Ignition technique for an in situ oil shale retort

DOEpatents

Cha, Chang Y.

1983-01-01

A generally flat combustion zone is formed across the entire horizontal cross-section of a fragmented permeable mass of formation particles formed in an in situ oil shale retort. The flat combustion zone is formed by either sequentially igniting regions of the surface of the fragmented permeable mass at successively lower elevations or by igniting the entire surface of the fragmented permeable mass and controlling the rate of advance of various portions of the combustion zone.

Isomer-dependent fragmentation dynamics of inner-shell photoionized difluoroiodobenzene

DOE PAGES

Ablikim, Utuq; Bomme, Cédric; Savelyev, Evgeny; ...

2017-05-11

The fragmentation dynamics of 2,6- and 3,5-difluoroiodobenzene after iodine 4d inner-shell photoionization with soft X-rays are studied using coincident electron and ion momentum imaging. By analyzing the momentum correlation between iodine and fluorine cations in three-fold ion coincidence events, we can distinguish the two isomers experimentally. Classical Coulomb explosion simulations are in overall agreement with the experimentally determined fragment ion kinetic energies and momentum correlations and point toward different fragmentation mechanisms and time scales. Finally, while most three-body fragmentation channels show clear evidence for sequential fragmentation on a time scale larger than the rotational period of the fragments, the breakupmore » into iodine and fluorine cations and a third charged co-fragment appears to occur within several hundred femtoseconds.« less

[The use of local vibration and ultrasound in the rehabilitation of urolithiasis patients with the "stone pathway" syndrome of the distal ureter].

PubMed

Li, A A; Nesterov, N I; Avilov, V Ia

1996-01-01

Sequential intrarectal impacts with local vibration and ultrasound on distal part of ureter in 60 patients with "stone pathway" promoted elimination of the stone fragments in 58 (96.7%) patients. The size of the urolith fragments varied from 1 to 5 mm.

The Off-Line Use of a Sequential Estimator.

DTIC Science & Technology

1980-07-01

S C SCHARTZ NOO1-80-C-0530 UNCLASSIFIED TR-4I’l EEEEEEEEE1-EEEEhE-mlllEllEEEEE -IIIEEEEEIII -iEiiiiEiiilEN 112.8 1.0,5 1111 3 2 1 1 2 .2’ � 1-12...question regarding t a e.%tent to which convergence can be assured. The results of sin,.-.ations are pre-sented. pJ 3 IBL OF COCUTS Abstract...2 fhapter 1. The Problem Statement - - 4..........----- ..hapter 2. $ome Difficulties With Sequential Processing - 6 Chapter 3 . Off

Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts.

PubMed

Boomsma, Wouter; Tian, Pengfei; Frellsen, Jes; Ferkinghoff-Borg, Jesper; Hamelryck, Thomas; Lindorff-Larsen, Kresten; Vendruscolo, Michele

2014-09-23

Methods of protein structure determination based on NMR chemical shifts are becoming increasingly common. The most widely used approaches adopt the molecular fragment replacement strategy, in which structural fragments are repeatedly reassembled into different complete conformations in molecular simulations. Although these approaches are effective in generating individual structures consistent with the chemical shift data, they do not enable the sampling of the conformational space of proteins with correct statistical weights. Here, we present a method of molecular fragment replacement that makes it possible to perform equilibrium simulations of proteins, and hence to determine their free energy landscapes. This strategy is based on the encoding of the chemical shift information in a probabilistic model in Markov chain Monte Carlo simulations. First, we demonstrate that with this approach it is possible to fold proteins to their native states starting from extended structures. Second, we show that the method satisfies the detailed balance condition and hence it can be used to carry out an equilibrium sampling from the Boltzmann distribution corresponding to the force field used in the simulations. Third, by comparing the results of simulations carried out with and without chemical shift restraints we describe quantitatively the effects that these restraints have on the free energy landscapes of proteins. Taken together, these results demonstrate that the molecular fragment replacement strategy can be used in combination with chemical shift information to characterize not only the native structures of proteins but also their conformational fluctuations.

On the Use of Adaptive Instructional Images Based on the Sequential-Global Dimension of the Felder-Silverman Learning Style Theory

ERIC Educational Resources Information Center

Filippidis, Stavros K.; Tsoukalas, Ioannis A.

2009-01-01

An adaptive educational system that uses adaptive presentation is presented. In this system fragments of different images present the same content and the system can choose the one most relevant to the user based on the sequential-global dimension of Felder-Silverman's learning style theory. In order to retrieve the learning style of each student…

Testing independence of fragment lengths within VNTR loci

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

Geisser, S.; Johnson, W.

1993-11-01

Methods that were devised to test independence of the bivariate fragment lengths obtained from VNTR loci are applied to several population databases. It is shown that for many of the probes independence (Hardy-Weinberg equilibrium) cannot be sustained. 3 refs., 3 tabs.

Dynamics of C2H 2 3 +→H++H++C 2 + investigated by 50-keV/u Ne8 + impact

NASA Astrophysics Data System (ADS)

Xu, S.; Zhu, X. L.; Feng, W. T.; Guo, D. L.; Zhao, Q.; Yan, S.; Zhang, P.; Zhao, D. M.; Gao, Y.; Zhang, S. F.; Yang, J.; Ma, X.

2018-06-01

Breakup dynamics of C2H 2 3 + → H++H++C 2 + induced by 50-keV/u Ne8 + ion impact is investigated employing a reaction microscope. All three ionic fragments in the final state are detected in coincidence, and their momentum vectors as well as the kinetic energies are determined. The kinetic-energy correlation spectrum of the two protons displays very rich structures. Utilizing the Newton diagrams and the Dalitz plots, different dissociation mechanisms corresponding to these structures are identified. It was found that, besides the concerted and sequential breakup, fragmentation mechanisms associated with different vibration modes including molecular bending and asymmetric stretching also make significant contributions. We analyzed the correlation between different fragmentation mechanisms and the kinetic-energy release (KER) and found that the sequential process occurs with higher KER while, in contrast, the concerted process mainly contributes to the lower KER. This behavior is entirely opposite to the breakup of the CO2 molecule.

Fluctuations and symmetry energy in nuclear fragmentation dynamics.

PubMed

Colonna, M

2013-01-25

Within a dynamical description of nuclear fragmentation, based on the liquid-gas phase transition scenario, we explore the relation between neutron-proton density fluctuations and nuclear symmetry energy. We show that, along the fragmentation path, isovector fluctuations follow the evolution of the local density and approach an equilibrium value connected to the local symmetry energy. Higher-density regions are characterized by smaller average asymmetry and narrower isotopic distributions. This dynamical analysis points out that fragment final state isospin fluctuations can probe the symmetry energy of the density domains from which fragments originate.

Affinity of hemoglobin for the cytoplasmic fragment of human erythrocyte membrane band 3. Equilibrium measurements at physiological pH using matrix-bound proteins: the effects of ionic strength, deoxygenation and of 2,3-diphosphoglycerate.

PubMed

Chétrite, G; Cassoly, R

1985-10-05

The cytoplasmic fragment of band 3 protein isolated from the human erythrocyte membrane was linked to a CNBr-activated Sepharose matrix in an attempt to measure, in batch experiments, its equilibrium binding constant with oxy- and deoxyhemoglobin at physiological pH and ionic strength values and in the presence or the absence of 2,3-diphosphoglycerate. All the experiments were done at pH 7.2, and equilibrium constants were computed on the basis of one hemoglobin tetramer bound per monomer of fragment. In 10 mM-phosphate buffer, a dissociation constant KD = 2 X 10(-4)M was measured for oxyhemoglobin and was shown to increase to 8 X 10(-4)M in the presence of 50 mM-NaCl. Association could not be demonstrated at higher salt concentrations. Diphosphoglycerate-stripped deoxyhemoglobin was shown to associate more strongly with the cytoplasmic fragment of band 3. In 10 mM-bis-Tris (pH 7.2) and in the presence of 120 mM-NaCl, a dissociation constant KD = 4 X 10(-4)M was measured. Upon addition of increasing amounts of 2,3-diphosphoglycerate, the complex formed between deoxyhemoglobin and the cytoplasmic fragment of band 3 was dissociated. On the reasonable assumption that the hemoglobin binding site present on band 3 fragment was not modified upon linking the protein to the Sepharose matrix, the results indicated that diphosphoglycerate-stripped deoxyhemoglobin or partially liganded hemoglobin tetramers in the T state could bind band 3 inside the intact human red blood cell.

Distributed Immune Systems for Wireless Network Information Assurance

DTIC Science & Technology

2010-04-26

ratio test (SPRT), where the goal is to optimize a hypothesis testing problem given a trade-off between the probability of errors and the...using cumulative sum (CUSUM) and Girshik-Rubin-Shiryaev (GRSh) statistics. In sequential versions of the problem the sequential probability ratio ...the more complicated problems, in particular those where no clear mean can be established. We developed algorithms based on the sequential probability

Effect of scrape-off-layer current on reconstructed tokamak equilibrium

DOE PAGES

King, J. R.; Kruger, S. E.; Groebner, R. J.; ...

2017-01-13

Methods are described that extend fields from reconstructed equilibria to include scrape-off-layer current through extrapolated parametrized and experimental fits. The extrapolation includes both the effects of the toroidal-field and pressure gradients which produce scrape-off-layer current after recomputation of the Grad-Shafranov solution. To quantify the degree that inclusion of scrape-off-layer current modifies the equilibrium, the χ-squared goodness-of-fit parameter is calculated for cases with and without scrape-off-layer current. The change in χ-squared is found to be minor when scrape-off-layer current is included however flux surfaces are shifted by up to 3 cm. Here the impact on edge modes of these scrape-off-layer modificationsmore » is also found to be small and the importance of these methods to nonlinear computation is discussed.« less

Method for rapid base sequencing in DNA and RNA

DOEpatents

Jett, J.H.; Keller, R.A.; Martin, J.C.; Moyzis, R.K.; Ratliff, R.L.; Shera, E.B.; Stewart, C.C.

1987-10-07

A method is provided for the rapid base sequencing of DNA or RNA fragments wherein a single fragment of DNA or RNA is provided with identifiable bases and suspended in a moving flow stream. An exonuclease sequentially cleaves individual bases from the end of the suspended fragment. The moving flow stream maintains the cleaved bases in an orderly train for subsequent detection and identification. In a particular embodiment, individual bases forming the DNA or RNA fragments are individually tagged with a characteristic fluorescent dye. The train of bases is then excited to fluorescence with an output spectrum characteristic of the individual bases. Accordingly, the base sequence of the original DNA or RNA fragment can be reconstructed. 2 figs.

Method for rapid base sequencing in DNA and RNA

DOEpatents

Jett, J.H.; Keller, R.A.; Martin, J.C.; Moyzis, R.K.; Ratliff, R.L.; Shera, E.B.; Stewart, C.C.

1990-10-09

A method is provided for the rapid base sequencing of DNA or RNA fragments wherein a single fragment of DNA or RNA is provided with identifiable bases and suspended in a moving flow stream. An exonuclease sequentially cleaves individual bases from the end of the suspended fragment. The moving flow stream maintains the cleaved bases in an orderly train for subsequent detection and identification. In a particular embodiment, individual bases forming the DNA or RNA fragments are individually tagged with a characteristic fluorescent dye. The train of bases is then excited to fluorescence with an output spectrum characteristic of the individual bases. Accordingly, the base sequence of the original DNA or RNA fragment can be reconstructed. 2 figs.

Method for rapid base sequencing in DNA and RNA

DOEpatents

Jett, James H.; Keller, Richard A.; Martin, John C.; Moyzis, Robert K.; Ratliff, Robert L.; Shera, E. Brooks; Stewart, Carleton C.

