, Yui; Nishikawa, Tomoki; Mori, Chiharu; Uwataki, Kimiko; Honoki, Kanya; Tsujiuchi, Toshifumi

2007-10-12

Mutations of the mitochondria DNA (mtDNA) displacement loop (D-loop) were investigated to clarify different changes of exogenous and endogenous liver carcinogenesis in rats. We induced hepatocellular carcinomas (HCCs) in rats with N-nitrosodiethylamine (DEN) and a choline-deficient l-amino acid-defined (CDAA) diet. DNAs were extracted from 10 HCCs induced by DEN and 10 HCCs induced by the CDAA diet. To identify mutations in mtDNA D-loop, polymerase chain reaction (PCR)-single strand conformation polymorphism (SSCP) analysis, followed by nucleotide sequencing, was performed. Mutations were detected in 5 out of 10 HCCs (50%) induced by DEN. Four out of 5 mutations were G/C to A/T transitions at positions 15707, 15717, 15930, and 16087, and one T/A to C/G transition at position 15559. By contrast, no mutations were found in 10 HCCs induced by the CDAA diet. These results demonstrated that mutations in mtDNA D-loop occur in rat HCCs induced by DEN but not by the CDAA diet, suggesting that mtDNA D-loop is a target of exogenous liver carcinogenesis in rats.

Multifunctional transducer

NASA Technical Reports Server (NTRS)

Feldstein, C.; Lewis, G. W.; Culler, V. H.; Merrbaum, S. (Inventor)

1981-01-01

Several parameters of a small region of a muscle tissue or other object, can be simultaneously measured using with minimal traumatizing or damage of the object, a trifunctional transducer which can determine the force applied by a muscle fiber, the displacement of the fiber, and the change in thickness of the fiber. The transducer has three legs with inner ends joined together and outer ends formed to piece the tissue and remain within it. Two of the legs are relatively stiff, to measure force applied by the tissue, and a third leg is relatively flexible to measure displacement of the tissue relative to one or both stiff legs, and with the three legs lying in a common plane so that the force and displacement measurements all relate to the same direction of muscle movements. A flexible loop is attached to one of the stiff legs to measure changes in muscle thickness, with the upper end of the loop fixed to the leg and the lower end of the loop bearing against the surface of the tissue and being free to slide on the leg.

Power modulation based fiber-optic loop-sensor having a dual measurement range

NASA Astrophysics Data System (ADS)

Nguyen, Nguyen Q.; Gupta, Nikhil

2009-08-01

A fiber-optic sensor is investigated in this work for potential applications in structural health monitoring. The sensor, called fiber-loop-sensor, is based on bending an optical fiber beyond a critical radius to obtain intensity losses and calibrating the losses with respect to the applied force or displacement. Additionally, in the present case, the use of single-mode optical fibers allows the appearance of several resonance peaks in the transmitted power-displacement graph. The intensity of one of these resonances can be tracked in a narrow range to obtain high sensitivity. Experimental results show that the resolution of 10-4 N for force and 10-5 m for displacement can be obtained in these sensors. The sensors are calibrated for various loop radii and for various loading rates. They are also tested under loading-unloading conditions for over 104 cycles to observe their fatigue behavior. The sensors show very repeatable response and no degradation in performance under these test conditions. Simple construction and instrumentation, high sensitivity, and low cost are the advantages of these sensors.

Detection of the Second Harmonic of Decay-less Kink Oscillations in the Solar Corona

NASA Astrophysics Data System (ADS)

Duckenfield, T.; Anfinogentov, S. A.; Pascoe, D. J.; Nakariakov, V. M.

2018-02-01

EUV observations of a multi-thermal coronal loop, taken by the Atmospheric Imaging Assembly of the Solar Dynamics Observatory, which exhibits decay-less kink oscillations are presented. The data cube of the quiet-Sun coronal loop was passed through a motion magnification algorithm to accentuate transverse oscillations. Time–distance maps are made from multiple slits evenly spaced along the loop axis and oriented orthogonal to the loop axis. Displacements of the intensity peak are tracked to generate time series of the loop displacement. Fourier analysis on the time series shows the presence of two periods within the loop: {P}1={10.3}-1.7+1.5 minutes and {P}2={7.4}-1.3+1.1 minutes. The longer period component is greatest in amplitude at the apex and remains in phase throughout the loop length. The shorter period component is strongest further down from the apex on both legs and displays an anti-phase behavior between the two loop legs. We interpret these results as the coexistence of the fundamental and second harmonics of the standing kink mode within the loop in the decay-less oscillation regime. An illustration of seismological application using the ratio P 1/2P 2 ∼ 0.7 to estimate the density scale height is presented. The existence of multiple harmonics has implications for understanding the driving and damping mechanisms for decay-less oscillations and adds credence to their interpretation as standing kink mode oscillations.

Assimilation of nicotinamide mononucleotide requires periplasmic AphA phosphatase in Salmonella enterica.

PubMed

Grose, Julianne H; Bergthorsson, Ulfar; Xu, Yaping; Sterneckert, Jared; Khodaverdian, Behzad; Roth, John R

2005-07-01

Salmonella enterica can obtain pyridine from exogenous nicotinamide mononucleotide (NMN) by three routes. In route 1, nicotinamide is removed from NMN in the periplasm and enters the cell as the free base. In route 2, described here, phosphate is removed from NMN in the periplasm by acid phosphatase (AphA), and the produced nicotinamide ribonucleoside (NmR) enters the cell via the PnuC transporter. Internal NmR is then converted back to NMN by the NmR kinase activity of NadR. Route 3 is seen only in pnuC* transporter mutants, which import NMN intact and can therefore grow on lower levels of NMN. Internal NMN produced by either route 2 or route 3 is deamidated to nicotinic acid mononucleotide and converted to NAD by the biosynthetic enzymes NadD and NadE.

An optimal open/closed-loop control method with application to a pre-stressed thin duralumin plate

NASA Astrophysics Data System (ADS)

Nadimpalli, Sruthi Raju

The excessive vibrations of a pre-stressed duralumin plate, suppressed by a combination of open-loop and closed-loop controls, also known as open/closed-loop control, is studied in this thesis. The two primary steps involved in this process are: Step (I) with an assumption that the closed-loop control law is proportional, obtain the optimal open-loop control by direct minimization of the performance measure consisting of energy at terminal time and a penalty on open-loop control force via calculus of variations. If the performance measure also involves a penalty on closed-loop control effort then a Fourier based method is utilized. Step (II) the energy at terminal time is minimized numerically to obtain optimal values of feedback gains. The optimal closed-loop control gains obtained are used to describe the displacement and the velocity of open-loop, closed-loop and open/closed-loop controlled duralumin plate.

Canonical DNA Repair Pathways Influence R-Loop-Driven Genome Instability.

PubMed

Stirling, Peter C; Hieter, Philip

2017-10-27

DNA repair defects create cancer predisposition in humans by fostering a higher rate of mutations. While DNA repair is quite well characterized, recent studies have identified previously unrecognized relationships between DNA repair and R-loop-mediated genome instability. R-loops are three-stranded nucleic acid structures in which RNA binds to genomic DNA to displace a loop of single-stranded DNA. Mutations in homologous recombination, nucleotide excision repair, crosslink repair, and DNA damage checkpoints have all now been linked to formation and function of transcription-coupled R-loops. This perspective will summarize recent literature linking DNA repair to R-loop-mediated genomic instability and discuss how R-loops may contribute to mutagenesis in DNA-repair-deficient cancers. Copyright © 2016 Elsevier Ltd. All rights reserved.

40 CFR 63.166 - Standards: Sampling connection systems.

Code of Federal Regulations, 2013 CFR

2013-07-01

... defined in 40 CFR part 261. (c) In-situ sampling systems and sampling systems without purges are exempt..., closed-loop, or closed-vent system, except as provided in § 63.162(b) of this subpart. Gases displaced...-purge, closed-loop, or closed-vent system as required in paragraph (a) of this section shall: (1) Return...

Variable-Displacement Hydraulic Drive Unit

NASA Technical Reports Server (NTRS)

Lang, D. J.; Linton, D. J.; Markunas, A.

1986-01-01

Hydraulic power controlled through multiple feedback loops. In hydraulic drive unit, power closely matched to demand, thereby saving energy. Hydraulic flow to and from motor adjusted by motor-control valve connected to wobbler. Wobbler angle determines motor-control-valve position, which in turn determines motor displacement. Concept applicable to machine tools, aircraft controls, and marine controls.

Studies of O18 impurity trapping at interstitial dislocation loops in ion implanted Fe (1 1 0) by ion channeling and ab initio calculations

NASA Astrophysics Data System (ADS)

Mathayan, Vairavel; Kothalamuthu, Saravanan; Gnanasekaran, Jaiganesh; Balakrishnan, Sundaravel; Panigrahi, Binaykumar

2018-01-01

The O18 and self ions are implanted at same depth in Fe (1 1 0) crystal and annealed to study the oxygen trapping under excess self interstitial defects. Rutherford backscattering spectrometry, nuclear reaction analysis and channeling measurements have been performed to determine the lattice site position of O18. The presence of dislocation loops is confirmed by energy-dependent dechanneling parameter measurements. From the tilt angular scans of Fe and O18 signals along 〈1 0 0〉, 〈1 1 0〉 axes, O18 is found to be displaced 0.2 Å from tetrahedral towards octahedral interstitial site in O18. Similar lattice site location of oxygen with the displacement of 0.37 Å is predicted by density functional theory calculations for the interaction of oxygen with 〈1 0 0〉 interstitial dislocation loop structure. Our results provide strong evidence on oxygen trapping at interstitial dislocation loops in the presence of excess interstitial defects in iron.

Eddy currents in a conducting sphere

NASA Technical Reports Server (NTRS)

Bergman, John; Hestenes, David

1986-01-01

This report analyzes the eddy current induced in a solid conducting sphere by a sinusoidal current in a circular loop. Analytical expressions for the eddy currents are derived as a power series in the vectorial displacement of the center of the sphere from the axis of the loop. These are used for first order calculations of the power dissipated in the sphere and the force and torque exerted on the sphere by the electromagnetic field of the loop.

Did template-directed nucleation precede molecular replication?

NASA Technical Reports Server (NTRS)

Orgel, Leslie E.

1986-01-01

It is proposed that mononucleotides incorporated into the surfaces of microcrystals of inorganic phosphates such as hydroxyapatite can act as templates to assemble complementary mononucleotides from solution, and that the phosphate groups of the assembled nucleotides can facilitate nucleation of a second hydroxyapatite crystal. This would provide a mechanism of replication that is subject to natural selection. The possible role of a replicating system of this kind in the origins of life on the earth is discussed.

Loop and void damage during heavy ion irradiation on nanocrystalline and coarse grained tungsten: Microstructure, effect of dpa rate, temperature, and grain size

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

El-Atwani, O.; Esquivel, E.; Efe, M.

Displacement damage, through heavy ion irradiation was studied on two tungsten grades (coarse grained tungsten (CGW) and nanocrystalline and ultrafine grained tungsten (NCW)) using different displacement per atom rates and different irradiation temperatures (RT and 1050 K). Percentage of <111> and <100> type loops at the irradiation conditions was determined. Irradiation damage in the microstructure was quantified using average loop areas and densities (method A) and loop areal fraction in the grain matrices under 2-beam diffraction conditions (method B). Average values of <111> and <100> loops were calculated from method A. Loop coalescence was shown to occur for CGW atmore » 0.25 dpa. Using both methods of quantifying microstructural damage, no effect of dpa rate was observed and damage in CGW was shown to be the same at RT and 1050 K. Swelling from voids observed at 1050 K was quantified. The loop damage in NCW was compared to CGW at the same diffraction and imaging conditions. NCW was shown to possess enhanced irradiation resistance at RT regarding loop damage and higher swelling resistance at 1050 K compared to CGW. For irradiation at 1050 K, the NCW was shown to have a similar defect densities to the CGW which is attributed to higher surface effects in the CGW, vacancy loop growth to voids and a better sink efficiency in the CGW deduced from the vacancy distribution profiles from Kinetic Monte Carlo simulations. Loop density and swelling was shown to have similar values in grains sizes that range from 80-600 nm. No loop or void denuded zones occurred at any of the irradiation conditions. This work has a collection of experiments and conclusions that are of vital importance to materials and nuclear communities.« less

Loop and void damage during heavy ion irradiation on nanocrystalline and coarse grained tungsten: Microstructure, effect of dpa rate, temperature, and grain size

DOE PAGES

El-Atwani, O.; Esquivel, E.; Efe, M.; ...

2018-02-20

Displacement damage, through heavy ion irradiation was studied on two tungsten grades (coarse grained tungsten (CGW) and nanocrystalline and ultrafine grained tungsten (NCW)) using different displacement per atom rates and different irradiation temperatures (RT and 1050 K). Percentage of <111> and <100> type loops at the irradiation conditions was determined. Irradiation damage in the microstructure was quantified using average loop areas and densities (method A) and loop areal fraction in the grain matrices under 2-beam diffraction conditions (method B). Average values of <111> and <100> loops were calculated from method A. Loop coalescence was shown to occur for CGW atmore » 0.25 dpa. Using both methods of quantifying microstructural damage, no effect of dpa rate was observed and damage in CGW was shown to be the same at RT and 1050 K. Swelling from voids observed at 1050 K was quantified. The loop damage in NCW was compared to CGW at the same diffraction and imaging conditions. NCW was shown to possess enhanced irradiation resistance at RT regarding loop damage and higher swelling resistance at 1050 K compared to CGW. For irradiation at 1050 K, the NCW was shown to have a similar defect densities to the CGW which is attributed to higher surface effects in the CGW, vacancy loop growth to voids and a better sink efficiency in the CGW deduced from the vacancy distribution profiles from Kinetic Monte Carlo simulations. Loop density and swelling was shown to have similar values in grains sizes that range from 80-600 nm. No loop or void denuded zones occurred at any of the irradiation conditions. This work has a collection of experiments and conclusions that are of vital importance to materials and nuclear communities.« less

Identification of Isn1 and Sdt1 as Glucose- and Vitamin-regulated Nicotinamide Mononucleotide and Nicotinic Acid Mononucleotide 5′-Nucleotidases Responsible for Production of Nicotinamide Riboside and Nicotinic Acid Riboside*

PubMed Central

Bogan, Katrina L.; Evans, Charles; Belenky, Peter; Song, Peng; Burant, Charles F.; Kennedy, Robert; Brenner, Charles

2009-01-01

Recently, we discovered that nicotinamide riboside and nicotinic acid riboside are biosynthetic precursors of NAD+, which are utilized through two pathways consisting of distinct enzymes. In addition, we have shown that exogenously supplied nicotinamide riboside is imported into yeast cells by a dedicated transporter, and it extends replicative lifespan on high glucose medium. Here, we show that nicotinamide riboside and nicotinic acid riboside are authentic intracellular metabolites in yeast. Secreted nicotinamide riboside was detected with a biological assay, and intracellular levels of nicotinamide riboside, nicotinic acid riboside, and other NAD+ metabolites were determined by a liquid chromatography-mass spectrometry method. A biochemical genomic screen indicated that three yeast enzymes possess nicotinamide mononucleotide 5′-nucleotidase activity in vitro. Metabolic profiling of knock-out mutants established that Isn1 and Sdt1 are responsible for production of nicotinamide riboside and nicotinic acid riboside in cells. Isn1, initially classified as an IMP-specific 5′-nucleotidase, and Sdt1, initially classified as a pyrimidine 5′-nucleotidase, are additionally responsible for dephosphorylation of pyridine mononucleotides. Sdt1 overexpression is growth-inhibitory to cells in a manner that depends on its active site and correlates with reduced cellular NAD+. Expression of Isn1 protein is positively regulated by the availability of nicotinic acid and glucose. These results reveal unanticipated and highly regulated steps in NAD+ metabolism. PMID:19846558

Identification of Isn1 and Sdt1 as glucose- and vitamin-regulated nicotinamide mononucleotide and nicotinic acid mononucleotide [corrected] 5'-nucleotidases responsible for production of nicotinamide riboside and nicotinic acid riboside.

PubMed

Bogan, Katrina L; Evans, Charles; Belenky, Peter; Song, Peng; Burant, Charles F; Kennedy, Robert; Brenner, Charles

2009-12-11

Recently, we discovered that nicotinamide riboside and nicotinic acid riboside are biosynthetic precursors of NAD(+), which are utilized through two pathways consisting of distinct enzymes. In addition, we have shown that exogenously supplied nicotinamide riboside is imported into yeast cells by a dedicated transporter, and it extends replicative lifespan on high glucose medium. Here, we show that nicotinamide riboside and nicotinic acid riboside are authentic intracellular metabolites in yeast. Secreted nicotinamide riboside was detected with a biological assay, and intracellular levels of nicotinamide riboside, nicotinic acid riboside, and other NAD(+) metabolites were determined by a liquid chromatography-mass spectrometry method. A biochemical genomic screen indicated that three yeast enzymes possess nicotinamide mononucleotide 5'-nucleotidase activity in vitro. Metabolic profiling of knock-out mutants established that Isn1 and Sdt1 are responsible for production of nicotinamide riboside and nicotinic acid riboside in cells. Isn1, initially classified as an IMP-specific 5'-nucleotidase, and Sdt1, initially classified as a pyrimidine 5'-nucleotidase, are additionally responsible for dephosphorylation of pyridine mononucleotides. Sdt1 overexpression is growth-inhibitory to cells in a manner that depends on its active site and correlates with reduced cellular NAD(+). Expression of Isn1 protein is positively regulated by the availability of nicotinic acid and glucose. These results reveal unanticipated and highly regulated steps in NAD(+) metabolism.

Documentation of programs that compute 1) quasi-static tilts produced by an expanding dislocation loop in an elastic and viscoelastic material, and 2) surface shear stresses, strains, and shear displacements produced by screw dislocations in a vertical slab with modulus contrast

USGS Publications Warehouse

McHugh, Stuart

1976-01-01

The material in this report can be grouped into two categories: 1) programs that compute tilts produced by a vertically oriented expanding rectangular dislocation loop in an elastic or viscoelastic material and 2) programs that compute the shear stresses, strains, and shear displacements in a three-phase half-space (i.e. a half-space containing a vertical slab). Each section describes the relevant theory, and provides a detailed guide to the operation of the programs. A series of examples is provided at the end of each section.

Top3-Rmi1 dissolve Rad51-mediated D loops by a topoisomerase-based mechanism.

PubMed

Fasching, Clare L; Cejka, Petr; Kowalczykowski, Stephen C; Heyer, Wolf-Dietrich

2015-02-19

The displacement loop (D loop) is a DNA strand invasion product formed during homologous recombination. Disruption of nascent D loops prevents recombination, and during synthesis-dependent strand annealing (SDSA), disruption of D loops extended by DNA polymerase ensures a non-crossover outcome. The proteins implicated in D loop disruption are DNA motor proteins/helicases that act by moving DNA junctions. Here we report that D loops can also be disrupted by DNA topoisomerase 3 (Top3), and this disruption depends on Top3's catalytic activity. Yeast Top3 specifically disrupts D loops mediated by yeast Rad51/Rad54; protein-free D loops or D loop mediated by bacterial RecA protein or human RAD51/RAD54 resist dissolution. Also, the human Topoisomerase IIIa-RMI1-RMI2 complex is capable of dissolving D loops. Consistent with genetic data, we suggest that the extreme growth defect and hyper-recombination phenotype of Top3-deficient yeast cells is partially a result of unprocessed D loops. Copyright © 2015 Elsevier Inc. All rights reserved.

A study of the effect of helium concentration and displacement damage on the microstructure of helium ion irradiated tungsten

NASA Astrophysics Data System (ADS)

Harrison, R. W.; Greaves, G.; Hinks, J. A.; Donnelly, S. E.

2017-11-01

Transmission electron microscopy (TEM) with in-situ He ion irradiation has been used to examine the damage microstructure of W when varying the helium concentration to displacement damage ratio, irradiation temperature and total dose. Irradiations employed 15, 60 or 85 keV He ions, at temperatures between 500 and 1000 °C up to doses of ∼3.0 DPA. Once nucleated and grown to an observable size in the TEM, bubble diameter as a function of irradiation dose did not measurably increase at irradiation temperatures of 500 °C between 1.0 and 3.0 DPA; this is attributed to the low mobility of vacancies and He/vacancy complexes at these temperatures. Bubble diameter increased slightly for irradiation temperatures of 750 °C and rapidly increased when irradiated at 1000 °C. Dislocation loops were observed at irradiation temperatures of 500 and 750 °C and no loops were observed at 1000 °C. Burgers vectors of the dislocations were determined to be b = ±½<111> type only and both vacancy and interstitial loops were observed. The proportion of interstitial loops increased with He-appm/DPA ratio and this is attributed to the concomitant increase in bubble areal density, which reduces the vacancy flux for both the growth of vacancy-type loops and the annihilation of interstitial clusters.

[Three-dimensional finite element analysis of maxillary incisor retraction with step-shaped vertical closing loop].

PubMed

Zhang, Sheng; Mai, Li-xiang; Liu, Cong-hua; Wang, Da-wei

2011-07-01

To investigate the displacement and stress distribution of upper incisors in three-dimensional (3D) space controlled by step-shaped vertical closing loop. The maxillary teeth and alveolar bone of a volunteer with normal occlusion were scanned with 3D spiral CT. Modeling and calculation were only carried out on right upper central incisor, lateral incisor and their alveolar bone in order to simplify the procedures. A 3D finite element model of archwire-brackets-upper incisors and periodontal tissues was developed using Ansys finite element package. Finally, a 3D finite element model of archwire-brackets-upper incisors and periodontal tissues was established based on mirror symmetry principle. The displacement of maxillary incisors and stress distribution in periodontal tissues were analyzed. When step-shaped vertical closing loop was simply drew back 1 mm, the maximum displacement of upper central incisor in labial and lingual direction were 5.29 × 10(-2) and 0.71 × 10(-2) mm; 10.47 × 10(-3) and 10.20 × 10(-3) mm in gingival and occlusal direction, 10.26 × 10(-3) and 1.63 × 10(-3) mm in medial and distal direction; the maximum displacement of upper lateral incisor in labial and lingual direction were 3.31 × 10(-2) and 0.41 × 10(-2) mm, 10.52 × 10(-3) and 5.10 × 10(-3) mm in gingival and occlusal direction, 6.29 × 10(-3) and 4.64 × 10(-3) mm in medial and distal direction, the displacement trend of them were moving lingually and gingivally similar to bodily movement. The stress peach of upper central incisor, periodontal ligament and alveolar bone were 31.35, 2.52 and 4.64 MPa, the stress peach of upper lateral incisor, periodontal ligament and alveolar bone were 19.59, 1.28 and 4.12 Mpa, the stress distribution of them were similar and the periodontal ligament buffered the stress imposed on the tooth.

Magnetic forces in high-Tc superconducting bearings

NASA Technical Reports Server (NTRS)

Moon, F. C.

1991-01-01

In September 1987, researchers at Cornell levitated a small rotor on superconducting bearings at 10,000 rpm. In April 1989, a speed of 120,000 rpm was achieved in a passive bearing with no active control. The bearing material used was YBa2Cu307. There is no evidence that the rotation speed has any significant effect on the lift force. Magnetic force measurements between a permanent rare-earth magnet and high T(sub c) superconducting material versus vertical and lateral displacements were made. A large hysteresis loop results for large displacements, while minor loops result for small displacements. These minor loops seem to give a slope proportional to the magnetic stiffness, and are probably indicative of flux pinning forces. Experiments of rotary speed versus time show a linear decay in a vacuum. Measurements of magnetic dipole over a high-T(sub c) superconducting disc of YBCO show that the lateral vibrations of levitated rotors were measured which indicates that transverse flux motion in the superconductor will create dissipation. As a result of these force measurements, an optimum shape for the superconductor bearing pads which gives good lateral and axial stability was designed. Recent force measurements on melt-quench processed superconductors indicate a substantial increase in levitation force and magnetic stiffness over free sintered materials. As a result, application of high-T(sub c) superconducting bearings are beginning to show great promise at this time.

Single nucleotide polymorphisms in the mitochondrial displacement loop and outcome of esophageal squamous cell carcinoma.

PubMed

Zhang, Ruixing; Wang, Rui; Zhang, Fengbin; Wu, Chensi; Fan, Haiyan; Li, Yan; Wang, Cuiju; Guo, Zhanjun

2010-11-26

Accumulation of single nucleotide polymorphisms (SNPs) in the displacement loop (D-loop) of mitochondrial DNA (mtDNA) has been described for different types of cancers and might be associated with cancer risk and disease outcome. We used a population-based series of esophageal squamous cell carcinoma (ESCC) patients for investigating the prediction power of SNPs in mitochondrial D-loop. The D-loop region of mtDNA was sequenced for 60 ESCC patients recorded in the Fourth Hospital of Hebei Medical University between 2003 and 2004. The 5 year survival curve were calculated with the Kaplan-Meier method and compared by the log-rank test at each SNP site, a multivariate survival analysis was also performed with the Cox proportional hazards method. The SNP sites of nucleotides 16274G/A, 16278C/T and 16399A/G were identified for prediction of post-operational survival by the log-rank test. In an overall multivariate analysis, the 16278 and 16399 alleles were identified as independent predictors of ESCC outcome. The length of survival of patients with the minor allele 16278T genotype was significantly shorter than that of patients with 16278C at the 16278 site (relative risk, 3.001; 95% CI, 1.029 - 8.756; p = 0.044). The length of survival of patients with the minor allele 16399G genotype was significantly shorter than that of patients with the more frequent allele 16399A at the 16399 site in ESCC patients (relative risk, 3.483; 95% CI, 1.068 - 11.359; p = 0.039). Genetic polymorphisms in the D-loop are independent prognostic markers for patients with ESCC. Accordingly, the analysis of genetic polymorphisms in the mitochondrial D-loop can help identify patient subgroups at high risk of a poor disease outcome.

Engineering Escherichia coli Nicotinic Acid Mononucleotide Adenylyltransferase for Fully Active Amidated NAD Biosynthesis.

PubMed

Wang, Xueying; Zhou, Yongjin J; Wang, Lei; Liu, Wujun; Liu, Yuxue; Peng, Chang; Zhao, Zongbao K

2017-07-01

NAD and its reduced form NADH function as essential redox cofactors and have major roles in determining cellular metabolic features. NAD can be synthesized through the deamidated and amidated pathways, for which the key reaction involves adenylylation of nicotinic acid mononucleotide (NaMN) and nicotinamide mononucleotide (NMN), respectively. In Escherichia coli , NAD de novo biosynthesis depends on the protein NadD-catalyzed adenylylation of NaMN to nicotinic acid adenine dinucleotide (NaAD), followed by NAD synthase-catalyzed amidation. In this study, we engineered NadD to favor NMN for improved amidated pathway activity. We designed NadD mutant libraries, screened by a malic enzyme-coupled colorimetric assay, and identified two variants, 11B4 (Y84V/Y118D) and 16D8 (A86W/Y118N), with a high preference for NMN. Whereas in the presence of NMN both variants were capable of enabling the viability of cells of E. coli BW25113-derived NAD-auxotrophic strain YJE003, for which the last step of the deamidated pathway is blocked, the 16D8 expression strain could grow without exogenous NMN and accumulated a higher cellular NAD(H) level than BW25113 in the stationary phase. These mutants established fully active amidated NAD biosynthesis and offered a new opportunity to manipulate NAD metabolism for biocatalysis and metabolic engineering. IMPORTANCE Adenylylation of nicotinic acid mononucleotide (NaMN) and adenylylation of nicotinamide mononucleotide (NMN), respectively, are the key steps in the deamidated and amidated pathways for NAD biosynthesis. In most organisms, canonical NAD biosynthesis follows the deamidated pathway. Here we engineered Escherichia coli NaMN adenylyltransferase to favor NMN and expressed the mutant enzyme in an NAD-auxotrophic E. coli strain that has the last step of the deamidated pathway blocked. The engineered strain survived in M9 medium, which indicated the implementation of a functional amidated pathway for NAD biosynthesis. These results enrich our understanding of NAD biosynthesis and are valuable for manipulation of NAD homeostasis for metabolic engineering. Copyright © 2017 American Society for Microbiology.

Calibration and optimization of an x-ray bendable mirror using displacement-measuring sensors.

PubMed

Vannoni, Maurizio; Martín, Idoia Freijo; Music, Valerija; Sinn, Harald

2016-07-25

We propose a method to control and to adjust in a closed-loop a bendable x-ray mirror using displacement-measuring devices. For this purpose, the usage of capacitive and interferometric sensors is investigated and compared. We installed the sensors in a bender setup and used them to continuously measure the position and shape of the mirror in the lab. The sensors are vacuum-compatible such that the same concept can also be applied in final conditions. The measurement is used to keep the calibration of the system and to create a closed-loop control compensating for external influences: in a demonstration measurement, using a 950 mm long bendable mirror, the mirror sagitta is kept stable inside a range of 10 nm Peak-To-Valley (P-V).

Activation of Latent Dihydroorotase from Aquifex aeolicus by Pressure*

PubMed Central

Hervé, Guy; Evans, Hedeel Guy; Fernado, Roshini; Patel, Chandni; Hachem, Fatme; Evans, David R.

2017-01-01

Elevated hydrostatic pressure was used to probe conformational changes of Aquifex aeolicus dihydroorotase (DHO), which catalyzes the third step in de novo pyrimidine biosynthesis. The isolated protein, a 45-kDa monomer, lacks catalytic activity but becomes active upon formation of a dodecameric complex with aspartate transcarbamoylase (ATC). X-ray crystallographic studies of the isolated DHO and of the complex showed that association induces several major conformational changes in the DHO structure. In the isolated DHO, a flexible loop occludes the active site blocking the access of substrates. The loop is mostly disordered but is tethered to the active site region by several electrostatic and hydrogen bonds. This loop becomes ordered and is displaced from the active site upon formation of DHO-ATC complex. The application of pressure to the complex causes its time-dependent dissociation and the loss of both DHO and ATC activities. Pressure induced irreversible dissociation of the obligate ATC trimer, and as a consequence the DHO is also inactivated. However, moderate hydrostatic pressure applied to the isolated DHO subunit mimics the complex formation and reversibly activates the isolated subunit in the absence of ATC, suggesting that the loop has been displaced from the active site. This effect of pressure is explained by the negative volume change associated with the disruption of ionic interactions and exposure of ionized amino acids to the solvent (electrostriction). The interpretation that the loop is relocated by pressure was validated by site-directed mutagenesis and by inhibition by small peptides that mimic the loop residues. PMID:27746403

A statistical study of decaying kink oscillations detected using SDO/AIA

NASA Astrophysics Data System (ADS)

Goddard, C. R.; Nisticò, G.; Nakariakov, V. M.; Zimovets, I. V.

2016-01-01

Context. Despite intensive studies of kink oscillations of coronal loops in the last decade, a large-scale statistically significant investigation of the oscillation parameters has not been made using data from the Solar Dynamics Observatory (SDO). Aims: We carry out a statistical study of kink oscillations using extreme ultraviolet imaging data from a previously compiled catalogue. Methods: We analysed 58 kink oscillation events observed by the Atmospheric Imaging Assembly (AIA) on board SDO during its first four years of operation (2010-2014). Parameters of the oscillations, including the initial apparent amplitude, period, length of the oscillating loop, and damping are studied for 120 individual loop oscillations. Results: Analysis of the initial loop displacement and oscillation amplitude leads to the conclusion that the initial loop displacement prescribes the initial amplitude of oscillation in general. The period is found to scale with the loop length, and a linear fit of the data cloud gives a kink speed of Ck = (1330 ± 50) km s-1. The main body of the data corresponds to kink speeds in the range Ck = (800-3300) km s-1. Measurements of 52 exponential damping times were made, and it was noted that at least 21 of the damping profiles may be better approximated by a combination of non-exponential and exponential profiles rather than a purely exponential damping envelope. There are nine additional cases where the profile appears to be purely non-exponential and no damping time was measured. A scaling of the exponential damping time with the period is found, following the previously established linear scaling between these two parameters.

Top3-Rmi1 dissolve Rad51-mediated D-loops by a topoisomerase-based mechanism

PubMed Central

Fasching, Clare L.; Cejka, Petr; Kowalczykowski, Stephen C.; Heyer, Wolf-Dietrich

2015-01-01

Summary The displacement loop (D-loop) is the DNA strand invasion product formed during homologous recombination. Disruption of nascent D-loops represents a mechanism of anti-recombination. During Synthesis-Dependent Strand Annealing D-loop disruption after extension of the invading strand is an integral step of the pathway and ensures a non-crossover outcome. The proteins implicated in D-loop disruption are DNA motor proteins/helicases acting by migrating DNA junctions. Here we report an unanticipated mechanism of D-loop dissolution mediated by DNA topoisomerase 3 (Top3) and dependent on its catalytic activity. D-loop dissolution catalyzed by yeast Top3 is highly specific for yeast Rad51/Rad54-mediated D-loops, whereas protein-free D-loops or D-loop mediated by bacterial RecA protein or human RAD51/RAD54 resist dissolution. Also the human Topoisomerase IIIα-RMI1–RMI2 complex is capable of dissolving D-loops. Consistent with genetic data, we suggest that the extreme growth defect and hyper-recombination phenotype of Top3-deficient yeast cells is in part a result of unprocessed D-loops. PMID:25699708

Development of a laser Doppler displacement encoder system with ultra-low-noise-level for linear displacement measurement with subnanometer resolution - Final CRADA Report

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

Shu, Deming

An U.S. DOE Cooperative Research and Development Agreement (CRADA) between ANL and Optodyne, Inc. has been established to develop a prototype laser Doppler displacement encoder system with ultra-low noise level for linear measurements to sub-nanometer resolution for synchrotron radiation applications. We have improved the heterodyne efficiency and reduced the detector shot noises by proper shielding and adding a low-pass filter. The laser Doppler displacement encoder system prototype demonstrated a ~ 1 nm system output noise floor with single reflection optics. With multiple-pass optical arrangement, 0.1 nm scale closed-loop feedback control is achieved.

Evolution of ion damage at 773K in Ni- containing concentrated solid-solution alloys

DOE PAGES

Shi, Shi; He, Mo-Rigen; Jin, Ke; ...

2018-01-10

Quantitative analysis of the impact of the compositional complexity in a series of Ni-containing concentrated solid-solution alloys, Ni, NiCo, NiFe, NiCoCr, NiCoFeCr, NiCoFeCrMn and NiCoFeCrPd, on the evolution of defects produced by 1 MeV Kr ion irradiation at 773 K is reported in this paper. The dynamics of the evolution of the damage structure during irradiation to a dose of 2 displacements per atom were observed directly by performing the ion irradiations in electron transparent foils in a transmission electron microscope coupled to an ion accelerator. The defect evolution was assessed through measurement of the defect density, defect size andmore » fraction of perfect and Frank loops. These three parameters were dependent on the alloying element as well as the number of elements. The population of loops was sensitive to the ion dose and alloy composition as faulted Frank loops were observed to unfault to perfect loops with increasing ion dose. Finally, these dependences are explained in terms of the influence of each element on the lifetime of the displacement cascade as well as on defect formation and migration energies.« less

Evolution of ion damage at 773K in Ni- containing concentrated solid-solution alloys

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

Shi, Shi; He, Mo-Rigen; Jin, Ke

Quantitative analysis of the impact of the compositional complexity in a series of Ni-containing concentrated solid-solution alloys, Ni, NiCo, NiFe, NiCoCr, NiCoFeCr, NiCoFeCrMn and NiCoFeCrPd, on the evolution of defects produced by 1 MeV Kr ion irradiation at 773 K is reported in this paper. The dynamics of the evolution of the damage structure during irradiation to a dose of 2 displacements per atom were observed directly by performing the ion irradiations in electron transparent foils in a transmission electron microscope coupled to an ion accelerator. The defect evolution was assessed through measurement of the defect density, defect size andmore » fraction of perfect and Frank loops. These three parameters were dependent on the alloying element as well as the number of elements. The population of loops was sensitive to the ion dose and alloy composition as faulted Frank loops were observed to unfault to perfect loops with increasing ion dose. Finally, these dependences are explained in terms of the influence of each element on the lifetime of the displacement cascade as well as on defect formation and migration energies.« less

The development of a cryogenic over-pressure pump

NASA Astrophysics Data System (ADS)

Alvarez, M.; Cease, H.; Flaugher, B.; Flores, R.; Garcia, J.; Lathrop, A.; Ruiz, F.

2014-01-01

A cryogenic over-pressure pump (OPP) was tested in the prototype telescope liquid nitrogen (LN2) cooling system for the Dark Energy Survey (DES) Project. This OPP consists of a process cylinder (PC), gas generator, and solenoid operated valves (SOVs). It is a positive displacement pump that provided intermittent liquid nitrogen (LN2) flow to an array of charge couple devices (CCDs) for the prototype Dark Energy Camera (DECam). In theory, a heater submerged in liquid would generate the drive gas in a closed loop cooling system. The drive gas would be injected into the PC to displace that liquid volume. However, due to limitations of the prototype closed loop nitrogen system (CCD cooling system) for DECam, a quasiclosed-loop nitrogen system was created. During the test of the OPP, the CCD array was cooled to its designed set point temperature of 173K. It was maintained at that temperature via electrical heaters. The performance of the OPP was captured in pressure, temperature, and flow rate in the CCD LN2 cooling system at Fermi National Accelerator Laboratory (FNAL).

Design and Analysis of a Compact Precision Positioning Platform Integrating Strain Gauges and the Piezoactuator

PubMed Central

Huang, Hu; Zhao, Hongwei; Yang, Zhaojun; Fan, Zunqiang; Wan, Shunguang; Shi, Chengli; Ma, Zhichao

2012-01-01

Miniaturization precision positioning platforms are needed for in situ nanomechanical test applications. This paper proposes a compact precision positioning platform integrating strain gauges and the piezoactuator. Effects of geometric parameters of two parallel plates on Von Mises stress distribution as well as static and dynamic characteristics of the platform were studied by the finite element method. Results of the calibration experiment indicate that the strain gauge sensor has good linearity and its sensitivity is about 0.0468 mV/μm. A closed-loop control system was established to solve the problem of nonlinearity of the platform. Experimental results demonstrate that for the displacement control process, both the displacement increasing portion and the decreasing portion have good linearity, verifying that the control system is available. The developed platform has a compact structure but can realize displacement measurement with the embedded strain gauges, which is useful for the closed-loop control and structure miniaturization of piezo devices. It has potential applications in nanoindentation and nanoscratch tests, especially in the field of in situ nanomechanical testing which requires compact structures. PMID:23012566

Microsatellites in the Eukaryotic DNA Mismatch Repair Genes as Modulators of Evolutionary Mutation Rate

NASA Technical Reports Server (NTRS)

Chang, Dong Kyung; Metzgar, David; Wills, Christopher; Boland, C. Richard

2003-01-01

All "minor" components of the human DNA mismatch repair (MMR) system-MSH3, MSH6, PMS2, and the recently discovered MLH3-contain mononucleotide microsatellites in their coding sequences. This intriguing finding contrasts with the situation found in the major components of the DNA MMR system-MSH2 and MLH1-and, in fact, most human genes. Although eukaryotic genomes are rich in microsatellites, non-triplet microsatellites are rare in coding regions. The recurring presence of exonal mononucleotide repeat sequences within a single family of human genes would therefore be considered exceptional.

Effect of GNSS receiver carrier phase tracking loops on earthquake monitoring performance

NASA Astrophysics Data System (ADS)

Clare, Adam; Lin, Tao; Lachapelle, Gérard

2017-06-01

This research focuses on the performance of GNSS receiver carrier phase tracking loops for early earthquake monitoring systems. An earthquake was simulated using a hardware simulator and position, velocity and acceleration displacements were obtained to recreate the dynamics of the 2011 Tohoku earthquake. Using a software defined receiver, GSNRx, tracking bandwidths of 5, 10, 15, 20, 30, 40 and 50 Hz along with integration times of 1, 5 and 10 ms were tested. Using the phase lock indicator, an adaptive tracking loop was designed and tested to maximize performance for this application.

Control of active reflector system for radio telescope

NASA Astrophysics Data System (ADS)

Zhou, Guo-hua; Li, Guo-ping; Zhang, Yong; Zhang, Zhen-chao

2016-10-01

According to the control requirements of the active reflector surface in the 110 m radio telescope at QiTai(QTT) Xinjiang, a new displacement actuator and a new displacement control system were designed and manufactured and then their characteristics were tested by a dual-frequency laser interferometer in the micro-displacement laboratory. The displacement actuator was designed by a scheme of high precision worm and roller screw structures, and the displacement control system was based on a ARM micro-processor. Finally, the S curve acceleration control methods were used to design the hardware platform and software algorithm for the active reflection surface of the control system. The test experiments were performed based on the laser metrology system on an active reflector close-loop antenna prototype for large radio telescope. Experimental results indicate that it achieves a 30 mm working stroke and 5 μm RMS motion resolution. The accuracy (standard deviation) is 3.67 mm, and the error between the determined and theoretical values is 0.04% when the rated load is 300 kg, the step is 2 mm and the stroke is 30mm. Furthermore, the active reflector integrated system was tested by the laser sensors with the accuracy of 0.25 μm RMS on 4-panel radio telescope prototype, the measurement results show that the integrated precision of the active reflector closed-loop control system is less than 5 μm RMS, and well satisfies the technical requirements of active reflector control system of the QTT radio telescope in 3 mm wavelength.

Anemometer calibrator

NASA Technical Reports Server (NTRS)

Bate, T.; Calkins, D. E.; Price, P.; Veikins, O.

1971-01-01

Calibrator generates accurate flow velocities over wide range of gas pressure, temperature, and composition. Both pressure and flow velocity can be maintained within 0.25 percent. Instrument is essentially closed loop hydraulic system containing positive displacement drive.

Label-free logic modules and two-layer cascade based on stem-loop probes containing a G-quadruplex domain.

PubMed

Guo, Yahui; Cheng, Junjie; Wang, Jine; Zhou, Xiaodong; Hu, Jiming; Pei, Renjun

2014-09-01

A simple, versatile, and label-free DNA computing strategy was designed by using toehold-mediated strand displacement and stem-loop probes. A full set of logic gates (YES, NOT, OR, NAND, AND, INHIBIT, NOR, XOR, XNOR) and a two-layer logic cascade were constructed. The probes contain a G-quadruplex domain, which was blocked or unfolded through inputs initiating strand displacement and the obviously distinguishable light-up fluorescent signal of G-quadruplex/NMM complex was used as the output readout. The inputs are the disease-specific nucleotide sequences with potential for clinic diagnosis. The developed versatile computing system based on our label-free and modular strategy might be adapted in multi-target diagnosis through DNA hybridization and aptamer-target interaction. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Suspension force control of bearingless permanent magnet slice motor based on flux linkage identification.

PubMed

Zhu, Suming; Zhu, Huangqiu

2015-07-01

The control accuracy and dynamic performance of suspension force are confined in the traditional bearingless permanent magnet slice motor (BPMSM) control strategies because the suspension force control is indirectly achieved by adopting a closed loop of displacement only. Besides, the phase information in suspension force control relies on accurate measurement of rotor position, making the control system more complex. In this paper, a new suspension force control strategy with displacement and radial suspension force double closed loops is proposed, the flux linkage of motor windings is identified based on voltage-current model and the flexibility of motor control can be improved greatly. Simulation and experimental results show that the proposed suspension force control strategy is effective to realize the stable operation of the BPMSM. Copyright © 2015 ISA. Published by Elsevier Ltd. All rights reserved.

Generation, Release, and Uptake of the NAD Precursor Nicotinic Acid Riboside by Human Cells.

PubMed

Kulikova, Veronika; Shabalin, Konstantin; Nerinovski, Kirill; Dölle, Christian; Niere, Marc; Yakimov, Alexander; Redpath, Philip; Khodorkovskiy, Mikhail; Migaud, Marie E; Ziegler, Mathias; Nikiforov, Andrey

2015-11-06

NAD is essential for cellular metabolism and has a key role in various signaling pathways in human cells. To ensure proper control of vital reactions, NAD must be permanently resynthesized. Nicotinamide and nicotinic acid as well as nicotinamide riboside (NR) and nicotinic acid riboside (NAR) are the major precursors for NAD biosynthesis in humans. In this study, we explored whether the ribosides NR and NAR can be generated in human cells. We demonstrate that purified, recombinant human cytosolic 5'-nucleotidases (5'-NTs) CN-II and CN-III, but not CN-IA, can dephosphorylate the mononucleotides nicotinamide mononucleotide and nicotinic acid mononucleotide (NAMN) and thus catalyze NR and NAR formation in vitro. Similar to their counterpart from yeast, Sdt1, the human 5'-NTs require high (millimolar) concentrations of nicotinamide mononucleotide or NAMN for efficient catalysis. Overexpression of FLAG-tagged CN-II and CN-III in HEK293 and HepG2 cells resulted in the formation and release of NAR. However, NAR accumulation in the culture medium of these cells was only detectable under conditions that led to increased NAMN production from nicotinic acid. The amount of NAR released from cells engineered for increased NAMN production was sufficient to maintain viability of surrounding cells unable to use any other NAD precursor. Moreover, we found that untransfected HeLa cells produce and release sufficient amounts of NAR and NR under normal culture conditions. Collectively, our results indicate that cytosolic 5'-NTs participate in the conversion of NAD precursors and establish NR and NAR as integral constituents of human NAD metabolism. In addition, they point to the possibility that different cell types might facilitate each other's NAD supply by providing alternative precursors. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Generation, Release, and Uptake of the NAD Precursor Nicotinic Acid Riboside by Human Cells*

PubMed Central

Kulikova, Veronika; Shabalin, Konstantin; Nerinovski, Kirill; Dölle, Christian; Niere, Marc; Yakimov, Alexander; Redpath, Philip; Khodorkovskiy, Mikhail; Migaud, Marie E.; Ziegler, Mathias; Nikiforov, Andrey

2015-01-01

NAD is essential for cellular metabolism and has a key role in various signaling pathways in human cells. To ensure proper control of vital reactions, NAD must be permanently resynthesized. Nicotinamide and nicotinic acid as well as nicotinamide riboside (NR) and nicotinic acid riboside (NAR) are the major precursors for NAD biosynthesis in humans. In this study, we explored whether the ribosides NR and NAR can be generated in human cells. We demonstrate that purified, recombinant human cytosolic 5′-nucleotidases (5′-NTs) CN-II and CN-III, but not CN-IA, can dephosphorylate the mononucleotides nicotinamide mononucleotide and nicotinic acid mononucleotide (NAMN) and thus catalyze NR and NAR formation in vitro. Similar to their counterpart from yeast, Sdt1, the human 5′-NTs require high (millimolar) concentrations of nicotinamide mononucleotide or NAMN for efficient catalysis. Overexpression of FLAG-tagged CN-II and CN-III in HEK293 and HepG2 cells resulted in the formation and release of NAR. However, NAR accumulation in the culture medium of these cells was only detectable under conditions that led to increased NAMN production from nicotinic acid. The amount of NAR released from cells engineered for increased NAMN production was sufficient to maintain viability of surrounding cells unable to use any other NAD precursor. Moreover, we found that untransfected HeLa cells produce and release sufficient amounts of NAR and NR under normal culture conditions. Collectively, our results indicate that cytosolic 5′-NTs participate in the conversion of NAD precursors and establish NR and NAR as integral constituents of human NAD metabolism. In addition, they point to the possibility that different cell types might facilitate each other's NAD supply by providing alternative precursors. PMID:26385918

Cardiovascular simulator improvement: pressure versus volume loop assessment.

PubMed

Fonseca, Jeison; Andrade, Aron; Nicolosi, Denys E C; Biscegli, José F; Leme, Juliana; Legendre, Daniel; Bock, Eduardo; Lucchi, Julio Cesar

2011-05-01

This article presents improvement on a physical cardiovascular simulator (PCS) system. Intraventricular pressure versus intraventricular volume (PxV) loop was obtained to evaluate performance of a pulsatile chamber mimicking the human left ventricle. PxV loop shows heart contractility and is normally used to evaluate heart performance. In many heart diseases, the stroke volume decreases because of low heart contractility. This pathological situation must be simulated by the PCS in order to evaluate the assistance provided by a ventricular assist device (VAD). The PCS system is automatically controlled by a computer and is an auxiliary tool for VAD control strategies development. This PCS system is according to a Windkessel model where lumped parameters are used for cardiovascular system analysis. Peripheral resistance, arteries compliance, and fluid inertance are simulated. The simulator has an actuator with a roller screw and brushless direct current motor, and the stroke volume is regulated by the actuator displacement. Internal pressure and volume measurements are monitored to obtain the PxV loop. Left chamber internal pressure is directly obtained by pressure transducer; however, internal volume has been obtained indirectly by using a linear variable differential transformer, which senses the diaphragm displacement. Correlations between the internal volume and diaphragm position are made. LabVIEW integrates these signals and shows the pressure versus internal volume loop. The results that have been obtained from the PCS system show PxV loops at different ventricle elastances, making possible the simulation of pathological situations. A preliminary test with a pulsatile VAD attached to PCS system was made. © 2011, Copyright the Authors. Artificial Organs © 2011, International Center for Artificial Organs and Transplantation and Wiley Periodicals, Inc.

RNA/DNA Hybrid Interactome Identifies DXH9 as a Molecular Player in Transcriptional Termination and R-Loop-Associated DNA Damage.

PubMed

Cristini, Agnese; Groh, Matthias; Kristiansen, Maiken S; Gromak, Natalia

2018-05-08

R-loops comprise an RNA/DNA hybrid and displaced single-stranded DNA. They play important biological roles and are implicated in pathology. Even so, proteins recognizing these structures are largely undefined. Using affinity purification with the S9.6 antibody coupled to mass spectrometry, we defined the RNA/DNA hybrid interactome in HeLa cells. This consists of known R-loop-associated factors SRSF1, FACT, and Top1, and yet uncharacterized interactors, including helicases, RNA processing, DNA repair, and chromatin factors. We validate specific examples of these interactors and characterize their involvement in R-loop biology. A top candidate DHX9 helicase promotes R-loop suppression and transcriptional termination. DHX9 interacts with PARP1, and both proteins prevent R-loop-associated DNA damage. DHX9 and other interactome helicases are overexpressed in cancer, linking R-loop-mediated DNA damage and disease. Our RNA/DNA hybrid interactome provides a powerful resource to study R-loop biology in health and disease. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Functions of Replication Protein A as a Sensor of R Loops and a Regulator of RNaseH1

PubMed Central

Nguyen, Hai Dang; Yadav, Tribhuwan; Giri, Sumanprava; Saez, Borja; Graubert, Timothy A.; Zou, Lee

2017-01-01

R loop, a transcription intermediate containing RNA:DNA hybrids and displaced single-stranded DNA (ssDNA), has emerged as a major source of genomic instability. RNaseH1, which cleaves the RNA in RNA:DNA hybrids, plays an important role in R loop suppression. Here, we show that replication protein A (RPA), a ssDNA-binding protein, interacts with RNaseH1 and colocalizes with both RNaseH1 and R loops in cells. In vitro, purified RPA directly enhances the association of RNaseH1 with RNA:DNA hybrids and stimulates the activity of RNaseH1 on R loops. An RPA binding-defective RNaseH1 mutant is not efficiently stimulated by RPA in vitro, fails to accumulate at R loops in cells, and loses the ability to suppress R loops and associated genomic instability. Thus, in addition to sensing DNA damage and replication stress, RPA is a sensor of R loops and a regulator of RNaseH1, extending the versatile role of RPA in suppression of genomic instability. PMID:28257700

Simple sequence repeats in Escherichia coli: abundance, distribution, composition, and polymorphism.

PubMed

Gur-Arie, R; Cohen, C J; Eitan, Y; Shelef, L; Hallerman, E M; Kashi, Y

2000-01-01

Computer-based genome-wide screening of the DNA sequence of Escherichia coli strain K12 revealed tens of thousands of tandem simple sequence repeat (SSR) tracts, with motifs ranging from 1 to 6 nucleotides. SSRs were well distributed throughout the genome. Mononucleotide SSRs were over-represented in noncoding regions and under-represented in open reading frames (ORFs). Nucleotide composition of mono- and dinucleotide SSRs, both in ORFs and in noncoding regions, differed from that of the genomic region in which they occurred, with 93% of all mononucleotide SSRs proving to be of A or T. Computer-based analysis of the fine position of every SSR locus in the noncoding portion of the genome relative to downstream ORFs showed SSRs located in areas that could affect gene regulation. DNA sequences at 14 arbitrarily chosen SSR tracts were compared among E. coli strains. Polymorphisms of SSR copy number were observed at four of seven mononucleotide SSR tracts screened, with all polymorphisms occurring in noncoding regions. SSR polymorphism could prove important as a genome-wide source of variation, both for practical applications (including rapid detection, strain identification, and detection of loci affecting key phenotypes) and for evolutionary adaptation of microbes.

A biological micro actuator: graded and closed-loop control of insect leg motion by electrical stimulation of muscles.

PubMed

Cao, Feng; Zhang, Chao; Vo Doan, Tat Thang; Li, Yao; Sangi, Daniyal Haider; Koh, Jie Sheng; Huynh, Ngoc Anh; Bin Aziz, Mohamed Fareez; Choo, Hao Yu; Ikeda, Kazuo; Abbeel, Pieter; Maharbiz, Michel M; Sato, Hirotaka

2014-01-01

In this study, a biological microactuator was demonstrated by closed-loop motion control of the front leg of an insect (Mecynorrhina torquata, beetle) via electrical stimulation of the leg muscles. The three antagonistic pairs of muscle groups in the front leg enabled the actuator to have three degrees of freedom: protraction/retraction, levation/depression, and extension/flexion. We observed that the threshold amplitude (voltage) required to elicit leg motions was approximately 1.0 V; thus, we fixed the stimulation amplitude at 1.5 V to ensure a muscle response. The leg motions were finely graded by alternation of the stimulation frequencies: higher stimulation frequencies elicited larger leg angular displacement. A closed-loop control system was then developed, where the stimulation frequency was the manipulated variable for leg-muscle stimulation (output from the final control element to the leg muscle) and the angular displacement of the leg motion was the system response. This closed-loop control system, with an optimized proportional gain and update time, regulated the leg to set at predetermined angular positions. The average electrical stimulation power consumption per muscle group was 148 µW. These findings related to and demonstrations of the leg motion control offer promise for the future development of a reliable, low-power, biological legged machine (i.e., an insect-machine hybrid legged robot).

Control of a flexible link by shaping the closed loop frequency response function through optimised feedback filters

NASA Astrophysics Data System (ADS)

Del Vescovo, D.; D'Ambrogio, W.

1995-01-01

A frequency domain method is presented to design a closed-loop control for vibration reduction flexible mechanisms. The procedure is developed on a single-link flexible arm, driven by one rotary degree of freedom servomotor, although the same technique may be applied to similar systems such as supports for aerospace antennae or solar panels. The method uses the structural frequency response functions (FRFs), thus avoiding system identification, that produces modeling uncertainties. Two closed-loops are implemented: the inner loop uses acceleration feedback with the aim of making the FRF similar to that of an equivalent rigid link; the outer loop feeds back displacements to achieve a fast positioning response and null steady state error. In both cases, the controller type is established a priori, while actual characteristics are defined by an optimisation procedure in which the relevant FRF is constrained into prescribed bounds and stability is taken into account.

Calorimetric thermal-vacuum performance characterization of the BAe 80 K space cryocooler

NASA Technical Reports Server (NTRS)

Kotsubo, V. Y.; Johnson, D. L.; Ross, R. G., Jr.

1992-01-01

A comprehensive characterization program is underway at JPL to generate test data on long-life, miniature Stirling-cycle cryocoolers for space application. The key focus of this paper is on the thermal performance of the British Aerospace (BAe) 80 K split-Stirling-cycle cryocooler as measured in a unique calorimetric thermal-vacuum test chamber that accurately simulates the heat-transfer interfaces of space. Two separate cooling fluid loops provide precise individual control of the compressor and displacer heatsink temperatures. In addition, heatflow transducers enable calorimetric measurements of the heat rejected separately by the compressor and displacer. Cooler thermal performance has been mapped for coldtip temperatures ranging from below 45 K to above 150 K, for heatsink temperatures ranging from 280 K to 320 K, and for a wide variety of operational variables including compressor-displacer phase, compressor-displacer stroke, drive frequency, and piston-displacer dc offset.

Simulation of magnetoelastic response of iron nanowire loop

NASA Astrophysics Data System (ADS)

Huang, Junping; Peng, Xianghe; Wang, Zhongchang; Hu, Xianzhi

2018-03-01

We analyzed the magnetoelastic responses of one-dimensional iron nanowire loop systems with quantum statistical mechanics, treating the particles in the systems as identical bosons with an arbitrary integer spin. Under the assumptions adopted, we demonstrated that the Hamiltonian of the system can be separated into two parts, corresponding to two Ising subsystems, describing the particle spin and the particle displacement, respectively. Because the energy of the particle motion at atomic scale is quantized, there should be more the strict constraint on the particle displacement Ising subsystem. Making use of the existing results for Ising system, the partition function of the system was derived into two parts, corresponding respectively to the two Ising subsystems. Then the Gibbs distribution was obtained by statistical mechanics, and the description for the magnetoelastic response was derived. The magnetoelastic responses were predicted with the developed approach, and the comparison with the results calculated with VASP demonstrates the validity of the developed approach.

A study of the vacancy loop formation probability in Ni-Cu and Ag-Pd alloys. [50-keV Kr sup + ions

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

Smalinskas, K.; Chen, Gengsheng; Haworth, J.

1992-04-01

The molten-zone model of vacancy loop formation from a displacement cascade predicts that the loop formation probability should scale with the melting temperature. To investigate this possibility the vacancy loop formation probability has been determined in a series of Cu-Ni and Ag-Pd alloys. The irradiations were performed at room temperature with 50 keV Kr+ ions and the resulting damage structure was examined by using transmission electron microscopy. In the Cu-Ni alloy series, the change in loop formation probability with increasing Ni concentration was complex, and at low- and high- nickel concentrations, the defect yield did not change in the predictedmore » manner. The defect yield was higher in the Cu-rich alloys than in the Ni-rich alloys. In the Ag-Pd alloy the change in the loop formation probability followed more closely the change in melting temperature, but no simple relationship was determined.« less

Initiator-catalyzed self-assembly of duplex-looped DNA hairpin motif based on strand displacement reaction for logic operations and amplified biosensing.

PubMed

Bi, Sai; Yue, Shuzhen; Wu, Qiang; Ye, Jiayan

2016-09-15

Here we program an initiator-catalyzed self-assembly of duplex-looped DNA hairpin motif based on strand displacement reaction. Due to the recycling of initiator and performance in a cascade manner, this system is versatilely extended to logic operations, including the construction of concatenated logic circuits with a feedback function and a biocomputing keypad-lock security system. Compared with previously reported molecular security systems, the prominent feature of our keypad lock is that it can be spontaneously reset and recycled with no need of any external stimulus and human intervention. Moreover, through integrating with an isothermal amplification technique of rolling circle amplification (RCA), this programming catalytic DNA self-assembly strategy readily achieves sensitive and selective biosensing of initiator. Importantly, a magnetic graphene oxide (MGO) is introduced to remarkably reduced background, which plays an important role in enhancing the signal-to-noise ratio and improving the detection sensitivity. Therefore, the proposed sophisticated DNA strand displacement-based methodology with engineering dynamic functions may find broad applications in the construction of programming DNA nanostructures, amplification biosensing platform, and large-scale DNA circuits. Copyright © 2016 Elsevier B.V. All rights reserved.

Displacement cascades and defects annealing in tungsten, Part I: Defect database from molecular dynamics simulations

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

Setyawan, Wahyu; Nandipati, Giridhar; Roche, Kenneth J.

Molecular dynamics simulations have been used to generate a comprehensive database of surviving defects due to displacement cascades in bulk tungsten. Twenty-one data points of primary knock-on atom (PKA) energies ranging from 100 eV (sub-threshold energy) to 100 keV (~780 × Ed, where Ed = 128 eV is the average displacement threshold energy) have been completed at 300 K, 1025 K and 2050 K. Within this range of PKA energies, two regimes of power-law energy-dependence of the defect production are observed. A distinct power-law exponent characterizes the number of Frenkel pairs produced within each regime. The two regimes intersect atmore » a transition energy which occurs at approximately 250 × Ed. The transition energy also marks the onset of the formation of large self-interstitial atom (SIA) clusters (size 14 or more). The observed defect clustering behavior is asymmetric, with SIA clustering increasing with temperature, while the vacancy clustering decreases. This asymmetry increases with temperature such that at 2050 K (~0.5 Tm) practically no large vacancy clusters are formed, meanwhile large SIA clusters appear in all simulations. The implication of such asymmetry on the long-term defect survival and damage accumulation is discussed. In addition, <100> {110} SIA loops are observed to form directly in the highest energy cascades, while vacancy <100> loops are observed to form at the lowest temperature and highest PKA energies, although the appearance of both the vacancy and SIA loops with Burgers vector of <100> type is relatively rare.« less

Decay-less kink oscillations in coronal loops

NASA Astrophysics Data System (ADS)

Anfinogentov, S.; Nisticò, G.; Nakariakov, V. M.

2013-12-01

Context. Kink oscillations of coronal loops in an off-limb active region are detected with the Imaging Assembly Array (AIA) instruments of the Solar Dynamics Observatory (SDO) at 171 Å. Aims: We aim to measure periods and amplitudes of kink oscillations of different loops and to determinate the evolution of the oscillation phase along the oscillating loop. Methods: Oscillating coronal loops were visually identified in the field of view of SDO/AIA and STEREO/EUVI-A: the loop length was derived by three-dimensional analysis. Several slits were taken along the loops to assemble time-distance maps. We identified oscillatory patterns and retrieved periods and amplitudes of the oscillations. We applied the cross-correlation technique to estimate the phase shift between oscillations at different segments of oscillating loops. Results: We found that all analysed loops show low-amplitude undamped transverse oscillations. Oscillation periods of loops in the same active region range from 2.5 to 11 min, and are different for different loops. The displacement amplitude is lower than 1 Mm. The oscillation phase is constant along each analysed loop. The spatial structure of the phase of the oscillations corresponds to the fundamental standing kink mode. We conclude that the observed behaviour is consistent with the empirical model in terms of a damped harmonic resonator affected by a non-resonant continuously operating external force. A movie is available in electronic form at http://www.aanda.org

The development of a microprocessor-controlled linearly-actuated valve assembly

NASA Technical Reports Server (NTRS)

Wall, R. H.

1984-01-01

The development of a proportional fluid control valve assembly is presented. This electromechanical system is needed for space applications to replace the current proportional flow controllers. The flow is controlled by a microprocessor system that monitors the control parameters of upstream pressure and requested volumetric flow rate. The microprocessor achieves the proper valve stem displacement by means of a digital linear actuator. A linear displacement sensor is used to measure the valve stem position. This displacement is monitored by the microprocessor system as a feedback signal to close the control loop. With an upstream pressure between 15 and 47 psig, the developed system operates between 779 standard CU cm/sec (SCCS) and 1543 SCCS.

Minor displacements in the insertion site provoke major differences in the induction of antibody responses by chimeric parvovirus-like particles.

PubMed

Rueda, P; Hurtado, A; del Barrio, M; Martínez-Torrecuadrada, J L; Kamstrup, S; Leclerc, C; Casal, J I

1999-10-10

An antigen-delivery system based on hybrid virus-like particles (VLPs) formed by the self-assembly of the capsid VP2 protein of canine parvovirus (CPV) and expressing foreign peptides was investigated. In this report, we have studied the effects of inserting the poliovirus C3:B epitope in the four loops and the C terminus of the CPV VP2 on the particle structure and immunogenicity. Epitope insertions in the four loops allowed the recovery of capsids in all of the mutants. However, only insertions of the C3:B epitope in VP2 residue 225 of the loop 2 were able to elicit a significant anti-peptide antibody response, but not poliovirus-neutralizing antibodies, probably because residue 225 is located in an small depression of the surface. To fine modulate the insertion site in loop 2, a cassette-mutagenesis was carried out to insert the epitope in adjacent positions 226, 227, and 228. The epitope C3:B inserted into these positions was well recognized by the specific monoclonal antibody C3 by immunoelectron microscopy. BALB/c mice immunized with these chimeric C3:B CPV:VLPs were able to elicit an strong neutralizing antibody response (>3 log(10) units) against poliovirus type 1 (Mahoney strain). Therefore, minor displacements in the insertion place cause dramatic changes in the accessibility of the epitope and the induction of antibody responses. Copyright 1999 Academic Press.

Simplified Real-Time Multiplex Detection of Loop-Mediated Isothermal Amplification Using Novel Mediator Displacement Probes with Universal Reporters.

PubMed

Becherer, Lisa; Bakheit, Mohammed; Frischmann, Sieghard; Stinco, Silvina; Borst, Nadine; Zengerle, Roland; von Stetten, Felix

2018-04-03

A variety of real-time detection techniques for loop-mediated isothermal amplification (LAMP) based on the change in fluorescence intensity during DNA amplification enable simultaneous detection of multiple targets. However, these techniques depend on fluorogenic probes containing target-specific sequences. That complicates the adaption to different targets leading to time-consuming assay optimization. Here, we present the first universal real-time detection technique for multiplex LAMP. The novel approach allows simple assay design and is easy to implement for various targets. The innovation features a mediator displacement probe and a universal reporter. During amplification of target DNA the mediator is displaced from the mediator displacement probe. Then it hybridizes to the reporter generating a fluorescence signal. The novel mediator displacement (MD) detection was validated against state-of-the-art molecular beacon (MB) detection by means of a HIV-1 RT-LAMP: MD surpassed MB detection by accelerated probe design (MD: 10 min, MB: 3-4 h), shorter times to positive (MD 4.1 ± 0.1 min shorter than MB, n = 36), improved signal-to-noise fluorescence ratio (MD: 5.9 ± 0.4, MB: 2.7 ± 0.4; n = 15), and showed equally good or better analytical performance parameters. The usability of one universal mediator-reporter set in different multiplex assays was successfully demonstrated for a biplex RT-LAMP of HIV-1 and HTLV-1 and a biplex LAMP of Haemophilus ducreyi and Treponema pallidum, both showing good correlation between target concentration and time to positive. Due to its simple implementation it is suggested to extend the use of the universal mediator-reporter sets to the detection of various other diagnostic panels.

Comparison between electric dipole and magnetic loop antennas for emitting whistler modes

NASA Astrophysics Data System (ADS)

Stenzel, R.; Urrutia, J. M.

2016-12-01

In a large uniform and unbounded laboratory plasma low frequency whistler modes are excited from an electric dipole and a magnetic loop. The excited waves are measured with a magnetic probe which resolves the three field components in 3D space and time. This yields the group velocity and energy density, from which one obtains the emitted power. The same rf generator is used for both antennas and the radiated power is measured under identical plasma conditions. The magnetic loop radiates 8000 times more power than the electric dipole. The reason is that the loop antenna carries a large conduction current while the electric dipole current is a much smaller displacement current through the sheath. The current, hence magnetic field excites whistlers, not the dipole electric field. Incidentally, a dipole antenna does not launch plane waves but m = 1 helicon modes. The findings suggest that active wave injections into the magnetosphere should be done with magnetic antennas. Two parallel dipoles connected at the free end could serve as an elongated loop.

Evolution of dislocation loops in austenitic stainless steels implanted with high concentration of hydrogen

NASA Astrophysics Data System (ADS)

Zheng, Zhongcheng; Gao, Ning; Tang, Rui; Yu, Yanxia; Zhang, Weiping; Shen, Zhenyu; Long, Yunxiang; Wei, Yaxia; Guo, Liping

2017-10-01

It has been found that under certain conditions, hydrogen retention would be strongly enhanced in irradiated austenitic stainless steels. To investigate the effect of the retained hydrogen on the defect microstructure, AL-6XN stainless steel specimens were irradiated with low energy (100 keV) H2+ so that high concentration of hydrogen was injected into the specimens while considerable displacement damage dose (up to 7 dpa) was also achieved. Irradiation induced dislocation loops and voids were characterised by transmission electron microscopy. For specimens irradiated to 7 dpa at 290 °C, dislocation loops with high number density were found and the void swelling was observed. At 380 °C, most of dislocation loops were unfaulted and tangled at 7 dpa, and the void swellings were observed at 5 dpa and above. Combining the data from low dose in previous work to high dose, four stages of dislocation loops evolution with hydrogen retention were suggested. Finally, molecular dynamics simulation was made to elucidate the division of large dislocation loops under irradiation.

High-stroke silicon-on-insulator MEMS nanopositioner: Control design for non-raster scan atomic force microscopy

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

Maroufi, Mohammad, E-mail: Mohammad.Maroufi@uon.edu.au; Fowler, Anthony G., E-mail: Anthony.Fowler@uon.edu.au; Bazaei, Ali, E-mail: Ali.Bazaei@newcastle.edu.au

A 2-degree of freedom microelectromechanical systems nanopositioner designed for on-chip atomic force microscopy (AFM) is presented. The device is fabricated using a silicon-on-insulator-based process and is designed as a parallel kinematic mechanism. It contains a central scan table and two sets of electrostatic comb actuators along each orthogonal axis, which provides displacement ranges greater than ±10 μm. The first in-plane resonance modes are located at 1274 Hz and 1286 Hz for the X and Y axes, respectively. To measure lateral displacements of the stage, electrothermal position sensors are incorporated in the design. To facilitate high-speed scans, the highly resonant dynamics ofmore » the system are controlled using damping loops in conjunction with internal model controllers that enable accurate tracking of fast sinusoidal set-points. To cancel the effect of sensor drift on controlled displacements, washout controllers are used in the damping loops. The feedback controlled nanopositioner is successfully used to perform several AFM scans in contact mode via a Lissajous scan method with a large scan area of 20 μm × 20 μm. The maximum scan rate demonstrated is 1 kHz.« less

Passive magnetic bearing for a motor-generator

DOEpatents

Post, Richard F [Walnut Creek, CA

2006-07-18

Conductive lap windings are interleaved with conventional loops in the stator of a motor-generator. The rotor provides magnetic induction lines that, when rotated, cut across the lap windings and the loops. When the rotor is laterally displaced from its equilibrium axis of rotation, its magnetic lines of induction induce a current in the interleaved lap windings. The induced current interacts with the magnetic lines of induction of the rotor in accordance with Lenz's law to generate a radial force that returns the rotor to its equilibrium axis of rotation.

Formation, levitation, and stability of prominences in the magnetized solar atmosphere

NASA Technical Reports Server (NTRS)

Drake, J. F.; Mok, Y.; Van Hoven, G.

1993-01-01

The dynamic formation of prominences in the initial magnetothermal equilibrium and their stability to sideward displacements are investigated focusing on the structure of the 2D solar atmosphere in the presence of coronal arcades or loops. A model based on 2D magnetohydrodynamic equations takes into account gravity, compressible flows, heating, radiation, anisotropic thermal conduction, and coupling to a deep chromosphere. It is found that prominences in simple arcades characterized by magnetic field with significant curvature at the apex are unstable to a lateral displacement.

Microgyroscope with closed loop output

NASA Technical Reports Server (NTRS)

Challoner, A. Dorian (Inventor); Gutierrez, Roman C. (Inventor); Tang, Tony K. (Inventor); Cargille, Donald R. (Inventor)

2002-01-01

A micro-gyroscope (10) having closed loop operation by a control voltage (V.sub.TY), that is demodulated by an output signal of the sense electrodes (S1, S2), providing Coriolis torque rebalance to prevent displacement of the micro-gyroscope (10) on the output axis (y-axis). The present invention provides wide-band, closed-loop operation for a micro-gyroscope (10) and allows the drive frequency to be closely tuned to a high Q sense axis resonance. A differential sense signal (S1-S2) is compensated and fed back by differentially changing the voltage on the drive electrodes to rebalance Coriolis torque. The feedback signal is demodulated in phase with the drive axis signal (K.sub..omega..crclbar..sub.x) to produce a measure of the Coriolis force.

Friction measurements in piston-cylinder apparatus using quartz-coesite reversible transition

NASA Technical Reports Server (NTRS)

Akella, J.

1979-01-01

The value of friction determined by monitoring piston displacement as a function of nominal pressure on compression and decompression cycles at 1273 K is compared with the friction value obtained by reversing the quartz-coesite transition at 1273 and 1073 K in a talc-glass-alsimag cell (Akella and Kennedy, 1971) and a low-friction salt cell (Mirwald et al., 1975). Quenching runs at 1273 K gave double values of friction of 0.25 GPa for the talc-glass-alsimag cell and 0.03 GPa for the salt cell. The piston-displacement technique gave somewhat higher values. Use of piston-displacement hysteresis loops in evaluating the actual pressure on a sample may lead to overestimates for decompression runs and underestimates for compression runs.

Manual and automatic control of surface effect ships. [operator steering servomechanisms analysis

NASA Technical Reports Server (NTRS)

Clement, W. F.; Shanahan, J. J.; Allen, R. W.

1975-01-01

A recent investigation of crew performance in the motion environment of a large generic high speed surface effect ship by means of a motion base simulation addressed some of the helmsman's control task with an external forward visual field of the seascape and navigation and steering displays in the pilot house. In addition to the primary steering control task, a subcritical speed tracking task provided a secondary surrogate for trimming the water speed of the craft. The results of helsmen's steering describing function measurements are presented, and some suggestions for their interpretation are offered. The likely steering loop closures comprise heading and lateral displacement for the course keeping task investigated. Also discussed is the manner in which these loop closures were implemented for automatic steering of the surface effect ship. Regardless of the influence of workload, steering technique, water speed and sea state, the helmsmen apparently adopted a disturbance regulation bandwidth of about 0.2 rad/sec for lateral displacement.

Irradiation effects in UO2 and CeO2

NASA Astrophysics Data System (ADS)

Ye, Bei; Oaks, Aaron; Kirk, Mark; Yun, Di; Chen, Wei-Ying; Holtzman, Benjamin; Stubbins, James F.

2013-10-01

Single crystal CeO2, as a surrogate material to UO2, was irradiated with 500 keV xenon ions at 800 °C while being observed using in situ transmission electron microscopy (TEM). Experimental results show the formation and growth of defect clusters including dislocation loops and cavities as a function of increasing atomic displacement dose. At high dose, the dislocation loop structure evolves into an extended dislocation line structure, which appears to remain stable to the high dose levels examined in this study. A high concentration of cavities was also present in the microstructure. Despite high atomic displacement doses, the specimen remained crystalline to a cumulated dose of 5 × 1015 ions/cm2, which is consistent with the known stability of the fluorite structure under high dose irradiation. Kinetic Monte Carlo calculations show that oxygen mobility is substantially higher in hypo-stoichiometric UO2/CeO2 than hyper-stoichiometric systems. This result is consistent with the ability of irradiation damage to recover even at intermediate irradiation temperatures.

Miniature Fourier transform spectrometer with a dual closed-loop controlled electrothermal micromirror.

PubMed

Han, Fengtian; Wang, Wei; Zhang, Xiaoyang; Xie, Huikai

2016-10-03

A large piston-displacement electrothermal micromirror with closed-loop control of both piston scan and tilting of the mirror plate is demonstrated for use in a miniature Fourier transform spectrometer. Constant scan velocity in an ultra large piston scan range has been demonstrated by the proposed closed-loop piston control scheme which can be easily implemented without considerably increasing system complexity. The experimental results show that the usable linear scan range generated by the micromirror has been extended up to 505 μm. The measured spectral resolution in a compact spectrometer reaches 20 cm^-1, or 0.57 nm at 532 nm wavelength. Compared to other presented systems, this microspectrometer will benefit from the closed-loop thermal actuator approach utilizing both the piston servo and tilt control to provide more consistent spectral response, improved spectral resolution and enhanced robustness to disturbances.

Simple Sequence Repeats in Escherichia coli: Abundance, Distribution, Composition, and Polymorphism

PubMed Central

Gur-Arie, Riva; Cohen, Cyril J.; Eitan, Yuval; Shelef, Leora; Hallerman, Eric M.; Kashi, Yechezkel

2000-01-01

Computer-based genome-wide screening of the DNA sequence of Escherichia coli strain K12 revealed tens of thousands of tandem simple sequence repeat (SSR) tracts, with motifs ranging from 1 to 6 nucleotides. SSRs were well distributed throughout the genome. Mononucleotide SSRs were over-represented in noncoding regions and under-represented in open reading frames (ORFs). Nucleotide composition of mono- and dinucleotide SSRs, both in ORFs and in noncoding regions, differed from that of the genomic region in which they occurred, with 93% of all mononucleotide SSRs proving to be of A or T. Computer-based analysis of the fine position of every SSR locus in the noncoding portion of the genome relative to downstream ORFs showed SSRs located in areas that could affect gene regulation. DNA sequences at 14 arbitrarily chosen SSR tracts were compared among E. coli strains. Polymorphisms of SSR copy number were observed at four of seven mononucleotide SSR tracts screened, with all polymorphisms occurring in noncoding regions. SSR polymorphism could prove important as a genome-wide source of variation, both for practical applications (including rapid detection, strain identification, and detection of loci affecting key phenotypes) and for evolutionary adaptation of microbes.[The sequence data described in this paper have been submitted to the GenBank data library under accession numbers AF209020–209030 and AF209508–209518.] PMID:10645951

Binding modes of phosphotriesterase-like lactonase complexed with δ-nonanoic lactone and paraoxon using molecular dynamics simulations.