1990-01-01

A method is provided for the rapid base sequencing of DNA or RNA fragments wherein a single fragment of DNA or RNA is provided with identifiable bases and suspended in a moving flow stream. An exonuclease sequentially cleaves individual bases from the end of the suspended fragment. The moving flow stream maintains the cleaved bases in an orderly train for subsequent detection and identification. In a particular embodiment, individual bases forming the DNA or RNA fragments are individually tagged with a characteristic fluorescent dye. The train of bases is then excited to fluorescence with an output spectrum characteristic of the individual bases. Accordingly, the base sequence of the original DNA or RNA fragment can be reconstructed.

Liquid chromatography, in combination with a quadrupole time-of-flight instrument (LC QTOF), with sequential window acquisition of all theoretical fragment-ion spectra (SWATH) acquisition: systematic studies on its use for screenings in clinical and forensic toxicology and comparison with information-dependent acquisition (IDA).

PubMed

Roemmelt, Andreas T; Steuer, Andrea E; Poetzsch, Michael; Kraemer, Thomas

2014-12-02

Forensic and clinical toxicological screening procedures are employing liquid chromatography-tandem mass spectrometry (LC-MS/MS) techniques with information-dependent acquisition (IDA) approaches more and more often. It is known that the complexity of a sample and the IDA settings might prevent important compounds from being triggered. Therefore, data-independent acquisition (DIA) methods should be more suitable for systematic toxicological analysis (STA). The DIA method sequential window acquisition of all theoretical fragment-ion spectra (SWATH), which uses Q1 windows of 20-35 Da for data-independent fragmentation, was systematically investigated for its suitability for STA. Quality of SWATH-generated mass spectra were evaluated with regard to mass error, relative abundance of the fragments, and library hits. With the Q1 window set to 20-25 Da, several precursors pass Q1 at the same time and are fragmented, thus impairing the library search algorithms to a different extent: forward fit was less affected than reverse fit and purity fit. Mass error was not affected. The relative abundance of the fragments was concentration dependent for some analytes and was influenced by cofragmentation, especially of deuterated analogues. Also, the detection rate of IDA compared to SWATH was investigated in a forced coelution experiment (up to 20 analytes coeluting). Even using several different IDA settings, it was observed that IDA failed to trigger relevant compounds. Screening results of 382 authentic forensic cases revealed that SWATH's detection rate was superior to IDA, which failed to trigger ∼10% of the analytes.

Degree of coupling and efficiency of energy converters far-from-equilibrium

NASA Astrophysics Data System (ADS)

Vroylandt, Hadrien; Lacoste, David; Verley, Gatien

2018-02-01

In this paper, we introduce a real symmetric and positive semi-definite matrix, which we call the non-equilibrium conductance matrix, and which generalizes the Onsager response matrix for a system in a non-equilibrium stationary state. We then express the thermodynamic efficiency in terms of the coefficients of this matrix using a parametrization similar to the one used near equilibrium. This framework, then valid arbitrarily far from equilibrium allows to set bounds on the thermodynamic efficiency by a universal function depending only on the degree of coupling between input and output currents. It also leads to new general power-efficiency trade-offs valid for macroscopic machines that are compared to trade-offs previously obtained from uncertainty relations. We illustrate our results on an unicycle heat to heat converter and on a discrete model of a molecular motor.

Mean-field crack networks on desiccated films and their applications: Girl with a Pearl Earring.

PubMed

Flores, J C

2017-02-15

Usual requirements for bulk and fissure energies are considered in obtaining the interdependence among external stress, thickness and area of crack polygons in desiccated films. The average area of crack polygons increases with thickness as a power-law of 4/3. The sequential fragmentation process is characterized by a topological factor related to a scaling finite procedure. Non-sequential overly tensioned (prompt) fragmentation is briefly discussed. Vermeer's painting, Girl with a Pearl Earring, is considered explicitly by using computational image tools and simple experiments and applying the proposed theoretical analysis. In particular, concerning the source of lightened effects on the girl's face, the left/right thickness layer ratio (≈1.34) and the stress ratio (≈1.102) are evaluated. Other master paintings are briefly considered.

Dancing Twins: Stellar Hierarchies That Formed Sequentially?

NASA Astrophysics Data System (ADS)

Tokovinin, Andrei

2018-04-01

This paper draws attention to the class of resolved triple stars with moderate ratios of inner and outer periods (possibly in a mean motion resonance) and nearly circular, mutually aligned orbits. Moreover, stars in the inner pair are twins with almost identical masses, while the mass sum of the inner pair is comparable to the mass of the outer component. Such systems could be formed either sequentially (inside-out) by disk fragmentation with subsequent accretion and migration, or by a cascade hierarchical fragmentation of a rotating cloud. Orbits of the outer and inner subsystems are computed or updated in four such hierarchies: LHS 1070 (GJ 2005, periods 77.6 and 17.25 years), HIP 9497 (80 and 14.4 years), HIP 25240 (1200 and 47.0 years), and HIP 78842 (131 and 10.5 years).

Probing peptide fragment ion structures by combining sustained off-resonance collision-induced dissociation and gas-phase H/D exchange (SORI-HDX) in Fourier transform ion-cyclotron resonance (FT-ICR) instruments.

PubMed

Somogyi, Arpád

2008-12-01

The usefulness of gas-phase H/D exchange is demonstrated to probe heterogeneous fragment and parent ion populations. Singly and multiply protonated peptides/proteins were fragmented by using sustained off-resonance irradiation collision-induced dissociation (SORI-CID). The fragments and the surviving precursor ions then all undergo H/D exchange in the gas-phase with either D(2)O or CD(3)OD under the same experimental conditions. Usually, 10 to 60 s of reaction time is adequate to monitor characteristic differences in the H/D exchange kinetic rates. These differences are then correlated to isomeric ion structures. The SORI-HDX method can be used to rapidly test fragment ion structures and provides useful insights into peptide fragmentation mechanisms.

Scaling Laws for Shapes of Food Fragments by Human Mastication

NASA Astrophysics Data System (ADS)

Kobayashi, Naoki; Kohyama, Kaoru; Sasaki, Yo; Matsushita, Mitsugu

2007-04-01

Scaling property of the shape of fragments which were produced by masticating raw carrots has been studied experimentally and theoretically. Mastication experiments showed that most fragments have more or less isotropic shapes which are independent of the number of chewing strokes, whereas larger fragments than a crossover size have complicated shapes. Since the crossover size had the structure which was dependent on the number of chewing strokes, we have tried to propose dynamic scaling hypothesis analogous to the case of growing self-affine interface. It was found that the dynamic scaling yields fairly accurate values of the scaling exponents. Our results will provide a new observation and insight of not only sequential fragmentation but also construction for physiological measurement.

Influence of fragment size and postoperative joint congruency on long-term outcome of posterior malleolar fractures.

PubMed

Drijfhout van Hooff, Cornelis Christiaan; Verhage, Samuel Marinus; Hoogendoorn, Jochem Maarten

2015-06-01

One of the factors contributing to long-term outcome of posterior malleolar fractures is the development of osteoarthritis. Based on biomechanical, cadaveric, and small population studies, fixation of posterior malleolar fracture fragments (PMFFs) is usually performed when fragment size exceeds 25-33%. However, the influence of fragment size on long-term clinical and radiological outcome size remains unclear. A retrospective cohort study of 131 patients treated for an isolated ankle fracture with involvement of the posterior malleolus was performed. Mean follow-up was 6.9 (range, 2.5-15.9) years. Patients were divided into groups depending on size of the fragment, small (<5%, n = 20), medium (5-25%, n = 86), or large (>25%, n = 25), and presence of step-off after operative treatment. We have compared functional outcome measures (AOFAS, AAOS), pain (VAS), and dorsiflexion restriction compared to the contralateral ankle and the incidence of osteoarthritis on X-ray. There were no nonunions, 56% of patients had no radiographic osteoarthritis, VAS was 10 of 100, and median clinical score was 90 of 100. More osteoarthritis occurred in ankle fractures with medium and large PMFFs compared to small fragments (small 16%, medium 48%, large 54%; P = .006). Also when comparing small with medium-sized fragments (P = .02), larger fragment size did not lead to a significantly decreased function (median AOFAS 95 vs 88, P = .16). If the PMFF size was >5%, osteoarthritis occurred more frequently when there was a postoperative step-off ≥1 mm in the tibiotalar joint surface (41% vs 61%, P = .02) (whether the posterior fragment had been fixed or not). In this group, fixing the PMFF did not influence development of osteoarthritis. However, in 42% of the cases with fixation of the fragment a postoperative step-off remained (vs 45% in the group without fixation). Osteoarthritis is 1 component of long-term outcome of malleolar fractures, and the results of this study demonstrate that there was more radiographic osteoarthritis in patients with medium and large posterior fragments than in those with small fragments. Radiographic osteoarthritis also occurred more frequently when postoperative step-off was 1 mm or more, whether the posterior fragment was fixed or not. However, clinical scores were not different for these groups. Level IV, retrospective case series. © The Author(s) 2015.

Ultra-Wide Band Non-reciprocity through Sequentially-Switched Delay Lines.

PubMed

Biedka, Mathew M; Zhu, Rui; Xu, Qiang Mark; Wang, Yuanxun Ethan

2017-01-06

Achieving non-reciprocity through unconventional methods without the use of magnetic material has recently become a subject of great interest. Towards this goal a time switching strategy known as the Sequentially-Switched Delay Line (SSDL) is proposed. The essential SSDL configuration consists of six transmission lines of equal length, along with five switches. Each switch is turned on and off sequentially to distribute and route the propagating electromagnetic wave, allowing for simultaneous transmission and receiving of signals through the device. Preliminary experimental results with commercial off the shelf parts are presented which demonstrated non-reciprocal behavior with greater than 40 dB isolation from 200 KHz to 200 MHz. The theory and experimental results demonstrated that the SSDL concept may lead to future on-chip circulators over multi-octaves of frequency.

Ultra-Wide Band Non-reciprocity through Sequentially-Switched Delay Lines

PubMed Central

Biedka, Mathew M.; Zhu, Rui; Xu, Qiang Mark; Wang, Yuanxun Ethan

2017-01-01

Achieving non-reciprocity through unconventional methods without the use of magnetic material has recently become a subject of great interest. Towards this goal a time switching strategy known as the Sequentially-Switched Delay Line (SSDL) is proposed. The essential SSDL configuration consists of six transmission lines of equal length, along with five switches. Each switch is turned on and off sequentially to distribute and route the propagating electromagnetic wave, allowing for simultaneous transmission and receiving of signals through the device. Preliminary experimental results with commercial off the shelf parts are presented which demonstrated non-reciprocal behavior with greater than 40 dB isolation from 200 KHz to 200 MHz. The theory and experimental results demonstrated that the SSDL concept may lead to future on-chip circulators over multi-octaves of frequency. PMID:28059132

Effectiveness of sequential automatic-manual home respiratory polygraphy scoring.