PubMed

Guan, Shanshan; Zhao, Li; Jin, Hanyong; Shan, Ning; Han, Weiwei; Wang, Song; Shan, Yaming

2017-02-01

Phosphotriesterase-like lactonases (PLLs) have received much attention because of their physical and chemical properties. They may have widespread applications in various fields. For example, they show potential for quorum-sensing signaling pathways and organophosphorus (OP) detoxification in agricultural science. However, the mechanism by which PLLs hydrolyze, which involves OP compounds and lactones and a variety of distinct catalytic efficiencies, has only rarely been explored. In the present study, molecular dynamics (MD) simulations were performed to characterize and contrast the structural dynamics of DrPLL, a member of the PLL superfamily in Deinococcus radiodurans, bound to two substrates, δ-nonanoic lactone and paraoxon. It has been observed that there is a 16-fold increase in the catalytic efficiency of the two mutant strains of DrPLL (F26G/C72I) vs. the wild-type enzyme toward the hydrolysis of paraoxon, but an explanation for this behavior is currently lacking. The analysis of the molecular trajectories of DrPLL bound to δ-nonanoic lactone indicated that lactone-induced conformational changes take place in loop 8, which is near the active site. Binding to paraoxon may lead to conformational displacement of loop 1 residues, which could lead to the deformation of the active site and so trigger the entry of the paraoxon into the active site. The efficiency of the F26G/C72I mutant was increased by decreasing the displacement of loop 1 residues and increasing the flexibility of loop 8 residues. These results provide a molecular-level explanation for the experimental behavior.

Epimerization of Alanyl-Alanine Induced by γ-Rays Irradiation in Aqueous Solutions.

PubMed

Munegumi, Toratane

2017-03-01

Living organisms have homochiral L-amino acids in proteins and homochiral D-mononucleotides in nucleic acids. The chemical evolutionary process to protein homochirality has been discussed for many years. Although many scenarios have been proposed for homochirality in the monomeric compounds, homochirality in amino acids and mononucleotides does not always guarantee homochirality in polypeptides and polynucleotides. Integrated scenarios containing the pathways from monomer to polymer should be proposed because in the pathways oligomers and polymers as well as monomers racemize (or epimerize), degrade, and condense. This research addresses epimerization and degradation of dipeptides under γ-rays irradiation by a cobalt-60 ( 60 Co) radiation source. The different rate constants of epimerization between diastereomeric dipeptides in the research suggest that the potential pathway toward homochirality could be much more complex.

Phase-locked loop based on nanoelectromechanical resonant-body field effect transistor

NASA Astrophysics Data System (ADS)

Bartsch, S. T.; Rusu, A.; Ionescu, A. M.

2012-10-01

We demonstrate the room-temperature operation of a silicon nanoelectromechanical resonant-body field effect transistor (RB-FET) embedded into phase-locked loop (PLL). The very-high frequency resonator uses on-chip electrostatic actuation and transistor-based displacement detection. The heterodyne frequency down-conversion based on resistive FET mixing provides a loop feedback signal with high signal-to-noise ratio. We identify key parameters for PLL operation, and analyze the performance of the RB-FET at the system level. Used as resonant mass detector, the experimental frequency stability in the ppm-range translates into sub atto-gram (10-18 g) sensitivity in high vacuum. The feedback and control system are generic and may be extended to other mechanical resonators with transistor properties, such as graphene membranes and carbon nanotubes.

COMMENT: Comment on 'Particle size dependent exchange bias and cluster-glass states in LaMn0.7Fe0.3O3 '

NASA Astrophysics Data System (ADS)

Geshev, J.

2009-02-01

Thakur et al (2008 J. Phys.: Condens. Matter 20 195215) have recently reported magnetization hysteresis loops shifted along the field axis of the cluster-glass compound LaMn0.7Fe0.3O3, attributed there to exchange bias induced at ferromagnetic/spin-glass-like interfaces. The present comment affirms that their results are insufficient for assigning the phenomenon solely to exchange bias since the corresponding field shift, if any, cannot be separated from that of a minor hysteresis loop of a ferromagnet, naturally displaced from the origin.

Rate of displacement for Jakob Type 1 lateral condyle fractures treated with a cast.

PubMed

Zale, C; Winthrop, Z A; Hennrikus, W

2018-04-01

The aim of this retrospective study is to report the rate of displacement of Jakob Type 1 lateral condyle fractures that were initially treated in a cast. We performed a retrospective review of all patients that were treated for a non-displaced (Jakob Type 1 < 2 mm) lateral condyle fracture of the humerus at our institution between 2002 and 2015. A total of 59 patients were initially treated with casting. Five fractures displaced and were converted to a closed pinning treatment plan with a conversion rate of 8.5%. There was a mean of 13.2 days (4 to 21) between treatment by initial casting and closed pinning. This study demonstrates an 8.5% displacement and conversion rate from cast treatment to closed pinning for initially non-displaced Jakob Type 1 lateral condyle fractures of the humerus. The internal oblique radiograph is most accurate to determine displacement. We recommend obtaining an internal oblique view at initial evaluation and at follow-up in the cast for lateral condyle fractures. To minimize movement at the fracture site, we recommend treating Jakob Type 1 lateral condyle fractures with a long arm cast with the elbow at 90° and the forearm in the supine position with a sling-loop design. IV - retrospective therapeutic study.

Usage of mitochondrial D-loop variation to predict risk for Huntington disease.

PubMed

Mousavizadeh, Kazem; Rajabi, Peyman; Alaee, Mahsa; Dadgar, Sepideh; Houshmand, Massoud

2015-08-01

Huntington's disease (HD) is an inherited autosomal neurodegenerative disease caused by the abnormal expansion of the CAG repeats in the Huntingtin (Htt) gene. It has been proven that mitochondrial dysfunction is contributed to the pathogenesis of Huntington's disease. The mitochondrial displacement loop (D-loop) is proven to accumulate mutations at a higher rate than other regions of mtDNA. Thus, we hypothesized that specific SNPs in the D-loop may contribute to the pathogenesis of Huntington's disease. In the present study, 30 patients with Huntington's disease and 463 healthy controls were evaluated for mitochondrial mutation sites within the D-loop region using PCR-sequencing method. Sequence analysis revealed 35 variations in HD group from Cambridge Mitochondrial Sequences. A significant difference (p < 0.05) was seen between patients and control group in eight SNPs. Polymorphisms at C16069T, T16126C, T16189C, T16519C and C16223T were correlated with an increased risk of HD while SNPs at C16150T, T16086C and T16195C were associated with a decreased risk of Huntington's disease.

A Simple Model for the Evolution of Multi-Stranded Coronal Loops

NASA Technical Reports Server (NTRS)

Fuentes, M. C. Lopez; Klimchuk, J. A.

2010-01-01

We develop and analyze a simple cellular automaton (CA) model that reproduces the main properties of the evolution of soft X-ray coronal loops. We are motivated by the observation that these loops evolve in three distinguishable phases that suggest the development, maintainance, and decay of a self-organized system. The model is based on the idea that loops are made of elemental strands that are heated by the relaxation of magnetic stress in the form of nanoflares. In this vision, usually called "the Parker conjecture" (Parker 1988), the origin of stress is the displacement of the strand footpoints due to photospheric convective motions. Modeling the response and evolution of the plasma we obtain synthetic light curves that have the same characteristic properties (intensity, fluctuations, and timescales) as the observed cases. We study the dependence of these properties on the model parameters and find scaling laws that can be used as observational predictions of the model. We discuss the implications of our results for the interpretation of recent loop observations in different wavelengths. Subject headings: Sun: corona - Sun: flares - Sun: magnetic topology - Sun: X-rays, gamma rays

Vibration isolation using extreme geometric nonlinearity

NASA Astrophysics Data System (ADS)

Virgin, L. N.; Santillan, S. T.; Plaut, R. H.

2008-08-01

A highly deformed, slender beam (or strip), attached to a vertically oscillating base, is used in a vibration isolation application to reduce the motion of a supported mass. The isolator is a thin strip that is bent so that the two ends are clamped together, forming a loop. The clamped ends are attached to an excitation source and the supported system is attached at the loop midpoint directly above the base. The strip is modeled as an elastica, and the resulting nonlinear boundary value problem is solved numerically using a shooting method. First the equilibrium shapes of the loop with varying static loads and lengths are studied. The analysis reveals a large degree of stiffness tunability; the stiffness is dependent on the geometric configuration, which itself is determined by the supported mass, loop length, and loop self-weight. Free vibration frequencies and mode shapes are also found. Finally, the case of forced vibration is studied, and the displacement transmissibility over a large range of forcing frequencies is determined for varying parameter values. Experiments using polycarbonate strips are conducted to verify equilibrium and dynamic behavior.

A fluorescence study of the molecular interactions of harmane with the nucleobases, their nucleosides and mononucleotides.

PubMed

Balón, M; Muñoz, M A; Carmona, C; Guardado, P; Galán, M

1999-07-19

Fluorescence binding studies of harmane to the elemental components of the nucleic acids were undertaken to investigate the origin of the interaction between the drug and DNA. Most of the tested substrates have been found to induce hypochromism in the absorption spectrum of harmane and to quench its fluorescence. The quenching process induced by the nucleobases and their nucleosides is mainly due to the formation of ground state 1:1 complexes. However, in the case of the mononucleotides a dynamic quenching component is also observed. This quenching component is likely due to the excited state interaction of harmane with the phosphate group of the nucleotides. UV-vis spectral changes and quenching measurements have been used to quantify the ground state association constants of the complexes and the quenching rate constants.

Enzymatic synthesis of polymers containing nicotinamide mononucleotide

NASA Technical Reports Server (NTRS)

Liu, Rihe

1995-01-01

Nicotinamide mononucleoside 5'-diphosphate in its reduced form is an excellent substrate for polynucleotide phosphorylase from Micrococcus luteus both in de novo polymerization reactions and in primer extension reactions. The oxidized form of the diphosphate is a much less efficient substrate; it can be used to extend primers but does not oligomerize in the absence of a primer. The cyanide adduct of the oxidized substrate, like the reduced substrate, polymerizes efficiently. Loss of cyanide yields high molecular weight polymers of the oxidized form. Terminal transferase from calf thymus accepts nicotinamide mononucleoside 5'-triphosphate as a substrate and efficiently adds one residue to the 3'-end of an oligodeoxynucleotide. T4 polynucleotide kinase accepts oligomers of nicotinamide mononucleotide as substrates. However, RNA polymerases do not incorporate nicotinamide mononucleoside 5'-triphosphate into products on any of the templates that we used.

Enzymatic Synthesis of Polymers Containing Nicotinamide Mononucleotide

NASA Technical Reports Server (NTRS)

Liu, Rihe; Orgel, Leslie E.

1995-01-01

Nicotinamide mononucleoside 5'-diphosphate in its reduced form is an excellent substrate for polynucleotide phosphorylase from Micrococcus luteus both in de novo polymerization reactions and in primer extension reactions. The oxidized form of the diphosphate is a much less efficient substrate; it can be used to extend primers but does not oligomerize in the absence of a primer. The cyanide adduct of the oxidized substrate, like the reduced substrate, polymerizes efficiently. Loss of cyanide yields high molecular weight polymers of the oxidized form. Terminal transferase from calf thymus accepts nicotinamide mononucleoside 5'-triphosphate as a substrate and efficiently adds one residue to the 3'-end of an oligodeoxynucleotide. T4 polynucleotide kinase accepts oligomers of nicotinamide mononucleotide as substrates. However, RNA polymerases do not incorporate nicotinamide mononucleoside 5'-triphosphate into products on any of the templates that we used.

Characterisation of radiation damage in W and W-based alloys from 2MeV self-ion near-bulk implantations

DOE PAGES

Yi, Xiaoou; Culham Science Centre, Abingdon; Jenkins, Michael L.; ...

2015-04-21

The displacement damage induced in bulk W and W-5 wt.% Re and W-5 wt.% Ta alloys by 2 MeV W + irradiation to doses 3.3×10 17 - 2.5×10 19 W +/m 2 at temperatures ranging from 300 to750°C has been characterized by transmission electron microscopy. An automated sizing and counting approach based on Image J has been proposed and performed for all irradiation data. In all cases the damage comprised dislocation loops, mostly of interstitial type, with Burgers vectors b = ½<111> (> 60%) and b = <100>. The diameters of loops did not exceed 20 nm, with the majoritymore » being ≤ 6 nm. The loop number density varied between 10 22 and 10 23 loops/m 3 . With increasing irradiation temperature, the loop size distributions shifted towards larger sizes, and there was a substantial decrease in loop number densities. The damage microstructure was less sensitive to dose than to temperature. Under the same irradiation conditions, loop number densities in the alloys were higher than in pure W but loops were smaller. In grains with normals close to z = <001>, loop strings developed in W at temperatures ≥ 500°C and doses ≥ 1.2 dpa, but such strings were not observed in the W-Re or W-Ta alloys. However, in other grain orientations complex structures appeared in all materials and dense dislocation networks formed at higher doses.« less

Detection of HbsAg and hATIII genetically modified goats (Caprahircus) by loop-mediated isothermal amplification.

PubMed

Tao, Chenyu; Zhang, Qingde; Zhai, Shanli; Liu, Bang

2013-11-01

In this study, sensitive and rapid detection systems were designed using a loop-mediated isothermal amplification (LAMP) method to detect the genetically modified goats. A set of 4 primers were designed for each exogenous nucleic acids HBsAg and hATIII. The DNA samples were first amplified with the outer and inner primers and released a single-stranded DNA,of which both ends were stem-loop structure. Then one inner primer hybridized with the loop, and initiated displacement synthesis in less than 1 h. The result could be visualized by both agarose gel electrophoresis and unaided eyes directly after adding SYBR GREEN 1. The detection limit of LAMP was ten copies of target molecules, indicating that LAMP was tenfold more sensitive than the classical PCR. Furthermore, all the samples of genetically modified goats were tested positively by LAMP, and the results demonstrated that the LAMP was a rapid and sensitive method for detecting the genetically modified organism.

Electron-Tunneling Magnetometer

NASA Technical Reports Server (NTRS)

Kaiser, William J.; Kenny, Thomas W.; Waltman, Steven B.

1993-01-01

Electron-tunneling magnetometer is conceptual solid-state device operating at room temperature, yet offers sensitivity comparable to state-of-art magnetometers such as flux gates, search coils, and optically pumped magnetometers, with greatly reduced volume, power consumption, electronics requirements, and manufacturing cost. Micromachined from silicon wafer, and uses tunneling displacement transducer to detect magnetic forces on cantilever-supported current loop.

Noncontact optical motion sensing for real-time analysis

NASA Astrophysics Data System (ADS)

Fetzer, Bradley R.; Imai, Hiromichi

1990-08-01

The adaptation of an image dissector tube (IDT) within the OPTFOLLOW system provides high resolution displacement measurement of a light discontinuity. Due to the high speed response of the IDT and the advanced servo loop circuitry, the system is capable of real time analysis of the object under test. The image of the discontinuity may be contoured by direct or reflected light and ranges spectrally within the field of visible light. The image is monitored to 500 kHz through a lens configuration which transposes the optical image upon the photocathode of the IDT. The photoelectric effect accelerates the resultant electrons through a photomultiplier and an enhanced current is emitted from the anode. A servo loop controls the electron beam, continually centering it within the IDT using magnetic focusing of deflection coils. The output analog voltage from the servo amplifier is thereby proportional to the displacement of the target. The system is controlled by a microprocessor with a 32kbyte memory and provides a digital display as well as instructional readout on a color monitor allowing for offset image tracking and automatic system calibration.

Digital control algorithms for microgravity isolation systems

NASA Technical Reports Server (NTRS)

Sinha, Alok; Wang, Yung-Peng

1992-01-01

New digital control algorithms were developed to achieve the desired acceleration transmissibility function. The attractive electromagnets have been taken as actuators. The relative displacement and the acceleration of the mass were used as feedback signals. Two approaches were developed to find that controller transfer function in Z-domain, which yields the desired transmissibility at each frequency. In the first approach, the controller transfer function is obtained by assuming that the desired transmissibility is known in Z-domain. Since the desired transmissibility H sub d(S) = 1/(tauS+1)(exp 2) is given in S-domain, the first task is to obtain the desired transmissibility in Z-domain. There are three methods to perform this task: bilinear transformation, and backward and forward rectangular rules. The bilinear transformation and backward rectangular rule lead to improper controller transfer functions, which are physically not realizable. The forward rectangular rule does lead to a physically realizable controller. However, this controller is found to be marginally stable because of a pole at Z=1. In order to eliminate this pole, a hybrid control structure is proposed. Here the control input is composed of two parts: analog and digital. The analog input simply represents the velocity (or the integral of acceleration) feedback; and the digital controller which uses only relative displacement signal, is then obtained to achieve the desired closed-loop transfer function. The stability analysis indicates that the controller transfer function is stable for typical values of sampling period. In the second approach, the aforementioned hybrid control structure is again used. First, an analog controller transfer function corresponding to relative displacement feedback is obtained to achieve the transmissibility as 1/(tauS+1)(exp 2). Then the transfer function for the digital control input is obtained by discretizing this analog controller transfer function via bilinear transformation. The stability of the resulting Z-domain closed loop system is analyzed. Also, the frequency response of the Z-domain closed-loop transfer function is determined to evaluate the performance of the control system.

Acoustic sensor for real-time control for the inductive heating process

DOEpatents

Kelley, John Bruce; Lu, Wei-Yang; Zutavern, Fred J.

2003-09-30

Disclosed is a system and method for providing closed-loop control of the heating of a workpiece by an induction heating machine, including generating an acoustic wave in the workpiece with a pulsed laser; optically measuring displacements of the surface of the workpiece in response to the acoustic wave; calculating a sub-surface material property by analyzing the measured surface displacements; creating an error signal by comparing an attribute of the calculated sub-surface material properties with a desired attribute; and reducing the error signal below an acceptable limit by adjusting, in real-time, as often as necessary, the operation of the inductive heating machine.

Athermalization in atomic force microscope based force spectroscopy using matched microstructure coupling.

PubMed

Torun, H; Finkler, O; Degertekin, F L

2009-07-01

The authors describe a method for athermalization in atomic force microscope (AFM) based force spectroscopy applications using microstructures that thermomechanically match the AFM probes. The method uses a setup where the AFM probe is coupled with the matched structure and the displacements of both structures are read out simultaneously. The matched structure displaces with the AFM probe as temperature changes, thus the force applied to the sample can be kept constant without the need for a separate feedback loop for thermal drift compensation, and the differential signal can be used to cancel the shift in zero-force level of the AFM.

Superconducting inductive displacement detection of a microcantilever

NASA Astrophysics Data System (ADS)

Vinante, A.

2014-07-01

We demonstrate a superconducting inductive technique to measure the displacement of a micromechanical resonator. In our scheme, a type I superconducting microsphere is attached to the free end of a microcantilever and approached to the loop of a dc Superconducting Quantum Interference Device (SQUID) microsusceptometer. A local magnetic field as low as 100 μT, generated by a field coil concentric to the SQUID, enables detection of the cantilever thermomechanical noise at 4.2 K. The magnetomechanical coupling and the magnetic spring are in good agreement with image method calculations assuming pure Meissner effect. These measurements are relevant to recent proposals of quantum magnetomechanics experiments based on levitating superconducting microparticles.

Heterogeneous dislocation loop formation near grain boundaries in a neutron-irradiated commercial FeCrAl alloy

NASA Astrophysics Data System (ADS)

Field, Kevin G.; Briggs, Samuel A.; Hu, Xunxiang; Yamamoto, Yukinori; Howard, Richard H.; Sridharan, Kumar

2017-01-01

FeCrAl alloys are an attractive class of materials for nuclear power applications because of their increased environmental compatibility compared with more traditional nuclear materials. Preliminary studies into the radiation tolerance of FeCrAl alloys under accelerated neutron testing between 300 and 400 °C have shown post-irradiation microstructures containing dislocation loops and a Cr-rich α‧ phase. Although these initial studies established the post-irradiation microstructures, there was little to no focus on understanding the influence of pre-irradiation microstructures on this response. In this study, a well-annealed commercial FeCrAl alloy, Alkrothal 720, was neutron irradiated to 1.8 displacements per atom (dpa) at 382 °C and then the effect of random high-angle grain boundaries on the spatial distribution and size of a〈100〉 dislocation loops, a/2〈111〉 dislocation loops, and black dot damage was analyzed using on-zone scanning transmission electron microscopy. Results showed a clear heterogeneous dislocation loop formation with a/2〈111〉 dislocation loops showing an increased number density and size, black dot damage showing a significant number density decrease, and a〈100〉 dislocation loops exhibiting an increased size in the vicinity of the grain boundary. These results suggest the importance of the pre-irradiation microstructure and, specifically, defect sink density spacing to the radiation tolerance of FeCrAl alloys.

Mechanical testing and finite element analysis of orthodontic teardrop loop.

PubMed

Coimbra, Maria Elisa Rodrigues; Penedo, Norman Duque; de Gouvêa, Jayme Pereira; Elias, Carlos Nelson; de Souza Araújo, Mônica Tirre; Coelho, Paulo Guilherme

2008-02-01

Understanding how teeth move in response to mechanical loads is an important aspect of orthodontic treatment. Treatment planning should include consideration of the appliances that will meet the desired loading of the teeth to result in optimized treatment outcomes. The purpose of this study was to evaluate the use of computer simulation to predict the force and the torsion obtained after the activation of tear drop loops of 3 heights. Seventy-five retraction loops were divided into 3 groups according to height (6, 7, and 8 mm). The loops were subjected to tensile load through displacements of 0.5, 1.0, 1.5, and 2.0 mm, and the resulting forces and torques were recorded. The loops were designed in AutoCAD software(2005; Autodesk Systems, Alpharetta, GA), and finite element analysis was performed with Ansys software(version 7.0; Swanson Analysis System, Canonsburg, PA). Statistical analysis of the mechanical experiment results was obtained by ANOVA and the Tukey post-hoc test (P < .01). The correlation test and the paired t test (P < .05) were used to compare the computer simulation with the mechanical experiment. The computer simulation accurately predicted the experimentally determined mechanical behavior of tear drop loops of different heights and should be considered an alternative for designing orthodontic appliances before treatment.

Study of nanometer-level precise phase-shift system used in electronic speckle shearography and phase-shift pattern interferometry

NASA Astrophysics Data System (ADS)

Jing, Chao; Liu, Zhongling; Zhou, Ge; Zhang, Yimo

2011-11-01

The nanometer-level precise phase-shift system is designed to realize the phase-shift interferometry in electronic speckle shearography pattern interferometry. The PZT is used as driving component of phase-shift system and translation component of flexure hinge is developed to realize micro displacement of non-friction and non-clearance. Closed-loop control system is designed for high-precision micro displacement, in which embedded digital control system is developed for completing control algorithm and capacitive sensor is used as feedback part for measuring micro displacement in real time. Dynamic model and control model of the nanometer-level precise phase-shift system is analyzed, and high-precision micro displacement is realized with digital PID control algorithm on this basis. It is proved with experiments that the location precision of the precise phase-shift system to step signal of displacement is less than 2nm and the location precision to continuous signal of displacement is less than 5nm, which is satisfied with the request of the electronic speckle shearography and phase-shift pattern interferometry. The stripe images of four-step phase-shift interferometry and the final phase distributed image correlated with distortion of objects are listed in this paper to prove the validity of nanometer-level precise phase-shift system.

Investigations of blue light-induced reactive oxygen species from flavin mononucleotide on inactivation of E. coli.

PubMed

Liang, Ji-Yuan; Cheng, Chien-Wei; Yu, Chin-Hao; Chen, Liang-Yü

2015-02-01

The micronutrients in many cellular processes, riboflavin, flavin mononucleotide (FMN), and flavin adenine dinucleotide (FAD) are photo-sensitive to UV and visible light for generating reactive oxygen species (ROS). Produced from phosphorylation of riboflavin, FMN is more water-soluble and rapidly transformed into free riboflavin after ingestion. This study investigated the application of visible blue light with FMN to development of an effective antimicrobial treatment. The photosensitization of bacterial viability with FMN was investigated by light quality, intensity, time, and irradiation dosage. The blue light-induced photochemical reaction with FMN could inactivate Escherichiacoli by the generated ROS in damaging nucleic acids, which was validated. This novel photodynamic technique could be a safe practice for photo-induced inactivation of environmental microorganism to achieve hygienic requirements in food processing. Copyright © 2015 Elsevier B.V. All rights reserved.

The interaction of the Eco R1 restriction enzyme E.coli with nucleotides

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

Hollis, Donald F.

1979-11-01

The Eco R1 restriction enzyme can be shown to be inhibited by nucleotides which correspond to any part of its known site of phosphodiesterase activity. A series of di-, tetra-, and hexa-nucleotide fragments were synthesized and their effect on the activity of the enzyme upon superhelical Co1 E1 DNA studied. The inhibition caused by the individual mononucleotides were also studied. In general all the nucleotide fragments showed some form of interaction with the enzyme system. Tetranucleotides were stronger inhibitors than dinucleotides, which in turn were stronger inhibitors than the mononucleotides. Within each category of inhibitors, those containing the phosphodiester bondmore » which is acted upon by the enzyme were the strongest inhibitors. Only those fragments which were consistent with the enzymes site of activity showed competitive inhibition kinetics. Nucleotides which do not fit within the site of phosphodiesterase activity show non-competitive inhibition kinetics.« less

Dislocation loop evolution during in-situ ion irradiation of model FeCrAl alloys

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

Haley, Jack C.; Briggs, Samuel A.; Edmondson, Philip D.

Model FeCrAl alloys of Fe-10%Cr-5%Al, Fe-12%Cr-4.5%Al, Fe-15%Cr-4%Al, and Fe-18%Cr-3%Al (in wt %) were irradiated with 1 MeV Kr++ ions in-situ with transmission electron microscopy to a dose of 2.5 displacements per atom (dpa) at 320 °C. In all cases, the microstructural damage consisted of dislocation loops with ½< 111 > and <100 > Burgers vectors. The proportion of ½< 111 > dislocation loops varied from ~50% in the Fe-10%Cr-5%Al model alloy and the Fe-18Cr%-3%Al model alloy to a peak of ~80% in the model Fe-15%Cr-4.5%Al alloy. The dislocation loop volume density increased with dose for all alloys and showed signsmore » of approaching an upper limit. The total loop populations at 2.5 dpa had a slight (and possibly insignificant) decline as the chromium content was increased from 10 to 15 wt %, but the Fe-18%Cr-3%Al alloy had a dislocation loop population ~50% smaller than the other model alloys. As a result, the largest dislocation loops in each alloy had image sizes of close to 20 nm in the micrographs, and the median diameters for all alloys ranged from 6 to 8 nm. Nature analysis by the inside-outside method indicated most dislocation loops were interstitial type.« less

Dislocation loop evolution during in-situ ion irradiation of model FeCrAl alloys

DOE PAGES

Haley, Jack C.; Briggs, Samuel A.; Edmondson, Philip D.; ...

2017-07-06

Model FeCrAl alloys of Fe-10%Cr-5%Al, Fe-12%Cr-4.5%Al, Fe-15%Cr-4%Al, and Fe-18%Cr-3%Al (in wt %) were irradiated with 1 MeV Kr++ ions in-situ with transmission electron microscopy to a dose of 2.5 displacements per atom (dpa) at 320 °C. In all cases, the microstructural damage consisted of dislocation loops with ½< 111 > and <100 > Burgers vectors. The proportion of ½< 111 > dislocation loops varied from ~50% in the Fe-10%Cr-5%Al model alloy and the Fe-18Cr%-3%Al model alloy to a peak of ~80% in the model Fe-15%Cr-4.5%Al alloy. The dislocation loop volume density increased with dose for all alloys and showed signsmore » of approaching an upper limit. The total loop populations at 2.5 dpa had a slight (and possibly insignificant) decline as the chromium content was increased from 10 to 15 wt %, but the Fe-18%Cr-3%Al alloy had a dislocation loop population ~50% smaller than the other model alloys. As a result, the largest dislocation loops in each alloy had image sizes of close to 20 nm in the micrographs, and the median diameters for all alloys ranged from 6 to 8 nm. Nature analysis by the inside-outside method indicated most dislocation loops were interstitial type.« less

A numerical study on flexoelectric bistable energy harvester

NASA Astrophysics Data System (ADS)

Kumar, Anuruddh; Sharma, Anshul; Vaish, Rahul; Kumar, Rajeev; Jain, Satish Chandra

2018-07-01

A flexoelectric energy harvesting can be a viable solution of energy source for low power devices and sensors due to its higher performance at nano/micro domain size. Numerical study has been performed on energy harvester based on flexoelectric phenomenon of dielectric materials. Cantilever type structure was opted here as it induces the polarization due to the breaking of lattice symmetry upon bending. Host layer of cantilever is made of barium strontium titanate (BST) as it has high flexoelectric coefficient, and electrodes are attached with the host layer to collect the charges. In this study, nonlinearity has been introduced using pair of magnets at the free end of the cantilever. Characteristics of the harvester performance (linear-non-linear) changes by varying the distance between magnets. Results revealed that the bistable energy harvester gives more operating frequency range when excitation is random as compared to the linear energy harvester. For the given dimension of the harvester, when magnets distance d = 6 mm, effective harvesting frequency ranges are 5-17.3 and 17.6-26 Hz as compared to linear harvester. Further, role of load resistance was investigated to understand the impact on the performance. Hysteresis loop between voltage and displacement significantly varies with the resistance. This hysteresis loop confirmed the backward coupling of flexoelectric layer, in which voltage affects the displacement due to actuation. Area under the hysteresis loop is maximum for optimum resistance value (20.4 kΩ) which confirms the maximum extraction of power during vibration.

Development Specification for the Portable Life Support System (PLSS) Thermal Loop Pump

NASA Technical Reports Server (NTRS)

Anchondo, Ian; Campbell, Colin

2017-01-01

The AEMU Thermal Loop Pump Development Specification establishes the requirements for design, performance, and testing of the Water Pump as part of the Thermal System of the Advanced Portable Life Support System (PLSS). It is envisioned that the Thermal Loop Pump is a positive displacement pump that provides a repeatable volume of flow against a given range of back-pressures provided by the various applications. The intention is to operate the pump at a fixed speed for the given application. The primary system is made up of two identical and redundant pumps of which only one is in operation at given time. The Auxiliary Loop Pump is an identical pump design to the primary pumps but is operated at half the flow rate. Inlet positive pressure to the pumps is provided by the upstream Flexible Supply Assembly (FSA-431 and FSA-531) which are physically located inside the suit volume and pressurized by suit pressure. An integrated relief valve, placed in parallel to the pump's inlet and outlet protects the pump and loop from over-pressurization. An integrated course filter is placed upstream of the pump's inlet to provide filtration and prevent potential debris from damaging the pump.

Dynamic tracking down-conversion signal processing method based on reference signal for grating heterodyne interferometer

NASA Astrophysics Data System (ADS)

Wang, Guochao; Yan, Shuhua; Zhou, Weihong; Gu, Chenhui

2012-08-01

Traditional displacement measurement systems by grating, which purely make use of fringe intensity to implement fringe count and subdivision, have rigid demands for signal quality and measurement condition, so they are not easy to realize measurement with nanometer precision. Displacement measurement with the dual-wavelength and single-grating design takes advantage of the single grating diffraction theory and the heterodyne interference theory, solving quite well the contradiction between large range and high precision in grating displacement measurement. To obtain nanometer resolution and nanometer precision, high-power subdivision of interference fringes must be realized accurately. A dynamic tracking down-conversion signal processing method based on the reference signal is proposed. Accordingly, a digital phase measurement module to realize high-power subdivision on field programmable gate array (FPGA) was designed, as well as a dynamic tracking down-conversion module using phase-locked loop (PLL). Experiments validated that a carrier signal after down-conversion can constantly maintain close to 100 kHz, and the phase-measurement resolution and phase precision are more than 0.05 and 0.2 deg, respectively. The displacement resolution and the displacement precision, corresponding to the phase results, are 0.139 and 0.556 nm, respectively.

Fiber-optic couplers as displacement sensors

NASA Astrophysics Data System (ADS)

Baruch, Martin C.; Gerdt, David W.; Adkins, Charles M.

2003-04-01

We introduce the novel concept of using a fiber-optic coupler as a versatile displacement sensor. Comparatively long fiber-optic couplers, with a coupling region of approximately 10 mm, are manufactured using standard communication SM fiber and placed in a looped-back configuration. The result is a displacement sensor, which is robust and highly sensitive over a wide dynamic range. This displacement sensor resolves 1-2 μm over distances of 1-1.5 mm and is characterized by the essential absence of a 'spring constant' plaguing other strain gauge-type sensors. Consequently, it is possible to couple to extremely weak vibrations, such as the skin displacement affected by arterial heart beat pulsations. Used as a wrist-worn heartbeat monitor, the fidelity of the arterial pulse signal has been shown to be so high that it is possible to not only determine heartbeat and breathing rates, but to implement a new single-point blood pressure measurement scheme which does not squeeze the arm. In an application as a floor vibration sensor for the non-intrusive monitoring of independently living elderly, the sensor has been shown to resolve the distinct vibration spectra of different persons and different events.

Disruption of the LOV-Jalpha helix interaction activates phototropin kinase activity.

PubMed

Harper, Shannon M; Christie, John M; Gardner, Kevin H

2004-12-28

Light plays a crucial role in activating phototropins, a class of plant photoreceptors that are sensitive to blue and UV-A wavelengths. Previous studies indicated that phototropin uses a bound flavin mononucleotide (FMN) within its light-oxygen-voltage (LOV) domain to generate a protein-flavin covalent bond under illumination. In the C-terminal LOV2 domain of Avena sativa phototropin 1, formation of this bond triggers a conformational change that results in unfolding of a helix external to this domain called Jalpha [Harper, S. M., et al. (2003) Science 301, 1541-1545]. Though the structural effects of illumination were characterized, it was unknown how these changes are coupled to kinase activation. To examine this, we made a series of point mutations along the Jalpha helix to disrupt its interaction with the LOV domain in a manner analogous to light activation. Using NMR spectroscopy and limited proteolysis, we demonstrate that several of these mutations displace the Jalpha helix from the LOV domain independently of illumination. When placed into the full-length phototropin protein, these point mutations display constitutive kinase activation, without illumination of the sample. These results indicate that unfolding of the Jalpha helix is the critical event in regulation of kinase signaling for the phototropin proteins.

Preparation, characterization and in vitro evaluation of a new nucleotide analogue prodrug cyclodextrin inclusion complexes.

PubMed

Diab, Roudayna; Jordheim, Lars P; Degobert, Ghania; Peyrottes, Suzanne; Périgaud, Christian; Dumontet, Charles; Fessi, Hatem

2009-01-01

Bis(tbutyl-S-acyl-2-thioethyl)-cytidine monophosophate is a new cytotoxic mononucleotide prodrug which have been developed to reverse the cellular resistance to nucleoside analogues. Unfortunately, its in vivo utilisation was hampered by its poor water solubility, raising the need of a molecular vector capable to mask its physicochemical characteristics although without affecting its cytotoxic activity. Hydroxypropyl-beta-cyclodextrin was used to prepare the prodrug inclusion complexes, allowing it to be solubilized in water and hence to be used for in vitro and in vivo experiments. A molar ratio of the cyclodextrin: prodrug of 3 was sufficient to obtain complete solubilization of the prodrug. The inclusion complex was characterized by differential scanning calorimetry, which revealed the disappearance of the melting peak of the prodrug suggesting the formation of inclusion complex. Proton Nuclear Magnetic Resonance spectroscopy provided a definitive proof of the inclusion complex formation, which was evidenced by the large chemical shift displacements observed for protons located in the interior of the hydrophobic cyclodextrin cavity. The complex retained its cytotoxic activity as shown by in vitro cell survival assays on murine leukemia cells. These results provided a basis for potential therapeutic applications of co-formulation of this new nucleotide analogue with hydroxypropyl-beta-CD in cancer therapy.

Stimulation of nicotinamide adenine dinucleotide biosynthetic pathways delays axonal degeneration after axotomy.

PubMed

Sasaki, Yo; Araki, Toshiyuki; Milbrandt, Jeffrey

2006-08-16

Axonal degeneration occurs in many neurodegenerative diseases and after traumatic injury and is a self-destructive program independent from programmed cell death. Previous studies demonstrated that overexpression of nicotinamide mononucleotide adenylyltransferase 1 (Nmnat1) or exogenous application of nicotinamide adenine dinucleotide (NAD) can protect axons of cultured dorsal root ganglion (DRG) neurons from degeneration caused by mechanical or neurotoxic injury. In mammalian cells, NAD can be synthesized from multiple precursors, including tryptophan, nicotinic acid, nicotinamide, and nicotinamide riboside (NmR), via multiple enzymatic steps. To determine whether other components of these NAD biosynthetic pathways are capable of delaying axonal degeneration, we overexpressed each of the enzymes involved in each pathway and/or exogenously administered their respective substrates in DRG cultures and assessed their capacity to protect axons after axotomy. Among the enzymes tested, Nmnat1 had the strongest protective effects, whereas nicotinamide phosphoribosyl transferase and nicotinic acid phosphoribosyl transferase showed moderate protective activity in the presence of their substrates. Strong axonal protection was also provided by Nmnat3, which is predominantly located in mitochondria, and an Nmnat1 mutant localized to the cytoplasm, indicating that the subcellular location of NAD production is not crucial for protective activity. In addition, we showed that exogenous application of the NAD precursors that are the substrates of these enzymes, including nicotinic acid mononucleotide, nicotinamide mononucleotide, and NmR, can also delay axonal degeneration. These results indicate that stimulation of NAD biosynthetic pathways via a variety of interventions may be useful in preventing or delaying axonal degeneration.

Phylogeny and strain typing of Escherichia coli, inferred from variation at mononucleotide repeat loci.

PubMed

Diamant, Eran; Palti, Yniv; Gur-Arie, Riva; Cohen, Helit; Hallerman, Eric M; Kashi, Yechezkel

2004-04-01

Multilocus sequencing of housekeeping genes has been used previously for bacterial strain typing and for inferring evolutionary relationships among strains of Escherichia coli. In this study, we used shorter intergenic sequences that contained simple sequence repeats (SSRs) of repeating mononucleotide motifs (mononucleotide repeats [MNRs]) to infer the phylogeny of pathogenic and commensal E. coli strains. Seven noncoding loci (four MNRs and three non-SSRs) were sequenced in 27 strains, including enterohemorrhagic (six isolates of O157:H7), enteropathogenic, enterotoxigenic, B, and K-12 strains. The four MNRs were also sequenced in 20 representative strains of the E. coli reference (ECOR) collection. Sequence polymorphism was significantly higher at the MNR loci, including the flanking sequences, indicating a higher mutation rate in the sequences flanking the MNR tracts. The four MNR loci were amplifiable by PCR in the standard ECOR A, B1, and D groups, but only one (yaiN) in the B2 group was amplified, which is consistent with previous studies that suggested that B2 is the most ancient group. High sequence compatibility was found between the four MNR loci, indicating that they are in the same clonal frame. The phylogenetic trees that were constructed from the sequence data were in good agreement with those of previous studies that used multilocus enzyme electrophoresis. The results demonstrate that MNR loci are useful for inferring phylogenetic relationships and provide much higher sequence variation than housekeeping genes. Therefore, the use of MNR loci for multilocus sequence typing should prove efficient for clinical diagnostics, epidemiology, and evolutionary study of bacteria.

Phylogeny and Strain Typing of Escherichia coli, Inferred from Variation at Mononucleotide Repeat Loci

PubMed Central

Diamant, Eran; Palti, Yniv; Gur-Arie, Riva; Cohen, Helit; Hallerman, Eric M.; Kashi, Yechezkel

2004-01-01

Multilocus sequencing of housekeeping genes has been used previously for bacterial strain typing and for inferring evolutionary relationships among strains of Escherichia coli. In this study, we used shorter intergenic sequences that contained simple sequence repeats (SSRs) of repeating mononucleotide motifs (mononucleotide repeats [MNRs]) to infer the phylogeny of pathogenic and commensal E. coli strains. Seven noncoding loci (four MNRs and three non-SSRs) were sequenced in 27 strains, including enterohemorrhagic (six isolates of O157:H7), enteropathogenic, enterotoxigenic, B, and K-12 strains. The four MNRs were also sequenced in 20 representative strains of the E. coli reference (ECOR) collection. Sequence polymorphism was significantly higher at the MNR loci, including the flanking sequences, indicating a higher mutation rate in the sequences flanking the MNR tracts. The four MNR loci were amplifiable by PCR in the standard ECOR A, B1, and D groups, but only one (yaiN) in the B2 group was amplified, which is consistent with previous studies that suggested that B2 is the most ancient group. High sequence compatibility was found between the four MNR loci, indicating that they are in the same clonal frame. The phylogenetic trees that were constructed from the sequence data were in good agreement with those of previous studies that used multilocus enzyme electrophoresis. The results demonstrate that MNR loci are useful for inferring phylogenetic relationships and provide much higher sequence variation than housekeeping genes. Therefore, the use of MNR loci for multilocus sequence typing should prove efficient for clinical diagnostics, epidemiology, and evolutionary study of bacteria. PMID:15066845

Profiles of the biosynthesis and metabolism of pyridine nucleotides in potatoes (Solanum tuberosum L.).

PubMed

Katahira, Riko; Ashihara, Hiroshi

2009-12-01

As part of a research program on nucleotide metabolism in potato tubers (Solanum tuberosum L.), profiles of pyridine (nicotinamide) metabolism were examined based on the in situ metabolic fate of radio-labelled precursors and the in vitro activities of enzymes. In potato tubers, [(3)H]quinolinic acid, which is an intermediate of de novo pyridine nucleotide synthesis, and [(14)C]nicotinamide, a catabolite of NAD, were utilised for pyridine nucleotide synthesis. The in situ tracer experiments and in vitro enzyme assays suggest the operation of multiple pyridine nucleotide cycles. In addition to the previously proposed cycle consisting of seven metabolites, we found a new cycle that includes newly discovered nicotinamide riboside deaminase which is also functional in potato tubers. This cycle bypasses nicotinamide and nicotinic acid; it is NAD --> nicotinamide mononucleotide --> nicotinamide riboside --> nicotinic acid riboside --> nicotinic acid mononucleotide --> nicotinic acid adenine dinucleotide --> NAD. Degradation of the pyridine ring was extremely low in potato tubers. Nicotinic acid glucoside is formed from nicotinic acid in potato tubers. Comparative studies of [carboxyl-(14)C]nicotinic acid metabolism indicate that nicotinic acid is converted to nicotinic acid glucoside in all organs of potato plants. Trigonelline synthesis from [carboxyl-(14)C]nicotinic acid was also found. Conversion was greater in green parts of plants, such as leaves and stem, than in underground parts of potato plants. Nicotinic acid utilised for the biosynthesis of these conjugates seems to be derived not only from the pyridine nucleotide cycle, but also from the de novo synthesis of nicotinic acid mononucleotide.

Super-resolution optical microscopy study of telomere structure.

PubMed

Phipps, Mary Lisa; Goodwin, Peter M; Martinez, Jennifer S; Goodwin, Edwin H

2016-09-01

Chromosome ends are shielded from exonucleolytic attack and inappropriate end-joining by terminal structures called telomeres; these structures are potential targets for anticancer drugs. Telomeres are composed of a simple DNA sequence (5?-TTAGGG-3? in humans) repeated more than a thousand times, a short 3? single-stranded overhang, and numerous proteins. Electron microscopy has shown that the 3? overhang pairs with the complementary strand at an internal site creating a small displacement loop and a large double-stranded “t-loop.” Our goal is to determine whether all telomeres adopt the t-loop configuration, or whether there are two or more distinct configurations. Progress in optimizing super-resolution (SR) microscopy for this ongoing investigation is reported here. Results suggest that under certain conditions sample preparation procedures may disrupt chromatin by causing loss of nucleosomes. This finding may limit the use of SR microscopy in telomere studies.

Hi-C and AIA observations of transverse magnetohydrodynamic waves in active regions

NASA Astrophysics Data System (ADS)

Morton, R. J.; McLaughlin, J. A.

2013-05-01

The recent launch of the High resolution Coronal imager (Hi-C) provided a unique opportunity of studying the EUV corona with unprecedented spatial resolution. We utilize these observations to investigate the properties of low-frequency (50-200 s) active region transverse waves, whose omnipresence had been suggested previously. The five-fold improvement in spatial resolution over SDO/AIA reveals coronal loops with widths 150-310 km and that these loops support transverse waves with displacement amplitudes <50 km. However, the results suggest that wave activity in the coronal loops is of low energy, with typical velocity amplitudes <3 km s-1. An extended time-series of SDO data suggests that low-energy wave behaviour is typical of the coronal structures both before and after the Hi-C observations. Appendix A and five movies associated to Figs. A.2-A.6 are available in electronic form at http://www.aanda.org

Super-resolution optical microscopy study of telomere structure

NASA Astrophysics Data System (ADS)

Phipps, Mary Lisa; Goodwin, Peter M.; Martinez, Jennifer S.; Goodwin, Edwin H.

2016-09-01

Chromosome ends are shielded from exonucleolytic attack and inappropriate end-joining by terminal structures called telomeres; these structures are potential targets for anticancer drugs. Telomeres are composed of a simple DNA sequence (5‧-TTAGGG-3‧ in humans) repeated more than a thousand times, a short 3‧ single-stranded overhang, and numerous proteins. Electron microscopy has shown that the 3‧ overhang pairs with the complementary strand at an internal site creating a small displacement loop and a large double-stranded "t-loop." Our goal is to determine whether all telomeres adopt the t-loop configuration, or whether there are two or more distinct configurations. Progress in optimizing super-resolution (SR) microscopy for this ongoing investigation is reported here. Results suggest that under certain conditions sample preparation procedures may disrupt chromatin by causing loss of nucleosomes. This finding may limit the use of SR microscopy in telomere studies.

Implementing Nonlinear Feedback Controllers Using DNA Strand Displacement Reactions.

PubMed

Sawlekar, Rucha; Montefusco, Francesco; Kulkarni, Vishwesh V; Bates, Declan G

2016-07-01

We show how an important class of nonlinear feedback controllers can be designed using idealized abstract chemical reactions and implemented via DNA strand displacement (DSD) reactions. Exploiting chemical reaction networks (CRNs) as a programming language for the design of complex circuits and networks, we show how a set of unimolecular and bimolecular reactions can be used to realize input-output dynamics that produce a nonlinear quasi sliding mode (QSM) feedback controller. The kinetics of the required chemical reactions can then be implemented as enzyme-free, enthalpy/entropy driven DNA reactions using a toehold mediated strand displacement mechanism via Watson-Crick base pairing and branch migration. We demonstrate that the closed loop response of the nonlinear QSM controller outperforms a traditional linear controller by facilitating much faster tracking response dynamics without introducing overshoots in the transient response. The resulting controller is highly modular and is less affected by retroactivity effects than standard linear designs.

Large-scale structure perturbation theory without losing stream crossing

NASA Astrophysics Data System (ADS)

McDonald, Patrick; Vlah, Zvonimir

2018-01-01

We suggest an approach to perturbative calculations of large-scale clustering in the Universe that includes from the start the stream crossing (multiple velocities for mass elements at a single position) that is lost in traditional calculations. Starting from a functional integral over displacement, the perturbative series expansion is in deviations from (truncated) Zel'dovich evolution, with terms that can be computed exactly even for stream-crossed displacements. We evaluate the one-loop formulas for displacement and density power spectra numerically in 1D, finding dramatic improvement in agreement with N-body simulations compared to the Zel'dovich power spectrum (which is exact in 1D up to stream crossing). Beyond 1D, our approach could represent an improvement over previous expansions even aside from the inclusion of stream crossing, but we have not investigated this numerically. In the process we show how to achieve effective-theory-like regulation of small-scale fluctuations without free parameters.

Results of aircraft open-loop tests of an experimental magnetic leader cable system for guidance during roll-out and turnoff

NASA Technical Reports Server (NTRS)

Bundick, W. Thomas; Middleton, David B.; Poole, William L.

1990-01-01

An experimental magnetic leader cable (MLC) system designed to measure aircraft lateral displacement from centerline and heading relative to centerline during rollout, turnoff, and taxi was tested at NASA's Wallops Flight Facility using NASA's Transport System Research Vehicle (TSRV), a modified B-737. The MLC system consisted of ground equipment that produced a magnetic field about a wire along runway centerline and airborne equipment that detected the strength and direction of this field and computed displacement and heading. Results of these tests indicate that estimates of aircraft displacement from centerline produced by the magnetic leader cable system using either of the two algorithms appear to be adequate for use by an automatic control system during rollout, turnoff, and taxi. Estimates of heading, however, are not sufficiently accurate for use, probably because of distortion of the magnetic field by the metal aircraft.

Effect of substrate bending on the piezoelectric measurement of PZT thin film

NASA Astrophysics Data System (ADS)

Xu, Xiaohui; Tang, Jianhong; He, Liangna

2009-05-01

Bonding conditions between PZT thin film and sample holder greatly affect the strain measurement of the PZT sample. The influence of various bonding conditions on the measured displacement were analyzed using finite element analysis (FEA). One-end fixed sample induces the maximum bending displacement. Experiments were performed on sol-gel derived PZT thin film. The voltage-displacement curve and "butterfly" loop were measured using laser Doppler method with phase detection. Experimental results agreed well with the simulated ones. The measured frequency dependence of piezoelectric response of PZT thin film indicated that, if the operating frequency was lower than 2 kHz, good bonding effect could be obtained when the entire back surface of the sample was glued to a rigid supporter using epoxy resin. A simple bonding model which considered the adhesives as a spring was used to estimate the frequency response of PZT thin film sample.

Improved approximations for control augmented structural synthesis

NASA Technical Reports Server (NTRS)

Thomas, H. L.; Schmit, L. A.

1990-01-01

A methodology for control-augmented structural synthesis is presented for structure-control systems which can be modeled as an assemblage of beam, truss, and nonstructural mass elements augmented by a noncollocated direct output feedback control system. Truss areas, beam cross sectional dimensions, nonstructural masses and rotary inertias, and controller position and velocity gains are treated simultaneously as design variables. The structural mass and a control-system performance index can be minimized simultaneously, with design constraints placed on static stresses and displacements, dynamic harmonic displacements and forces, structural frequencies, and closed-loop eigenvalues and damping ratios. Intermediate design-variable and response-quantity concepts are used to generate new approximations for displacements and actuator forces under harmonic dynamic loads and for system complex eigenvalues. This improves the overall efficiency of the procedure by reducing the number of complete analyses required for convergence. Numerical results which illustrate the effectiveness of the method are given.

Cardiac looping may be driven by compressive loads resulting from unequal growth of the heart and pericardial cavity. Observations on a physical simulation model

PubMed Central

Bayraktar, Meriç; Männer, Jörg

2014-01-01

The transformation of the straight embryonic heart tube into a helically wound loop is named cardiac looping. Such looping is regarded as an essential process in cardiac morphogenesis since it brings the building blocks of the developing heart into an approximation of their definitive topographical relationships. During the past two decades, a large number of genes have been identified which play important roles in cardiac looping. However, how genetic information is physically translated into the dynamic form changes of the looping heart is still poorly understood. The oldest hypothesis of cardiac looping mechanics attributes the form changes of the heart loop (ventral bending → simple helical coiling → complex helical coiling) to compressive loads resulting from growth differences between the heart and the pericardial cavity. In the present study, we have tested the physical plausibility of this hypothesis, which we call the growth-induced buckling hypothesis, for the first time. Using a physical simulation model, we show that growth-induced buckling of a straight elastic rod within the confined space of a hemispherical cavity can generate the same sequence of form changes as observed in the looping embryonic heart. Our simulation experiments have furthermore shown that, under bilaterally symmetric conditions, growth-induced buckling generates left- and right-handed helices (D-/L-loops) in a 1:1 ratio, while even subtle left- or rightward displacements of the caudal end of the elastic rod at the pre-buckling state are sufficient to direct the buckling process toward the generation of only D- or L-loops, respectively. Our data are discussed with respect to observations made in biological “models.” We conclude that compressive loads resulting from unequal growth of the heart and pericardial cavity play important roles in cardiac looping. Asymmetric positioning of the venous heart pole may direct these forces toward a biased generation of D- or L-loops. PMID:24772086

TEM characterization of irradiated microstructure of Fe-9%Cr ODS and ferritic-martensitic alloys

NASA Astrophysics Data System (ADS)

Swenson, M. J.; Wharry, J. P.

2018-04-01

The objective of this study is to evaluate the effects of irradiation dose and dose rate on defect cluster (i.e. dislocation loops and voids) evolution in a model Fe-9%Cr oxide dispersion strengthened steel and commercial ferritic-martensitic steels HCM12A and HT9. Complimentary irradiations using Fe2+ ions, protons, or neutrons to doses ranging from 1 to 100 displacements per atom (dpa) at 500 °C are conducted on each alloy. The irradiated microstructures are characterized using transmission electron microscopy (TEM). Dislocation loops exhibit limited growth after 1 dpa upon Fe2+ and proton irradiation, while any voids observed are small and sparse. The average size and number density of loops are statistically invariant between Fe2+, proton, and neutron irradiated specimens at otherwise fixed irradiation conditions of ∼3 dpa, 500 °C. Therefore, we conclude that higher dose rate charged particle irradiations can reproduce the neutron irradiated loop microstructure with temperature shift governed by the invariance theory; this temperature shift is ∼0 °C for the high sink strength alloys studied herein.

Experimental Research on Seismic Performance of Four-Element Variable Cross-Sectional Concrete Filled Steel Tubular Laced Columns

NASA Astrophysics Data System (ADS)

Ou, Zhijing; Lin, Jianmao; Chen, Shengfu; Lin, Wen

2017-10-01

A total of 7 experimental tests were conducted to investigate seismic performance of four element variable cross-sectional Concrete Filled Steel Tubular (CFST) laced columns. The experimental parameters are longitudinal slope and arrangement type of lacing tubes. The rules on hysteresis loop, ductility, energy expenditure, and stiffness degradation of specimens are researched. Test results indicate that all specimens have good seismic performance; their hysteresis loops are full without obvious shrinkage. With the increase of longitudinal slope, the horizontal carrying capacity increases, energy dissipation capacity improve, and there is slightly increase in stiffness degradation. The influence of arrangement type of lacing tubes on displacement ductility of specimens is big.

Regenerable Air Purification System for Gas-Phase Contaminant Control

NASA Technical Reports Server (NTRS)

Constantinescu, Ileana C.; Finn, John E.; LeVan, M. Douglas; Lung, Bernadette (Technical Monitor)

2000-01-01

Tests of a pre-prototype regenerable air purification system (RAPS) that uses water vapor to displace adsorbed contaminants from an adsorbent column have been performed at NASA Ames Research Center. A unit based on this design can be used for removing trace gas-phase contaminants from spacecraft cabin air or from polluted process streams including incinerator exhaust. During the normal operation mode, contaminants are removed from the air on the column. Regeneration of the column is performed on-line. During regeneration, contaminants are displaced and destroyed inside the closed oxidation loop. In this presentation we discuss initial experimental results for the performance of RAPS in the removal and treatment of several important spacecraft contaminant species from air.

Analytical interferences of mercuric chloride preservative in environmental water samples: Determination of organic compounds isolated by continuous liquid-liquid extraction or closed-loop stripping

USGS Publications Warehouse

Foreman, W.T.; Zaugg, S.D.; Falres, L.M.; Werner, M.G.; Leiker, T.J.; Rogerson, P.F.

1992-01-01

Analytical interferences were observed during the determination of organic compounds in groundwater samples preserved with mercuric chloride. The nature of the interference was different depending on the analytical isolation technique employed. (1) Water samples extracted with dichloromethane by continuous liquid-liquid extraction (CLLE) and analyzed by gas chromatography/mass spectrometry revealed a broad HgCl2 'peak' eluting over a 3-5-min span which interfered with the determination of coeluting organic analytes. Substitution of CLLE for separatory funnel extraction in EPA method 508 also resulted in analytical interferences from the use of HgCl2 preservative. (2) Mercuric chloride was purged, along with organic contaminants, during closed-loop stripping (CLS) of groundwater samples and absorbed onto the activated charcoal trap. Competitive sorption of the HgCl2 by the trap appeared to contribute to the observed poor recoveries for spiked organic contaminants. The HgCl2 was not displaced from the charcoal with the dichloromethane elution solvent and required strong nitric acid to achieve rapid, complete displacement. Similar competitive sorption mechanisms might also occur in other purge and trap methods when this preservative is used.

H∞ Robust Control of a Large-Piston MEMS Micromirror for Compact Fourier Transform Spectrometer Systems.

PubMed

Chen, Huipeng; Li, Mengyuan; Zhang, Yi; Xie, Huikai; Chen, Chang; Peng, Zhangming; Su, Shaohui

2018-02-08

Incorporating linear-scanning micro-electro-mechanical systems (MEMS) micromirrors into Fourier transform spectral acquisition systems can greatly reduce the size of the spectrometer equipment, making portable Fourier transform spectrometers (FTS) possible. How to minimize the tilting of the MEMS mirror plate during its large linear scan is a major problem in this application. In this work, an FTS system has been constructed based on a biaxial MEMS micromirror with a large-piston displacement of 180 μm, and a biaxial H∞ robust controller is designed. Compared with open-loop control and proportional-integral-derivative (PID) closed-loop control, H∞ robust control has good stability and robustness. The experimental results show that the stable scanning displacement reaches 110.9 μm under the H∞ robust control, and the tilting angle of the MEMS mirror plate in that full scanning range falls within ±0.0014°. Without control, the FTS system cannot generate meaningful spectra. In contrast, the FTS yields a clean spectrum with a full width at half maximum (FWHM) spectral linewidth of 96 cm -1 under the H∞ robust control. Moreover, the FTS system can maintain good stability and robustness under various driving conditions.

H∞ Robust Control of a Large-Piston MEMS Micromirror for Compact Fourier Transform Spectrometer Systems

PubMed Central

Li, Mengyuan; Zhang, Yi; Chen, Chang; Peng, Zhangming; Su, Shaohui

2018-01-01

Incorporating linear-scanning micro-electro-mechanical systems (MEMS) micromirrors into Fourier transform spectral acquisition systems can greatly reduce the size of the spectrometer equipment, making portable Fourier transform spectrometers (FTS) possible. How to minimize the tilting of the MEMS mirror plate during its large linear scan is a major problem in this application. In this work, an FTS system has been constructed based on a biaxial MEMS micromirror with a large-piston displacement of 180 μm, and a biaxial H∞ robust controller is designed. Compared with open-loop control and proportional-integral-derivative (PID) closed-loop control, H∞ robust control has good stability and robustness. The experimental results show that the stable scanning displacement reaches 110.9 μm under the H∞ robust control, and the tilting angle of the MEMS mirror plate in that full scanning range falls within ±0.0014°. Without control, the FTS system cannot generate meaningful spectra. In contrast, the FTS yields a clean spectrum with a full width at half maximum (FWHM) spectral linewidth of 96 cm−1 under the H∞ robust control. Moreover, the FTS system can maintain good stability and robustness under various driving conditions. PMID:29419765

A two-concentric-loop iterative method in estimation of displacement height and roughness length for momentum and sensible heat.

PubMed

Zhao, Wenguang; Qualls, Russell J; Berliner, Pedro R

2008-11-01

A two-concentric-loop iterative (TCLI) method is proposed to estimate the displacement height and roughness length for momentum and sensible heat by using the measurements of wind speed and air temperature at two heights, sensible heat flux above the crop canopy, and the surface temperature of the canopy. This method is deduced theoretically from existing formulae and equations. The main advantage of this method is that data measured not only under near neutral conditions, but also under unstable and slightly stable conditions can be used to calculate the scaling parameters. Based on the data measured above an Acacia Saligna agroforestry system, the displacement height (d0) calculated by the TCLI method and by a conventional method are compared. Under strict neutral conditions, the two methods give almost the same results. Under unstable conditions, d0 values calculated by the conventional method are systematically lower than those calculated by the TCLI method, with the latter exhibiting only slightly lower values than those seen under strictly neutral conditions. Computation of the average values of the scaling parameters for the agroforestry system showed that the displacement height and roughness length for momentum are 68% and 9.4% of the average height of the tree canopy, respectively, which are similar to percentages found in the literature. The calculated roughness length for sensible heat is 6.4% of the average height of the tree canopy, a little higher than the percentages documented in the literature. When wind direction was aligned within 5 degrees of the row direction of the trees, the average displacement height calculated was about 0.6 m lower than when the wind blew across the row direction. This difference was statistically significant at the 0.0005 probability level. This implies that when the wind blows parallel to the row direction, the logarithmic profile of wind speed is shifted lower to the ground, so that, at a given height, the wind speeds are faster than when the wind blows perpendicular to the row direction.

Quantitative bioluminescent detection of bacteria

NASA Technical Reports Server (NTRS)

Chappelle, E. W.; Picciolo, G. L.

1976-01-01

Phosphoflavins in sample are measured using photobacterial luciferase assay technique for flavin mononucleotide (FMN). Boiling perchloric acid is used to rupture cells to free bound flavin and to hydrolyze flavin adenine dinucleotide to FMN. Base-stabilized water solution of sodium borohydride is used as reactant.

Rocket Propellant Ducts (Cryogenic Fuel Lines): First Cut Approximations and Design Guidance

NASA Technical Reports Server (NTRS)

Brewer, William V.

1998-01-01

The design team has to set parameters before analysis can take place. Analysis is customarily a thorough and time consuming process which can take weeks or even months. Only when analysis is complete can the designer obtain feedback. If margins are negative, the process must be repeated to a greater or lesser degree until satisfactory results are achieved. Reduction of the number of iterations thru this loop would beneficially conserve time and resources. The task was to develop relatively simple, easy to use, guidelines and analytic tools that allow the designer to evaluate what effect various alternatives may have on performance as the design progresses. "Easy to use" is taken to mean closed form approximations and the use of graphic methods. "Simple" implies that 2-d and quasi 3-d approximations be exploited to whatever degree is useful before more resource intensive methods are applied. The objective is to avoid the grosser violation of performance margins at the outset. Initial efforts are focused on thermal expansion/contraction and rigid body kinematics as they relate to propellant duct displacements in the gimbal plane loop (GPL). The purpose of the loop is to place two flexible joints on the same two orthogonal intersecting axes as those of the rocket motor gimbals. This supposes the ducting will flex predictably with independent rotations corresponding to those of the motor gimbal actions. It can be shown that if GPL joint axes do not coincide with motor gimbal axes, displacement incompatibilities result in less predictable movement of the ducts.

The comparative biomechanics of the reinforced interdental crossover and the Stout loop composite splints for mandibular fracture repair in dogs.

PubMed

Kitshoff, A M; de Rooster, H; Ferreira, S M; Burger, D; Steenkamp, G

2013-01-01

To describe a new technique, the reinforced interdental crossover composite splint (RIC), for transverse mandibular fracture repair in dogs. This technique was compared biomechanically with the established reinforced interdental Stout loop composite splint (RIS) technique. Six pairs of mandibles from young adult small breed dogs were used for the study. Osteotomies were created in a standardized fashion and fixed with either RIC or RIS. All composite splint constructs were tested biomechanically with a cantilever bending force, using a single column testing machine at a rate of 2 mm/min. The time of application, amount of composite used, ultimate force, stiffness, total displacement, and total energy absorbed during displacement of the rostral mandibular segment were calculated and compared between the two groups. No significant difference was found when comparing the time of application of the RIC and the RIS techniques. All implants failed by either composite resin fracture over the region of the osteotomy or by fracture between the first and second molar followed by detachment of the resin from the lingual enamel surface of the first molar. Differences between the RIC and RIS in force (80.5 N ± 40.3 and 51.8 N ± 27.4. respectively) and stiffness (16.2 N/mm ± 4.4 and 10.1 N/mm ± 4.1 respectively) were significant (p = 0.03). However differences between the two techniques in displacement and total energy absorbed were not significant. In experimentally fractured mandibles of young adult dogs there is evidence that RIC is biomechanically similar to RIS.

High-resolution observations of active region moss and its dynamics

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

Morton, R. J.; McLaughlin, J. A., E-mail: richard.morton@northumbria.ac.uk

2014-07-10

The High Resolution Coronal Imager has provided the sharpest view of the EUV corona to date. In this paper, we exploit its impressive resolving power to provide the first analysis of the fine-scale structure of moss in an active region. The data reveal that the moss is made up of a collection of fine threads that have widths with a mean and standard deviation of 440 ± 190 km (FWHM). The brightest moss emission is located at the visible head of the fine-scale structure and the fine structure appears to extend into the lower solar atmosphere. The emission decreases alongmore » the features, implying that the lower sections are most likely dominated by cooler transition region plasma. These threads appear to be the cool, lower legs of the hot loops. In addition, the increased resolution allows for the first direct observation of physical displacements of the moss fine structure in a direction transverse to its central axis. Some of these transverse displacements demonstrate periodic behavior, which we interpret as a signature of kink (Alfvénic) waves. Measurements of the properties of the transverse motions are made and the wave motions have means and standard deviations of 55 ± 37 km for the transverse displacement amplitude, 77 ± 33 s for the period, and 4.7 ± 2.5 km s{sup –1} for the velocity amplitude. The presence of waves in the transition region of hot loops could have important implications for the heating of active regions.« less

Genome-Wide Characterization and Linkage Mapping of Simple Sequence Repeats in Mei (Prunus mume Sieb. et Zucc.)

PubMed Central

Sun, Lidan; Yang, Weiru; Zhang, Qixiang; Cheng, Tangren; Pan, Huitang; Xu, Zongda; Zhang, Jie; Chen, Chuguang

2013-01-01

Because of its popularity as an ornamental plant in East Asia, mei (Prunus mume Sieb. et Zucc.) has received increasing attention in genetic and genomic research with the recent shotgun sequencing of its genome. Here, we performed the genome-wide characterization of simple sequence repeats (SSRs) in the mei genome and detected a total of 188,149 SSRs occurring at a frequency of 794 SSR/Mb. Mononucleotide repeats were the most common type of SSR in genomic regions, followed by di- and tetranucleotide repeats. Most of the SSRs in coding sequences (CDS) were composed of tri- or hexanucleotide repeat motifs, but mononucleotide repeats were always the most common in intergenic regions. Genome-wide comparison of SSR patterns among the mei, strawberry (Fragaria vesca), and apple (Malus×domestica) genomes showed mei to have the highest density of SSRs, slightly higher than that of strawberry (608 SSR/Mb) and almost twice as high as that of apple (398 SSR/Mb). Mononucleotide repeats were the dominant SSR motifs in the three Rosaceae species. Using 144 SSR markers, we constructed a 670 cM-long linkage map of mei delimited into eight linkage groups (LGs), with an average marker distance of 5 cM. Seventy one scaffolds covering about 27.9% of the assembled mei genome were anchored to the genetic map, depending on which the macro-colinearity between the mei genome and Prunus T×E reference map was identified. The framework map of mei constructed provides a first step into subsequent high-resolution genetic mapping and marker-assisted selection for this ornamental species. PMID:23555708

Mycobacterial nicotinate mononucleotide adenylyltransferase: Structure, mechanism, and implications for drug discovery

DOE PAGES

Rodionova, Irina A.; Zuccola, Harmon J.; Sorci, Leonardo; ...

2015-01-28

Nicotinate mononucleotide adenylyltransferase NadD is an essential enzyme in the biosynthesis of the NAD cofactor, which has been implicated as a target for developing new antimycobacterial therapies. Here we report the crystal structure of Mycobacterium tuberculosis NadD ( MtNadD) at a resolution of 2.4 Å. A remarkable new feature of the MtNadD structure, compared with other members of this enzyme family, is a 310 helix that locks the active site in an over-closed conformation. As a result, MtNadD is rendered inactive as it is topologically incompatible with substrate binding and catalysis. Directed mutagenesis was also used to further dissect themore » structural elements that contribute to the interactions of the two MtNadD substrates, i.e. ATP and nicotinic acid mononucleotide (NaMN). For inhibitory profiling of partially active mutants and wild type MtNadD, we used a small molecule inhibitor of MtNadD with moderate affinity ( Ki ~ 25 μM) and antimycobacterial activity (MIC 80) ~ 40-80 μM). This analysis revealed interferences with some of the residues in the NaMN binding subsite consistent with the competitive inhibition observed for the NaMN substrate (but not ATP). A detailed steady-state kinetic analysis of MtNadD suggests that ATP must first bind to allow efficient NaMN binding and catalysis. This sequential mechanism is consistent with the requirement of transition to catalytically competent (open) conformation hypothesized from structural modeling. A possible physiological significance of this mechanism is to enable the down-regulation of NAD synthesis under ATP-limiting dormancy conditions. Lastly, these findings point to a possible new strategy for designing inhibitors that lock the enzyme in the inactive over-closed conformation.« less

Identification of a nicotinamide/nicotinate mononucleotide adenylyltransferase in Giardia lamblia (GlNMNAT).

PubMed

Forero-Baena, Nicolás; Sánchez-Lancheros, Diana; Buitrago, July Constanza; Bustos, Victor; Ramírez-Hernández, María Helena

2015-01-01

Giardia lamblia is an intestinal protozoan parasite that causes giardiasis, a disease of high prevalence in Latin America, Asia and Africa. Giardiasis leads to poor absorption of nutrients, severe electrolyte loss and growth retardation. In addition to its clinical importance, this parasite is of special biological interest due to its basal evolutionary position and simplified metabolism, which has not been studied thoroughly. One of the most important and conserved metabolic pathways is the biosynthesis of nicotinamide adenine dinucleotide (NAD). This molecule is widely known as a coenzyme in multiple redox reactions and as a substrate in cellular processes such as synthesis of Ca 2+ mobilizing agents, DNA repair and gene expression regulation. There are two pathways for NAD biosynthesis, which converge at the step catalyzed by nicotinamide/nicotinate mononucleotide adenylyltransferase (NMNAT, EC 2.7.7.1/18). Using bioinformatics tools, we found two NMNAT sequences in Giardia lamblia ( glnmnat-a and glnmnat-b ). We first verified the identity of the sequences in silico . Subsequently, glnmnat-a was cloned into an expression vector. The recombinant protein (His-GlNMNAT) was purified by nickel-affinity binding and was used in direct in vitro enzyme assays assessed by C18-HPLC, verifying adenylyltransferase activity with both nicotinamide (NMN) and nicotinic acid (NAMN) mononucleotides. Optimal reaction pH and temperature were 7.3 and 26 °C. Michaelis-Menten kinetics were observed for NMN and ATP, but saturation was not accomplished with NAMN, implying low affinity yet detectable activity with this substrate. Double-reciprocal plots showed no cooperativity for this enzyme. This represents an advance in the study of NAD metabolism in Giardia spp.

Screening for microsatellite instability target genes in colorectal cancers

PubMed Central

Vilkki, S; Launonen, V; Karhu, A; Sistonen, P; Vastrik, I; Aaltonen, L

2002-01-01

Background: Defects in the DNA repair system lead to genetic instability because replication errors are not corrected. This type of genetic instability is a key event in the malignant progression of HNPCC and a subset of sporadic colon cancers and mutation rates are particularly high at short repetitive sequences. Somatic deletions of coding mononucleotide repeats have been detected, for example, in the TGFßRII and BAX genes, and recently many novel target genes for microsatellite instability (MSI) have been proposed. Novel target genes are likely to be discovered in the future. More data should be created on background mutation rates in MSI tumours to evaluate mutation rates observed in the candidate target genes. Methods: Mutation rates in 14 neutral intronic repeats were evaluated in MSI tumours. Bioinformatic searches combined with keywords related to cancer and tumour suppressor or CRC related gene homology were used to find new candidate MSI target genes. By comparison of mutation frequencies observed in intronic mononucleotide repeats versus exonic coding repeats of potential MSI target genes, the significance of the exonic mutations was estimated. Results: As expected, the length of an intronic mononucleotide repeat correlated positively with the number of slippages for both G/C and A/T repeats (p=0.0020 and p=0.0012, respectively). BRCA1, CtBP1, and Rb1 associated CtIP and other candidates were found in a bioinformatic search combined with keywords related to cancer. Sequencing showed a significantly increased mutation rate in the exonic A9 repeat of CtIP (25/109=22.9%) as compared with similar intronic repeats (p≤0.001). Conclusions: We propose a new candidate MSI target gene CtIP to be evaluated in further studies. PMID:12414815

New Insights into the Phylogeny and Molecular Classification of Nicotinamide Mononucleotide Deamidases

PubMed Central

Sánchez-Carrón, Guiomar; Martínez-Moñino, Ana Belén; Sola-Carvajal, Agustín; Takami, Hideto; García-Carmona, Francisco; Sánchez-Ferrer, Álvaro

2013-01-01

Nicotinamide mononucleotide (NMN) deamidase is one of the key enzymes of the bacterial pyridine nucleotide cycle (PNC). It catalyzes the conversion of NMN to nicotinic acid mononucleotide, which is later converted to NAD+ by entering the Preiss-Handler pathway. However, very few biochemical data are available regarding this enzyme. This paper represents the first complete molecular characterization of a novel NMN deamidase from the halotolerant and alkaliphilic bacterium Oceanobacillus iheyensis (OiPncC). The enzyme was active over a broad pH range, with an optimum at pH 7.4, whilst maintaining 90 % activity at pH 10.0. Surprisingly, the enzyme was quite stable at such basic pH, maintaining 61 % activity after 21 days. As regard temperature, it had an optimum at 65 °C but its stability was better below 50 °C. OiPncC was a Michaelian enzyme towards its only substrate NMN, with a K m value of 0.18 mM and a kcat/K m of 2.1 mM-1 s-1. To further our understanding of these enzymes, a complete phylogenetic and structural analysis was carried out taking into account the two Pfam domains usually associated with them (MocF and CinA). This analysis sheds light on the evolution of NMN deamidases, and enables the classification of NMN deamidases into 12 different subgroups, pointing to a novel domain architecture never before described. Using a Logo representation, conserved blocks were determined, providing new insights on the crucial residues involved in the binding and catalysis of both CinA and MocF domains. The analysis of these conserved blocks within new protein sequences could permit the more efficient data curation of incoming NMN deamidases. PMID:24340054

Sensitive immobilization-free electrochemical DNA sensor based on isothermal circular strand displacement polymerization reaction.

PubMed

Xuan, Feng; Luo, Xiaoteng; Hsing, I-Ming

2012-05-15

A highly sensitive electrochemical DNA sensor that requires no probe immobilization has been developed based on a target recycling mechanism utilizing a DNA polymerase with a strand displacement activity. The electrochemical detection is realized by taking advantage of the difference in diffusivity between a free ferrocene-labeled peptide nucleic acid (Fc-PNA) and a Fc-PNA hybridized with a complementary DNA, while the DNA polymerase-assisted target recycling leads to signal generation and amplification. The hybridization of the target DNA opens up a stem-loop template DNA with the Fc-PNA hybridized to its extruded 5' end and allows a DNA primer to anneal and be extended by the DNA polymerase, which results in sequential displacement of the target DNA and the Fc-PNA from the template DNA. The displaced target DNA will hybridize with another template DNA, triggering another round of primer extension and strand displacement. The released Fc-PNA, due to its neutral backbone, has much higher diffusivity towards a negatively charged electrode, compared to that when it is hybridized with a negatively charged DNA. Therefore, a significantly enhanced signal of Fc can be observed. The outstanding sensitivity and simplicity make this approach a promising candidate for next-generation electrochemical DNA sensing technologies. Copyright © 2012 Elsevier B.V. All rights reserved.

The effects of spaceflight on open-loop and closed-loop postural control mechanisms: human neurovestibular studies on SLS-2

NASA Technical Reports Server (NTRS)

Collins, J. J.; De Luca, C. J.; Pavlik, A. E.; Roy, S. H.; Emley, M. S.; Young, L. R. (Principal Investigator)

1995-01-01

Stabilogram-diffusion analysis was used to examine how prolonged periods in microgravity affect the open-loop and closed-loop postural control mechanisms. It was hypothesized that following spaceflight: (1) the effective stochastic activity of the open-loop postural control schemes in astronauts is increased; (2) the effective stochastic activity and uncorrelated behavior, respectively, of the closed-loop postural control mechanisms in astronauts are increased; and (3) astronauts utilized open-loop postural controls schemes for shorter time intervals and smaller displacements. Four crew members and two alternates from the 14-day Spacelab Life Sciences 2 Mission were included in the study. Each subject was tested under eyes-open, quiet-standing conditions on multiple preflight and postflight days. The subjects' center-of-pressure trajectories were measured with a force platform and analyzed according to stabilogram-diffusion analysis. It was found that the effective stochastic activity of the open-loop postural control schemes in three of the four crew members was increased following spaceflight. This result is interpreted as an indication that there may be in-flight adaptations to higher-level descending postural control pathways, e.g., a postflight increase in the tonic activation of postural muscles. This change may also be the consequence of a compensatory (e.g., "stiffening") postural control strategy that is adopted by astronauts to account for general feeling of postflight unsteadiness. The crew members, as a group, did not exhibit any consistent preflight/postflight differences in the steady-state behavior of their closed-loop postural control mechanisms or in the functional interaction of their open-loop and closed-loop postural control mechanisms. These results are interpreted as indications that although there may be in-flight adaptations to the vestibular system and/or proprioceptive system, input from the visual system can compensate for such changes during undisturbed stance.