PubMed

Masa, Juan F; Corral, Jaime; Pereira, Ricardo; Duran-Cantolla, Joaquin; Cabello, Marta; Hernández-Blasco, Luis; Monasterio, Carmen; Alonso-Fernandez, Alberto; Chiner, Eusebi; Vázquez-Polo, Francisco-José; Montserrat, Jose M

2013-04-01

Automatic home respiratory polygraphy (HRP) scoring functions can potentially confirm the diagnosis of sleep apnoea-hypopnoea syndrome (SAHS) (obviating technician scoring) in a substantial number of patients. The result would have important management and cost implications. The aim of this study was to determine the diagnostic cost-effectiveness of a sequential HRP scoring protocol (automatic and then manual for residual cases) compared with manual HRP scoring, and with in-hospital polysomnography. We included suspected SAHS patients in a multicentre study and assigned them to home and hospital protocols at random. We constructed receiver operating characteristic (ROC) curves for manual and automatic scoring. Diagnostic agreement for several cut-off points was explored and costs for two equally effective alternatives were calculated. Of 366 randomised patients, 348 completed the protocol. Manual scoring produced better ROC curves than automatic scoring. There was no sensitive automatic or subsequent manual HRP apnoea-hypopnoea index (AHI) cut-off point. The specific cut-off points for automatic and subsequent manual HRP scorings (AHI >25 and >20, respectively) had a specificity of 93% for automatic and 94% for manual scorings. The costs of manual protocol were 9% higher than sequential HRP protocol; these were 69% and 64%, respectively, of the cost of the polysomnography. A sequential HRP scoring protocol is a cost-effective alternative to polysomnography, although with limited cost savings compared to HRP manual scoring.

Auctions with Dynamic Populations: Efficiency and Revenue Maximization

NASA Astrophysics Data System (ADS)

Said, Maher

We study a stochastic sequential allocation problem with a dynamic population of privately-informed buyers. We characterize the set of efficient allocation rules and show that a dynamic VCG mechanism is both efficient and periodic ex post incentive compatible; we also show that the revenue-maximizing direct mechanism is a pivot mechanism with a reserve price. We then consider sequential ascending auctions in this setting, both with and without a reserve price. We construct equilibrium bidding strategies in this indirect mechanism where bidders reveal their private information in every period, yielding the same outcomes as the direct mechanisms. Thus, the sequential ascending auction is a natural institution for achieving either efficient or optimal outcomes.

Shot noise enhancement from non-equilibrium plasmons in Luttinger liquid junctions.

PubMed

Kim, Jaeuk U; Kinaret, Jari M; Choi, Mahn-Soo

2005-06-29

We consider a quantum wire double junction system with each wire segment described by a spinless Luttinger model, and study theoretically shot noise in this system in the sequential tunnelling regime. We find that the non-equilibrium plasmonic excitations in the central wire segment give rise to qualitatively different behaviour compared to the case with equilibrium plasmons. In particular, shot noise is greatly enhanced by them, and exceeds the Poisson limit. We show that the enhancement can be explained by the emergence of several current-carrying processes, and that the effect disappears if the channels effectively collapse to one because of fast plasmon relaxation processes, for example.

Shot noise enhancement from non-equilibrium plasmons in Luttinger liquid junctions

NASA Astrophysics Data System (ADS)

Kim, Jaeuk U.; Kinaret, Jari M.; Choi, Mahn-Soo

2005-06-01

We consider a quantum wire double junction system with each wire segment described by a spinless Luttinger model, and study theoretically shot noise in this system in the sequential tunnelling regime. We find that the non-equilibrium plasmonic excitations in the central wire segment give rise to qualitatively different behaviour compared to the case with equilibrium plasmons. In particular, shot noise is greatly enhanced by them, and exceeds the Poisson limit. We show that the enhancement can be explained by the emergence of several current-carrying processes, and that the effect disappears if the channels effectively collapse to one because of fast plasmon relaxation processes, for example.

PARVMEC: An Efficient, Scalable Implementation of the Variational Moments Equilibrium Code

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

Seal, Sudip K; Hirshman, Steven Paul; Wingen, Andreas

The ability to sustain magnetically confined plasma in a state of stable equilibrium is crucial for optimal and cost-effective operations of fusion devices like tokamaks and stellarators. The Variational Moments Equilibrium Code (VMEC) is the de-facto serial application used by fusion scientists to compute magnetohydrodynamics (MHD) equilibria and study the physics of three dimensional plasmas in confined configurations. Modern fusion energy experiments have larger system scales with more interactive experimental workflows, both demanding faster analysis turnaround times on computational workloads that are stressing the capabilities of sequential VMEC. In this paper, we present PARVMEC, an efficient, parallel version of itsmore » sequential counterpart, capable of scaling to thousands of processors on distributed memory machines. PARVMEC is a non-linear code, with multiple numerical physics modules, each with its own computational complexity. A detailed speedup analysis supported by scaling results on 1,024 cores of a Cray XC30 supercomputer is presented. Depending on the mode of PARVMEC execution, speedup improvements of one to two orders of magnitude are reported. PARVMEC equips fusion scientists for the first time with a state-of-theart capability for rapid, high fidelity analyses of magnetically confined plasmas at unprecedented scales.« less

Sequential Auctions in Uncertain Information Settings

NASA Astrophysics Data System (ADS)

Fatima, Shaheen; Wooldridge, Michael; Jennings, Nicholas R.

This paper analyzes sequential auctions for private value objects using second-price sealed-bid rules. Now, the equilibrium bids for such auctions depend on the information uncertainty of the bidders. Specifically, there are three key auction parameters that the bidders could be uncertain about: the valuations of the objects for sale, the number of objects for sale, and the number of participating bidders. We analyse the bidding behaviour for each of these three sources of uncertainty. For each setting, we first find the equilibrium bidding strategies for the individual auctions that comprise a series. Then we analyze the effect of these uncertainties on the computational and economic properties of the equilibrium solution. The former analysis is essential if we want to use software agents to bid on our behalf. The latter is essential because both the auctioneer and the bidders want to know how these uncertainties affect their profits. Thus we compare the outcomes for these settings from the perspective of the bidders (i.e., in terms of their profits), from the perspective of the auctioneer (i.e., in terms of his revenue), and from a global perspective (i.e., in terms of auction efficiency).

Energy Flow in Dense Off-Equilibrium Plasma

DTIC Science & Technology

2016-07-15

akT e in our system100 i e T T Teller 1966 Smoking Gun Experiment: Laser Breakdown in COLD gas In going from room to liquid Nitrogen temperature...oflaser breakdown have revealed a new phase of off-equilibrium plasma that has a tensile strength similar to a liquid , and reduced ion-electron...approved for public release. Part 1: Energy Balance in Sonoluminescing Dense Plasma Sonoluminescence occurs from rapid implosion of gas bubbles caused to

How well can step-off and gap distances be reduced when treating intra-articular distal radius fractures with fragment specific fixation when using fluoroscopy.

PubMed

Thiart, M; Ikram, A; Lamberts, R P

2016-12-01

Although fragment specific fixation has proved to be an effective treatment regime, it has not been established how successfully this treatment could be performed using fluoroscopy and what the added value of arthroscopy could be. Establish gap and step-off distances after in intra-articular distal radius fractures that have been treated with fragment specific fixation while using fluoroscopy. Forty-four patients with an intra-articular distal radius fracture were treated with fragment specific fixation while using fluoroscopy. After the treatment of the intra-articular distal radius fracture with fragment specific fixation and the use of fluoroscopy, but before the completion of the surgical intervention, all gap, and step-off distances were determined by using arthroscopy. In addition, the joint was checked for any other wrist pathologies. Arthroscopy after the surgical intervention showed that in 37 patients no gap distances could be detected, while in six patients a gap distance of≤2mm was found and in one patient, a gap distance of 3mm. Similarly, arthroscopy revealed no step-off distances in 33 patients, while in 11 patients a step-off distance of≤2mm was found. Although additional wrist pathologies were found in 48% of our population, only one patient needed surgical intervention. Three months after the surgical intervention wrist flexion was 41±10°, wrist extension 51±17°, ulnar deviation 19±10°, radial deviation 32±12° while patients could pronate and supinate their wrist to 85±5° and 74±20°, respectively. Intra-articular distal radius fractures can be treated successfully with fragment specific fixation and the use of fluoroscopy. As almost all gap and step-off distances could be reduced to an acceptable level, the scope for arthroscopy to further improve this treatment regime is limited. The functional outcome scores that were found 3 months after the surgical intervention were similar to what has been reported in other studies using different treatment option. These findings suggest that fragment specific fixation is a good alternative for treating intra-articular distal radius fractures. As in most cases, only fluoroscopy is needed for fragment specific fixation, this treatment technique is a good treatment option for resource-limited hospitals, setting who do not have access to arthroscopy. III, case-control study. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

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

Holland, Troy Michael; Kress, Joel David; Bhat, Kabekode Ghanasham

Year 1 Objectives (August 2016 – December 2016) – The original Independence model is a sequentially regressed set of parameters from numerous data sets in the Aspen Plus modeling framework. The immediate goal with the basic data model is to collect and evaluate those data sets relevant to the thermodynamic submodels (pure substance heat capacity, solvent mixture heat capacity, loaded solvent heat capacities, and volatility data). These data are informative for the thermodynamic parameters involved in both vapor-liquid equilibrium, and in the chemical equilibrium of the liquid phase.

High data rate coding for the space station telemetry links.

NASA Technical Reports Server (NTRS)

Lumb, D. R.; Viterbi, A. J.

1971-01-01

Coding systems for high data rates were examined from the standpoint of potential application in space-station telemetry links. Approaches considered included convolutional codes with sequential, Viterbi, and cascaded-Viterbi decoding. It was concluded that a high-speed (40 Mbps) sequential decoding system best satisfies the requirements for the assumed growth potential and specified constraints. Trade-off studies leading to this conclusion are viewed, and some sequential (Fano) algorithm improvements are discussed, together with real-time simulation results.

Long-Tailed Distributions in Biological Systems:. Revisit to Lognormals

NASA Astrophysics Data System (ADS)

Kobayashi, N.; Kohyama, K.; Moriyama, O.; Sasaki, Y.; Matsushita, M.; Matsushita, S.

2007-07-01

Long-tailed distributions in biological systems have been studied. First, we found that lognormal distributions show excellent fit with various data for the duration distribution of disability in aged people, irrespective of their severity and gender. The robust lognormal distribution of disability implies that the incidence of diseases can be completed by many independent subprocesses in succession. Next, we studied food fragmentation by human mastication. A lognormal distribution well fits to the entire region for masticated food fragments for a small number of chewing strokes. Furthermore, the tail of the fragment-size distribution changes from the lognormal distribution to a power-law one as the chewing stroke number increases. The good data fitting by the lognormal and power-law distribution implies that two functions of mastication, a sequential fragmentation with cascade and randomness and a lower threshold for fragment size, may affect the size distribution of masticated food fragments.

Structural characterization by both positive and negative electrospray ion trap mass spectrometry of oligogalacturonates purified by high-performance anion-exchange chromatography.

PubMed

Quéméner, Bernard; Désiré, Cédric; Debrauwer, Laurent; Rathahao, Estelle

2003-01-17

The off-line coupling of high-performance anion-exchange chromatography to electrospray ion trap mass spectrometry (ESI-IT-MS) is described. Two sets of isocratic conditions were optimised for the semi-preparative purification of oligogalacturonates of degree of polymerisation from 4 to 6 by monitoring eluates with either pulsed amperometric detection or evaporative light scattering detection in the presence of an online Dionex Carbohydrate Membrane Desalter (CMD). In these conditions, purified oligogalacturonate solutions were suitable, without further desalting steps, for infusion ESI-IT-MS experiments. This paper provides some interesting features of positive and negative ESI-IT-multiple MS (MSn) of these acidic oligosaccharides. The spectra acquired in both ion modes show characteristic fragments resulting from glycosidic bond and cross-ring cleavages. Under negative ionization conditions, the fragmentation of the singly-charged [M-H]- ions, as well as the Ci-, and Zi-, fragment ions through sequential MSn experiments, was always dominated by product ions from C- and Z-type glycosidic cleavages. All spectra also displayed 0.2 A-type cross-ring cleavage ions which carry linkage information. Collision-induced dissociation (CID) spectra of sodium-cationized species obtained under positive ionization conditions were more complex. Successive MSn experiments also led to the 0.2 A-type cross-ring cleavage ions observed together with B- and Y-type ions. The presence of the 0.2 A ion series was related to Mr 60 (C2H4O2) losses. Combined with the absence of the Mr 30 (CH2O) and the Mr 90 (C3H6O3) ions, these ions were indicative of 1-4 type glycosidic linkage.