Reversible Solid Adhesion for Defense Applications

DTIC Science & Technology

2008-01-31

sensitive. Referring to Fig. 2(a), using the two closed-loop piezoelectric ( PZT ) actuators, the vertical and horizontal velocities of the...approaching/retracting contacting surfaces can be independently controlled. The displacement resolution of the vertical PZT actuator is 0.6 nm, and the total...interfacial forces are measured using the prototype custom-made capacity-type force transducer which is attached directly on the upper PZT actuator. In order

Absorption by DNA single strands of adenine isolated in vacuo: The role of multiple chromophores

NASA Astrophysics Data System (ADS)

Nielsen, Lisbeth Munksgaard; Pedersen, Sara Øvad; Kirketerp, Maj-Britt Suhr; Nielsen, Steen Brøndsted

2012-02-01

The degree of electronic coupling between DNA bases is a topic being up for much debate. Here we report on the intrinsic electronic properties of isolated DNA strands in vacuo free of solvent, which is a good starting point for high-level excited states calculations. Action spectra of DNA single strands of adenine reveal sign of exciton coupling between stacked bases from blueshifted absorption bands (˜3 nm) relative to that of the dAMP mononucleotide (one adenine base). The bands are blueshifted by about 10 nm compared to those of solvated strands, which is a shift similar to that for the adenine molecule and the dAMP mononucleotide. Desolvation has little effect on the bandwidth, which implies that inhomogenous broadening of the absorption bands in aqueous solution is of minor importance compared to, e.g., conformational disorder. Finally, at high photon energies, internal conversion competes with electron detachment since dissociation of the bare photoexcited ions on the microsecond time scale is measured.

NRK1 controls nicotinamide mononucleotide and nicotinamide riboside metabolism in mammalian cells.

PubMed

Ratajczak, Joanna; Joffraud, Magali; Trammell, Samuel A J; Ras, Rosa; Canela, Núria; Boutant, Marie; Kulkarni, Sameer S; Rodrigues, Marcelo; Redpath, Philip; Migaud, Marie E; Auwerx, Johan; Yanes, Oscar; Brenner, Charles; Cantó, Carles

2016-10-11

NAD + is a vital redox cofactor and a substrate required for activity of various enzyme families, including sirtuins and poly(ADP-ribose) polymerases. Supplementation with NAD + precursors, such as nicotinamide mononucleotide (NMN) or nicotinamide riboside (NR), protects against metabolic disease, neurodegenerative disorders and age-related physiological decline in mammals. Here we show that nicotinamide riboside kinase 1 (NRK1) is necessary and rate-limiting for the use of exogenous NR and NMN for NAD + synthesis. Using genetic gain- and loss-of-function models, we further demonstrate that the role of NRK1 in driving NAD + synthesis from other NAD + precursors, such as nicotinamide or nicotinic acid, is dispensable. Using stable isotope-labelled compounds, we confirm NMN is metabolized extracellularly to NR that is then taken up by the cell and converted into NAD + . Our results indicate that mammalian cells require conversion of extracellular NMN to NR for cellular uptake and NAD + synthesis, explaining the overlapping metabolic effects observed with the two compounds.

NRK1 controls nicotinamide mononucleotide and nicotinamide riboside metabolism in mammalian cells

PubMed Central

Ratajczak, Joanna; Joffraud, Magali; Trammell, Samuel A. J.; Ras, Rosa; Canela, Núria; Boutant, Marie; Kulkarni, Sameer S.; Rodrigues, Marcelo; Redpath, Philip; Migaud, Marie E.; Auwerx, Johan; Yanes, Oscar; Brenner, Charles; Cantó, Carles

2016-01-01

NAD+ is a vital redox cofactor and a substrate required for activity of various enzyme families, including sirtuins and poly(ADP-ribose) polymerases. Supplementation with NAD+ precursors, such as nicotinamide mononucleotide (NMN) or nicotinamide riboside (NR), protects against metabolic disease, neurodegenerative disorders and age-related physiological decline in mammals. Here we show that nicotinamide riboside kinase 1 (NRK1) is necessary and rate-limiting for the use of exogenous NR and NMN for NAD+ synthesis. Using genetic gain- and loss-of-function models, we further demonstrate that the role of NRK1 in driving NAD+ synthesis from other NAD+ precursors, such as nicotinamide or nicotinic acid, is dispensable. Using stable isotope-labelled compounds, we confirm NMN is metabolized extracellularly to NR that is then taken up by the cell and converted into NAD+. Our results indicate that mammalian cells require conversion of extracellular NMN to NR for cellular uptake and NAD+ synthesis, explaining the overlapping metabolic effects observed with the two compounds. PMID:27725675

Self-sustained oscillations of a shock wave interacting with a boundary layer on a supercritical airfoil

NASA Technical Reports Server (NTRS)

Ventres, C. S.; Howe, M. S.

1984-01-01

A theory is proposed of the self-sustaining oscillations of a weak shock on an airfoi in steady, transonic flow. The interaction of the shock with the boundary layer on the airfoil produces displacement thickness fluctuations which convect downstream and generate sound by interaction with the trailing edge. A feedback loop is established when this sound impinges on the shock wave, resulting in the production of further fluctuations in the displacement thickness. The details are worked out for an idealized mean boundary layer velocity profile, but strong support for the basic hypotheses of the theory is provided by a comparison with recent experiments involving the generation of acoustic 'tone bursts' by a supercritical airfoil section.

Self-sustained oscillations of a shock wave interacting with a boundary layer on a supercritical airfoil

NASA Technical Reports Server (NTRS)

Ventres, C. S.; Howe, M. S.

1983-01-01

A theory is proposed of the self-sustaining oscillations of a weak shock on an airfoil in steady, transonic flow. The interaction of the shock with the boundary layer on the airfoil produces displacement thickness fluctuations which convect downstream and generate sound by interaction with the trailing edge. A feedback loop is established when this sound impinges on the shock wave, resulting in the production of further fluctuations in the displacement thickness. The details are worked out for an idealized mean boundary layer velocity profile, but strong support for the basic hypotheses of the theory is provided by a comparison with recent experiments involving the generation of acoustic "tone bursts' by a supercritical airfoil section.

Ultrasensitive measurement of microcantilever displacement below the shot-noise limit

DOE PAGES

Pooser, Raphael C.; Lawrie, Benjamin J.

2015-04-23

The displacement of micro-electro-mechanical-systems (MEMs) cantilevers is used to measure a variety of phe- nomena in devices ranging from force microscopes for single spin detection[1] to biochemical sensors[2] to un- cooled thermal imaging systems[3]. The displacement readout is often performed optically with segmented de- tectors or interference measurements. Until recently, var- ious noise sources have limited the minimum detectable displacement in MEMs systems, but it is now possible to minimize all other sources[4] so that the noise level of the coherent light eld, called the shot noise limit (SNL), becomes the dominant source. Light sources dis- playing quantum-enhanced statistics belowmore » this limit are available[5, 6], with applications in gravitational wave astronomy[7] and bioimaging[8], but direct displacement measurements of MEMS cantilevers below the SNL have been impossible until now. Here, we demonstrate the rst direct measurement of a MEMs cantilever displace- ment with sub-SNL sensitivity, thus enabling ultratrace sensing, imaging, and microscopy applications. By com- bining multi-spatial-mode quantum light sources with a simple dierential measurement, we show that sub-SNL MEMs displacement sensitivity is highly accessible com- pared to previous eorts that measured the displacement of macroscopic mirrors with very distinct spatial struc- tures crafted with multiple optical parametric ampliers and locking loops[9]. We apply this technique to a com- mercially available microcantilever in order to detect dis- placements 60% below the SNL at frequencies where the microcantilever is shot-noise-limited. These results sup- port a new class of quantum MEMS sensor whose ulti- mate signal to noise ratio is determined by the correla- tions possible in quantum optics systems.« less

Ultrasensitive measurement of microcantilever displacement below the shot-noise limit

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

Pooser, Raphael C.; Lawrie, Benjamin J.

The displacement of micro-electro-mechanical-systems (MEMs) cantilevers is used to measure a variety of phe- nomena in devices ranging from force microscopes for single spin detection[1] to biochemical sensors[2] to un- cooled thermal imaging systems[3]. The displacement readout is often performed optically with segmented de- tectors or interference measurements. Until recently, var- ious noise sources have limited the minimum detectable displacement in MEMs systems, but it is now possible to minimize all other sources[4] so that the noise level of the coherent light eld, called the shot noise limit (SNL), becomes the dominant source. Light sources dis- playing quantum-enhanced statistics belowmore » this limit are available[5, 6], with applications in gravitational wave astronomy[7] and bioimaging[8], but direct displacement measurements of MEMS cantilevers below the SNL have been impossible until now. Here, we demonstrate the rst direct measurement of a MEMs cantilever displace- ment with sub-SNL sensitivity, thus enabling ultratrace sensing, imaging, and microscopy applications. By com- bining multi-spatial-mode quantum light sources with a simple dierential measurement, we show that sub-SNL MEMs displacement sensitivity is highly accessible com- pared to previous eorts that measured the displacement of macroscopic mirrors with very distinct spatial struc- tures crafted with multiple optical parametric ampliers and locking loops[9]. We apply this technique to a com- mercially available microcantilever in order to detect dis- placements 60% below the SNL at frequencies where the microcantilever is shot-noise-limited. These results sup- port a new class of quantum MEMS sensor whose ulti- mate signal to noise ratio is determined by the correla- tions possible in quantum optics systems.« less

Hyperthermophilic Archaeon Thermococcus kodakarensis Utilizes a Four-Step Pathway for NAD+ Salvage through Nicotinamide Deamination.

PubMed

Hachisuka, Shin-Ichi; Sato, Takaaki; Atomi, Haruyuki

2018-06-01

Many organisms possess pathways that regenerate NAD + from its degradation products, and two pathways are known to salvage NAD + from nicotinamide (Nm). One is a four-step pathway that proceeds through deamination of Nm to nicotinic acid (Na) by Nm deamidase and phosphoribosylation to nicotinic acid mononucleotide (NaMN), followed by adenylylation and amidation. Another is a two-step pathway that does not involve deamination and directly proceeds with the phosphoribosylation of Nm to nicotinamide mononucleotide (NMN), followed by adenylylation. Judging from genome sequence data, the hyperthermophilic archaeon Thermococcus kodakarensis is supposed to utilize the four-step pathway, but the fact that the adenylyltransferase encoded by TK0067 recognizes both NMN and NaMN also raises the possibility of a two-step salvage mechanism. Here, we examined the substrate specificity of the recombinant TK1676 protein, annotated as nicotinic acid phosphoribosyltransferase. The TK1676 protein displayed significant activity toward Na and phosphoribosyl pyrophosphate (PRPP) and only trace activity with Nm and PRPP. We further performed genetic analyses on TK0218 (quinolinic acid phosphoribosyltransferase) and TK1650 (Nm deamidase), involved in de novo biosynthesis and four-step salvage of NAD + , respectively. The ΔTK0218 mutant cells displayed growth defects in a minimal synthetic medium, but growth was fully restored with the addition of Na or Nm. The ΔTK0218 ΔTK1650 mutant cells did not display growth in the minimal medium, and growth was restored with the addition of Na but not Nm. The enzymatic and genetic analyses strongly suggest that NAD + salvage in T. kodakarensis requires deamination of Nm and proceeds through the four-step pathway. IMPORTANCE Hyperthermophiles must constantly deal with increased degradation rates of their biomolecules due to their high growth temperatures. Here, we identified the pathway that regenerates NAD + from nicotinamide (Nm) in the hyperthermophilic archaeon Thermococcus kodakarensis The organism utilizes a four-step pathway that initially hydrolyzes the amide bond of Nm to generate nicotinic acid (Na), followed by phosphoribosylation, adenylylation, and amidation. Although the two-step pathway, consisting of only phosphoribosylation of Nm and adenylylation, seems to be more efficient, Nm mononucleotide in the two-step pathway is much more thermolabile than Na mononucleotide, the corresponding intermediate in the four-step pathway. Although NAD + itself is thermolabile, this may represent an example of a metabolism that has evolved to avoid the use of thermolabile intermediates. Copyright © 2018 American Society for Microbiology.

Reanalysis and revision of the complete mitochondrial genome of Rachycentron canadum (Teleostei, Perciformes, Rachycentridae).

PubMed

Musika, Jidapa; Khongchatee, Adison; Phinchongsakuldit, Jaros

2014-08-01

The complete mitochondrial genome of cobia, Rachycentron canadum, was reanalyzed and revised. The genome is 18,008 bp in length, containing 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region or displacement loop (D-loop). The gene arrangement is identical to that observed in most vertebrates. Base composition on the heavy strand is 30.14% A, 25.22% C, 15.80% G and 28.84% T. The D-loop region exhibits an A + T rich pattern, containing short tandem repeats of TATATACATGG, TATATGCACAA and TATATGCACGG. The mitochondrial genome studied differs from the previously published genome in two segments; the control region to 12S and ND5 to tRNA(Glu). The 12S sequence also differs from those published in the databases. Phylogeny analyses revealed that the differences could be due to errors in sequence assembly and/or sample misidentification of the previous studies.

Dislocation loop formation in model FeCrAl alloys after neutron irradiation below 1 dpa

DOE PAGES

Field, Kevin G.; Briggs, Samuel A.; Sridharan, Kumar; ...

2017-08-01

FeCrAl alloys with varying compositions and microstructures are under consideration for accident-tolerant fuel cladding, but limited details exist on dislocation loop formation and growth for this class of alloys under neutron irradiation. Four model FeCrAl alloys with chromium contents ranging from 10.01 to 17.51 wt % and alunimum contents of 4.78 to 2.93 wt % were neutron irradiated to doses of 0.3–0.8 displacements per atom (dpa) at temperatures of 335–355°C. On-zone STEM imaging revealed a mixed population of black dots and larger dislocation loops with either a/2< 111 > or a< 100 > Burgers vectors. Weak composition dependencies were observedmore » and varied depending on whether the defect size, number density, or ratio of defect types was of interest. Here, the results were found to mirror those of previous studies on FeCrAl and FeCr alloys irradiated under similar conditions, although distinct differences exist.« less

Dislocation loop formation in model FeCrAl alloys after neutron irradiation below 1 dpa

NASA Astrophysics Data System (ADS)

Field, Kevin G.; Briggs, Samuel A.; Sridharan, Kumar; Yamamoto, Yukinori; Howard, Richard H.

2017-11-01

FeCrAl alloys with varying compositions and microstructures are under consideration for accident-tolerant fuel cladding, but limited details exist on dislocation loop formation and growth for this class of alloys under neutron irradiation. Four model FeCrAl alloys with chromium contents ranging from 10.01 to 17.51 wt % and aluminum contents of 4.78 to 2.93 wt % were neutron irradiated to doses of 0.3-0.8 displacements per atom (dpa) at temperatures of 335-355 °C. On-zone STEM imaging revealed a mixed population of black dots and larger dislocation loops with either a / 2 〈 111 〉 or a 〈 100 〉 Burgers vectors. Weak composition dependencies were observed and varied depending on whether the defect size, number density, or ratio of defect types was of interest. Results were found to mirror those of previous studies on FeCrAl and FeCr alloys irradiated under similar conditions, although distinct differences exist.

Comparison of three-dimensional orthodontic load systems of different commercial archwires for space closure.

PubMed

Gajda, Steven; Chen, Jie

2012-03-01

To experimentally quantify the effects of the loop design on three-dimensional orthodontic load systems of two types of commercial closing loop archwires: Teardrop and Keyhole. An orthodontic force tester and custom-made dentoform were used to measure the load systems produced on two teeth during simulated space closure. The system included three force components along and three moment components about three clinically defined axes on two target teeth: the left maxillary canine and the lateral incisor. The archwires were attached to the dentoform and were activated following a standard clinical procedure. The resulting six load components produced by the two archwires were reported and compared. The results were also compared with those of the T-loop archwire published previously. The three designs deliver similar loading patterns; however, the component magnitudes are dependent on the design. All of the designs result in lingual tipping of the teeth, canine lingual-mesial displacement, canine crown-mesial-in rotation, and incisor crown-distal-in rotation.

Effect of a Near Fault on the Seismic Response of a Base-Isolated Structure with a Soft Storey

NASA Astrophysics Data System (ADS)

Athamnia, B.; Ounis, A.; Abdeddaim, M.

2017-12-01

This study focuses on the soft-storey behavior of RC structures with lead core rubber bearing (LRB) isolation systems under near and far-fault motions. Under near-fault ground motions, seismic isolation devices might perform poorly because of large isolator displacements caused by large velocity and displacement pulses associated with such strong motions. In this study, four different structural models have been designed to study the effect of soft-storey behavior under near-fault and far-fault motions. The seismic analysis for isolated reinforced concrete buildings is carried out using a nonlinear time history analysis method. Inter-story drifts, absolute acceleration, displacement, base shear forces, hysteretic loops and the distribution of plastic hinges are examined as a result of the analysis. These results show that the performance of a base isolated RC structure is more affected by increasing the height of a story under nearfault motion than under far-fault motion.

Large-scale structure perturbation theory without losing stream crossing

DOE PAGES

McDonald, Patrick; Vlah, Zvonimir

2018-01-10

Here, we suggest an approach to perturbative calculations of large-scale clustering in the Universe that includes from the start the stream crossing (multiple velocities for mass elements at a single position) that is lost in traditional calculations. Starting from a functional integral over displacement, the perturbative series expansion is in deviations from (truncated) Zel’dovich evolution, with terms that can be computed exactly even for stream-crossed displacements. We evaluate the one-loop formulas for displacement and density power spectra numerically in 1D, finding dramatic improvement in agreement with N-body simulations compared to the Zel’dovich power spectrum (which is exact in 1D upmore » to stream crossing). Beyond 1D, our approach could represent an improvement over previous expansions even aside from the inclusion of stream crossing, but we have not investigated this numerically. In the process we show how to achieve effective-theory-like regulation of small-scale fluctuations without free parameters.« less

Large-scale structure perturbation theory without losing stream crossing

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

McDonald, Patrick; Vlah, Zvonimir

Here, we suggest an approach to perturbative calculations of large-scale clustering in the Universe that includes from the start the stream crossing (multiple velocities for mass elements at a single position) that is lost in traditional calculations. Starting from a functional integral over displacement, the perturbative series expansion is in deviations from (truncated) Zel’dovich evolution, with terms that can be computed exactly even for stream-crossed displacements. We evaluate the one-loop formulas for displacement and density power spectra numerically in 1D, finding dramatic improvement in agreement with N-body simulations compared to the Zel’dovich power spectrum (which is exact in 1D upmore » to stream crossing). Beyond 1D, our approach could represent an improvement over previous expansions even aside from the inclusion of stream crossing, but we have not investigated this numerically. In the process we show how to achieve effective-theory-like regulation of small-scale fluctuations without free parameters.« less

Standing Kink modes in three-dimensional coronal loops

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

Pascoe, D. J.; De Moortel, I., E-mail: dpascoe@mcs.st-andrews.ac.uk

2014-04-01

So far, the straight flux tube model proposed by Edwin and Roberts is the most commonly used tool in practical coronal seismology, in particular, to infer values of the (coronal) magnetic field from observed, standing kink mode oscillations. In this paper, we compare the period predicted by this basic model with three-dimensional (3D) numerical simulations of standing kink mode oscillations, as the period is a crucial parameter in the seismological inversion to determine the magnetic field. We perform numerical simulations of standing kink modes in both straight and curved 3D coronal loops and consider excitation by internal and external drivers.more » The period of oscillation for the displacement of dense coronal loops is determined by the loop length and the kink speed, in agreement with the estimate based on analytical theory for straight flux tubes. For curved coronal loops embedded in a magnetic arcade and excited by an external driver, a secondary mode with a period determined by the loop length and external Alfvén speed is also present. When a low number of oscillations is considered, these two periods can result in a single, non-resolved (broad) peak in the power spectrum, particularly for low values of the density contrast for which the two periods will be relatively similar. In that case (and for this particular geometry), the presence of this additional mode would lead to ambiguous seismological estimates of the magnetic field strength.« less

Interactive Retro-Deformation of Terrain for Reconstructing 3D Fault Displacements.

PubMed

Westerteiger, R; Compton, T; Bernadin, T; Cowgill, E; Gwinner, K; Hamann, B; Gerndt, A; Hagen, H

2012-12-01

Planetary topography is the result of complex interactions between geological processes, of which faulting is a prominent component. Surface-rupturing earthquakes cut and move landforms which develop across active faults, producing characteristic surface displacements across the fault. Geometric models of faults and their associated surface displacements are commonly applied to reconstruct these offsets to enable interpretation of the observed topography. However, current 2D techniques are limited in their capability to convey both the three-dimensional kinematics of faulting and the incremental sequence of events required by a given reconstruction. Here we present a real-time system for interactive retro-deformation of faulted topography to enable reconstruction of fault displacement within a high-resolution (sub 1m/pixel) 3D terrain visualization. We employ geometry shaders on the GPU to intersect the surface mesh with fault-segments interactively specified by the user and transform the resulting surface blocks in realtime according to a kinematic model of fault motion. Our method facilitates a human-in-the-loop approach to reconstruction of fault displacements by providing instant visual feedback while exploring the parameter space. Thus, scientists can evaluate the validity of traditional point-to-point reconstructions by visually examining a smooth interpolation of the displacement in 3D. We show the efficacy of our approach by using it to reconstruct segments of the San Andreas fault, California as well as a graben structure in the Noctis Labyrinthus region on Mars.

Hardening Mechanisms of Silicon Nanospheres: A Molecular Dynamics Study

DTIC Science & Technology

2011-05-01

in single oxide system 111 Figure 5.9 Dislocation motion in double oxide systems 112 x Figure 5.10 Dislocation response to incremental...addressed as no single dislocation loops were ever separated and no diffraction peaks indicative of the -Sn phase were observed. The load vs. displacement...as the diamond cubic structure has angle dependent covalent bonds. Therefore, other potentials have been 20 developed that model the

Increasing the computational efficient of digital cross correlation by a vectorization method

NASA Astrophysics Data System (ADS)

Chang, Ching-Yuan; Ma, Chien-Ching

2017-08-01

This study presents a vectorization method for use in MATLAB programming aimed at increasing the computational efficiency of digital cross correlation in sound and images, resulting in a speedup of 6.387 and 36.044 times compared with performance values obtained from looped expression. This work bridges the gap between matrix operations and loop iteration, preserving flexibility and efficiency in program testing. This paper uses numerical simulation to verify the speedup of the proposed vectorization method as well as experiments to measure the quantitative transient displacement response subjected to dynamic impact loading. The experiment involved the use of a high speed camera as well as a fiber optic system to measure the transient displacement in a cantilever beam under impact from a steel ball. Experimental measurement data obtained from the two methods are in excellent agreement in both the time and frequency domain, with discrepancies of only 0.68%. Numerical and experiment results demonstrate the efficacy of the proposed vectorization method with regard to computational speed in signal processing and high precision in the correlation algorithm. We also present the source code with which to build MATLAB-executable functions on Windows as well as Linux platforms, and provide a series of examples to demonstrate the application of the proposed vectorization method.

Structural pathway of regulated substrate transfer and threading through an Hsp100 disaggregase.

PubMed

Deville, Célia; Carroni, Marta; Franke, Kamila B; Topf, Maya; Bukau, Bernd; Mogk, Axel; Saibil, Helen R

2017-08-01

Refolding aggregated proteins is essential in combating cellular proteotoxic stress. Together with Hsp70, Hsp100 chaperones, including Escherichia coli ClpB, form a powerful disaggregation machine that threads aggregated polypeptides through the central pore of tandem adenosine triphosphatase (ATPase) rings. To visualize protein disaggregation, we determined cryo-electron microscopy structures of inactive and substrate-bound ClpB in the presence of adenosine 5'- O -(3-thiotriphosphate), revealing closed AAA+ rings with a pronounced seam. In the substrate-free state, a marked gradient of resolution, likely corresponding to mobility, spans across the AAA+ rings with a dynamic hotspot at the seam. On the seam side, the coiled-coil regulatory domains are locked in a horizontal, inactive orientation. On the opposite side, the regulatory domains are accessible for Hsp70 binding, substrate targeting, and activation. In the presence of the model substrate casein, the polypeptide threads through the entire pore channel and increased nucleotide occupancy correlates with higher ATPase activity. Substrate-induced domain displacements indicate a pathway of regulated substrate transfer from Hsp70 to the ClpB pore, inside which a spiral of loops contacts the substrate. The seam pore loops undergo marked displacements, along with ordering of the regulatory domains. These asymmetric movements suggest a mechanism for ATPase activation and substrate threading during disaggregation.

A Redox 2-Cys Mechanism Regulates the Catalytic Activity of Divergent Cyclophilins1[W

PubMed Central

Campos, Bruna Medéia; Sforça, Mauricio Luis; Ambrosio, Andre Luis Berteli; Domingues, Mariane Noronha; Brasil de Souza, Tatiana de Arruda Campos; Barbosa, João Alexandre Ribeiro Gonçalvez; Leme, Adriana Franco Paes; Perez, Carlos Alberto; Whittaker, Sara Britt-Marie; Murakami, Mario Tyago; Zeri, Ana Carolina de Matos; Benedetti, Celso Eduardo

2013-01-01

The citrus (Citrus sinensis) cyclophilin CsCyp is a target of the Xanthomonas citri transcription activator-like effector PthA, required to elicit cankers on citrus. CsCyp binds the citrus thioredoxin CsTdx and the carboxyl-terminal domain of RNA polymerase II and is a divergent cyclophilin that carries the additional loop KSGKPLH, invariable cysteine (Cys) residues Cys-40 and Cys-168, and the conserved glutamate (Glu) Glu-83. Despite the suggested roles in ATP and metal binding, the functions of these unique structural elements remain unknown. Here, we show that the conserved Cys residues form a disulfide bond that inactivates the enzyme, whereas Glu-83, which belongs to the catalytic loop and is also critical for enzyme activity, is anchored to the divergent loop to maintain the active site open. In addition, we demonstrate that Cys-40 and Cys-168 are required for the interaction with CsTdx and that CsCyp binds the citrus carboxyl-terminal domain of RNA polymerase II YSPSAP repeat. Our data support a model where formation of the Cys-40-Cys-168 disulfide bond induces a conformational change that disrupts the interaction of the divergent and catalytic loops, via Glu-83, causing the active site to close. This suggests a new type of allosteric regulation in divergent cyclophilins, involving disulfide bond formation and a loop-displacement mechanism. PMID:23709667

Propagating wave in active region-loops, located over the solar disk observed by the Interface Region Imaging Spectrograph

NASA Astrophysics Data System (ADS)

Zhang, B.; Hou, Y. J.; Zhang, J.

2018-03-01

Aims: We aim to ascertain the physical parameters of a propagating wave over the solar disk detected by the Interface Region Imaging Spectrograph (IRIS). Methods: Using imaging data from the IRIS and the Solar Dynamic Observatory (SDO), we tracked bright spots to determine the parameters of a propagating transverse wave in active region (AR) loops triggered by activation of a filament. Deriving the Doppler velocity of Si IV line from spectral observations of IRIS, we have determined the rotating directions of active region loops which are relevant to the wave. Results: On 2015 December 19, a filament was located on the polarity inversion line of the NOAA AR 12470. The filament was activated and then caused a C1.1 two-ribbon flare. Between the flare ribbons, two rotation motions of a set of bright loops were observed to appear in turn with opposite directions. Following the end of the second rotation, a propagating wave and an associated transverse oscillation were detected in these bright loops. In 1400 Å channel, there was bright material flowing along the loops in a wave-like manner, with a period of 128 s and a mean amplitude of 880 km. For the transverse oscillation, we tracked a given loop and determine the transverse positions of the tracking loop in a limited longitudinal range. In both of 1400 Å and 171 Å channels, approximately four periods are distinguished during the transverse oscillation. The mean period of the oscillation is estimated as 143 s and the displacement amplitude as between 1370 km and 690 km. We interpret these oscillations as a propagating kink wave and obtain its speed of 1400 km s-1. Conclusions: Our observations reveal that a flare associated with filament activation could trigger a kink propagating wave in active region loops over the solar disk. Movies associated to Figs. 1-4 are available at http://https://www.aanda.org

Active member vibration control for a 4 meter primary reflector support structure

NASA Technical Reports Server (NTRS)

Umland, J. W.; Chen, G.-S.

1992-01-01

The design and testing of a new low voltage piezoelectric active member with integrated load cell and displacement sensor is described. This active member is intended for micron level vibration and structural shape control of the Precision Segmented Reflector test-bed. The test-bed is an erectable 4 meter diameter backup support truss for a 2.4 meter focal length parabolic reflector. Active damping of the test-bed is then demonstrated using the newly developed active members. The control technique used is referred to as bridge feedback. With this technique the internal sensors are used in a local feedback loop to match the active member's input impedance to the structure's load impedance, which then maximizes vibrational energy dissipation. The active damping effectiveness is then evaluated from closed loop frequency responses.

Cecal volvulus as a complication of gastric banding.

PubMed

Fakhro, Abdulla; O'Riordan, James M; Lawler, Leo P; O'Connell, P Ronan

2009-12-01

Surgery is an increasingly important management option for patients with obesity. Laparoscopic adjustable gastric banding is a procedure employed to treat morbid obesity refractory to medical therapy. It works by reducing the capacity of the stomach and promoting early satiety. We report the unusual case of a 33-year-old female who presented acutely 2 years following laparoscopic adjustable gastric banding with cecal volvulus and closed loop obstruction caused by displacement of the connecting tube.

NAD(P)H:Flavin Mononucleotide Oxidoreductase Inactivation during 2,4,6-Trinitrotoluene Reduction

PubMed Central

Riefler, R. Guy; Smets, Barth F.

2002-01-01

Bacteria readily transform 2,4,6-trinitrotoluene (TNT), a contaminant frequently found at military bases and munitions production facilities, by reduction of the nitro group substituents. In this work, the kinetics of nitroreduction were investigated by using a model nitroreductase, NAD(P)H:flavin mononucleotide (FMN) oxidoreductase. Under mediation by NAD(P)H:FMN oxidoreductase, TNT rapidly reacted with NADH to form 2-hydroxylamino-4,6-dinitrotoluene and 4-hydroxylamino-2,6-dinitrotoluene, whereas 2-amino-4,6-dinitrotoluene and 4-amino-2,6-dinitrotoluene were not produced. Progressive loss of activity was observed during TNT reduction, indicating inactivation of the enzyme during transformation. It is likely that a nitrosodinitrotoluene intermediate reacted with the NAD(P)H:FMN oxidoreductase, leading to enzyme inactivation. A half-maximum constant with respect to NADH, KN, of 394 μM was measured, indicating possible NADH limitation under typical cellular conditions. A mathematical model that describes the inactivation process and NADH limitation provided a good fit to TNT reduction profiles. This work represents the first step in developing a comprehensive enzyme level understanding of nitroarene biotransformation. PMID:11916686

YCL047C/POF1 Is a Novel Nicotinamide Mononucleotide Adenylyltransferase (NMNAT) in Saccharomyces cerevisiae*

PubMed Central

Kato, Michiko; Lin, Su-Ju

2014-01-01

NAD+ is an essential metabolic cofactor involved in various cellular biochemical processes. Nicotinamide riboside (NR) is an endogenously produced key pyridine metabolite that plays important roles in the maintenance of NAD+ pool. Using a NR-specific cell-based screen, we identified mutants that exhibit altered NR release phenotype. Yeast cells lacking the ORF YCL047C/POF1 release considerably more NR compared with wild type, suggesting that POF1 plays an important role in NR/NAD+ metabolism. The amino acid sequence of Pof1 indicates that it is a putative nicotinamide mononucleotide adenylyltransferase (NMNAT). Unlike other yeast NMNATs, Pof1 exhibits NMN-specific adenylyltransferase activity. Deletion of POF1 significantly lowers NAD+ levels and decreases the efficiency of NR utilization, resistance to oxidative stress, and NR-induced life span extension. We also show that NR is constantly produced by multiple nucleotidases and that the intracellular NR pools are likely to be compartmentalized, which contributes to the regulation of NAD+ homeostasis. Our findings may contribute to the understanding of the molecular basis and regulation of NAD+ metabolism in higher eukaryotes. PMID:24759102

New chloroplast microsatellite markers suitable for assessing genetic diversity of Lolium perenne and other related grass species

PubMed Central

Diekmann, Kerstin; Hodkinson, Trevor R.; Barth, Susanne

2012-01-01

Background and Aims Lolium perenne (perennial ryegrass) is the most important forage grass species of temperate regions. We have previously released the chloroplast genome sequence of L. perenne ‘Cashel’. Here nine chloroplast microsatellite markers are published, which were designed based on knowledge about genetically variable regions within the L. perenne chloroplast genome. These markers were successfully used for characterizing the genetic diversity in Lolium and different grass species. Methods Chloroplast genomes of 14 Poaceae taxa were screened for mononucleotide microsatellite repeat regions and primers designed for their amplification from nine loci. The potential of these markers to assess genetic diversity was evaluated on a set of 16 Irish and 15 European L. perenne ecotypes, nine L. perenne cultivars, other Lolium taxa and other grass species. Key Results All analysed Poaceae chloroplast genomes contained more than 200 mononucleotide repeats (chloroplast simple sequence repeats, cpSSRs) of at least 7 bp in length, concentrated mainly in the large single copy region of the genome. Nucleotide composition varied considerably among subfamilies (with Pooideae biased towards poly A repeats). The nine new markers distinguish L. perenne from all non-Lolium taxa. TeaCpSSR28 was able to distinguish between all Lolium species and Lolium multiflorum due to an elongation of an A8 mononucleotide repeat in L. multiflorum. TeaCpSSR31 detected a considerable degree of microsatellite length variation and single nucleotide polymorphism. TeaCpSSR27 revealed variation within some L. perenne accessions due to a 44-bp indel and was hence readily detected by simple agarose gel electrophoresis. Smaller insertion/deletion events or single nucleotide polymorphisms detected by these new markers could be visualized by polyacrylamide gel electrophoresis or DNA sequencing, respectively. Conclusions The new markers are a valuable tool for plant breeding companies, seed testing agencies and the wider scientific community due to their ability to monitor genetic diversity within breeding pools, to trace maternal inheritance and to distinguish closely related species. PMID:22419761

New chloroplast microsatellite markers suitable for assessing genetic diversity of Lolium perenne and other related grass species.

PubMed

Diekmann, Kerstin; Hodkinson, Trevor R; Barth, Susanne

2012-11-01

Lolium perenne (perennial ryegrass) is the most important forage grass species of temperate regions. We have previously released the chloroplast genome sequence of L. perenne 'Cashel'. Here nine chloroplast microsatellite markers are published, which were designed based on knowledge about genetically variable regions within the L. perenne chloroplast genome. These markers were successfully used for characterizing the genetic diversity in Lolium and different grass species. Chloroplast genomes of 14 Poaceae taxa were screened for mononucleotide microsatellite repeat regions and primers designed for their amplification from nine loci. The potential of these markers to assess genetic diversity was evaluated on a set of 16 Irish and 15 European L. perenne ecotypes, nine L. perenne cultivars, other Lolium taxa and other grass species. All analysed Poaceae chloroplast genomes contained more than 200 mononucleotide repeats (chloroplast simple sequence repeats, cpSSRs) of at least 7 bp in length, concentrated mainly in the large single copy region of the genome. Nucleotide composition varied considerably among subfamilies (with Pooideae biased towards poly A repeats). The nine new markers distinguish L. perenne from all non-Lolium taxa. TeaCpSSR28 was able to distinguish between all Lolium species and Lolium multiflorum due to an elongation of an A(8) mononucleotide repeat in L. multiflorum. TeaCpSSR31 detected a considerable degree of microsatellite length variation and single nucleotide polymorphism. TeaCpSSR27 revealed variation within some L. perenne accessions due to a 44-bp indel and was hence readily detected by simple agarose gel electrophoresis. Smaller insertion/deletion events or single nucleotide polymorphisms detected by these new markers could be visualized by polyacrylamide gel electrophoresis or DNA sequencing, respectively. The new markers are a valuable tool for plant breeding companies, seed testing agencies and the wider scientific community due to their ability to monitor genetic diversity within breeding pools, to trace maternal inheritance and to distinguish closely related species.

Characterization and mutational analysis of a nicotinamide mononucleotide deamidase from Agrobacterium tumefaciens showing high thermal stability and catalytic efficiency

PubMed Central

Martínez-Moñino, Ana Belén; Zapata-Pérez, Rubén; García-Saura, Antonio Ginés; Gil-Ortiz, Fernando; Pérez-Gilabert, Manuela

2017-01-01

NAD+ has emerged as a crucial element in both bioenergetic and signaling pathways since it acts as a key regulator of cellular and organismal homeostasis. Among the enzymes involved in its recycling, nicotinamide mononucleotide (NMN) deamidase is one of the key players in the bacterial pyridine nucleotide cycle, where it catalyzes the conversion of NMN into nicotinic acid mononucleotide (NaMN), which is later converted to NAD+ in the Preiss-Handler pathway. The biochemical characteristics of bacterial NMN deamidases have been poorly studied, although they have been investigated in some firmicutes, gamma-proteobacteria and actinobacteria. In this study, we present the first characterization of an NMN deamidase from an alphaproteobacterium, Agrobacterium tumefaciens (AtCinA). The enzyme was active over a broad pH range, with an optimum at pH 7.5. Moreover, the enzyme was quite stable at neutral pH, maintaining 55% of its activity after 14 days. Surprisingly, AtCinA showed the highest optimal (80°C) and melting (85°C) temperatures described for an NMN deamidase. The above described characteristics, together with its high catalytic efficiency, make AtCinA a promising biocatalyst for the production of pure NaMN. In addition, six mutants (C32A, S48A, Y58F, Y58A, T105A and R145A) were designed to study their involvement in substrate binding, and two (S31A and K63A) to determine their contribution to the catalysis. However, only four mutants (C32A, S48A Y58F and T105A) showed activity, although with reduced catalytic efficiency. These results, combined with a thermal and structural analysis, reinforce the Ser/Lys catalytic dyad mechanism as the most plausible among those proposed. PMID:28388636

Characterization of frequencies and distribution of single nucleotide insertions/deletions in the human genome.

PubMed

Tan, Ene-Choo; Li, Haixia

2006-07-19

Most of the studies on single nucleotide variations are on substitutions rather than insertions/deletions. In this study, we examined the distribution and characteristics of single nucleotide insertions/deletions (SNindels), using data available from dbSNP for all the human chromosomes. There are almost 300,000 SNindels in the database, of which only 0.8% are validated. They occur at the frequency of 0.887 per 10 kb on average for the whole genome, or approximately 1 for every 11,274 bp. More than half occur in regions with mononucleotide repeats the longest of which is 47 bases. Overall the mononucleotide repeats involving C and G are much shorter than those for A and T. About 12% are surrounded by palindromes. There is general correlation between chromosome size and total number for each chromosome. Inter-chromosomal variation in density ranges from 0.6 to 21.7 per kilobase. The overall spectrum shows very high proportion of SNindel of types -/A and -/T at over 81%. The proportion of -/A and -/T SNindels for each chromosome is correlated to its AT content. Less than half of the SNindels are within or near known genes and even fewer (<0.183%) in coding regions, and more than 1.4% of -/C and -/G are in coding compared to 0.2% for -/A and -/T types. SNindels of -/A and -/T types make up 80% of those found within untranslated regions but less than 40% of those within coding regions. A separate analysis using the subset of 2324 validated SNindels showed slightly less AT bias of 74%, SNindels not within mononucleotide repeats showed even less AT bias at 58%. Density of validated SNindels is 0.007/10 kb overall and 90% are found within or near genes. Among all chromosomes, Y has the lowest numbers and densities for all SNindels, validated SNindels, and SNindels not within repeats.

Direct Observation of Sink-Dependent Defect Evolution in Nanocrystalline Iron under Irradiation

DOE PAGES

El Atwani, Osman; Nathaniel, James; Leff, Asher C.; ...

2017-05-12

Crystal defects generated during irradiation can result in severe changes in morphology and an overall degradation of mechanical properties in a given material. Nanomaterials have been proposed as radiation damage tolerant materials, due to the hypothesis that defect density decreases with grain size refinement due to the increase in grain boundary surface area. The lower defect density should arise from grain boundary-point defect absorption and enhancement of interstitial-vacancy annihilation. In this study, low energy helium ion irradiation on free-standing iron thin films were performed at 573 K. Interstitial loops of a 0 /2 [111] Burgers vector were directly observed asmore » a result of the displacement damage. Loop density trends with grain size demonstrated an increase in the nanocrystalline (<100 nm) regime, but scattered behavior in the transition from the nanocrystalline to the ultra-fine regime (100–500 nm). To examine the validity of such trends, loop density and area for different grains at various irradiation doses were compared and revealed efficient defect absorption in the nanocrystalline grain size regime, but loop coalescence in the ultra-fine grain size regime. Lastly, a relationship between the denuded zone formation, a measure of grain boundary absorption efficiency, grain size, grain boundary type and misorientation angle is determined.« less

Direct Observation of Sink-Dependent Defect Evolution in Nanocrystalline Iron under Irradiation

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

El Atwani, Osman; Nathaniel, James; Leff, Asher C.

Crystal defects generated during irradiation can result in severe changes in morphology and an overall degradation of mechanical properties in a given material. Nanomaterials have been proposed as radiation damage tolerant materials, due to the hypothesis that defect density decreases with grain size refinement due to the increase in grain boundary surface area. The lower defect density should arise from grain boundary-point defect absorption and enhancement of interstitial-vacancy annihilation. In this study, low energy helium ion irradiation on free-standing iron thin films were performed at 573 K. Interstitial loops of a 0 /2 [111] Burgers vector were directly observed asmore » a result of the displacement damage. Loop density trends with grain size demonstrated an increase in the nanocrystalline (<100 nm) regime, but scattered behavior in the transition from the nanocrystalline to the ultra-fine regime (100–500 nm). To examine the validity of such trends, loop density and area for different grains at various irradiation doses were compared and revealed efficient defect absorption in the nanocrystalline grain size regime, but loop coalescence in the ultra-fine grain size regime. Lastly, a relationship between the denuded zone formation, a measure of grain boundary absorption efficiency, grain size, grain boundary type and misorientation angle is determined.« less

Rapid and Sensitive Isothermal Detection of Nucleic-acid Sequence by Multiple Cross Displacement Amplification.

PubMed

Wang, Yi; Wang, Yan; Ma, Ai-Jing; Li, Dong-Xun; Luo, Li-Juan; Liu, Dong-Xin; Jin, Dong; Liu, Kai; Ye, Chang-Yun

2015-07-08

We have devised a novel amplification strategy based on isothermal strand-displacement polymerization reaction, which was termed multiple cross displacement amplification (MCDA). The approach employed a set of ten specially designed primers spanning ten distinct regions of target sequence and was preceded at a constant temperature (61-65 °C). At the assay temperature, the double-stranded DNAs were at dynamic reaction environment of primer-template hybrid, thus the high concentration of primers annealed to the template strands without a denaturing step to initiate the synthesis. For the subsequent isothermal amplification step, a series of primer binding and extension events yielded several single-stranded DNAs and single-stranded single stem-loop DNA structures. Then, these DNA products enabled the strand-displacement reaction to enter into the exponential amplification. Three mainstream methods, including colorimetric indicators, agarose gel electrophoresis and real-time turbidity, were selected for monitoring the MCDA reaction. Moreover, the practical application of the MCDA assay was successfully evaluated by detecting the target pathogen nucleic acid in pork samples, which offered advantages on quick results, modest equipment requirements, easiness in operation, and high specificity and sensitivity. Here we expounded the basic MCDA mechanism and also provided details on an alternative (Single-MCDA assay, S-MCDA) to MCDA technique.

A strand graph semantics for DNA-based computation

PubMed Central

Petersen, Rasmus L.; Lakin, Matthew R.; Phillips, Andrew

2015-01-01

DNA nanotechnology is a promising approach for engineering computation at the nanoscale, with potential applications in biofabrication and intelligent nanomedicine. DNA strand displacement is a general strategy for implementing a broad range of nanoscale computations, including any computation that can be expressed as a chemical reaction network. Modelling and analysis of DNA strand displacement systems is an important part of the design process, prior to experimental realisation. As experimental techniques improve, it is important for modelling languages to keep pace with the complexity of structures that can be realised experimentally. In this paper we present a process calculus for modelling DNA strand displacement computations involving rich secondary structures, including DNA branches and loops. We prove that our calculus is also sufficiently expressive to model previous work on non-branching structures, and propose a mapping from our calculus to a canonical strand graph representation, in which vertices represent DNA strands, ordered sites represent domains, and edges between sites represent bonds between domains. We define interactions between strands by means of strand graph rewriting, and prove the correspondence between the process calculus and strand graph behaviours. Finally, we propose a mapping from strand graphs to an efficient implementation, which we use to perform modelling and simulation of DNA strand displacement systems with rich secondary structure. PMID:27293306

Concerted action of the MutLβ heterodimer and Mer3 helicase regulates the global extent of meiotic gene conversion

PubMed Central

Duroc, Yann; Kumar, Rajeev; Ranjha, Lepakshi; Adam, Céline; Guérois, Raphaël; Md Muntaz, Khan; Marsolier-Kergoat, Marie-Claude; Dingli, Florent; Laureau, Raphaëlle; Loew, Damarys; Llorente, Bertrand; Charbonnier, Jean-Baptiste; Cejka, Petr; Borde, Valérie

2017-01-01

Gene conversions resulting from meiotic recombination are critical in shaping genome diversification and evolution. How the extent of gene conversions is regulated is unknown. Here we show that the budding yeast mismatch repair related MutLβ complex, Mlh1-Mlh2, specifically interacts with the conserved meiotic Mer3 helicase, which recruits it to recombination hotspots, independently of mismatch recognition. This recruitment is essential to limit gene conversion tract lengths genome-wide, without affecting crossover formation. Contrary to expectations, Mer3 helicase activity, proposed to extend the displacement loop (D-loop) recombination intermediate, does not influence the length of gene conversion events, revealing non-catalytical roles of Mer3. In addition, both purified Mer3 and MutLβ preferentially recognize D-loops, providing a mechanism for limiting gene conversion in vivo. These findings show that MutLβ is an integral part of a new regulatory step of meiotic recombination, which has implications to prevent rapid allele fixation and hotspot erosion in populations. DOI: http://dx.doi.org/10.7554/eLife.21900.001 PMID:28051769

Regulated Formation of lncRNA-DNA Hybrids Enables Faster Transcriptional Induction and Environmental Adaptation.

PubMed

Cloutier, Sara C; Wang, Siwen; Ma, Wai Kit; Al Husini, Nadra; Dhoondia, Zuzer; Ansari, Athar; Pascuzzi, Pete E; Tran, Elizabeth J

2016-02-04

Long non-coding (lnc)RNAs, once thought to merely represent noise from imprecise transcription initiation, have now emerged as major regulatory entities in all eukaryotes. In contrast to the rapidly expanding identification of individual lncRNAs, mechanistic characterization has lagged behind. Here we provide evidence that the GAL lncRNAs in the budding yeast S. cerevisiae promote transcriptional induction in trans by formation of lncRNA-DNA hybrids or R-loops. The evolutionarily conserved RNA helicase Dbp2 regulates formation of these R-loops as genomic deletion or nuclear depletion results in accumulation of these structures across the GAL cluster gene promoters and coding regions. Enhanced transcriptional induction is manifested by lncRNA-dependent displacement of the Cyc8 co-repressor and subsequent gene looping, suggesting that these lncRNAs promote induction by altering chromatin architecture. Moreover, the GAL lncRNAs confer a competitive fitness advantage to yeast cells because expression of these non-coding molecules correlates with faster adaptation in response to an environmental switch. Copyright © 2016 Elsevier Inc. All rights reserved.

A deeper analysis of the epitope/paratope of PLY-5, a mouse monoclonal antibody which recognises the conserved undecapeptide tryptophan-rich loop (ECTGLAWEWWR) of bacterial cholesterol-dependent cytolysins.

PubMed

González-Menéndez, Pedro; García-Ocaña, Marcos; de los Toyos, Juan R

2013-01-04

A previous study showed that the minimal epitope recognised by the PLY-5 mAb in the conserved undecapeptide Trp-rich loop of bacterial CDCs should consist of WEWWRT (Jacobs et al., 1999) [5]. Now, through immunoscreening of amino acid substitution analogues, it is concluded that the second Trp and the Arg residues are essential in the PLY-5 epitope. The E residue is an auxiliary epitope contributor. Antibody modelling and docking simulations provided support for these findings. For recognition by the antibody, the Trp-rich loop flipped out, mimicking the mechanism of membrane insertion. The displaced second Trp was seen to establish aromatic stacking interactions with aromatic residues of the antibody paratope and the notably extruded guanidium tip of the arginine residue mediated electrostatic interactions with well-exposed carboxylic groups of glutamic residues on the surface of the paratope. Thus, the epitope/paratope interaction is mainly mediated by aromatic and by ionic interactions. Copyright © 2012 Elsevier Inc. All rights reserved.

Comparison of three-dimensional orthodontic load systems of different commercial archwires for space closure

PubMed Central

Gajda, Steven; Chen, Jie

2014-01-01

Objective To experimentally quantify the effects of the loop design on three-dimensional orthodontic load systems of two types of commercial closing loop archwires: Teardrop and Keyhole. Materials and Methods An orthodontic force tester and custom-made dentoform were used to measure the load systems produced on two teeth during simulated space closure. The system included three force components along and three moment components about three clinically defined axes on two target teeth: the left maxillary canine and the lateral incisor. The archwires were attached to the dentoform and were activated following a standard clinical procedure. Results The resulting six load components produced by the two archwires were reported and compared. The results were also compared with those of the T-loop archwire published previously. Conclusions The three designs deliver similar loading patterns; however, the component magnitudes are dependent on the design. All of the designs result in lingual tipping of the teeth, canine lingual-mesial displacement, canine crown-mesial-in rotation, and incisor crown-distal-in rotation. PMID:21879793

A new photoelectrochemical biosensors based on DNA conformational changes and isothermal circular strand-displacement polymerization reaction.

PubMed

Zhang, Xiaoru; Xu, Yunpeng; Zhao, Yanqing; Song, Weiling

2013-01-15

We report a strategy for the transduction of DNA hybridization into a readily detectable photoelectrochemical signal by means of a conformational change analogous to electrochemical DNA (E-DNA) approach. To demonstrate the effect of distance change for photosensitizer to the surface of electrode on the change of photocurrent, photosensitizer Ru(bpy)(2)(dcbpy)(2+) tagged DNA stem-loop structures were self-assembled onto a nanogold modified ITO electrode. Hybridization induced a large conformational change in DNA structure, which in turn significantly altered the electron-transfer tunneling distance between the electrode and photosensitizer. The resulting change in photocurrent was proportional to the concentration of DNA in the range of 1.0×10(-10)-8.0×10(-9)M. In order to improve the sensitivity of the photoelectrochemical biosensor, an amplified detection method based on isothermal strand displacement polymerization reaction was employed. With multiple rounds of isothermal strand replication, which led to strand displacement and constituted consecutive signal amplification, a detection limit of 9.4×10(-14)M target DNA was achieved. Copyright © 2012 Elsevier B.V. All rights reserved.

Low-Field and High-Field Characterization of THUNDER Actuators

NASA Technical Reports Server (NTRS)

Ounaies, Z.; Mossi, K.; Smith, R.; Bernd, J.; Bushnell, Dennis M. (Technical Monitor)

2001-01-01

THUNDER (THin UNimorph DrivER) actuators are pre-stressed piezoelectric devices developed at NASA Langley Research Center (LaRC) that exhibit enhanced strain capabilities. As a result, they are of interest in a variety of aerospace applications. Characterization of their performance as a function of electric field, temperature and frequency is needed in order to optimize their operation. Towards that end, a number of THUNDER devices were obtained from FACE International Co. with a stainless steel substrate varying in thickness from 1 mil to 20 mils. The various devices were evaluated to determine low-field and high-field displacement its well as the polarization hysteresis loops. The thermal stability of these drivers was evaluated by two different methods. First, the samples were thermally cycled under electric field by systematically increasing the maximum temperature from 25 C to 200 C while the displacement was being measured. Second, the samples were isothermally aged at 0 C, 50 C, 100 C. and 150 C in air, and the isothermal decay of the displacement was measured at room temperature as a function of time.

R-loops cause genomic instability in T helper lymphocytes from patients with Wiskott-Aldrich syndrome.

PubMed

Sarkar, Koustav; Han, Seong-Su; Wen, Kuo-Kuang; Ochs, Hans D; Dupré, Loïc; Seidman, Michael M; Vyas, Yatin M

2017-12-15

Wiskott-Aldrich syndrome (WAS), X-linked thrombocytopenia (XLT), and X-linked neutropenia, which are caused by WAS mutations affecting Wiskott-Aldrich syndrome protein (WASp) expression or activity, manifest in immunodeficiency, autoimmunity, genomic instability, and lymphoid and other cancers. WASp supports filamentous actin formation in the cytoplasm and gene transcription in the nucleus. Although the genetic basis for XLT/WAS has been clarified, the relationships between mutant forms of WASp and the diverse features of these disorders remain ill-defined. We sought to define how dysfunctional gene transcription is causally linked to the degree of T H cell deficiency and genomic instability in the XLT/WAS clinical spectrum. In human T H 1- or T H 2-skewing cell culture systems, cotranscriptional R-loops (RNA/DNA duplex and displaced single-stranded DNA) and DNA double-strand breaks (DSBs) were monitored in multiple samples from patients with XLT and WAS and in normal T cells depleted of WASp. WASp deficiency provokes increased R-loops and R-loop-mediated DSBs in T H 1 cells relative to T H 2 cells. Mechanistically, chromatin occupancy of serine 2-unphosphorylated RNA polymerase II is increased, and that of topoisomerase 1, an R-loop preventing factor, is decreased at R-loop-enriched regions of IFNG and TBX21 (T H 1 genes) in T H 1 cells. These aberrations accompany increased unspliced (intron-retained) and decreased spliced mRNA of IFNG and TBX21 but not IL13 (T H 2 gene). Significantly, increased cellular load of R-loops and DSBs, which are normalized on RNaseH1-mediated suppression of ectopic R-loops, inversely correlates with disease severity scores. Transcriptional R-loop imbalance is a novel molecular defect causative in T H 1 immunodeficiency and genomic instability in patients with WAS. The study proposes that cellular R-loop load could be used as a potential biomarker for monitoring symptom severity and prognostic outcome in the XLT-WAS clinical spectrum and could be targeted therapeutically. Copyright © 2017 American Academy of Allergy, Asthma & Immunology. All rights reserved.

MacA is a second cytochrome c peroxidase of Geobacter sulfurreducens.

PubMed

Seidel, Julian; Hoffmann, Maren; Ellis, Katie E; Seidel, Antonia; Spatzal, Thomas; Gerhardt, Stefan; Elliott, Sean J; Einsle, Oliver

2012-04-03

The metal-reducing δ-proteobacterium Geobacter sulfurreducens produces a large number of c-type cytochromes, many of which have been implicated in the transfer of electrons to insoluble metal oxides. Among these, the dihemic MacA was assigned a central role. Here we have produced G. sulfurreducens MacA by recombinant expression in Escherichia coli and have solved its three-dimensional structure in three different oxidation states. Sequence comparisons group MacA into the family of diheme cytochrome c peroxidases, and the protein indeed showed hydrogen peroxide reductase activity with ABTS(-2) as an electron donor. The observed K(M) was 38.5 ± 3.7 μM H(2)O(2) and v(max) was 0.78 ± 0.03 μmol of H(2)O(2)·min(-1)·mg(-1), resulting in a turnover number k(cat) = 0.46 · s(-1). In contrast, no Fe(III) reductase activity was observed. MacA was found to display electrochemical properties similar to other bacterial diheme peroxidases, in addition to the ability to electrochemically mediate electron transfer to the soluble cytochrome PpcA. Differences in activity between CcpA and MacA can be rationalized with structural variations in one of the three loop regions, loop 2, that undergoes conformational changes during reductive activation of the enzyme. This loop is adjacent to the active site heme and forms an open loop structure rather than a more rigid helix as in CcpA. For the activation of the protein, the loop has to displace the distal ligand to the active site heme, H93, in loop 1. A H93G variant showed an unexpected formation of a helix in loop 2 and disorder in loop 1, while a M297H variant that altered the properties of the electron transfer heme abolished reductive activation.

MacA is a Second Cytochrome c Peroxidase of Geobacter sulfurreducens

PubMed Central

Seidel, Julian; Hoffmann, Maren; Ellis, Katie E.; Seidel, Antonia; Spatzal, Thomas; Gerhardt, Stefan; Elliott, Sean J.

2012-01-01

The metal-reducing δ-proteobacterium Geobacter sulfurreducens produces a large number of c-type cytochromes, many of which have been implicated in the transfer of electrons to insoluble metal oxides. Among these, the dihemic MacA was assigned a central role. Here we have produced G. sulfurreducens MacA by recombinant expression in Escherichia coli and have solved its three-dimensional structure in three different oxidation states. Sequence comparisons group MacA into the family of diheme cytochrome c peroxidases, and the protein indeed showed hydrogen peroxide reductase activity with ABTS2– as an electron donor. The observed KM was 38.5 ± 3.7 μM H2O2 and vmax was 0.78 ± 0.03 μmol H2O2·min–1·mg–1, resulting in a turnover number kcat = 0.46 · s–1. In contrast, no Fe(III) reductase activity was observed. MacA was found to display similar electrochemical properties to other bacterial diheme peroxidases, in additional to the ability to electrochemically mediate electron transfer to the soluble cytochrome PpcA. Differences in activity between CcpA and MacA can be rationalized with structural variations in one of the three loop regions, loop 2, that undergo conformational changes during reductive activation of the enzyme. This loop is adjacent to the active site heme and forms an open loop structure rather than a more rigid helix as in CcpA. For the activation of the protein the loop has to displace the distal ligand to the active site heme, H93, in loop 1. A H93G variant showed an unexpected formation of a helix in loop 2 and disorder in loop 1, while a M297H variant that altered the properties of the electron transfer heme abolished reductive activation. PMID:22417533

Electron Densities in Solar Flare Loops, Chromospheric Evaporation Upflows, and Acceleration Sites

NASA Technical Reports Server (NTRS)

Aschwanden, Markus J.; Benz, Arnold O.

1996-01-01

We compare electron densities measured at three different locations in solar flares: (1) in Soft X-Ray (SXR) loops, determined from SXR emission measures and loop diameters from Yohkoh Soft X-Ray Telescope maps (n(sub e, sup SXR) = (0.2-2.5) x 10(exp 11)/ cu cm); (2) in chromospheric evaporation upflows, inferred from plasma frequency cutoffs of decimetric radio bursts detected with the 0.1-3 GHz spectrometer Phoenix of ETH Zuerich (n(sub e, sup upflow) = (0.3-11) x 10(exp 10)/cu cm; and (3) in acceleration sites, inferred from the plasma frequency at the separatrix between upward-accelerated (type III bursts) and downward-accelerated (reverse-drift bursts) electron beams [n(sub e, sup acc) = (0.6-10) x 10(exp 9)/cu cm]. The comparison of these density measurements, obtained from 44 flare episodes (during 14 different flares), demonstrates the compatibility of flare plasma density diagnostics with SXR and radio methods. The density in the upflowing plasma is found to be somewhat lower than in the filled loops, having ratios in a range n(sub e, sup upflow)/n(sub e, sup SXR) = 0.02-1.3, and a factor of 3.6 higher behind the upflow front. The acceleration sites are found to have a much lower density than the SXR-bright flare loops, i.e., n(sub e, sup acc)/n(sub e, sup SXR) = 0.005- 0.13, and thus must be physically displaced from the SXR-bright flare loops. The scaling law between electron time-of-flight distances l' and loop half-lengths s, l'/s = 1.4 +/- 0.3, recently established by Aschwanden et al. suggests that the centroid of the acceleration region is located above the SXR-bright flare loop, as envisioned in cusp geometries (e.g., in magnetic reconnection models).

Shear wave transducer for boreholes

DOEpatents

Mao, N.H.

1984-08-23

A technique and apparatus is provided for estimating in situ stresses by measuring stress-induced velocity anisotropy around a borehole. Two sets each of radially and tangentially polarized transducers are placed inside the hole with displacement directions either parallel or perpendicular to the principal stress directions. With this configuration, relative travel times are measured by both a pulsed phase-locked loop technique and a cross correlation of digitized waveforms. The biaxial velocity data are used to back-calculate the applied stress.

Shear wave transducer for stress measurements in boreholes

DOEpatents

Mao, Nai-Hsien

1987-01-01

A technique and apparatus for estimating in situ stresses by measuring stress-induced velocity anisotropy around a borehole. Two sets each of radially and tangentially polarized transducers are placed inside the hole with displacement directions either parallel or perpendicular to the principal stress directions. With this configuration, relative travel times are measured by both a pulsed phase-locked loop technique and a cross correlation of digitized waveforms. The biaxial velocity data is used to back-calculate the applied stress.

Design and implementation of active members for precision space structures

NASA Technical Reports Server (NTRS)

Webster, M. S.; Fanson, J. L.; Lurie, B. J.; O'Brien, J. F.

1992-01-01

This paper describes the development and implementation of an active member in a precision truss structure. The active member utilizes a piezoelectric actuator motor imbedded in a steel case with built-in displacement sensor. This active member is used in structural quieting. Collocated active damping control loops are designed in order to impedance match piezoelectric active members to the structure. Results from application of these controllers and actuators to the JPL Phase B testbed are given.

DNA damage mediated transcription arrest: Step back to go forward.

PubMed

Mullenders, Leon

2015-12-01

The disturbance of DNA helix conformation by bulky DNA damage poses hindrance to transcription elongating due to stalling of RNA polymerase at transcription blocking lesions. Stalling of RNA polymerase provokes the formation of R-loops, i.e. the formation of a DNA-RNA hybrid and a displaced single stranded DNA strand as well as displacement of spliceosomes. R-loops are processed into DNA single and double strand breaks by NER factors depending on TC-NER factors leading to genome instability. Moreover, stalling of RNA polymerase induces a strong signal for cell cycle arrest and apoptosis. These toxic and mutagenic effects are counteracted by a rapid recruitment of DNA repair proteins to perform transcription coupled nucleotide excision repair (TC-NER) to remove the blocking DNA lesions and to restore transcription. Recent studies have highlighted the role of backtracking of RNA polymerase to facilitate TC-NER and identified novel factors that play key roles in TC-NER and in restoration of transcription. On the molecular level these factors facilitate stability of the repair complex by promotion and regulation of various post-translational modifications of NER factors and chromatin substrate. In addition, the continuous flow of new factors that emerge from screening assays hints to several regulatory levels to safeguard the integrity of transcription elongation after disturbance by DNA damage that have yet to be explored. Copyright © 2015 Elsevier B.V. All rights reserved.

Listeria monocytogenes PdeE, a phosphodiesterase that contributes to virulence and has hydrolytic activity against cyclic mononucleotides and cyclic dinucleotides

USDA-ARS?s Scientific Manuscript database

We have identified and partially characterized a putative HD domain hydrolase, LMOf2365_2464, which is highly expressed during listerial intracellular replication. LMOf2365_2464 is annotated as a putative HD domain-containing hydrolase. The ability of an isogenic mutant strain, F2365'2464, to adhere...

Microstructural evolution of NF709 (20Cr–25Ni–1.5MoNbTiN) under neutron irradiation

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

Kim, Byoungkoo; Tan, Lizhen; Xu, C.

In this study, because of its superior creep and corrosion resistance as compared with general austenitic stainless steels, NF709 has emerged as a candidate structural material for advanced nuclear reactors. To obtain fundamental information about the radiation resistance of this material, this study examined the microstructural evolution of NF709 subjected to neutron irradiation to 3 displacements per atom at 500 °C. Transmission electron microscopy, scanning electron microscopy, and high-energy x-ray diffraction were employed to characterize radiation-induced segregation, Frank loops, voids, as well as the formation and reduction of precipitates. Radiation hardening of ~76% was estimated by nanoindentation, approximately consistent withmore » the calculation according to the dispersed barrier-hardening model, suggesting Frank loops as the primary hardening source.« less

Improving atomic force microscopy imaging by a direct inverse asymmetric PI hysteresis model.

PubMed

Wang, Dong; Yu, Peng; Wang, Feifei; Chan, Ho-Yin; Zhou, Lei; Dong, Zaili; Liu, Lianqing; Li, Wen Jung

2015-02-03

A modified Prandtl-Ishlinskii (PI) model, referred to as a direct inverse asymmetric PI (DIAPI) model in this paper, was implemented to reduce the displacement error between a predicted model and the actual trajectory of a piezoelectric actuator which is commonly found in AFM systems. Due to the nonlinearity of the piezoelectric actuator, the standard symmetric PI model cannot precisely describe the asymmetric motion of the actuator. In order to improve the accuracy of AFM scans, two series of slope parameters were introduced in the PI model to describe both the voltage-increase-loop (trace) and voltage-decrease-loop (retrace). A feedforward controller based on the DIAPI model was implemented to compensate hysteresis. Performance of the DIAPI model and the feedforward controller were validated by scanning micro-lenses and standard silicon grating using a custom-built AFM.

High temperature skin friction measurement

NASA Technical Reports Server (NTRS)

Tcheng, Ping; Holmes, Harlan K.; Supplee, Frank H., Jr.

1989-01-01

Skin friction measurement in the NASA Langley hypersonic propulsion facility is described. The sensor configuration utilized an existing balance, modified to provide thermal isolation and an increased standoff distance. For test run times of about 20 sec and ambient-air cooling of the test section and balance, the modified balance performed satisfactorily, even when it was subjected to acoustic and structural vibration. The balance is an inertially balanced closed-loop servo system where the current to a moving-coil motor needed to restore or null the output from the position sensor is a measure of the force or skin friction tending to displace the moving element. The accuracy of the sensor is directly affected by the position sensor in the feedback loop, in this case a linear-variable differential transformer which has proven to be influenced by temperature gradients.

Microstructural evolution of NF709 (20Cr–25Ni–1.5MoNbTiN) under neutron irradiation

DOE PAGES

Kim, Byoungkoo; Tan, Lizhen; Xu, C.; ...

2015-12-30

In this study, because of its superior creep and corrosion resistance as compared with general austenitic stainless steels, NF709 has emerged as a candidate structural material for advanced nuclear reactors. To obtain fundamental information about the radiation resistance of this material, this study examined the microstructural evolution of NF709 subjected to neutron irradiation to 3 displacements per atom at 500 °C. Transmission electron microscopy, scanning electron microscopy, and high-energy x-ray diffraction were employed to characterize radiation-induced segregation, Frank loops, voids, as well as the formation and reduction of precipitates. Radiation hardening of ~76% was estimated by nanoindentation, approximately consistent withmore » the calculation according to the dispersed barrier-hardening model, suggesting Frank loops as the primary hardening source.« less

Electromagnetic Modeling of the Passive Stabilization Loop at EAST

NASA Astrophysics Data System (ADS)

Ji, Xiang; Song, Yuntao; Wu, Songtao; Wang, Zhibin; Shen, Guang; Liu, Xufeng; Cao, Lei; Zhou, Zibo; Peng, Xuebing; Wang, Chenghao

2012-09-01

A passive stabilization loop (PSL) has been designed and manufactured in order to enhance the control of vertical instability and accommodate the new stage for high-performance plasma at EAST. Eddy currents are induced by vertical displacement events (VDEs) and disruption, which can produce a magnetic field to control the vertical instability of the plasma in a short timescale. A finite element model is created and meshed using ANSYS software. Based on the simulation of plasma VDEs and disruption, the distribution and decay curve of the eddy currents on the PSL are obtained. The largest eddy current is 200 kA and the stress is 68 MPa at the outer current bridge, which is the weakest point of the PSL because of the eddy currents and the magnetic fields. The analysis results provide the supporting data for the structural design.

Sensitivity of coronal loop sausage mode frequencies and decay rates to radial and longitudinal density inhomogeneities: a spectral approach

NASA Astrophysics Data System (ADS)

Cally, Paul S.; Xiong, Ming

2018-01-01

Fast sausage modes in solar magnetic coronal loops are only fully contained in unrealistically short dense loops. Otherwise they are leaky, losing energy to their surrounds as outgoing waves. This causes any oscillation to decay exponentially in time. Simultaneous observations of both period and decay rate therefore reveal the eigenfrequency of the observed mode, and potentially insight into the tubes’ nonuniform internal structure. In this article, a global spectral description of the oscillations is presented that results in an implicit matrix eigenvalue equation where the eigenvalues are associated predominantly with the diagonal terms of the matrix. The off-diagonal terms vanish identically if the tube is uniform. A linearized perturbation approach, applied with respect to a uniform reference model, is developed that makes the eigenvalues explicit. The implicit eigenvalue problem is easily solved numerically though, and it is shown that knowledge of the real and imaginary parts of the eigenfrequency is sufficient to determine the width and density contrast of a boundary layer over which the tubes’ enhanced internal densities drop to ambient values. Linearized density kernels are developed that show sensitivity only to the extreme outside of the loops for radial fundamental modes, especially for small density enhancements, with no sensitivity to the core. Higher radial harmonics do show some internal sensitivity, but these will be more difficult to observe. Only kink modes are sensitive to the tube centres. Variation in internal and external Alfvén speed along the loop is shown to have little effect on the fundamental dimensionless eigenfrequency, though the associated eigenfunction becomes more compact at the loop apex as stratification increases, or may even displace from the apex.

Pseudo Dynamic Testing and Seismic Rehabilitation of Iraqi Brick, Bearing and Shear Walls

DTIC Science & Technology

2008-04-01

R es ea rc h L ab or at or y Approved for public release; distribution is unlimited. ERDC/CERL TR-08-6 April 2008 Pseudo Dynamic Testing and...Model 307-50 and one Satec 100 kip servo-hydraulic actuator controlled by closed-loop servo controllers and an Instron 8800 multi-axis controller and RS...Plus testing software.* The Satec actuator was operated in displacement control mode, and the 50 kip CGS actuators were operated in modal control

Bidirectional amplifier

DOEpatents

Wright, James T.

1986-01-01

A bilateral circuit is operable for transmitting signals in two directions without generation of ringing due to feedback caused by the insertion of the circuit. The circuit may include gain for each of the signals to provide a bidirectional amplifier. The signals are passed through two separate paths, with a unidirectional amplifier in each path. A controlled sampling device is provided in each path for sampling the two signals. Any feedback loop between the two signals is disrupted by providing a phase displacement between the control signals for the two sampling devices.

Bidirectional amplifier

DOEpatents

Wright, J.T.

1984-02-02

A bilateral circuit is operable for transmitting signals in two directions without generation of ringing due to feedback caused by the insertion of the circuit. The circuit may include gain for each of the signals to provide a bidirectional amplifier. The signals are passed through two separate paths, with a unidirectional amplifier in each path. A controlled sampling device is provided in each path for sampling the two signals. Any feedback loop between the two signals is disrupted by providing a phase displacement between the control signals for the two sampling devices.

Nicotinamide mononucleotide inhibits JNK activation to reverse Alzheimer disease.

PubMed

Yao, Zhiwen; Yang, Wenhao; Gao, Zhiqiang; Jia, Peng

2017-04-24

Amyloid-β (Aβ) oligomers have been accepted as major neurotoxic agents in the therapy of Alzheimer's disease (AD). It has been shown that the activity of nicotinamide adenine dinucleotide (NAD+) is related with the decline of Aβ toxicity in AD. Nicotinamide mononucleotide (NMN), the important precursor of NAD+, is produced during the reaction of nicotinamide phosphoribosyl transferase (Nampt). This study aimed to figure out the potential therapeutic effects of NMN and its underlying mechanisms in APPswe/PS1dE9 (AD-Tg) mice. We found that NMN gave rise to a substantial improvement in behavioral measures of cognitive impairments compared to control AD-Tg mice. In addition, NMN treatment significantly decreased β-amyloid production, amyloid plaque burden, synaptic loss, and inflammatory responses in transgenic animals. Mechanistically, NMN effectively controlled JNK activation. Furthermore, NMN potently progressed nonamyloidogenic amyloid precursor protein (APP) and suppressed amyloidogenic APP by mediating the expression of APP cleavage secretase in AD-Tg mice. Based on our findings, it was suggested that NMN substantially decreases multiple AD-associated pathological characteristically at least partially by the inhibition of JNK activation. Copyright © 2017 Elsevier B.V. All rights reserved.

1H NMR study of the hetero-association of flavin-mononucleotide with mutagenic dyes: ethidium bromide and proflavine

NASA Astrophysics Data System (ADS)

Evstigneev, M. P.; Mukhina, Yu. V.; Davies, D. B.

The hetero-association of the vitamin B2 derivative, flavin-mononucleotide (FMN), with a mutagenic dye, ethidium bromide (EB) or proflavine (PF), has been studied by 1D and 2D 500 MHz 1H NMR spectroscopy. The variations of proton chemical shifts of both the vitamin and dye as a function of concentration and temperature were analysed in terms of the structural and thermodynamical properties of the FMN-EB and FMN-PF complexes in solution. The structures of the complexes were also investigated by observed intermolecular ROE contacts and molecular mechanics calculations. The results show that the 1 : 1 hetero-association complexes in solution are more stable than the self-association complexes, which is consistent with formation of an intermolecular hydrogen-bond in the hetero-complexes of FMN-EB and FMN-PF. Hence it is possible that the toxicity of aromatic molecules such as EB and PF may be reduced in vitro by the presence of FMN, partly because of the known antimutagenic action of FMN and partly because it has been shown in this work that there is an effective intermolecular association between the mutagens and the vitamin.

YCL047C/POF1 is a novel nicotinamide mononucleotide adenylyltransferase (NMNAT) in Saccharomyces cerevisiae.

PubMed

Kato, Michiko; Lin, Su-Ju

2014-05-30

NAD(+) is an essential metabolic cofactor involved in various cellular biochemical processes. Nicotinamide riboside (NR) is an endogenously produced key pyridine metabolite that plays important roles in the maintenance of NAD(+) pool. Using a NR-specific cell-based screen, we identified mutants that exhibit altered NR release phenotype. Yeast cells lacking the ORF YCL047C/POF1 release considerably more NR compared with wild type, suggesting that POF1 plays an important role in NR/NAD(+) metabolism. The amino acid sequence of Pof1 indicates that it is a putative nicotinamide mononucleotide adenylyltransferase (NMNAT). Unlike other yeast NMNATs, Pof1 exhibits NMN-specific adenylyltransferase activity. Deletion of POF1 significantly lowers NAD(+) levels and decreases the efficiency of NR utilization, resistance to oxidative stress, and NR-induced life span extension. We also show that NR is constantly produced by multiple nucleotidases and that the intracellular NR pools are likely to be compartmentalized, which contributes to the regulation of NAD(+) homeostasis. Our findings may contribute to the understanding of the molecular basis and regulation of NAD(+) metabolism in higher eukaryotes. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Recent African origin of modern humans revealed by complete sequences of hominoid mitochondrial DNAs.

PubMed Central

Horai, S; Hayasaka, K; Kondo, R; Tsugane, K; Takahata, N

1995-01-01

We analyzed the complete mitochondrial DNA (mtDNA) sequences of three humans (African, European, and Japanese), three African apes (common and pygmy chimpanzees, and gorilla), and one orangutan in an attempt to estimate most accurately the substitution rates and divergence times of hominoid mtDNAs. Nonsynonymous substitutions and substitutions in RNA genes have accumulated with an approximately clock-like regularity. From these substitutions and under the assumption that the orangutan and African apes diverged 13 million years ago, we obtained a divergence time for humans and chimpanzees of 4.9 million years. This divergence time permitted calibration of the synonymous substitution rate (3.89 x 10(-8)/site per year). To obtain the substitution rate in the displacement (D)-loop region, we compared the three human mtDNAs and measured the relative abundance of substitutions in the D-loop region and at synonymous sites. The estimated substitution rate in the D-loop region was 7.00 x 10(-8)/site per year. Using both synonymous and D-loop substitutions, we inferred the age of the last common ancestor of the human mtDNAs as 143,000 +/- 18,000 years. The shallow ancestry of human mtDNAs, together with the observation that the African sequence is the most diverged among humans, strongly supports the recent African origin of modern humans, Homo sapiens sapiens. PMID:7530363

Ferroelectriclike and pyroelectric behavior of CaCu{sub 3}Ti{sub 4}O{sub 12} ceramics

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

Shri Prakash, B.; Varma, K. B. R.

2007-02-19

A ferroelectriclike hysteresis loop was obtained at room temperature for CaCu{sub 3}Ti{sub 4}O{sub 12} (CCTO) ceramic. The remnant polarization and coercive field for 1100 deg. C/5 h sintered CaCu{sub 3}Ti{sub 4}O{sub 12} ceramics were 0.063 {mu}C/cm{sup 2} and 195 V/cm, respectively. Remnant polarization increased while the coercive field decreased with increase in sintering temperature/duration, implying that these were microstructural dependent. The observation of the hysteresis loop for CCTO ceramic was corroborated by its pyroelectric behavior, and the pyroelectric current at room temperature was -0.0028 nA. These findings were attributed to the presence of mixed-valent Ti ions, apart from off centermore » displacement of Ti ions in TiO{sub 6} octahedra.« less

Improving Atomic Force Microscopy Imaging by a Direct Inverse Asymmetric PI Hysteresis Model

PubMed Central

Wang, Dong; Yu, Peng; Wang, Feifei; Chan, Ho-Yin; Zhou, Lei; Dong, Zaili; Liu, Lianqing; Li, Wen Jung

2015-01-01

A modified Prandtl–Ishlinskii (PI) model, referred to as a direct inverse asymmetric PI (DIAPI) model in this paper, was implemented to reduce the displacement error between a predicted model and the actual trajectory of a piezoelectric actuator which is commonly found in AFM systems. Due to the nonlinearity of the piezoelectric actuator, the standard symmetric PI model cannot precisely describe the asymmetric motion of the actuator. In order to improve the accuracy of AFM scans, two series of slope parameters were introduced in the PI model to describe both the voltage-increase-loop (trace) and voltage-decrease-loop (retrace). A feedforward controller based on the DIAPI model was implemented to compensate hysteresis. Performance of the DIAPI model and the feedforward controller were validated by scanning micro-lenses and standard silicon grating using a custom-built AFM. PMID:25654719

MD simulation of plastic deformation nucleation in stressed crystallites under irradiation

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

Korchuganov, A. V., E-mail: avkor@ispms.tsc.ru; Zolnikov, K. P., E-mail: kost@ispms.tsc.ru; Kryzhevich, D. S., E-mail: kryzhev@ispms.tsc.ru

2016-12-15

The investigation of plastic deformation nucleation in metals and alloys under irradiation and mechanical loading is one of the topical issues of materials science. Specific features of nucleation and evolution of the defect system in stressed and irradiated iron, vanadium, and copper crystallites were studied by molecular dynamics simulation. Mechanical loading was performed in such a way that the modeled crystallite volume remained unchanged. The energy of the primary knock-on atom initiating a cascade of atomic displacements in a stressed crystallite was varied from 0.05 to 50 keV. It was found that atomic displacement cascades might cause global structural transformationsmore » in a region far larger than the radiation-damaged area. These changes are similar to the ones occurring in the process of mechanical loading of samples. They are implemented by twinning (in iron and vanadium) or through the formation of partial dislocation loops (in copper).« less

Regenerable Incinerator Exhaust Purification and Trace Contaminant Control System

NASA Technical Reports Server (NTRS)

Finn, John E.; Cho, Shelia Y.; LeVan, M. Douglas

2003-01-01

In this novel approach to air purification, contaminants removed from a process air stream by a high-capacity adsorbent are displaced periodically by a warm, high-humidity, reverse-flow air stream. Displaced contaminants flow into a closed regeneration loop, in which organic compounds are oxidized catalytically and acid gases are removed by a gas- water contactor (which also serves as the source of the water vapor). These features are expected to result in a design that has few expendables and lower energy consumption than alternative regenerable techniques. The joint project between NASA Ames Research Center and Vanderbilt University has completed its third year. Breadboard development continues at NASA Ames, while Vanderbilt has completed most of its adsorption equilibria development. Vanderbilt has completed its fixed-bed apparatus for investigation of dynamic adsorption and desorption processes for trace organic compounds and water vapor, and is continuing its development of the mathematical model describing the column dynamics.

Simultaneous VLA observations of a flare at 6 and 20 centimeter wavelengths

NASA Technical Reports Server (NTRS)

Velusamy, T.; Kundu, M. R.; Schmahl, E. J.; Mccabe, M.

1987-01-01

Using the Very Large Array at 6 and 20 cm wavelengths, a May 15, 1980 solar flare was mapped. The 1B flare, as observed in H alpha at Mees Solar Observatory, Maui, Hawaii, appeared as two sequential flares occurring at different neutral lines. The peaks of the time profile at 20 cm were delayed with respect to the 6 cm counterparts, but they were related to each other and to the H alpha activity. At 20 cm, precursor activity occurred, and an oppositely polarized source an arcminute away from the main burst may have triggered the flare. The main 20 cm emission appeared to be displaced limbward from the 6 cm burst. If both the 6 and 20 cm emission originated in the same system of loops, it is inferred that the apparent lateral displacement was caused by a height difference of 33,000 km in the sources of emission.

Inadequate interaction between open- and closed-loop postural control in phobic postural vertigo.

PubMed

Wuehr, M; Pradhan, C; Novozhilov, S; Krafczyk, S; Brandt, T; Jahn, K; Schniepp, R

2013-05-01

Phobic postural vertigo (PPV) is characterized by a subjective dizziness and postural imbalance. Changes in postural control strategy may cause the disturbed postural performance in PPV. A better understanding of the mechanisms behind this change in strategy is required to improve the diagnostic tools and therapeutic options for this prevalent disorder. Here we apply stabilogram diffusion analysis (SDA) to examine the characteristics and modes of interaction of open- and closed-loop processes that make up the postural control scheme in PPV. Twenty patients with PPV and 20 age-matched healthy controls were recorded on a stabilometer platform with eyes open and with eyes closed. Spatio-temporal changes of the center of pressure (CoP) displacement were analyzed by means of SDA and complementary CoP amplitude measures. (1) Open-loop control mechanisms in PPV were disturbed because of a higher diffusion activity (p < 0.001). (2) The interaction of open- and closed-loop processes was altered in that the sensory feedback threshold of the system was lowered (p = 0.010). These two changes were comparable to those observed in healthy subjects during more demanding balance conditions such as standing with eyes closed. These data indicate that subjective imbalance in PPV is associated with characteristic changes in the coordination of open- and closed-loop mechanisms of postural control. Patients with PPV use sensory feedback inadequately during undisturbed stance, and this impairs postural performance. These changes are compatible with higher levels of anti-gravity muscle activity and co-contraction during the conscious concentration on control of postural stability.

Evidence and age-related distribution of mtDNA D-loop point mutations in skeletal muscle from healthy subjects and mitochondrial patients.

PubMed

Del Bo, Roberto; Bordoni, Andreina; Martinelli Boneschi, Filippo; Crimi, Marco; Sciacco, Monica; Bresolin, Nereo; Scarlato, Guglielmo; Comi, Giacomo Pietri

2002-10-15

The progressive accumulation of mitochondrial DNA (mtDNA) alterations, ranging from single mutations to large-scale deletions, in both the normal ageing process and pathological conditions is a relevant phenomenon in terms of frequency and heteroplasmic degree. Recently, two point mutations (A189G and T408A) within the Displacement loop (D-loop) region, the control region for mtDNA replication, were shown to occur in skeletal muscles from aged individuals. We evaluated the presence and the heteroplasmy levels of these two mutations in muscle biopsies from 91 unrelated individuals of different ages (21 healthy subjects and 70 patients affected by mitochondrial encephalomyopathies). Overall, both mutations significantly accumulate with age. However, a different relationship was discovered among the different subgroups of patients: a higher number of A189G positive subjects younger than 53 years was detected in the subgroup of multiple-deleted patients; furthermore, a trend towards an increased risk for the mutations was evidenced among patients carrying multiple deletions when compared to healthy controls. These findings support the idea that a common biological mechanism determines the accumulation of somatic point mutations in the D-loop region, both in healthy subjects and in mitochondrial myopathy patients. At the same time, it appears that disorders caused by mutations of nuclear genes controlling mtDNA replication (the "mtDNA multiple deletions" syndromes) present a temporal advantage to mutate in the D-loop region. This observation may be relevant to the definition of the molecular pathogenesis of these latter syndromes. Copyright 2002 Elsevier Science B.V.

Postural control model interpretation of stabilogram diffusion analysis

NASA Technical Reports Server (NTRS)

Peterka, R. J.

2000-01-01

Collins and De Luca [Collins JJ. De Luca CJ (1993) Exp Brain Res 95: 308-318] introduced a new method known as stabilogram diffusion analysis that provides a quantitative statistical measure of the apparently random variations of center-of-pressure (COP) trajectories recorded during quiet upright stance in humans. This analysis generates a stabilogram diffusion function (SDF) that summarizes the mean square COP displacement as a function of the time interval between COP comparisons. SDFs have a characteristic two-part form that suggests the presence of two different control regimes: a short-term open-loop control behavior and a longer-term closed-loop behavior. This paper demonstrates that a very simple closed-loop control model of upright stance can generate realistic SDFs. The model consists of an inverted pendulum body with torque applied at the ankle joint. This torque includes a random disturbance torque and a control torque. The control torque is a function of the deviation (error signal) between the desired upright body position and the actual body position, and is generated in proportion to the error signal, the derivative of the error signal, and the integral of the error signal [i.e. a proportional, integral and derivative (PID) neural controller]. The control torque is applied with a time delay representing conduction, processing, and muscle activation delays. Variations in the PID parameters and the time delay generate variations in SDFs that mimic real experimental SDFs. This model analysis allows one to interpret experimentally observed changes in SDFs in terms of variations in neural controller and time delay parameters rather than in terms of open-loop versus closed-loop behavior.

SLIPPING MAGNETIC RECONNECTION, CHROMOSPHERIC EVAPORATION, IMPLOSION, AND PRECURSORS IN THE 2014 SEPTEMBER 10 X1.6-CLASS SOLAR FLARE

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

Dudík, Jaroslav; Karlický, Marian; Dzifčáková, Elena

2016-05-20

We investigate the occurrence of slipping magnetic reconnection, chromospheric evaporation, and coronal loop dynamics in the 2014 September 10 X-class flare. Slipping reconnection is found to be present throughout the flare from its early phase. Flare loops are seen to slip in opposite directions toward both ends of the ribbons. Velocities of 20–40 km s{sup −1} are found within time windows where the slipping is well resolved. The warm coronal loops exhibit expanding and contracting motions that are interpreted as displacements due to the growing flux rope that subsequently erupts. This flux rope existed and erupted before the onset ofmore » apparent coronal implosion. This indicates that the energy release proceeds by slipping reconnection and not via coronal implosion. The slipping reconnection leads to changes in the geometry of the observed structures at the Interface Region Imaging Spectrograph slit position, from flare loop top to the footpoints in the ribbons. This results in variations of the observed velocities of chromospheric evaporation in the early flare phase. Finally, it is found that the precursor signatures, including localized EUV brightenings as well as nonthermal X-ray emission, are signatures of the flare itself, progressing from the early phase toward the impulsive phase, with the tether-cutting being provided by the slipping reconnection. The dynamics of both the flare and outlying coronal loops is found to be consistent with the predictions of the standard solar flare model in three dimensions.« less

Experimental Evaluation of an Invasive Medical Instrument Based on a Displacement Measurement System.

PubMed

Fotiadis, Dimitris A; Astaras, Alexandros; Bamidis, Panagiotis D; Papathanasiou, Kostas; Kalfas, Anestis

2015-09-01

This paper presents a novel method for tracking the position of a medical instrument's tip. The system is based on phase locking a high frequency signal transmitted from the medical instrument's tip to a reference signal. Displacement measurement is established having the loop open, in order to get a low frequency voltage representing the medical instrument's movement; therefore, positioning is established by means of conventional measuring techniques. The voltage-controlled oscillator stage of the phase-locked loop (PLL), combined to an appropriate antenna, comprises the associated transmitter located inside the medical instrument tip. All the other low frequency PLL components, low noise amplifier and mixer, are located outside the human body, forming the receiver part of the system. The operating details of the proposed system were coded in Verilog-AMS. Simulation results indicate robust medical instrument tracking in 1-D. Experimental evaluation of the proposed position tracking system is also presented. The experiments described in this paper are based on a transmitter moving opposite a stationary receiver performing either constant velocity or uniformly accelerated movement, and also together with two stationary receivers performing constant velocity movement again. This latter setup is implemented in order to demonstrate the prototype's accuracy for planar (2-D) motion measurements. Error analysis and time-domain analysis are presented for system performance characterization. Furthermore, preliminary experimental assessment using a saline solution container to more closely approximate the human body as a radio frequency wave transmission medium has proved the system's capability of operating underneath the skin.

Three Degree of Freedom Parallel Mechanical Linkage

NASA Technical Reports Server (NTRS)

Adelstein, Bernard D. (Inventor)

1998-01-01

A three degree of freedom parallel mechanism or linkage that couples three degree of freedom translational displacements at an endpoint, such as a handle, a hand grip, or a robot tool, to link rotations about three axes that are fixed with respect to a common base or ground link. The mechanism includes a three degree of freedom spherical linkage formed of two closed loops, and a planar linkage connected to the endpoint. The closed loops are rotatably interconnected, and made of eight rigid links connected by a plurality of single degree of freedom revolute joints. Three of these revolute joints are base joints and are connected to a common ground. such that the axis lines passing through the revolute joints intersect at a common fixed center point K forming the center of a spherical work volume in which the endpoint is capable of moving. 'Me three degrees of freedom correspond to the spatial displacement of the endpoint, for instance. The mechanism provides a new overall spatial kinematic linkage composed of a minimal number of rigid links and rotary joints. The mechanism has improved mechanical stiffness, and conveys mechanical power bidirectionally between the human operator and the electromechanical actuators. It does not require gears, belts. cable, screw or other types of transmission elements, and is useful in applications requiring full backdrivability. Thus, this invention can serve as the mechanical linkage for actively powered devices such as compliant robotic manipulators and force-reflecting hand controllers, and passive devices such as manual input devices for computers and other systems.

A Self-Circulating Heat Exchanger for Use in Stirling and Thermoacoustic-Stirling Engines

NASA Astrophysics Data System (ADS)

Backhaus, Scott; Reid, Robert S.

2005-02-01

A major technical hurdle to the implementation of large Stirling engines or thermoacoustic engines is the reliability, performance, and manufacturability of the hot heat exchanger that brings high-temperature heat into the engine. Unlike power conversion devices that utilize steady flow, the oscillatory nature of the flow in Stirling and thermoacoustic engines restricts the length of a traditional hot heat exchanger to a peak-to-peak gas displacement, which is usually around 0.2 meters or less. To overcome this restriction, a new hot heat exchanger has been devised that uses a fluid diode in a looped pipe, which is resonantly driven by the oscillating gas pressure in the engine itself, to circulate the engine's working fluid around the loop. Instead of thousands of short, intricately interwoven passages that must be individually sealed, this new design consists of a few pipes that are typically 10 meters long. This revolutionary approach eliminates thousands of hermetic joints, pumps the engine's working fluid to and from a remote heat source without using moving parts, and does so without compromising on heat transfer surface area. Test data on a prototype loop integrated with a 1-kW thermoacoustic engine will be presented.

Real-Time Sequence-Validated Loop-Mediated Isothermal Amplification Assays for Detection of Middle East Respiratory Syndrome Coronavirus (MERS-CoV)

PubMed Central

Bhadra, Sanchita; Jiang, Yu Sherry; Kumar, Mia R.; Johnson, Reed F.; Hensley, Lisa E.; Ellington, Andrew D.

2015-01-01

The Middle East respiratory syndrome coronavirus (MERS-CoV), an emerging human coronavirus, causes severe acute respiratory illness with a 35% mortality rate. In light of the recent surge in reported infections we have developed asymmetric five-primer reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays for detection of MERS-CoV. Isothermal amplification assays will facilitate the development of portable point-of-care diagnostics that are crucial for management of emerging infections. The RT-LAMP assays are designed to amplify MERS-CoV genomic loci located within the open reading frame (ORF)1a and ORF1b genes and upstream of the E gene. Additionally we applied one-step strand displacement probes (OSD) for real-time sequence-specific verification of LAMP amplicons. Asymmetric amplification effected by incorporating a single loop primer in each assay accelerated the time-to-result of the OSD-RT-LAMP assays. The resulting assays could detect 0.02 to 0.2 plaque forming units (PFU) (5 to 50 PFU/ml) of MERS-CoV in infected cell culture supernatants within 30 to 50 min and did not cross-react with common human respiratory pathogens. PMID:25856093

Multiple maternal origins of Indonesian crowing chickens revealed by mitochondrial DNA analysis.

PubMed

Ulfah, Maria; Perwitasari, Dyah; Jakaria, Jakaria; Muladno, Muhammad; Farajallah, Achmad

2017-03-01

The utilization of Indonesian crowing chickens is increasing; as such, assessing their genetic structures is important to support the conservation of their genetic resources. This study analyzes the matrilineal evolution of Indonesian crowing chickens based on the mtDNA displacement loop D-loop region to clarify their phylogenetic relationships, possible maternal origin, and possible routes of chicken dispersal. The neighbor-joining tree reveals that the majority of Indonesian crowing chickens belong to haplogroups B, D, and E, but haplogroup D harbored most of them. The Bayesian analysis also reveals that Indonesian crowing chickens derive from Bekisar chicken, a hybrid of the green junglefowl, suggesting the possible contribution of green junglefowl to chicken domestication. There appear at least three maternal lineages of Indonesian chicken origins indicated by the median network profile of mtDNA D-loop haplotypes, namely (1) Chinese; (2) Chinese, Indian, and other Southeast Asian chickens; and (3) Indian, Chinese, Southeast Asian, Japanese, and European chickens. Chicken domestication might be centered in China, India, Indonesia, and other Southeast Asian countries, supporting multiple maternal origins of Indonesian crowing chickens. A systematic breeding program of indigenous chickens will be very important to retain the genetic diversity for future use and conservation.

Lysophospholipid presentation by CD1d and recognition by a human Natural Killer T-cell receptor

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

López-Sagaseta, Jacinto; Sibener, Leah V.; Kung, Jennifer E.

2014-10-02

Invariant Natural Killer T (iNKT) cells use highly restricted {alpha}{beta} T cell receptors (TCRs) to probe the repertoire of lipids presented by CD1d molecules. Here, we describe our studies of lysophosphatidylcholine (LPC) presentation by human CD1d and its recognition by a native, LPC-specific iNKT TCR. Human CD1d presenting LPC adopts an altered conformation from that of CD1d presenting glycolipid antigens, with a shifted {alpha}1 helix resulting in an open A pocket. Binding of the iNKT TCR requires a 7-{angstrom} displacement of the LPC headgroup but stabilizes the CD1d-LPC complex in a closed conformation. The iNKT TCR CDR loop footprint onmore » CD1d-LPC is anchored by the conserved positioning of the CDR3{alpha} loop, whereas the remaining CDR loops are shifted, due in part to amino-acid differences in the CDR3{beta} and J{beta} segment used by this iNKT TCR. These findings provide insight into how lysophospholipids are presented by human CD1d molecules and how this complex is recognized by some, but not all, human iNKT cells.« less

Structure of the S. aureus PI-specific phospholipase C reveals modulation of active site access by a titratable π-cation latched loop†

PubMed Central

Goldstein, Rebecca; Cheng, Jiongjia; Stec, Boguslaw; Roberts, Mary F.

2012-01-01

Staphylococcus aureus secretes a phosphatidylinositol-specific phospholipase C (PIPLC) as a virulence factor that is unusual in exhibiting higher activity at acidic pH values than other enzymes in this class. We have determined the crystal structure of this enzyme at pH 4.6 and pH 7.5. Under slightly basic conditions, the S. aureus PI-PLC structure closely follows the conformation of other bacterial PI-PLCs. However, when crystallized under acidic conditions, a large section of mobile loop at the αβ-barrel rim in the vicinity of the active site shows ~10 Å shift. This loop displacement at acidic pH is the result of a titratable intramolecular π-cation interaction between His258 and Phe249. This was verified by a structure of the mutant protein H258Y crystallized at pH 4.6, which does not exhibit the large loop shift. The intramolecular π-cation interaction for S. aureus PI-PLC provides an explanation for the activity of the enzyme at acid pH and also suggests how phosphatidylcholine, as a competitor for Phe249, may kinetically activate this enzyme. PMID:22390775

Experimental investigation of active rib stitch knitted architecture for flow control applications

NASA Astrophysics Data System (ADS)

Abel, Julianna M.; Mane, Poorna; Pascoe, Benjamin; Luntz, Jonathan; Brei, Diann

2010-04-01

Actively manipulating flow characteristics around the wing can enhance the high-lift capability and reduce drag; thereby, increasing fuel economy, improving maneuverability and operation over diverse flight conditions which enables longer, more varied missions. Active knits, a novel class of cellular structural smart material actuator architectures created by continuous, interlocked loops of stranded active material, produce distributed actuation that can actively manipulate the local surface of the aircraft wing to improve flow characteristics. Rib stitch active knits actuate normal to the surface, producing span-wise discrete periodic arrays that can withstand aerodynamic forces while supplying the necessary displacement for flow control. This paper presents a preliminary experimental investigation of the pressuredisplacement actuation performance capabilities of a rib stitch active knit based upon shape memory alloy (SMA) wire. SMA rib stitch prototypes in both individual form and in stacked and nestled architectures were experimentally tested for their quasi-static load-displacement characteristics, verifying the parallel and series relationships of the architectural configurations. The various configurations tested demonstrated the potential of active knits to generate the required level of distributed surface displacements while under aerodynamic level loads for various forms of flow control.

Initial Computations of Vertical Displacement Events with NIMROD

NASA Astrophysics Data System (ADS)

Bunkers, Kyle; Sovinec, C. R.

2014-10-01

Disruptions associated with vertical displacement events (VDEs) have potential for causing considerable physical damage to ITER and other tokamak experiments. We report on initial computations of generic axisymmetric VDEs using the NIMROD code [Sovinec et al., JCP 195, 355 (2004)]. An implicit thin-wall computation has been implemented to couple separate internal and external regions without numerical stability limitations. A simple rectangular cross-section domain generated with the NIMEQ code [Howell and Sovinec, CPC (2014)] modified to use a symmetry condition at the midplane is used to test linear and nonlinear axisymmetric VDE computation. As current in simulated external coils for large- R / a cases is varied, there is a clear n = 0 stability threshold which lies below the decay-index criterion for the current-loop model of a tokamak to model VDEs [Mukhovatov and Shafranov, Nucl. Fusion 11, 605 (1971)]; a scan of wall distance indicates the offset is due to the influence of the conducting wall. Results with a vacuum region surrounding a resistive wall will also be presented. Initial nonlinear computations show large vertical displacement of an intact simulated tokamak. This effort is supported by U.S. Department of Energy Grant DE-FG02-06ER54850.

Knotless anchors with sutures external to the anchor body may be at risk for suture cutting through osteopenic bone

PubMed Central

Ono, Y.; Woodmass, J. M.; Nelson, A. A.; Boorman, R. S.; Thornton, G. M.

2016-01-01

Objectives This study evaluated the mechanical performance, under low-load cyclic loading, of two different knotless suture anchor designs: sutures completely internal to the anchor body (SpeedScrew) and sutures external to the anchor body and adjacent to bone (MultiFIX P). Methods Using standard suture loops pulled in-line with the rotator cuff (approximately 60°), anchors were tested in cadaveric bone and foam blocks representing normal to osteopenic bone. Mechanical testing included preloading to 10 N and cyclic loading for 500 cycles from 10 N to 60 N at 60 mm/min. The parameters evaluated were initial displacement, cyclic displacement and number of cycles and load at 3 mm displacement relative to preload. Video recording throughout testing documented the predominant source of suture displacement and the distance of ‘suture cutting through bone’. Results In cadaveric bone and foam blocks, MultiFIX P anchors had significantly greater initial displacement, and lower number of cycles and lower load at 3 mm displacement than SpeedScrew anchors. Video analysis revealed ‘suture cutting through bone’ as the predominant source of suture displacement in cadaveric bone (qualitative) and greater ‘suture cutting through bone’ comparing MultiFIX P with SpeedScrew anchors in foam blocks (quantitative). The greater suture displacement in MultiFIX P anchors was predominantly from suture cutting through bone, which was enhanced in an osteopenic bone model. Conclusions Anchors with sutures external to the anchor body are at risk for suture cutting through bone since the suture eyelet is at the distal tip of the implant and the suture directly abrades against the bone edge during cyclic loading. Suture cutting through bone may be a significant source of fixation failure, particularly in osteopenic bone. Cite this article: Y. Ono, J. M. Woodmass, A. A. Nelson, R. S. Boorman, G. M. Thornton, I. K. Y. Lo. Knotless anchors with sutures external to the anchor body may be at risk for suture cutting through osteopenic bone. Bone Joint Res 2016;5:269–275. DOI: 10.1302/2046-3758.56.2000535. PMID:27357383

Knotless anchors with sutures external to the anchor body may be at risk for suture cutting through osteopenic bone.

PubMed

Ono, Y; Woodmass, J M; Nelson, A A; Boorman, R S; Thornton, G M; Lo, I K Y

2016-06-01

This study evaluated the mechanical performance, under low-load cyclic loading, of two different knotless suture anchor designs: sutures completely internal to the anchor body (SpeedScrew) and sutures external to the anchor body and adjacent to bone (MultiFIX P). Using standard suture loops pulled in-line with the rotator cuff (approximately 60°), anchors were tested in cadaveric bone and foam blocks representing normal to osteopenic bone. Mechanical testing included preloading to 10 N and cyclic loading for 500 cycles from 10 N to 60 N at 60 mm/min. The parameters evaluated were initial displacement, cyclic displacement and number of cycles and load at 3 mm displacement relative to preload. Video recording throughout testing documented the predominant source of suture displacement and the distance of 'suture cutting through bone'. In cadaveric bone and foam blocks, MultiFIX P anchors had significantly greater initial displacement, and lower number of cycles and lower load at 3 mm displacement than SpeedScrew anchors. Video analysis revealed 'suture cutting through bone' as the predominant source of suture displacement in cadaveric bone (qualitative) and greater 'suture cutting through bone' comparing MultiFIX P with SpeedScrew anchors in foam blocks (quantitative). The greater suture displacement in MultiFIX P anchors was predominantly from suture cutting through bone, which was enhanced in an osteopenic bone model. Anchors with sutures external to the anchor body are at risk for suture cutting through bone since the suture eyelet is at the distal tip of the implant and the suture directly abrades against the bone edge during cyclic loading. Suture cutting through bone may be a significant source of fixation failure, particularly in osteopenic bone.Cite this article: Y. Ono, J. M. Woodmass, A. A. Nelson, R. S. Boorman, G. M. Thornton, I. K. Y. Lo. Knotless anchors with sutures external to the anchor body may be at risk for suture cutting through osteopenic bone. Bone Joint Res 2016;5:269-275. DOI: 10.1302/2046-3758.56.2000535. © 2016 Lo et al.

Scientific Research Program for Power, Energy, and Thermal Technologies. Task Order 0001: Energy, Power, and Thermal Technologies and Processes Experimental Research. Subtask: Thermal Management of Electromechanical Actuation System for Aircraft Primary Flight Control Surfaces

DTIC Science & Technology

2014-05-01

utilizing buoyancy differences in vapor and liquid phases to pump the heat transfer fluid between the evaporator and condenser. In this particular...Virtual Instrumentation Engineering Workbench LHP Loop Heat Pipe LVDT Linear Voltage Displacement Transducer MACE Micro -technologies for Air...Bland 1992). This type of duty cycle lends itself to thermal energy storage, which when coupled with an effective heat transfer mechanism can

Single molecule actuation and detection on a lab-on-a-chip magnetoresistive platform

NASA Astrophysics Data System (ADS)

Chaves, R. C.; Bensimon, D.; Freitas, P. P.

2011-03-01

On-chip magnetic tweezers based on current loops were integrated with magnetoresistive sensors. Magnetic forces up to 1.0±0.3pN are produced to actuate on DNA anchored to the surface of a flow cell and labeled with micrometer-sized magnetic beads. The levitation of the beads stretches the immobilized DNA. The relative position of the magnetic beads is monitored using spin-valve sensors. A bead vertical displacement resolution of 60nm is derived for DNA molecular motor activity in a tweezer steady current regime.

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

Gerard, R.; Malekian, C.; Meessen, O.

The Leak Before Break (LBB) concept allows to eliminate from the design basis the double-ended guillotine break of the primary loop piping, provided it can be demonstrated by a fracture mechanics analysis that a through-wall flaw, of a size giving rise to a leakage still well detectable by the plant leak detection systems, remains stable even under accident conditions (including the Safe Shutdown Earthquake (SSE)). This concept was successfully applied to the primary loop piping of several Belgian Pressurized Water Reactor (PWR) units, operated by the Utility Electrabel. One of the main benefits is to permit justification of supports inmore » the primary loop and justification of the integrity of the reactor pressure vessel and internals in case of a Loss Of Coolant Accident (LOCA) in stretch-out conditions. For two of the Belgian PWR units, the LBB approach also made it possible to reduce the number of large hydraulic snubbers installed on the primary coolant pumps. Last but not least, the LBB concept also facilitates the steam generator replacement operations, by eliminating the need for some pipe whip restraints located close to the steam generator. In addition to the U.S. regulatory requirements, the Belgian safety authorities impose additional requirements which are described in details in a separate paper. An novel aspect of the studies performed in Belgium is the way in which residual loads in the primary loop are taken into account. Such loads may result from displacements imposed to close the primary loop in a steam generator replacement operation, especially when it is performed using the {open_quote}two cuts{close_quotes} technique. The influence of such residual loads on the LBB margins is discussed in details and typical results are presented.« less

Effect of neutron irradiation on defect evolution in Ti 3SiC 2 and Ti 2AlC

DOE PAGES

Tallman, Darin J.; He, Lingfeng; Garcia-Diaz, Brenda L.; ...

2015-10-23

Here, we report on the characterization of defects formed in polycrystalline Ti 3SiC 2 and Ti 2AlC samples exposed to neutron irradiation – up to 0.1 displacements per atom (dpa) at 350 ± 40 °C or 695 ± 25 °C, and up to 0.4 dpa at 350 ± 40 °C. Black spots are observed in both Ti 3SiC 2 and Ti 2AlC after irradiation to both 0.1 and 0.4 dpa at 350 °C. After irradiation to 0.1 dpa at 695 °C, small basal dislocation loops, with a Burgers vector of b = 1/2 [0001] are observed in both materials. Atmore » 9 ± 3 and 10 ± 5 nm, the loop diameters in the Ti 3SiC 2 and Ti 2AlC samples, respectively, were comparable. At 1 × 10 23 loops/m 3, the dislocation loop density in Ti 2AlC was ≈1.5 orders of magnitude greater than in Ti 3SiC 2, at 3 x 10 21 loops/m3. After irradiation at 350 °C, extensive microcracking was observed in Ti 2AlC, but not in Ti 3SiC 2. The room temperature electrical resistivities increased as a function of neutron dose for all samples tested, and appear to saturate in the case of Ti 3SiC 2. The MAX phases are unequivocally more neutron radiation tolerant than the impurity phases TiC and Al 2O 3. Based on these results, Ti 3SiC 2 appears to be a more promising MAX phase candidate for high temperature nuclear applications than Ti 2AlC.« less

Expression, Purification, and Characterization of a Recombinant Flavin Reductase from the Luminescent Marine Bacterium "Photobacterium Leiognathi": A Set of Exercises for Students

ERIC Educational Resources Information Center

Crowley, Thomas E.

2010-01-01

In "Photobacterium," the flavin reductase encoded by "lux"G regenerates the reduced form of flavin mononucleotide (FMN). Reduced FMN is one of the substrates of the luciferase enzyme that catalyzes a light-emitting reaction. A set of experiments, that employs a "lux"G-expression plasmid construct (pGhis) and is suitable for an undergraduate…

Molecular dynamics simulation of dioxygen pathways through mini singlet oxygen generator (miniSOG), a genetically encoded marker and killer protein.

PubMed

Pietra, Francesco

2014-12-01

In this work, molecular dynamics (MD) simulations of the permeation of proteins by small gases of biological significance have been extended from gas carrier, sensor, and enzymatic proteins to genetically encoded tags and killer proteins. To this end, miniSOG was taken as an example of current high interest, using a biased form of MD, called random-acceleration MD. Various egress gates and binding pockets for dioxygen, as an indistinguishable mimic of singlet dioxygen, were found on both above and below the isoalloxazine plane of the flavin mononucleotide cofactor in miniSOG. Of such gates and binding pockets, those lying within two opposite cones, coaxial with a line normal to the isoalloxazine plane, and with the vertex at the center of such a plane are those most visited by the escaping gas molecule. Out of residues most capable of quenching (1) O2 , Y30, lying near the base of one such a cone, and H85, near the base of the opposite cone, are held to be most responsible for the reduced quantum yield of (1) O2 with folded miniSOG with respect to free flavin mononucleotide in solution. Copyright © 2014 Verlag Helvetica Chimica Acta AG, Zürich.

A Modified Shuttle Plasmid Facilitates Expression of a Flavin Mononucleotide-Based Fluorescent Protein in Treponema denticola ATCC 35405

PubMed Central

Godovikova, Valentina; Goetting-Minesky, M. Paula; Shin, Jae M.; Kapila, Yvonne L.; Rickard, Alexander H.

2015-01-01

Oral pathogens, including Treponema denticola, initiate the dysregulation of tissue homeostasis that characterizes periodontitis. However, progress of research on the roles of T. denticola in microbe-host interactions and signaling, microbial communities, microbial physiology, and molecular evolution has been hampered by limitations in genetic methodologies. This is typified by an extremely low transformation efficiency and inability to transform the most widely studied T. denticola strain with shuttle plasmids. Previous studies have suggested that robust restriction-modification (R-M) systems in T. denticola contributed to these problems. To facilitate further molecular genetic analysis of T. denticola behavior, we optimized existing protocols such that shuttle plasmid transformation efficiency was increased by >100-fold over prior reports. Here, we report routine transformation of T. denticola ATCC 35405 with shuttle plasmids, independently of both plasmid methylation status and activity of the type II restriction endonuclease encoded by TDE0911. To validate the utility of this methodological advance, we demonstrated expression and activity in T. denticola of a flavin mononucleotide-based fluorescent protein (FbFP) that is active under anoxic conditions. Addition of routine plasmid-based fluorescence labeling to the Treponema toolset will enable more-rigorous and -detailed studies of the behavior of this organism. PMID:26162875

Nicotinamide mononucleotide (NMN) supplementation ameliorates the impact of maternal obesity in mice: comparison with exercise.

PubMed

Uddin, Golam Mezbah; Youngson, Neil A; Doyle, Bronte M; Sinclair, David A; Morris, Margaret J

2017-11-08

Maternal overnutrition increases the risk of long-term metabolic dysfunction in offspring. Exercise improves metabolism partly by upregulating mitochondrial biogenesis or function, via increased levels of nicotinamide adenine dinucleotide (NAD + ). We have shown that the NAD + precursor, nicotinamide mononucleotide (NMN) can reverse some of the negative consequences of high fat diet (HFD) consumption. To investigate whether NMN can impact developmentally-set metabolic deficits, we compared treadmill exercise and NMN injection in offspring of obese mothers. Five week old lean and obese female C57BL6/J mice were mated with chow fed males. Female offspring weaned onto HFD were given treadmill exercise for 9 weeks, or NMN injection daily for 18 days. Maternal obesity programmed increased adiposity and liver triglycerides, with decreased glucose tolerance, liver NAD + levels and citrate synthase activity in offspring. Both interventions reduced adiposity, and showed a modest improvement in glucose tolerance and improved markers of mitochondrial function. NMN appeared to have stronger effects on liver fat catabolism (Hadh) and synthesis (Fasn) than exercise. The interventions appeared to exert the most global benefit in mice that were most metabolically challenged (HFD-consuming offspring of obese mothers). This work encourages further study to confirm the suitability of NMN for use in reversing metabolic dysfunction linked to programming by maternal obesity.

Assimilation of Endogenous Nicotinamide Riboside Is Essential for Calorie Restriction-mediated Life Span Extension in Saccharomyces cerevisiae*

PubMed Central

Lu, Shu-Ping; Kato, Michiko; Lin, Su-Ju

2009-01-01

NAD+ (nicotinamide adenine dinucleotide) is an essential cofactor involved in various biological processes including calorie restriction-mediated life span extension. Administration of nicotinamide riboside (NmR) has been shown to ameliorate deficiencies related to aberrant NAD+ metabolism in both yeast and mammalian cells. However, the biological role of endogenous NmR remains unclear. Here we demonstrate that salvaging endogenous NmR is an integral part of NAD+ metabolism. A balanced NmR salvage cycle is essential for calorie restriction-induced life span extension and stress resistance in yeast. Our results also suggest that partitioning of the pyridine nucleotide flux between the classical salvage cycle and the NmR salvage branch might be modulated by the NAD+-dependent Sir2 deacetylase. Furthermore, two novel deamidation steps leading to nicotinic acid mononucleotide and nicotinic acid riboside production are also uncovered that further underscore the complexity and flexibility of NAD+ metabolism. In addition, utilization of extracellular nicotinamide mononucleotide requires prior conversion to NmR mediated by a periplasmic phosphatase Pho5. Conversion to NmR may thus represent a strategy for the transport and assimilation of large nonpermeable NAD+ precursors. Together, our studies provide a molecular basis for how NAD+ homeostasis factors confer metabolic flexibility. PMID:19416965

In vitro evaluation of nicotinamide riboside analogs against Haemophilus influenzae.

PubMed Central

Godek, C P; Cynamon, M H

1990-01-01

Exogenous NAD, nicotinamide mononucleotide, or nicotinamide riboside is required for the growth of Haemophilus influenzae. These compounds have been defined as the V-factor growth requirement. We have previously shown that the internalization of nicotinamide riboside is energy dependent and carrier mediated with saturation kinetics. Thionicotinamide riboside, 3-pyridinealdehyde riboside, 3-acetylpyridine riboside, and 3-aminopyridine riboside were prepared from their corresponding NAD analogs. These compounds and several other nicotinamide riboside analogs were evaluated for their ability to support the growth of H. influenzae and for their ability to block the uptake of [carbonyl-14C]nicotinamide riboside by H. influenzae. 3-Aminopyridine riboside blocked the uptake of [carbonyl-14C]nicotinamide riboside and inhibited the growth of H. influenzae when NAD, nicotinamide mononucleotide, or nicotinamide riboside served as the V factor. The antibacterial activity of 3-aminopyridine riboside was found to be specific for H. influenzae but had no effect on the growth of Staphylococcus aureus or Escherichia coli. In additional experiments by reversed-phase high-performance liquid chromatography, it was determined that whole cells of H. influenzae degrade 3-aminopyridine adenine dinucleotide to 3-aminopyridine riboside, which is then internalized. Inside the cell, 3-aminopyridine riboside has the ability to interfere with the growth of H. influenzae by an undetermined mechanism. Images PMID:2145800

In vitro evaluation of nicotinamide riboside analogs against Haemophilus influenzae.

PubMed

Godek, C P; Cynamon, M H

1990-08-01

Exogenous NAD, nicotinamide mononucleotide, or nicotinamide riboside is required for the growth of Haemophilus influenzae. These compounds have been defined as the V-factor growth requirement. We have previously shown that the internalization of nicotinamide riboside is energy dependent and carrier mediated with saturation kinetics. Thionicotinamide riboside, 3-pyridinealdehyde riboside, 3-acetylpyridine riboside, and 3-aminopyridine riboside were prepared from their corresponding NAD analogs. These compounds and several other nicotinamide riboside analogs were evaluated for their ability to support the growth of H. influenzae and for their ability to block the uptake of [carbonyl-14C]nicotinamide riboside by H. influenzae. 3-Aminopyridine riboside blocked the uptake of [carbonyl-14C]nicotinamide riboside and inhibited the growth of H. influenzae when NAD, nicotinamide mononucleotide, or nicotinamide riboside served as the V factor. The antibacterial activity of 3-aminopyridine riboside was found to be specific for H. influenzae but had no effect on the growth of Staphylococcus aureus or Escherichia coli. In additional experiments by reversed-phase high-performance liquid chromatography, it was determined that whole cells of H. influenzae degrade 3-aminopyridine adenine dinucleotide to 3-aminopyridine riboside, which is then internalized. Inside the cell, 3-aminopyridine riboside has the ability to interfere with the growth of H. influenzae by an undetermined mechanism.

Assimilation of endogenous nicotinamide riboside is essential for calorie restriction-mediated life span extension in Saccharomyces cerevisiae.

PubMed

Lu, Shu-Ping; Kato, Michiko; Lin, Su-Ju

2009-06-19

NAD(+) (nicotinamide adenine dinucleotide) is an essential cofactor involved in various biological processes including calorie restriction-mediated life span extension. Administration of nicotinamide riboside (NmR) has been shown to ameliorate deficiencies related to aberrant NAD(+) metabolism in both yeast and mammalian cells. However, the biological role of endogenous NmR remains unclear. Here we demonstrate that salvaging endogenous NmR is an integral part of NAD(+) metabolism. A balanced NmR salvage cycle is essential for calorie restriction-induced life span extension and stress resistance in yeast. Our results also suggest that partitioning of the pyridine nucleotide flux between the classical salvage cycle and the NmR salvage branch might be modulated by the NAD(+)-dependent Sir2 deacetylase. Furthermore, two novel deamidation steps leading to nicotinic acid mononucleotide and nicotinic acid riboside production are also uncovered that further underscore the complexity and flexibility of NAD(+) metabolism. In addition, utilization of extracellular nicotinamide mononucleotide requires prior conversion to NmR mediated by a periplasmic phosphatase Pho5. Conversion to NmR may thus represent a strategy for the transport and assimilation of large nonpermeable NAD(+) precursors. Together, our studies provide a molecular basis for how NAD(+) homeostasis factors confer metabolic flexibility.

Quantification of riboflavin, flavin mononucleotide, and flavin adenine dinucleotide in mammalian model cells by CE with LED-induced fluorescence detection.

PubMed

Hühner, Jens; Ingles-Prieto, Álvaro; Neusüß, Christian; Lämmerhofer, Michael; Janovjak, Harald

2015-02-01

Cultured mammalian cells essential are model systems in basic biology research, production platforms of proteins for medical use, and testbeds in synthetic biology. Flavin cofactors, in particular flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), are critical for cellular redox reactions and sense light in naturally occurring photoreceptors and optogenetic tools. Here, we quantified flavin contents of commonly used mammalian cell lines. We first compared three procedures for extraction of free and noncovalently protein-bound flavins and verified extraction using fluorescence spectroscopy. For separation, two CE methods with different BGEs were established, and detection was performed by LED-induced fluorescence with limit of detections (LODs 0.5-3.8 nM). We found that riboflavin (RF), FMN, and FAD contents varied significantly between cell lines. RF (3.1-14 amol/cell) and FAD (2.2-17.0 amol/cell) were the predominant flavins, while FMN (0.46-3.4 amol/cell) was found at markedly lower levels. Observed flavin contents agree with those previously extracted from mammalian tissues, yet reduced forms of RF were detected that were not described previously. Quantification of flavins in mammalian cell lines will allow a better understanding of cellular redox reactions and optogenetic tools. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Monitoring techniques for high accuracy interference fit assembly processes

NASA Astrophysics Data System (ADS)

Liuti, A.; Vedugo, F. Rodriguez; Paone, N.; Ungaro, C.

2016-06-01

In the automotive industry, there are many assembly processes that require a high geometric accuracy, in the micrometer range; generally open-loop controllers cannot meet these requirements. This results in an increased defect rate and high production costs. This paper presents an experimental study of interference fit process, aimed to evaluate the aspects which have the most impact on the uncertainty in the final positioning. The press-fitting process considered, consists in a press machine operating with a piezoelectric actuator to press a plug into a sleeve. Plug and sleeve are designed and machined to obtain a known interference fit. Differential displacement and velocity measurements of the plug with respect to the sleeve are measured by a fiber optic differential laser Doppler vibrometer. Different driving signals of the piezo actuator allow to have an insight into the differences between a linear and a pulsating press action. The paper highlights how the press-fit assembly process is characterized by two main phases: the first is an elastic deformation of the plug and sleeve, which produces a reversible displacement, the second is a sliding of the plug with respect to the sleeve, which results in an irreversible displacement and finally realizes the assembly. The simultaneous measurements of the displacement and the force have permitted to define characteristic features in the signal useful to identify the start of the irreversible movement. These indicators could be used to develop a control logic in a press assembly process.

Altered characteristics of balance control in obese older adults.

PubMed

Melzer, Itshak; Oddsson, Lars I E

2016-01-01

Obesity is one of the most significant epidemiological trends of the last decades. Recently it was found that obese individuals show postural instability. Balance control mechanisms in obese older adults were less studied. Therefore we aimed to investigate the effect of obesity on balance control mechanisms in older adults. Parameters from Stabilogram-Diffusion Analysis (SDA) and measures from summary statistics of foot centre-of-pressure (COP) displacements along the anterior-posterior (AP) and mediolateral (ML) directions in eyes open and eyes closed conditions were used to characterize postural control in 22 obese (30-<35kg/m(2)), 26 overweight (25-<30kg/m(2)), and 18 normal weight subjects (18.5-<25kg/m(2)). Obese group subjects demonstrated significantly greater transition displacement, transition time interval, and short-term scaling exponent in the ML-direction compared with the normal weight group (eyes open and closed). In the AP-direction the obese group showed greater transition displacement (eyes open) and short-term scaling exponent (eyes open and closed). Average AP-COP and ML-COP ranges of COP sway were higher in the obese group compared with the normal weight group (eyes open and closed). This work indicates an altered postural control process in obese older adults. A greater sway displacement before closed-loop feedback mechanisms are called into play was seen in the ML direction that may lead to a higher risk of instability and fall events. Copyright © 2015 Asia Oceania Association for the Study of Obesity. Published by Elsevier Ltd. All rights reserved.

Research on hysteresis loop considering the prestress effect and electrical input dynamics for a giant magnetostrictive actuator

NASA Astrophysics Data System (ADS)

Zhu, Yuchuan; Yang, Xulei; Wereley, Norman M.

2016-08-01

In this paper, focusing on the application-oriented giant magnetostrictive material (GMM)-based electro-hydrostatic actuator, which features an applied magnetic field at high frequency and high amplitude, and concentrating on the static and dynamic characteristics of a giant magnetostrictive actuator (GMA) considering the prestress effect on the GMM rod and the electrical input dynamics involving the power amplifier and the inductive coil, a methodology for studying the static and dynamic characteristics of a GMA using the hysteresis loop as a tool is developed. A GMA that can display the preforce on the GMM rod in real-time is designed, and a magnetostrictive model dependent on the prestress on a GMM rod instead of the existing quadratic domain rotation model is proposed. Additionally, an electrical input dynamics model to excite GMA is developed according to the simplified circuit diagram, and the corresponding parameters are identified by the experimental data. A dynamic magnetization model with the eddy current effect is deduced according to the Jiles-Atherton model and the Maxwell equations. Next, all of the parameters, including the electrical input characteristics, the dynamic magnetization and the mechanical structure of GMA, are identified by the experimental data from the current response, magnetization response and displacement response, respectively. Finally, a comprehensive comparison between the model results and experimental data is performed, and the results show that the test data agree well with the presented model results. An analysis on the relation between the GMA displacement response and the parameters from the electrical input dynamics, magnetization dynamics and mechanical structural dynamics is performed.

PARACEST Properties of a Dinuclear Neodymium(III) Complex Bound to DNA or Carbonate

PubMed Central

Nwe, Kido; Andolina, Christopher M.; Huang, Ching-Hui; Morrow, Janet R.

2009-01-01

A dinuclear Nd(III) macrocyclic complex of 1 (1,4-bis[1-(4,7,10-tris(carbamoylmethyl)-1,4,7,10-tetraazacyclododecane]-p-xylene) and mononuclear complexes of 1,4,7-tris-1,4,7,10-tetraazacyclododecane 2, and 1,4,7-tris[(N-N-diethyl)carbamoylmethyl]-1,4,7,10-tetraazacyclododecane, 3, are prepared. Complexes of 1 and 2 give rise to a PARACEST (paramagnetic chemical exchange saturation transfer) peak from exchangeable amide protons that resonate approximately 12 ppm downfield from the bulk water proton resonance. The dinuclear Nd(III) complex is promising as a PARACEST contrast agent for MRI applications because it has an optimal pH of 7.5 and the rate constant for amide proton exchange (2700 s−1) is nearly as large as it can be within slow exchange conditions with bulk water. Dinuclear Ln2(1) complexes (Ln(III) = Nd(III), Eu(III)) bind tightly to anionic ligands including carbonate, diethylphosphate and DNA. The CEST amide peak of Nd2(1) is enhanced by certain DNA sequences that contain hairpin loops, but decreases in the presence of diethyl phosphate or carbonate. Direct excitation luminescence studies of Eu2(1) show that double-stranded and hairpin loop DNA sequences displace one water ligand on each Eu(III) center. DNA displaces carbonate ion despite the low dissociation constant for the Eu2(1) carbonate complex (Kd = 15 µM). Enhancement of the CEST effect of a lanthanide complex by binding to DNA is a promising step toward the preparation of PARACEST agents containing DNA scaffolds. PMID:19555071

PARACEST properties of a dinuclear neodymium(III) complex bound to DNA or carbonate.

PubMed

Nwe, Kido; Andolina, Christopher M; Huang, Ching-Hui; Morrow, Janet R

2009-07-01

A dinuclear Nd(III) macrocyclic complex of 1 (1,4-bis[1-(4,7,10-tris(carbamoylmethyl)-1,4,7,10-tetraazacyclododecane]-p-xylene) and mononuclear complexes of 1,4,7-tris-1,4,7,10-tetraazacyclododecane, 2, and 1,4,7-tris[(N-N-diethyl)carbamoylmethyl]-1,4,7,10-tetraazacyclododecane, 3, are prepared. Complexes of 1 and 2 give rise to a PARACEST (paramagnetic chemical exchange saturation transfer) peak from exchangeable amide protons that resonate approximately 12 ppm downfield from the bulk water proton resonance. The dinuclear Nd(III) complex is promising as a PARACEST contrast agent for MRI applications, because it has an optimal pH of 7.5 and the rate constant for amide proton exchange (2700 s(-1)) is nearly as large as it can be within slow exchange conditions with bulk water. Dinuclear Ln(2)(1) complexes (Ln(III) = Nd(III), Eu(III)) bind tightly to anionic ligands including carbonate, diethyl phosphate, and DNA. The CEST amide peak of Nd(2)(1) is enhanced by certain DNA sequences that contain hairpin loops, but decreases in the presence of diethyl phosphate or carbonate. Direct excitation luminescence studies of Eu(2)(1) show that double-stranded and hairpin-loop DNA sequences displace one water ligand on each Eu(III) center. DNA displaces carbonate ion despite the low dissociation constant for the Eu(2)(1) carbonate complex (K(d) = 15 microM). Enhancement of the CEST effect of a lanthanide complex by binding to DNA is a promising step toward the preparation of PARACEST agents containing DNA scaffolds.

Method of Bonding Optical Elements with Near-Zero Displacement

NASA Technical Reports Server (NTRS)

Robinson, David; McClelland, Ryan; Byron, Glenn; Evans, Tyler

2012-01-01

The International X-ray Project seeks to build an x-ray telescope using thousands of pieces of thin and flexible glass mirror segments. Each mirror segment must be bonded into a housing in nearly perfect optical alignment without distortion. Forces greater than 0.001 Newton, or displacements greater than 0.5 m of the glass, cause unacceptable optical distortion. All known epoxies shrink as they cure. Even the epoxies with the least amount of shrinkage (<0.01%) cause unacceptable optical distortion and misalignment by pulling the mirror segments towards the housing as it cures. A related problem is that the shrinkage is not consistent or predictable so that it cannot be accounted for in the setup (i.e., if all of the bonds shrunk an equal amount, there would be no problem). A method has been developed that allows two components to be joined with epoxy in such a way that reduces the displacement caused by epoxy shrinking as it cures to less than 200 nm. The method involves using ultraviolet-cured epoxy with a displacement sensor and a nanoactuator in a control loop. The epoxy is cured by short-duration exposures to UV light. In between each exposure, the nano-actuator zeroes out the displacement caused by epoxy shrinkage and thermal expansion. After a few exposures, the epoxy has cured sufficiently to prevent further displacement of the two components. Bonding of optical elements has been done for many years, but most optics are thick and rigid elements that resist micro-Newton-level forces without causing distortion. When bonding thin glass optics such as the 0.40-mm thick IXO X-ray mirrors, forces in the micro- and milli-Newton levels cause unacceptable optical figure error. This innovation can now repeatedly and reliably bond a thin glass mirror to a metal housing with less than 0.2 m of displacement (<200 nm). This is an enabling technology that allows the installation of virtually stress-free, undistorted thin optics onto structures. This innovation is applicable to the bonding of thin optical elements, or any thin/flexible structures, that must be attached in an undistorted, consistent, and aligned way.

Egocentric and Allocentric Localization During Induced Motion

PubMed Central

Post, Robert B.; Welch, Robert B.; Whitney, David

2009-01-01

This research examined motor measures of the apparent egocentric location and perceptual measures of the apparent allocentric location of a target that was being seen to undergo induced motion (IM). In Experiments 1 and 3, subjects fixated a stationary dot (IM target) while a rectangular surround stimulus (inducing stimulus) oscillated horizontally. The inducing stimulus motion caused the IM target to appear to move in the opposite direction. In Experiment 1, two dots (flashed targets) were flashed above and below the IM target when the surround had reached its leftmost or rightmost displacement from the subject’s midline. Subjects pointed open loop at either the apparent egocentric location of the IM target or at the bottom of the two flashed targets. On separate trials, subjects made judgments of the Vernier alignment of the IM target with the flashed targets at the endpoints of the surround’s oscillation. The pointing responses were displaced in the direction of the previously seen IM for the IM target and to a lesser degree for the bottom flashed target. However, the allocentric Vernier judgments demonstrated no perceptual displacement of the IM target relative to the flashed targets. Thus, IM results in a dissociation of egocentric location measures from allocentric location measures. In Experiment 2, pointing and Vernier measures were obtained with stationary horizontally displaced surrounds and there was no dissociation of egocentric location measures from allocentric location measures. These results indicate that the Roelofs effect did not produce the pattern of results in Experiment 1. In Experiment 3, pointing and Vernier measures were obtained when the surround was at the midpoint of an oscillation. In this case, egocentric pointing responses were displaced in the direction of surround motion (opposite IM) for the IM target and to a greater degree for the bottom flashed target. However, there was no apparent displacement of the IM target relative to the flashed targets in the allocentric Vernier judgments. Therefore, in Experiment 3 egocentric location measures were again dissociated from allocentric location measures. The results of this experiment also demonstrate that IM does not generate an allocentric displacement illusion analogous to the “flash-lag” effect. PMID:18751688

Closed loop kinesthetic feedback for postural control rehabilitation.

PubMed

Vérité, Fabien; Bachta, Wael; Morel, Guillaume

2014-01-01

Postural control rehabilitation may benefit from the use of smart devices providing biofeedback. This approach consists of increasing the patients perception of their postural state. Namely, postural state is monitored and fed back in real time to the patients through one or more sensory channels. This allows implementing rehabilitation exercises where the patients control their posture with the help of additional sensory inputs. In this paper, a closed loop control of the Center-Of-Pressure (CoP) based on kinesthetic feedback is proposed as a new form of biofeedback. The motion of a one Degree of Freedom (DoF) translational device, lightly touched by the patient's forefinger, is servoed to the patient's CoP position extracted from the measurements of a force plate on which he/she stands. As a result, the patient's CoP can be controllably displaced. A first set of experiments is used to prove the feasibility of this closed-loop control under ideal conditions favoring the perception of the kinesthetic feedback, while the subject is totally unaware of the context. A second set of experiments is then proposed to evaluate the robustness of this approach under experimental conditions that are more realistic with regards to the clinical context of a rehabilitation program involving biofeedback-based exercises.

Mechanism and manipulation of DNA:RNA hybrid G-quadruplex formation in transcription of G-rich DNA.

PubMed

Zhang, Jia-yu; Zheng, Ke-wei; Xiao, Shan; Hao, Yu-hua; Tan, Zheng

2014-01-29

We recently reported that a DNA:RNA hybrid G-quadruplex (HQ) forms during transcription of DNA that bears two or more tandem guanine tracts (G-tract) on the nontemplate strand. Putative HQ-forming sequences are enriched in the nearby 1000 nt region right downstream of transcription start sites in the nontemplate strand of warm-blooded animals, and HQ regulates transcription under both in vitro and in vivo conditions. Therefore, knowledge of the mechanism of HQ formation is important for understanding the biological function of HQ as well as for manipulating gene expression by targeting HQ. In this work, we studied the mechanism of HQ formation using an in vitro T7 transcription model. We show that RNA synthesis initially produces an R-loop, a DNA:RNA heteroduplex formed by a nascent RNA transcript and the template DNA strand. In the following round of transcription, the RNA in the R-loop is displaced, releasing the RNA in single-stranded form (ssRNA). Then the G-tracts in the RNA can jointly form HQ with those in the nontemplate DNA strand. We demonstrate that the structural cascade R-loop → ssRNA → HQ offers opportunities to intercept HQ formation, which may provide a potential method to manipulate gene expression.

The analysis and compensation of errors of precise simple harmonic motion control under high speed and large load conditions based on servo electric cylinder

NASA Astrophysics Data System (ADS)

Ma, Chen-xi; Ding, Guo-qing

2017-10-01

Simple harmonic waves and synthesized simple harmonic waves are widely used in the test of instruments. However, because of the errors caused by clearance of gear and time-delay error of FPGA, it is difficult to control servo electric cylinder in precise simple harmonic motion under high speed, high frequency and large load conditions. To solve the problem, a method of error compensation is proposed in this paper. In the method, a displacement sensor is fitted on the piston rod of the electric cylinder. By using the displacement sensor, the real-time displacement of the piston rod is obtained and fed back to the input of servo motor, then a closed loop control is realized. There is compensation of pulses in the next period of the synthetic waves. This paper uses FPGA as the processing core. The software mainly comprises a waveform generator, an Ethernet module, a memory module, a pulse generator, a pulse selector, a protection module, an error compensation module. A durability of shock absorbers is used as the testing platform. The durability mainly comprises a single electric cylinder, a servo motor for driving the electric cylinder, and the servo motor driver.

Discovery of d-amino acid oxidase inhibitors based on virtual screening against the lid-open enzyme conformation.

PubMed

Szilágyi, Bence; Skok, Žiga; Rácz, Anita; Frlan, Rok; Ferenczy, György G; Ilaš, Janez; Keserű, György M

2018-06-01

d-Amino acid oxidase (DAAO) inhibitors are typically small polar compounds with often suboptimal pharmacokinetic properties. Features of the native binding site limit the operational freedom of further medicinal chemistry efforts. We therefore initiated a structure based virtual screening campaign based on the X-ray structures of DAAO complexes where larger ligands shifted the loop (lid opening) covering the native binding site. The virtual screening of our in-house collection followed by the in vitro test of the best ranked compounds led to the identification of a new scaffold with micromolar IC 50 . Subsequent SAR explorations enabled us to identify submicromolar inhibitors. Docking studies supported by in vitro activity measurements suggest that compounds bind to the active site with a salt-bridge characteristic to DAAO inhibitor binding. In addition, displacement of and interaction with the loop covering the active site contributes significantly to the activity of the most potent compounds. Copyright © 2018 Elsevier Ltd. All rights reserved.

Wavelet Transform Analysis of the Power Spectrum of Centre of Pressure Signals to Detect the Critical Point Interval of Postural Control

NASA Astrophysics Data System (ADS)

Singh, Neeraj Kumar; Snoussi, Hichem; Hewson, David; Duchêne, Jacques

The aim of this study was to develop a method to detecting the critical point interval (CPI) when sensory feedback is used as part of a closed-loop postural control strategy. Postural balance was evaluated using centre of pressure (COP) displacements from a force plate for 17 control and 10 elderly subjects under eyes open, eyes closed, and vibration conditions. A modified local-maximum-modulus wavelet transform analysis using the power spectrum of COP signals was used to calculate CPI. Lower CPI values indicate increased closed-loop postural control with a quicker response to sensory input. Such a strategy requires greater energy expenditure due to the repeated muscular interventions to remain stable. The CPI for elderly occurred significantly quicker than for controls, indicating tighter control of posture. Similar results were observed for eyes closed and vibration conditions. The CPI parameter can be used to detect differences in postural control due to ageing.

Writing and compiling code into biochemistry.

PubMed

Shea, Adam; Fett, Brian; Riedel, Marc D; Parhi, Keshab

2010-01-01

This paper presents a methodology for translating iterative arithmetic computation, specified as high-level programming constructs, into biochemical reactions. From an input/output specification, we generate biochemical reactions that produce output quantities of proteins as a function of input quantities performing operations such as addition, subtraction, and scalar multiplication. Iterative constructs such as "while" loops and "for" loops are implemented by transferring quantities between protein types, based on a clocking mechanism. Synthesis first is performed at a conceptual level, in terms of abstract biochemical reactions - a task analogous to high-level program compilation. Then the results are mapped onto specific biochemical reactions selected from libraries - a task analogous to machine language compilation. We demonstrate our approach through the compilation of a variety of standard iterative functions: multiplication, exponentiation, discrete logarithms, raising to a power, and linear transforms on time series. The designs are validated through transient stochastic simulation of the chemical kinetics. We are exploring DNA-based computation via strand displacement as a possible experimental chassis.

Microstructural evolution of type 304 and 316 stainless steels under neutron irradiation at LWR relevant conditions

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

Tan, Lizhen; Stoller, Roger E.; Field, Kevin G.

Extension of light water reactors' useful life will expose austenitic internal core components to irradiation damage levels beyond 100 displacements per atom (dpa), which will lead to profound microstructural evolution and consequent degradation of macroscopic properties. Microstructural evolution, including Frank loops, cavities, precipitates, and segregation at boundaries and the resultant radiation hardening in type 304 and 316 stainless steel (SS) variants, were studied in this work via experimental characterization and multiple simulation methods. Experimental data for up to 40 heats of type 304SS and 316SS variants irradiated in different reactors to 0.6–120 dpa at 275–375°C were either generated from thismore » work or collected from literature reports. These experimental data were then combined with models of Frank loop and cavity evolution, computational thermodynamics and precipitation, and ab initio and rate theory integrated radiation-induced segregation models to provide insights into microstructural evolution and degradation at higher radiation doses.« less

Control of a multidegree of freedom standing wave ultrasonic motor driven precise positioning system

NASA Astrophysics Data System (ADS)

Ferreira, Antoine; Minotti, Patrice

1997-04-01

A newly developed positioning system incorporating a multidegree of freedom standing wave ultrasonic motor (SWUM) is presented and its advantageous features, operating principles, and some experimental results are described. The principle of motorization is based on the conversion, through frictional contact, of a stationary bending vibration sustained in a slotted metallic resonator, into rigid body displacements. A small autonomous multidegree of freedom nanopositioner using a SWUM motor is presented for fine positioning in scanning tunneling microscopy. The positioning system is achieved via the simultaneous operation of two identical pulse width modulation servo-control systems, each having a laser vibrometer position feedback loop. The closed loop position schemes are theoretically considered and their results are demonstrated and evaluated in practice. Evaluations of experimental tests indicate that a positioning resolution less than 100 nm are successfully achieved for an unlimited X-Y travel range with linear speeds between 1 mm s-1 and few cm s-1.

Microstructural evolution of type 304 and 316 stainless steels under neutron irradiation at LWR relevant conditions

DOE PAGES

Tan, Lizhen; Stoller, Roger E.; Field, Kevin G.; ...

2015-12-11

Extension of light water reactors' useful life will expose austenitic internal core components to irradiation damage levels beyond 100 displacements per atom (dpa), which will lead to profound microstructural evolution and consequent degradation of macroscopic properties. Microstructural evolution, including Frank loops, cavities, precipitates, and segregation at boundaries and the resultant radiation hardening in type 304 and 316 stainless steel (SS) variants, were studied in this work via experimental characterization and multiple simulation methods. Experimental data for up to 40 heats of type 304SS and 316SS variants irradiated in different reactors to 0.6–120 dpa at 275–375°C were either generated from thismore » work or collected from literature reports. These experimental data were then combined with models of Frank loop and cavity evolution, computational thermodynamics and precipitation, and ab initio and rate theory integrated radiation-induced segregation models to provide insights into microstructural evolution and degradation at higher radiation doses.« less

Adaptive optics self-calibration using differential OTF (dOTF)

NASA Astrophysics Data System (ADS)

Rodack, Alexander T.; Knight, Justin M.; Codona, Johanan L.; Miller, Kelsey L.; Guyon, Olivier

2015-09-01

We demonstrate self-calibration of an adaptive optical system using differential OTF [Codona, JL; Opt. Eng. 0001; 52(9):097105-097105. doi:10.1117/1.OE.52.9.097105]. We use a deformable mirror (DM) along with science camera focal plane images to implement a closed-loop servo that both flattens the DM and corrects for non-common-path aberrations within the telescope. The pupil field modification required for dOTF measurement is introduced by displacing actuators near the edge of the illuminated pupil. Simulations were used to develop methods to retrieve the phase from the complex amplitude dOTF measurements for both segmented and continuous sheet MEMS DMs and tests were performed using a Boston Micromachines continuous sheet DM for verification. We compute the actuator correction updates directly from the phase of the dOTF measurements, reading out displacements and/or slopes at segment and actuator positions. Through simulation, we also explore the effectiveness of these techniques for a variety of photons collected in each dOTF exposure pair.

Biologically inspired design of feedback control systems implemented using DNA strand displacement reactions.

PubMed

Foo, Mathias; Sawlekar, Rucha; Kulkarni, Vishwesh V; Bates, Declan G

2016-08-01

The use of abstract chemical reaction networks (CRNs) as a modelling and design framework for the implementation of computing and control circuits using enzyme-free, entropy driven DNA strand displacement (DSD) reactions is starting to garner widespread attention in the area of synthetic biology. Previous work in this area has demonstrated the theoretical plausibility of using this approach to design biomolecular feedback control systems based on classical proportional-integral (PI) controllers, which may be constructed from CRNs implementing gain, summation and integrator operators. Here, we propose an alternative design approach that utilises the abstract chemical reactions involved in cellular signalling cycles to implement a biomolecular controller - termed a signalling-cycle (SC) controller. We compare the performance of the PI and SC controllers in closed-loop with a nonlinear second-order chemical process. Our results show that the SC controller outperforms the PI controller in terms of both performance and robustness, and also requires fewer abstract chemical reactions to implement, highlighting its potential usefulness in the construction of biomolecular control circuits.

A novel electrochemical biosensor for ultrasensitive and specific detection of DNA based on molecular beacon mediated circular strand displacement and rolling circle amplification.

PubMed

Cheng, Wei; Zhang, Wei; Yan, Yurong; Shen, Bo; Zhu, Dan; Lei, Pinhua; Ding, Shijia

2014-12-15

A novel electrochemical biosensing strategy was developed for ultrasensitive and specific detection of target DNA using a cascade signal amplification based on molecular beacon (MB) mediated circular strand displacement (CSD), rolling circle amplification (RCA), biotin-strepavidin system, and enzymatic amplification. The target DNA hybridized with the loop portion of MB probe immobilized on the gold electrode and triggered the CSD, leading to multiple biotin-tagged DNA duplex. Furthermore, via biotin-streptavidin interaction, the RCA was implemented, producing long massive tandem-repeat DNA sequences for binding numerous biotinylated detection probes. This enabled an ultrasensitive electrochemical readout by further employing the streptavidin-alkaline phosphatase. The proposed biosensor showed very high sensitivity and selectivity with a dynamic response range from 1 fM to 100 pM. The proposed strategy could have the potential for applying in clinical molecular diagnostics and environmental monitoring. Copyright © 2014 Elsevier B.V. All rights reserved.

Magnetization Processes in Ribbons of Soft Magnetic Amorphous Alloys

NASA Astrophysics Data System (ADS)

Skulkina, N. A.; Ivanov, O. A.; Mazeeva, A. K.; Kuznetsov, P. A.; Stepanova, E. A.; Blinova, O. V.; Mikhalitsyna, E. A.

2018-02-01

Using iron-based (Fe-B-Si-C; Fe-Ni-Si-B) and cobalt-based (Co-Fe-Ni-Cr-Mn-Si-B) soft magnetic alloys as examples, we have studied the dependences of the remanence measured using minor hysteresis loops on the maximum induction. The different degrees of stabilization of the 180° and 90° domain walls allows these dependences to be used to analyze the magnetization processes that occur in the rapidly quenched soft magnetic alloys. It has been established from the B r( B m) dependences that, in the ribbons of soft magnetic amorphous alloys, the processes of the rotation of the magnetization oriented perpendicular to the ribbon plane start before the end of the processes of the displacement of the walls of domains with planar magnetization. After the end of the magnetization rotation processes, the magnetization processes can be interpreted as the displacement of the domain walls with a planar magnetization accompanied by a decrease in their number and a transition to a bistable state.

Magnetic bearings for a high-performance optical disk buffer, volume 1

NASA Technical Reports Server (NTRS)

Hockney, Richard; Adler, Karen; Anastas, George, Jr.; Downer, James; Flynn, Frederick; Goldie, James; Gondhalekar, Vijay; Hawkey, Timothy; Johnson, Bruce

1990-01-01

The innovation investigated in this project was the application of magnetic bearing technology to the translator head of an optical-disk data storage device. Both the capability for space-based applications and improved performance are expected to result. The phase 1 effort produced: (1) detailed specifications for both the translator-head and rotary-spindel bearings; (2) candidate hardware configurations for both bearings with detail definition for the translator head; (3) required characteristics for the magnetic bearing control loops; (4) position sensor selection; and (5) definition of the required electronic functions. The principal objective of Phase 2 was the design, fabrication, assembly, and test of the magnetic bearing system for the translator head. The scope of work included: (1) mechanical design of each of the required components; (2) electrical design of the required circuitry; (3) fabrication of the component parts and bread-board electronics; (4) generation of a test plan; and (5) integration of the prototype unit and performance testing. The project has confirmed the applicability of magnetic bearing technology to suspension of the translator head of the optical disk device, and demonstrated the achievement of all performance objectives. The magnetic bearing control loops perform well, achieving 100 Hz nominal bandwidth with phase margins between 37 and 63 degrees. The worst-case position resolution is 0.02 micron in the displacement loops and 1 micron rad in the rotation loops, The system is very robust to shock disturbances, recovering smoothly even when collisions occur between the translator and frame. The unique start-up/shut-down circuit has proven very effective.

Electrostatic networks control plug stabilization in the PapC usher.

PubMed

Pham, Thieng; Henderson, Nadine S; Werneburg, Glenn T; Thanassi, David G; Delcour, Anne H

2015-01-01

The PapC usher, a β-barrel pore in the outer membrane of uropathogenic Escherichia coli, is used for assembly of the P pilus, a key virulence factor in bacterial colonization of human kidney cells. Each PapC protein is composed of a 24-stranded β-barrel channel, flanked by N- and C-terminal globular domains protruding into the periplasm, and occluded by a plug domain (PD). The PD is displaced from the channel towards the periplasm during pilus biogenesis, but the molecular mechanism for PD displacement remains unclear. Two structural features within the β-barrel, an α-helix and β5-6 hairpin loop, may play roles in controlling plug stabilization. Here we have tested clusters of residues at the interface of the plug, barrel, α-helix and hairpin, which participate in electrostatic networks. To assess the roles of these residues in plug stabilization, we used patch-clamp electrophysiology to compare the activity of wild-type and mutant PapC channels containing alanine substitutions at these sites. Mutations interrupting each of two salt bridge networks were relatively ineffective in disrupting plug stabilization. However, mutation of two pairs of arginines located at the inner and the outer surfaces of the PD resulted in an enhanced propensity for plug displacement. One arginine pair involved in a repulsive interaction between the linkers that tether the plug to the β-barrel was particularly sensitive to mutation. These results suggest that plug displacement, which is necessary for pilus assembly and translocation, may require a weakening of key electrostatic interactions between the plug linkers, and the plug and the α-helix.

Erythroid pyrimidine 5'-nucleotidase: cloning, developmental expression, and regulation by cAMP and in vivo hypoxia.

PubMed

Mass, Markus; Simo, Erika; Dragon, Stefanie

2003-12-01

A characteristic process of terminal erythroid differentiation is the degradation of ribosomal RNA into mononucleotides. The pyrimidine mononucleotides can be dephosphorylated by pyrimidine 5'-nucleotidase (P5N-I). In humans, a lack of this enzyme causes hemolytic anemia with ribosomal structures and trinucleotides retained in the red blood cells (RBCs). Although the protein/nucleotide sequence of P5N-I is known in mammals, the onset and regulation of P5N-I during erythroid maturation is unknown. However, in circulating chicken embryonic RBCs, the enzyme is induced together with carbonic anhydrase (CAII) and 2,3-bisphosphoglycerate (2,3-BPG) by norepinephrine (NE) and adenosine, which are released by the embryo under hypoxic conditions. Here, we present the chicken P5N-I sequence and the gene expression of P5N-I during RBC maturation; the profile of gene expression follows the enzyme activity with a rise between days 13 and 16 of embryonic development. The p5n-I expression is induced (1) in definitive but not primitive RBCs by stimulation of beta-adrenergic/adenosine receptors, and (2) in definitive RBCs by hypoxic incubation of the chicken embryo. Since embryonic RBCs increase their hemoglobin-oxygen affinity by degradation of nucleotides such as uridine triphosphate (UTP) and cytidine triphosphate (CTP), the induction of p5n-I expression can be seen as an adaptive response to hypoxia.

Abiotic Synthesis of Nucleic Acids: Hypochromicity and Future Research

NASA Technical Reports Server (NTRS)

Glass, K.; Oye, M.; Deamer, D.; Vercoutere, W.

2017-01-01

The earliest forms of life would likely have a protocellular form, with a membrane encapsulating some form of linear charged polymer. These polymers could have enzymatic as well as genetic properties. We can simulate plausible prebiotic conditions in the laboratory to test hypotheses related to this concept. In earlier work we have shown that mononucleotides organized within a multilamellar lipid matrix can produce oligomers in the anhydrous phase of dehydration- rehydration cycles (Rajamani, 2008). If mononucleotides are in solution at millimolar concentrations, then oligomers resembling RNA are synthesized and exist in a steady state with their monomers DeGuzman, 2014). We have used conventional and novel techniques to demonstrate that secondary structures stabilized by hydrogen bonds may be present in the condensation products produced in dehydration- rehydration cycles that simulate hydrothermal fields that were present on the early Earth. Gel electrophoresis data corroborates the presence of up to 200-base pair length RNA fragments in products of Hydration-Dehydration experiments. Furthermore, hypochromicity measurements demonstrate a degree of hypochromicity found in single RNA strand of known sequence, as well as results that indicate this is true also for a sample of complementary strands of RNA. Analysis of ionic current signatures of known RNA hairpin molecule as measured using a nanopore detector indicate a significant variability in pattern, different from the signatures produced by DNA hairpin molecules. This informs how we may interpret nanopore data gathered from prebiotic simulations.

Infrequent widespread microsatellite instability in hepatocellular carcinomas.

PubMed

Yamamoto, H; Itoh, F; Fukushima, H; Kaneto, H; Sasaki, S; Ohmura, T; Satoh, T; Karino, Y; Endo, T; Toyota, J; Imai, K

2000-03-01

Widespread or high-frequency microsatellite instability (MSI) due to the defective DNA mismatch repair (MMR) occurs in the majority of hereditary non-polyposis colorectal cancer and a subset of sporadic malignant tumors. The incidence of MSI and underlying DNA MMR defects have been well characterized in gastrointestinal carcinogenesis, but not in hepatocarcinogenesis. To address the issue, we analyzed 55 Japanese hepatocellular carcinomas using several indicators of DNA MMR defects, such as microsatellite analysis, loss of heterozygosity (LOH) and mutation analysis of MMR genes, methylation of hMLH1 promoter, and frameshift mutations of mononucleotide repeat sequences within possible target genes. Mutation of beta2-microglobulin gene, which is presumably involved in MSI-positive tumor cell escape from immune surveillance was also examined. Some of these analyses were also carried out in 9 human liver cancer cell lines. None of the 3 quasi-monomorphic mononucleotide markers sensitive for MSI, BAT26, BAT25, and BAT34C4 presented shortened unstable alleles in any of the carcinoma, cirrhosis, chronic hepatitis tissues, or cell lines. LOH at MMR genes was infrequent (4.4 approximately 7.1%), and no mutations were detected. Neither hMLH1 hypermethylation nor frameshift mutation in the target genes was detected. No mutations were found in beta2-microglobulin. Widespread MSI due to the defective DNA MMR appears to play little if any part in Japanese hepatocarcinogenesis.