Sequential vs. simultaneous photokilling by mitochondrial and lysosomal photodamage

NASA Astrophysics Data System (ADS)

Kessel, David

2017-02-01

We previously reported that a low level of lysosomal photoda mage can markedly promote the subsequent efficacy of PDT directed at mitochondria. This involves release of Ca2+ from photo damaged lysosomes, cleavage of the autophagy-associated protein ATG5 after activation of calpain and an interaction between the ATG5 fragment and mitochondria resulting in enhanced apoptosis. Inhibition of calpain activity abolished th is effect. We examined permissible irradiation sequences. Lysosomal photodamage must occur first with the `enhancement' effect showing a short half-life ( 15 min), presumably reflecting the survival of the ATG5 fragment. Simultaneous photo damage to both loci was found to be as effective as the sequential protocol. Since Photofrin can target both lysosomes and mitochondria for photo damage, this broad spectrum of photo damage may explain the efficacy of this photo sensitizing agent in spite of a sub-optimal absorbance profile at a sub- optimal wavelength for tissue transparency.

Secondary Fragmentation of Comet Shoemaker-Levy 9 and the Ramifications for the Progenitor's Breakup in July 1992

NASA Technical Reports Server (NTRS)

Sekanina, Z.; Chodas, P. W.; Yeomans, D. K.

1998-01-01

Comprehensive analysis of discrete events of secondary fragmentation leads to a conceptually new understanding of the process of disintegration of comet Shoemaker-Levy 9. We submit that the jovian tidal forces inflicted extensive cracks throughout the interior of the original nucleus but did not split it apart. The initial disruption was apparently accomplished by stresses exerted on the cracked object by its fast rotation during the early post-perijove period of time. We argue that this disruption was in fact a rapid sequence of episodes during July 1992 that gave birth to the 12 on-train, or primary, fragments: A, C, D, E, G, H, K, L, Q (later Q(sub 1)), R, S, and W. The discrete events of secondary fragmentation, which gave birth to the off-train fragments, are understood in this scenario as stochastic manifestations of the continuing process of progressive disintegration. Of the 13 off-train fragments considered, nine were secondary--B, F, G(sub 2), M, N, P (later P(sub 2) or P(sub 2a)), Q(sub 2), U, and V--and four tertiary (J, P(sub 1), P(sub 2b), and T). The separation parameters of 11 off-train fragments were determined. The vectorial distribution of separation velocities of these fragments shows a strong concentration toward a great circle, unquestionably an effect of the approximately conserved angular momentum of the progenitor comet since the time of its initial disruption. Also apparent is their clumping (except for P(sub 1)) to a segment along the great circle, implying that the fragments were consistently released from one side of their parents, thus explaining for the first time why the off-train fragments preferentially appeared on one side of the nuclear train. In order to obtain a consistent solution, our model requires that the points of separation be on the antisolar side of the parent fragments, where thermal stresses are likely to enhance the effect of rotation. The episodes of secondary fragmentation are found to have nine months after the close encounter with Jupiter in early July 1992, and the separation velocities ranged between 0.36 and 1.7 m/s. The spin-axis position is determined to have been nearly in the jovicentric orbit plane, which rules out the Asphaug-Benz-Solem strengthless aggregate model as a plausible breakup hypothesis. Since the separation velocities are rotational in nature, they cannot substantially exceed the critical limit for centrifugal breakup and offer an estimate for the original nuclear dimensions. The comet's nucleus is found to have been approximately 10 km in diameter and spinning rapidly. With the exception of P(sub 1) and apparently also P(sub 2) and F, no nongravitational deceleration was detected in the motions of the off-train fragments. Serious doubts are cast on continuing appreciable activity of any of these fragments. Indeed, when it was necessary to introduce a deceleration into the equations of motion, the effect appears to have been due to the action of solar radiation pressure on the centroid of centimeter-sized particulates in the disintegrating condensations.

Morphological Transformation between Nanocoils and Nanoribbons via Defragmentation Structural Rearrangement or Fragmentation-recombination Mechanism

NASA Astrophysics Data System (ADS)

Zhang, Yibin; Zheng, Yingxuan; Xiong, Wei; Peng, Cheng; Zhang, Yifan; Duan, Ran; Che, Yanke; Zhao, Jincai

2016-06-01

Kinetic control over the assembly pathways towards novel metastable functional materials or far-from-equilibrium systems has been much less studied compared to the thermodynamic equilibrium self-assembly. Herein, we report the distinct morphological transformation between nanocoils and nanoribbons in the self-assembly of unsymmetric perylene diimide (PDI) molecules. We demonstrate that the morphological transformation of the kinetically trapped assemblies into the thermodynamically stable forms proceeds via two distinct mechanisms, i.e., a direct structural rearrangement (molecule 1 or 2) and a fragmentation-recombination mechanism (molecule 4), respectively. The subtle interplay of the steric hindrance of the bulky substituents and the flexibility of the linker structure between the bulky moiety and the perylene core was demonstrated to enable the effective modulation of the energetic landscape of the assemblies and thus modulation of the assembly pathways. Herein, our work presents a new approach to control the self-assembly pathways and thereby can be used to achieve novel far-from-equilibrium systems.

On gamesmen and fair men: explaining fairness in non-cooperative bargaining games.

PubMed

Suleiman, Ramzi

2018-02-01

Experiments on bargaining games have repeatedly shown that subjects fail to use backward induction, and that they only rarely make demands in accordance with the subgame perfect equilibrium. In a recent paper, we proposed an alternative model, termed 'economic harmony' in which we modified the individual's utility by defining it as a function of the ratio between the actual and aspired pay-offs. We also abandoned the notion of equilibrium, in favour of a new notion of 'harmony', defined as the intersection of strategies, at which all players are equally satisfied. We showed that the proposed model yields excellent predictions of offers in the ultimatum game, and requests in the sequential common pool resource dilemma game. Strikingly, the predicted demand in the ultimatum game is equal to the famous Golden Ratio (approx. 0.62 of the entire pie). The same prediction was recently derived independently by Schuster (Schuster 2017. Sci. Rep. 7 , 5642). In this paper, we extend the solution to bargaining games with alternating offers. We show that the derived solution predicts the opening demands reported in several experiments, on games with equal and unequal discount factors and game horizons. Our solution also predicts several unexplained findings, including the puzzling 'disadvantageous counter-offers', and the insensitivity of opening demands to variations in the players' discount factors, and game horizon. Strikingly, we find that the predicted opening demand in the alternating offers game is also equal to the Golden Ratio.

On gamesmen and fair men: explaining fairness in non-cooperative bargaining games

PubMed Central

2018-01-01

Experiments on bargaining games have repeatedly shown that subjects fail to use backward induction, and that they only rarely make demands in accordance with the subgame perfect equilibrium. In a recent paper, we proposed an alternative model, termed ‘economic harmony’ in which we modified the individual's utility by defining it as a function of the ratio between the actual and aspired pay-offs. We also abandoned the notion of equilibrium, in favour of a new notion of ‘harmony’, defined as the intersection of strategies, at which all players are equally satisfied. We showed that the proposed model yields excellent predictions of offers in the ultimatum game, and requests in the sequential common pool resource dilemma game. Strikingly, the predicted demand in the ultimatum game is equal to the famous Golden Ratio (approx. 0.62 of the entire pie). The same prediction was recently derived independently by Schuster (Schuster 2017. Sci. Rep. 7, 5642). In this paper, we extend the solution to bargaining games with alternating offers. We show that the derived solution predicts the opening demands reported in several experiments, on games with equal and unequal discount factors and game horizons. Our solution also predicts several unexplained findings, including the puzzling ‘disadvantageous counter-offers’, and the insensitivity of opening demands to variations in the players' discount factors, and game horizon. Strikingly, we find that the predicted opening demand in the alternating offers game is also equal to the Golden Ratio. PMID:29515877

The greenhouse of Titan.

NASA Technical Reports Server (NTRS)

Sagan, C.

1973-01-01

Analysis of non-gray radiative equilibrium and gray convective equilibrium on Titan suggests that a massive molecular-hydrogen greenhouse effect may be responsible for the disagreement between the observed IR temperatures and the equilibrium temperature of an atmosphereless Titan. Calculations of convection indicate a probable minimum optical depth of 14 which corresponds to a molecular hydrogen shell of substantial thickness with total pressures of about 0.1 bar. It is suggested that there is an equilibrium between outgassing and blow-off on the one hand and accretion from the protons trapped in a hypothetical Saturnian magnetic field on the other, in the present atmosphere of Titan. It is believed that an outgassing equivalent to the volatilization of a few kilometers of subsurface ice is required to maintain the present blow-off rate without compensation for all geological time. The presence of an extensive hydrogen corona around Titan is postulated, with surface temperatures up to 200 K.

Generalized Boltzmann-Type Equations for Aggregation in Gases

NASA Astrophysics Data System (ADS)

Adzhiev, S. Z.; Vedenyapin, V. V.; Volkov, Yu. A.; Melikhov, I. V.

2017-12-01

The coalescence and fragmentation of particles in a dispersion system are investigated by applying kinetic theory methods, namely, by generalizing the Boltzmann kinetic equation to coalescence and fragmentation processes. Dynamic equations for the particle concentrations in the system are derived using the kinetic equations of motion. For particle coalescence and fragmentation, equations for the particle momentum, coordinate, and mass distribution functions are obtained and the coalescence and fragmentation coefficients are calculated. The equilibrium mass and velocity distribution functions of the particles in the dispersion system are found in the approximation of an active terminal group (Becker-Döring-type equation). The transition to a continuum description is performed.

iHADAMAC: A complementary tool for sequential resonance assignment of globular and highly disordered proteins

NASA Astrophysics Data System (ADS)

Feuerstein, Sophie; Plevin, Michael J.; Willbold, Dieter; Brutscher, Bernhard

2012-01-01

An experiment, iHADAMAC, is presented that yields information on the amino-acid type of individual residues in a protein by editing the 1H- 15N correlations into seven different 2D spectra, each corresponding to a different class of amino-acid types. Amino-acid type discrimination is realized via a Hadamard encoding scheme based on four different spin manipulations as recently introduced in the context of the sequential HADAMAC experiment. Both sequential and intra-residue HADAMAC experiments yield highly complementary information that greatly facilitate resonance assignment of proteins with high frequency degeneracy, as demonstrated here for a 188-residue intrinsically disordered protein fragment of the hepatitis C virus protein NS5A.

Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction.

PubMed

de Oliveira, Saulo H P; Law, Eleanor C; Shi, Jiye; Deane, Charlotte M

2018-04-01

Most current de novo structure prediction methods randomly sample protein conformations and thus require large amounts of computational resource. Here, we consider a sequential sampling strategy, building on ideas from recent experimental work which shows that many proteins fold cotranslationally. We have investigated whether a pseudo-greedy search approach, which begins sequentially from one of the termini, can improve the performance and accuracy of de novo protein structure prediction. We observed that our sequential approach converges when fewer than 20 000 decoys have been produced, fewer than commonly expected. Using our software, SAINT2, we also compared the run time and quality of models produced in a sequential fashion against a standard, non-sequential approach. Sequential prediction produces an individual decoy 1.5-2.5 times faster than non-sequential prediction. When considering the quality of the best model, sequential prediction led to a better model being produced for 31 out of 41 soluble protein validation cases and for 18 out of 24 transmembrane protein cases. Correct models (TM-Score > 0.5) were produced for 29 of these cases by the sequential mode and for only 22 by the non-sequential mode. Our comparison reveals that a sequential search strategy can be used to drastically reduce computational time of de novo protein structure prediction and improve accuracy. Data are available for download from: http://opig.stats.ox.ac.uk/resources. SAINT2 is available for download from: https://github.com/sauloho/SAINT2. saulo.deoliveira@dtc.ox.ac.uk. Supplementary data are available at Bioinformatics online.