Loss of heterozygosity and microsatellite instability are rare in sporadic dedifferentiated liposarcoma: a study of 43 well-characterized cases.

PubMed

Davis, Jessica L; Grenert, James P; Horvai, Andrew E

2014-06-01

Defects in mismatch repair proteins have been identified in Lynch syndrome-associated liposarcomas, as well as in rare sporadic sarcomas. However, it is unclear if mismatch repair defects have a role in sarcoma tumorigenesis. Microsatellite instability is a surrogate marker of mismatch repair defects. To determine whether sporadic dedifferentiated liposarcomas display microsatellite instability and, if so, to evaluate whether such instability differs between the lipogenic and nonlipogenic components of these tumors. The diagnoses of conventional dedifferentiated liposarcoma were confirmed by a combination of morphologic, immunophenotypic, and molecular studies. Standard fluorescence-based polymerase chain reaction, including 5 mononucleotide microsatellite markers (BAT25, BAT26, NR21, NR24, and MONO27), as well as 2 pentanucleotide repeat markers (Penta C and Penta D), was used to test for instability and loss of heterozygosity. We demonstrated only a single case (1 of 43) with microsatellite instability at one mononucleotide marker. No sarcomas showed high-level microsatellite instability. However, loss of heterozygosity at the pentanucleotide markers was observed in 8 of 43 cases. The presence of loss of heterozygosity was overrepresented in the nonlipogenic (dedifferentiated) components compared with the paired lipogenic (well differentiated) components. Mismatch repair defects do not contribute to sporadic dedifferentiated liposarcoma tumorigenesis. Whether the observed loss of heterozygosity drives tumorigenesis in liposarcoma, for example by affecting tumor suppressor or cell cycle regulator genes, remains to be determined.

Upstream mononucleotide A-repeats play a cis-regulatory role in mammals through the DICER1 and Ago proteins.

PubMed

Aporntewan, Chatchawit; Pin-on, Piyapat; Chaiyaratana, Nachol; Pongpanich, Monnat; Boonyaratanakornkit, Viroj; Mutirangura, Apiwat

2013-10-01

A-repeats are the simplest form of tandem repeats and are found ubiquitously throughout genomes. These mononucleotide repeats have been widely believed to be non-functional 'junk' DNA. However, studies in yeasts suggest that A-repeats play crucial biological functions, and their role in humans remains largely unknown. Here, we showed a non-random pattern of distribution of sense A- and T-repeats within 20 kb around transcription start sites (TSSs) in the human genome. Different distributions of these repeats are observed upstream and downstream of TSSs. Sense A-repeats are enriched upstream, whereas sense T-repeats are enriched downstream of TSSs. This enrichment directly correlates with repeat size. Genes with different functions contain different lengths of repeats. In humans, tissue-specific genes are enriched for short repeats of <10 bp, whereas housekeeping genes are enriched for long repeats of ≥10 bp. We demonstrated that DICER1 and Argonaute proteins are required for the cis-regulatory role of A-repeats. Moreover, in the presence of a synthetic polymer that mimics an A-repeat, protein binding to A-repeats was blocked, resulting in a dramatic change in the expression of genes containing upstream A-repeats. Our findings suggest a length-dependent cis-regulatory function of A-repeats and that Argonaute proteins serve as trans-acting factors, binding to A-repeats.

Nicotinamide mononucleotide inhibits post-ischemic NAD(+) degradation and dramatically ameliorates brain damage following global cerebral ischemia.

PubMed

Park, Ji H; Long, Aaron; Owens, Katrina; Kristian, Tibor

2016-11-01

Nicotinamide adenine dinucleotide (NAD(+)) is an essential cofactor for multiple cellular metabolic reactions and has a central role in energy production. Brain ischemia depletes NAD(+) pools leading to bioenergetics failure and cell death. Nicotinamide mononucleotide (NMN) is utilized by the NAD(+) salvage pathway enzyme, nicotinamide adenylyltransferase (Nmnat) to generate NAD(+). Therefore, we examined whether NMN could protect against ischemic brain damage. Mice were subjected to transient forebrain ischemia and treated with NMN or vehicle at the start of reperfusion or 30min after the ischemic insult. At 2, 4, and 24h of recovery, the proteins poly-ADP-ribosylation (PAR), hippocampal NAD(+) levels, and expression levels of NAD(+) salvage pathway enzymes were determined. Furthermore, animal's neurologic outcome and hippocampal CA1 neuronal death was assessed after six days of reperfusion. NMN (62.5mg/kg) dramatically ameliorated the hippocampal CA1 injury and significantly improved the neurological outcome. Additionally, the post-ischemic NMN treatment prevented the increase in PAR formation and NAD(+) catabolism. Since the NMN administration did not affect animal's temperature, blood gases or regional cerebral blood flow during recovery, the protective effect was not a result of altered reperfusion conditions. These data suggest that administration of NMN at a proper dosage has a strong protective effect against ischemic brain injury. Published by Elsevier Inc.

Actions of p-synephrine on hepatic enzyme activities linked to carbohydrate metabolism and ATP levels in vivo and in the perfused rat liver.

PubMed

Maldonado, Marcos Rodrigues; Bracht, Lívia; de Sá-Nakanishi, Anacharis Babeto; Corrêa, Rúbia Carvalho Gomes; Comar, Jurandir Fernando; Peralta, Rosane Marina; Bracht, Adelar

2018-01-01

p-Synephrine is one of the main active components of the fruit of Citrus aurantium (bitter orange). Extracts of the bitter orange and other preparations containing p-synephrine have been used worldwide to promote weight loss and for sports performance. The purpose of the study was to measure the action of p-synephrine on hepatic enzyme activities linked to carbohydrate and energy metabolism and the levels of adenine mononucleotides. Enzymes and adenine mononucleotides were measured in the isolated perfused rat liver and in vivo after oral administration of the drug (50 and 300 mg/kg) by using standard techniques. p-Synephrine increased the activity of glycogen phosphorylase in vivo and in the perfused liver. It decreased, however, the activities of pyruvate kinase and pyruvate dehydrogenase also in vivo and in the perfused liver. p-Synephrine increased the hepatic pools of adenosine diphosphate and adenosine triphosphate. Stimulation of glycogen phosphorylase is consistent with the reported increased glycogenolysis in the perfused liver and increased glycemia in rats. The decrease in the pyruvate dehydrogenase activity indicates that p-synephrine is potentially capable of inhibiting the transformation of carbohydrates into lipids. The capability of increasing the adenosine triphosphate-adenosine diphosphate pool indicates a beneficial effect of p-synephrine on the cellular energetics. Copyright © 2017 John Wiley & Sons, Ltd.

Coenzyme Recognition and Gene Regulation by a Flavin Mononucleotide Riboswitch

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

Serganov, A.; Huang, L; Patel, D

2009-01-01

The biosynthesis of several protein cofactors is subject to feedback regulation by riboswitches. Flavin mononucleotide (FMN)-specific riboswitches also known as RFN elements, direct expression of bacterial genes involved in the biosynthesis and transport of riboflavin (vitamin B2) and related compounds. Here we present the crystal structures of the Fusobacterium nucleatum riboswitch bound to FMN, riboflavin and antibiotic roseoflavin. The FMN riboswitch structure, centred on an FMN-bound six-stem junction, does not fold by collinear stacking of adjacent helices, typical for folding of large RNAs. Rather, it adopts a butterfly-like scaffold, stapled together by opposingly directed but nearly identically folded peripheral domains.more » FMN is positioned asymmetrically within the junctional site and is specifically bound to RNA through interactions with the isoalloxazine ring chromophore and direct and Mg{sup 2+}-mediated contacts with the phosphate moiety. Our structural data, complemented by binding and footprinting experiments, imply a largely pre-folded tertiary RNA architecture and FMN recognition mediated by conformational transitions within the junctional binding pocket. The inherent plasticity of the FMN-binding pocket and the availability of large openings make the riboswitch an attractive target for structure-based design of FMN-like antimicrobial compounds. Our studies also explain the effects of spontaneous and antibiotic-induced deregulatory mutations and provided molecular insights into FMN-based control of gene expression in normal and riboflavin-overproducing bacterial strains.« less

Ligand binding phenomena that pertain to the metabolic function of renalase.

PubMed

Beaupre, Brett A; Roman, Joseph V; Hoag, Matthew R; Meneely, Kathleen M; Silvaggi, Nicholas R; Lamb, Audrey L; Moran, Graham R

2016-12-15

Renalase catalyzes the oxidation of isomers of β-NAD(P)H that carry the hydride in the 2 or 6 positions of the nicotinamide base to form β-NAD(P) + . This activity is thought to alleviate inhibition of multiple β-NAD(P)-dependent enzymes of primary and secondary metabolism by these isomers. Here we present evidence for a variety of ligand binding phenomena relevant to the function of renalase. We offer evidence of the potential for primary metabolism inhibition with structures of malate dehydrogenase and lactate dehydrogenase bound to the 6-dihydroNAD isomer. The previously observed preference of renalase from Pseudomonas for NAD-derived substrates over those derived from NADP is accounted for by the structure of the enzyme in complex with NADPH. We also show that nicotinamide nucleosides and mononucleotides reduced in the 2- and 6-positions are renalase substrates, but bind weakly. A seven-fold enhancement of acquisition (k red /K d ) for 6-dihydronicotinamide riboside was observed for human renalase in the presence of ADP. However, generally the addition of complement ligands, AMP for mononucleotide or ADP for nucleoside substrates, did not enhance the reductive half-reaction. Non-substrate nicotinamide nucleosides or nucleotides bind weakly suggesting that only β-NADH and β-NADPH compete with dinucleotide substrates for access to the active site. Copyright © 2016 Elsevier Inc. All rights reserved.

SelTarbase, a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunology

PubMed Central

Woerner, Stefan M.; Yuan, Yan P.; Benner, Axel; Korff, Sebastian; von Knebel Doeberitz, Magnus; Bork, Peer

2010-01-01

About 15% of human colorectal cancers and, at varying degrees, other tumor entities as well as nearly all tumors related to Lynch syndrome are hallmarked by microsatellite instability (MSI) as a result of a defective mismatch repair system. The functional impact of resulting mutations depends on their genomic localization. Alterations within coding mononucleotide repeat tracts (MNRs) can lead to protein truncation and formation of neopeptides, whereas alterations within untranslated MNRs can alter transcription level or transcript stability. These mutations may provide selective advantage or disadvantage to affected cells. They may further concern the biology of microsatellite unstable cells, e.g. by generating immunogenic peptides induced by frameshifts mutations. The Selective Targets database (http://www.seltarbase.org) is a curated database of a growing number of public MNR mutation data in microsatellite unstable human tumors. Regression calculations for various MSI–H tumor entities indicating statistically deviant mutation frequencies predict TGFBR2, BAX, ACVR2A and others that are shown or highly suspected to be involved in MSI tumorigenesis. Many useful tools for further analyzing genomic DNA, derived wild-type and mutated cDNAs and peptides are integrated. A comprehensive database of all human coding, untranslated, non-coding RNA- and intronic MNRs (MNR_ensembl) is also included. Herewith, SelTarbase presents as a plenty instrument for MSI-carcinogenesis-related research, diagnostics and therapy. PMID:19820113

Characterization of fine-grain piezoceramic stack actuators

NASA Astrophysics Data System (ADS)

Davis, Christopher L.; Morris, Donald G.; Calkins, Frederick T.

2001-07-01

Samples of fine grain piezoelectric ceramics (less than or equal to 1 micrometers ) exhibit increased mechanical strength and improved machinability over conventional materials, which should result in actuators which have increased reliability with fewer rejected parts. The focus of the work presented here is to compare the properties of several fine grain and conventional actuators provided by TRS Ceramics. Specimens are constructed of TRS200 (a PZT-5A or DOD Type II equivalent material) and TRS600 (a PZT-5H or DOD Type VI equivalent material). All of the actuators consist of ceramic wafers bonded together with electrodes between them to form a stack. Several actuator overall dimensions and two wafer thicknesses (250 micrometers and 500 micrometers ) are investigated as well as material which has been subjected to hot isopress. The two main figures of merit in the stack actuator comparisons are free strain and blocked stress. Strain and stress loops are measured under a variety of field levels, including negative fields up to the coercive limit (full butterfly loops were not performed). Also compared are values of energy density and hysteresis in the strain, stress and electric displacement vs. field loops. Stack longevity is addressed through duration tests in which stacks are used to drive representative mechanical impedance for an extended period. Results show that fine grain stacks completed 109 continuous actuation cycles with no sign of performance degradation.

Structure of the myotonic dystrophy type 2 RNA and designed small molecules that reduce toxicity.

PubMed

Childs-Disney, Jessica L; Yildirim, Ilyas; Park, HaJeung; Lohman, Jeremy R; Guan, Lirui; Tran, Tuan; Sarkar, Partha; Schatz, George C; Disney, Matthew D

2014-02-21

Myotonic dystrophy type 2 (DM2) is an incurable neuromuscular disorder caused by a r(CCUG) expansion (r(CCUG)(exp)) that folds into an extended hairpin with periodically repeating 2×2 nucleotide internal loops (5'CCUG/3'GUCC). We designed multivalent compounds that improve DM2-associated defects using information about RNA-small molecule interactions. We also report the first crystal structure of r(CCUG) repeats refined to 2.35 Å. Structural analysis of the three 5'CCUG/3'GUCC repeat internal loops (L) reveals that the CU pairs in L1 are each stabilized by one hydrogen bond and a water-mediated hydrogen bond, while CU pairs in L2 and L3 are stabilized by two hydrogen bonds. Molecular dynamics (MD) simulations reveal that the CU pairs are dynamic and stabilized by Na(+) and water molecules. MD simulations of the binding of the small molecule to r(CCUG) repeats reveal that the lowest free energy binding mode occurs via the major groove, in which one C residue is unstacked and the cross-strand nucleotides are displaced. Moreover, we modeled the binding of our dimeric compound to two 5'CCUG/3'GUCC motifs, which shows that the scaffold on which the RNA-binding modules are displayed provides an optimal distance to span two adjacent loops.

Structure of the Myotonic Dystrophy Type 2 RNA and Designed Small Molecules That Reduce Toxicity

PubMed Central

Park, HaJeung; Lohman, Jeremy R.; Guan, Lirui; Tran, Tuan; Sarkar, Partha; Schatz, George C.; Disney, Matthew D.

2014-01-01

Myotonic dystrophy type 2 (DM2) is an untreatable neuromuscular disorder caused by a r(CCUG) expansion (r(CCUG)exp) that folds into an extended hairpin with periodically repeating 2×2 nucleotide internal loops (5’CCUG/3’GUCC). We designed multivalent compounds that improve DM2-associated defects using information about RNA-small molecule interactions. We also report the first crystal structure of r(CCUG)exp refined to 2.35 Å. Structural analysis of the three 5’CCUG/3’GUCC repeat internal loops (L) reveals that the CU pairs in L1 are each stabilized by one hydrogen bond and a water-mediated hydrogen bond while CU pairs in L2 and L3 are stabilized by two hydrogen bonds. Molecular dynamics (MD) simulations reveal that the CU pairs are dynamic and stabilized by Na+ and water molecules. MD simulations of the binding of the small molecule to r(CCUG) repeats reveal that the lowest free energy binding mode occurs via the major groove, in which one C residue is unstacked and the cross-strand nucleotides are displaced. Moreover, we modeled the binding of our dimeric compound to two 5’CCUG/3’GUCC motifs, which shows that the scaffold on which the RNA-binding modules are displayed provides an optimal distance to span two adjacent loops. PMID:24341895

Studies of Xenopus laevis mitochondrial DNA: D-loop mapping and characterization of DNA-binding proteins

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

Cairns, S.S.

1987-01-01

In X. laevis oocytes, mitochondrial DNA accumulates to 10/sup 5/ times the somatic cell complement, and is characterized by a high frequency of a triple-stranded displacement hoop structure at the origin of replication. To map the termini of the single strands, it was necessary to correct the nucleotide sequence of the D-loop region. The revised sequence of 2458 nucleotides contains 54 discrepancies in comparison to a previously published sequence. Radiolabeling of the nascent strands of the D-loop structure either at the 5' end or at the 3' end identifies a major species with a length of 1670 nucleotides. Cleavage ofmore » the 5' labeled strands reveals two families of ends located near several matches to an element, designated CSB-1, that is conserved in this location in several vertebrate genomes. Cleavage of 3' labeled strands produced one fragment. The unique 3' end maps to about 15 nucleotides preceding the tRNA/sup Pro/ gene. A search for proteins which may bind to mtDNA in this region to regulate nucleic acid synthesis has identified three activities in lysates of X. laevis mitochondria. The DNA-binding proteins were assayed by monitoring their ability to retard the migration of labeled double- or single-stranded DNA fragments in polyacrylamide gels. The DNA binding preference was determined by competition with an excess of either ds- or ssDNA.« less

Theory of electric creep and electromechanical coupling with domain evolution for non-poled and fully poled ferroelectric ceramics

PubMed Central

Xia, Xiaodong; Wang, Yang; Zhong, Zheng

2016-01-01

Unlike mechanical creep with inelastic deformation, electric creep with domain evolution is a rarely studied subject. In this paper, we present a theory of electric creep and related electromechanical coupling for both non-poled and fully poled ferroelectric ceramics. We consider electric creep to be a time-dependent process, with an initial condition lying on the D (electric displacement) versus E (electric field) hysteresis loop. Both processes are shown to share the same Gibbs free energy and thermodynamic driving force, but relative to creep, the hysteresis loop is just a field-dependent process. With this view, we develop a theory with a single thermodynamic driving force but with two separate kinetic equations, one for the field-dependent loops in terms of a Lorentzian-like function and the other for the time-dependent D in terms of a dissipation potential. We use the 0°–90° and then 90°–180° switches to attain these goals. It is demonstrated that the calculated results are in broad agreement with two sets of experiments, one for a non-poled PIC-151 and the other for a fully poled PZT-5A. The theory also shows that creep polarization tends to reach a saturation state with time and that the saturated polarization has its maximum at the coercive field. PMID:27843406

Singularity-free dislocation dynamics with strain gradient elasticity

NASA Astrophysics Data System (ADS)

Po, Giacomo; Lazar, Markus; Seif, Dariush; Ghoniem, Nasr

2014-08-01

The singular nature of the elastic fields produced by dislocations presents conceptual challenges and computational difficulties in the implementation of discrete dislocation-based models of plasticity. In the context of classical elasticity, attempts to regularize the elastic fields of discrete dislocations encounter intrinsic difficulties. On the other hand, in gradient elasticity, the issue of singularity can be removed at the outset and smooth elastic fields of dislocations are available. In this work we consider theoretical and numerical aspects of the non-singular theory of discrete dislocation loops in gradient elasticity of Helmholtz type, with interest in its applications to three dimensional dislocation dynamics (DD) simulations. The gradient solution is developed and compared to its singular and non-singular counterparts in classical elasticity using the unified framework of eigenstrain theory. The fundamental equations of curved dislocation theory are given as non-singular line integrals suitable for numerical implementation using fast one-dimensional quadrature. These include expressions for the interaction energy between two dislocation loops and the line integral form of the generalized solid angle associated with dislocations having a spread core. The single characteristic length scale of Helmholtz elasticity is determined from independent molecular statics (MS) calculations. The gradient solution is implemented numerically within our variational formulation of DD, with several examples illustrating the viability of the non-singular solution. The displacement field around a dislocation loop is shown to be smooth, and the loop self-energy non-divergent, as expected from atomic configurations of crystalline materials. The loop nucleation energy barrier and its dependence on the applied shear stress are computed and shown to be in good agreement with atomistic calculations. DD simulations of Lome-Cottrell junctions in Al show that the strength of the junction and its configuration are easily obtained, without ad-hoc regularization of the singular fields. Numerical convergence studies related to the implementation of the non-singular theory in DD are presented.

Action of nucleotide phosphotransferase of Escherichia coli on nicotinamide riboside and nicotinamide mononucleotide.

PubMed Central

Brunngraber, E F; Chargaff, E

1977-01-01

The action of the nucleotide phosphotransferase of Escherichia coli on nicotinamide riboside and on its 5'-phosphate results in the addition of one phosphate moiety to each of the substrates. Although the proof is not conclusive, it is likely that the phosphate group is transferred to the 3'-hydroxyl of the ribose. This is in contrast to the behavior of the enzyme toward NAD in which only the adenylic acid portion is phosphorylated enzymically. PMID:144913

Measurement of whole tire profile

NASA Astrophysics Data System (ADS)

Yang, Yongyue; Jiao, Wenguang

2010-08-01

In this paper, a precision measuring device is developed for obtaining characteristic curve of tire profile and its geometric parameters. It consists of a laser displacement measurement unit, a closed-loop precision two-dimensional coordinate table, a step motor control system and a fast data acquisition and analysis system. Based on the laser trigonometry, a data map of tire profile and coordinate values of all points can be obtained through corresponding data transformation. This device has a compact structure, a convenient control, a simple hardware circuit design and a high measurement precision. Experimental results indicate that measurement precision can meet the customer accuracy requirement of +/-0.02 mm.

Multiparameter measurement using a double-Y-shaped suspended-core fiber in a fiber loop configuration

NASA Astrophysics Data System (ADS)

Silva, S. F.; Baierl, H.; Auguste, J.-L.; Jamier, R.; Roy, P.; Baptista, J. M.; Santos, J. L.; Frazão, O.

2014-05-01

Cardiovascular health of the human population is a major concern for medical clinicians, with cardiovascular diseases responsible for 48% of all deaths worldwide, according to the World Health Organisation. Therefore the development of new practicable and economical diagnostic tools to scrutinise the cardiovascular health of humans is a major driver for clinicians. We offer a new technique to obtain seismocardiographic signals covering both ballistocardiography (below 20Hz) and audible heart sounds (20Hz upwards). The detection scheme is based upon an array of curvature/displacement sensors using fibre optic long period gratings interrogated using a variation of the derivative spectroscopy interrogation technique

Balance control and anti‐gravity muscle activity during the experience of fear at heights

PubMed Central

Wuehr, Max; Kugler, Guenter; Schniepp, Roman; Eckl, Maria; Pradhan, Cauchy; Jahn, Klaus; Huppert, Doreen; Brandt, Thomas

2014-01-01

Abstract Fear of heights occurs when a visual stimulus causes the apprehension of losing balance and falling. A moderate form of visual height intolerance (vHI) affects about one third of the general population and has relevant consequences for the quality of life. A quantitative evaluation of balance mechanisms in persons susceptible to vHI during height exposure is missing. VHI‐related changes in postural control were assessed by center‐of‐pressure displacements and electromyographic recordings of selected leg, arm, and neck muscles in 16 subjects with vHI while standing at heights on an emergency balcony versus standing in the laboratory at ground level. Characteristics of open‐ and closed‐loop postural control were analyzed. Body sway and muscle activity parameters were correlated with the subjective estimates of fear at heights. During height exposure, (1) open‐loop control was disturbed by a higher diffusion activity (P < 0.001) and (2) the sensory feedback threshold for closed‐loop control was lowered (P < 0.010). Altered postural control was predominantly associated with increased co‐contraction of leg muscles. Body sway and leg and neck muscle co‐contraction correlated with the severity of subjective anxiety (P < 0.050). Alterations in postural control diminished if there were nearby stationary contrasts in the visual surrounding or if subjects stood with eyes closed. The performance of a cognitive dual task also improved impaired balance. Visual heights have two behavioral effects in vHI subjects: A change occurs in (1) open‐ and closed‐loop postural control strategy and (2) co‐contraction of anti‐gravity leg and neck muscles, both of which depend on the severity of evoked fear at heights. PMID:24744901

DNA Methylation-a Potential Source of Mitochondria DNA Base Mismatch in the Development of Diabetic Retinopathy.

PubMed

Mishra, Manish; Kowluru, Renu A

2018-04-21

In the development of diabetic retinopathy, retinal mitochondria are dysfunctional, and mitochondrial DNA (mtDNA) is damaged with increased base mismatches and hypermethylated cytosines. DNA methylation is also a potential source of mutation, and in diabetes, the noncoding region, the displacement loop (D-loop), experiences more methylation and base mismatches than other regions of the mtDNA. Our aim was to investigate a possible crosstalk between mtDNA methylation and base mismatches in the development of diabetic retinopathy. The effect of inhibition of Dnmts (by 5-aza-2'-deoxycytidine or Dnmt1-siRNA) on glucose-induced mtDNA base mismatches was investigated in human retinal endothelial cells by surveyor endonuclease digestion and validated by Sanger sequencing. The role of deamination factors on increased base mismatches was determined in the cells genetically modulated for mitochondrial superoxide dismutase (Sod2) or cytidine-deaminase (APOBEC3A). The results were confirmed in an in vivo model using retinal microvasculature from diabetic mice overexpressing Sod2. Inhibition of DNA methylation, or regulation of cytosine deamination, significantly inhibited an increase in base mismatches at the D-loop and prevented mitochondrial dysfunction. Overexpression of Sod2 in mice also prevented diabetes-induced D-loop hypermethylation and increase in base mismatches. The crosstalk between DNA methylation and base mismatches continued even after termination of hyperglycemia, suggesting its role in the metabolic memory phenomenon associated with the progression of diabetic retinopathy. Inhibition of DNA methylation limits the availability of methylated cytosine for deamination, suggesting a crosstalk between DNA methylation and base mismatches. Thus, regulation of DNA methylation, or its deamination, should impede the development of diabetic retinopathy by preventing formation of base mismatches and mitochondrial dysfunction.

Balance control and anti-gravity muscle activity during the experience of fear at heights.

PubMed

Wuehr, Max; Kugler, Guenter; Schniepp, Roman; Eckl, Maria; Pradhan, Cauchy; Jahn, Klaus; Huppert, Doreen; Brandt, Thomas

2014-02-01

Fear of heights occurs when a visual stimulus causes the apprehension of losing balance and falling. A moderate form of visual height intolerance (vHI) affects about one third of the general population and has relevant consequences for the quality of life. A quantitative evaluation of balance mechanisms in persons susceptible to vHI during height exposure is missing. VHI-related changes in postural control were assessed by center-of-pressure displacements and electromyographic recordings of selected leg, arm, and neck muscles in 16 subjects with vHI while standing at heights on an emergency balcony versus standing in the laboratory at ground level. Characteristics of open- and closed-loop postural control were analyzed. Body sway and muscle activity parameters were correlated with the subjective estimates of fear at heights. During height exposure, (1) open-loop control was disturbed by a higher diffusion activity (P < 0.001) and (2) the sensory feedback threshold for closed-loop control was lowered (P < 0.010). Altered postural control was predominantly associated with increased co-contraction of leg muscles. Body sway and leg and neck muscle co-contraction correlated with the severity of subjective anxiety (P < 0.050). Alterations in postural control diminished if there were nearby stationary contrasts in the visual surrounding or if subjects stood with eyes closed. The performance of a cognitive dual task also improved impaired balance. Visual heights have two behavioral effects in vHI subjects: A change occurs in (1) open- and closed-loop postural control strategy and (2) co-contraction of anti-gravity leg and neck muscles, both of which depend on the severity of evoked fear at heights.

The development of a closed-loop flight controller with panel method integration for gust alleviation using biomimetic feathers on aircraft wings

NASA Astrophysics Data System (ADS)

Blower, Christopher J.; Lee, Woody; Wickenheiser, Adam M.

2012-04-01

This paper presents the development of a biomimetic closed-loop flight controller that integrates gust alleviation and flight control into a single distributed system. Modern flight controllers predominantly rely on and respond to perturbations in the global states, resulting in rotation or displacement of the entire aircraft prior to the response. This bio-inspired gust alleviation system (GAS) employs active deflection of electromechanical feathers that react to changes in the airflow, i.e. the local states. The GAS design is a skeletal wing structure with a network of featherlike panels installed on the wing's surfaces, creating the airfoil profile and replacing the trailing-edge flaps. In this study, a dynamic model of the GAS-integrated wing is simulated to compute gust-induced disturbances. The system implements continuous adjustment to flap orientation to perform corrective responses to inbound gusts. MATLAB simulations, using a closed-loop LQR integrated with a 2D adaptive panel method, allow analysis of the morphing structure's aerodynamic data. Non-linear and linear dynamic models of the GAS are compared to a traditional single control surface baseline wing. The feedback loops synthesized rely on inertial changes in the global states; however, variations in number and location of feather actuation are compared. The bio-inspired system's distributed control effort allows the flight controller to interchange between the single and dual trailing edge flap profiles, thereby offering an improved efficiency to gust response in comparison to the traditional wing configuration. The introduction of aero-braking during continuous gusting flows offers a 25% reduction in x-velocity deviation; other flight parameters can be reduced in magnitude and deviation through control weighting optimization. Consequently, the GAS demonstrates enhancements to maneuverability and stability in turbulent intensive environments.

In-Situ RBS Channelling Studies Of Ion Implanted Semiconductors And Insulators

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

Wendler, E.

2011-06-01

The experimental set-up at the ion beam facility in Jena allows the performance of Rutherford backscattering spectrometry (RBS) in channeling configuration at any temperature between 15 K and room temperature without changing the environment or the temperature of the sample. Doing RBS channeling studies at 15 K increases the sensitivity to defects, because the influence of lattice vibrations is reduced. Thus, the very early processes of ion induced damage formation can be studied and the cross section of damage formation per ion in virgin material, P, can be determined. At 15 K ion-beam induced damage formation itself can be investigated,more » because the occurrence of thermal effects can be widely excluded. In AlAs, GaN, and ZnO the cross section P measured at 15 K can be used to estimate the displacement energy for the heavier component, which is in reasonable agreement with other experiments or theoretical calculations. For a given ion species (here Ar ions) the measured cross section P exhibits a quadratic dependence P{proportional_to}P{sub SRIM}{sup 2} with P{sub SRIM} being the value calculated with SRIM using established displacement energies from other sources. From these results the displacement energy of AlN can be estimated to about 40 eV. Applying the computer code DICADA to calculate the depth distribution of displaced lattice atoms from the channeling spectra, indirect information about the type of defects produced during ion implantation at 15 K can be obtained. In some materials like GaN or ZnO the results indicate the formation of extended defects most probably dislocation loops and thus suggest an athermal mobility of defect at 15 K.« less

A closed-loop phase-locked interferometer for wide bandwidth position sensing

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

Fleming, Andrew J., E-mail: Andrew.Fleming@Newcastle.edu.au; Routley, Ben S., E-mail: Ben.Routley@Newcastle.edu.au

This article describes a position sensitive interferometer with closed-loop control of the reference mirror. A calibrated nanopositioner is used to lock the interferometer phase to the most sensitive point in the interferogram. In this configuration, large low-frequency movements of the sensor mirror can be detected from the control signal applied to the nanopositioner and high-frequency short-range signals can be measured directly from the photodiode. It is demonstrated that these two signals are complementary and can be summed to find the total displacement. The resulting interferometer has a number of desirable characteristics: it is optically simple, does not require polarization ormore » modulation to detect the direction of motion, does not require fringe-counting or interpolation electronics, and has a bandwidth equal to that of the photodiode. Experimental results demonstrate the frequency response analysis of a high-speed positioning stage. The proposed instrument is ideal for measuring the frequency response of nanopositioners, electro-optical components, MEMs devices, ultrasonic devices, and sensors such as surface acoustic wave detectors.« less

MEMS closed-loop control incorporating a memristor as feedback sensing element

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

Garcia, Ernest J.; Almeida, Sergio F.; Mireles, Jr., Jose

In this work the integration of a memristor with a MEMS parallel plate capacitor coupled by an amplification stage is simulated. It is shown that the MEMS upper plate position can be controlled up to 95% of the total gap. Due to its common operation principle, the change in the MEMS plate position can be interpreted by the change in the memristor resistance, or memristance. A memristance modulation of ~1 KΩ was observed. A polynomial expression representing the MEMS upper plate displacement as a function of the memristance is presented. Thereafter a simple design for a voltage closed-loop control ismore » presented showing that the MEMS upper plate can be stabilized up to 95% of the total gap using the memristor as a feedback sensing element. As a result, the memristor can play important dual roles in overcoming the limited operation range of MEMS parallel plate capacitors and in simplifying read-out circuits of those devices by representing the motion of the upper plate in the form of resistance change instead of capacitance change.« less

A continuum model for dynamic analysis of the Space Station

NASA Technical Reports Server (NTRS)

Thomas, Segun

1989-01-01

Dynamic analysis of the International Space Station using MSC/NASTRAN had 1312 rod elements, 62 beam elements, 489 nodes and 1473 dynamic degrees of freedom. A realtime, man-in-the-loop simulation of such a model is impractical. This paper discusses the mathematical model for realtime dynamic simulation of the Space Station. Several key questions in structures and structural dynamics are addressed. First, to achieve a significant reduction in the number of dynamic degrees of freedom, a continuum equivalent representation of the Space Station truss structure which accounted for the unsymmetry of the basic configuration and resulted in the coupling of extensional and transverse deformation, is developed. Next, dynamic equations for the continuum equivalent of the Space Station truss structure are formulated using a matrix version of Kane's dynamical equations. Flexibility is accounted for by using a theory that accommodates extension, bending in two principal planes and shear displacement. Finally, constraint equations suitable for dynamic analysis of flexible bodies with closed loop configuration are developed and solution of the resulting system of equations is based on the zero eigenvalue theorem.

MEMS closed-loop control incorporating a memristor as feedback sensing element

DOE PAGES

Garcia, Ernest J.; Almeida, Sergio F.; Mireles, Jr., Jose; ...

2015-12-01

In this work the integration of a memristor with a MEMS parallel plate capacitor coupled by an amplification stage is simulated. It is shown that the MEMS upper plate position can be controlled up to 95% of the total gap. Due to its common operation principle, the change in the MEMS plate position can be interpreted by the change in the memristor resistance, or memristance. A memristance modulation of ~1 KΩ was observed. A polynomial expression representing the MEMS upper plate displacement as a function of the memristance is presented. Thereafter a simple design for a voltage closed-loop control ismore » presented showing that the MEMS upper plate can be stabilized up to 95% of the total gap using the memristor as a feedback sensing element. As a result, the memristor can play important dual roles in overcoming the limited operation range of MEMS parallel plate capacitors and in simplifying read-out circuits of those devices by representing the motion of the upper plate in the form of resistance change instead of capacitance change.« less

Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a.

PubMed

Swarts, Daan C; van der Oost, John; Jinek, Martin

2017-04-20

The CRISPR-associated protein Cas12a (Cpf1), which has been repurposed for genome editing, possesses two distinct nuclease activities: endoribonuclease activity for processing its own guide RNAs and RNA-guided DNase activity for target DNA cleavage. To elucidate the molecular basis of both activities, we determined crystal structures of Francisella novicida Cas12a bound to guide RNA and in complex with an R-loop formed by a non-cleavable guide RNA precursor and a full-length target DNA. Corroborated by biochemical experiments, these structures reveal the mechanisms of guide RNA processing and pre-ordering of the seed sequence in the guide RNA that primes Cas12a for target DNA binding. Furthermore, the R-loop complex structure reveals the strand displacement mechanism that facilitates guide-target hybridization and suggests a mechanism for double-stranded DNA cleavage involving a single active site. Together, these insights advance our mechanistic understanding of Cas12a enzymes and may contribute to further development of genome editing technologies. Copyright © 2017 Elsevier Inc. All rights reserved.

Structural basis of arrestin-3 activation and signaling

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

Chen, Qiuyan; Perry, Nicole A.; Vishnivetskiy, Sergey A.

A unique aspect of arrestin-3 is its ability to support both receptor-dependent and receptor-independent signaling. Here, we show that inositol hexakisphosphate (IP6) is a non-receptor activator of arrestin-3 and report the structure of IP6-activated arrestin-3 at 2.4-Å resolution. IP6-activated arrestin-3 exhibits an inter-domain twist and a displaced C-tail, hallmarks of active arrestin. IP6 binds to the arrestin phosphate sensor, and is stabilized by trimerization. Analysis of the trimerization surface, which is also the receptor-binding surface, suggests a feature called the finger loop as a key region of the activation sensor. We show that finger loop helicity and flexibility may underliemore » coupling to hundreds of diverse receptors and also promote arrestin-3 activation by IP6. Importantly, we show that effector-binding sites on arrestins have distinct conformations in the basal and activated states, acting as switch regions. These switch regions may work with the inter-domain twist to initiate and direct arrestin-mediated signaling.« less

Cloverleaf microgyroscope with electrostatic alignment and tuning

NASA Technical Reports Server (NTRS)

Challoner, A. Dorian (Inventor); Gutierrez, Roman C. (Inventor); Tang, Tony K. (Inventor)

2007-01-01

A micro-gyroscope (10) having closed loop output operation by a control voltage (V.sub.ty), that is demodulated by a drive axis (x-axis) signal V.sub.thx of the sense electrodes (S1, S2), providing Coriolis torque rebalance to prevent displacement of the micro-gyroscope (10) on the output axis (y-axis) V.sub.thy.about.0. Closed loop drive axis torque, V.sub.tx maintains a constant drive axis amplitude signal, V.sub.thx. The present invention provides independent alignment and tuning of the micro-gyroscope by using separate electrodes and electrostatic bias voltages to adjust alignment and tuning. A quadrature amplitude signal, or cross-axis transfer function peak amplitude is used to detect misalignment that is corrected to zero by an electrostatic bias voltage adjustment. The cross-axis transfer function is either V.sub.thy/V.sub.ty or V.sub.tnx/V.sub.tx. A quadrature signal noise level, or difference in natural frequencies estimated from measurements of the transfer functions is used to detect residual mistuning, that is corrected to zero by a second electrostatic bias voltage adjustment.

Real-Time Adaptive Control of a Magnetic Levitation System with a Large Range of Load Disturbance.

PubMed

Zhang, Zhizhou; Li, Xiaolong

2018-05-11

In an idle light-load or a full-load condition, the change of the load mass of a suspension system is very significant. If the control parameters of conventional control methods remain unchanged, the suspension performance of the control system deteriorates rapidly or even loses stability when the load mass changes in a large range. In this paper, a real-time adaptive control method for a magnetic levitation system with large range of mass changes is proposed. First, the suspension control system model of the maglev train is built up, and the stability of the closed-loop system is analyzed. Then, a fast inner current-loop is used to simplify the design of the suspension control system, and an adaptive control method is put forward to ensure that the system is still in a stable state when the load mass varies in a wide range. Simulations and experiments show that when the load mass of the maglev system varies greatly, the adaptive control method is effective to suspend the system stably with a given displacement.

Real-Time Adaptive Control of a Magnetic Levitation System with a Large Range of Load Disturbance

PubMed Central

Zhang, Zhizhou; Li, Xiaolong

2018-01-01

In an idle light-load or a full-load condition, the change of the load mass of a suspension system is very significant. If the control parameters of conventional control methods remain unchanged, the suspension performance of the control system deteriorates rapidly or even loses stability when the load mass changes in a large range. In this paper, a real-time adaptive control method for a magnetic levitation system with large range of mass changes is proposed. First, the suspension control system model of the maglev train is built up, and the stability of the closed-loop system is analyzed. Then, a fast inner current-loop is used to simplify the design of the suspension control system, and an adaptive control method is put forward to ensure that the system is still in a stable state when the load mass varies in a wide range. Simulations and experiments show that when the load mass of the maglev system varies greatly, the adaptive control method is effective to suspend the system stably with a given displacement. PMID:29751610

Annealing effect on microstructural recovery in 316L and A533B

NASA Astrophysics Data System (ADS)

Hashimoto, N.; Goto, S.; Inoue, S.; Suzuki, E.

2017-11-01

An austenitic model alloy (316L) and a low alloy steel (A533B) were exposed to constant or fluctuating temperature after electron irradiation to a cumulative damage level of 1 displacement per atom. 316L model alloy was exposed to LWR operating temperature during electron irradiation, and were exposed to a higher temperature at a high heating and cooling rates. The annealing experiment after irradiation to 316L resulted in the change in irradiation-induced microstructure; both the size and the number density of Frank loop and black dots were decreased, while the volume fraction of void was increased. In the case of A533B, the aging experiment after electron irradiation resulted in the shrinkage or the disappearance of black dots and the growth of dislocation loops. It is suggested that during annealing and/or aging at a high temperature the excess vacancies could be provided and flew into each defect feature, resulting in that interstitial type feature could be diminished, while vacancy type increased in volume fraction if exists.

Low Young's moduli induced D-E loop dispersion and its effect on the energy discharging performance of PVDF and P(VDF-co-HFP) films

NASA Astrophysics Data System (ADS)

Xia, Weimin; Chen, Bing; Liu, Yang; Wang, Qing; Zhang, Zhicheng

2018-03-01

Large-scale stretched films of PVDF and its copolymer P(VDF-co-HFP) with various molar contents of VDF were found to possess the considerable breakdown electric fields of about 900 MV/m. Under such a high electric field, soft polymer films with lower Young's moduli are larger compressed, giving rise to a constraining of reversal of dipoles and thereby a depressing of the dielectric response. Consequently, the displacement-electric field loops at above 700 MV/m show a dispersion phenomenon, which agrees with the reduction of in phase dielectric constant from 10 to 7 in soft P(VDF-co-HFP) 85/15mol% thick film caused by ultra-high isostatic pressure of about 400Mpa. Comparatively, in mechanically stretched PVDF and 95.5/4.5mol% P(VDF-co-HFP) thick films with a relatively high hardness, the considerable discharged energy densities of 27.1 J/cm3 and 27.7 J/cm3 were obtained, providing an effective way to achieve high discharging performance for these fluoropolymers.

3D Imaging of a Dislocation Loop at the Onset of Plasticity in an Indented Nanocrystal.

PubMed

Dupraz, M; Beutier, G; Cornelius, T W; Parry, G; Ren, Z; Labat, S; Richard, M-I; Chahine, G A; Kovalenko, O; De Boissieu, M; Rabkin, E; Verdier, M; Thomas, O

2017-11-08

Structural quality and stability of nanocrystals are fundamental problems that bear important consequences for the performances of small-scale devices. Indeed, at the nanoscale, their functional properties are largely influenced by elastic strain and depend critically on the presence of crystal defects. It is thus of prime importance to be able to monitor, by noninvasive means, the stability of the microstructure of nano-objects against external stimuli such as mechanical load. Here we demonstrate the potential of Bragg coherent diffraction imaging for such measurements, by imaging in 3D the evolution of the microstructure of a nanocrystal exposed to in situ mechanical loading. Not only could we observe the evolution of the internal strain field after successive loadings, but we also evidenced a transient microstructure hosting a stable dislocation loop. The latter is fully characterized from its characteristic displacement field. The mechanical behavior of this small crystal is clearly at odds with what happens in bulk materials where many dislocations interact. Moreover, this original in situ experiment opens interesting possibilities for the investigation of plastic deformation at the nanoscale.

Modeling of a viscoelastic damper and its application in structural control.

PubMed

Mehrabi, M H; Suhatril, Meldi; Ibrahim, Zainah; Ghodsi, S S; Khatibi, Hamed

2017-01-01

Conventional seismic rehabilitation methods may not be suitable for some buildings owing to their high cost and time-consuming foundation work. In recent years, viscoelastic dampers (VEDs) have been widely used in many mid- and high-rise buildings. This study introduces a viscoelastic passive control system called rotary rubber braced damper (RRBD). The RRBD is an economical, lightweight, and easy-to-assemble device. A finite element model considering nonlinearity, large deformation, and material damage is developed to conduct a parametric study on different damper sizes under pushover cyclic loading. The fundamental characteristics of this VED system are clarified by analyzing building structures under cyclic loading. The result show excellent energy absorption and stable hysteresis loops in all specimens. Additionally, by using a sinusoidal shaking table test, the effectiveness of the RRBD to manage the response displacement and acceleration of steel frames is considered. The RRBD functioned at early stages of lateral displacement, indicating that the system is effective for all levels of vibration. Moreover, the proposed damper shows significantly better performance in terms of the column compression force resulting from the brace action compared to chevron bracing (CB).

Helium bubbles aggravated defects production in self-irradiated copper

NASA Astrophysics Data System (ADS)

Wu, FengChao; Zhu, YinBo; Wu, Qiang; Li, XinZhu; Wang, Pei; Wu, HengAn

2017-12-01

Under the environment of high radiation, materials used in fission and fusion reactors will internally accumulate numerous lattice defects and bubbles. With extensive studies focused on bubble resolution under irradiation, the mutually effects between helium bubbles and displacement cascades in irradiated materials remain unaddressed. Therefore, the defects production and microstructure evolution under self-irradiation events in vicinity of helium bubbles are investigated by preforming large scale molecular dynamics simulations in single-crystal copper. When subjected to displacement cascades, distinguished bubble resolution categories dependent on bubble size are observed. With the existence of bubbles, radiation damage is aggravated with the increasing bubble size, represented as the promotion of point defects and dislocations. The atomic mechanisms of heterogeneous dislocation structures are attributed to different helium-vacancy cluster modes, transforming from the resolved gas trapped with vacancies to the biased absorption of vacancies by the over-pressured bubble. In both cases, helium impedes the recombination of point defects, leading to the accelerated formation of interstitial loops. The results and insight obtained here might contribute to understand the underlying mechanism of transmutant solute on the long-term evolution of irradiated materials.

Localization and phosphorylation of Plasmodium falciparum nicotinamide/nicotinate mononucleotide adenylyltransferase (PfNMNAT) in intraerythrocytic stages.

PubMed

Nieto, Carlos A; Sánchez, Lina M; Sánchez, Diana M; Díaz, Gonzalo J; Ramírez, María H

2018-04-11

Nicotinamide adenine dinucleotide (NAD+) is an essential molecule in the energy metabolism of living beings, and it has various cellular functions. The main enzyme in the biosynthesis of this nucleotide is nicotinamide/nicotinate mononucleotide adenylyltransferase (NMNAT, EC 2.7.7.1/18) because it is the convergence point for all known biosynthetic pathways. NMNATs have divergences in both the number of isoforms detected and their distribution, depending on the organism. In the laboratory of basic research in biochemistry (LIBBIQ: acronym in Spanish) the NMNATs of protozoan parasites (Leishmania braziliensis, Plasmodium falciparum, Trypanosoma cruzi, and Giardia duodenalis) have been studied, analysing their catalytic properties through the use of proteins. Recombinants and their cellular distribution essentially. In 2014, O'Hara et al. determined the cytoplasmic localization of NMNAT of P. falciparum, using a transgene coupled to GFP, however, the addition of labels to the study protein can modify several of its characteristics, including its sub-cellular localization. This study confirms the cytoplasmic localization of this protein in the parasite through recognition of the endogenous protein in the different stages of the asexual life cycle. Additionally, the study found that PfNMNAT could be a phosphorylation target at serine, tyrosine and threonine residues, and it shows variations during the asexual life cycle. These experiments confirmed that the parasite is situated in the cytoplasm, fulfilling the required functions of NAD+ in this compartment, the PfNMNAT is regulated in post-transcription processes, and can be regulated by phosphorylation in its residues.

The transport and metabolism of the uridine mononucleotides by rat jejunum in vitro.

PubMed Central

Bronk, J R; Hastewell, J G

1989-01-01

1. Both uridine 3'-monophosphate (3'-UMP) and uridine 5'-monophosphate (5'-UMP) when perfused through the lumen of isolated rat jejunum gave rise to uracil as the only transported pyrimidine appearing in the serosal medium; neither the nucleotide nor the nucleoside could be detected in the serosal fluid. 2. There was a low level of the nucleoside, uridine, in the luminal fluid after the nucleotide had passed through the jejunal segment. Luminal nucleoside appearance was more marked from the 3' form of the nucleotide. 3. The hydrolysis of the nucleotides to the nucleoside form occurred via a brush-border membrane enzyme, which had the same maximal velocity (Vmax) for the two nucleotides (699 +/- 35 and 747 +/- 10 nmol min-1 (mg protein)-1 for 3'-UMP and 5'-UMP, respectively) but a different Michaelis constant (Km) so that 3'-UMP (Km = 58 +/- 3 microM) hydrolysis is favoured over 5'-UMP hydrolysis (Km = 108 +/- microM) at lower concentrations. 4. At 0.05 mM, luminal 3'-UMP gave rise to a higher rate of serosal uracil appearance than luminal 5'-UMP, but at higher luminal concentrations (0.1-0.2 mM) the rate of serosal uracil appearance was the same from both nucleotides. 5. The transmural transport of uracil from the uridine mononucleotides is discussed with reference to the metabolism and compartmentalization of the small intestine responsible for the appearance of the free pyrimidine in the serosal fluid. PMID:2778724

Nicotinamide riboside kinases display redundancy in mediating nicotinamide mononucleotide and nicotinamide riboside metabolism in skeletal muscle cells.

PubMed

Fletcher, Rachel S; Ratajczak, Joanna; Doig, Craig L; Oakey, Lucy A; Callingham, Rebecca; Da Silva Xavier, Gabriella; Garten, Antje; Elhassan, Yasir S; Redpath, Philip; Migaud, Marie E; Philp, Andrew; Brenner, Charles; Canto, Carles; Lavery, Gareth G

2017-08-01

Augmenting nicotinamide adenine dinucleotide (NAD + ) availability may protect skeletal muscle from age-related metabolic decline. Dietary supplementation of NAD + precursors nicotinamide mononucleotide (NMN) and nicotinamide riboside (NR) appear efficacious in elevating muscle NAD + . Here we sought to identify the pathways skeletal muscle cells utilize to synthesize NAD + from NMN and NR and provide insight into mechanisms of muscle metabolic homeostasis. We exploited expression profiling of muscle NAD + biosynthetic pathways, single and double nicotinamide riboside kinase 1/2 (NRK1/2) loss-of-function mice, and pharmacological inhibition of muscle NAD + recycling to evaluate NMN and NR utilization. Skeletal muscle cells primarily rely on nicotinamide phosphoribosyltransferase (NAMPT), NRK1, and NRK2 for salvage biosynthesis of NAD + . NAMPT inhibition depletes muscle NAD + availability and can be rescued by NR and NMN as the preferred precursors for elevating muscle cell NAD + in a pathway that depends on NRK1 and NRK2. Nrk2 knockout mice develop normally and show subtle alterations to their NAD+ metabolome and expression of related genes. NRK1, NRK2, and double KO myotubes revealed redundancy in the NRK dependent metabolism of NR to NAD + . Significantly, these models revealed that NMN supplementation is also dependent upon NRK activity to enhance NAD + availability. These results identify skeletal muscle cells as requiring NAMPT to maintain NAD + availability and reveal that NRK1 and 2 display overlapping function in salvage of exogenous NR and NMN to augment intracellular NAD + availability.

Recognition of Nucleoside Monophosphate Substrates by Haemophilus influenzae Class C Acid Phosphatase

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

Singh, Harkewal; Schuermann, Jonathan P.; Reilly, Thomas J.

2010-12-08

The e (P4) phosphatase from Haemophilus influenzae functions in a vestigial NAD{sup +} utilization pathway by dephosphorylating nicotinamide mononucleotide to nicotinamide riboside. P4 is also the prototype of class C acid phosphatases (CCAPs), which are nonspecific 5{prime},3{prime}-nucleotidases localized to the bacterial outer membrane. To understand substrate recognition by P4 and other class C phosphatases, we have determined the crystal structures of a substrate-trapping mutant P4 enzyme complexed with nicotinamide mononucleotide, 5{prime}-AMP, 3{prime}-AMP, and 2{prime}-AMP. The structures reveal an anchor-shaped substrate-binding cavity comprising a conserved hydrophobic box that clamps the nucleotide base, a buried phosphoryl binding site, and three solvent-filled pocketsmore » that contact the ribose and the hydrogen-bonding edge of the base. The span between the hydrophobic box and the phosphoryl site is optimal for recognizing nucleoside monophosphates, explaining the general preference for this class of substrate. The base makes no hydrogen bonds with the enzyme, consistent with an observed lack of base specificity. Two solvent-filled pockets flanking the ribose are key to the dual recognition of 5{prime}-nucleotides and 3{prime}-nucleotides. These pockets minimize the enzyme's direct interactions with the ribose and provide sufficient space to accommodate 5{prime} substrates in an anti conformation and 3{prime} substrates in a syn conformation. Finally, the structures suggest that class B acid phosphatases and CCAPs share a common strategy for nucleotide recognition.« less

Blue light induced reactive oxygen species from flavin mononucleotide and flavin adenine dinucleotide on lethality of HeLa cells.

PubMed

Yang, Ming-Yeh; Chang, Chih-Jui; Chen, Liang-Yü

2017-08-01

Photodynamic therapy (PDT) is a safe and non-invasive treatment for cancers and microbial infections. Various photosensitizers and light sources have been developed for clinical cancer therapies. Flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) are the cofactor of enzymes and are used as photosensitizers in this study. Targeting hypoxia and light-triggering reactive oxygen species (ROS) are experimental strategies for poisoning tumor cells in vitro. HeLa cells are committed to apoptosis when treated with FMN or FAD and exposed to visible blue light (the maximum emitted wavelength of blue light is 462nm). Under blue light irradiation at 3.744J/cm 2 (=0.52mW/cm 2 irradiated for 2h), the minimal lethal dose is 3.125μM and the median lethal doses (LD 50 ) for FMN and FAD are 6.5μM and 7.2μM, respectively. Individual exposure to visible blue light irradiation or riboflavin photosensitizers does not produce cytotoxicity and no side effects are observed in this study. The western blotting results also show that an intrinsic apoptosis pathway is activated by the ROS during photolysis of riboflavin analogues. Blue light triggers the cytotoxicity of riboflavins on HeLa cells in vitro. Based on these results, this is a feasible and efficient of PDT with an intrinsic photosensitizer for cancer research. Copyright © 2017 Elsevier B.V. All rights reserved.

Uptake and Metabolism of Antibiotics Roseoflavin and 8-Demethyl-8-Aminoriboflavin in Riboflavin-Auxotrophic Listeria monocytogenes.

PubMed

Matern, Andreas; Pedrolli, Danielle; Großhennig, Stephanie; Johansson, Jörgen; Mack, Matthias

2016-12-01

The riboflavin analogs roseoflavin (RoF) and 8-demethyl-8-aminoriboflavin (AF) are produced by the bacteria Streptomyces davawensis and Streptomyces cinnabarinus Riboflavin analogs have the potential to be used as broad-spectrum antibiotics, and we therefore studied the metabolism of riboflavin (vitamin B 2 ), RoF, and AF in the human pathogen Listeria monocytogenes, a bacterium which is a riboflavin auxotroph. We show that the L. monocytogenes protein Lmo1945 is responsible for the uptake of riboflavin, RoF, and AF. Following import, these flavins are phosphorylated/adenylylated by the bifunctional flavokinase/flavin adenine dinucleotide (FAD) synthetase Lmo1329 and adenylylated by the unique FAD synthetase Lmo0728, the first monofunctional FAD synthetase to be described in bacteria. Lmo1329 generates the cofactors flavin mononucleotide (FMN) and FAD, whereas Lmo0728 produces FAD only. The combined activities of Lmo1329 and Lmo0728 are responsible for the intracellular formation of the toxic cofactor analogs roseoflavin mononucleotide (RoFMN), roseoflavin adenine dinucleotide (RoFAD), 8-demethyl-8-aminoriboflavin mononucleotide (AFMN), and 8-demethyl-8-aminoriboflavin adenine dinucleotide (AFAD). In vivo reporter gene assays and in vitro transcription/translation experiments show that the L. monocytogenes FMN riboswitch Rli96, which controls expression of the riboflavin transport gene lmo1945, is negatively affected by riboflavin/FMN and RoF/RoFMN but not by AF/AFMN. Treatment of L. monocytogenes with RoF or AF leads to drastically reduced FMN/FAD levels. We suggest that the reduced flavin cofactor levels in combination with concomitant synthesis of inactive cofactor analogs (RoFMN, RoFAD, AFMN, and AFAD) explain why RoF and AF contribute to antibiotic activity in L. monocytogenes IMPORTANCE: The riboflavin analogs roseoflavin (RoF) and 8-demethyl-8-aminoriboflavin (AF) are small molecules which are produced by Streptomyces davawensis and Streptomyces cinnabarinus RoF and AF were reported to have antibacterial activity, and we studied how these compounds are metabolized by the human bacterial pathogen Listeria monocytogenes We found that the L. monocytogenes protein Lmo1945 mediates uptake of AF and RoF and that the combined activities of the enzymes Lmo1329 and Lmo0728 are responsible for the conversion of AF and RoF to toxic cofactor analogs. Comparative studies with RoF and AF (a weaker antibiotic) suggest that the reduction in FMN/FAD levels and the formation of inactive FMN/FAD analogs explain to a large extent the antibiotic activity of AF and RoF. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

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

Joseph, J.S.; Saikatendu, K.S.; Subramanian, V.

Mature nonstructural protein-15 (nsp15) from the severe acute respiratory syndrome coronavirus (SARS-CoV) contains a novel uridylate-specific Mn{sup 2+}-dependent endoribonuclease (NendoU). Structure studies of the full-length form of the obligate hexameric enzyme from two CoVs, SARS-CoV and murine hepatitis virus, and its monomeric homologue, XendoU from Xenopus laevis, combined with mutagenesis studies have implicated several residues in enzymatic activity and the N-terminal domain as the major determinant of hexamerization. However, the tight link between hexamerization and enzyme activity in NendoUs has remained an enigma. Here, we report the structure of a trimmed, monomeric form of SARS-CoV nsp15 (residues 28 to 335)more » determined to a resolution of 2.9 Angstroms. The catalytic loop (residues 234 to 249) with its two reactive histidines (His 234 and His 249) is dramatically flipped by {approx}120 degrees into the active site cleft. Furthermore, the catalytic nucleophile Lys 289 points in a diametrically opposite direction, a consequence of an outward displacement of the supporting loop (residues 276 to 295). In the full-length hexameric forms, these two loops are packed against each other and are stabilized by intimate intersubunit interactions. Our results support the hypothesis that absence of an adjacent monomer due to deletion of the hexamerization domain is the most likely cause for disruption of the active site, offering a structural basis for why only the hexameric form of this enzyme is active.« less

Complete nucleotide sequence of pig (Sus scrofa) mitochondrial genome and dating evolutionary divergence within Artiodactyla.

PubMed

Lin, C S; Sun, Y L; Liu, C Y; Yang, P C; Chang, L C; Cheng, I C; Mao, S J; Huang, M C

1999-08-05

The complete nucleotide sequence of the pig (Sus scrofa) mitochondrial genome, containing 16613bp, is presented in this report. The genome is not a specific length because of the presence of the variable numbers of tandem repeats, 5'-CGTGCGTACA in the displacement loop (D-loop). Genes responsible for 12S and 16S rRNAs, 22 tRNAs, and 13 protein-coding regions are found. The genome carries very few intergenic nucleotides with several instances of overlap between protein-coding or tRNA genes, except in the D-loop region. For evaluating the possible evolutionary relationships between Artiodactyla and Cetacea, the nucleotide substitutions and amino acid sequences of 13 protein-coding genes were aligned by pairwise comparisons of the pig, cow, and fin whale. By comparing these sequences, we suggest that there is a closer relationship between the pig and cow than that between either of these species and fin whale. In addition, the accumulation of transversions and gaps in pig 12S and 16S rRNA genes was compared with that in other eutherian species, including cow, fin whale, human, horse, and harbor seal. The results also reveal a close phylogenetic relationship between pig and cow, as compared to fin whale and others. Thus, according to the sequence differences of mitochondrial rRNA genes in eutherian species, the evolutionary separation of pig and cow occurred about 53-60 million years ago.

Observations of Upward Propagating Waves in the Transition Region and Corona above Sunspots

NASA Astrophysics Data System (ADS)

Hou, Zhenyong; Huang, Zhenghua; Xia, Lidong; Li, Bo; Fu, Hui

2018-03-01

We present observations of persistent oscillations of some bright features in the upper-chromosphere/transition region above sunspots taken by IRIS SJ 1400 Å and upward propagating quasi-periodic disturbances along coronal loops rooted in the same region taken by the AIA 171 Å passband. The oscillations of the features are cyclic oscillatory motions without any obvious damping. The amplitudes of the spatial displacements of the oscillations are about 1″. The apparent velocities of the oscillations are comparable to the sound speed in the chromosphere, but the upward motions are slightly larger than that of the downward. The intensity variations can take 24%–53% of the background, suggesting nonlinearity of the oscillations. The FFT power spectra of the oscillations show a dominant peak at a period of about 3 minutes, which is consistent with the omnipresent 3 minute oscillations in sunspots. The amplitudes of the intensity variations of the upward propagating coronal disturbances are 10%–15% of the background. The coronal disturbances have a period of about 3 minutes, and propagate upward along the coronal loops with apparent velocities in a range of 30 ∼ 80 km s‑1. We propose a scenario in which the observed transition region oscillations are powered continuously by upward propagating shocks, and the upward propagating coronal disturbances can be the recurrent plasma flows driven by shocks or responses of degenerated shocks that become slow magnetic-acoustic waves after heating the plasma in the coronal loops at their transition-region bases.

The cell pole: the site of cross talk between the DNA uptake and genetic recombination machinery.

PubMed

Kidane, Dawit; Ayora, Silvia; Sweasy, Joann B; Graumann, Peter L; Alonso, Juan C

2012-01-01

Natural transformation is a programmed mechanism characterized by binding of free double-stranded (ds) DNA from the environment to the cell pole in rod-shaped bacteria. In Bacillus subtilis some competence proteins, which process the dsDNA and translocate single-stranded (ss) DNA into the cytosol, recruit a set of recombination proteins mainly to one of the cell poles. A subset of single-stranded binding proteins, working as "guardians", protects ssDNA from degradation and limit the RecA recombinase loading. Then, the "mediators" overcome the inhibitory role of guardians, and recruit RecA onto ssDNA. A RecA·ssDNA filament searches for homology on the chromosome and, in a process that is controlled by "modulators", catalyzes strand invasion with the generation of a displacement loop (D-loop). A D-loop resolvase or "resolver" cleaves this intermediate, limited DNA replication restores missing information and a DNA ligase seals the DNA ends. However, if any step fails, the "rescuers" will repair the broken end to rescue chromosomal transformation. If the ssDNA does not share homology with resident DNA, but it contains information for autonomous replication, guardian and mediator proteins catalyze plasmid establishment after inhibition of RecA. DNA replication and ligation reconstitute the molecule (plasmid transformation). In this review, the interacting network that leads to a cross talk between proteins of the uptake and genetic recombination machinery will be placed into prospective.

The cell pole: The site of cross talk between the DNA uptake and genetic recombination machinery

PubMed Central

Kidane, Dawit; Ayora, Silvia; Sweasy, Joann; Graumann, Peter L.; Alonso, Juan C.

2012-01-01

Natural transformation is a programmed mechanism characterized by binding of free double-stranded (ds) DNA from the environment to the cell pole in rod-shaped bacteria. In Bacillus subtilis some competence proteins, which process the dsDNA and translocate single-stranded (ss) DNA into the cytosol, recruit a set of recombination proteins mainly to one of the cell poles. A subset of single-stranded binding proteins, working as “guardians”, protect ssDNA from degradation and limit the RecA recombinase loading. Then, the “mediators” overcome the inhibitory role of guardians, and recruit RecA onto ssDNA. A RecA·ssDNA filament searches for homology on the chromosome and, in a process that is controlled by “modulators”, catalyzes strand invasion with the generation of a displacement loop (D-loop). A D-loop resolvase or “resolver” cleaves this intermediate, limited DNA replication restores missing information and a DNA ligase seals the DNA ends. However, if any step fails, the “rescuers” will repair the broken end to rescue chromosomal transformation. If the ssDNA does not share homology with resident DNA, but it contains information for autonomous replication, guardian and mediator proteins catalyze plasmid establishment after inhibition of RecA. DNA replication and ligation reconstitute the molecule (plasmid transformation). In this review, the interacting network that leads to a cross talk between proteins of the uptake and genetic recombination machinery will be placed into prospective. PMID:23046409

Transverse kink oscillations in the presence of twist

NASA Astrophysics Data System (ADS)

Terradas, J.; Goossens, M.

2012-12-01

Context. Magnetic twist is thought to play an important role in coronal loops. The effects of magnetic twist on stable magnetohydrodynamic (MHD) waves is poorly understood because they are seldom studied for relevant cases. Aims: The goal of this work is to study the fingerprints of magnetic twist on stable transverse kink oscillations. Methods: We numerically calculated the eigenmodes of propagating and standing MHD waves for a model of a loop with magnetic twist. The azimuthal component of the magnetic field was assumed to be small in comparison to the longitudinal component. We did not consider resonantly damped modes or kink instabilities in our analysis. Results: For a nonconstant twist the frequencies of the MHD wave modes are split, which has important consequences for standing waves. This is different from the degenerated situation for equilibrium models with constant twist, which are characterised by an azimuthal component of the magnetic field that linearly increases with the radial coordinate. Conclusions: In the presence of twist standing kink solutions are characterised by a change in polarisation of the transverse displacement along the tube. For weak twist, and in the thin tube approximation, the frequency of standing modes is unaltered and the tube oscillates at the kink speed of the corresponding straight tube. The change in polarisation is linearly proportional to the degree of twist. This has implications with regard to observations of kink modes, since the detection of this variation in polarisation can be used as an indirect method to estimate the twist in oscillating loops.

A cascade autocatalytic strand displacement amplification and hybridization chain reaction event for label-free and ultrasensitive electrochemical nucleic acid biosensing.

PubMed

Chen, Zhiqiang; Liu, Ying; Xin, Chen; Zhao, Jikuan; Liu, Shufeng

2018-08-15

Herein, an autocatalytic strand displacement amplification (ASDA) strategy was proposed for the first time, which was further ingeniously coupled with hybridization chain reaction (HCR) event for the isothermal, label-free and multiple amplification toward nucleic acid detection. During the ASDA module, the target recognition opens the immobilized hairpin probe (IP) and initiates the annealing of the auxiliary DNA strand (AS) with the opened IP for the successive polymerization and nicking reaction in the presence of DNA polymerase and nicking endonuclease. This induces the target recycling and generation of a large amount of intermediate DNA sequences, which can be used as target analogy to execute the autocatalytic strand displacement amplification. Simultaneously, the introduced AS strand can propagate the HCR between two hairpins (H1 and H2) to form a linear DNA concatamer with cytosine (C)-rich loop region, which can facilitate the in-situ synthesis of silver nanoclusters (AgNCs) as electrochemical tags for further amplification toward target responses. With current cascade ASDA and HCR strategy, the detection of target DNA could be achieved with a low detection limit of about 0.16 fM and a good selectivity. The developed biosensor also exhibits the distinct advantages of flexibility and simplicity in probe design and biosensor fabrication, and label-free electrochemical detection, thus opens a promising avenue for the detection of nucleic acid with low abundance in bioanalysis and clinical biomedicine. Copyright © 2018 Elsevier B.V. All rights reserved.

Voltammetric determination of attomolar levels of a sequence derived from the genom of hepatitis B virus by using molecular beacon mediated circular strand displacement and rolling circle amplification.

PubMed

Huang, Shan; Feng, Mengmeng; Li, Jiawen; Liu, Yi; Xiao, Qi

2018-03-03

The authors describe an electrochemical method for the determination of the single-stranded DNA (ssDNA) oligonucleotide with a sequence derived from the genom of hepatitis B virus (HBV). It is making use of circular strand displacement (CSD) and rolling circle amplification (RCA) strategies mediated by a molecular beacon (MB). This ssDNA hybridizes with the loop portion of the MB immobilized on the surface of a gold electrode, while primer DNA also hybridizes with the rest of partial DNA sequences of MB. This triggers the MB-mediated CSD. The RCA is then initiated to produce a long DNA strand with multiple tandem-repeat sequences, and this results in a significant increase of the differential pulse voltammetric response of the electrochemical probe Methylene Blue at a rather low working potential of -0.24 V (vs. Ag/AgCl). Under optimal experimental conditions, the assay displays an ultrahigh sensitivity (with a 2.6 aM detection limit) and excellent selectivity. Response is linear in the 10 to 700 aM DNA concentration range. Graphical abstract Schematic of a voltammetric method for the determination of attomolar levels of target DNA. It is based on molecular beacon mediated circular strand displacement and rolling circle amplification strategies. Under optimal experimental conditions, the assay displays an ultrahigh sensitivity with a 2.6 aM detection limit and excellent selectivity.

Identification and cloning of four riboswitches from Burkholderia pseudomallei strain K96243

NASA Astrophysics Data System (ADS)

Munyati-Othman, Noor; Fatah, Ahmad Luqman Abdul; Piji, Mohd Al Akmarul Fizree Bin Md; Ramlan, Effirul Ikhwan; Raih, Mohd Firdaus

2015-09-01

Structured RNAs referred as riboswitches have been predicted to be present in the genome sequence of Burkholderia pseudomallei strain K96243. Four of the riboswitches were identified and analyzed through BLASTN, Rfam search and multiple sequence alignment. The RNA aptamers belong to the following riboswitch classifications: glycine riboswitch, cobalamin riboswitch, S-adenosyl-(L)-homocysteine (SAH) riboswitch and flavin mononucleotide (FMN) riboswitch. The conserved nucleotides for each aptamer were identified and were marked on the secondary structure generated by RNAfold. These riboswitches were successfully amplified and cloned for further study.

Free-Piston Stirling Power Conversion Unit for Fission Surface Power, Phase I Final Report

NASA Technical Reports Server (NTRS)

Wood, J. Gary; Buffalino, Andrew; Holliday, Ezekiel; Penswick, Barry; Gedeon, David

2010-01-01

This report summarizes the design of a 12 kW dual opposed free-piston Stirling convertor and controller for potential future use in space missions. The convertor is heated via a pumped NaK loop and cooling is provided by a pumped water circuit. Convertor efficiency is projected at 27 percent (AC electrical out/heat in). The controller converts the AC electrical output to 120 Vdc and is projected at 91 percent efficiency. A mechanically simple arrangement, based on proven technology, was selected in which the piston is resonated almost entirely by the working space pressure swing, while the displacer is resonated by planar mechanical springs in the bounce space.

Nonlinear random response prediction using MSC/NASTRAN

NASA Technical Reports Server (NTRS)

Robinson, J. H.; Chiang, C. K.; Rizzi, S. A.

1993-01-01

An equivalent linearization technique was incorporated into MSC/NASTRAN to predict the nonlinear random response of structures by means of Direct Matrix Abstract Programming (DMAP) modifications and inclusion of the nonlinear differential stiffness module inside the iteration loop. An iterative process was used to determine the rms displacements. Numerical results obtained for validation on simple plates and beams are in good agreement with existing solutions in both the linear and linearized regions. The versatility of the implementation will enable the analyst to determine the nonlinear random responses for complex structures under combined loads. The thermo-acoustic response of a hexagonal thermal protection system panel is used to highlight some of the features of the program.

Apparatus for establishing flow of a fluid mass having a known velocity

NASA Technical Reports Server (NTRS)

Price, P.; Veikins, O.; Bate, E. R., Jr.; Jones, R. H. (Inventor)

1974-01-01

An apparatus for establishing a flow of fluid mass, such as gas, having a known velocity is introduced. The apparatus is characterized by an hermetically sealed chamber conforming to a closed-loop configuration and including a throat and a plurality of axially displaceable pistons for sweeping through the throat a stream of gas including a core and an unsheared boundary layer. Within the throat there is a cylindrical coring body concentrically related to the throat for receiving the core, and a chamber surrounding the cylindrical body for drawing off the boundary layer, whereby the velocity of the core is liberated from the effects of the velocity of the boundary layer.

Cyclic biomechanical testing of biocomposite lateral row knotless anchors in a human cadaveric model.

PubMed

Barber, F Alan; Bava, Eric D; Spenciner, David B; Piccirillo, Justin

2013-06-01

The purpose of this study was to assess the mechanical performance of biocomposite knotless lateral row anchors based on both anchor design and the direction of pull. Two lateral row greater tuberosity insertion sites (anterior and posterior) were identified in matched pairs of fresh-frozen human cadaveric shoulders DEXA (dual energy X-ray absorptiometry) scanned to verify comparability. The humeri were stripped of all soft tissue and 3 different biocomposite knotless lateral row anchors: HEALIX Knotless BR (DePuy Mitek, Raynham MA), BioComposite PushLock (Arthrex, Naples, FL), and Bio-SwiveLock (Arthrex). Fifty-two anchors were distributed among the insertion locations and tested them with either an anatomic or axial pull. A fixed-gauge loop (15 mm) of 2 high-strength sutures from each anchor was created. After a 10-Nm preload, anchors were cycled from 10 to 45 Nm at 0.5 Hz for 200 cycles and tested to failure at 4.23 mm/second. The load to reach 3 mm and 5 mm displacement, ultimate failure load, displacement at ultimate failure, and failure mode were recorded. Threaded anchors (Bio-SwiveLock, P = .03; HEALIX Knotless, P = .014) showed less displacement with anatomic testing than did the nonthreaded anchor (BioComposite PushLock), and the HEALIX Knotless showed less overall displacement than did the other 2 anchors. The Bio-SwiveLock exhibited greater failure loads than did the other 2 anchors (P < .05). Comparison of axial and anatomic loading showed no maximum load differences for all anchors as a whole (P = .1084). Yet, anatomic pulling produced higher failure loads than did axial pulling for the Bio-SwiveLock but not for the BioComposite PushLock or the HEALIX Knotless. The nonthreaded anchor (BioComposite PushLock) displayed lower failure loads than did both threaded anchors with axial pulling. Threaded biocomposite anchors (HEALIX Knotless BR and Bio-SwiveLock) show less anatomic loading displacement and higher axial failure loads than do the nonthreaded (BioComposite PushLock) anchor. The HEALIX Knotless BR anchor showed less displacement than did the BioComposite PushLock and Bio-SwiveLock anchors. Neither axial nor anatomic loading had an effect on overall anchor displacement. Because of the strength profiles exhibited, this study supports the use of biocomposite anchors, which have definite advantages over polyetheretherketone (PEEK) and metal products. However, the nonthreaded BioComposite PushLock anchor cannot be recommended. Copyright © 2013 Arthroscopy Association of North America. All rights reserved.

Forensic applicability of multi-allelic InDels with mononucleotide homopolymer structures.

PubMed

Zhang, Shu; Zhu, Qiang; Chen, Xiaogang; Zhao, Yuancun; Zhao, Xiaohong; Yang, Yiwen; Gao, Zehua; Fang, Ting; Wang, Yufang; Zhang, Ji

2018-04-27

Insertion/deletion polymorphisms (InDels), which possess the characteristics of low mutation rates and a short amplicon size, have been regarded as promising markers for forensic DNA analysis. InDels can be classified as bi-allelic or multi-allelic, depending on the number of alleles. Many studies have explored the use of bi-allelic InDels in forensic applications, such as individual identification and ancestry inference. However, multi-allelic InDels have received relatively little attention. In this study, InDels with 2-6 alleles and a minor allele frequency ≥0.01, in Chinese Southern Han (CHS), were retrieved from the 1000 Genomes Project Phase III. Based on the structural analysis of all retrieved InDels, 17 multi-allelic markers with mononucleotide homopolymer structures were selected and combined in one multiplex PCR reaction system. Sensitivity, species specificity and applicability in forensic case work of the multiplex were analyzed. A total of 218 unrelated individuals from a Chinese Han population were genotyped. The combined discriminatory power (CDP), the combined match probability (CMP) and the cumulative probability of exclusion (CPE) were 0.9999999999609, 3.91E-13 and 0.9956, respectively. The results demonstrated that this InDel multiplex panel was highly informative in the investigated population and most of the 26 populations of the 1000 Genomes Project. The data also suggested that multi-allelic InDel markers with monomeric base pair expansions are useful for forensic applications. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

IDENTIFICATION OF NICOTINAMIDE MONONUCLEOTIDE DEAMIDASE OF THE BACTERIAL PYRIDINE NUCLEOTIDE CYCLE REVEALS A NOVEL BROADLY CONSERVED AMIDOHYDROLASE FAMILY

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

Galeazzi, Luca; Bocci, Paolo; Amici, Adolfo

2011-09-27

The pyridine nucleotide cycle (PNC) is a network of salvage and recycling routes maintaining homeostasis of NAD(P) cofactor pool in the cell. Nicotinamide mononucleotide (NMN) deamidase (EC 3.5.1.42), one of the key enzymes of the bacterial PNC was originally described in Enterobacteria, but the corresponding gene eluded identification for over 30 years. A genomics-based reconstruction of NAD metabolism across hundreds bacterial species suggested that NMN deamidase reaction is the only possible way of nicotinamide salvage in the marine bacterium Shewanella oneidensis. This prediction was verified via purification of native NMN deamidase from S. oneidensis followed by the identification of themore » respective gene, termed pncC. Enzymatic characterization of the PncC protein, as well as phenotype analysis of deletion mutants, confirmed its proposed biochemical and physiological function in S. oneidensis. Of the three PncC homologs present in E. coli, NMN deamidase activity was confirmed only for the recombinant purified product of the ygaD gene. A comparative analysis at the level of sequence and three dimensional structure, which is available for one of the PncC family member, shows no homology with any previously described amidohydrolases. Multiple alignment analysis of functional and non functional PncC homologs, together with NMN docking experiments, allowed us to tentatively identify the active site area and conserved residues therein. An observed broad phylogenomic distribution of predicted functional PncCs in bacterial kingdom is consistent with a possible role in detoxification of NMN, resulting from NAD utilization by DNA ligase.« less

NadN and e (P4) are essential for utilization of NAD and nicotinamide mononucleotide but not nicotinamide riboside in Haemophilus influenzae.