Novel strategies to construct complex synthetic vectors to produce DNA molecular weight standards.

PubMed

Chen, Zhe; Wu, Jianbing; Li, Xiaojuan; Ye, Chunjiang; Wenxing, He

2009-05-01

DNA molecular weight standards (DNA markers, nucleic acid ladders) are commonly used in molecular biology laboratories as references to estimate the size of various DNA samples in electrophoresis process. One method of DNA marker production is digestion of synthetic vectors harboring multiple DNA fragments of known sizes by restriction enzymes. In this article, we described three novel strategies-sequential DNA fragment ligation, screening of ligation products by polymerase chain reaction (PCR) with end primers, and "small fragment accumulation"-for constructing complex synthetic vectors and minimizing the mass differences between DNA fragments produced from restrictive digestion of synthetic vectors. The strategy could be applied to construct various complex synthetic vectors to produce any type of low-range DNA markers, usually available commercially. In addition, the strategy is useful for single-step ligation of multiple DNA fragments for construction of complex synthetic vectors and other applications in molecular biology field.

Sequential memory: Binding dynamics

NASA Astrophysics Data System (ADS)

Afraimovich, Valentin; Gong, Xue; Rabinovich, Mikhail

2015-10-01

Temporal order memories are critical for everyday animal and human functioning. Experiments and our own experience show that the binding or association of various features of an event together and the maintaining of multimodality events in sequential order are the key components of any sequential memories—episodic, semantic, working, etc. We study a robustness of binding sequential dynamics based on our previously introduced model in the form of generalized Lotka-Volterra equations. In the phase space of the model, there exists a multi-dimensional binding heteroclinic network consisting of saddle equilibrium points and heteroclinic trajectories joining them. We prove here the robustness of the binding sequential dynamics, i.e., the feasibility phenomenon for coupled heteroclinic networks: for each collection of successive heteroclinic trajectories inside the unified networks, there is an open set of initial points such that the trajectory going through each of them follows the prescribed collection staying in a small neighborhood of it. We show also that the symbolic complexity function of the system restricted to this neighborhood is a polynomial of degree L - 1, where L is the number of modalities.

Sequential memory: Binding dynamics.

PubMed

Afraimovich, Valentin; Gong, Xue; Rabinovich, Mikhail

2015-10-01

Temporal order memories are critical for everyday animal and human functioning. Experiments and our own experience show that the binding or association of various features of an event together and the maintaining of multimodality events in sequential order are the key components of any sequential memories-episodic, semantic, working, etc. We study a robustness of binding sequential dynamics based on our previously introduced model in the form of generalized Lotka-Volterra equations. In the phase space of the model, there exists a multi-dimensional binding heteroclinic network consisting of saddle equilibrium points and heteroclinic trajectories joining them. We prove here the robustness of the binding sequential dynamics, i.e., the feasibility phenomenon for coupled heteroclinic networks: for each collection of successive heteroclinic trajectories inside the unified networks, there is an open set of initial points such that the trajectory going through each of them follows the prescribed collection staying in a small neighborhood of it. We show also that the symbolic complexity function of the system restricted to this neighborhood is a polynomial of degree L - 1, where L is the number of modalities.

Synthesizing a novel genetic sequential logic circuit: a push-on push-off switch

PubMed Central

Lou, Chunbo; Liu, Xili; Ni, Ming; Huang, Yiqi; Huang, Qiushi; Huang, Longwen; Jiang, Lingli; Lu, Dan; Wang, Mingcong; Liu, Chang; Chen, Daizhuo; Chen, Chongyi; Chen, Xiaoyue; Yang, Le; Ma, Haisu; Chen, Jianguo; Ouyang, Qi

2010-01-01

Design and synthesis of basic functional circuits are the fundamental tasks of synthetic biologists. Before it is possible to engineer higher-order genetic networks that can perform complex functions, a toolkit of basic devices must be developed. Among those devices, sequential logic circuits are expected to be the foundation of the genetic information-processing systems. In this study, we report the design and construction of a genetic sequential logic circuit in Escherichia coli. It can generate different outputs in response to the same input signal on the basis of its internal state, and ‘memorize' the output. The circuit is composed of two parts: (1) a bistable switch memory module and (2) a double-repressed promoter NOR gate module. The two modules were individually rationally designed, and they were coupled together by fine-tuning the interconnecting parts through directed evolution. After fine-tuning, the circuit could be repeatedly, alternatively triggered by the same input signal; it functions as a push-on push-off switch. PMID:20212522

Synthesizing a novel genetic sequential logic circuit: a push-on push-off switch.

PubMed

Lou, Chunbo; Liu, Xili; Ni, Ming; Huang, Yiqi; Huang, Qiushi; Huang, Longwen; Jiang, Lingli; Lu, Dan; Wang, Mingcong; Liu, Chang; Chen, Daizhuo; Chen, Chongyi; Chen, Xiaoyue; Yang, Le; Ma, Haisu; Chen, Jianguo; Ouyang, Qi

2010-01-01

Design and synthesis of basic functional circuits are the fundamental tasks of synthetic biologists. Before it is possible to engineer higher-order genetic networks that can perform complex functions, a toolkit of basic devices must be developed. Among those devices, sequential logic circuits are expected to be the foundation of the genetic information-processing systems. In this study, we report the design and construction of a genetic sequential logic circuit in Escherichia coli. It can generate different outputs in response to the same input signal on the basis of its internal state, and 'memorize' the output. The circuit is composed of two parts: (1) a bistable switch memory module and (2) a double-repressed promoter NOR gate module. The two modules were individually rationally designed, and they were coupled together by fine-tuning the interconnecting parts through directed evolution. After fine-tuning, the circuit could be repeatedly, alternatively triggered by the same input signal; it functions as a push-on push-off switch.

Contextual view of Warner's Ranch. First of three sequential views ...

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

Contextual view of Warner's Ranch. First of three sequential views (from west to east) of the buildings in relation to the surrounding geography. Ranch House on right. Note approximate locations of Overland Trail on right and San Diego cutoff branching off to left. Camera facing northwest. - Warner Ranch, Ranch House, San Felipe Road (State Highway S2), Warner Springs, San Diego County, CA

Increasing methylation of the calcitonin gene during disease progression in sequential samples from CML patients.

PubMed

Mills, K I; Guinn, B A; Walsh, V A; Burnett, A K

1996-09-01

In chronic myeloid leukaemia (CML), disease progression from the initial chronic phase to the acute phase or blast crisis has previously been shown to be correlated with progressive increases in hyper-methylation of the calcitonin gene, located at chromosome 11p15. However, sequential studies of individual patients were not performed in these investigations. We have analysed 44 samples from nine patients with typical Philadelphia chromosome positive CML throughout their disease progression to determine the methylation state of the calcitonin gene at these time points. Densitometry was used to quantitate the ratio of the normal 2.0 kb Hpa II fragments, indicating normal methylation status of the gene, compared to the intensity of the abnormal, hyper-methylated, 2.6-3.1 kb Hpa II fragments. We found a gradual increase in the ratio of methylated:unmethylated calcitonin gene during chronic phase with a dramatic rise at blast crisis. Further, the ratio of the abnormal hypermethylated 3.1 kb fragments to the methylated 2.6 kb fragment resulted in the identification of a clonal expansion of abnormally methylated cells. This expansion of cells with hypermethylation of the calcitonin gene during chronic phase was shown to coincide with the presence of a mutation in the p53 gene. The data presented in this study would suggest that an increased methylation status of the calcitonin gene during disease progression may indicate the expansion of abnormal blast cell populations and subsequent progression to blast crisis.

Feeding group responses of a Neotropical termite assemblage to rain forest fragmentation.

PubMed

Davies, Richard G

2002-10-01

Biomass collapse and its associated microclimatic stresses within recently isolated rain forest fragments may negatively affect species diversity of most resident taxa. However, for some decomposer organisms, increased resource availability via accompanying tree die-off may effect positive responses, at least for a time, with implications for rates of nutrient cycling and greenhouse gas release. This study investigates the early effects of forest fragmentation on a Neotropical termite assemblage. Numbers of encounters (surrogate for relative abundance) and species richness of wood and leaf-litter feeders, soil feeders, and the whole assemblage, were studied across true forest islands and mainland sites at a hydroelectric reservoir in French Guiana. Results showed no overall effect of fragmentation on either total termite encounters or species richness. However, numbers of encounters and species richness of wood and leaf-litter feeders showed positive responses to forest fragmentation. By contrast, soil feeders showed a negative response for numbers of encounters and no significant effect for species richness. Environmental data suggest that increased tree die-off, and other edge effects associated with biomass collapse, were underway at the time of sampling. Resulting increase in resource availability may therefore explain the positive influence on wood and leaf-litter feeders. A possible decrease in predation pressure from ants with decrease in island size was not tested for, but was a likely effect of the flooded matrix habitat. Fragmentation effects on soil feeder encounters may be due to the energetic and microclimatic constraints of feeding lower down the humification gradient of termite food substrates, but were not sufficient to affect species richness. The patterns revealed suggest that rates of wood decomposition following tree die-off, and of soil nutrient cycling, under different rain forest fragmentation scenarios, merit further study.

[60 years of the equilibrium theory of insular biogeography: problems of testing, results of the field studies, applied importance].

PubMed

Akatov, V V

2012-01-01

A review is presented of publications dealing with analysis of species richness of island biological communities and habitat islands based on the equilibrium theory of insular biogeography by MacArthur and Wilson (1963). Principal points of the theory are considered along with its shortcomings, problems and results of its testing. Also, possibilities are appraised for using recommendations elaborated on the base of the theory in nature conservation practice. The results of island and habitat island biota studies indicate that in many cases data corroborate the equilibrium theory while in many other cases they do not. In particular, for cenoses fragmented 50-250 years ago, especially for the ones formed by long living species, there have been no conspicuous effects of species relaxation detected. At that, the theory prediction of substantial reduction in species richness of fragmented communities in the long run is hardly disputed. The results of studies conducted in the field of insular biogeography are taken as a basis for recommendations on the long-term conservation of isolated communities integrity, although mostly they are of qualitative nature.

The involvement of immunoglobulin E isotype switch in scleroderma skin tissue.

PubMed

Ohtsuka, Tsutomu; Yamazaki, Soji

2005-08-01

The involvement of mast cell, which is activated by immunoglobulin E (IgE), has been reported in the formation of systemic sclerosis (SSc) abnormality. IgE is generated with isotype switch. During isotype switch, switch circles resulting from direct mu to epsilon, or from sequential mu to gamma via epsilon switching will be created. We studied whether switching occurs in SSc. We used nested polymerase chain reaction to analyze the S fragments from switch circles. Fifty-two patients with SSc, and 62 healthy women were studied. Neither of 62 normal skin tissues showed direct switch, nor sequential switch. Neither of seven normal whole blood cells showed direct switch, nor sequential switch. In 52SSc skin tissues, three (5.8%) showed direct switch, and two (3.8%) showed sequential switch. As a result, five (9.6%) of SSc skin tissue showed immunogobulin E class switch. These results were confirmed by DNA sequencing. These results demonstrated that isotype switch to the epsilon locus achieved by direct and/or sequential switch are involved in SSc skin.