PubMed

Kemmer, G; Reilly, T J; Schmidt-Brauns, J; Zlotnik, G W; Green, B A; Fiske, M J; Herbert, M; Kraiss, A; Schlör, S; Smith, A; Reidl, J

2001-07-01

Haemophilus influenzae has an absolute requirement for NAD (factor V) because it lacks almost all the biosynthetic enzymes necessary for the de novo synthesis of that cofactor. Factor V can be provided as either nicotinamide adenosine dinucleotide (NAD), nicotinamide mononucleotide (NMN), or nicotinamide riboside (NR) in vitro, but little is known about the source or the mechanism of uptake of these substrates in vivo. As shown by us earlier, at least two gene products are involved in the uptake of NAD, the outer membrane lipoprotein e (P4), which has phosphatase activity and is encoded by hel, and a periplasmic NAD nucleotidase, encoded by nadN. It has also been observed that the latter gene product is essential for H. influenzae growth on media supplemented with NAD. In this report, we describe the functions and substrates of these two proteins as they act together in an NAD utilization pathway. Data are provided which indicate that NadN harbors not only NAD pyrophosphatase but also NMN 5'-nucleotidase activity. The e (P4) protein is also shown to have NMN 5'-nucleotidase activity, recognizing NMN as a substrate and releasing NR as its product. Insertion mutants of nadN or deletion and site-directed mutants of hel had attenuated growth and a reduced uptake phenotype when NMN served as substrate. A hel and nadN double mutant was only able to grow in the presence of NR, whereas no uptake of NMN was observed.

NadN and e (P4) Are Essential for Utilization of NAD and Nicotinamide Mononucleotide but Not Nicotinamide Riboside in Haemophilus influenzae

PubMed Central

Kemmer, Gabriele; Reilly, Thomas J.; Schmidt-Brauns, Joachim; Zlotnik, Gary W.; Green, Bruce A.; Fiske, Michael J.; Herbert, Mark; Kraiß, Anita; Schlör, Stefan; Smith, Arnold; Reidl, Joachim

2001-01-01

Haemophilus influenzae has an absolute requirement for NAD (factor V) because it lacks almost all the biosynthetic enzymes necessary for the de novo synthesis of that cofactor. Factor V can be provided as either nicotinamide adenosine dinucleotide (NAD), nicotinamide mononucleotide (NMN), or nicotinamide riboside (NR) in vitro, but little is known about the source or the mechanism of uptake of these substrates in vivo. As shown by us earlier, at least two gene products are involved in the uptake of NAD, the outer membrane lipoprotein e (P4), which has phosphatase activity and is encoded by hel, and a periplasmic NAD nucleotidase, encoded by nadN. It has also been observed that the latter gene product is essential for H. influenzae growth on media supplemented with NAD. In this report, we describe the functions and substrates of these two proteins as they act together in an NAD utilization pathway. Data are provided which indicate that NadN harbors not only NAD pyrophosphatase but also NMN 5′-nucleotidase activity. The e (P4) protein is also shown to have NMN 5′-nucleotidase activity, recognizing NMN as a substrate and releasing NR as its product. Insertion mutants of nadN or deletion and site-directed mutants of hel had attenuated growth and a reduced uptake phenotype when NMN served as substrate. A hel and nadN double mutant was only able to grow in the presence of NR, whereas no uptake of NMN was observed. PMID:11395461

Clinical impact of endometrial cancer stratified by genetic mutational profiles, POLE mutation, and microsatellite instability.

PubMed

Haruma, Tomoko; Nagasaka, Takeshi; Nakamura, Keiichiro; Haraga, Junko; Nyuya, Akihiro; Nishida, Takeshi; Goel, Ajay; Masuyama, Hisashi; Hiramatsu, Yuji

2018-01-01

The molecular characterization of endometrial cancer (EC) can facilitate identification of various tumor subtypes. Although EC patients with POLE mutations reproducibly demonstrate better prognosis, the outcome of patients with microsatellite instability (MSI) remains controversial. This study attempted to interrogate whether genetic stratification of EC can identify distinct subsets with prognostic significance. A cohort of 138 EC patients who underwent surgical resection with curative intent was enrolled. Sanger sequencing was used to evaluate mutations in the POLE and KRAS genes. MSI analysis was performed using four mononucleotide repeat markers and methylation status of the MLH1 promoter was measured by a fluorescent bisulfite polymerase chain reaction (PCR). Protein expression for mismatch repair (MMR) proteins was evaluated by immunohistochemistry (IHC). Extensive hypermethylation of the MLH1 promoter was observed in 69.6% ECs with MLH1 deficiency and 3.5% with MMR proficiency, but in none of the ECs with loss of other MMR genes (P < .0001). MSI-positive and POLE mutations were found in 29.0% and 8.7% EC patients, respectively. Our MSI analysis showed a sensitivity of 92.7% for EC patients with MMR deficiency, and a specificity of 97.9% for EC patients with MMR proficiency. In univariate and multivariate analyses, POLE mutations and MSI status was significantly associated with progression-free survival (P = 0.0129 and 0.0064, respectively) but not with endometrial cancer-specific survival. This study provides significant evidence that analyses of proofreading POLE mutations and MSI status based on mononucleotide repeat markers are potentially useful biomarkers to identify EC patients with better prognosis.

Electron microscopy observations of radiation damage in irradiated and annealed tungsten

NASA Astrophysics Data System (ADS)

Grzonka, J.; Ciupiński, Ł.; Smalc-Koziorowska, J.; Ogorodnikova, O. V.; Mayer, M.; Kurzydłowski, K. J.

2014-12-01

In the present work tungsten samples were irradiated with W6+ ions with a kinetic energy of 20 MeV in order to simulate radiation damage by fast neutrons. Two samples with cumulative damage of 2.3 and 6.36 displacements per atom were produced. The scanning transmission electron microscopy investigations were carried out in order to determine structure changes resulting from the irradiation. The evolution of the damage with post implantation annealing in the temperature range 673-1100 K was also assessed. Damage profiles were studied at cross-sections. Scanning transmission electron microscopy studies of the lamellae after annealing revealed aggregation of defects and rearrangement as well as partial healing of dislocations at higher temperatures. The results confirm the higher density of radiation-induced dislocations in the near surface area of the sample (1.8 * 1014 m-2) in comparison with a deeper damage area (1.5 * 1014 m-2). Significant decrease of dislocation density was observed after annealing with a concurrent growth of dislocation loops. Transmission electron microscopy analyses show that the dislocation loops are perfect dislocations with the Burgers vectors of b = ½[ 1 1 1].

Atomic force microscopy capable of vibration isolation with low-stiffness Z-axis actuation.

PubMed

Ito, Shingo; Schitter, Georg

2018-03-01

For high-resolution imaging without bulky external vibration isolation, this paper presents an atomic force microscope (AFM) capable of vibration isolation with its internal Z-axis (vertical) actuators moving the AFM probe. Lorentz actuators (voice coil actuators) are used for the Z-axis actuation, and flexures guiding the motion are designed to have a low stiffness between the mover and the base. The low stiffness enables a large Z-axis actuation of more than 700 µm and mechanically isolates the probe from floor vibrations at high frequencies. To reject the residual vibrations, the probe tracks the sample by using a displacement sensor for feedback control. Unlike conventional AFMs, the Z-axis actuation attains a closed-loop control bandwidth that is 35 times higher than the first mechanical resonant frequency. The closed-loop AFM system has robustness against the flexures' nonlinearity and uses the first resonance for better sample tracking. For further improvement, feedforward control with a vibration sensor is combined, and the resulting system rejects 98.4% of vibrations by turning on the controllers. The AFM system is demonstrated by successful AFM imaging in a vibrational environment. Copyright © 2017 Elsevier B.V. All rights reserved.

Compliance and control characteristics of an additive manufactured-flexure stage

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

Lee, ChaBum; Tarbutton, Joshua A.

2015-04-15

This paper presents a compliance and positioning control characteristics of additive manufactured-nanopositioning system consisted of the flexure mechanism and voice coil motor (VCM). The double compound notch type flexure stage was designed to utilize the elastic deformation of two symmetrical four-bar mechanisms to provide a millimeter-level working range. Additive manufacturing (AM) process, stereolithography, was used to fabricate the flexure stage. The AM stage was inspected by using 3D X-ray computerized tomography scanner: air-voids and shape irregularity. The compliance, open-loop resonance peak, and damping ratio of the AM stage were measured 0.317 mm/N, 80 Hz, and 0.19, respectively. The AM stagemore » was proportional-integral-derivative positioning feedback-controlled and the capacitive type sensor was used to measure the displacement. As a result, the AM flexure mechanism was successfully 25 nm positioning controlled within 500 μm range. The resonance peak was found approximately at 280 Hz in closed-loop. This research showed that the AM flexure mechanism and the VCM can provide millimeter range with high precision and can be a good alternative to an expensive metal-based flexure mechanism and piezoelectric transducer.« less

Untangleing the effects of chain rigidity on the structure and dynamics of strongly adsorbed polymer melts

DOE PAGES

Carrillo, Jan-Michael Y.; Cheng, Shiwang; Kumar, Rajeev; ...

2015-06-11

Here, we present a detailed analysis of coarse-grained molecular dynamics simulations of semiflexible polymer melts in contact with a strongly adsorbing substrate. We have characterized the segments in the interfacial layer by counting the number of trains, loops, tails and unadsorbed segments. For more rigid chains, a tail and an adsorbed segment (a train) dominate while loops are more prevalent in more flexible chains. The tails exhibit a non-uniformly stretched conformation akin to the polydispersed pseudobrush envisioned by Guiselin. To probe the dynamics of the segments we computed the layer z-resolved intermediate coherent collective dynamics structure factor, S(q, t, z),more » mean-square displacement of segments, and the 2nd Legendre polynomial of the time-autocorrelation of unit bond vectors, 2[n i(t,z)•n i(0,z)]>. Our results show that segmental dynamics is slower for stiffer chains and there is a strong correlation between the structure and dynamics in the interfacial layer. There is no glassy layer, and the slowing down in dynamics of stiffer chains in the adsorbed region can be attributed to the densification and the more persistent layering of segments.« less

Economic analysis of municipal wastewater utilization for thermoelectric power production

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

Safari, I.; Walker, M.; Abbasian, J.

2011-01-01

The thermoelectric power industry in the U.S. uses a large amount of freshwater. The large water demand is increasingly a problem, especially for new power plant development, as availability of freshwater for new uses diminishes in the United States. Reusing non-traditional water sources, such as treated municipal wastewater, provides one option to mitigate freshwater usage in the thermoelectric power industry. The amount of freshwater withdrawal that can be displaced with non-traditional water sources at a particular location requires evaluation of the water management and treatment requirements, considering the quality and abundance of the non-traditional water sources. This paper presents themore » development of an integrated costing model to assess the impact of degraded water treatment, as well as the implications of increased tube scaling in the main condenser. The model developed herein is used to perform case studies of various treatment, condenser cleaning and condenser configurations to provide insight into the ramifications of degraded water use in the cooling loops of thermoelectric power plants. Further, this paper lays the groundwork for the integration of relationships between degraded water quality, scaling characteristics and volatile emission within a recirculating cooling loop model.« less

The role of niobium carbide in radiation induced segregation behaviour of type 347 austenitic stainless steel

NASA Astrophysics Data System (ADS)

Ahmedabadi, Parag; Kain, Vivekanand; Gupta, Manu; Samajdar, I.; Sharma, S. C.; Bhagwat, P.; Chowdhury, R.

2011-08-01

The effect of niobium carbide precipitates on radiation induced segregation (RIS) behaviour in type 347 stainless steel was investigated. The material in the as-received condition was irradiated using double-loop 4.8 MeV protons at 300 °C for 0.43 dpa (displacement per atom). The RIS in the proton irradiated specimen was characterized using double-loop electrochemical potentiokinetic reactivation (DL-EPR) test followed by atomic force microscopic examination. The nature of variation of DL-EPR values with the depth matched with the variation of the calculated irradiation damage (dpa) with the depth. The attack on grain boundaries during EPR tests was negligible indicating absence of chromium depletion zones. The interface between niobium carbide and the matrix acts as a sink for point defects generated during irradiation and this had reduced point defect flux toward grain boundaries. The attack was noticed at a few large cluster of niobium carbide after the DL-EPR test at the depth of maximum attack for the irradiated specimen. Pit-like features were not observed within the matrix indicating the absence of chromium depletion regions within the matrix.

Experiment study on RC frame retrofitted by the external structure

NASA Astrophysics Data System (ADS)

Liu, Chunyang; Shi, Junji; Hiroshi, Kuramoto; Taguchi, Takashi; Kamiya, Takashi

2016-09-01

A new retrofitting method is proposed herein for reinforced concrete (RC) structures through attachment of an external structure. The external structure consists of a fiber concrete encased steel frame, connection slab and transverse beams. The external structure is connected to the existing structure through a connection slab and transverse beams. Pseudostatic experiments were carried out on one unretrofitted specimen and three retrofitted frame specimens. The characteristics, including failure mode, crack pattern, hysteresis loops behavior, relationship of strain and displacement of the concrete slab, are demonstrated. The results show that the load carrying capacity is obviously increased, and the extension length of the slab and the number of columns within the external frame are important influence factors on the working performance of the existing structure. In addition, the displacement difference between the existing structure and the outer structure was caused mainly by three factors: shear deformation of the slab, extraction of transverse beams, and drift of the conjunction part between the slab and the existing frame. Furthermore, the total deformation determined by the first two factors accounted for approximately 80% of the damage, therefore these factors should be carefully considered in engineering practice to enhance the effects of this new retrofitting method.

Atomic force microscopy studies of human rhinovirus topology and molecular forces.

PubMed

Kienberger, Ferry; Zhu, Rong; Rankl, Christian; Gruber, Hermann J; Blaas, Dieter; Hinterdorfer, Peter

2010-01-01

Dynamic force microscopy (DFM) allows for imaging of the structure and assessment of the function of biological specimens in their physiological environment. In DFM, the cantilever is oscillated at a given frequency and touches the sample only at the end of its downward movement. Accordingly, the problem of lateral forces displacing or even destroying biomolecules is virtually inexistent as the contact time and friction forces are greatly reduced. Here, we describe the use of DFM in studies of human rhinovirus serotype 2 (HRV2). The capsid of HRV2 was reproducibly imaged without any displacement of the virus. Release of the genomic RNA from the virions was initiated by exposure to low-pH buffer and snapshots of the extrusion process were obtained. DFM of the single-stranded RNA genome of an HRV showed loops protruding from a condensed RNA core, 20-50 nm in height. The mechanical rigidity of the RNA was determined by single molecule pulling experiments. From fitting RNA stretching curves to the worm-like-chain (WLC) model a persistence length of 1.0+/-0.17 nm was obtained. Copyright (c) 2010 Elsevier Inc. All rights reserved.

3D active stabilization system with sub-micrometer resolution.

PubMed

Kursu, Olli; Tuukkanen, Tuomas; Rahkonen, Timo; Vähäsöyrinki, Mikko

2012-01-01

Stable positioning between a measurement probe and its target from sub- to few micrometer scales has become a prerequisite in precision metrology and in cellular level measurements from biological tissues. Here we present a 3D stabilization system based on an optoelectronic displacement sensor and custom piezo-actuators driven by a feedback control loop that constantly aims to zero the relative movement between the sensor and the target. We used simulations and prototyping to characterize the developed system. Our results show that 95% attenuation of movement artifacts is achieved at 1 Hz with stabilization performance declining to ca. 70% attenuation at 10 Hz. Stabilization bandwidth is limited by mechanical resonances within the displacement sensor that occur at relatively low frequencies, and are attributable to the sensor's high force sensitivity. We successfully used brain derived micromotion trajectories as a demonstration of complex movement stabilization. The micromotion was reduced to a level of ∼1 µm with nearly 100 fold attenuation at the lower frequencies that are typically associated with physiological processes. These results, and possible improvements of the system, are discussed with a focus on possible ways to increase the sensor's force sensitivity without compromising overall system bandwidth.

Collider tests of the Renormalizable Coloron Model

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

Bai, Yang; Dobrescu, Bogdan A.

The coloron, a massive version of the gluon present in gauge extensions of QCD, has been searched for at the LHC as a dijet or top quark pair resonance. We point out that in the Renormalizable Coloron Model (ReCoM) with a minimal field content to break the gauge symmetry, a color-octet scalar and a singlet scalar are naturally lighter than the coloron because they are pseudo Nambu-Goldstone bosons. Consequently, the coloron may predominantly decay into scalar pairs, leading to novel signatures at the LHC. When the color-octet scalar is lighter than the singlet, or when the singlet mass is above roughly 1 TeV, the signatures consist of multi-jet resonances of multiplicity up to 12, including topologies with multi-prong jet substructure, slightly displaced vertices, and sometimes a top quark pair. When the singlet is the lightest ReCoM boson and lighter than about 1 TeV, its main decays (more » $W^+W^-$, $$\\gamma Z$$, $ZZ$) arise at three loops. The LHC signatures then involve two or four boosted electroweak bosons, often originating from highly displaced vertices, plus one or two pairs of prompt jets or top quarks.« less

A novel instrument for generating angular increments of 1 nanoradian

NASA Astrophysics Data System (ADS)

Alcock, Simon G.; Bugnar, Alex; Nistea, Ioana; Sawhney, Kawal; Scott, Stewart; Hillman, Michael; Grindrod, Jamie; Johnson, Iain

2015-12-01

Accurate generation of small angles is of vital importance for calibrating angle-based metrology instruments used in a broad spectrum of industries including mechatronics, nano-positioning, and optic fabrication. We present a novel, piezo-driven, flexure device capable of reliably generating micro- and nanoradian angles. Unlike many such instruments, Diamond Light Source's nano-angle generator (Diamond-NANGO) does not rely on two separate actuators or rotation stages to provide coarse and fine motion. Instead, a single Physik Instrumente NEXLINE "PiezoWalk" actuator provides millimetres of travel with nanometre resolution. A cartwheel flexure efficiently converts displacement from the linear actuator into rotary motion with minimal parasitic errors. Rotation of the flexure is directly measured via a Magnescale "Laserscale" angle encoder. Closed-loop operation of the PiezoWalk actuator, using high-speed feedback from the angle encoder, ensures that the Diamond-NANGO's output drifts by only ˜0.3 nrad rms over ˜30 min. We show that the Diamond-NANGO can reliably move with unprecedented 1 nrad (˜57 ndeg) angular increments over a range of >7000 μrad. An autocollimator, interferometer, and capacitive displacement sensor are used to independently confirm the Diamond-NANGO's performance by simultaneously measuring the rotation of a reflective cube.

A novel instrument for generating angular increments of 1 nanoradian.

PubMed

Alcock, Simon G; Bugnar, Alex; Nistea, Ioana; Sawhney, Kawal; Scott, Stewart; Hillman, Michael; Grindrod, Jamie; Johnson, Iain

2015-12-01

Accurate generation of small angles is of vital importance for calibrating angle-based metrology instruments used in a broad spectrum of industries including mechatronics, nano-positioning, and optic fabrication. We present a novel, piezo-driven, flexure device capable of reliably generating micro- and nanoradian angles. Unlike many such instruments, Diamond Light Source's nano-angle generator (Diamond-NANGO) does not rely on two separate actuators or rotation stages to provide coarse and fine motion. Instead, a single Physik Instrumente NEXLINE "PiezoWalk" actuator provides millimetres of travel with nanometre resolution. A cartwheel flexure efficiently converts displacement from the linear actuator into rotary motion with minimal parasitic errors. Rotation of the flexure is directly measured via a Magnescale "Laserscale" angle encoder. Closed-loop operation of the PiezoWalk actuator, using high-speed feedback from the angle encoder, ensures that the Diamond-NANGO's output drifts by only ∼0.3 nrad rms over ∼30 min. We show that the Diamond-NANGO can reliably move with unprecedented 1 nrad (∼57 ndeg) angular increments over a range of >7000 μrad. An autocollimator, interferometer, and capacitive displacement sensor are used to independently confirm the Diamond-NANGO's performance by simultaneously measuring the rotation of a reflective cube.

3D Active Stabilization System with Sub-Micrometer Resolution

PubMed Central

Rahkonen, Timo; Vähäsöyrinki, Mikko

2012-01-01

Stable positioning between a measurement probe and its target from sub- to few micrometer scales has become a prerequisite in precision metrology and in cellular level measurements from biological tissues. Here we present a 3D stabilization system based on an optoelectronic displacement sensor and custom piezo-actuators driven by a feedback control loop that constantly aims to zero the relative movement between the sensor and the target. We used simulations and prototyping to characterize the developed system. Our results show that 95 % attenuation of movement artifacts is achieved at 1 Hz with stabilization performance declining to ca. 70 % attenuation at 10 Hz. Stabilization bandwidth is limited by mechanical resonances within the displacement sensor that occur at relatively low frequencies, and are attributable to the sensor's high force sensitivity. We successfully used brain derived micromotion trajectories as a demonstration of complex movement stabilization. The micromotion was reduced to a level of ∼1 µm with nearly 100 fold attenuation at the lower frequencies that are typically associated with physiological processes. These results, and possible improvements of the system, are discussed with a focus on possible ways to increase the sensor's force sensitivity without compromising overall system bandwidth. PMID:22900045

Modeling of a viscoelastic damper and its application in structural control

PubMed Central

Ibrahim, Zainah; Ghodsi, S. S.; Khatibi, Hamed

2017-01-01

Conventional seismic rehabilitation methods may not be suitable for some buildings owing to their high cost and time-consuming foundation work. In recent years, viscoelastic dampers (VEDs) have been widely used in many mid- and high-rise buildings. This study introduces a viscoelastic passive control system called rotary rubber braced damper (RRBD). The RRBD is an economical, lightweight, and easy-to-assemble device. A finite element model considering nonlinearity, large deformation, and material damage is developed to conduct a parametric study on different damper sizes under pushover cyclic loading. The fundamental characteristics of this VED system are clarified by analyzing building structures under cyclic loading. The result show excellent energy absorption and stable hysteresis loops in all specimens. Additionally, by using a sinusoidal shaking table test, the effectiveness of the RRBD to manage the response displacement and acceleration of steel frames is considered. The RRBD functioned at early stages of lateral displacement, indicating that the system is effective for all levels of vibration. Moreover, the proposed damper shows significantly better performance in terms of the column compression force resulting from the brace action compared to chevron bracing (CB). PMID:28570657

State transition of a non-Ohmic damping system in a corrugated plane.

PubMed

Lü, Kun; Bao, Jing-Dong

2007-12-01

Anomalous transport of a particle subjected to non-Ohmic damping of the power delta in a tilted periodic potential is investigated via Monte Carlo simulation of the generalized Langevin equation. It is found that the system exhibits two relative motion modes: the locked state and the running state. In an environment of sub-Ohmic damping (0=2D_(eff)(delta){t(delta_eff} . Our result shows that the effective power index delta_(eff) can be enhanced and is a nonmonotonic function of the temperature and the driving force. The mixture of the two motion modes also leads to a breakdown of the hysteresis loop of the mobility.

A novel oscillation control for MEMS vibratory gyroscopes using a modified electromechanical amplitude modulation technique

NASA Astrophysics Data System (ADS)

Ma, Wei; Lin, Yiyu; Liu, Siqi; Zheng, Xudong; Jin, Zhonghe

2017-02-01

This paper reports a novel oscillation control algorithm for MEMS vibratory gyroscopes using a modified electromechanical amplitude modulation (MEAM) technique, which enhances the robustness against the frequency variation of the driving mode, compared to the conventional EAM (CEAM) scheme. In this approach, the carrier voltage exerted on the proof mass is frequency-modulated by the drive resonant frequency. Accordingly, the pick-up signal from the interface circuit involves a constant-frequency component that contains the amplitude and phase information of the vibration displacement. In other words, this informational detection signal is independent of the mechanical resonant frequency, which varies due to different batches, imprecise micro-fabrication and changing environmental temperature. In this paper, the automatic gain control loop together with the phase-locked loop are simultaneously analyzed using the averaging method and Routh-Hurwitz criterion, deriving the stability condition and the parameter optimization rules of the transient response. Then, a simulation model based on the real system is set up to evaluate the control algorithm. Further, the proposed MEAM method is tested using a field-programmable-gate-array based digital platform on a capacitive vibratory gyroscope. By optimizing the control parameters, the transient response of the drive amplitude reveals a settling time of 45.2 ms without overshoot, according well with the theoretical prediction and simulation results. The first measurement results show that the amplitude variance of the drive displacement is 12 ppm in an hour while the phase standard deviation is as low as 0.0004°. The mode-split gyroscope operating under atmospheric pressure demonstrates an outstanding performance. By virtue of the proposed MEAM method, the bias instability and angle random walk are measured to be 0.9° h-1 (improved by 2.4 times compared to the CEAM method) and 0.068° (√h)-1 (improved by 1.4 times), respectively.

Mitochondrial DNA mutation screening of male patients with obstructive sleep apnea-hypopnea syndrome.

PubMed

Huang, Xiao-Ying; Li, Hong; Xu, Xiao-Mei; Wang, Liang-Xing

2014-08-01

The aim of the present study was to analyze the differences between the genes of the mitochondrial DNA (mtDNA) displacement loop (D-loop) region and the Cambridge Reference sequence, in order to screen the mutation sites and investigate the correlation between mutations, clinical parameters and complications associated with obstructive sleep apnea-hypopnea syndrome (OSAHS). mtDNA was obtained from male patients with OSAHS in the Zhejiang Province. In total, 60 male patients with OSAHS and 102 healthy adults were assessed to determine the levels of fasting blood glucose, total cholesterol, triglyceride (TG) and high-density and low-density lipoproteins (LDL). Furthermore, peripheral mtDNA was extracted and bidirectional sequencing was conducted to enable mutation screening. In the mtDNA D-loop region, 178 mutation sites were identified, of which 115 sites were present in the two groups. The number of non-common sites in the OSAHS group was significantly higher compared with the control group (P<0.05). No statistically significant difference was observed in the mutations among the mild, moderate and severe OSAHS groups (P>0.05). A total of 21 cases in the severe OSAHS group exhibited mutation rates of >10%. In the control group, there were 24 cases where the np73A-G and np263A-G mutations were predominant. The np303-np315 region was identified to be the highly variable region and various mutation forms were observed. Statistically significant differences were observed in the neck perimeter, TG and LDL levels among the OSAHS-no-mutation subgroups (P<0.05) and LDL was shown to be associated with an mtDNA mutation in the OSAHS group. Numerous polymorphic mutation sites were identified in the mtDNA D-loop region of the OSAHS group. Therefore, mtDNA mutation sites may be closely associated with the clinical manifestations and complications of OSAHS.

Vibration nullification of MEMS device using input shaping

NASA Astrophysics Data System (ADS)

Jordan, Scott; Lawrence, Eric M.

2003-07-01

The active silicon microstructures known as Micro-Electromechanical Systems (MEMS) are improving many existing technologies through simplification and cost reduction. Many industries have already capitalized on MEMS technology such as those in fields as diverse as telecommunications, computing, projection displays, automotive safety, defense and biotechnology. As they grow in sophistication and complexity, the familiar pressures to further reduce costs and increase performance grow for those who design and manufacture MEMS devices and the engineers who specify them for their end applications. One example is MEMS optical switches that have evolved from simple, bistable on/off elements to microscopic, freelypositionable beam steering optics. These can be actuated to discrete angular positions or to continuously-variable angular states through applied command signals. Unfortunately, elaborate closed-loop actuation schemes are often necessitated in order to stabilize the actuation. Furthermore, preventing one actuated micro-element from vibrationally cross-coupling with its neighbors is another reason costly closed-loop approaches are thought to be necessary. The Laser Doppler Vibrometer (LDV) is a valuable tool for MEMS characterization that provides non-contact, real-time measurements of velocity and/or displacement response. The LDV is a proven technology for production metrology to determine dynamical behaviors of MEMS elements, which can be a sensitive indicator of manufacturing variables such as film thickness, etch depth, feature tolerances, handling damage and particulate contamination. They are also important for characterizing the actuation dynamics of MEMS elements for implementation of a patented controls technique called Input Shaping«, which we show here can virtually eliminate the vibratory resonant response of MEMS elements even when subjected to the most severe actuation profiles. In this paper, we will demonstrate the use of the LDV to determine how the application of this compact, efficient algorithm can improve the performance of both open- and closed-loop MEMS devices, eliminating the need for costly closed-loop approaches. This can greatly reduce the complexity, cost and yield of MEMS design and manufacture.

Coupling of Lever Arm Swing and Biased Brownian Motion in Actomyosin

PubMed Central

Nie, Qing-Miao; Togashi, Akio; Sasaki, Takeshi N.; Takano, Mitsunori; Sasai, Masaki; Terada, Tomoki P.

2014-01-01

An important unresolved problem associated with actomyosin motors is the role of Brownian motion in the process of force generation. On the basis of structural observations of myosins and actins, the widely held lever-arm hypothesis has been proposed, in which proteins are assumed to show sequential structural changes among observed and hypothesized structures to exert mechanical force. An alternative hypothesis, the Brownian motion hypothesis, has been supported by single-molecule experiments and emphasizes more on the roles of fluctuating protein movement. In this study, we address the long-standing controversy between the lever-arm hypothesis and the Brownian motion hypothesis through in silico observations of an actomyosin system. We study a system composed of myosin II and actin filament by calculating free-energy landscapes of actin-myosin interactions using the molecular dynamics method and by simulating transitions among dynamically changing free-energy landscapes using the Monte Carlo method. The results obtained by this combined multi-scale calculation show that myosin with inorganic phosphate (Pi) and ADP weakly binds to actin and that after releasing Pi and ADP, myosin moves along the actin filament toward the strong-binding site by exhibiting the biased Brownian motion, a behavior consistent with the observed single-molecular behavior of myosin. Conformational flexibility of loops at the actin-interface of myosin and the N-terminus of actin subunit is necessary for the distinct bias in the Brownian motion. Both the 5.5–11 nm displacement due to the biased Brownian motion and the 3–5 nm displacement due to lever-arm swing contribute to the net displacement of myosin. The calculated results further suggest that the recovery stroke of the lever arm plays an important role in enhancing the displacement of myosin through multiple cycles of ATP hydrolysis, suggesting a unified movement mechanism for various members of the myosin family. PMID:24762409

Coupling of lever arm swing and biased Brownian motion in actomyosin.

PubMed

Nie, Qing-Miao; Togashi, Akio; Sasaki, Takeshi N; Takano, Mitsunori; Sasai, Masaki; Terada, Tomoki P

2014-04-01

An important unresolved problem associated with actomyosin motors is the role of Brownian motion in the process of force generation. On the basis of structural observations of myosins and actins, the widely held lever-arm hypothesis has been proposed, in which proteins are assumed to show sequential structural changes among observed and hypothesized structures to exert mechanical force. An alternative hypothesis, the Brownian motion hypothesis, has been supported by single-molecule experiments and emphasizes more on the roles of fluctuating protein movement. In this study, we address the long-standing controversy between the lever-arm hypothesis and the Brownian motion hypothesis through in silico observations of an actomyosin system. We study a system composed of myosin II and actin filament by calculating free-energy landscapes of actin-myosin interactions using the molecular dynamics method and by simulating transitions among dynamically changing free-energy landscapes using the Monte Carlo method. The results obtained by this combined multi-scale calculation show that myosin with inorganic phosphate (Pi) and ADP weakly binds to actin and that after releasing Pi and ADP, myosin moves along the actin filament toward the strong-binding site by exhibiting the biased Brownian motion, a behavior consistent with the observed single-molecular behavior of myosin. Conformational flexibility of loops at the actin-interface of myosin and the N-terminus of actin subunit is necessary for the distinct bias in the Brownian motion. Both the 5.5-11 nm displacement due to the biased Brownian motion and the 3-5 nm displacement due to lever-arm swing contribute to the net displacement of myosin. The calculated results further suggest that the recovery stroke of the lever arm plays an important role in enhancing the displacement of myosin through multiple cycles of ATP hydrolysis, suggesting a unified movement mechanism for various members of the myosin family.

Mitochondria DNA replication and DNA methylation in the metabolic memory associated with continued progression of diabetic retinopathy.

PubMed

Tewari, Shikha; Zhong, Qing; Santos, Julia M; Kowluru, Renu A

2012-07-24

Diabetic retinopathy fails to halt after cessation of hyperglycemic insult, and a vicious cycle of mitochondria damage continues. The aim of our study was to investigate the effect of termination of hyperglycemia on retinal mtDNA replication, and elucidate the mechanism responsible for the continued mtDNA damage. Polymerase gamma 1 (POLG1), the catalytic subunit of the mitochondrial DNA replication enzyme, and the damage to the displacement loop region of mtDNA (D-loop) were analyzed in the retina from streptozotocin-diabetic rats maintained in poor glycemic control (PC, glycated hemoglobin ∼11%) or in good glycemic control (GC, glycated hemoglobin ∼6%) for 6 months, or in PC for three months followed by GC for three months (Rev). To understand the mechanism DNA methylation status of POLG1 promoter was investigated by methylation-specific PCR. The key parameters were confirmed in the isolated retinal endothelial cells exposed to high glucose, followed by normal glucose. POLG1 continued to be down-regulated, the D-loop region damaged, and the CpG islands at the regulatory region of POLG hyper-methylated even after three months of GC that had followed three months of PC (Rev group). Similar results were observed in the retinal endothelial cells exposed to normal glucose after being exposed to high glucose. Continued hypermethylation of the CpG sites at the regulatory region of POLG affects its binding to the mtDNA, compromising the transcriptional activity. Modulation of DNA methylation using pharmaceutic or molecular means could help maintain mitochondria homeostasis, and prevent further progression of diabetic retinopathy.

Interaction between Gravitropism and Phototropism in Sporangiophores of Phycomyces blakesleeanus1

PubMed Central

Grolig, Franz; Eibel, Peter; Schimek, Christine; Schapat, Tanja; Dennison, David S.; Galland, Paul A.

2000-01-01

The interaction between gravitropism and phototropism was analyzed for sporangiophores of Phycomyces blakesleeanus. Fluence rate-response curves for phototropism were generated under three different conditions: (a) for stationary sporangiophores, which reached photogravitropic equilibrium; (b) for sporangiophores, which were clinostated head-over during phototropic stimulation; and (c) for sporangiophores, which were subjected to centrifugal accelerations of 2.3g to 8.4g. For blue light (454 nm), clinostating caused an increase of the slope of the fluence rate-response curves and an increase of the maximal bending angles at saturating fluence rates. The absolute threshold remained, however, practically unaffected. In contrast to the results obtained with blue light, no increase of the slope of the fluence rate-response curves was obtained with near-ultraviolet light at 369 nm. Bilateral irradiation with near-ultraviolet or blue light enhanced gravitropism, whereas symmetric gravitropic stimulation caused a partial suppression of phototropism. Gravitropism and phototropism appear to be tightly linked by a tonic feedback loop that allows the respective transduction chains a mutual influence over each other. The use of tropism mutants allowed conclusions to be drawn about the tonic feedback loop with the gravitropic and phototropic transduction chains. The results from clinostating mutants that lack octahedral crystals (implicated as statoliths) showed that these crystals are not involved in the tonic feedback loop. At elevated centrifugal accelerations, the fluence-rate-response curves for photogravitropic equilibrium were displaced to higher fluence rates and the slope decreased. The results indicate that light transduction possesses a logarithmic transducer, whereas gravi-transduction uses a linear one. PMID:10859206

Interaction between gravitropism and phototropism in sporangiophores of Phycomyces blakesleeanus.

PubMed

Grolig, F; Eibel, P; Schimek, C; Schapat, T; Dennison, D S; Galland, P A

2000-06-01

The interaction between gravitropism and phototropism was analyzed for sporangiophores of Phycomyces blakesleeanus. Fluence rate-response curves for phototropism were generated under three different conditions: (a) for stationary sporangiophores, which reached photogravitropic equilibrium; (b) for sporangiophores, which were clinostated head-over during phototropic stimulation; and (c) for sporangiophores, which were subjected to centrifugal accelerations of 2.3g to 8.4g. For blue light (454 nm), clinostating caused an increase of the slope of the fluence rate-response curves and an increase of the maximal bending angles at saturating fluence rates. The absolute threshold remained, however, practically unaffected. In contrast to the results obtained with blue light, no increase of the slope of the fluence rate-response curves was obtained with near-ultraviolet light at 369 nm. Bilateral irradiation with near-ultraviolet or blue light enhanced gravitropism, whereas symmetric gravitropic stimulation caused a partial suppression of phototropism. Gravitropism and phototropism appear to be tightly linked by a tonic feedback loop that allows the respective transduction chains a mutual influence over each other. The use of tropism mutants allowed conclusions to be drawn about the tonic feedback loop with the gravitropic and phototropic transduction chains. The results from clinostating mutants that lack octahedral crystals (implicated as statoliths) showed that these crystals are not involved in the tonic feedback loop. At elevated centrifugal accelerations, the fluence-rate-response curves for photogravitropic equilibrium were displaced to higher fluence rates and the slope decreased. The results indicate that light transduction possesses a logarithmic transducer, whereas gravi-transduction uses a linear one.

A new driving method for piezo deformable mirrors: open loop control and MOAO made easy

NASA Astrophysics Data System (ADS)

Ouattara, Issa; Gach, Jean-Luc; Amram, Philippe

2016-07-01

This paper presents the design and the realisation of a technique to attenuate the hysteresis nonlinear phenomenon of piezoelectric actuators. Piezoelectric actuator are widely utilised for deformable mirrors used for MOAO and power laser beam shaping techniques. The nonlinearities of piezo are usually iteratively compensa- ted using closed-loop set-ups. In open-loop control, the hysteresis and the creep of the piezo cannot be corrected, thus this nonlinearities must be removed or at least minimised. The concept has been demonstrated on high displacement Amplified Piezoelectric Actuators (APA) mounted in a Fabry-Perot interferometer. The hysteresis attenuation technique aims to assist the Fabry-Perots nano-positioning control system to attain its main scientific specification. In such system, each APA has a maximum stroke of 270 μm within a 170 V (-20 V to +150 V) range and is used to position a high reflective mirror plate. The Fabry-Perots nano-positioning control system is specified to limit the APAs positioning steady-state noise to 3nm rms, but the hysteresis limits the positioning accuracy. In order to attenuate hysteresis, a hybrid amplifier circuit built with a high power operational amplifier has been designed and applied for each APA. The experiments results show that the hysteresis effect has almost been eliminated, and consequently the positioning steady-state noise can significantly been reduced. Because of the excellent results of this hybrid amplifier, a patent application has been introduced in June 12, 2015 under number No.1555381 and is being reviewed now.

Design of a prototype position actuator for the primary mirror segments of the European Extremely Large Telescope

NASA Astrophysics Data System (ADS)

Jiménez, A.; Morante, E.; Viera, T.; Núñez, M.; Reyes, M.

2010-07-01

European Extremely Large Telescope (E-ELT) based in 984 primary mirror segments achieving required optical performance; they must position relatively to adjacent segments with relative nanometer accuracy. CESA designed M1 Position Actuators (PACT) to comply with demanding performance requirements of EELT. Three PACT are located under each segment controlling three out of the plane degrees of freedom (tip, tilt, piston). To achieve a high linear accuracy in long operational displacements, PACT uses two stages in series. First stage based on Voice Coil Actuator (VCA) to achieve high accuracies in very short travel ranges, while second stage based on Brushless DC Motor (BLDC) provides large stroke ranges and allows positioning the first stage closer to the demanded position. A BLDC motor is used achieving a continuous smoothly movement compared to sudden jumps of a stepper. A gear box attached to the motor allows a high reduction of power consumption and provides a great challenge for sizing. PACT space envelope was reduced by means of two flat springs fixed to VCA. Its main characteristic is a low linear axial stiffness. To achieve best performance for PACT, sensors have been included in both stages. A rotary encoder is included in BLDC stage to close position/velocity control loop. An incremental optical encoder measures PACT travel range with relative nanometer accuracy and used to close the position loop of the whole actuator movement. For this purpose, four different optical sensors with different gratings will be evaluated. Control strategy show different internal closed loops that work together to achieve required performance.

Spherical nanoindentation study of the deformation micromechanisms of LiTaO{sub 3} single crystals

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

Anasori, B.; Barsoum, M. W.; Sickafus, K. E.

2011-07-15

Herein, spherical nanoindentation (NI) was used to investigate the room temperature deformation behavior of C-plane LiTaO{sub 3} single crystals loaded along the [0001] direction as a function of ion irradiation. When the NI load-displacement curves of 3 different nanoindenter radii (1.4 {mu}m, 5 {mu}m, and 21 {mu}m) were converted to NI stress-strain curves, good agreement between them was found. The surface first deforms elastically - with a Young's modulus of 205 {+-} 5 GPa, calculated from the stiffness versus contact radii curves and 207 {+-} 3 GPa measured using a Berkovich tip - and then plastically deforms at {approx_equal} 6more » GPa. Repeated loading into the same location results in large, reproducible, fully reversible, nested hysteresis loops attributed to the formation of incipient kink bands (IKBs). The latter are coaxial fully reversible dislocation loops that spontaneously shrink when the load is removed. The IKBs most probably nucleate within the (1012) twins that form near the surface. The sharper radii resulted in twin nucleation at lower stresses. The changes in the reversible loops' shape and areas can be related to the width of the twins that form. The latter were proportional to the nanoindenter tip radii and confirmed by scanning electron microscopy and by the fact that larger threshold stresses were needed for IKB nucleation with the smaller tip sizes. No effect of irradiation was observed on the NI response, presumably because of the mildness of the irradiation damage.« less

Design of the deformable mirror demonstration CubeSat (DeMi)

NASA Astrophysics Data System (ADS)

Douglas, Ewan S.; Allan, Gregory; Barnes, Derek; Figura, Joseph S.; Haughwout, Christian A.; Gubner, Jennifer N.; Knoedler, Alex A.; LeClair, Sarah; Murphy, Thomas J.; Skouloudis, Nikolaos; Merck, John; Opperman, Roedolph A.; Cahoy, Kerri L.

2017-09-01

The Deformable Mirror Demonstration Mission (DeMi) was recently selected by DARPA to demonstrate in-space operation of a wavefront sensor and Microelectromechanical system (MEMS) deformable mirror (DM) payload on a 6U CubeSat. Space telescopes designed to make high-contrast observations using internal coronagraphs for direct characterization of exoplanets require the use of high-actuator density deformable mirrors. These DMs can correct image plane aberrations and speckles caused by imperfections, thermal distortions, and diffraction in the telescope and optics that would otherwise corrupt the wavefront and allow leaking starlight to contaminate coronagraphic images. DeMi is provide on-orbit demonstration and performance characterization of a MEMS deformable mirror and closed loop wavefront sensing. The DeMi payload has two operational modes, one mode that images an internal light source and another mode which uses an external aperture to images stars. Both the internal and external modes include image plane and pupil plane wavefront sensing. The objectives of the internal measurement of the 140-actuator MEMS DM actuator displacement are characterization of the mirror performance and demonstration of closed-loop correction of aberrations in the optical path. Using the external aperture to observe stars of magnitude 2 or brighter, assuming 3-axis stability with less than 0.1 degree of attitude knowledge and jitter below 10 arcsec RMSE, per observation, DeMi will also demonstrate closed loop wavefront control on an astrophysical target. We present an updated payload design, results from simulations and laboratory optical prototyping, as well as present our design for accommodating high-voltage multichannel drive electronics for the DM on a CubeSat.

Rise Time Reduction of Thermal Actuators Operated in Air and Water through Optimized Pre-Shaped Open-Loop Driving.

PubMed

Larsen, T; Doll, J C; Loizeau, F; Hosseini, N; Peng, A W; Fantner, G; Ricci, A J; Pruitt, B L

2017-01-01

Electrothermal actuators have many advantages compared to other actuators used in Micro-Electro-Mechanical Systems (MEMS). They are simple to design, easy to fabricate and provide large displacements at low voltages. Low voltages enable less stringent passivation requirements for operation in liquid. Despite these advantages, thermal actuation is typically limited to a few kHz bandwidth when using step inputs due to its intrinsic thermal time constant. However, the use of pre-shaped input signals offers a route for reducing the rise time of these actuators by orders of magnitude. We started with an electrothermally actuated cantilever having an initial 10-90% rise time of 85 μs in air and 234 μs in water for a standard open-loop step input. We experimentally characterized the linearity and frequency response of the cantilever when operated in air and water, allowing us to obtain transfer functions for the two cases. We used these transfer functions, along with functions describing desired reduced rise-time system responses, to numerically simulate the required input signals. Using these pre-shaped input signals, we improved the open-loop 10-90% rise time from 85 μs to 3 μs in air and from 234 μs to 5 μs in water, an improvement by a factor of 28 and 47, respectively. Using this simple control strategy for MEMS electrothermal actuators makes them an attractive alternative to other high speed micromechanical actuators such as piezoelectric stacks or electrostatic comb structures which are more complex to design, fabricate, or operate.

Oligomerization of mononucleotides on montmorillonite: A potential approach to the prebiotic synthesis of RNA. [Abstract only

NASA Technical Reports Server (NTRS)

Ferris, James P.; Ertem, Goezen; Ding, Zi Ping; Prabahar, Joseph

1994-01-01

The condensation of the 5'-phosphorimidazolide of adenosine (ImpA) on montmorillonite in a pH 8 aqueous solution yields oligomers containing up to 10 monomer units. The regiospecificity of 3',5'-phosphodiester bond formation is enhanced by addition of 10% diadenosine pyrophosphate (AppA) to the reaction mixture. A series of activated derivatives of 5'-AMP was prepared to investigate the effect of the leaving group on oligomer formation. The benzimidazole and p-dimethylamino-pyridine derivatives gave the best yields of oligomers. Factors important for oligomer formation is discussed.

Oligomerization reactions of deoxyribonucleotides on montmorillonite clay - The effect of mononucleotide structure on phosphodiester bond formation

NASA Technical Reports Server (NTRS)

Ferris, James P.; KAMALUDDIN

1989-01-01

The formation of oligomers from deoxynucleotides, catalyzed by Na(+)-montmorillonite, was investigated with special attention given to the effect of the monomer structure on the phosphodiester bond formation. It was found that adenine deoxynucleotides bind more strongly to montmorillonite than do the corresponding ribonucleotides and thymidine nucleotides. Tetramers of 2-prime-dpA were detected in the reaction of 2-prime-d-5-prime-AMP with a water-soluble carbodiimide EDAC in the presence of Na(+)-montmorillonite, illustrating the possible role of minerals in the formation of biopolymers on the primitive earth.

Light production in the luminous fishes Photoblepharon and Anomalops from the Banda Islands.

PubMed

Haneda, Y; Tsuji, F I

1971-07-09

The unresolved mechanism of light production in Photoblepharon and Anomalops has been reinvestigated in fresh and preserved material. Based on biochemical evidence obtained with emulsions and cell-free extracts of the organs, especially the stimulation of light with reduced flavin mononucleotide, and on electron microscopy of organ sections showing the presence of numerous bacteria, we conclude that the light is produced by symbiotic luminous bacteria. Because of the continuing failure to cultivate the luminous bacteria and because of their morphology, we suggest that the bacteria are of a primitive type called bacteroids.

Structure, recognition and adaptive binding in RNA aptamer complexes.

PubMed

Patel, D J; Suri, A K; Jiang, F; Jiang, L; Fan, P; Kumar, R A; Nonin, S

1997-10-10

Novel features of RNA structure, recognition and discrimination have been recently elucidated through the solution structural characterization of RNA aptamers that bind cofactors, aminoglycoside antibiotics, amino acids and peptides with high affinity and specificity. This review presents the solution structures of RNA aptamer complexes with adenosine monophosphate, flavin mononucleotide, arginine/citrulline and tobramycin together with an example of hydrogen exchange measurements of the base-pair kinetics for the AMP-RNA aptamer complex. A comparative analysis of the structures of these RNA aptamer complexes yields the principles, patterns and diversity associated with RNA architecture, molecular recognition and adaptive binding associated with complex formation.

Monte Carlo study of the magnetic properties in a bilayer dendrimer structure with non-magnetic layers

NASA Astrophysics Data System (ADS)

Jabar, A.; Masrour, R.

2017-12-01

In this paper, we study the Ruderman-Kittel-Kasuya-Yosida (RKKY) interactions and magnetic layer effects on the bilayer transitions of a spin-5/2 Blume-Capel model formed by two magnetic blocs separated by a non-magnetic spacer of finite thickness. The thermalization process of magnetization for systems sizes has been given. We have shown that the magnetic order in the two magnetic blocs depend on the thickness of the magnetic layer. In the total magnetization profiles, the susceptibility peaks correspond to the reduced critical temperature. This critical temperature is displaced towards higher temperatures when increasing the number of magnetic layers. In addition, we have discussed and interpreted the behaviors of the magnetic hysteresis loops.

Regenerable Air Purification System for Gas-Phase Contaminant Control

NASA Technical Reports Server (NTRS)

Constantinescu, Ileana C.; Qi, Nan; LeVan, M. Douglas; Finn, Cory K.; Finn, John E.; Luna, Bernadette (Technical Monitor)

2000-01-01

A regenerable air purification system (RAPS) that uses water vapor to displace adsorbed contaminants from an. adsorbent column into a closed oxidation loop is under development through cooperative R&D between Vanderbilt University and NASA Ames Research Center. A unit based on this design can be used for removing trace gas-phase contaminants from spacecraft cabin air or from polluted process streams including incinerator exhaust. Recent work has focused on fabrication and operation of a RAPS breadboard at NASA Ames, and on measurement of adsorption isotherm data for several important organic compounds at Vanderbilt. These activities support the use and validation of RAPS modeling software also under development at Vanderbilt, which will in turn be used to construct a prototype system later in the project.

Verification of polarising optics for the LISA optical bench.

PubMed

Dehne, Marina; Tröbs, Michael; Heinzel, Gerhard; Danzmann, Karsten

2012-12-03

The Laser Interferometer Space Antenna (LISA) is a space-based interferometric gravitational wave detector. In the current baseline design for the optical bench, the use of polarising optics is foreseen to separate optical beams. Therefore it is important to investigate the influence of polarising components on the interferometer sensitivity and validate that the required picometre stability in the low-frequency band (1 mHz - 1 Hz) is achievable. This paper discusses the design of the experiment and the implemented stabilisation loops. A displacement readout fulfilling the requirement in the whole frequency band is presented. Alternatively, we demonstrate improvement of the noise performance by implementing various algorithms in data post-processing, which leads to an additional robustness for the LISA mission.

Multi-instrument observations of a failed flare eruption associated with MHD waves in a loop bundle

NASA Astrophysics Data System (ADS)

Nisticò, G.; Polito, V.; Nakariakov, V. M.; Del Zanna, G.

2017-04-01

Context. We present observations of a B7.9-class flare that occurred on the 24th January, 2015, using the Atmospheric Imaging Assembly (AIA) of the Solar Dynamics Observatory (SDO), the EUV Imaging Spectrometer (EIS) and the X-Ray Telescope of Hinode. The flare triggers the eruption of a dense cool plasma blob as seen in AIA 171 Å, which is unable to completely break out and remains confined within a local bundle of active region loops. During this process, transverse oscillations of the threads are observed. The cool plasma is then observed to descend back to the chromosphere along each loop strand. At the same time, a larger diffuse co-spatial loop observed in the hot wavebands of SDO/AIA and Hinode/XRT is formed, exhibiting periodic intensity variations along its length. Aims: The formation and evolution of magnetohydrodynamic (MHD) waves depend upon the values of the local plasma parameters (e.g. density, temperature and magnetic field), which can hence be inferred by coronal seismology. In this study we aim to assess how the observed MHD modes are affected by the variation of density and temperature. Methods: We combined analysis of EUV/X-ray imaging and spectroscopy using SDO/AIA, Hinode/EIS and XRT. Results: The transverse oscillations of the cool loop threads are interpreted in terms of vertically polarised kink oscillations. The fitting procedure applied to the loop displacement time series gives a period of 3.5 to 4 min, and an amplitude of 5 Mm. The oscillations are strongly damped showing very low quality factor (1.5-2), which is defined as the ratio of the damping time and the oscillation period. The weak variation of the period of the kink wave, which is estimated from the fitting analysis, is in agreement with the density variations due to the presence of the plasma blob inferred from the intensity light curve at 171 Å. The coexisting intensity oscillations along the hot loop are interpreted as a slow MHD wave with a period of 10 min and phase speed of approximately 436 km s-1. Comparison between the fast and slow modes allows for the determination of the Alfvén speed, and consequently magnetic field values. The plasma-β inferred from the analysis is estimated to be approximately 0.1-0.3. Conclusions: We show that the evolution of the detected waves is determined by the temporal variations of the local plasma parameters, caused by the flare heating and the consequent cooling. We apply coronal seismology to both waves obtaining estimates of the background plasma parameters. Movies are available at http://www.aanda.org

Enzyme architecture: the effect of replacement and deletion mutations of loop 6 on catalysis by triosephosphate isomerase.

PubMed

Zhai, Xiang; Go, Maybelle K; O'Donoghue, AnnMarie C; Amyes, Tina L; Pegan, Scott D; Wang, Yan; Loria, J Patrick; Mesecar, Andrew D; Richard, John P

2014-06-03

Two mutations of the phosphodianion gripper loop in chicken muscle triosephosphate isomerase (cTIM) were examined: (1) the loop deletion mutant (LDM) formed by removal of residues 170-173 [Pompliano, D. L., et al. (1990) Biochemistry 29, 3186-3194] and (2) the loop 6 replacement mutant (L6RM), in which the N-terminal hinge sequence of TIM from eukaryotes, 166-PXW-168 (X = L or V), is replaced by the sequence from archaea, 166-PPE-168. The X-ray crystal structure of the L6RM shows a large displacement of the side chain of E168 from that for W168 in wild-type cTIM. Solution nuclear magnetic resonance data show that the L6RM results in significant chemical shift changes in loop 6 and surrounding regions, and that the binding of glycerol 3-phosphate (G3P) results in chemical shift changes for nuclei at the active site of the L6RM that are smaller than those of wild-type cTIM. Interactions with loop 6 of the L6RM stabilize the enediolate intermediate toward the elimination reaction catalyzed by the LDM. The LDM and L6RM result in 800000- and 23000-fold decreases, respectively, in kcat/Km for isomerization of GAP. Saturation of the LDM, but not the L6RM, by substrate and inhibitor phosphoglycolate is detected by steady-state kinetic analyses. We propose, on the basis of a comparison of X-ray crystal structures for wild-type TIM and the L6RM, that ligands bind weakly to the L6RM because a large fraction of the ligand binding energy is utilized to overcome destabilizing electrostatic interactions between the side chains of E168 and E129 that are predicted to develop in the loop-closed enzyme. Similar normalized yields of DHAP, d-DHAP, and d-GAP are formed in LDM- and L6RM-catalyzed reactions of GAP in D2O. The smaller normalized 12-13% yield of DHAP and d-DHAP observed for the mutant cTIM-catalyzed reactions compared with the 79% yield of these products for wild-type cTIM suggests that these mutations impair the transfer of a proton from O-2 to O-1 at the initial enediolate phosphate intermediate. No products are detected for the LDM-catalyzed isomerization reactions in D2O of [1-(13)C]GA and HPi, but the L6RM-catalyzed reaction in the presence of 0.020 M dianion gives a 2% yield of the isomerization product [2-(13)C,2-(2)H]GA.

Nicotinamide mononucleotide protects against pro-inflammatory cytokine-mediated impairment of mouse islet function.

PubMed

Caton, P W; Kieswich, J; Yaqoob, M M; Holness, M J; Sugden, M C

2011-12-01

Nicotinamide phosphoribosyltransferase (NAMPT), the rate-limiting enzyme for NAD(+) biosynthesis, exists as intracellular NAMPT (iNAMPT) and extracellular NAMPT (eNAMPT). eNAMPT, secreted from adipose tissue, promotes insulin secretion. Administration of nicotinamide mononucleotide (NMN), a product of the eNAMPT reaction, corrects impaired islet function in Nampt ( +/- ) mice. One of its potential targets is the NAD(+)-dependent deacetylase sirtuin 1. We hypothesised that altered NAMPT activity might contribute to the suppression of islet function associated with inflammation, and aimed to determine whether NMN could improve cytokine-mediated islet dysfunction. Acute effects of NMN on cytokine-mediated islet dysfunction were examined in islets incubated with TNFα and IL1β, and in mice fed a fructose-rich diet (FRD) for 16 weeks. Changes in iNAMPT, eNAMPT and inflammation levels were determined in FRD-fed mice. FRD-fed mice displayed markedly lower levels of circulating eNAMPT, with impaired insulin secretion and raised islet expression of Il1b. NMN administration lowered Il1b expression and restored suppressed insulin secretion in FRD-fed mice. NMN also restored insulin secretion in islets cultured with pro-inflammatory cytokines. The changes in islet function corresponded with changes in key markers of islet function and differentiation. The anti-inflammatory effects of NMN were partially blocked by inhibition of sirtuin 1. Chronic fructose feeding causes severe islet dysfunction in mice. Onset of beta cell failure in FRD-fed mice may occur via lowered secretion of eNAMPT, leading to increased islet inflammation and impaired beta cell function. Administration of exogenous NMN to FRD-fed mice corrects inflammation-induced islet dysfunction. Modulation of this pathway may be an attractive target for amelioration of islet dysfunction associated with inflammation.

Detection and identification of 1-methylethyl and methyl radicals generated by irradiating tea tree (Melaleuca alternifolia) oil with visible light (436 nm) in the presence of flavin mononucleotide and ferrous ion.

PubMed

Mori, H-M; Iwahashi, H

2013-08-01

Here, we determined the electron spin resonance (ESR) spectra of standard reaction mixtures (I) containing 25 μM flavin mononucleotide (FMN), 0.018% tea tree (Melaleuca alternifolia) oil, 1.9 M acetonitrile, 20 mM phosphate buffer (pH 7.4), 0.1 M α-(4-pyridyl-1-oxide)-N-tert-butylnitrone (4-POBN), and 1.0 mM FeSO₄(NH₄)₂SO₄ irradiated with 436 nm visible light (7.8 J/cm²). Prominent ESR signals (αN = 1.58 mT and αHβ = 0.26 mT) were detected, suggesting that free radicals form in the standard reaction. In order to know whether singlet oxygen (¹O₂) is involved in the radical formation or not, ESR measurement was performed for the standard D₂O reaction mixture (I) which contained 25 μM FMN, 0.0036% tea tree oil, 1.9 M acetonitrile-d3, 20 mM phosphate buffer (pH 7.4), 0.1 M 4-POBN and 1.0 mM FeSO₄ in D₂O. The ESR peak height of the standard D₂O reaction increased to 169 ± 24% of the control. Thus, ¹O₂ seems to be involved in the formation of the radicals because D₂O increases the lifetime of singlet oxygen. High-performance liquid chromatography-ESR-mass spectrometry analyses detected 1-methylethyl and methyl radicals in the standard reaction. The radicals appear to form through the reaction of ferrous ion with α-terpinene endoperoxide (ascaridole), which generated from the reaction of α-terpinene with ¹O₂. The 1-methylethyl and methyl radicals may exert a pro-oxidant effect under these conditions.

Interaction of DNA and mononucleotides with theophylline investigated using electrochemical biosensors and biosensing.

PubMed

Nemčeková, Katarína; Labuda, Ján; Milata, Viktor; Blaškovičová, Jana; Sochr, Jozef

2018-05-03

The understanding of DNA-drug interaction mechanism is among the important aspects of biological studies for drug design, discovery and pharmaceutical development processes. Published rather detailed FTIR and UV-visible spectroscopic studies on the interactions of theophylline, theobromine and caffeine with calf thymus DNA have shown effective binding of these methylxanthine derivatives to DNA and RNA involving H-bonds. However, to our knowledge, there is no such investigation using electrochemical approach. As a novelty of the study, in this paper the bioelectrochemical approach has been chosen for the investigation of an interaction of low molecular salmon sperm dsDNA, ssDNA and mononucleotides with theophylline (TP) in aqueous phosphate buffered medium using DNA-based electrochemical biosensors and biosensing in solution phase. Exploitation of the electrochemical approach via changes in square wave voltammetric responses of deoxyguanosine (dGuo) and deoxyadenosine (dAdo) provided a new indication on preferential association of TP with dGuo in the case of double helical dsDNA structure which was not reported previously. Moreover, an attachment of TP molecules outside DNA was found in the presence of high concentration of 3.3 × 10 -4  M TP in solution which diminishes the electron transfer and leads to the difficulties in quantitative evaluation of the TP and dGuo voltammetric responses. The changes in UV-vis and FTIR spectra obtained in the same medium confirmed the association interaction of TP with both nucleobases. Utilizing the model and the published energies of hydrogen bonding stabilization, the formation of a DNA-TP complex was predicted through the intermolecular H-bonds between TP and the NH-CO moiety of guanine and the N-NH 2 moiety of adenine. Copyright © 2018 Elsevier B.V. All rights reserved.

Optimizing doped libraries by using genetic algorithms

NASA Astrophysics Data System (ADS)

Tomandl, Dirk; Schober, Andreas; Schwienhorst, Andreas

1997-01-01

The insertion of random sequences into protein-encoding genes in combination with biologicalselection techniques has become a valuable tool in the design of molecules that have usefuland possibly novel properties. By employing highly effective screening protocols, a functionaland unique structure that had not been anticipated can be distinguished among a hugecollection of inactive molecules that together represent all possible amino acid combinations.This technique is severely limited by its restriction to a library of manageable size. Oneapproach for limiting the size of a mutant library relies on `doping schemes', where subsetsof amino acids are generated that reveal only certain combinations of amino acids in a proteinsequence. Three mononucleotide mixtures for each codon concerned must be designed, suchthat the resulting codons that are assembled during chemical gene synthesis represent thedesired amino acid mixture on the level of the translated protein. In this paper we present adoping algorithm that `reverse translates' a desired mixture of certain amino acids into threemixtures of mononucleotides. The algorithm is designed to optimally bias these mixturestowards the codons of choice. This approach combines a genetic algorithm with localoptimization strategies based on the downhill simplex method. Disparate relativerepresentations of all amino acids (and stop codons) within a target set can be generated.Optional weighing factors are employed to emphasize the frequencies of certain amino acidsand their codon usage, and to compensate for reaction rates of different mononucleotidebuilding blocks (synthons) during chemical DNA synthesis. The effect of statistical errors thataccompany an experimental realization of calculated nucleotide mixtures on the generatedmixtures of amino acids is simulated. These simulations show that the robustness of differentoptima with respect to small deviations from calculated values depends on their concomitantfitness. Furthermore, the calculations probe the fitness landscape locally and allow apreliminary assessment of its structure.

Genetic Control of Biosynthesis and Transport of Riboflavin and Flavin Nucleotides and Construction of Robust Biotechnological Producers†

PubMed Central

Abbas, Charles A.; Sibirny, Andriy A.

2011-01-01

Summary: Riboflavin [7,8-dimethyl-10-(1′-d-ribityl)isoalloxazine, vitamin B2] is an obligatory component of human and animal diets, as it serves as the precursor of flavin coenzymes, flavin mononucleotide, and flavin adenine dinucleotide, which are involved in oxidative metabolism and other processes. Commercially produced riboflavin is used in agriculture, medicine, and the food industry. Riboflavin synthesis starts from GTP and ribulose-5-phosphate and proceeds through pyrimidine and pteridine intermediates. Flavin nucleotides are synthesized in two consecutive reactions from riboflavin. Some microorganisms and all animal cells are capable of riboflavin uptake, whereas many microorganisms have distinct systems for riboflavin excretion to the medium. Regulation of riboflavin synthesis in bacteria occurs by repression at the transcriptional level by flavin mononucleotide, which binds to nascent noncoding mRNA and blocks further transcription (named the riboswitch). In flavinogenic molds, riboflavin overproduction starts at the stationary phase and is accompanied by derepression of enzymes involved in riboflavin synthesis, sporulation, and mycelial lysis. In flavinogenic yeasts, transcriptional repression of riboflavin synthesis is exerted by iron ions and not by flavins. The putative transcription factor encoded by SEF1 is somehow involved in this regulation. Most commercial riboflavin is currently produced or was produced earlier by microbial synthesis using special selected strains of Bacillus subtilis, Ashbya gossypii, and Candida famata. Whereas earlier RF overproducers were isolated by classical selection, current producers of riboflavin and flavin nucleotides have been developed using modern approaches of metabolic engineering that involve overexpression of structural and regulatory genes of the RF biosynthetic pathway as well as genes involved in the overproduction of the purine precursor of riboflavin, GTP. PMID:21646432

Development of Pineapple Microsatellite Markers and Germplasm Genetic Diversity Analysis

PubMed Central

Tong, Helin; Chen, You; Wang, Jingyi; Chen, Yeyuan; Sun, Guangming; He, Junhu; Wu, Yaoting

2013-01-01

Two methods were used to develop pineapple microsatellite markers. Genomic library-based SSR development: using selectively amplified microsatellite assay, 86 sequences were generated from pineapple genomic library. 91 (96.8%) of the 94 Simple Sequence Repeat (SSR) loci were dinucleotide repeats (39 AC/GT repeats and 52 GA/TC repeats, accounting for 42.9% and 57.1%, resp.), and the other three were mononucleotide repeats. Thirty-six pairs of SSR primers were designed; 24 of them generated clear bands of expected sizes, and 13 of them showed polymorphism. EST-based SSR development: 5659 pineapple EST sequences obtained from NCBI were analyzed; among 1397 nonredundant EST sequences, 843 were found containing 1110 SSR loci (217 of them contained more than one SSR locus). Frequency of SSRs in pineapple EST sequences is 1SSR/3.73 kb, and 44 types were found. Mononucleotide, dinucleotide, and trinucleotide repeats dominate, accounting for 95.6% in total. AG/CT and AGC/GCT were the dominant type of dinucleotide and trinucleotide repeats, accounting for 83.5% and 24.1%, respectively. Thirty pairs of primers were designed for each of randomly selected 30 sequences; 26 of them generated clear and reproducible bands, and 22 of them showed polymorphism. Eighteen pairs of primers obtained by the one or the other of the two methods above that showed polymorphism were selected to carry out germplasm genetic diversity analysis for 48 breeds of pineapple; similarity coefficients of these breeds were between 0.59 and 1.00, and they can be divided into four groups accordingly. Amplification products of five SSR markers were extracted and sequenced, corresponding repeat loci were found and locus mutations are mainly in copy number of repeats and base mutations in the flanking region. PMID:24024187

Excited-state dynamics of mononucleotides and DNA strands in a deep eutectic solvent.

PubMed

Zhang, Yuyuan; de La Harpe, Kimberly; Hariharan, Mahesh; Kohler, Bern

2018-04-17

The photophysics of several mono- and oligonucleotides were investigated in a deep eutectic solvent for the first time. The solvent glyceline, prepared as a 1 : 2 mole ratio mixture of choline chloride and glycerol, was used to study excited-state deactivation in a non-aqueous solvent by the use of steady-state and time-resolved spectroscopy. DNA strands in glyceline retain the secondary structures that are present in aqueous solution to some degree, thus enabling a study of the effects of solvent properties on the excited states of stacked bases and stacked base pairs. The excited-state lifetime of the mononucleotide 5'-AMP in glyceline is 630 fs, or twice as long as in aqueous solution. Even slower relaxation is seen for 5'-TMP in glyceline, and a possible triplet state with a lifetime greater than 3 ns is observed. Circular dichroism spectra show that the single strand (dA)18 and the duplex d(AT)9·d(AT)9 adopt similar structures in glyceline and in aqueous solution. Despite having similar conformations in both solvents, femtosecond transient absorption experiments reveal striking changes in the dynamics. Excited-state decay and vibrational cooling generally take place more slowly in glyceline than in water. Additionally, the fraction of long-lived excited states in both oligonucleotide systems is lower in glyceline than in aqueous solution. For a DNA duplex, water is suggested to favor decay pathways involving intrastrand charge separation, while the deep eutectic solvent favors interstrand deactivation channels involving neutral species. Slower solvation dynamics in the viscous deep eutectic solvent may also play a role. These results demonstrate that the dynamics of excitations in stacked bases and stacked base pairs depend not only on conformation, but are also highly sensitive to the solvent.

Genetic control of biosynthesis and transport of riboflavin and flavin nucleotides and construction of robust biotechnological producers.

PubMed

Abbas, Charles A; Sibirny, Andriy A

2011-06-01

Riboflavin [7,8-dimethyl-10-(1'-d-ribityl)isoalloxazine, vitamin B₂] is an obligatory component of human and animal diets, as it serves as the precursor of flavin coenzymes, flavin mononucleotide, and flavin adenine dinucleotide, which are involved in oxidative metabolism and other processes. Commercially produced riboflavin is used in agriculture, medicine, and the food industry. Riboflavin synthesis starts from GTP and ribulose-5-phosphate and proceeds through pyrimidine and pteridine intermediates. Flavin nucleotides are synthesized in two consecutive reactions from riboflavin. Some microorganisms and all animal cells are capable of riboflavin uptake, whereas many microorganisms have distinct systems for riboflavin excretion to the medium. Regulation of riboflavin synthesis in bacteria occurs by repression at the transcriptional level by flavin mononucleotide, which binds to nascent noncoding mRNA and blocks further transcription (named the riboswitch). In flavinogenic molds, riboflavin overproduction starts at the stationary phase and is accompanied by derepression of enzymes involved in riboflavin synthesis, sporulation, and mycelial lysis. In flavinogenic yeasts, transcriptional repression of riboflavin synthesis is exerted by iron ions and not by flavins. The putative transcription factor encoded by SEF1 is somehow involved in this regulation. Most commercial riboflavin is currently produced or was produced earlier by microbial synthesis using special selected strains of Bacillus subtilis, Ashbya gossypii, and Candida famata. Whereas earlier RF overproducers were isolated by classical selection, current producers of riboflavin and flavin nucleotides have been developed using modern approaches of metabolic engineering that involve overexpression of structural and regulatory genes of the RF biosynthetic pathway as well as genes involved in the overproduction of the purine precursor of riboflavin, GTP.

Loop-mediated isothermal amplification (LAMP) assays for rapid detection and differentiation of Nosema apis and N. ceranae in honeybees.

PubMed

Ptaszyńska, Aneta A; Borsuk, Grzegorz; Woźniakowski, Grzegorz; Gnat, Sebastian; Małek, Wanda

2014-08-01

Nosemosis is a contagious disease of honeybees (Apis mellifera) manifested by increased winter mortality, poor spring build-up and even the total extinction of infected bee colonies. In this paper, loop-mediated isothermal amplifications (LAMP) were used for the first time to identify and differentiate N. apis and N. ceranae, the causative agents of nosemosis. LAMP assays were performed at a constant temperature of 60 °C using two sets of six species-specific primers, recognising eight distinct fragments of 16S rDNA gene and GspSSD polymerase with strand displacement activity. The optimal time for LAMP and its Nosema species sensitivity and specificity were assessed. LAMP only required 30 min for robust identification of the amplicons. Ten-fold serial dilutions of total DNA isolated from bees infected with microsporidia were used to determine the detection limit of N. apis and N. ceranae DNAs by LAMP and standard PCR assays. LAMP appeared to be 10(3) -fold more sensitive than a standard PCR in detecting N. apis and N. ceranae. LAMP methods developed by us are highly Nosema species specific and allow to identify and differentiate N. apis and N. ceranae. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Active vibration and noise control of vibro-acoustic system by using PID controller

NASA Astrophysics Data System (ADS)

Li, Yunlong; Wang, Xiaojun; Huang, Ren; Qiu, Zhiping

2015-07-01

Active control simulation of the acoustic and vibration response of a vibro-acoustic cavity of an airplane based on a PID controller is presented. A full numerical vibro-acoustic model is developed by using an Eulerian model, which is a coupled model based on the finite element formulation. The reduced order model, which is used to design the closed-loop control system, is obtained by the combination of modal expansion and variable substitution. Some physical experiments are made to validate and update the full-order and the reduced-order numerical models. Optimization of the actuator placement is employed in order to get an effective closed-loop control system. For the controller design, an iterative method is used to determine the optimal parameters of the PID controller. The process is illustrated by the design of an active noise and vibration control system for a cavity structure. The numerical and experimental results show that a PID-based active control system can effectively suppress the noise inside the cavity using a sound pressure signal as the controller input. It is also possible to control the noise by suppressing the vibration of the structure using the structural displacement signal as the controller input. For an airplane cavity structure, considering the issue of space-saving, the latter is more suitable.

Subsonic Ultra Green Aircraft Research: Phase II- Volume III-Truss Braced Wing Aeroelastic Test Report

NASA Technical Reports Server (NTRS)

Bradley, Marty K.; Allen, Timothy J.; Droney, Christopher

2014-01-01

This Test Report summarizes the Truss Braced Wing (TBW) Aeroelastic Test (Task 3.1) work accomplished by the Boeing Subsonic Ultra Green Aircraft Research (SUGAR) team, which includes the time period of February 2012 through June 2014. The team consisted of Boeing Research and Technology, Boeing Commercial Airplanes, Virginia Tech, and NextGen Aeronautics. The model was fabricated by NextGen Aeronautics and designed to meet dynamically scaled requirements from the sized full scale TBW FEM. The test of the dynamically scaled SUGAR TBW half model was broken up into open loop testing in December 2013 and closed loop testing from January 2014 to April 2014. Results showed the flutter mechanism to primarily be a coalescence of 2nd bending mode and 1st torsion mode around 10 Hz, as predicted by analysis. Results also showed significant change in flutter speed as angle of attack was varied. This nonlinear behavior can be explained by including preload and large displacement changes to the structural stiffness and mass matrices in the flutter analysis. Control laws derived from both test system ID and FEM19 state space models were successful in suppressing flutter. The control laws were robust and suppressed flutter for a variety of Mach, dynamic pressures, and angle of attacks investigated.

Towards precision constraints on gravity with the Effective Field Theory of Large-Scale Structure

NASA Astrophysics Data System (ADS)

Bose, Benjamin; Koyama, Kazuya; Lewandowski, Matthew; Vernizzi, Filippo; Winther, Hans A.

2018-04-01

We compare analytical computations with numerical simulations for dark-matter clustering, in general relativity and in the normal branch of DGP gravity (nDGP). Our analytical frameword is the Effective Field Theory of Large-Scale Structure (EFTofLSS), which we use to compute the one-loop dark-matter power spectrum, including the resummation of infrared bulk displacement effects. We compare this to a set of 20 COLA simulations at redshifts z = 0, z = 0.5, and z = 1, and fit the free parameter of the EFTofLSS, called the speed of sound, in both ΛCDM and nDGP at each redshift. At one-loop at z = 0, the reach of the EFTofLSS is kreach ≈ 0.14 Mpc‑1 for both ΛCDM and nDGP. Along the way, we compare two different infrared resummation schemes and two different treatments of the time dependence of the perturbative expansion, concluding that they agree to approximately 1% over the scales of interest. Finally, we use the ratio of the COLA power spectra to make a precision measurement of the difference between the speeds of sound in ΛCDM and nDGP, and verify that this is proportional to the modification of the linear coupling constant of the Poisson equation.

Loop-mediated isothermal amplification (LAMP): a versatile technique for detection of micro-organisms.

PubMed

Wong, Y-P; Othman, S; Lau, Y-L; Radu, S; Chee, H-Y

2018-03-01

Loop-mediated isothermal amplification (LAMP) amplifies DNA with high specificity, efficiency and rapidity under isothermal conditions by using a DNA polymerase with high displacement strand activity and a set of specifically designed primers to amplify targeted DNA strands. Following its first discovery by Notomi et al. ( Nucleic Acids Res 28: E63), LAMP was further developed over the years which involved the combination of this technique with other molecular approaches, such as reverse transcription and multiplex amplification for the detection of infectious diseases caused by micro-organisms in humans, livestock and plants. In this review, available types of LAMP techniques will be discussed together with their applications in detection of various micro-organisms. Up to date, there are varieties of LAMP detection methods available including colorimetric and fluorescent detection, real-time monitoring using turbidity metre and detection using lateral flow device which will also be highlighted in this review. Apart from that, commercialization of LAMP technique had also been reported such as lyophilized form of LAMP reagents kit and LAMP primer sets for detection of pathogenic micro-organisms. On top of that, advantages and limitations of this molecular detection method are also described together with its future potential as a diagnostic method for infectious disease. © 2017 The Society for Applied Microbiology.