Sequential ranging integration times in the presence of CW interference in the ranging channel

NASA Technical Reports Server (NTRS)

Mathur, Ashok; Nguyen, Tien

1986-01-01

The Deep Space Network (DSN), managed by the Jet Propulsion Laboratory for NASA, is used primarily for communication with interplanetary spacecraft. The high sensitivity required to achieve planetary communications makes the DSN very susceptible to radio-frequency interference (RFI). In this paper, an analytical model is presented of the performance degradation of the DSN sequential ranging subsystem in the presence of downlink CW interference in the ranging channel. A trade-off between the ranging component integration times and the ranging signal-to-noise ratio to achieve a desired level of range measurement accuracy and the probability of error in the code components is also presented. Numerical results presented illustrate the required trade-offs under various interference conditions.

Effecting skin renewal: a multifaceted approach.

PubMed

Widgerow, Alan D; Grekin, Steven K

2011-06-01

The skin undergoes intrinsic aging as a normal course, but exposure to ultraviolet (UV) light results in major cumulative damage that manifests as the typical aged photodamaged skin. UV irradiation produces a sequence of changes within the skin layers starting with signaling processes following DNA damage and culminating in nonabsorbed fragmentation of collagen and other proteins within the extracellular matrix. These fragments promote the synthesis of matrix metalloproteinases (MMPs) that further aggravate the damage to the ground substance and add to fragment accumulation. This study describes a unique sequential approach to controlling this photodamage - inhibition of signaling, inhibition of MMPs, proteasome stimulation and mopping up of fragments, stimulation of procollagen and collagen production, and uniform packaging of new collagen fibers. Thus, a multifaceted approach is introduced with presentation of a unique product formulation based on these research principles. © 2011 Wiley Periodicals, Inc.

Evolutionary behaviour, trade-offs and cyclic and chaotic population dynamics.

PubMed

Hoyle, Andy; Bowers, Roger G; White, Andy

2011-05-01

Many studies of the evolution of life-history traits assume that the underlying population dynamical attractor is stable point equilibrium. However, evolutionary outcomes can change significantly in different circumstances. We present an analysis based on adaptive dynamics of a discrete-time demographic model involving a trade-off whose shape is also an important determinant of evolutionary behaviour. We derive an explicit expression for the fitness in the cyclic region and consequently present an adaptive dynamic analysis which is algebraic. We do this fully in the region of 2-cycles and (using a symbolic package) almost fully for 4-cycles. Simulations illustrate and verify our results. With equilibrium population dynamics, trade-offs with accelerating costs produce a continuously stable strategy (CSS) whereas trade-offs with decelerating costs produce a non-ES repellor. The transition to 2-cycles produces a discontinuous change: the appearance of an intermediate region in which branching points occur. The size of this region decreases as we move through the region of 2-cycles. There is a further discontinuous fall in the size of the branching region during the transition to 4-cycles. We extend our results numerically and with simulations to higher-period cycles and chaos. Simulations show that chaotic population dynamics can evolve from equilibrium and vice-versa.

Analyzing Communication Architectures Using Commercial Off-The-Shelf (COTS) Modeling and Simulation Tools

DTIC Science & Technology

1998-06-01

4] By 2010, we should be able to change how we conduct the most intense joint operations. Instead of relying on massed forces and sequential ...not independent, sequential steps. Data probes to support the analysis phase were required to complete the logical models. This generated a need...Networks) Identify Granularity (System Level) - Establish Physical Bounds or Limits to Systems • Determine System Test Configuration and Lineup

Sequential Probability Ratio Testing with Power Projective Base Method Improves Decision-Making for BCI

PubMed Central

Liu, Rong

2017-01-01

Obtaining a fast and reliable decision is an important issue in brain-computer interfaces (BCI), particularly in practical real-time applications such as wheelchair or neuroprosthetic control. In this study, the EEG signals were firstly analyzed with a power projective base method. Then we were applied a decision-making model, the sequential probability ratio testing (SPRT), for single-trial classification of motor imagery movement events. The unique strength of this proposed classification method lies in its accumulative process, which increases the discriminative power as more and more evidence is observed over time. The properties of the method were illustrated on thirteen subjects' recordings from three datasets. Results showed that our proposed power projective method outperformed two benchmark methods for every subject. Moreover, with sequential classifier, the accuracies across subjects were significantly higher than that with nonsequential ones. The average maximum accuracy of the SPRT method was 84.1%, as compared with 82.3% accuracy for the sequential Bayesian (SB) method. The proposed SPRT method provides an explicit relationship between stopping time, thresholds, and error, which is important for balancing the time-accuracy trade-off. These results suggest SPRT would be useful in speeding up decision-making while trading off errors in BCI. PMID:29348781

Statistical prescission point model of fission fragment angular distributions

NASA Astrophysics Data System (ADS)

John, Bency; Kataria, S. K.

1998-03-01

In light of recent developments in fission studies such as slow saddle to scission motion and spin equilibration near the scission point, the theory of fission fragment angular distribution is examined and a new statistical prescission point model is developed. The conditional equilibrium of the collective angular bearing modes at the prescission point, which is guided mainly by their relaxation times and population probabilities, is taken into account in the present model. The present model gives a consistent description of the fragment angular and spin distributions for a wide variety of heavy and light ion induced fission reactions.

Extension of the BRYNTRN code to monoenergetic light ion beams

NASA Technical Reports Server (NTRS)

Cucinotta, Francis A.; Wilson, John W.; Badavi, Francis F.

1994-01-01

A monoenergetic version of the BRYNTRN transport code is extended to beam transport of light ions (H-2, H-3, He-3, and He-4) in shielding materials (thick targets). The redistribution of energy in nuclear reactions is included in transport solutions that use nuclear fragmentation models. We also consider an equilibrium target-fragment spectrum for nuclei with mass number greater than four to include target fragmentation effects in the linear energy transfer (LET) spectrum. Illustrative results for water and aluminum shielding, including energy and LET spectra, are discussed for high-energy beams of H-2 and He-4.

A heuristic for landscape management

Treesearch

Martín Alfonso B. Mendoza; Jesús S. Zepeta; Juan José A. Fajardo

2006-01-01

The development of landscape ecology has stressed out the importance of spatial and sequential relationships as explanations to forest stand dynamics, and for other natural ambiences. This presentation offers a specific design that introduces spatial considerations into forest planning with the idea of regulating fragmentation and connectivity in commercial forest...

Disentangling the photodissociation pathways of small lead clusters by time-resolved monitoring of their delayed decays: the case of {{{\\rm{P}}{\\rm{b}}}_{31}}^{+}

NASA Astrophysics Data System (ADS)

Wolfram, Markus; König, Stephan; Bandelow, Steffi; Fischer, Paul; Jankowski, Alexander; Marx, Gerrit; Schweikhard, Lutz

2018-02-01

Lead clusters {{{{Pb}}}{n}}+/- in the size range between about n = 15 and 40 have recently shown to exhibit complex dissociation spectra due to sequential and competing decays. In order to disentangle the pathways the exemplary {{{{Pb}}}31}+ clusters have been stored and size selected in a Penning trap and irradiated by nanosecond laser pulses. We present time-resolved measurements at time scales from several tens of microseconds to several hundreds of milliseconds. The study results in strong evidence that {{{{Pb}}}31}+ decays not only by neutral monomer evaporation but also by neutral heptamers breaking off. In addition, the decays are further followed to smaller products. The corresponding decay and growth times show that {{{{Pb}}}30}+ also dissociates by either monomer evaporation or heptamer break-off. Furthermore, the product {{{{Pb}}}17}+ may well be a result of heptamer break-off from {{{{Pb}}}24}+—as the second step of a sequential heptamer decay.

Microsecond Unfolding Kinetics of Sheep Prion Protein Reveals an Intermediate that Correlates with Susceptibility to Classical Scrapie

PubMed Central

Chen, Kai-Chun; Xu, Ming; Wedemeyer, William J.; Roder, Heinrich

2011-01-01

The microsecond folding and unfolding kinetics of ovine prion proteins (ovPrP) were measured under various solution conditions. A fragment comprising residues 94–233 of the full-length ovPrP was studied for four variants with differing susceptibilities to classical scrapie in sheep. The observed biexponential unfolding kinetics of ovPrP provides evidence for an intermediate species. However, in contrast to previous results for human PrP, there is no evidence for an intermediate under refolding conditions. Global analysis of the kinetic data, based on a sequential three-state mechanism, quantitatively accounts for all folding and unfolding data as a function of denaturant concentration. The simulations predict that an intermediate accumulates under both folding and unfolding conditions, but is observable only in unfolding experiments because the intermediate is optically indistinguishable from the native state. The relative population of intermediates in two ovPrP variants, both transiently and under destabilizing equilibrium conditions, correlates with their propensities for classical scrapie. The variant susceptible to classical scrapie has a larger population of the intermediate state than the resistant variant. Thus, the susceptible variant should be favored to undergo the PrPC to PrPSc conversion and oligomerization. PMID:21889460

Information Performances and Illative Sequences: Sequential Organization of Explanations of Chemical Phase Equilibrium

ERIC Educational Resources Information Center

Brown, Nathaniel James Swanton

2009-01-01

While there is consensus that conceptual change is surprisingly difficult, many competing theories of conceptual change co-exist in the literature. This dissertation argues that this discord is partly the result of an inadequate account of the unwritten rules of human social interaction that underlie the field's preferred…

Out-of-equilibrium dynamics driven by localized time-dependent perturbations at quantum phase transitions

NASA Astrophysics Data System (ADS)

Pelissetto, Andrea; Rossini, Davide; Vicari, Ettore

2018-03-01

We investigate the quantum dynamics of many-body systems subject to local (i.e., restricted to a limited space region) time-dependent perturbations. If the system crosses a quantum phase transition, an off-equilibrium behavior is observed, even for a very slow driving. We show that, close to the transition, time-dependent quantities obey scaling laws. In first-order transitions, the scaling behavior is universal, and some scaling functions can be computed exactly. For continuous transitions, the scaling laws are controlled by the standard critical exponents and by the renormalization-group dimension of the perturbation at the transition. Our protocol can be implemented in existing relatively small quantum simulators, paving the way for a quantitative probe of the universal off-equilibrium scaling behavior, without the need to manipulate systems close to the thermodynamic limit.

Self-consistent field for fragmented quantum mechanical model of large molecular systems.

PubMed

Jin, Yingdi; Su, Neil Qiang; Xu, Xin; Hu, Hao

2016-01-30

Fragment-based linear scaling quantum chemistry methods are a promising tool for the accurate simulation of chemical and biomolecular systems. Because of the coupled inter-fragment electrostatic interactions, a dual-layer iterative scheme is often employed to compute the fragment electronic structure and the total energy. In the dual-layer scheme, the self-consistent field (SCF) of the electronic structure of a fragment must be solved first, then followed by the updating of the inter-fragment electrostatic interactions. The two steps are sequentially carried out and repeated; as such a significant total number of fragment SCF iterations is required to converge the total energy and becomes the computational bottleneck in many fragment quantum chemistry methods. To reduce the number of fragment SCF iterations and speed up the convergence of the total energy, we develop here a new SCF scheme in which the inter-fragment interactions can be updated concurrently without converging the fragment electronic structure. By constructing the global, block-wise Fock matrix and density matrix, we prove that the commutation between the two global matrices guarantees the commutation of the corresponding matrices in each fragment. Therefore, many highly efficient numerical techniques such as the direct inversion of the iterative subspace method can be employed to converge simultaneously the electronic structure of all fragments, reducing significantly the computational cost. Numerical examples for water clusters of different sizes suggest that the method shall be very useful in improving the scalability of fragment quantum chemistry methods. © 2015 Wiley Periodicals, Inc.