Observational Evidence for the Causes and Consequences of Chromospheric Reconnection

NASA Astrophysics Data System (ADS)

Yan, Limei; He, Jiansen; Xia, Lidong; Jiao, Fangran

2015-05-01

The chromospheric anemone jets with an inverse “Y” shape are ubiquitous, as revealed by the Solar Optical Telescope observations. These jets are considered to be consequences of chromospheric magnetic reconnections. Although these jets have been studied intensively, the dynamics and their driving causes remain unclear observationally. In this work, we report a case of a chromospheric jet showing complete observational evidence for the cause and consequence of chromospheric intermittent reconnection. The intermittent eruption of this jet shows two distinct quasi-periods, 50-60 s and 600-700 s. The short-period eruptions may be related to the plasmoid-induced reconnection, and the long-period ones may be interpreted as sequences of cycles of energy storage and release during magnetic reconnections. The observations also reveal Alfvénic waves with a mean period around 88 s and a maximum transverse displacement around 0.″26. The jet is hosted by a loop moving smoothly with a horizontal speed of ˜0.4 km s-1. Our results provide observational evidence supporting the magnetic reconnection model of the formation of the chromospheric jets with related products, in which the loop advection drives intermittent magnetic reconnections, and the reconnection outflows carrying plasmoids collide further with the ambient field lines and finally excite waves and jets.

On a common critical state in localized and diffuse failure modes

NASA Astrophysics Data System (ADS)

Zhu, Huaxiang; Nguyen, Hien N. G.; Nicot, François; Darve, Félix

2016-10-01

Accurately modeling the critical state mechanical behavior of granular material largely relies on a better understanding and characterizing the critical state fabric in different failure modes, i.e. localized and diffuse failure modes. In this paper, a mesoscopic scale is introduced, in which the organization of force-transmission paths (force-chains) and cells encompassed by contacts (meso-loops) can be taken into account. Numerical drained biaxial tests using a discrete element method are performed with different initial void ratios, in order to investigate the critical state fabric on the meso-scale in both localized and diffuse failure modes. According to the displacement and strain fields extracted from tests, the failure mode and failure area of each specimen are determined. Then convergent critical state void ratios are observed in failure area of specimens. Different mechanical features of two kinds of meso-structures (force-chains and meso-loops) are investigated, to clarify whether there exists a convergent meso-structure inside the failure area of granular material, as the signature of critical state. Numerical results support a positive answer. Failure area of both localized and diffuse failure modes therefore exhibits the same fabric in critical state. Hence, these two failure modes prove to be homological with respect to the concept of the critical state.

Features of primary damage by high energy displacement cascades in concentrated Ni-based alloys

DOE PAGES

Béland, Laurent Karim; Lu, Chenyang; Osetskiy, Yuri N.; ...

2016-02-25

Alloying of Ni with Fe or Co reduces primary damage production under ion irradiation. Similar results have been obtained from classical molecular dynamics simulations of 1, 10, 20, and 40 keV collision cascades in Ni, NiFe, and NiCo. In all cases, a mix of imperfect stacking fault tetrahedra, faulted loops with a 1/3 {111} Burgers vector, and glissile interstitial loops with a 1/2 {110} Burgers vector were formed, along with small sessile point defect complexes and clusters. Primary damage reduction occurs by three mechanisms. First, Ni-Co, Ni-Fe, Co-Co, and Fe-Fe short-distance repulsive interactions are stiffer than Ni-Ni interactions, which leadmore » to a decrease in damage formation during the transition from the supersonic ballistic regime to the sonic regime. This largely controls final defect production. Second, alloying decreases thermal conductivity, leading to a longer thermal spike lifetime. The associated annealing reduces final damage production. These two mechanisms are especially important at cascades energies less than 40 keV. Third, at the higher energies, the production of large defect clusters by subcascades is inhibited in the alloys. A number of challenges and limitations pertaining to predictive atomistic modeling of alloys under high-energy particle irradiation are discussed.« less

Transient response of an active nonlinear sandwich piezolaminated plate

NASA Astrophysics Data System (ADS)

Oveisi, Atta; Nestorović, Tamara

2017-04-01

In this paper, the dynamic modelling and active vibration control of a piezolaminated plate with geometrical nonlinearities are investigated using a semi-analytical approach. For active vibration control purposes, the core orthotropic elastic layer is assumed to be perfectly bonded with two piezo-layers on its top and bottom surfaces which act as sensor and actuator, respectively. In the modelling procedure, the piezo-layers are assumed to be connected via a proportional derivative (PD) feedback control law. Hamilton's principle is employed to acquire the strong form of the dynamic equation in terms of additional higher order strain expressions by means of von Karman strain-displacement correlation. The obtained nonlinear partial differential equation (NPDE) is converted to a system of nonlinear ordinary differential equations (NODEs) by engaging Galerkin method and using the orthogonality of shape functions for the simply supported boundary conditions. Then, the resulting system of NODEs is solved numerically by employing the built-in Mathematica function, "NDSolve". Next, the vibration attenuation performance is evaluated and sensitivity of the closed-loop system is investigated for several control parameters and the external disturbance parameters. The proposed solution in open loop configuration is validated by finite element (FE) package ABAQUS both in the spatial domain and for the time-/frequency-dependent response.

The effect of main urine inhibitors on the activity of different DNA polymerases in loop-mediated isothermal amplification.

PubMed

Jevtuševskaja, Jekaterina; Krõlov, Katrin; Tulp, Indrek; Langel, Ülo

2017-04-01

The use of rapid amplification methods to detect pathogens in biological samples is mainly limited by the amount of pathogens present in the sample and the presence of inhibiting substances. Inhibitors can affect the amplification efficiency by either binding to the polymerase, interacting with the DNA, or interacting with the polymerase during primer extension. Amplification is performed using DNA polymerase enzymes and even small changes in their activity can influence the sensitivity and robustness of molecular assays Methods: The main purpose of this research was to examine which compounds present in urine inhibit polymerases with strand displacement activity. To quantify the inhibition, we employed quantitative loop-mediated isothermal amplification Results: The authors found that the presence of BSA, Mg 2+, and urea at physiologically relevant concentrations, as well as acidic or alkaline conditions did not affect the activity of any of the tested polymerases. However, addition of salt significantly affected the activity of the tested polymerases. These findings may aid in the development of more sensitive, robust, cost effective isothermal amplification based molecular assays suitable for both point-of-care testing and on-site screening of pathogens directly from unprocessed urine which avoid the need for long and tedious DNA purification steps prior to amplification.

Crystal structure of the zymogen form of the group A Streptococcus virulence factor SpeB: an integrin-binding cysteine protease.

PubMed

Kagawa, T F; Cooney, J C; Baker, H M; McSweeney, S; Liu, M; Gubba, S; Musser, J M; Baker, E N

2000-02-29

Pathogenic bacteria secrete protein toxins that weaken or disable their host, and thereby act as virulence factors. We have determined the crystal structure of streptococcal pyrogenic exotoxin B (SpeB), a cysteine protease that is a major virulence factor of the human pathogen Streptococcus pyogenes and participates in invasive disease episodes, including necrotizing fasciitis. The structure, determined for the 40-kDa precursor form of SpeB at 1.6-A resolution, reveals that the protein is a distant homologue of the papain superfamily that includes the mammalian cathepsins B, K, L, and S. Despite negligible sequence identity, the protease portion has the canonical papain fold, albeit with major loop insertions and deletions. The catalytic site differs from most other cysteine proteases in that it lacks the Asn residue of the Cys-His-Asn triad. The prosegment has a unique fold and inactivation mechanism that involves displacement of the catalytically essential His residue by a loop inserted into the active site. The structure also reveals the surface location of an integrin-binding Arg-Gly-Asp (RGD) motif that is a feature unique to SpeB among cysteine proteases and is linked to the pathogenesis of the most invasive strains of S. pyogenes.

Low mitochondrial DNA diversity of Japanese Polled and Kuchinoshima feral cattle.

PubMed

Mannen, Hideyuki; Yonesaka, Riku; Noda, Aoi; Shimogiri, Takeshi; Oshima, Ichiro; Katahira, Kiyomi; Kanemaki, Misao; Kunieda, Tetsuo; Inayoshi, Yousuke; Mukai, Fumio; Sasazaki, Shinji

2017-05-01

This study aims to estimate the mitochondrial genetic diversity and structure of Japanese Polled and Kuchinoshima feral cattle, which are maintained in small populations. We determined the mitochondrial DMA (mtDNA) displacement loop (D-loop) sequences for both cattle populations and analyzed these in conjunction with previously published data from Northeast Asian cattle populations. Our findings showed that Japanese native cattle have a predominant, Asian-specific mtDNA haplogroup T4 with high frequencies (0.43-0.81). This excluded Kuchinoshima cattle (32 animals), which had only one mtDNA haplotype belonging to the haplogroup T3. Japanese Polled showed relatively lower mtDNA diversity in the average sequence divergence (0.0020) than other Wagyu breeds (0.0036-0.0047). Japanese Polled have been maintained in a limited area of Yamaguchi, and the population size is now less than 200. Therefore, low mtDNA diversity in the Japanese Polled could be explained by the decreasing population size in the last three decades. We found low mtDNA diversity in both Japanese Polled and Kuchinoshima cattle. The genetic information obtained in this study will be useful for maintaining these populations and for understanding the origin of Japanese native cattle. © 2016 Japanese Society of Animal Science.

Advanced Bode Plot Techniques for Ultrasonic Transducers

NASA Astrophysics Data System (ADS)

DeAngelis, D. A.; Schulze, G. W.

The Bode plot, displayed as either impedance or admittance versus frequency, is the most basic test used by ultrasonic transducer designers. With simplicity and ease-of-use, Bode plots are ideal for baseline comparisons such as spacing of parasitic modes or impedance, but quite often the subtleties that manifest as poor process control are hard to interpret or are nonexistence. In-process testing of transducers is time consuming for quantifying statistical aberrations, and assessments made indirectly via the workpiece are difficult. This research investigates the use of advanced Bode plot techniques to compare ultrasonic transducers with known "good" and known "bad" process performance, with the goal of a-priori process assessment. These advanced techniques expand from the basic constant voltage versus frequency sweep to include constant current and constant velocity interrogated locally on transducer or tool; they also include up and down directional frequency sweeps to quantify hysteresis effects like jumping and dropping phenomena. The investigation focuses solely on the common PZT8 piezoelectric material used with welding transducers for semiconductor wire bonding. Several metrics are investigated such as impedance, displacement/current gain, velocity/current gain, displacement/voltage gain and velocity/voltage gain. The experimental and theoretical research methods include Bode plots, admittance loops, laser vibrometry and coupled-field finite element analysis.

Crack stability in a representative piping system under combined inertial and seismic/dynamic displacement-controlled stresses. Subtask 1.3 final report

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

Scott, P.; Olson, R.; Wilkowski, O.G.

1997-06-01

This report presents the results from Subtask 1.3 of the International Piping Integrity Research Group (IPIRG) program. The objective of Subtask 1.3 is to develop data to assess analysis methodologies for characterizing the fracture behavior of circumferentially cracked pipe in a representative piping system under combined inertial and displacement-controlled stresses. A unique experimental facility was designed and constructed. The piping system evaluated is an expansion loop with over 30 meters of 16-inch diameter Schedule 100 pipe. The experimental facility is equipped with special hardware to ensure system boundary conditions could be appropriately modeled. The test matrix involved one uncracked andmore » five cracked dynamic pipe-system experiments. The uncracked experiment was conducted to evaluate piping system damping and natural frequency characteristics. The cracked-pipe experiments evaluated the fracture behavior, pipe system response, and stability characteristics of five different materials. All cracked-pipe experiments were conducted at PWR conditions. Material characterization efforts provided tensile and fracture toughness properties of the different pipe materials at various strain rates and temperatures. Results from all pipe-system experiments and material characterization efforts are presented. Results of fracture mechanics analyses, dynamic finite element stress analyses, and stability analyses are presented and compared with experimental results.« less

Performance of a continuous flow ventricular assist device: magnetic bearing design, construction, and testing.

PubMed

Allaire, P; Hilton, E; Baloh, M; Maslen, E; Bearnson, G; Noh, D; Khanwilkar, P; Olsen, D

1998-06-01

A new centrifugal continuous flow ventricular assist device, the CFVAD III, which is fully magnetic bearing suspended, has been developed. It has only one moving part (the impeller), has no contact (magnetic suspension), is compact, and has minimal heating. A centrifugal impeller of 2 inch outer diameter is driven by a permanent magnet brushless DC motor. This paper discusses the design, construction, testing, and performance of the magnetic bearings in the unit. The magnetic suspension consists of an inlet side magnetic bearing and an outlet side magnetic bearing, each divided into 8 pole segments to control axial and radial displacements as well as angular displacements. The magnetic actuators are composed of several different materials to minimize size and weight while having sufficient load capacity to support the forces on the impeller. Flux levels in the range of 0.1 T are employed in the magnetic bearings. Self sensing electronic circuits (without physical sensors) are employed to determine the impellar position and provide the feedback control signal needed for the magnetic bearing control loops. The sensors provide position sensitivity of approximately 0.025 mm. A decentralized 5 axis controller has been developed using modal control techniques. Proportional integral derivative controls are used for each axis to levitate the magnetically supported impeller.

Theoretical and experimental research on machine tool servo system for ultra-precision position compensation on CNC lathe

NASA Astrophysics Data System (ADS)

Ma, Zhichao; Hu, Leilei; Zhao, Hongwei; Wu, Boda; Peng, Zhenxing; Zhou, Xiaoqin; Zhang, Hongguo; Zhu, Shuai; Xing, Lifeng; Hu, Huang

2010-08-01

The theories and techniques for improving machining accuracy via position control of diamond tool's tip and raising resolution of cutting depth on precise CNC lathes have been extremely focused on. A new piezo-driven ultra-precision machine tool servo system is designed and tested to improve manufacturing accuracy of workpiece. The mathematical model of machine tool servo system is established and the finite element analysis is carried out on parallel plate flexure hinges. The output position of diamond tool's tip driven by the machine tool servo system is tested via a contact capacitive displacement sensor. Proportional, integral, derivative (PID) feedback is also implemented to accommodate and compensate dynamical change owing cutting forces as well as the inherent non-linearity factors of the piezoelectric stack during cutting process. By closed loop feedback controlling strategy, the tracking error is limited to 0.8 μm. Experimental results have shown the proposed machine tool servo system could provide a tool positioning resolution of 12 nm, which is much accurate than the inherent CNC resolution magnitude. The stepped shaft of aluminum specimen with a step increment of cutting depth of 1 μm is tested, and the obtained contour illustrates the displacement command output from controller is accurately and real-time reflected on the machined part.

Nonlinear mathematical modeling and sensitivity analysis of hydraulic drive unit

NASA Astrophysics Data System (ADS)

Kong, Xiangdong; Yu, Bin; Quan, Lingxiao; Ba, Kaixian; Wu, Liujie

2015-09-01

The previous sensitivity analysis researches are not accurate enough and also have the limited reference value, because those mathematical models are relatively simple and the change of the load and the initial displacement changes of the piston are ignored, even experiment verification is not conducted. Therefore, in view of deficiencies above, a nonlinear mathematical model is established in this paper, including dynamic characteristics of servo valve, nonlinear characteristics of pressure-flow, initial displacement of servo cylinder piston and friction nonlinearity. The transfer function block diagram is built for the hydraulic drive unit closed loop position control, as well as the state equations. Through deriving the time-varying coefficient items matrix and time-varying free items matrix of sensitivity equations respectively, the expression of sensitivity equations based on the nonlinear mathematical model are obtained. According to structure parameters of hydraulic drive unit, working parameters, fluid transmission characteristics and measured friction-velocity curves, the simulation analysis of hydraulic drive unit is completed on the MATLAB/Simulink simulation platform with the displacement step 2 mm, 5 mm and 10 mm, respectively. The simulation results indicate that the developed nonlinear mathematical model is sufficient by comparing the characteristic curves of experimental step response and simulation step response under different constant load. Then, the sensitivity function time-history curves of seventeen parameters are obtained, basing on each state vector time-history curve of step response characteristic. The maximum value of displacement variation percentage and the sum of displacement variation absolute values in the sampling time are both taken as sensitivity indexes. The sensitivity indexes values above are calculated and shown visually in histograms under different working conditions, and change rules are analyzed. Then the sensitivity indexes values of four measurable parameters, such as supply pressure, proportional gain, initial position of servo cylinder piston and load force, are verified experimentally on test platform of hydraulic drive unit, and the experimental research shows that the sensitivity analysis results obtained through simulation are approximate to the test results. This research indicates each parameter sensitivity characteristics of hydraulic drive unit, the performance-affected main parameters and secondary parameters are got under different working conditions, which will provide the theoretical foundation for the control compensation and structure optimization of hydraulic drive unit.

Reverse Anterior Cruciate Ligament Reconstruction Fixation: A Biomechanical Comparison Study of Tibial Cross-Pin and Femoral Interference Screw Fixation.

PubMed

Lawley, Richard J; Klein, Samuel E; Chudik, Steven C

2017-03-01

To evaluate the biomechanical performance of tibial cross-pin (TCP) fixation relative to femoral cross-pin (FCP), femoral interference screw (FIS), and tibial interference screw (TIS) fixation. We randomized 40 porcine specimens (20 tibias and 20 femurs) to TIS fixation (group 1, n = 10), FIS fixation (group 2, n = 10), TCP fixation (group 3, n = 10), or FCP fixation (group 4, n = 10) and performed biomechanical testing to compare ultimate load, stiffness, yield load, cyclic displacement, and load at 5-mm displacement. We performed cross-pin fixation of the looped end and interference screw fixation of the free ends of 9-mm-diameter bovine extensor digitorum communis tendon grafts. Graft fixation constructs were cyclically loaded and then loaded to failure in line with the tunnels. Regarding yield load, FIS was superior to TIS (704 ± 125 N vs 504 ± 118 N, P = .002), TCP was superior to TIS (1,449 ± 265 N vs 504 ± 118 N, P < .001), and TCP was superior to FCP (1,449 ± 265 N vs 792 ± 397 N, P < .001). Cyclic displacement for FCP was superior to TCP. Cyclic displacement for TIS versus FIS showed no statistically significant difference (2.5 ± 1.0 mm vs 2.2 ± 0.6 mm, P = .298). Interference screw fixation consistently failed by graft slippage, whereas TCP fixation failed by tibial bone failure. FCP fixation failed by either femoral bone failure or failure elsewhere in the testing apparatus. Regarding yield load, TCP fixation performed biomechanically superior to the clinically proven FCP at time zero. Because TIS fixation shows the lowest yield strength, it represents the weak link, and combined TCP-FIS fixation theoretically would be biomechanically superior relative to combined FCP-TIS fixation with regard to yield load. Cyclic displacement showed a small difference in favor of FCP over TCP fixation and no difference between TIS and FIS. Time-zero biomechanics of TCP fixation paired with FIS fixation show that this method of fixation can be considered a potential alternative to current practice and may pose clinical benefits in different clinical scenarios of anterior cruciate ligament reconstruction. Copyright © 2016 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

Structural and thermodynamic analysis of the hetero-association of theophylline with aromatic drug molecules

NASA Astrophysics Data System (ADS)

Andrejuk, D. D.; Hernandez Santiago, A. A.; Khomich, V. V.; Voronov, V. K.; Davies, D. B.; Evstigneev, M. P.

2008-10-01

The hetero-association of theophylline (THP) with other biologically-active aromatic molecules ( e.g. the anti-cancer drugs daunomycin and novantrone, the antibiotic norfloxacin, the vitamin flavin-mononucleotide and two mutagens ethidium bromide and proflavine) has been studied by NMR in aqueous-salt solution (0.1 M Na-phosphate buffer, p D 7.1). It was found that THP shows an essentially similar hetero-association ability as caffeine (CAF) towards aromatic drugs, except for novantrone (NOV), which has much less affinity to THP than CAF as a result of energetically unfavourable orthogonal orientation of the chromophores of THP and NOV in the hetero-complex.

Clays in prebiological chemistry

NASA Technical Reports Server (NTRS)

Rao, M.; Oro, J.; Odom, D. G.

1980-01-01

The ways in which clays have been utilized in studies of prebiological chemistry are reviewed, and an assessment is given of the possible role of clays in prebiological systems. The adsorption of organic molecules on clays has been demonstrated, as has the synthesis of bioorganic monomers in the presence of clays. For instance, amino acids, purines and pyrimidines have been obtained from carbon monoxide and nitric acid in the presence of clays at relatively high temperatures (250-325 C). The oligomerization of biochemical monomers, mediated by clays, has also been shown to result in the formation of polymer molecules basic to life. Clays have also been found to affect the condensation of mononucleotides to oligonucleotides.

Horizontal versus vertical orientation of the loop for tension band wiring of transverse patella fractures.

PubMed

Lee, Sang Ki; Hwang, Yoon Sub; Choy, Won Sik

2014-03-01

Conventional operative treatments of patella fractures are frequently associated with implant failure or displacement. Recent biomechanical studies showed that the orientation of the wire loop and the site of the wire twist can affect the fixation strength. The purpose of this study was to compare the clinical outcome of the tension band technique with loops in different orientations and different knot positions. For this retrospective study, 72 patella fractures (71 patients) were fixed with figure-of-eight configurations in combination with 2 K-wires. Patients were divided into 3 groups according to the orientation of tension band construct. A total of 40 patella fractures were placed with figure-of-eight configurations in a vertical orientation either with 1 wire twist (group 1; 16 patella fractures) or with 2 wire twists at the adjacent corners (group 2; 24 patella fractures). Thirty-two patella fractures were placed with figure-of-eight configurations in a horizontal orientation with 2 wire twists at the adjacent corners (group 3). Range of motion, complication rates, and knee scoring scales (Hospital for Special Surgery and Lysholm) were assessed during serial follow-up. Satisfactory reductions were achieved in all groups, but functional results in the early stage were different. Group 3 had better Hospital for Special Surgery and Lysholm scores at 3 months postoperatively; however, at 6 months and 1 year postoperatively, all groups had similar scores. At the 1-year follow-up, all groups achieved acceptable flexion and range of motion. The overall complication rate was lower in the horizontal group (12.5%). Placing the figure-of-eight tension band construct in a horizontal orientation can provide functional benefits in the early stage after patella fractures. Copyright 2014, SLACK Incorporated.

Optimization of Sensing and Feedback Control for Vibration/Flutter of Rotating Disk by PZT Actuators via Air Coupled Pressure

PubMed Central

Yan, Tianhong; Xu, Xinsheng; Han, Jianqiang; Lin, Rongming; Ju, Bingfeng; Li, Qing

2011-01-01

In this paper, a feedback control mechanism and its optimization for rotating disk vibration/flutter via changes of air-coupled pressure generated using piezoelectric patch actuators are studied. A thin disk rotates in an enclosure, which is equipped with a feedback control loop consisting of a micro-sensor, a signal processor, a power amplifier, and several piezoelectric (PZT) actuator patches distributed on the cover of the enclosure. The actuator patches are mounted on the inner or the outer surfaces of the enclosure to produce necessary control force required through the airflow around the disk. The control mechanism for rotating disk flutter using enclosure surfaces bonded with sensors and piezoelectric actuators is thoroughly studied through analytical simulations. The sensor output is used to determine the amount of input to the actuator for controlling the response of the disk in a closed loop configuration. The dynamic stability of the disk-enclosure system, together with the feedback control loop, is analyzed as a complex eigenvalue problem, which is solved using Galerkin’s discretization procedure. The results show that the disk flutter can be reduced effectively with proper configurations of the control gain and the phase shift through the actuations of PZT patches. The effectiveness of different feedback control methods in altering system characteristics and system response has been investigated. The control capability, in terms of control gain, phase shift, and especially the physical configuration of actuator patches, are also evaluated by calculating the complex eigenvalues and the maximum displacement produced by the actuators. To achieve a optimal control performance, sizes, positions and shapes of PZT patches used need to be optimized and such optimization has been achieved through numerical simulations. PMID:22163788

Optimization of sensing and feedback control for vibration/flutter of rotating disk by PZT actuators via air coupled pressure.

PubMed

Yan, Tianhong; Xu, Xinsheng; Han, Jianqiang; Lin, Rongming; Ju, Bingfeng; Li, Qing

2011-01-01

In this paper, a feedback control mechanism and its optimization for rotating disk vibration/flutter via changes of air-coupled pressure generated using piezoelectric patch actuators are studied. A thin disk rotates in an enclosure, which is equipped with a feedback control loop consisting of a micro-sensor, a signal processor, a power amplifier, and several piezoelectric (PZT) actuator patches distributed on the cover of the enclosure. The actuator patches are mounted on the inner or the outer surfaces of the enclosure to produce necessary control force required through the airflow around the disk. The control mechanism for rotating disk flutter using enclosure surfaces bonded with sensors and piezoelectric actuators is thoroughly studied through analytical simulations. The sensor output is used to determine the amount of input to the actuator for controlling the response of the disk in a closed loop configuration. The dynamic stability of the disk-enclosure system, together with the feedback control loop, is analyzed as a complex eigenvalue problem, which is solved using Galerkin's discretization procedure. The results show that the disk flutter can be reduced effectively with proper configurations of the control gain and the phase shift through the actuations of PZT patches. The effectiveness of different feedback control methods in altering system characteristics and system response has been investigated. The control capability, in terms of control gain, phase shift, and especially the physical configuration of actuator patches, are also evaluated by calculating the complex eigenvalues and the maximum displacement produced by the actuators. To achieve a optimal control performance, sizes, positions and shapes of PZT patches used need to be optimized and such optimization has been achieved through numerical simulations.

Extensive interbreeding occurred among multiple matriarchal ancestors during the domestication of dogs: evidence from inter- and intraspecies polymorphisms in the D-loop region of mitochondrial DNA between dogs and wolves.

PubMed

Tsuda, K; Kikkawa, Y; Yonekawa, H; Tanabe, Y

1997-08-01

To test the hypothesis that the domestic dogs are derived from several different ancestral gray wolf populations, we compared the sequence of the displacement (D)-loop region of the mitochondrial DNA (mtDNA) from 24 breeds of domestic dog (34 individual dogs) and 3 subspecies of gray wolf (Canis lupus lupus, C.l. pallipes and C.l. chanco; 19 individuals). The intraspecific sequence variations within domestic dogs (0.00-3.19%) and within wolves (0.00-2.88%) were comparable to the interspecific variations between domestic dogs and wolves (0.30-3.35%). A repetitive sequence with repeat units (TACACGTA/GCG) that causes the size variation in the D-loop region was also found in both dogs and wolves. However, no nucleotide substitutions or repetitive arrays were specific for domestic dogs or for wolves. These results showed that there is a close genetic relationship between dogs and wolves. Two major clades appeared in the phylogenetic trees constructed by neighbor-joining and by the maximum parsimony method; one clade containing Chinese wolf (C.l. chanco) showed extensive variations while the other showed only slight variation. This showed that there were two major genetic components both in domestic dogs and in wolves. However, neither clades nor haplotypes specific for any dog breed were observed, whereas subspecies-specific clades were found in Asiatic wolves. These results suggested that the extant breeds of domestic dogs have maintained a large degree of mtDNA polymorphisms introduced from their ancestral wolf populations, and that extensive interbreedings had occurred among multiple matriarchal origins.

Atomistic simulation study of influence of Al2O3-Al interface on dislocation interaction and prismatic loop formation during nano-indentation on Al2O3-coated aluminum.

PubMed

Mishra, Srishti; Meraj, Md; Pal, Snehanshu

2018-06-19

A large-scale molecular dynamics (MD) simulation of nano-indentation was carried out to provide insight into the influence of the Al-Al 2 O 3 interface on dislocation evolution and deformation behavior of Al substrate coated with Al 2 O 3 thin film. Adaptive common neighbor analysis (a-CNA), centro-symmetry parameter (CSP) estimation, and dislocation extraction algorithm (DXA) were implemented to represent structural evolution during nano-indentation deformation. The absence of elastic regime was observed in the P-h curve for this simulated nano-indentation test of Al 2 O 3 thin film coated Al specimen. The displacement of oxygen atoms from Al 2 O 3 to Al partly through the interface greatly influences the plastic deformation behavior of the specimen during nano-indentation. Prismatic dislocation loops, which are formed due to pinning of Shockley partials (1/6 < 112>) by Stair-rod (1/6 < 110>) and Hirth dislocation (1/3 < 001>), were observed in all cases studied in this work. Pile-up of atoms was also observed and the extent of the pile-up was found to vary with the test temperature. A distorted stacking fault tetrahedron (SFT) is formed when a nano-indentation test is carried out at 100 K. The presence of a prismatic dislocation loop, SFT and dislocation forest caused strain hardening and, consequently, there is an increase in hardness as indentation depth increases. Graphical abstract Figure illustrates nano-indentation model set up along with load vs. depth curve and distorted stacking fault tetrahedron.

Crystal Structure of the Pseudomonas aeruginosa BEL-1 Extended-Spectrum β-Lactamase and Its Complexes with Moxalactam and Imipenem

PubMed Central

Pozzi, Cecilia; De Luca, Filomena; Benvenuti, Manuela; Poirel, Laurent; Nordmann, Patrice; Rossolini, Gian Maria

2016-01-01

BEL-1 is an acquired class A extended-spectrum β-lactamase (ESBL) found in Pseudomonas aeruginosa clinical isolates from Belgium which is divergent from other ESBLs (maximum identity of 54% with GES-type enzymes). This enzyme is efficiently inhibited by clavulanate, imipenem, and moxalactam. Crystals of BEL-1 were obtained at pH 5.6, and the structure of native BEL-1 was determined from orthorhombic and monoclinic crystal forms at 1.60-Å and 1.48-Å resolution, respectively. By soaking native BEL-1 crystals, complexes with imipenem (monoclinic form, 1.79-Å resolution) and moxalactam (orthorhombic form, 1.85-Å resolution) were also obtained. In the acyl-enzyme complexes, imipenem and moxalactam differ by the position of the α-substituent and of the carbonyl oxygen (in or out of the oxyanion hole). More surprisingly, the Ω-loop, which includes the catalytically relevant residue Glu166, was found in different conformations in the various subunits, resulting in the Glu166 side chain being rotated out of the active site or even in displacement of its Cα atom up to approximately 10 Å. A BEL-1 variant showing the single Leu162Phe substitution (BEL-2) confers a higher level of resistance to CAZ, CTX, and FEP and shows significantly lower Km values than BEL-1, especially with oxyiminocephalosporins. BEL-1 Leu162 is located at the beginning of the Ω-loop and is surrounded by Phe72, Leu139, and Leu148 (contact distances, 3.5 to 3.9 Å). This small hydrophobic cavity could not reasonably accommodate the bulkier Phe162 found in BEL-2 without altering neighboring residues or the Ω-loop itself, thus likely causing an important alteration of the enzyme kinetic properties. PMID:27671060

Microstructural evolution in fast-neutron-irradiated austenitic stainless steels

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

Stoller, R.E.

1987-12-01

The present work has focused on the specific problem of fast-neutron-induced radiation damage to austenitic stainless steels. These steels are used as structural materials in current fast fission reactors and are proposed for use in future fusion reactors. Two primary components of the radiation damage are atomic displacements (in units of displacements per atom, or dpa) and the generation of helium by nuclear transmutation reactions. The radiation environment can be characterized by the ratio of helium to displacement production, the so-called He/dpa ratio. Radiation damage is evidenced microscopically by a complex microstructural evolution and macroscopically by density changes and alteredmore » mechanical properties. The purpose of this work was to provide additional understanding about mechanisms that determine microstructural evolution in current fast reactor environments and to identify the sensitivity of this evolution to changes in the He/dpa ratio. This latter sensitivity is of interest because the He/dpa ratio in a fusion reactor first wall will be about 30 times that in fast reactor fuel cladding. The approach followed in the present work was to use a combination of theoretical and experimental analysis. The experimental component of the work primarily involved the examination by transmission electron microscopy of specimens of a model austenitic alloy that had been irradiated in the Oak Ridge Research Reactor. A major aspect of the theoretical work was the development of a comprehensive model of microstructural evolution. This included explicit models for the evolution of the major extended defects observed in neutron irradiated steels: cavities, Frank faulted loops and the dislocation network. 340 refs., 95 figs., 18 tabs.« less

Long-wave instabilities of two interlaced helical vortices

NASA Astrophysics Data System (ADS)

Quaranta, H. U.; Brynjell-Rahkola, M.; Leweke, T.; Henningson, D. S.

2016-09-01

We present a comparison between experimental observations and theoretical predictions concerning long-wave displacement instabilities of the helical vortices in the wake of a two-bladed rotor. Experiments are performed with a small-scale rotor in a water channel, using a set-up that allows the individual triggering of various instability modes at different azimuthal wave numbers, leading to local or global pairing of successive vortex loops. The initial development of the instability and the measured growth rates are in good agreement with the predictions from linear stability theory, based on an approach where the helical vortex system is represented by filaments. At later times, local pairing develops into large-scale distortions of the vortices, whereas for global pairing the non-linear evolution returns the system almost to its initial geometry.

An Adaptive Control Technology for Safety of a GTM-like Aircraft

NASA Technical Reports Server (NTRS)

Matsutani, Megumi; Crespo, Luis G.; Annaswamy, Anuradha; Jang, Jinho

2010-01-01

An adaptive control architecture for safe performance of a transport aircraft subject to various adverse conditions is proposed and verified in this report. This architecture combines a nominal controller based on a Linear Quadratic Regulator with integral action, and an adaptive controller that accommodates actuator saturation and bounded disturbances. The effectiveness of the baseline controller and its adaptive augmentation are evaluated using a stand-alone control veri fication methodology. Case studies that pair individual parameter uncertainties with critical flight maneuvers are studied. The resilience of the controllers is determined by evaluating the degradation in closed-loop performance resulting from increasingly larger deviations in the uncertain parameters from their nominal values. Symmetric and asymmetric actuator failures, flight upsets, and center of gravity displacements, are some of the uncertainties considered.

On the IR-resummation in the EFTofLSS

NASA Astrophysics Data System (ADS)

Senatore, Leonardo; Trevisan, Gabriele

2018-05-01

We propose a simplification for the IR-resummation scheme of [1] and also include its next-to-leading order corrections coming from the tree-level three-point function of the long displacement field. First we show that the new simplified formula shares the same properties of the resummation of [2]. In Fourier space, the IR-resummed power spectrum has no residual wiggles and the two-loop calculation matches the non-linear power spectrum of the Dark Sky simulation at z=0 up to ksimeq0.34 h Mpc‑1 within cosmic variance. Then, we find that the additional subleading terms (although parametrically infrared-enhanced) modify the leading-order IR-resummed correlation function only in a marginal way, implying that the IR-resummation scheme can robustly predict the shape of the BAO peak.

Application of SPM interferometry in MEMS vibration measurement

NASA Astrophysics Data System (ADS)

Tang, Chaowei; He, Guotian; Xu, Changbiao; Zhao, Lijuan; Hu, Jun

2007-12-01

The resonant frequency measurement of cantilever has an important position in MEMS(Micro Electro Mechanical Systems) research. Meanwhile the SPM interferometry is a high-precision optical measurement technique, which can be used in physical quantity measurement of vibration, displacement, surface profile. Hence, in this paper we propose to apply SPM(SPM) interferometry in measuring the vibration of MEMS cantilever and in the experiment the vibration of MEMS cantilever was driven by light source. Then this kind of vibration was measured in nm precision. Finally the relational characteristics of MEMS cantilever vibration under optical excitation can be gotten and the measurement principle is analyzed. This method eliminates the influence on the measuring precision caused by external interference and light intensity change through feedback control loop. Experiment results prove that this measurement method has a good effect.

Development of a Compact Efficient Cooling Pump for Space Suit Life Support Systems

NASA Technical Reports Server (NTRS)

vanBoeyen, Roger W.; Reeh, Jonathan A.; Trevino, Luis

2008-01-01

With the increasing demands placed on extravehicular activity (EVA) for the International Space Station (ISS) assembly and maintenance, along with planned lunar and Martian missions, the need for increased human productivity and capability becomes ever more critical. This is most readily achieved by reduction in space suit weight and volume, and increased hardware reliability, durability, and operating lifetime. Considerable progress has been made with each successive generation of space suit design; from the Apollo A7L suit, to the current Shuttle Extravehicular Mobile Unit (EMU) suit, and the next generation Constellation Space Suit Element (CSSE). However, one area of space suit design which has continued to lag is the fluid pump used to drive the water cooling loop of the Primary Life Support System (PLSS). The two main types of fluid pumps typically used in space applications are rotodynamic pumps (pumping is achieved through a rotary vaned impeller) and displacement pumps (which includes rotary and diaphragm pumps). The rotating and moving parts found in the pumps and electric motor add significantly to the susceptibility to wear and friction, thermal mismatch, and complexity of the pumps. Electric motor-driven pumps capable of achieving high operational reliability are necessarily large, heavy, and energy inefficient. This report describes a development effort conducted for NASA by Lynntech, Inc., who recently demonstrated the feasibility of an electrochemically-driven fluid cooling pump. With no electric motor and minimal lightweight components, an electrochemically-driven pump is expected to be significantly smaller, lighter and achieve a longer life time than conventional rotodynamic and displacement pumps. By employing sulfonated polystyrene-based proton exchange membranes, rather than conventional Nafion membranes, a significant reduction in the actuator power consumption was demonstrated. It was also demonstrated that these membranes possess the necessary mechanical strength, durability, and temperature range for long life space operation. The preliminary design for a Phase II prototype pump compares very favorably to the fluid cooling pumps currently used in space suit portable life support systems (PLSS). Characteristics of the electrochemically-driven pump are described and the benefits of the technology as a replacement for electric motor pumps in mechanically pumped single-phase fluid loops (MPFLs) is discussed.

L-Band Transmit/Receive Module for Phase-Stable Array Antennas

NASA Technical Reports Server (NTRS)

Andricos, Constantine; Edelstein, Wendy; Krimskiy, Vladimir

2008-01-01

Interferometric synthetic aperture radar (InSAR) has been shown to provide very sensitive measurements of surface deformation and displacement on the order of 1 cm. Future systematic measurements of surface deformation will require this capability over very large areas (300 km) from space. To achieve these required accuracies, these spaceborne sensors must exhibit low temporal decorrelation and be temporally stable systems. An L-band (24-cmwavelength) InSAR instrument using an electronically steerable radar antenna is suited to meet these needs. In order to achieve the 1-cm displacement accuracy, the phased array antenna requires phase-stable transmit/receive (T/R) modules. The T/R module operates at L-band (1.24 GHz) and has less than 1- deg absolute phase stability and less than 0.1-dB absolute amplitude stability over temperature. The T/R module is also high power (30 W) and power efficient (60-percent overall efficiency). The design is currently implemented using discrete components and surface mount technology. The basic T/R module architecture is augmented with a calibration loop to compensate for temperature variations, component variations, and path loss variations as a function of beam settings. The calibration circuit consists of an amplitude and phase detector, and other control circuitry, to compare the measured gain and phase to a reference signal and uses this signal to control a precision analog phase shifter and analog attenuator. An architecture was developed to allow for the module to be bidirectional, to operate in both transmit and receive mode. The architecture also includes a power detector used to maintain a transmitter power output constant within 0.1 dB. The use of a simple, stable, low-cost, and high-accuracy gain and phase detector made by Analog Devices (AD8302), combined with a very-high efficiency T/R module, is novel. While a self-calibrating T/R module capability has been sought for years, a practical and cost-effective solution has never been demonstrated. By adding the calibration loop to an existing high-efficiency T/R module, there is a demonstrated order-of-magnitude improvement in the amplitude and phase stability.

Functional anticodon architecture of human tRNALys3 includes disruption of intraloop hydrogen bonding by the naturally occurring amino acid modification, t6A.

PubMed

Stuart, J W; Gdaniec, Z; Guenther, R; Marszalek, M; Sochacka, E; Malkiewicz, A; Agris, P F

2000-11-07

The structure of the human tRNA(Lys3) anticodon stem and loop domain (ASL(Lys3)) provides evidence of the physicochemical contributions of N6-threonylcarbamoyladenosine (t(6)A(37)) to tRNA(Lys3) functions. The t(6)A(37)-modified anticodon stem and loop domain of tRNA(Lys3)(UUU) (ASL(Lys3)(UUU)- t(6)A(37)) with a UUU anticodon is bound by the appropriately programmed ribosomes, but the unmodified ASL(Lys3)(UUU) is not [Yarian, C., Marszalek, M., Sochacka, E., Malkiewicz, A., Guenther, R., Miskiewicz, A., and Agris, P. F., Biochemistry 39, 13390-13395]. The structure, determined to an average rmsd of 1.57 +/- 0.33 A (relative to the mean structure) by NMR spectroscopy and restrained molecular dynamics, is the first reported of an RNA in which a naturally occurring hypermodified nucleoside was introduced by automated chemical synthesis. The ASL(Lys3)(UUU)-t(6)A(37) loop is significantly different than that of the unmodified ASL(Lys3)(UUU), although the five canonical base pairs of both ASL(Lys3)(UUU) stems are in the standard A-form of helical RNA. t(6)A(37), 3'-adjacent to the anticodon, adopts the form of a tricyclic nucleoside with an intraresidue H-bond and enhances base stacking on the 3'-side of the anticodon loop. Critically important to ribosome binding, incorporation of the modification negates formation of an intraloop U(33).A(37) base pair that is observed in the unmodified ASL(Lys3)(UUU). The anticodon wobble position U(34) nucleobase in ASL(Lys3)(UUU)-t(6)A(37) is significantly displaced from its position in the unmodified ASL and directed away from the codon-binding face of the loop resulting in only two anticodon bases for codon binding. This conformation is one explanation for ASL(Lys3)(UUU) tendency to prematurely terminate translation and -1 frame shift. At the pH 5.6 conditions of our structure determination, A(38) is protonated and positively charged in ASL(Lys3)(UUU)-t(6)A(37) and the unmodified ASL(Lys3)(UUU). The ionized carboxylic acid moiety of t(6)A(37) possibly neutralizes the positive charge of A(+)(38). The protonated A(+)(38) can base pair with C(32), but t(6)A(37) may weaken the interaction through steric interference. From these results, we conclude that ribosome binding cannot simply be an induced fit of the anticodon stem and loop, otherwise the unmodified ASL(Lys3)(UUU) would bind as well as ASL(Lys3)(UUU)-t(6)A(37). t(6)A(37) and other position 37 modifications produce the open, structured loop required for ribosomal binding.

Persistent Doppler Shift Oscillations Observed with HINODE-EIS in the Solar Corona: Spectroscopic Signatures of Alfvenic Waves and Recurring Upflows

NASA Technical Reports Server (NTRS)

Tian, Hui; McIntosh, Scott W.; Wang, Tongjiang; Offman, Leon; De Pontieu, Bart; Innes, Davina E.; Peter, Hardi

2012-01-01

Using data obtained by the EUV Imaging Spectrometer on board Hinode, we have performed a survey of obvious and persistent (without significant damping) Doppler shift oscillations in the corona. We have found mainly two types of oscillations from February to April in 2007. One type is found at loop footpoint regions, with a dominant period around 10 minutes. They are characterized by coherent behavior of all line parameters (line intensity, Doppler shift, line width, and profile asymmetry), and apparent blueshift and blueward asymmetry throughout almost the entire duration. Such oscillations are likely to be signatures of quasi-periodic upflows (small-scale jets, or coronal counterpart of type-II spicules), which may play an important role in the supply of mass and energy to the hot corona. The other type of oscillation is usually associated with the upper part of loops. They are most clearly seen in the Doppler shift of coronal lines with formation temperatures between one and two million degrees. The global wavelets of these oscillations usually peak sharply around a period in the range of three to six minutes. No obvious profile asymmetry is found and the variation of the line width is typically very small. The intensity variation is often less than 2%. These oscillations are more likely to be signatures of kink/Alfv´en waves rather than flows. In a few cases, there seems to be a p/2 phase shift between the intensity and Doppler shift oscillations, which may suggest the presence of slow-mode standing waves according to wave theories. However, we demonstrate that such a phase shift could also be produced by loops moving into and out of a spatial pixel as a result of Alfv´enic oscillations. In this scenario, the intensity oscillations associated with Alfv´enic waves are caused by loop displacement rather than density change. These coronal waves may be used to investigate properties of the coronal plasma and magnetic field.

Effects of neutron irradiation of Ti 3SiC 2 and Ti 3AlC 2 in the 121–1085 °C temperature range

DOE PAGES

Tallman, Darin J.; He, Lingfeng; Gan, Jian; ...

2016-11-19

Herein we report on the formation of defects in response to neutron irradiation of polycrystalline Ti 3SiC 2 and Ti 3AlC 2 samples exposed to doses of 0.14±0.01, 1.6±0.1, and 3.4±0.1 displacements per atom (dpa) at irradiation temperatures of 121±12, 735±6 and 1085±68 °C. After irradiation to 0.14 dpa at 121 °C and 735 °C, black spots are observed in both Ti 3SiC 2 and Ti 3AlC 2. After irradiation to 1.6 and 3.4 dpa at 735 °C, basal dislocation loops, with a Burgers vector of b = ½ [0001] are observed in Ti 3SiC 2, with loop diameters ofmore » 21±6 and 30±8 nm for 1.6 dpa and 3.4 dpa, respectively. In Ti3AlC2, larger dislocation loops, 75±34 nm in diameter are observed after 3.4 dpa at 735 °C, in addition to stacking faults. Impurity particles of TiC, as well as stacking fault TiC platelets in the MAX phases, are seen to form extensive dislocation loops under all conditions. Voids are observed at grain boundaries and within stacking faults after 3.4 dpa irradiation, with extensive void formation in the TiC regions at 1085 °C. Remarkably, denuded zones on the order of 1 µm are observed in Ti 3SiC 2 after irradiation to 3.4 dpa at 735 °C. Small grains, 3-5 µm in diameter, are damage free after irradiation at 1085 °C at this dose. The presence of the A-layer in the MAX phases is seen to provide enhanced irradiation tolerance. Based on these results, and up to 3.41 dpa, Ti 3SiC 2 remains a promising candidate for high temperature nuclear applications.« less

Effects of neutron irradiation of Ti 3SiC 2 and Ti 3AlC 2 in the 121–1085 °C temperature range

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

Tallman, Darin J.; He, Lingfeng; Gan, Jian

Herein we report on the formation of defects in response to neutron irradiation of polycrystalline Ti 3SiC 2 and Ti 3AlC 2 samples exposed to doses of 0.14±0.01, 1.6±0.1, and 3.4±0.1 displacements per atom (dpa) at irradiation temperatures of 121±12, 735±6 and 1085±68 °C. After irradiation to 0.14 dpa at 121 °C and 735 °C, black spots are observed in both Ti 3SiC 2 and Ti 3AlC 2. After irradiation to 1.6 and 3.4 dpa at 735 °C, basal dislocation loops, with a Burgers vector of b = ½ [0001] are observed in Ti 3SiC 2, with loop diameters ofmore » 21±6 and 30±8 nm for 1.6 dpa and 3.4 dpa, respectively. In Ti3AlC2, larger dislocation loops, 75±34 nm in diameter are observed after 3.4 dpa at 735 °C, in addition to stacking faults. Impurity particles of TiC, as well as stacking fault TiC platelets in the MAX phases, are seen to form extensive dislocation loops under all conditions. Voids are observed at grain boundaries and within stacking faults after 3.4 dpa irradiation, with extensive void formation in the TiC regions at 1085 °C. Remarkably, denuded zones on the order of 1 µm are observed in Ti 3SiC 2 after irradiation to 3.4 dpa at 735 °C. Small grains, 3-5 µm in diameter, are damage free after irradiation at 1085 °C at this dose. The presence of the A-layer in the MAX phases is seen to provide enhanced irradiation tolerance. Based on these results, and up to 3.41 dpa, Ti 3SiC 2 remains a promising candidate for high temperature nuclear applications.« less

Study on torsional fretting wear behavior of a ball-on-socket contact configuration simulating an artificial cervical disk.

PubMed

Wang, Song; Wang, Fei; Liao, Zhenhua; Wang, Qingliang; Liu, Yuhong; Liu, Weiqiang

2015-10-01

A ball-on-socket contact configuration was designed to simulate an artificial cervical disk in structure. UHMWPE (ultra high molecular weight polyethylene) hot pressed by powders and Ti6Al4V alloy were selected as the material combination of ball and socket. The socket surface was coated by a ~500 nm C-DLC (carbon ion implantation-diamond like carbon) mixed layer to improve its surface nano hardness and wear resistance. The torsional fretting wear behavior of the ball-on-socket model was tested at different angular displacements under 25% bovine serum lubrication with an axial force of 100 N to obtain more realistic results with that in vivo. The fretting running regimes and wear damage characteristics as well as wear mechanisms for both ball and socket were studied based on 2D (two dimension) optical microscope, SEM (scanning electron microscope) and 3D (three dimension) profiles. With the increase of angular displacement amplitude from 1° to 7°, three types of T-θ (Torsional torque-angular displacement amplitude) curves (i.e., linear, elliptical and parallelogram loops) corresponding to running regimes of PSR (partial slip regime), MR (mixed regime) and SR (slip regime) were observed and analyzed. Both the central region and the edge zone of the ball and socket were damaged. The worn surfaces were characterized by wear scratches and wear debris. In addition, more severe wear damage and more wear debris appeared on the central region of the socket at higher angular displacement amplitude. The dominant damage mechanism was a mix of surface scratch, adhesive wear and abrasive wear for the UHMWPE ball while that for the coated socket was abrasive wear by PE particles and some polishing and rolling process on the raised overgrown DLC grains. The frictional kinetic behavior, wear type, damage region and damage mechanism for the ball-on-socket model revealed significant differences with those of a ball-on-flat contact while showing better consistency with that of in vitro cervical prosthesis simulations according to the literature. Copyright © 2015. Published by Elsevier B.V.

The hip fluid seal--Part II: The effect of an acetabular labral tear, repair, resection, and reconstruction on hip stability to distraction.

PubMed

Nepple, Jeffrey J; Philippon, Marc J; Campbell, Kevin J; Dornan, Grant J; Jansson, Kyle S; LaPrade, Robert F; Wijdicks, Coen A

2014-04-01

The acetabular labrum is theorized to be important to normal hip function by providing stability to distraction forces through the suction effect of the hip fluid seal. The purpose of this study was to determine the relative contributions of the hip capsule and labrum to the distractive stability of the hip, and to characterize hip stability to distraction forces in six labral conditions: intact labrum, labral tear, labral repair (looped vs. through sutures), partial resection, labral reconstruction with iliotibial band, and complete resection. Eight cadaveric hips with a mean age of 47.8 years (SD 4.3, range 41-51 years) were included. For each condition, the hip seal was broken by distracting the hip at a rate of 0.33 mm/s while the required force, energy, and negative intra-articular pressure were measured. For comparisons between labral conditions, measurements were normalized to the intact labral state (percent of intact). The relative contribution of the labrum to distractive stability was greatest at 1 and 2 mm of displacement, where it was significantly greater than the role of the capsule and accounted for 77 % (SD 27 %, p = 0.006) and 70 % (SD 7 %, p = 0.009) of total distractive stability, respectively. The relative contribution of the capsule to distractive stability increased with progressive displacement, providing 41 % (SD 49 %) and 52 % (SD 53 %) of distractive stability at 3 and 5 mm of distraction, respectively. The maximal distraction force required to break the hip seal in the intact labral state (capsule removed) varied from 124 to 150 N. Labral tear, partial resection, and complete resection resulted in average maximal distraction forces of 76 % (SD 34 %), 29 % (SD 26 %), and 27 % (SD 22 %), respectively, compared to the intact state. Through type labral repairs resulted in significantly greater improvements (from the labral tear state) in maximal negative pressure generated, compared to looped type repairs (median increase; +32 vs. -9 %, p = 0.029). Labral reconstruction resulted in a mean maximal distraction force of 66 % (SD 35 %), with a significant improvement of 37 % compared to partial labral resection (p < 0.001). The acetabular labrum was the primary hip stabilizer to distraction forces at small displacements (1-2 mm). Partial labral resection significantly decreased the distractive strength of the hip fluid seal. Labral reconstruction significantly improved distractive stability, compared to partial labral resection. The results of this study may provide insight into the relative importance of the capsule and labrum to distractive stability of the hip and may help to explain hip microinstability in the setting of labral disease.

High Speed, High Temperature, Fault Tolerant Operation of a Combination Magnetic-Hydrostatic Bearing Rotor Support System for Turbomachinery

NASA Technical Reports Server (NTRS)

Jansen, Mark; Montague, Gerald; Provenza, Andrew; Palazzolo, Alan

2004-01-01

Closed loop operation of a single, high temperature magnetic radial bearing to 30,000 RPM (2.25 million DN) and 540 C (1000 F) is discussed. Also, high temperature, fault tolerant operation for the three axis system is examined. A novel, hydrostatic backup bearing system was employed to attain high speed, high temperature, lubrication free support of the entire rotor system. The hydrostatic bearings were made of a high lubricity material and acted as journal-type backup bearings. New, high temperature displacement sensors were successfully employed to monitor shaft position throughout the entire temperature range and are described in this paper. Control of the system was accomplished through a stand alone, high speed computer controller and it was used to run both the fault-tolerant PID and active vibration control algorithms.

Vaginal Pessary for Uterine Repositioning During High-Intensity Focused Ultrasound Ablation of Uterine Leiomyomas

PubMed Central

Pulanic, Tajana Klepac; Venkatesan, Aradhana M.; Segars, James; Sokka, Sham; Wood, Bradford J.; Stratton, Pamela

2015-01-01

In order to ensure safe magnetic resonance-guided high-intensity focused ultrasound ablation of uterine leiomyomas, ultrasound beam path should be free of intervening scar and bowel. Pre-treatment magnetic resonance imaging of a 9cm long and 7.7cm wide leiomyomatous uterus in a 39-year-old woman with menorrhagia and abdominopelvic pain initially demonstrated a focused ultrasound treatment path without bowel between the uterus and abdominal wall. On the day of ablation, however, multiple loops of bowel were observed in the ultrasound beam path by magnetic resonance imaging. Uterine repositioning was accomplished with a 76 mm donut vaginal pessary which anteverted the fundus and successfully displaced bowel. A vaginal pessary may aid in repositioning an axial or retroverted uterus to enable ablation of uterine leiomyomas. PMID:26584482

Vaginal Pessary for Uterine Repositioning during High-Intensity Focused Ultrasound Ablation of Uterine Leiomyomas.

PubMed

Klepac Pulanic, Tajana; Venkatesan, Aradhana M; Segars, James; Sokka, Sham; Wood, Bradford J; Stratton, Pamela

2016-01-01

In order to ensure safe magnetic resonance-guided, high-intensity focused, ultrasound ablation of uterine leiomyomas, the ultrasound beam path should be free of intervening scar and bowel. Pre-treatment MRI of a 9-cm long and 7.7-cm wide leiomyomatous uterus in a 39-year-old woman with menorrhagia and abdominopelvic pain initially demonstrated a focused ultrasound treatment path without a bowel between the uterus and the abdominal wall. On the day of ablation, however, multiple loops of bowel were observed in the ultrasound beam path by MRI. Uterine repositioning was accomplished with a 76-mm donut vaginal pessary, which anteverted the fundus and successfully displaced the bowel. A vaginal pessary may aid in repositioning an axial or retroverted uterus to enable ablation of uterine leiomyomas. © 2015 S. Karger AG, Basel.

Modeling and Positioning of a PZT Precision Drive System.

PubMed

Liu, Che; Guo, Yanling

2017-11-08

The fact that piezoelectric ceramic transducer (PZT) precision drive systems in 3D printing are faced with nonlinear problems with respect to positioning, such as hysteresis and creep, has had an extremely negative impact on the precision of laser focusing systems. To eliminate the impact of PZT nonlinearity during precision drive movement, mathematical modeling and theoretical analyses of each module comprising the system were carried out in this study, a micro-displacement measurement circuit based on Position Sensitive Detector (PSD) is constructed, followed by the establishment of system closed-loop control and creep control models. An XL-80 laser interferometer (Renishaw, Wotton-under-Edge, UK) was used to measure the performance of the precision drive system, showing that system modeling and control algorithms were correct, with the requirements for precision positioning of the drive system satisfied.

Mechatronics Interface for Computer Assisted Prostate Surgery Training

NASA Astrophysics Data System (ADS)

Altamirano del Monte, Felipe; Padilla Castañeda, Miguel A.; Arámbula Cosío, Fernando

2006-09-01

In this work is presented the development of a mechatronics device to simulate the interaction of the surgeon with the surgical instrument (resectoscope) used during a Transurethral Resection of the Prostate (TURP). Our mechatronics interface is part of a computer assisted system for training in TURP, which is based on a 3D graphics model of the prostate which can be deformed and resected interactively by the user. The mechatronics interface, is the device that the urology residents will manipulate to simulate the movements performed during surgery. Our current prototype has five degrees of freedom, which are enough to have a realistic simulation of the surgery movements. Two of these degrees of freedom are linear, to determinate the linear displacement of the resecting loop and the other three are rotational to determinate three directions and amounts of rotation.

Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications.

PubMed

Huang, Lei; Ma, Fei; Chapman, Alec; Lu, Sijia; Xie, Xiaoliang Sunney

2015-01-01

We present a survey of single-cell whole-genome amplification (WGA) methods, including degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR), multiple displacement amplification (MDA), and multiple annealing and looping-based amplification cycles (MALBAC). The key parameters to characterize the performance of these methods are defined, including genome coverage, uniformity, reproducibility, unmappable rates, chimera rates, allele dropout rates, false positive rates for calling single-nucleotide variations, and ability to call copy-number variations. Using these parameters, we compare five commercial WGA kits by performing deep sequencing of multiple single cells. We also discuss several major applications of single-cell genomics, including studies of whole-genome de novo mutation rates, the early evolution of cancer genomes, circulating tumor cells (CTCs), meiotic recombination of germ cells, preimplantation genetic diagnosis (PGD), and preimplantation genomic screening (PGS) for in vitro-fertilized embryos.

Modeling and Positioning of a PZT Precision Drive System

PubMed Central

Liu, Che; Guo, Yanling

2017-01-01

The fact that piezoelectric ceramic transducer (PZT) precision drive systems in 3D printing are faced with nonlinear problems with respect to positioning, such as hysteresis and creep, has had an extremely negative impact on the precision of laser focusing systems. To eliminate the impact of PZT nonlinearity during precision drive movement, mathematical modeling and theoretical analyses of each module comprising the system were carried out in this study, a micro-displacement measurement circuit based on Position Sensitive Detector (PSD) is constructed, followed by the establishment of system closed-loop control and creep control models. An XL-80 laser interferometer (Renishaw, Wotton-under-Edge, UK) was used to measure the performance of the precision drive system, showing that system modeling and control algorithms were correct, with the requirements for precision positioning of the drive system satisfied. PMID:29117140

Structural control sensors for the CASES GTF

NASA Technical Reports Server (NTRS)

Davis, Hugh W.; Bukley, Angelia P.

1993-01-01

CASES (Controls, Astrophysics and Structures Experiment in Space) is a proposed space experiment to collect x-ray images of the galactic center and solar disk with unprecedented resolution. This requires precision pointing and suppression of vibrations in the long flexible structure that comprises the 32-m x-ray telescope optical bench. Two separate electro-optical sensor systems are provided for the ground test facility (GTF). The Boom Motion Tracker (BMT) measures eigenvector data for post-mission use in system identification. The Tip Displacement Sensor (TDS) measures boom tip position and is used as feedback for the closed-loop control system that stabilizes the boom. Both the BMT and the TDS have met acceptance specifications and were delivered to MSFC in February 1992. This paper describes the sensor concept, the sensor configuration as implemented in the GTF, and the results of characterization and performance testing.

Three-dimensional particle tracking velocimetry algorithm based on tetrahedron vote

NASA Astrophysics Data System (ADS)

Cui, Yutong; Zhang, Yang; Jia, Pan; Wang, Yuan; Huang, Jingcong; Cui, Junlei; Lai, Wing T.

2018-02-01

A particle tracking velocimetry algorithm based on tetrahedron vote, which is named TV-PTV, is proposed to overcome the limited selection problem of effective algorithms for 3D flow visualisation. In this new cluster-matching algorithm, tetrahedrons produced by the Delaunay tessellation are used as the basic units for inter-frame matching, which results in a simple algorithmic structure of only two independent preset parameters. Test results obtained using the synthetic test image data from the Visualisation Society of Japan show that TV-PTV presents accuracy comparable to that of the classical algorithm based on new relaxation method (NRX). Compared with NRX, TV-PTV possesses a smaller number of loops in programming and thus a shorter computing time, especially for large particle displacements and high particle concentration. TV-PTV is confirmed practically effective using an actual 3D wake flow.

Predicting the NMR spectra of nucleotides by DFT calculations: cyclic uridine monophosphate.

PubMed

Bagno, Alessandro; Rastrelli, Federico; Saielli, Giacomo

2008-06-01

We present an experimental and quantum chemical NMR study of the mononucleotide cyclic uridine monophosphate in water. Spectral parameters ((1)H and (13)C chemical shifts and (1)H--(1)H, (13)C--(1)H, (31)P--(13)C and (31)P--(1)H spin-spin coupling constants) have been carefully obtained experimentally and calculated using DFT methods including the solvent effect and the conformational flexibility of the solute. This study confirms that the (1)H and (13)C spectra of polar, flexible molecules in aqueous solution can be predicted with a high level of accuracy, comparable to that obtained for less complex systems. Copyright (c) 2008 John Wiley & Sons, Ltd

Embryo Sexing and Sex Chromosomal Chimerism Analysis by Loop-Mediated Isothermal Amplification in Cattle and Water Buffaloes

PubMed Central

HIRAYAMA, Hiroki; KAGEYAMA, Soichi; MORIYASU, Satoru; SAWAI, Ken; MINAMIHASHI, Akira

2013-01-01

Abstract In domestic animals of the family Bovidae, sex preselection of offspring has been demanded for convenience of milk/beef production and animal breeding. Development of the nonsurgical embryo transfer technique and sexing methods of preimplantation embryos made it possible. Sexing based on detection of Y chromosome-specific DNA sequences is considered the most reliable method to date. PCR enables amplification of a target sequence from a small number of blastomeres. However, it requires technical skill and is time consuming. Furthermore, PCR has the risk of false positives because of DNA contamination during handling of the PCR products in duplicate PCR procedures and/or electrophoresis. Therefore, for embryo sexing to become widely used in the cattle embryo transfer industry, a simple, rapid and precise sexing method needs to be developed. Loop-mediated isothermal amplification (LAMP) is a novel DNA amplification method, and the reaction is carried out under isothermal conditions (range, 60 to 65 C) using DNA polymerase with strand displacement activity. When the target DNA is amplified by LAMP, a white precipitate derived from magnesium pyrophosphate (a by-product of the LAMP reaction) is observed. It is noteworthy that LAMP does not need special reagents or electrophoresis to detect the amplified DNA. This review describes the development and application of an embryo sexing method using LAMP in cattle and water buffaloes. PMID:23965599

DACS II - A distributed thermal/mechanical loads data acquisition and control system

NASA Technical Reports Server (NTRS)

Zamanzadeh, Behzad; Trover, William F.; Anderson, Karl F.

1987-01-01

A distributed data acquisition and control system has been developed for the NASA Flight Loads Research Facility. The DACS II system is composed of seven computer systems and four array processors configured as a main computer system, three satellite computer systems, and 13 analog input/output systems interconnected through three independent data networks. Up to three independent heating and loading tests can be run concurrently on different test articles or the entire system can be used on a single large test such as a full scale hypersonic aircraft. Thermal tests can include up to 512 independent adaptive closed loop control channels. The control system can apply up to 20 MW of heating to a test specimen while simultaneously applying independent mechanical loads. Each thermal control loop is capable of heating a structure at rates of up to 150 F per second over a temperature range of -300 to +2500 F. Up to 64 independent mechanical load profiles can be commanded along with thermal control. Up to 1280 analog inputs monitor temperature, load, displacement and strain on the test specimens with real time data displayed on up to 15 terminals as color plots and tabular data displays. System setup and operation is accomplished with interactive menu-driver displays with extensive facilities to assist the users in all phases of system operation.

OBSERVATIONAL EVIDENCE FOR THE CAUSES AND CONSEQUENCES OF CHROMOSPHERIC RECONNECTION

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

Yan, Limei; Xia, Lidong; Jiao, Fangran

The chromospheric anemone jets with an inverse “Y” shape are ubiquitous, as revealed by the Solar Optical Telescope observations. These jets are considered to be consequences of chromospheric magnetic reconnections. Although these jets have been studied intensively, the dynamics and their driving causes remain unclear observationally. In this work, we report a case of a chromospheric jet showing complete observational evidence for the cause and consequence of chromospheric intermittent reconnection. The intermittent eruption of this jet shows two distinct quasi-periods, 50–60 s and 600–700 s. The short-period eruptions may be related to the plasmoid-induced reconnection, and the long-period ones may bemore » interpreted as sequences of cycles of energy storage and release during magnetic reconnections. The observations also reveal Alfvénic waves with a mean period around 88 s and a maximum transverse displacement around 0.″26. The jet is hosted by a loop moving smoothly with a horizontal speed of ∼0.4 km s{sup −1}. Our results provide observational evidence supporting the magnetic reconnection model of the formation of the chromospheric jets with related products, in which the loop advection drives intermittent magnetic reconnections, and the reconnection outflows carrying plasmoids collide further with the ambient field lines and finally excite waves and jets.« less

A New Type of Motor: Pneumatic Step Motor

PubMed Central

Stoianovici, Dan; Patriciu, Alexandru; Petrisor, Doru; Mazilu, Dumitru; Kavoussi, Louis

2011-01-01

This paper presents a new type of pneumatic motor, a pneumatic step motor (PneuStep). Directional rotary motion of discrete displacement is achieved by sequentially pressurizing the three ports of the motor. Pulsed pressure waves are generated by a remote pneumatic distributor. The motor assembly includes a motor, gearhead, and incremental position encoder in a compact, central bore construction. A special electronic driver is used to control the new motor with electric stepper indexers and standard motion control cards. The motor accepts open-loop step operation as well as closed-loop control with position feedback from the enclosed sensor. A special control feature is implemented to adapt classic control algorithms to the new motor, and is experimentally validated. The speed performance of the motor degrades with the length of the pneumatic hoses between the distributor and motor. Experimental results are presented to reveal this behavior and set the expectation level. Nevertheless, the stepper achieves easily controllable precise motion unlike other pneumatic motors. The motor was designed to be compatible with magnetic resonance medical imaging equipment, for actuating an image-guided intervention robot, for medical applications. For this reason, the motors were entirely made of nonmagnetic and dielectric materials such as plastics, ceramics, and rubbers. Encoding was performed with fiber optics, so that the motors are electricity free, exclusively using pressure and light. PneuStep is readily applicable to other pneumatic or hydraulic precision-motion applications. PMID:21528106

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

Ghassemi-Armaki, Hassan; Leff, Asher C.; Taheri, Mitra L.

Compression-compression cyclic deformation of nanocrystalline NiTi tubes intended for medical stents and with an outer diameter of 1 mm and wall thickness of 70 μm was studied using micropillars produced by FIB with the loading axis orthogonal to the tube axis. These micropillars were cycled in a displacement-controlled mode using a nanoindenter equipped with a flat punch to strain levels of 4, 6 and 8% in each cycle and specimens were subjected to several hundred cycles. Furthermore, the cyclic response of two NiTi tubes, one with Af of 17 °C and the other with an Af of -5 °C ismore » compared. The texture of the tube with the Af of -5 °C was measured at the microscopic level using transmission electron microscopy and at the macroscopic level by X-ray diffraction and good agreement was noted. Characteristics such as i) a reduction in the forward transformation stress, ii) increase in maximum stress for a given displacement amplitude, and iii) a reduction in the hysteresis loop area, all with increasing number of cycles, observed typically during cyclic deformation of conventional macroscopic specimens, were captured in the micropillar cyclic tests. Our observations lead to the conclusion that micropillar compression testing in a cyclic mode can enable characterizing the orientation-dependent response in such small dimension components that see complex loading in service, and additionally provide an opportunity for calibrating constitutive equations in micromechanical models.« less

Biochemical studies of the Saccharomyces cerevisiae Mph1 helicase on junction-containing DNA structures

PubMed Central

Kang, Young-Hoon; Munashingha, Palinda Ruvan; Lee, Chul-Hwan; Nguyen, Tuan Anh; Seo, Yeon-Soo

2012-01-01

Saccharomyces cerevisiae Mph1 is a 3–5′ DNA helicase, required for the maintenance of genome integrity. In order to understand the ATPase/helicase role of Mph1 in genome stability, we characterized its helicase activity with a variety of DNA substrates, focusing on its action on junction structures containing three or four DNA strands. Consistent with its 3′ to 5′ directionality, Mph1 displaced 3′-flap substrates in double-fixed or equilibrating flap substrates. Surprisingly, Mph1 displaced the 5′-flap strand more efficiently than the 3′ flap strand from double-flap substrates, which is not expected for a 3–5′ DNA helicase. For this to occur, Mph1 required a threshold size (>5 nt) of 5′ single-stranded DNA flap. Based on the unique substrate requirements of Mph1 defined in this study, we propose that the helicase/ATPase activity of Mph1 play roles in converting multiple-stranded DNA structures into structures cleavable by processing enzymes such as Fen1. We also found that the helicase activity of Mph1 was used to cause structural alterations required for restoration of replication forks stalled due to damaged template. The helicase properties of Mph1 reported here could explain how it resolves D-loop structure, and are in keeping with a model proposed for the error-free damage avoidance pathway. PMID:22090425

Controlling the error on target motion through real-time mesh adaptation: Applications to deep brain stimulation.

PubMed

Bui, Huu Phuoc; Tomar, Satyendra; Courtecuisse, Hadrien; Audette, Michel; Cotin, Stéphane; Bordas, Stéphane P A

2018-05-01

An error-controlled mesh refinement procedure for needle insertion simulations is presented. As an example, the procedure is applied for simulations of electrode implantation for deep brain stimulation. We take into account the brain shift phenomena occurring when a craniotomy is performed. We observe that the error in the computation of the displacement and stress fields is localised around the needle tip and the needle shaft during needle insertion simulation. By suitably and adaptively refining the mesh in this region, our approach enables to control, and thus to reduce, the error whilst maintaining a coarser mesh in other parts of the domain. Through academic and practical examples we demonstrate that our adaptive approach, as compared with a uniform coarse mesh, increases the accuracy of the displacement and stress fields around the needle shaft and, while for a given accuracy, saves computational time with respect to a uniform finer mesh. This facilitates real-time simulations. The proposed methodology has direct implications in increasing the accuracy, and controlling the computational expense of the simulation of percutaneous procedures such as biopsy, brachytherapy, regional anaesthesia, or cryotherapy. Moreover, the proposed approach can be helpful in the development of robotic surgeries because the simulation taking place in the control loop of a robot needs to be accurate, and to occur in real time. Copyright © 2018 John Wiley & Sons, Ltd.

Highly selective detection of single-nucleotide polymorphisms using a quartz crystal microbalance biosensor based on the toehold-mediated strand displacement reaction.

PubMed

Wang, Dingzhong; Tang, Wei; Wu, Xiaojie; Wang, Xinyi; Chen, Gengjia; Chen, Qiang; Li, Na; Liu, Feng

2012-08-21

Toehold-mediated strand displacement reaction (SDR) is first introduced to develop a simple quartz crystal microbalance (QCM) biosensor without an enzyme or label at normal temperature for highly selective and sensitive detection of single-nucleotide polymorphism (SNP) in the p53 tumor suppressor gene. A hairpin capture probe with an external toehold is designed and immobilized on the gold electrode surface of QCM. A successive SDR is initiated by the target sequence hybridization with the toehold domain and ends with the unfolding of the capture probe. Finally, the open-loop capture probe hybridizes with the streptavidin-coupled reporter probe as an efficient mass amplifier to enhance the QCM signal. The proposed biosensor displays remarkable specificity to target the p53 gene fragment against single-base mutant sequences (e.g., the largest discrimination factor is 63 to C-C mismatch) and high sensitivity with the detection limit of 0.3 nM at 20 °C. As the crucial component of the fabricated biosensor for providing the high discrimination capability, the design rationale of the capture probe is further verified by fluorescence sensing and atomic force microscopy imaging. Additionally, a recovery of 84.1% is obtained when detecting the target sequence in spiked HeLa cells lysate, demonstrating the feasibility of employing this biosensor in detecting SNPs in biological samples.

Meandering instability of a viscous thread

NASA Astrophysics Data System (ADS)

Morris, Stephen W.; Dawes, Jonathan H. P.; Ribe, Neil M.; Lister, John R.

2008-06-01

A viscous thread falling from a nozzle onto a surface exhibits the famous rope-coiling effect, in which the thread buckles to form loops. If the surface is replaced by a belt moving with speed U , the rotational symmetry of the buckling instability is broken and a wealth of interesting states are observed [see S. Chiu-Webster and J. R. Lister, J. Fluid Mech. 569, 89 (2006)]. We experimentally studied this “fluid-mechanical sewing machine” in a more precise apparatus. As U is reduced, the steady catenary thread bifurcates into a meandering state in which the thread displacements are only transverse to the motion of the belt. We measured the amplitude and frequency ω of the meandering close to the bifurcation. For smaller U , single-frequency meandering bifurcates to a two-frequency “figure-8” state, which contains a significant 2ω component and parallel as well as transverse displacements. This eventually reverts to single-frequency coiling at still smaller U . More complex, highly hysteretic states with additional frequencies are observed for larger nozzle heights. We propose to understand this zoology in terms of the generic amplitude equations appropriate for resonant interactions between two oscillatory modes with frequencies ω and 2ω . The form of the amplitude equations captures both the axisymmetry of the U=0 coiling state and the symmetry-breaking effects induced by the moving belt.

Thread amplitudes and frequencies in a fluid mechanical `sewing machine'

NASA Astrophysics Data System (ADS)

Morris, Stephen W.; Dawes, J. H. P.; Lister, John; Dalziel, Stuart

2006-11-01

A viscous thread falling on a surface exhibits the famous rope- coiling effect, in which the thread buckles to form loops. If the surface is replaced by a belt moving at speed U, the rotational symmetry of the buckling instability is broken and a wealth of interesting states are observed (1). We experimentally studied this fluid mechanical `sewing machine' in a new, more precise apparatus. As U is reduced, the stretched thread bifurcates into a meandering state in which the thread displacements are only transverse to the motion of the belt. We measured the amplitudes A and frequency φ of the meandering close to the bifurcation. For small U, single- frequency meandering bifurcates to a two-frequency `figure 8' state, which contains a significant 2φ component and parallel as well as transverse displacements. This eventually reverts to single-frequency coiling at smaller U. More complex, highly hysteretic states with additional harmonics are observed for larger nozzle heights. We propose to understand this zoology in terms of the generic amplitude equations appropriate for resonant interactions between three oscillatory modes with frequencies φ, 2φ and 3φ. The form of the amplitude equations captures both the axisymmetry of the U=0 coiling state and the symmetry-breaking effects induced by the moving belt.(1) Chiu-Webster and Lister, J. Fluid Mech., in press.

Meandering instability of a viscous thread.

PubMed

Morris, Stephen W; Dawes, Jonathan H P; Ribe, Neil M; Lister, John R

2008-06-01

A viscous thread falling from a nozzle onto a surface exhibits the famous rope-coiling effect, in which the thread buckles to form loops. If the surface is replaced by a belt moving with speed U , the rotational symmetry of the buckling instability is broken and a wealth of interesting states are observed [see S. Chiu-Webster and J. R. Lister, J. Fluid Mech. 569, 89 (2006)]. We experimentally studied this "fluid-mechanical sewing machine" in a more precise apparatus. As U is reduced, the steady catenary thread bifurcates into a meandering state in which the thread displacements are only transverse to the motion of the belt. We measured the amplitude and frequency omega of the meandering close to the bifurcation. For smaller U , single-frequency meandering bifurcates to a two-frequency "figure-8" state, which contains a significant 2omega component and parallel as well as transverse displacements. This eventually reverts to single-frequency coiling at still smaller U . More complex, highly hysteretic states with additional frequencies are observed for larger nozzle heights. We propose to understand this zoology in terms of the generic amplitude equations appropriate for resonant interactions between two oscillatory modes with frequencies omega and 2omega . The form of the amplitude equations captures both the axisymmetry of the U=0 coiling state and the symmetry-breaking effects induced by the moving belt.

Numerical Simulation of Hysteretic Live Load Effect in a Soil-Steel Bridge

NASA Astrophysics Data System (ADS)

Sobótka, Maciej

2014-03-01

The paper presents numerical simulation of hysteretic live load effect in a soil-steel bridge. The effect was originally identified experimentally by Machelski [1], [2]. The truck was crossing the bridge one way and the other in the full-scale test performed. At the same time, displacements and stress in the shell were measured. The major conclusion from the research was that the measured quantities formed hysteretic loops. A numerical simulation of that effect is addressed in the present work. The analysis was performed using Flac finite difference code. The methodology of solving the mechanical problems implemented in Flac enables us to solve the problem concerning a sequence of load and non-linear mechanical behaviour of the structure. The numerical model incorporates linear elastic constitutive relations for the soil backfill, for the steel shell and the sheet piles, being a flexible substructure for the shell. Contact zone between the shell and the soil backfill is assumed to reflect elastic-plastic constitutive model. Maximum shear stress in contact zone is limited by the Coulomb condition. The plastic flow rule is described by dilation angle ψ = 0. The obtained results of numerical analysis are in fair agreement with the experimental evidence. The primary finding from the performed simulation is that the slip in the interface can be considered an explanation of the hysteresis occurrence in the charts of displacement and stress in the shell.

Deformation twinning in irradiated ferritic/martensitic steels

NASA Astrophysics Data System (ADS)

Wang, K.; Dai, Y.; Spätig, P.

2018-04-01

Two different ferritic/martensitic steels were tensile tested to gain insight into the mechanisms of embrittlement induced by the combined effects of displacement damage and helium after proton/neutron irradiation in SINQ, the Swiss spallation neutron source. The irradiation conditions were in the range: 15.8-19.8 dpa (displacement per atom) with 1370-1750 appm He at 245-300 °C. All the samples fractured in brittle mode with intergranular or cleavage fracture surfaces when tested at room temperature (RT) or 300 °C. After tensile test, transmission electron microscopy (TEM) was employed to investigate the deformation microstructures. TEM-lamella samples were extracted directly below the intergranular fracture surfaces or cleavage surfaces by using the focused ion beam technique. Deformation twinning was observed in irradiated specimens at high irradiation dose. Only twins with {112} plane were observed in all of the samples. The average thickness of twins is about 40 nm. Twins initiated at the fracture surface, became gradually thinner with distance away from the fracture surface and finally stopped in the matrix. Novel features such as twin-precipitate interactions, twin-grain boundary and/or twin-lath boundary interactions were observed. Twinning bands were seen to be arrested by grain boundaries or large precipitates, but could penetrate martensitic lath boundaries. Unlike the case of defect free channels, small defect-clusters, dislocation loops and dense small helium bubbles were observed inside twins.

Exchange bias for core/shell magnetic nanoparticles

NASA Astrophysics Data System (ADS)

Lemos, C. G. O.; Figueiredo, W.; Santos, M.

2015-09-01

We study the properties of a finite magnetic system to model a magnetic nanoparticle, which is formed by a reduced number of magnetic dipole moments due to the spin of the atoms. The nanoparticle is of the type core/shell where the shell is formed by spins interacting through an antiferromagnetic exchange coupling while for the spins belonging to the core the coupling is ferromagnetic. The interaction between the spins at the interface core/shell can be either ferro or antiferromagnetic. To describe the states of the spins we used the XY model in which the spins are considered as continuous variables, free to point in any direction of the xy plane. We also consider a magnetocrystalline anisotropy, exchange anisotropy and the Zeeman effect. Our model is studied in a lattice with square symmetry, using the Monte Carlo method along with the Metropolis prescription. The results show that in the absence of an external magnetic field and exchange anisotropy, the system continuously goes to a disordered state from an ordered state at a well defined temperature. In the presence of external magnetic fields the system displays the exchange bias phenomenon, that is, the displacement of the hysteresis loops, due to the introduction of the exchange anisotropy term. However, this displacement depends on the core and shell sizes, as well as on the magnitude of the coupling between the shell and the core moments.

Analysis of vertical stability limits and vertical displacement event behavior on NSTX-U

NASA Astrophysics Data System (ADS)

Boyer, Mark; Battaglia, Devon; Gerhardt, Stefan; Menard, Jonathan; Mueller, Dennis; Myers, Clayton; Sabbagh, Steven; Smith, David

2017-10-01

The National Spherical Torus Experiment Upgrade (NSTX-U) completed its first run campaign in 2016, including commissioning a larger center-stack and three new tangentially aimed neutral beam sources. NSTX-U operates at increased aspect ratio due to the larger center-stack, making vertical stabilization more challenging. Since ST performance is improved at high elongation, improvements to the vertical control system were made, including use of multiple up-down-symmetric flux loop pairs for real-time estimation, and filtering to remove noise. Similar operating limits to those on NSTX (in terms of elongation and internal inductance) were achieved, now at higher aspect ratio. To better understand the observed limits and project to future operating points, a database of vertical displacement events and vertical oscillations observed during the plasma current ramp-up on NSTX/NSTX-U has been generated. Shots were clustered based on the characteristics of the VDEs/oscillations, and the plasma parameter regimes associated with the classes of behavior were studied. Results provide guidance for scenario development during ramp-up to avoid large oscillations at the time of diverting, and provide the means to assess stability of target scenarios for the next campaign. Results will also guide plans for improvements to the vertical control system. Work supported by U.S. D.O.E. Contract No. DE-AC02-09CH11466.

Looping probabilities of elastic chains: a path integral approach.

PubMed

Cotta-Ramusino, Ludovica; Maddocks, John H

2010-11-01

We consider an elastic chain at thermodynamic equilibrium with a heat bath, and derive an approximation to the probability density function, or pdf, governing the relative location and orientation of the two ends of the chain. Our motivation is to exploit continuum mechanics models for the computation of DNA looping probabilities, but here we focus on explaining the novel analytical aspects in the derivation of our approximation formula. Accordingly, and for simplicity, the current presentation is limited to the illustrative case of planar configurations. A path integral formalism is adopted, and, in the standard way, the first approximation to the looping pdf is obtained from a minimal energy configuration satisfying prescribed end conditions. Then we compute an additional factor in the pdf which encompasses the contributions of quadratic fluctuations about the minimum energy configuration along with a simultaneous evaluation of the partition function. The original aspects of our analysis are twofold. First, the quadratic Lagrangian describing the fluctuations has cross-terms that are linear in first derivatives. This, seemingly small, deviation from the structure of standard path integral examples complicates the necessary analysis significantly. Nevertheless, after a nonlinear change of variable of Riccati type, we show that the correction factor to the pdf can still be evaluated in terms of the solution to an initial value problem for the linear system of Jacobi ordinary differential equations associated with the second variation. The second novel aspect of our analysis is that we show that the Hamiltonian form of these linear Jacobi equations still provides the appropriate correction term in the inextensible, unshearable limit that is commonly adopted in polymer physics models of, e.g. DNA. Prior analyses of the inextensible case have had to introduce nonlinear and nonlocal integral constraints to express conditions on the relative displacement of the end points. Our approximation formula for the looping pdf is of quite general applicability as, in contrast to most prior approaches, no assumption is made of either uniformity of the elastic chain, nor of a straight intrinsic shape. If the chain is uniform the Jacobi system evaluated at certain minimum energy configurations has constant coefficients. In such cases our approximate pdf can be evaluated in an entirely explicit, closed form. We illustrate our analysis with a planar example of this type and compute an approximate probability of cyclization, i.e., of forming a closed loop, from a uniform elastic chain whose intrinsic shape is an open circular arc.

Closed loop control of a cylindrical tube type Ionic Polymer Metal Composite (IPMC)

NASA Astrophysics Data System (ADS)

Mead, Benjamin T.

The goal of this research is to provide a framework for the integration of tube type, cylindrical Ionic Polymer Metal-Composite (IPMC) into conventional devices. IPMCs are one of the most widely used types of electro-active polymer actuator, due to their low electric driving potential and large deformation range. For this research a tube type IPMC was investigated. This IPMC has a circular cross section with four separate electrodes on its surface and a hole through the middle. The four electrodes allow for biaxial bending and accurate control of the tip location. One of the main advantages of using this type of IPMC is the ability to embed a specific tool and accurately control the tool tip location using the large deflection range of the IPMC. This ability has widespread applications including in the biomedical field for use in active catheter procedures. First, this relatively new type of IPMC is investigated and characterized. The processes and materials used are described and the functional design is explored. Before the modeling process beings the basic functions of the IPMC are investigated. To this end force and displacement experiments are performed to describe the activation of the tube type IPMC. This data will be used later to verify and calibrate the mathematical simulations. Second, a three dimensional multi-physics finite element model is developed using COMSOL 4.3a. This model will automatically couple three physics packages and provide a description of the fluid interactions within the tube type IPMC. This model is then compared against the experimental displacement results to calibrate the simulation. Using this simulation design parameters are declared including, overall diameter, and tool hole size. The performance of the IPMC is then simulated while varying these parameters. Third, an electro-mechanical model of the IPMC is developed. This macroscopic model is used to relate the input voltage to an associated tip deflection. Several model types used for this purpose are tested and discussed. After determining a suitable type a mathematical electro-mechanical model is developed. Using this model several closed loop control systems are proposed. Once a final decision is reached the closed loop control system is implemented in the experimental setup. Several tests are designed to test the effectiveness of the closed loop system and mathematical models. Finally several improvements are made to enhance the users experience using IPMCs as well as incorporating them into conventional devices. To provide a better user interface the experimental control system is extended to allow the user to input controls via a standard computer mouse. This will allow a shorter operator training time and hopefully a wider array of real world uses for IPMCs. Attempts are also made to establish permanent connections to the IPMC. A tube type IPMC is meant to be used as part of a total system. To this end soldered connections to the IPMC are made. One of the main expected applications of tube type IPMCs are as active catheters. In this application the IPMC would be placed in-line with the plastic catheter line. As a proof of concept the IPMC is installed onto the tip of a conventional catheter line.

Loss of MSH3 protein expression is frequent in MLH1-deficient colorectal cancer and is associated with disease progression.

PubMed

Plaschke, Jens; Krüger, Stefan; Jeske, Birgit; Theissig, Franz; Kreuz, Friedmar R; Pistorius, Steffen; Saeger, Hans D; Iaccarino, Ingram; Marra, Giancarlo; Schackert, Hans K

2004-02-01

Mononucleotide repeat sequences are particularly prone to frameshift mutations in tumors with biallelic inactivation of the mismatch repair (MMR) genes MLH1 or MSH2. In these tumors, several genes harboring mononucleotide repeats in their coding region have been proposed as targets involved in tumor progression, among which are also the MMR genes MSH3 and MSH6. We have analyzed the expression of the MSH3 and MSH6 proteins by immunohistochemistry in 31 colorectal carcinomas in which MLH1 was inactivated. Loss of MSH3 expression was identified in 15 tumors (48.5%), whereas all tumors expressed MSH6. Frameshift mutations at coding microsatellites were more frequent in MSH3 (16 of 31) than in MSH6 (3 of 31; Fisher's exact test, P < 0.001). Frameshift mutations and allelic losses of MSH3 were more frequent in MSH3-negative tumors compared with those with normal expression (22 mutations in 30 alleles versus 8 mutations in 28 alleles; chi(2), P = 0.001). Biallelic inactivation was evident or inferred for 60% of MSH3-negative tumors but none of the tumors with normal MSH3 expression. In contrast, we did not identify frameshift mutations in the (A)8 tract of MSH3 in a control group of 18 colorectal carcinomas in which the MMR deficiency was based on the inactivation of MSH2. As it has been suggested that mutations of MSH3 might play a role in tumor progression, we studied the association between MSH3 expression and disease stage assessed by lymph node and distant metastases status. Dukes stages C and D were more frequent in primary tumors with loss of MSH3 expression (9 of 13), compared with tumors with retained expression (1 of 14; Fisher's exact test, P = 0.001), suggesting that MSH3 abrogation may be a predictor of metastatic disease or even favor tumor cell spread in MLH1-deficient colorectal cancers.

Head to Head Comparison of Short-Term Treatment with the NAD(+) Precursor Nicotinamide Mononucleotide (NMN) and 6 Weeks of Exercise in Obese Female Mice.

PubMed

Uddin, Golam M; Youngson, Neil A; Sinclair, David A; Morris, Margaret J

2016-01-01

Obesity is well known to be a major cause of several chronic metabolic diseases, which can be partially counteracted by exercise. This is due, in part, to an upregulation of mitochondrial activity through increased nicotinamide adenine dinucleotide (NAD(+)). Recent studies have shown that NAD(+) levels can be increased by using the NAD(+) precursor, nicotinamide mononucleotide (NMN) leading to the suggestion that NMN could be a useful intervention in diet related metabolic disorders. In this study we compared the metabolic, and especially mitochondrial-associated, effects of exercise and NMN in ameliorating the consequences of high-fat diet (HFD) induced obesity in mice. Sixty female 5 week old C57BL6/J mice were allocated across five groups: Chow sedentary: CS; Chow exercise: CEX; HFD sedentary: HS; HFD NMN: HNMN; HFD exercise: HEX (12/group). After 6 weeks of diet, exercise groups underwent treadmill exercise (15 m/min for 45 min), 6 days per week for 6 weeks. NMN or vehicle (500 mg/kg body weight) was injected (i.p.) daily for the last 17 days. No significant alteration in body weight was observed in response to exercise or NMN. The HFD significantly altered adiposity, glucose tolerance, plasma insulin, NADH levels and citrate synthase activity in muscle and liver. HEX and HNMN groups both showed significantly improved glucose tolerance compared to the HS group. NAD(+) levels were increased significantly both in muscle and liver by NMN whereas exercise increased NAD(+) only in muscle. Both NMN and exercise ameliorated the HFD-induced reduction in liver citrate synthase activity. However, exercise, but not NMN, ameliorated citrate synthase activity in muscle. Overall these data suggest that while exercise and NMN-supplementation can induce similar reversal of the glucose intolerance induced by obesity, they are associated with tissue-specific effects and differential alterations to mitochondrial function in muscle and liver.

The origin of life in geothermal hot springs: Darwin's warm little pond revisited

NASA Astrophysics Data System (ADS)

Deamer, D.

2016-12-01

The origin of life in geothermal hot springs: Darwin's warm little pond revisited David Deamer and Bruce Damer, Department of Biomolecular Engineering, University of California, Santa Cruz CA 95064 We are exploring ways in which mononucleotides can undergo polymerization and encapsulation in the presence of an organizing matrix (1, 2, 3). When mixtures of amphiphilic lipids and mononucleotides are exposed to cycles of dehydration and rehydration, the lipids concentrate and organize the monomers within multilamellar liquid-crystalline matrices that self-assemble in the dry state. The chemical potential driving the polymerization reaction is supplied by the anhydrous conditions in which water becomes a leaving group, with heat providing activation energy. Upon rehydration, the polymeric products are encapsulated in trillions of microscopic compartments. Each compartment is unique in its composition and contents, and can be considered to be an experiment in a natural version of combinatorial chemistry that would be ubiquitous in the prebiotic environment. There are specific thermodynamic and kinetic considerations required for this process to work which are related to cycles of evaporation and rehydration, ionic composition, salt concentration, pH and temperature. These conditions are present in hydrothermal fields associated with volcanic activity on today's Earth and can be compared with the range of possible conditions on Enceladus to estimate the probability that life can emerge on an icy world with a subsurface salty liquid ocean. 1. De Guzman V, Shenasa H, Vercoutere W, Deamer D (2014) Generation of oligonucleotides under hydrothermal conditions by non-enzymatic polymerization. J Mol Evol 78:251-262 2. Deamer D. 2012. Liquid crystalline nanostructures: organizing matrices for non-enzymatic nucleic acid polymerization. Chem Soc Rev. 41:5375-9. 3. Damer B, Deamer D. 2015. Coupled phases and combinatorial selection in fluctuating hydrothermal pools: a scenario to guide experimental approaches to the origin of cellular life. Life 5:872-87.

A set of primers for analyzing chloroplast DNA diversity in Citrus and related genera.

PubMed

Cheng, Yunjiang; de Vicente, M Carmen; Meng, Haijun; Guo, Wenwu; Tao, Nengguo; Deng, Xiuxin

2005-06-01

Chloroplast simple sequence repeat (cpSSR) markers in Citrus were developed and used to analyze chloroplast diversity of Citrus and closely related genera. Fourteen cpSSR primer pairs from the chloroplast genomes of tobacco (Nicotiana tabacum L.) and Arabidopsis were found useful for analyzing the Citrus chloroplast genome (cpDNA) and recoded with the prefix SPCC (SSR Primers for Citrus Chloroplast). Eleven of the 14 primer pairs revealed some degree of polymorphism among 34 genotypes of Citrus, Fortunella, Poncirus and some of their hybrids, with polymorphism information content (PIC) values ranging from 0.057 to 0.732, and 18 haplotypes were identified. The cpSSR data were analyzed with NTSYS-pc software, and the genetic relationships suggested by the unweighted pair group method based on arithmetic means (UPGMA) dendrogram were congruent with previous taxonomic investigations: the results showed that all samples fell into seven major clusters, i.e., Citrus medica L., Poncirus, Fortunella, C. ichangensis Blanco, C. reticulata Swingle, C. aurantifolia (Christm.) Swingle and C. grandis (L.) Osbeck. The results of previous studies combined with our cpSSR analyses revealed that: (1) Calamondin (C. madurensis Swingle) is the result of hybridization between kumquat (Fortunella) and mandarin (C. reticulata), where kumquat acted as the female parent; (2) Ichang papeda (C. ichangensis) has a unique taxonomic status; and (3) although Bendiguangju mandarin (C. reticulata) and Satsuma mandarin (C. reticulata) are similar in fruit shape and leaf morphology, they have different maternal parents. Bendiguangju mandarin has the same cytoplasm as sweet orange (C. sinensis), whereas Satsuma mandarin has the cytoplasm of C. reticulata. Seventeen PCR products from SPCC1 and 21 from SPCC11 were cloned and sequenced. The results revealed that mononucleotide repeats as well as insertions and deletions of small segments of DNA were associated with SPCC1 polymorphism, whereas polymorphism generated by SPCC11 was essentially due to the variation in length of the mononucleotide repeats.

Musclelike joint mechanism driven by dielectric elastomer actuator for robotic applications

NASA Astrophysics Data System (ADS)

Jung, Ho Sang; Cho, Kyeong Ho; Park, Jae Hyeong; Yang, Sang Yul; Kim, Youngeun; Kim, Kihyeon; Nguyen, Canh Toan; Phung, Hoa; Tien Hoang, Phi; Moon, Hyungpil; Koo, Ja Choon; Ryeol Choi, Hyouk

2018-07-01

The purpose of this study is to develop an artificial muscle actuator suitable for robotic applications, and to demonstrate the feasibility of applying this actuator to an arm mechanism, and controlling it delicately and smoothly like a human being. To accomplish this, we perform the procedures that integrate the soft actuator, called the single body dielectric elastomer actuator, which is very flexible and capable of high speed operation, and the displacement amplification mechanism called the sliding filament joint mechanism, which mimics the sliding filament model of human muscles. In this paper, we describe the characteristics and control method of the actuation system that consists of actuator, mechanism, and embedded controller, and show the experimental results of the closed-loop position and static stiffness control of the robotic arm application. Finally, based on the results, we evaluate the performance of this application.

An innovative re-centering SMA-lead damper and its application to steel frame structures

NASA Astrophysics Data System (ADS)

Li, Hong-Nan; Liu, Ming-Ming; Fu, Xing

2018-07-01

In this paper, an innovative re-centering damper is presented to reduce the residual deflection of civil structures under strong earthquakes. The schematic diagram of the proposed re-centering SMA-lead damper (RSLD) is provided first. Then the mechanical behaviors of all the sub-components are measured by the testing machine, followed by the proposal of mechanical model of the RSLD. Based on the experimental results, the mechanical model factors for each sub-component are determined by the data fitting method, which is then used to simulate the hysteresis loops of the damper. Meanwhile the experiment of the fabricated RSLD is carried out to study the influence of the loading rate and displacement amplitude on the mechanical properties. Finally, the response analysis of a six-story steel frame structure installed with different damper position configurations is performed, and the results reveal that the proposed RSLD has an outstanding re-centering capacity.

Feedback equilibrium control during human standing

PubMed Central

Alexandrov, Alexei V.; AA, Frolov; FB, Horak; P, Carlson-Kuhta; S, Park

2006-01-01

Equilibrium maintenance during standing in humans was investigated with a 3-joint (ankle, knee and hip) sagittal model of body movement. The experimental paradigm consisted of sudden perturbations of humans in quiet stance by backward displacements of the support platform. Data analysis was performed using eigenvectors of motion equation. The results supported three conclusions. First, independent feedback control of movements along eigenvectors (eigenmovements) can adequately describe human postural responses to stance perturbations. This conclusion is consistent with previous observations (Alexandrov et al., 2001b) that these same eigenmovements are also independently controlled in a feed-forward manner during voluntary upper-trunk bending. Second, independent feedback control of each eigenmovement is sufficient to provide its stability. Third, the feedback loop in each eigenmovement can be modeled as a linear visco-elastic spring with delay. Visco-elastic parameters and time-delay values result from the combined contribution of passive visco-elastic mechanisms and sensory systems of different modalities. PMID:16228222

Irradiation Microstructure of Austenitic Steels and Cast Steels Irradiated in the BOR-60 Reactor at 320°C

NASA Astrophysics Data System (ADS)

Yang, Yong; Chen, Yiren; Huang, Yina; Allen, Todd; Rao, Appajosula

Reactor internal components are subjected to neutron irradiation in light water reactors, and with the aging of nuclear power plants around the world, irradiation-induced material degradations are of concern for reactor internals. Irradiation-induced defects resulting from displacement damage are critical for understanding degradation in structural materials. In the present work, microstructural changes due to irradiation in austenitic stainless steels and cast steels were characterized using transmission electron microscopy. The specimens were irradiated in the BOR-60 reactor, a fast breeder reactor, up to 40 dpa at 320°C. The dose rate was approximately 9.4x10-7 dpa/s. Void swelling and irradiation defects were analyzed for these specimens. A high density of faulted loops dominated the irradiated-altered microstructures. Along with previous TEM results, a dose dependence of the defect structure was established at 320°C.

Design and control of six degree-of-freedom active vibration isolation table.

PubMed

Hong, Jinpyo; Park, Kyihwan

2010-03-01

A six-axis active vibration isolation system (AVIS) is designed by using the direct driven guide and ball contact mechanisms in order to have no cross-coupling between actuators. The point contact configuration gives an advantage of having an easy assembly of eight voice coil actuators to an upper and a base plate. A voice coil actuator is used since it can provide a large displacement and sufficient bandwidth required for vibration control. The AVIS is controlled considering the effect of flexible vibration mode in the upper plate and velocity sensor dynamics. A loop shaping technique and phase margin condition are applied to design a vibration controller. The performances of the AVIS are investigated in the frequency domain and finally validated by comparing with the passive isolation system. The scanning profiles of the specimen are compared together by using the atomic force microscope. The robustness of the AVIS is verified by showing the impulse response.

Independent mitochondrial origin and historical genetic differentiation in North Eastern Asian cattle.

PubMed

Mannen, H; Kohno, M; Nagata, Y; Tsuji, S; Bradley, D G; Yeo, J S; Nyamsamba, D; Zagdsuren, Y; Yokohama, M; Nomura, K; Amano, T

2004-08-01

In order to clarify the origin and genetic diversity of cattle in North Eastern Asia, this study examined mitochondrial displacement loop sequence variation and frequencies of Bos taurus and Bos indicus Y chromosome haplotypes in Japanese, Mongolian, and Korean native cattle. In mitochondrial analyses, 20% of Mongolian cattle carried B. indicus mitochondrial haplotypes, but Japanese and Korean cattle carried only B. taurus haplotypes. In contrast, all samples revealed B. taurus Y chromosome haplotypes. This may be due to the import of zebu and other cattle during the Mongol Empire era with subsequent crossing with native taurine cattle. B. taurus mtDNA sequences fall into several geographically distributed haplogroups and one of these, termed here T4, is described in each of the test samples, but has not been observed in Near Eastern, European or African cattle. This may have been locally domesticated from an East Eurasian strain of Bos primigenius.

Induced Fit in Protein Multimerization: The HFBI Case

PubMed Central

Riccardi, Laura

2016-01-01

Hydrophobins, produced by filamentous fungi, are small amphipathic proteins whose biological functions rely on their unique surface-activity properties. Understanding the mechanistic details of the multimerization process is of primary importance to clarify the interfacial activity of hydrophobins. We used free energy calculations to study the role of a flexible β-hairpin in the multimerization process in hydrophobin II from Trichoderma reesei (HFBI). We characterized how the displacement of this β-hairpin controls the stability of the monomers/dimers/tetramers in solution. The regulation of the oligomerization equilibrium of HFBI will necessarily affect its interfacial properties, fundamental for its biological function and for technological applications. Moreover, we propose possible routes for the multimerization process of HFBI in solution. This is the first case where a mechanism by which a flexible loop flanking a rigid patch controls the protein-protein binding equilibrium, already known for proteins with charged binding hot-spots, is described within a hydrophobic patch. PMID:27832079

Development of a Compact, Efficient Cooling Pump for Space Suit Life Support Systems

NASA Technical Reports Server (NTRS)

van Boeyen, Roger; Reeh, Jonathan; Trevino, Luis

2009-01-01

A compact, low-power electrochemically-driven fluid cooling pump is currently being developed by Lynntech, Inc. With no electric motor and minimal lightweight components, the pump is significantly lighter than conventional rotodynamic and displacement pumps. Reliability and robustness is achieved with the absence of rotating or moving components (apart from the bellows). By employing sulfonated polystyrene-based proton exchange membranes, rather than conventional Nafion membranes, a significant reduction in the actuator power consumption was demonstrated. Lynntech also demonstrated that these membranes possess the necessary mechanical strength, durability, and temperature range for long life space operation. The preliminary design for a Phase II prototype pump compares very favorably to the fluid cooling pumps currently used in space suit primary life support systems (PLSSs). Characteristics of the electrochemically-driven pump are described and the benefits of the technology as a replacement for electric motor pumps in mechanically pumped single-phase fluid loops is discussed.

Disruption of a coronal streamer by an eruptive prominence and coronal mass ejection

NASA Technical Reports Server (NTRS)

Illing, R. M. E.; Hundhausen, A. J.

1986-01-01

The coronal mass ejection of August 18, 1980 is analyzed using images from the coronagraph on the Solar Maximum Mission (SMM) satellite. The event occurred at the site of a large coronal helmet streamer and evolved into the three-part structure of a bright frontal shell, followed by a relatively dark space surrounding a bright filamentary core as seen in many mass ejections of the SMM epoch. The bright core can be identified as material from a prominence whose eruption was observed from the ground. The mass of the frontal shell is equal to that of the coronal helmet streamer, indicating that the shell is the coronal material previously in the helmet streamer, displaced and set into motion by the erupting prominence and surrounding cavity. The mass ejected in the bright core (or prominences) is estimated to be 50 percent larger than the 'coronal' material in the front loop.

Microstructural evolution of pure tungsten neutron irradiated with a mixed energy spectrum

NASA Astrophysics Data System (ADS)

Koyanagi, Takaaki; Kumar, N. A. P. Kiran; Hwang, Taehyun; Garrison, Lauren M.; Hu, Xunxiang; Snead, Lance L.; Katoh, Yutai

2017-07-01

Microstructures of single-crystal bulk tungsten (W) and polycrystalline W foil with a strong grain texture were investigated using transmission electron microscopy following neutron irradiation at ∼90-800 °C to 0.03-4.6 displacements per atom (dpa) in the High Flux Isotope Reactor with a mixed energy spectrum. The dominant irradiation defects were dislocation loops and small clusters at ∼90 °C. Additional voids were formed in W irradiated at above 460 °C. Voids and precipitates involving transmutation rhenium and osmium were the dominant defects at more than ∼1 dpa. We found a new phenomenon of microstructural evolution in irradiated polycrystalline W: Re- and Os-rich precipitation along grain boundaries. Comparison of results between this study and previous studies using different irradiation facilities revealed that the microstructural evolution of pure W is highly dependent on the neutron energy spectrum in addition to the irradiation temperature and dose.

Design and control of six degree-of-freedom active vibration isolation table

NASA Astrophysics Data System (ADS)

Hong, Jinpyo; Park, Kyihwan

2010-03-01

A six-axis active vibration isolation system (AVIS) is designed by using the direct driven guide and ball contact mechanisms in order to have no cross-coupling between actuators. The point contact configuration gives an advantage of having an easy assembly of eight voice coil actuators to an upper and a base plate. A voice coil actuator is used since it can provide a large displacement and sufficient bandwidth required for vibration control. The AVIS is controlled considering the effect of flexible vibration mode in the upper plate and velocity sensor dynamics. A loop shaping technique and phase margin condition are applied to design a vibration controller. The performances of the AVIS are investigated in the frequency domain and finally validated by comparing with the passive isolation system. The scanning profiles of the specimen are compared together by using the atomic force microscope. The robustness of the AVIS is verified by showing the impulse response.

Developments and Control of Biocompatible Conducting Polymer for Intracorporeal Continuum Robots.

PubMed

Chikhaoui, Mohamed Taha; Benouhiba, Amine; Rougeot, Patrick; Rabenorosoa, Kanty; Ouisse, Morvan; Andreff, Nicolas

2018-04-30

Dexterity of robots is highly required when it comes to integration for medical applications. Major efforts have been conducted to increase the dexterity at the distal parts of medical robots. This paper reports on developments toward integrating biocompatible conducting polymers (CP) into inherently dexterous concentric tube robot paradigm. In the form of tri-layer thin structures, CP micro-actuators produce high strains while requiring less than 1 V for actuation. Fabrication, characterization, and first integrations of such micro-actuators are presented. The integration is validated in a preliminary telescopic soft robot prototype with qualitative and quantitative performance assessment of accurate position control for trajectory tracking scenarios. Further, CP micro-actuators are integrated to a laser steering system in a closed-loop control scheme with displacements up to 5 mm. Our first developments aim toward intracorporeal medical robotics, with miniaturized actuators to be embedded into continuum robots.

Measurement of vertical stability metrics in KSTAR

NASA Astrophysics Data System (ADS)

Hahn, Sang-Hee; Humphreys, D. A.; Mueller, D.; Bak, J. G.; Eidietis, N. W.; Kim, H.-S.; Ko, J. S.; Walker, M. L.; Kstar Team

2017-10-01

The paper summarizes results of multi-year ITPA experiments regarding measurement of the vertical stabilization capability of KSTAR discharges, including most recent measurements at the highest achievable elongation (κ 2.0 - 2.1). The measurements of the open-loop growth rate of VDE (γz) and the maximum controllable vertical displacement (ΔZmax) are done by the release-and-catch method. The dynamics of the vertical movement of the plasma is verified by both relevant magnetic reconstructions and non-magnetic diagnostics. The measurements of γz and ΔZmax were done for different plasma currents, βp, internal inductances, elongations and different configurations of the vessel conductors that surround the plasma as the first wall. Effects of control design choice and diagnostics noise are discussed, and comparison with the axisymmetric plasma response model is given for partial accounting for the measured control capability. This work supported by Ministry of Science, ICT, and Future Planning under KSTAR project.

Optical fiber sensors and signal processing for intelligent structure monitoring

NASA Technical Reports Server (NTRS)

Rogowski, Robert; Claus, R. O.; Lindner, D. K.; Thomas, Daniel; Cox, Dave

1988-01-01

The analytic and experimental performance of optical fiber sensors for the control of vibration of large aerospace and other structures are investigated. In particular, model domain optical fiber sensor systems, are being studied due to their apparent potential as distributed, low mass sensors of vibration over appropriate ranges of both low frequency and low amplitude displacements. Progress during the past three months is outlined. Progress since September is divided into work in the areas of experimental hardware development, analytical analysis, control design and sensor development. During the next six months, tests of a prototype closed-loop control system for a beam are planned which will demonstrate the solution of several optical fiber instrumentation device problems, the performance of the control system theory which incorporates the model of the modal domain sensor, and the potential for distributed control which this sensor approach offers.

Proton irradiation study of GFR candidate ceramics

NASA Astrophysics Data System (ADS)

Gan, Jian; Yang, Yong; Dickson, Clayton; Allen, Todd

2009-06-01

This work investigated the microstructural response of SiC, ZrC and ZrN irradiated with 2.6 MeV protons at 800 °C to a fluence of 2.75 × 10 19 protons/cm 2, corresponding to 0.71-1.8 displacement per atom (dpa), depending on the material. The change of lattice constant evaluated using HOLZ patterns is not observed. In comparison to Kr ion irradiation at 800 °C to 10 dpa from the previous studies, the proton irradiated ZrC and ZrN at 1.8 dpa show less irradiation damage to the lattice structure. The proton irradiated ZrC exhibits faulted loops which are not observed in the Kr ion irradiated sample. ZrN shows the least microstructural change from proton irradiation. The microstructure of 6H-SiC irradiated to 0.71 dpa consists of black dot defects at high density.

GOES I/M image navigation and registration

NASA Technical Reports Server (NTRS)

Fiorello, J. L., Jr.; Oh, I. H.; Kelly, K. A.; Ranne, L.

1989-01-01

Image Navigation and Registration (INR) is the system that will be used on future Geostationary Operational Environmental Satellite (GOES) missions to locate and register radiometric imagery data. It consists of a semiclosed loop system with a ground-based segment that generates coefficients to perform image motion compensation (IMC). The IMC coefficients are uplinked to the satellite-based segment, where they are used to adjust the displacement of the imagery data due to movement of the imaging instrument line-of-sight. The flight dynamics aspects of the INR system is discussed in terms of the attitude and orbit determination, attitude pointing, and attitude and orbit control needed to perform INR. The modeling used in the determination of orbit and attitude is discussed, along with the method of on-orbit control used in the INR system, and various factors that affect stability. Also discussed are potential error sources inherent in the INR system and the operational methods of compensating for these errors.

How main-chains of proteins explore the free-energy landscape in native states.

PubMed

Senet, Patrick; Maisuradze, Gia G; Foulie, Colette; Delarue, Patrice; Scheraga, Harold A

2008-12-16

Understanding how a single native protein diffuses on its free-energy landscape is essential to understand protein kinetics and function. The dynamics of a protein is complex, with multiple relaxation times reflecting a hierarchical free-energy landscape. Using all-atom molecular dynamics simulations of an alpha/beta protein (crambin) and a beta-sheet polypeptide (BS2) in their "native" states, we demonstrate that the mean-square displacement of dihedral angles, defined by 4 successive C(alpha) atoms, increases as a power law of time, t(alpha), with an exponent alpha between 0.08 and 0.39 (alpha = 1 corresponds to Brownian diffusion), at 300 K. Residues with low exponents are located mainly in well-defined secondary elements and adopt 1 conformational substate. Residues with high exponents are found in loops/turns and chain ends and exist in multiple conformational substates, i.e., they move on multiple-minima free-energy profiles.

Morphology variation, composition alteration and microstructure changes in ion-irradiated 1060 aluminum alloy

NASA Astrophysics Data System (ADS)

Wan, Hao; Si, Naichao; Wang, Quan; Zhao, Zhenjiang

2018-02-01

Morphology variation, composition alteration and microstructure changes in 1060 aluminum irradiated with 50 keV helium ions were characterized by field emission scanning electron microscopy (FESEM) equipped with x-ray elemental scanning, 3D measuring laser microscope and transmission electron microscope (TEM). The results show that, helium ions irradiation induced surface damage and Si-rich aggregates in the surfaces of irradiated samples. Increasing the dose of irradiation, more damages and Si-rich aggregates would be produced. Besides, defects such as dislocations, dislocation loops and dislocation walls were the primary defects in the ion implanted layer. The forming of surface damages were related with preferentially sputtering of Al component. While irradiation-enhanced diffusion and irradiation-induced segregation resulted in the aggregation of impurity atoms. And the aggregation ability of impurity atoms were discussed based on the atomic radius, displacement energy, lattice binding energy and surface binding energy.

How main-chains of proteins explore the free-energy landscape in native states

PubMed Central

Senet, Patrick; Maisuradze, Gia G.; Foulie, Colette; Delarue, Patrice; Scheraga, Harold A.

2008-01-01

Understanding how a single native protein diffuses on its free-energy landscape is essential to understand protein kinetics and function. The dynamics of a protein is complex, with multiple relaxation times reflecting a hierarchical free-energy landscape. Using all-atom molecular dynamics simulations of an α/β protein (crambin) and a β-sheet polypeptide (BS2) in their “native” states, we demonstrate that the mean-square displacement of dihedral angles, defined by 4 successive Cα atoms, increases as a power law of time, tα, with an exponent α between 0.08 and 0.39 (α = 1 corresponds to Brownian diffusion), at 300 K. Residues with low exponents are located mainly in well-defined secondary elements and adopt 1 conformational substate. Residues with high exponents are found in loops/turns and chain ends and exist in multiple conformational substates, i.e., they move on multiple-minima free-energy profiles. PMID:19073932

Fiber cavity ring-down using an optical time-domain reflectometer

NASA Astrophysics Data System (ADS)

Passos, D. J.; Silva, S. O.; Fernandes, J. R. A.; Marques, M. B.; Frazão, O.

2014-12-01

This work presented a demonstration of the potential for a fiber based cavity ring-down (CRD) using an optical time-domain reflectometer (OTDR). The OTDR was used to send the impulses down into about 20 km of a standard single optical fiber, at the end of which the fiber cavity ring-down was placed. The OTDR measured no appreciable losses, so other CRDs multiplexed could be spliced in parallel along the same optical fiber. To demonstrate the behavior and sensitivity of the proposed configuration, a displacement sensor based on a fiber taper with a diameter of 50 μm was placed inside the fiber loop, and the induced losses were measured on the CRD signal — a sensitivity of 11.8 ± 0.5 μs/mm was achieved. The dynamic range of the sensing head used in this configuration was about 2 mm. Finally, this work was also compared with different works published in the literature.

A novel active disturbance rejection based tracking design for laser system with quadrant photodetector

NASA Astrophysics Data System (ADS)

Manojlović, Stojadin M.; Barbarić, Žarko P.; Mitrović, Srđan T.

2015-06-01

A new tracking design for laser systems with different arrangements of a quadrant photodetector, based on the principle of active disturbance rejection control is suggested. The detailed models of quadrant photodetector with standard add-subtract, difference-over-sum and diagonal-difference-over-sum algorithms for displacement signals are included in the control loop. Target moving, non-linearity of a photodetector, parameter perturbations and exterior disturbances are treated as a total disturbance. Active disturbance rejection controllers with linear extended state observers for total disturbance estimation and rejection are designed. Proposed methods are analysed in frequency domain to quantify their stability characteristics and disturbance rejection performances. It is shown through simulations, that tracking errors are effectively compensated, providing the laser spot positioning in the area near the centre of quadrant photodetector where the mentioned algorithms have the highest sensitivity, which provides tracking of the manoeuvring targets with high accuracy.

Dermatoglyphic features in Prader-Willi syndrome with respect to chromosomal findings

PubMed Central

Reed, Terry; Butler, Merlin G.

2017-01-01

Dermatoglyphic findings were compared in 38 Prader-Willi syndrome (PWS) patients and 270 normal controls. Twenty-one of the PWS patients had an interstitial deletion of the proximal long arm of chromosome 15 and seventeen PWS cases had normal chromosomes. Findings in PWS are not diagnostic but do show some consistent deviations that can be used in the clinical evaluation of PWS patients. These include a displacement of the axial triradius away from the normal proximal position, an excess of whorls primarily on the thumbs, radial termination of the palmar A mainline, and lack of arches on the big toe. Deletion PWS patients were much more homogeneous than non-deletion cases with respect to plantar patterns. The previously reported deficit of plantar pattern intensity was restricted only to deletion PWS and was characterized by a lack of plantar interdigital II–IV patterns with almost exclusively hallucal distal loops. PMID:6713710

Experimental investigation of leaky lamb modes by an optically induced grating.

PubMed

Van de Rostyne, Kris; Glorieux, Christ; Gao, Weimin; Lauriks, Walter; Thoen, Jan

2002-09-01

By removing the symmetry of a free plate configuration, fluid loading significantly modifies the nature of acoustic waves travelling along a plate, and it even gives existence to new acoustic modes. We present theoretical predictions for the existence, dispersive behavior, and spatial distribution of leaky Lamb waves in a fluid-loaded film. Although Lamb modes are often investigated by studying the radiated fluid waves resulting from their leakage, here their properties are assessed by detecting the wave displacements directly using laser beam deflection. By using crossed laser beam excitation, the detection and analysis of the different modes is done at a fixed wavelength, allowing one to verify the existence, the velocity, and the damping of each predicted mode in a simple and unambiguous way. Our theoretical predictions for the nature of the modes in a water-loaded Plexiglas film, including parts of looping modes, are experimentally confirmed.

Binding constants of phenylalanine for the four mononucleotides

NASA Technical Reports Server (NTRS)

Khaled, M. A.; Mullins, D. W., Jr.; Lacey, J. C., Jr.

1984-01-01

Earlier work has shown that several properties of amino acids correlate directly with properties of their anticodonic nucleotides. Furthermore, in precipitation studies with thermal proteinoids and homopolyribonucleotides, an anticodonic preference was displayed between Lys-rich, Pro-rich and Gly-rich thermal proteinoids and their anticodonic polyribonucleotides. However, Phe-rich thermal proteinoid displayed a preference for its codonic nucleotide, poly U. This inconsistency seemed to be explained by a folding in of the hydrophobic residues of Phe causing the proteinoid to appear more hydrophilic. The present work used nuclear magnetic resonance techniques to resolve a limited question: to which of the four nucleotides does Phe bind most strongly? The results show quite clearly that Phe binds most strongly to its anticodonic nucleotide, AMP.

Hydrogen bonding in the neutron structure of the mononucleotide 5'-UMP disodium salt

NASA Astrophysics Data System (ADS)

Chitra, R.; Ranjan-Choudhury, R.; Ramanadham, M.

Disodium uridine 5'-monophosphate heptahydrate (5'-UMPNa2), Na2[C9H11N2O9P].7H2O, crystallises in space group C2221 with a=22.985, b=8.911 and c=19.494Å. A neutron beam of λ=1.216Å was used; Z=8 and V=3992.75Å3. Data consisted of 1785 unique reflections. Na ions were connected to the main molecule through water molecules and sugar oxygens. One of the Na ions occupied a special position, and the other at a general position was partially disordered. The uracil base was planar, and had anti conformation about the glycosidic bond. The sugar had C(2') endo conformation and was gauche-gauche.

5-kWe Free-piston Stirling Engine Convertor

NASA Technical Reports Server (NTRS)

Chapman, Peter A.; Vitale, Nicholas A.; Walter, Thomas J.

2008-01-01

The high reliability, long life, and efficient operation of Free-Piston Stirling Engines (FPSEs) make them an attractive power system to meet future space power requirements with less mass, better efficiency, and less total heat exchanger area than other power convertor options. FPSEs are also flexible in configuration as they can be coupled with many potential heat sources and various heat input systems, heat rejection systems, and power management and distribution systems. Development of a 5-kWe Stirling Convertor Assembly (SCA) is underway to demonstrate the viability of an FPSE for space power. The design is a scaled-down version of the successful 12.5-kWe Component Test Power Converter (CTPC) developed under NAS3-25463. The ultimate efficiency target is 25% overall convertor efficiency (electrical power out over heat in). For the single cylinder prototype now in development, cost and time constraints required use of economical and readily available materials (steel versus beryllium) and components (a commercially available linear alternator) and thus lower efficiency. The working gas is helium at 150 bar mean pressure. The design consists of a displacer suspended on internally pumped gas bearings and a power piston/alternator supported on flexures. Non-contacting clearance seals are used between internal volumes. Heat to and from the prototype convertor is done via pumped liquid loops passing through shell and tube heat exchangers. The preliminary and detail designs of the convertor, controller, and support systems (heating loop, cooling loop, and helium supply system) are complete and all hardware is on order. Assembly and test of the prototype at Foster- Miller is planned for early 2008, when work will focus on characterizing convertor dynamics and steady-state operation to determine maximum power output and system efficiency. The device will then be delivered to Auburn University where assessments will include start-up and shutdown characterization and transient response to temperature and load variations. Future activities may include testing at NASA GRC.

A tiny event producing an interplanetary type III burst

NASA Astrophysics Data System (ADS)

Alissandrakis, C. E.; Nindos, A.; Patsourakos, S.; Kontogeorgos, A.; Tsitsipis, P.

2015-10-01

Aims: We investigate the conditions under which small-scale energy release events in the low corona gave rise to strong interplanetary (IP) type III bursts. Methods: We analyzed observations of three tiny events, detected by the Nançay Radio Heliograph (NRH), two of which produced IP type III bursts. We took advantage of the NRH positioning information and of the high cadence of AIA/SDO data to identify the associated extreme-UV (EUV) emissions. We measured positions and time profiles of the metric and EUV sources. Results: We found that the EUV events that produced IP type III bursts were located near a coronal hole boundary, while the one that did not was located in a closed magnetic field region. In all three cases tiny flaring loops were involved, without any associated mass eruption. In the best observed case, the radio emission at the highest frequency (435 MHz) was displaced by ~55'' with respect to the small flaring loop. The metric type III emission shows a complex structure in space and in time, indicative of multiple electron beams, despite the low intensity of the events. From the combined analysis of dynamic spectra and NRH images, we derived the electron beam velocity as well as the height, ambient plasma temperature, and density at the level of formation of the 160 MHz emission. From the analysis of the differential emission measure derived from the AIA images, we found that the first evidence of energy release was at the footpoints, and this was followed by the development of flaring loops and subsequent cooling. Conclusions: Even small energy release events can accelerate enough electrons to give rise to powerful IP type III bursts. The proximity of the electron acceleration site to open magnetic field lines facilitates the escape of the electrons into the interplanetary space. The offset between the site of energy release and the metric type III location warrants further investigation. The movie is available in electronic form at http://www.aanda.org

Crystal Structure of the Pseudomonas aeruginosa BEL-1 Extended-Spectrum β-Lactamase and Its Complexes with Moxalactam and Imipenem.

PubMed

Pozzi, Cecilia; De Luca, Filomena; Benvenuti, Manuela; Poirel, Laurent; Nordmann, Patrice; Rossolini, Gian Maria; Mangani, Stefano; Docquier, Jean-Denis

2016-12-01

BEL-1 is an acquired class A extended-spectrum β-lactamase (ESBL) found in Pseudomonas aeruginosa clinical isolates from Belgium which is divergent from other ESBLs (maximum identity of 54% with GES-type enzymes). This enzyme is efficiently inhibited by clavulanate, imipenem, and moxalactam. Crystals of BEL-1 were obtained at pH 5.6, and the structure of native BEL-1 was determined from orthorhombic and monoclinic crystal forms at 1.60-Å and 1.48-Å resolution, respectively. By soaking native BEL-1 crystals, complexes with imipenem (monoclinic form, 1.79-Å resolution) and moxalactam (orthorhombic form, 1.85-Å resolution) were also obtained. In the acyl-enzyme complexes, imipenem and moxalactam differ by the position of the α-substituent and of the carbonyl oxygen (in or out of the oxyanion hole). More surprisingly, the Ω-loop, which includes the catalytically relevant residue Glu166, was found in different conformations in the various subunits, resulting in the Glu166 side chain being rotated out of the active site or even in displacement of its Cα atom up to approximately 10 Å. A BEL-1 variant showing the single Leu162Phe substitution (BEL-2) confers a higher level of resistance to CAZ, CTX, and FEP and shows significantly lower K m values than BEL-1, especially with oxyiminocephalosporins. BEL-1 Leu162 is located at the beginning of the Ω-loop and is surrounded by Phe72, Leu139, and Leu148 (contact distances, 3.5 to 3.9 Å). This small hydrophobic cavity could not reasonably accommodate the bulkier Phe162 found in BEL-2 without altering neighboring residues or the Ω-loop itself, thus likely causing an important alteration of the enzyme kinetic properties. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Biomechanical evaluation of different suture techniques for arthroscopic transtibial pull-out repair of posterior medial meniscus root tears.

PubMed

Feucht, Matthias J; Grande, Eduardo; Brunhuber, Johannes; Burgkart, Rainer; Imhoff, Andreas B; Braun, Sepp

2013-12-01

A tear of the posterior medial meniscus root (PMMR) is increasingly recognized as a serious knee joint injury. Several suture techniques for arthroscopic transtibial pull-out repair have been described; however, only limited data about the biomechanical properties of these techniques are currently available. There are significant differences between the tested suture techniques, with more complex suture configurations providing superior biomechanical properties. Controlled laboratory study. A total of 40 porcine medial menisci were randomly assigned to 1 of 4 groups (10 specimens each) according to suture technique: two simple stitches (TSS), horizontal mattress suture (HMS), modified Mason-Allen suture (MMA), and two modified loop stitches (TLS). Meniscus-suture constructs were subjected to cyclic loading followed by load-to-failure testing in a servohydraulic material testing machine. During cyclic loading, the HMS and TLS groups showed a significantly higher displacement after 100, 500, and 1000 cycles compared with the TSS and MMA groups. After 1000 cycles, the highest displacement was found for the TLS group, with significant differences compared with all other groups. During load-to-failure testing, the highest maximum load and yield load were observed for the MMA group, with statistically significant differences compared with the TSS and TLS groups. With regard to stiffness, the TSS and MMA groups showed significantly higher values compared with the HMS and TLS groups. The MMA technique provided the best biomechanical properties with regard to cyclic loading and load-to-failure testing. The TSS technique seems to be a valuable alternative. Both the HMS and TLS techniques have the disadvantage of lower stiffness and higher displacement during cyclic loading. Using a MMA technique may improve healing rates and avoid progressive extrusion of the medial meniscus after transtibial pull-out repair of PMMR tears. The TSS technique may be used as an alternative that is easier to perform, but a more careful rehabilitation program is possibly necessary to avoid early failure.

Large Stroke High Fidelity PZN-PT Single-Crystal "Stake" Actuator.

PubMed

Huang, Yu; Xia, Yuexue; Lin, Dian Hua; Yao, Kui; Lim, Leong Chew

2017-10-01

A new piezoelectric actuator design, called "Stake" actuator, is proposed and demonstrated in this paper. As an example, the stake actuator is made of four d 32 -mode PZN-5.5%PT single crystals (SCs), each of 25 mm ( L ) ×8 mm ( W ) ×0.4 mm (T) in dimensions, bonded with the aid of polycarbonate edge guide-cum-stiffeners into a square-pipe configuration for improved bending and twisting strengths and capped with top and bottom pedestals made of 1.5-mm-thick anodized aluminum. The resultant stake actuator measured 9 mm ×9 mm ×28 mm. The hollow structure is a key design feature, which optimizes SC usage efficiency and lowers the overall cost of the actuator. The displacement-voltage responses, blocking forces, resonance characteristics of the fabricated stake actuator, as well as the load and temperature effects, are measured and discussed. Since d 32 is negative for [011]-poled SC, the "Stake" actuator contracts in the axial direction when a positive-polarity field is applied to the crystals. Biased drive is thus recommended when extensional displacement is desired. The SC stake actuator has negligible (<1%) hysteresis and a large linear strain range of >0.13% when driven up to +300 V (i.e., 0.75 kV/mm), which is close to the rhombohedral-to-orthorhombic transformation field ( E RO ) of 0.85 kV/mm of the SC used. The stake actuator displays a stroke of [Formula: see text] (at +300 V) despite its small overall dimensions, and has a blocking force of 114 N. The SC d 32 stake actuator fabricated displays more than 30% larger axial strain than the state-of-the-art PZT stack actuators of comparable length as well as moderate blocking forces. Said actuators are thus ideal for applications when large displacements with simple open-loop control are preferred.

Mountain-Top-to-Mountain-Top Optical Link Demonstration. Part 2

NASA Technical Reports Server (NTRS)

Biswas, A.; Wright, M. W.

2002-01-01

A mountain-top-to-mountain-top optical communications demonstration was conducted between the JPL Table Mountain Facility (TMF), Wrightwood, California, and Strawberry Peak (SP), Lake Arrowhead, California, during the months of August and September of 2000. The link was nearly horizontal at an altitude of 2 km and spanned a range of 46.8 km. A 780-nm multibeam beacon broadcast from TMF was received by the JPL Optical Communications Demonstrator (OCD) located at SP. The received beacon was utilized as a pointing reference to retransmit an 852-nm communications laser beam, modulated at 400 Mb/s by a PN7 pseudo-random bit stream (PRBS) sequence. The long atmospheric path resulted in atmospheric-turbulence-induced angle-of-arrival fluctuations of the beacon at the OCD aperture. A .ne-steering control loop was used to track the resulting beacon centroid motion and update the pointing of the communications laser beam transmitted from SP to TMF. Fried parameters, or r0, inferred from focal spot sizes received at SP were 4 to 5 cm whereas, using the spot sizes received at TMF, they were 2 to 3 cm. In both cases, theory predicts larger r0 values. The predicted angle-of-arrival fluctuations compare well with measured rms displacements exhibited by the focal spots at either end of the link. An uncompensated error of 1.1 rad in the x-axis and 2 rad in the y-axis was obtained using centroid data logged by the OCD. Average bit-error rates of 10-5 were recorded for extended periods of time. An atmospheric coherence length r0 of 3 to 5 cm was inferred using the focal-plane spot size measured on the CCD tracking sensor and compared to a predicted value of 5 to 7 cm using reasonable atmospheric models. The irradiance bounds required for the CCD tracking sensor to perform centroiding was found to range from 2000 to 3000 integrated pixel counts, although a more reliable range was 600 to 3000, indicating a dynamic range of 6 to 11 dB. The motion of the spot on the focal plane was also recorded and yielded rms angle-of-arrival-induced focal-plane displacement of 9 to 11 m, compared to a predicted value of 7.8 to 11 m. The irradiance measurements made with the OCD clearly indicate that best tracking performance is obtained when the mean received signal is 2000 to 2200 counts. The best tracking performance resulted in an rms uncompensated error of 1.1 rad. The uncompensated error appeared to increase with either an increase or decrease in mean beacon-signal level. The rms uncompensated error determined by deriving the beacon displacement power spectral density from the beacon centroid-versustime data and the rejection function of the control loop yielded a higher value of 3.4 rad.

Structures of rat cytosolic PEPCK: insight into the mechanism of phosphorylation and decarboxylation of oxaloacetic acid.

PubMed

Sullivan, Sarah M; Holyoak, Todd

2007-09-04

The structures of the rat cytosolic isoform of phosphoenolpyruvate carboxykinase (PEPCK) reported in the PEPCK-Mn2+, -Mn2+-oxaloacetic acid (OAA), -Mn2+-OAA-Mn2+-guanosine-5'-diphosphate (GDP), and -Mn2+-Mn2+-guanosine-5'-tri-phosphate (GTP) complexes provide insight into the mechanism of phosphoryl transfer and decarboxylation mediated by this enzyme. OAA is observed to bind in a number of different orientations coordinating directly to the active site metal. The Mn2+-OAA and Mn2+-OAA-Mn2+GDP structures illustrate inner-sphere coordination of OAA to the manganese ion through the displacement of two of the three water molecules coordinated to the metal in the holo-enzyme by the C3 and C4 carbonyl oxygens. In the PEPCK-Mn2+-OAA complex, an alternate bound conformation of OAA is present. In this conformation, in addition to the previous interactions, the C1 carboxylate is directly coordinated to the active site Mn2+, displacing all of the waters coordinated to the metal in the holo-enzyme. In the PEPCK-Mn2+-GTP structure, the same water molecule displaced by the C1 carboxylate of OAA is displaced by one of the gamma-phosphate oxygens of the triphosphate nucleotide. The structures are consistent with a mechanism of direct in-line phosphoryl transfer, supported by the observed stereochemistry of the reaction. In the catalytically competent binding mode, the C1 carboxylate of OAA is sandwiched between R87 and R405 in an environment that would serve to facilitate decarboxylation. In the reverse reaction, these two arginines would form the CO2 binding site. Comparison of the Mn2+-OAA-Mn2+GDP and Mn2+-Mn2+GTP structures illustrates a marked difference in the bound conformations of the nucleotide substrates in which the GTP nucleotide is bound in a high-energy state resulting from the eclipsing of all three of the phosphoryl groups along the triphosphate chain. This contrasts a previously determined structure of PEPCK in complex with a triphosphate nucleotide analogue in which the analogue mirrors the conformation of GDP as opposed to GTP. Last, the structures illustrate a correlation between conformational changes in the P-loop, the nucleotide binding site, and the active site lid that are important for catalysis.

Mitochondrial DNA evolution in mice.

PubMed

Ferris, S D; Sage, R D; Prager, E M; Ritte, U; Wilson, A C

1983-11-01

This study extends knowledge of mitochondrial DNA (mtDNA) diversity in mice to include 208 animals belonging to eight species in the subgenus Mus. Highly purified mtDNA from each has been subjected to high-resolution restriction mapping with respect to the known sequence of one mouse mtDNA. Variation attributed to base substitutions was encountered at about 200 of the 300 cleavage sites examined, and a length mutation was located in or near the displacement loop. The variability of different functional regions in this genome was as follows, from least to most: ribosomal RNA, transfer RNA, known proteins, displacement loop and unidentified reading frames. --Phylogenetic analysis confirmed the utility of the Sage and Marshall revision of mouse classification, according to which there are at least four species of commensal mice and three species of aboriginal mice in the complex that was formerly considered to be one species. The most thoroughly studied of these species is Mus domesticus, the house mouse of Western Europe and the Mediterranean region, which is the mitochondrial source of all 50 of the laboratory strains examined and of the representatives of wild house mice introduced by Europeans to North and South America during the past few hundred years. --The level of mtDNA variation among wild representatives of M. domesticus is similar to that for the Eastern European house mouse (M. musculus) and several other mammalian species. By contrast, among the many laboratory strains that are known or suspected to stem from the pet mouse trade, there is little interstrain variation, most strains having the "old inbred" type of domesticus mtDNA, whose frequency in the 145 wild mice examined is low, about 0.04. Also notable is the apparent homogeneity of mtDNA in domesticus races that have fixed six or more fused chromosomes and the close relationship of some of these mtDNAs to those of karyotypically normal mice. --In addition, this paper discusses fossil and other evidence for the view that in mice, as in many other mammals, the average rate of point mutational divergence in mtDNA is 2-4% per million years. From this, it is estimated that the commensal association between mice and our ancestors began more than a million years ago, i.e., at an early stage in the evolution of Homo erectus.

Mitochondrial DNA Evolution in Mice

PubMed Central

Ferris, Stephen D.; Sage, Richard D.; Prager, Ellen M.; Ritte, Uzi; Wilson, Allan C.

1983-01-01

This study extends knowledge of mitochondrial DNA (mtDNA) diversity in mice to include 208 animals belonging to eight species in the subgenus Mus. Highly purified mtDNA from each has been subjected to high-resolution restriction mapping with respect to the known sequence of one mouse mtDNA. Variation attributed to base substitutions was encountered at about 200 of the 300 cleavage sites examined, and a length mutation was located in or near the displacement loop. The variability of different functional regions in this genome was as follows, from least to most: ribosomal RNA, transfer RNA, known proteins, displacement loop and unidentified reading frames.—Phylogenetic analysis confirmed the utility of the Sage and Marshall revision of mouse classification, according to which there are at least four species of commensal mice and three species of aboriginal mice in the complex that was formerly considered to be one species. The most thoroughly studied of these species is Mus domesticus, the house mouse of Western Europe and the Mediterranean region, which is the mitochondrial source of all 50 of the laboratory strains examined and of the representatives of wild house mice introduced by Europeans to North and South America during the past few hundred years.—The level of mtDNA variation among wild representatives of (M. musculus) and several other mammalian species. By contrast, among the many laboratory strains that are known or suspected to stem from the pet mouse trade, there is little interstrain variation, most strains having the "old inbred" type of domesticus mtDNA, whose frequency in the 145 wild mice examined is low, about 0.04. Also notable is the apparent homogeneity of mtDNA in domesticus races that have fixed six or more fused chromosomes and the close relationship of some of these mtDNAs to those of karyotypically normal mice.—In addition, this paper discusses fossil and other evidence for the view that in mice, as in many other mammals, the average rate of point mutational divergence in mtDNA is 2–4% per million years. From this, it is estimated that the commensal association between mice and our ancestors began more than a million years ago, i.e., at an early stage in the evolution of Homo erectus. PMID:6315529

A right-handed signalling pathway drives heart looping in vertebrates

PubMed Central

Ocaña, Oscar H.; Coskun, Hakan; Minguillón, Carolina; Murawala, Prayag; Tanaka, Elly M.; Galcerán, Joan; Muñoz-Chapuli, Ramón; Nieto, M. Angela

2017-01-01

The majority of animals show external bilateral symmetry, precluding the observation of multiple internal left-right (L/R) asymmetries that are fundamental for organ packaging and function1,2. In vertebrates, left identity is mediated by the left-specific Nodal-Pitx2 axis that is repressed on the right-hand side by the epithelial-mesenchymal transition (EMT) inducer Snail13,4. Despite some existing evidence3,5, it remains unclear whether an equivalent instructive pathway provides right-hand specific information to the embryo. Here we show that in zebrafish, BMP mediates the L/R asymmetric activation of another EMT inducer, Prrx1a, in the lateral plate mesoderm (LPM) with higher levels on the right. Prrx1a drives L/R differential cell movements towards the midline leading to a leftward displacement of the cardiac posterior pole through an actomyosin-dependent mechanism. Downregulation of Prrx1a prevents heart looping and leads to mesocardia. Two parallel and mutually repressed pathways, respectively driven by Nodal and BMP on the left and right LPM, converge on the asymmetric activation of Pitx2 and Prrx1, two transcription factors that integrate left and right information to govern heart morphogenesis. This mechanism is conserved in the chicken embryo and, in the mouse, Snail1 fulfills the role played by Prrx1 in fish and chick. Thus, a differential L/R EMT produces asymmetric cell movements and forces, more prominent from the right, that drive heart laterality in vertebrates. PMID:28880281

Measurement of dynamic magnetization induced by a pulsed field: Proposal for a new rock magnetism method

NASA Astrophysics Data System (ADS)

Kodama, Kazuto

2015-02-01

This study proposes a new method for measuring transient magnetization of natural samples induced by a pulsed field with duration of 11 ms using a pulse magnetizer. An experimental system was constructed, consisting of a pair of differential sensing coils connected with a high-speed digital oscilloscope for data acquisition. The data were transferred to a computer to obtain an initial magnetization curve and a descending branch of a hysteresis loop in a rapidly changing positive field. This system was tested with synthetic samples (permalloy ribbon, aluminum plate, and nickel powder) as well as two volcanic rock samples. Results from the synthetic samples showed considerable differences from those measured by a quasi-static method using a vibrating sample magnetometer (VSM). These differences were principally due to the time-dependent magnetic properties or to electromagnetic effects, such as magnetic viscosity, eddy current loss, or magnetic relaxation. Results from the natural samples showed that the transient magnetization-field curves were largely comparable to the corresponding portions of the hysteresis loops. However, the relative magnetization (scaled to the saturation magnetization) at the end of a pulse was greater than that measured by a VSM. This discrepancy, together with the occurrence of rapid exponential decay after a pulse, indicates magnetic relaxations that could be interpreted in terms of domain wall displacement. These results suggest that with further developments, the proposed technique can become a useful tool for characterizing magnetic particles contained in a variety of natural materials.

Influence of laser surface treated on the characterization and corrosion behavior of Al-Fe aerospace alloys

NASA Astrophysics Data System (ADS)

Pariona, Moisés Meza; Teleginski, Viviane; dos Santos, Kelly; de Lima, Angela A. O. C.; Zara, Alfredo J.; Micene, Katieli Tives; Riva, Rudimar

2013-07-01

In this research laser surface remelting without protective coating with a 2 kW Yb-fiber laser (IPG YLR-2000S) was applied in the Al-1.5 wt.%Fe alloy in order to investigate the layer treated with different techniques of superficial characterization, thereby, the technique of optical microscopy, atomic force microscopy and low-angle X-ray diffraction were used. The present work mainly focuses on the corrosion study by diverse techniques in aggressive environment of the laser-treated area and the substrate material was carried out, thereby, at open circuit potential testing, the results have shown a displacement to more anodic values in the corrosion potential for the laser-treated specimen when compared to the untreated specimen; in potentiodynamic polarization tests have shown that as a result of the laser treatment, the corrosion current can be reduced by as much as ten times, and a passive region was obtained, which served as an effective barrier for reducing anodic dissolution and finally, the result in cyclic polarization curves of the untreated sample there was a greater area of the hysteresis loop, implying that it is more susceptible to corrosion. This study was complemented by other techniques mentioned above in order to elucidate this study. Laser surface remelting process has definitely modified the surface film, which results in higher corrosion resistance, a large range of passivation and a lower area of the hysteresis loop.

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

Broome, S. T.; Bauer, S. J.; Hansen, F. D.

Design, analysis and performance assessment of potential salt repositories for heat-generating nuclear waste require knowledge of thermal, mechanical, and fluid transport properties of reconsolidating granular salt. So, to inform salt repository evaluations, we have undertaken an experimental program to determine Bulk and Young’s moduli and Poisson’s ratio of reconsolidated granular salt as a function of porosity and temperature and to establish the deformational processes by which the salt reconsolidates. Our tests were conducted at 100, 175, and 250 °C. In hydrostatic tests, confining pressure is increased to 20 MPa with periodic unload/reload loops to determine K. Volume strain increases withmore » increasing temperature. In shear tests at 2.5 and 5 MPa confining pressure, after confining pressure is applied, the crushed salt is subjected to a differential stress, with periodic unload/reload loops to determine E and ν. At predetermined differential stress levels the stress is held constant and the salt consolidates. Displacement gages mounted on the samples show little lateral deformation until the samples reach a porosity of ~10 %. Interestingly, vapor is vented only for 250 °C tests and condenses at the vent port. It is hypothesized that the brine originates from fluid inclusions, which were made accessible by heating and intragranular deformational processes including decrepitation. Furthermore, identification and documentation of consolidation processes are inferred from optical and scanning electron microstructural observations. As a result, densification at low porosity is enhanced by water film on grain boundaries that enables solution-precipitation phenomena.« less

Test Methodology Development for Experimental Structural Assessment of ASC Planar Spring Material for Long-Term Durability

NASA Technical Reports Server (NTRS)

Yun, Gunjin; Abdullah, A. B. M.; Binienda, Wieslaw; Krause, David L.; Kalluri, Sreeramesh

2014-01-01

A vibration-based testing methodology has been developed that will assess fatigue behavior of the metallic material of construction for the Advanced Stirling Convertor displacer (planar) spring component. To minimize the testing duration, the test setup is designed for base-excitation of a multiplespecimen arrangement, driven in a high-frequency resonant mode; this allows completion of fatigue testing in an accelerated period. A high performance electro-dynamic exciter (shaker) is used to generate harmonic oscillation of cantilever beam specimens, which are clasped on the shaker armature with specially-designed clamp fixtures. The shaker operates in closed-loop control with dynamic specimen response feedback provided by a scanning laser vibrometer. A test coordinator function synchronizes the shaker controller and the laser vibrometer to complete the closed-loop scheme. The test coordinator also monitors structural health of the test specimens throughout the test period, recognizing any change in specimen dynamic behavior. As this may be due to fatigue crack initiation, the test coordinator terminates test progression and then acquires test data in an orderly manner. Design of the specimen and fixture geometry was completed by finite element analysis such that peak stress does not occur at the clamping fixture attachment points. Experimental stress evaluation was conducted to verify the specimen stress predictions. A successful application of the experimental methodology was demonstrated by validation tests with carbon steel specimens subjected to fully-reversed bending stress; high-cycle fatigue failures were induced in such specimens using higher-than-prototypical stresses

Model identification of terfenol-D magnetostrictive actuator for precise positioning control

NASA Astrophysics Data System (ADS)

Saleem, Ashraf; Ghodsi, Mojtaba; Mesbah, Mostefa; Ozer, Abdullah

2016-04-01

Feedback control strategies are desirable for disturbance rejection of human-induced vibrations in civil engineering structures as human walking forces cannot easily be measured. In relation to human-induced vibration control studies, most past researches have focused on floors and footbridges and the widely used linear controller implemented in the trials has been the direct velocity feedback (DVF) scheme. With appropriate compensation to enhance its robustness, it has been shown to be effective at damping out the problematic modes of vibration of the structures in which the active vibration control systems have been implemented. The work presented here introduces a disturbance observer (DOB) that is used with an outer-loop DVF controller. Results of analytical studies presented in this work based on the dynamic properties of a walkway bridge structure demonstrate the potential of this approach for enhancing the vibration mitigation performance offered by a purely DVF controller. For example, estimates of controlled frequency response functions indicate improved attenuation of vibration around the dominant frequency of the walkway bridge structure as well as at higher resonant frequencies. Controlled responses from three synthesized walking excitation forces on a walkway bridge structure model show that the inclusion of the disturbance observer with an outer loop DVF has potential to improve on the vibration mitigation performance by about 3.5% at resonance and 6-10% off-resonance. These are realised with hard constraints being imposed on the low frequency actuator displacements.

Incorporating a disturbance observer with direct velocity feedback for control of human-induced vibrations

NASA Astrophysics Data System (ADS)

Nyawako, Donald; Reynolds, Paul; Hudson, Emma

2016-04-01

Feedback control strategies are desirable for disturbance rejection of human-induced vibrations in civil engineering structures as human walking forces cannot easily be measured. In relation to human-induced vibration control studies, most past researches have focused on floors and footbridges and the widely used linear controller implemented in the trials has been the direct velocity feedback (DVF) scheme. With appropriate compensation to enhance its robustness, it has been shown to be effective at damping out the problematic modes of vibration of the structures in which the active vibration control systems have been implemented. The work presented here introduces a disturbance observer (DOB) that is used with an outer-loop DVF controller. Results of analytical studies presented in this work based on the dynamic properties of a walkway bridge structure demonstrate the potential of this approach for enhancing the vibration mitigation performance offered by a purely DVF controller. For example, estimates of controlled frequency response functions indicate improved attenuation of vibration around the dominant frequency of the walkway bridge structure as well as at higher resonant frequencies. Controlled responses from three synthesized walking excitation forces on a walkway bridge structure model show that the inclusion of the disturbance observer with an outer loop DVF has potential to improve on the vibration mitigation performance by about 3.5% at resonance and 6-10% off-resonance. These are realised with hard constraints being imposed on the low frequency actuator displacements.

Ion channeling study of defects in compound crystals using Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Turos, A.; Jozwik, P.; Nowicki, L.; Sathish, N.

2014-08-01

Ion channeling is a well-established technique for determination of structural properties of crystalline materials. Defect depth profiles have been usually determined basing on the two-beam model developed by Bøgh (1968) [1]. As long as the main research interest was focused on single element crystals it was considered as sufficiently accurate. New challenge emerged with growing technological importance of compound single crystals and epitaxial heterostructures. Overlap of partial spectra due to different sublattices and formation of complicated defect structures makes the two beam method hardly applicable. The solution is provided by Monte Carlo computer simulations. Our paper reviews principal aspects of this approach and the recent developments in the McChasy simulation code. The latter made it possible to distinguish between randomly displaced atoms (RDA) and extended defects (dislocations, loops, etc.). Hence, complex defect structures can be characterized by the relative content of these two components. The next refinement of the code consists of detailed parameterization of dislocations and dislocation loops. Defect profiles for variety of compound crystals (GaN, ZnO, SrTiO3) have been measured and evaluated using the McChasy code. Damage accumulation curves for RDA and extended defects revealed non monotonous defect buildup with some characteristic steps. Transition to each stage is governed by the different driving force. As shown by the complementary high resolution XRD measurements lattice strain plays here the crucial role and can be correlated with the concentration of extended defects.

Mitochondrial DNA analyses revealed low genetic diversity in the endangered Indian wild ass Equus hemionus khur.

PubMed

Khaire, Devendra; Atkulwar, Ashwin; Farah, Sameera; Baig, Mumtaz

2017-09-01

The Indian wild ass Equus hemionus khur, belonging to ass-like equid branch, inhabits the dry and arid desert of the Little Rann of Kutch, Gujarat. The E. h. khur is the sole survivor of Asiatic wild ass species/subspecies in South Asia. To provide first ever insights into the genetic diversity, phylogeny, and demography of the endangered Indian wild ass, we sampled 52 free-ranging individuals from the Little Rann of Kutch by using a non-invasive methodology. The sequencing of 230 bp in cytochrome b (Cyt b) and displacement loop (D-loop) region revealed that current ∼4000 extant population of Indian wild ass harbours low genetic diversity. Phylogenetic analyses confirmed that E. h. khur, E. h. onager, and E. h. kulan belong to a single strict monophyletic clade. Therefore, we suggest the delimitation of the five E. hemionus subspecies in vogue to a single species E. hemionus. The application of molecular clock confirmed that the Asiatic wild ass had undergone diversification 0.65 Million years ago. Demographic measurements assessed using a Bayesian skyline plot demonstrated decline in the maternal effective population size of the Indian wild ass during different periods; these periods coincided with the origin and rise of the Indus civilization in the northwest of the Indian subcontinent during the Neolithic. In conclusion, maintaining high genetic diversity in the existing isolated population of 4000 Indian wild asses inhabiting the wild ass sanctuary is important compared with subspecies preservation alone.

Laparoscopic Band-Separated One Anastomosis Gastric Bypass.

PubMed

Ospanov, Oral B

2016-09-01

This video demonstrates laparoscopic band-separated one anastomosis gastric bypass-combining the advantages of banding and gastric bypass without stapler and cutter use. This is basically a gastrojejunal loop bypass above an obstructive band in the upper stomach. An adjustable low pressure "Medsil" gastric band was introduced in the abdomen and retracted through the retrogastric tunnel. The front wall of the stomach below the band was displaced in the upward direction through the ring band, increasing the size of the anterior portion of the stomach pouch so that a gastroenteroanastomosis could be created at this point. Gastro-gastric sutures were placed to create a gastro-gastric plication around the band and hold it in position. The band tubing was exteriorized and connected to a special port, which was secured to the abdominal wall fascia. A jejunal loop was created about 200 cm from the ligament of Treitz and anastomosed to the gastric pouch by hand using Vicryl 2/0 sutures. Between November 2015 and February 2016, the study was performed on 10 patients. The average operating time for all cases was 75 min (range 63-87). There was no morbidity or mortality. No complications were observed, including band erosion and band infection. Operation costs were about $2000 lower with this method than with standard gastric bypass surgery. Postop the patients lost weight by 3-4 kg per month. Preliminary results show that laparoscopic band-separated one anastomosis gastric bypass have feasibility, safety, efficacy, and reduced operating costs.

Step-wise addition of disulfide bridge in firefly luciferase controls color shift through a flexible loop: a thermodynamic perspective.

PubMed

Nazari, Mahboobeh; Hosseinkhani, Saman; Hassani, Leila

2013-02-01

Multi-color bioluminescence is developed using the introduction of single/double disulfide bridges in firefly luciferase. The bioluminescence reaction, which uses luciferin, Mg(2+)-ATP and molecular oxygen to yield an electronically excited oxyluciferin, is carried out by the luciferase and emits visible light. The bioluminescence color of firefly luciferases is determined by the luciferase sequence and assay conditions. It has been proposed that the stability of a protein may increase through the introduction of a disulfide bridge that decreases the configurational entropy of unfolding. Single and double disulfide bridges are introduced into Photinus pyralis firefly luciferase to make separate mutant enzymes with a single/double bridge (C(81)-A(105)C, L(306)C-L(309)C, P(451)C-V(469)C; C(81)-A(105)C/P(451)C-V(469)C, and A(296)C-A(326)C/P(451)C-V(469)C). By introduction of disulfide bridges using site-directed mutagenesis in Photinus pyralis luciferase the color of emitted light was changed to red or kept in different extents. The bioluminescence color shift occurred with displacement of a critical loop in the luciferase structure without any change in green emitter mutants. Thermodynamic analysis revealed that among mutants, L(306)C-L(309)C shows a remarkable stability against urea denaturation and also a considerable increase in kinetic stability and a clear shift in bioluminescence spectra towards red.

Commande en boucle fermee sur un profil d'aile deformable dans la soufflerie Price-Paidoussis

NASA Astrophysics Data System (ADS)

Brossard, Jeremy

The purpose of the ATR-42 project is to apply the concept of morphing wings by fabricating a morphing composite wing model of the Regional Transport Aircraft-42 to reduce drag and improve the aerodynamic performance. A control-command system coupled to an actuator mechanism will morph the wing skin. However, for best results, the control of the deformation must be studied carefully to insure the precision. Thus, a dual digitalexperimental approach is required. The solution proposed in this paper focuses on the controlled deformation of the upper wing of the ATR-42. A composite wing model with morphing capabilities was built and tested in the wind tunnel to evaluate its aerodynamic performance and serve as reference. A deformation mechanism, consisting of two engines and two camshafts, was subsequently designed and integrated within this model to obtain the optimum wing shapes according to the different flight condition. A control loop position was modeled in Matlab / Simulink and implemented experimentally to control the mechanism. Two types of results have been obtained. The first set concerned regulation and the second concerned aerodynamics. The control loop has achieved the desired skin displacement with an accuracy of 5%. Deformations of the upper skin were performed by a actuation system driven by motors, limitations supply were assured by the regulation architecture. For several flight conditions, the pressure measurements, validated with simulation results, have confirmed a reduction of the induced drag, compared to the original ATR-42 airfoil drag reduction.