Synthesis of the carbocyclic core of the cornexistins by ring-closing metathesis.

PubMed

Clark, J Stephen; Marlin, Frederic; Nay, Bastien; Wilson, Claire

2003-01-09

An advanced intermediate in the synthesis of the phytotoxins cornexistin and hydroxycornexistin has been synthesized. Sequential palladium-mediated sp(2)-sp(3) fragment coupling and ring-closing diene metathesis have been used to construct the nine-membered carbocyclic core found in the natural products. [reaction--see text

Capsule Escape Tests - Wallops Island

NASA Image and Video Library

1959-05-14

Caption: Off the pad abort shot at Wallops using Langley PARD designed full scale capsule with Recruit rocket and extended skirt main parachute. Shows sequential images of launch and capsule splashdown.

Strategy to obtain axenic cultures from field-collected samples of the cyanobacterium Phormidium animalis.

PubMed

Vázquez-Martínez, Guadalupe; Rodriguez, Mario H; Hernández-Hernández, Fidel; Ibarra, Jorge E

2004-04-01

An efficient strategy, based on a combination of procedures, was developed to obtain axenic cultures from field-collected samples of the cyanobacterium Phormidium animalis. Samples were initially cultured in solid ASN-10 medium, and a crude separation of major contaminants from P. animalis filaments was achieved by washing in a series of centrifugations and resuspensions in liquid medium. Then, manageable filament fragments were obtained by probe sonication. Fragmentation was followed by forceful washing, using vacuum-driven filtration through an 8-microm pore size membrane and an excess of water. Washed fragments were cultured and treated with a sequential exposure to four different antibiotics. Finally, axenic cultures were obtained from serial dilutions of treated fragments. Monitoring under microscope examination and by inoculation in Luria-Bertani (LB) agar plates indicated either axenicity or the degree of contamination throughout the strategy.

Ultrafast fragmentation dynamics of triply charged carbon dioxide: Vibrational-mode-dependent molecular bond breakage

NASA Astrophysics Data System (ADS)

Yang, HongJiang; Wang, Enliang; Dong, WenXiu; Gong, Maomao; Shen, Zhenjie; Tang, Yaguo; Shan, Xu; Chen, Xiangjun

2018-05-01

The a b i n i t i o molecular dynamics (MD) simulations using an atom-centered density matrix propagation method have been carried out to investigate the fragmentation of the ground-state triply charged carbon dioxide, CO23 +→C+ + Oa+ + Ob+ . Ten thousands of trajectories have been simulated. By analyzing the momentum correlation of the final fragments, it is demonstrated that the sequential fragmentation dominates in the three-body dissociation, consistent with our experimental observations which were performed by electron collision at impact energy of 1500 eV. Furthermore, the MD simulations allow us to have detailed insight into the ultrafast evolution of the molecular bond breakage at a very early stage, within several tens of femtoseconds, and the result shows that the initial nuclear vibrational mode plays a decisive role in switching the dissociation pathways.

Sequential power-up circuit

DOEpatents

Kronberg, James W.

1992-01-01

A sequential power-up circuit for starting several electrical load elements in series to avoid excessive current surge, comprising a voltage ramp generator and a set of voltage comparators, each comparator having a different reference voltage and interfacing with a switch that is capable of turning on one of the load elements. As the voltage rises, it passes the reference voltages one at a time and causes the switch corresponding to that voltage to turn on its load element. The ramp is turned on and off by a single switch or by a logic-level electrical signal. The ramp rate for turning on the load element is relatively slow and the rate for turning the elements off is relatively fast. Optionally, the duration of each interval of time between the turning on of the load elements is programmable.

Hospital's activity-based financing system and manager-physician [corrected] interaction.

PubMed

Crainich, David; Leleu, Hervé; Mauleon, Ana

2011-10-01

This paper examines the consequences of the introduction of an activity-based reimbursement system on the behavior of physicians and hospital's managers. We consider a private for-profit sector where both hospitals and physicians are initially paid on a fee-for-service basis. We show that the benefit of the introduction of an activity-based system depends on the type of interaction between managers and physicians (simultaneous or sequential decision-making games). It is shown that, under the activity-based system, a sequential interaction with physician leader could be beneficial for both agents in the private sector. We further model an endogenous timing game à la Hamilton and Slutsky (Games Econ Behav 2: 29-46, 1990) in which the type of interaction is determined endogenously. We show that, under the activity-based system, the sequential interaction with physician leader is the unique subgame perfect equilibrium.

Folding pathway of a multidomain protein depends on its topology of domain connectivity

PubMed Central

Inanami, Takashi; Terada, Tomoki P.; Sasai, Masaki

2014-01-01

How do the folding mechanisms of multidomain proteins depend on protein topology? We addressed this question by developing an Ising-like structure-based model and applying it for the analysis of free-energy landscapes and folding kinetics of an example protein, Escherichia coli dihydrofolate reductase (DHFR). DHFR has two domains, one comprising discontinuous N- and C-terminal parts and the other comprising a continuous middle part of the chain. The simulated folding pathway of DHFR is a sequential process during which the continuous domain folds first, followed by the discontinuous domain, thereby avoiding the rapid decrease in conformation entropy caused by the association of the N- and C-terminal parts during the early phase of folding. Our simulated results consistently explain the observed experimental data on folding kinetics and predict an off-pathway structural fluctuation at equilibrium. For a circular permutant for which the topological complexity of wild-type DHFR is resolved, the balance between energy and entropy is modulated, resulting in the coexistence of the two folding pathways. This coexistence of pathways should account for the experimentally observed complex folding behavior of the circular permutant. PMID:25267632

Breccia Formation at a Complex Impact Crater: Slate Islands, Lake Superior, Ontario, Canada

NASA Technical Reports Server (NTRS)

Dressler, B. O.; Sharpton, V. L.

1997-01-01

The Slate Islands impact structure is the eroded remnant of a approximately 30-32 km-diameter complex impact structure located in northern Lake Superior, Ontario, Canada. Target rocks are Archean supracrustal and igneous rocks and Proterozoic metavolcanics, metasediments, and diabase. A wide variety of breccias occurs on the islands, many of which contain fragments exhibiting shock metamorphic features. Aphanitic, narrow and inclusion-poor pseudotachylite veins, commonly with more or less parallel boundaries and apophyses branching off them, represent the earliest breccias formed during the compression stage of the impact process. Coarse-grained, polymictic elastic matrix breccias form small to very large, inclusion-rich dikes and irregularly shaped bodies that may contain altered glass fragments. These breccias have sharp contacts with their host rocks and include a wide range of fragment types some of which were transported over minimum distances of approximately 2 km away from the center of the structure. They cut across pseudotachylite veins and contain inclusions of them. Field and petrographic evidence indicate that these polymictic breccias formed predominantly during the excavation and central uplift stages of the impact process. Monomictic breccias, characterized by angular fragments and transitional contacts with their host rocks, occur in parautochthonous target rocks, mainly on the outlying islands of the Slate Islands archipelago. A few contain fragmented and disrupted, coarse-grained, polymictic clastic matrix breccia dikes. This is an indication that at least some of these monomictic breccias formed late in the impact process and that they are probably related to a late crater modification stage. A small number of relatively large occurrences of glass-poor, suevitic breccias occur at the flanks of the central uplift and along the inner flank of the outer ring of the Slate Islands complex crater. A coarse, glass-free, allogenic breccia, containing shatter-coned fragments derived from Proterozoic target rocks (upper target strata), observed at two locations may be analogous to the 'Bunt Breccia' of the Ries crater in Germany. At one of these locations this breccia lies close to a crater suevite deposit. At the other, it overlies parautochthonous, monomictic breccia. The State Islands impact breccias are superbly exposed, much better than breccias in most other terrestrial impact structures. Observations, including those indicative of multiple and and sequential processes, provide insight on how impact breccias form and how they relate to the various phases of the impact process. Eventually they will lead to an improved understanding of planetary impact processes.

Optimal control of a coupled partial and ordinary differential equations system for the assimilation of polarimetry Stokes vector measurements in tokamak free-boundary equilibrium reconstruction with application to ITER

NASA Astrophysics Data System (ADS)

Faugeras, Blaise; Blum, Jacques; Heumann, Holger; Boulbe, Cédric

2017-08-01

The modelization of polarimetry Faraday rotation measurements commonly used in tokamak plasma equilibrium reconstruction codes is an approximation to the Stokes model. This approximation is not valid for the foreseen ITER scenarios where high current and electron density plasma regimes are expected. In this work a method enabling the consistent resolution of the inverse equilibrium reconstruction problem in the framework of non-linear free-boundary equilibrium coupled to the Stokes model equation for polarimetry is provided. Using optimal control theory we derive the optimality system for this inverse problem. A sequential quadratic programming (SQP) method is proposed for its numerical resolution. Numerical experiments with noisy synthetic measurements in the ITER tokamak configuration for two test cases, the second of which is an H-mode plasma, show that the method is efficient and that the accuracy of the identification of the unknown profile functions is improved compared to the use of classical Faraday measurements.

Reactive solute transport in streams: 1. Development of an equilibrium- based model

USGS Publications Warehouse

Runkel, Robert L.; Bencala, Kenneth E.; Broshears, Robert E.; Chapra, Steven C.

1996-01-01

An equilibrium-based solute transport model is developed for the simulation of trace metal fate and transport in streams. The model is formed by coupling a solute transport model with a chemical equilibrium submodel based on MINTEQ. The solute transport model considers the physical processes of advection, dispersion, lateral inflow, and transient storage, while the equilibrium submodel considers the speciation and complexation of aqueous species, precipitation/dissolution and sorption. Within the model, reactions in the water column may result in the formation of solid phases (precipitates and sorbed species) that are subject to downstream transport and settling processes. Solid phases on the streambed may also interact with the water column through dissolution and sorption/desorption reactions. Consideration of both mobile (water-borne) and immobile (streambed) solid phases requires a unique set of governing differential equations and solution techniques that are developed herein. The partial differential equations describing physical transport and the algebraic equations describing chemical equilibria are coupled using the sequential iteration approach.

Influence of primary fragment excitation energy and spin distributions on fission observables

NASA Astrophysics Data System (ADS)

Litaize, Olivier; Thulliez, Loïc; Serot, Olivier; Chebboubi, Abdelaziz; Tamagno, Pierre

2018-03-01

Fission observables in the case of 252Cf(sf) are investigated by exploring several models involved in the excitation energy sharing and spin-parity assignment between primary fission fragments. In a first step the parameters used in the FIFRELIN Monte Carlo code "reference route" are presented: two parameters for the mass dependent temperature ratio law and two constant spin cut-off parameters for light and heavy fragment groups respectively. These parameters determine the initial fragment entry zone in excitation energy and spin-parity (E*, Jπ). They are chosen to reproduce the light and heavy average prompt neutron multiplicities. When these target observables are achieved all other fission observables can be predicted. We show here the influence of input parameters on the saw-tooth curve and we discuss the influence of a mass and energy-dependent spin cut-off model on gamma-rays related fission observables. The part of the model involving level densities, neutron transmission coefficients or photon strength functions remains unchanged.

Comparative study of the molecularly imprinted polymers prepared by reversible addition-fragmentation chain transfer "bulk" polymerization and traditional radical "bulk" polymerization.

PubMed

Ma, Yue; Pan, Guoqing; Zhang, Ying; Guo, Xianzhi; Zhang, Huiqi

2013-05-01

Bisphenol A (BPA) and propranolol-imprinted polymers have been prepared via both reversible addition-fragmentation chain transfer "bulk" polymerization (RAFTBP) and traditional radical "bulk" polymerization (TRBP) under similar reaction conditions, and their equilibrium binding properties were compared in detail for the first time. The chemical compositions, specific surface areas, equilibrium bindings, and selectivity of the obtained molecularly imprinted polymers (MIPs) were systematically characterized. The experimental results showed that the MIPs with molecular imprinting effects and quite fast binding kinetics could be readily prepared via RAFTBP, but they did not show improved template binding properties in comparison with those prepared via TRBP, which is in sharp contrast to many previous reports. This could be attributed to the heavily interrupted equilibrium between the dormant species and active radicals in the RAFT mechanism because of the occurrence of fast gelation during RAFTBP. The findings presented here strongly demonstrates that the application of controlled radical polymerizations (CRPs) in molecular imprinting does not always benefit the binding properties of the resultant MIPs, which is of significant importance for the rational use of CRPs in generating MIPs with improved properties. Copyright © 2013 John Wiley & Sons, Ltd.

Equilibria, prudent compromises, and the "waiting" game.

PubMed

Sim, Kwang Mong

2005-08-01

While evaluation of many e-negotiation agents are carried out through empirical studies, this work supplements and complements existing literature by analyzing the problem of designing market-driven agents (MDAs) in terms of equilibrium points and stable strategies. MDAs are negotiation agents designed to make prudent compromises taking into account factors such as time preference, outside option, and rivalry. This work shows that 1) in a given market situation, an MDA negotiates optimally because it makes minimally sufficient concession, and 2) by modeling negotiation of MDAs as a game gamma of incomplete information, it is shown that the strategies adopted by MDAs are stable. In a bilateral negotiation, it is proven that the strategy pair of two MDAs forms a sequential equilibrium for gamma. In a multilateral negotiation, it is shown that the strategy profile of MDAs forms a market equilibrium for gamma.

When and how to operate the posterior malleolus fragment in trimalleolar fractures: a systematic literature review.

PubMed

Verhage, Samuel Marinus; Hoogendoorn, Jochem Maarten; Krijnen, Pieta; Schipper, Inger Birgitta

2018-05-12

Whether or not and how to fixate the posterior malleolus fracture seems to depend on the fracture fragment size and its amount of dislocation, but clear guidelines for daily practice are lacking. In this review, we summarize the literature on preferred treatment of the posterior fragment in trimalleolar fractures. A systematic review of publications between January 1995 and April 30 2017 on this topic in the PubMed, Embase, and Cochrane databases was performed according to the PRISMA statement. Seventeen (2 prospective and 15 retrospective) of the 180 identified studies were included. Six studies report on indications for fixation of posterior malleolus fracture fragments. Eleven studies compare different fixation approaches and techniques for the posterior fragment. Meta-analysis was not possible due to varying fixation criteria and outcomes. There was no clear association between posterior fragment size and functional outcome or development of osteoarthritis. The non-anatomical reduction of the fragment was of more influence on outcome. Radiological and functional outcome was better after open reduction and internal fixation via the posterolateral approach than after percutaneous anterior-to-posterior screw fixation. The posterior fragment size is not a clear indication for its fixation. A step-off, however, seems an important indicator for developing posttraumatic osteoarthritis and worse functional outcome. Posterior fragments involving the intra-articular surface need to be reduced and fixated to prevent postoperative persisting step-off. Furthermore, fixation of the posterior malleolus via an open posterolateral approach seems superior to percutaneous anterior-to-posterior fixation. However, these results need to be confirmed in a prospective comparative trial. Therapeutic level II.

Fast antibody fragment motion: flexible linkers act as entropic spring

PubMed Central

Stingaciu, Laura R.; Ivanova, Oxana; Ohl, Michael; Biehl, Ralf; Richter, Dieter

2016-01-01

A flexible linker region between three fragments allows antibodies to adjust their binding sites to an antigen or receptor. Using Neutron Spin Echo Spectroscopy we observed fragment motion on a timescale of 7 ns with motional amplitudes of about 1 nm relative to each other. The mechanistic complexity of the linker region can be described by a spring model with Brownian motion of the fragments in a harmonic potential. Displacements, timescale, friction and force constant of the underlying dynamics are accessed. The force constant exhibits a similar strength to an entropic spring, with friction of the fragment matching the unbound state. The observed fast motions are fluctuations in pre-existing equilibrium configurations. The Brownian motion of domains in a harmonic potential is the appropriate model to examine functional hinge motions dependent on the structural topology and highlights the role of internal forces and friction to function. PMID:27020739

Fast antibody fragment motion: flexible linkers act as entropic spring

DOE PAGES

Stingaciu, Laura R.; Ivanova, Oxana; Ohl, Michael; ...

2016-03-29

A flexible linker region between three fragments allows antibodies to adjust their binding sites to an antigen or receptor. Using Neutron Spin Echo Spectroscopy we observed fragment motion on a timescale of 7 ns with motional amplitudes of about 1 nm relative to each other. The mechanistic complexity of the linker region can be described by a spring model with Brownian motion of the fragments in a harmonic potential. Displacements, timescale, friction and force constant of the underlying dynamics are accessed. The force constant exhibits a similar strength to an entropic spring, with friction of the fragment matching the unboundmore » state. The observed fast motions are fluctuations in pre-existing equilibrium configurations. In conclusion, the Brownian motion of domains in a harmonic potential is the appropriate model to examine functional hinge motions dependent on the structural topology and highlights the role of internal forces and friction to function.« less

Fast antibody fragment motion: flexible linkers act as entropic spring.

PubMed

Stingaciu, Laura R; Ivanova, Oxana; Ohl, Michael; Biehl, Ralf; Richter, Dieter

2016-03-29

A flexible linker region between three fragments allows antibodies to adjust their binding sites to an antigen or receptor. Using Neutron Spin Echo Spectroscopy we observed fragment motion on a timescale of 7 ns with motional amplitudes of about 1 nm relative to each other. The mechanistic complexity of the linker region can be described by a spring model with Brownian motion of the fragments in a harmonic potential. Displacements, timescale, friction and force constant of the underlying dynamics are accessed. The force constant exhibits a similar strength to an entropic spring, with friction of the fragment matching the unbound state. The observed fast motions are fluctuations in pre-existing equilibrium configurations. The Brownian motion of domains in a harmonic potential is the appropriate model to examine functional hinge motions dependent on the structural topology and highlights the role of internal forces and friction to function.

Understanding the Periodic Table of Elements via Iconic Mapping and Sequential Diagramming: The Roundhouse Strategy

ERIC Educational Resources Information Center

Ward, Robin E.; Lee, William D.

2006-01-01

Roundhouse is a visually creative information-processing tool (J. E. Trowbridge and J. H. Wandersee 1998). The procedure requires learners to construct knowledge using "mindful" connections to replace less effective practices of memorizing fragmented information. Students create observable organization schemes of related ideas and icons in a…

Sequential power-up circuit

DOEpatents

Kronberg, J.W.

1992-06-02

A sequential power-up circuit for starting several electrical load elements in series to avoid excessive current surge, comprising a voltage ramp generator and a set of voltage comparators, each comparator having a different reference voltage and interfacing with a switch that is capable of turning on one of the load elements. As the voltage rises, it passes the reference voltages one at a time and causes the switch corresponding to that voltage to turn on its load element. The ramp is turned on and off by a single switch or by a logic-level electrical signal. The ramp rate for turning on the load element is relatively slow and the rate for turning the elements off is relatively fast. Optionally, the duration of each interval of time between the turning on of the load elements is programmable. 2 figs.

40 CFR 63.680 - Applicability and designation of affected sources.

Code of Federal Regulations, 2014 CFR

2014-07-01

... for the treatment, recycling, or recovery of off-site material. Distillation means a process, either... equilibrium within the distillation unit. (ii) Fractionation process used for the treatment, recycling, or... process used for the treatment, recycling, or recovery of off-site material. Thin-film evaporation means a...

Responsible Grammar Rebels: Using the Hunger Games Trilogy to Teach the Intentional Sentence Fragment

ERIC Educational Resources Information Center

Simmons, Amber M.

2016-01-01

Building off of students' interest in popular apocalyptic/dystopian literature, this article explores how passages from Suzanne Collins's "The Hunger Games" trilogy aided in teaching students how to successfully rebel against traditional grammar rules, looking at fragments as intentional stylistic choices. Employing the values of…

A Classroom Auction with Externalities: Applied to Mergers and Acquisitions

ERIC Educational Resources Information Center

Meister, J. Patrick; Anderson, Kyle J.

2007-01-01

The authors describe an in-class exercise in which students participate in an auction to buy US Airways. The exercise is based on events of late 1995, in which neither United nor American Airlines decided to bid for US Airways. Two teams of students participate in an English auction. Students learn that the equilibrium of the sequential game is…

Mesoscale modeling of vacancy-mediated Si segregation near an edge dislocation in Ni under irradiation

NASA Astrophysics Data System (ADS)

Li, Zebo; Trinkle, Dallas R.

2017-04-01

We use a continuum method informed by transport coefficients computed using self-consistent mean field theory to model vacancy-mediated diffusion of substitutional Si solutes in FCC Ni near an a/2 [1 1 ¯0 ] (111 ) edge dislocation. We perform two sequential simulations: first under equilibrium boundary conditions and then under irradiation. The strain field around the dislocation induces heterogeneity and anisotropy in the defect transport properties and determines the steady-state vacancy and Si distributions. At equilibrium both vacancies and Si solutes diffuse to form Cottrell atmospheres with vacancies accumulating in the compressive region above the dislocation core while Si segregates to the tensile region below the core. Irradiation raises the bulk vacancy concentration, driving vacancies to flow into the dislocation core. The out-of-equilibrium vacancy fluxes drag Si atoms towards the core, causing segregation to the compressive region, despite Si being an oversized solute in Ni.

Chemical reactions simulated by ground-water-quality models

USGS Publications Warehouse

Grove, David B.; Stollenwerk, Kenneth G.

1987-01-01

Recent literature concerning the modeling of chemical reactions during transport in ground water is examined with emphasis on sorption reactions. The theory of transport and reactions in porous media has been well documented. Numerous equations have been developed from this theory, to provide both continuous and sequential or multistep models, with the water phase considered for both mobile and immobile phases. Chemical reactions can be either equilibrium or non-equilibrium, and can be quantified in linear or non-linear mathematical forms. Non-equilibrium reactions can be separated into kinetic and diffusional rate-limiting mechanisms. Solutions to the equations are available by either analytical expressions or numerical techniques. Saturated and unsaturated batch, column, and field studies are discussed with one-dimensional, laboratory-column experiments predominating. A summary table is presented that references the various kinds of models studied and their applications in predicting chemical concentrations in ground waters.

Biological Implications of Dynamical Phases in Non-equilibrium Networks

NASA Astrophysics Data System (ADS)

Murugan, Arvind; Vaikuntanathan, Suriyanarayanan

2016-03-01

Biology achieves novel functions like error correction, ultra-sensitivity and accurate concentration measurement at the expense of free energy through Maxwell Demon-like mechanisms. The design principles and free energy trade-offs have been studied for a variety of such mechanisms. In this review, we emphasize a perspective based on dynamical phases that can explain commonalities shared by these mechanisms. Dynamical phases are defined by typical trajectories executed by non-equilibrium systems in the space of internal states. We find that coexistence of dynamical phases can have dramatic consequences for function vs free energy cost trade-offs. Dynamical phases can also provide an intuitive picture of the design principles behind such biological Maxwell Demons.

Ecological impacts of tropical forest fragmentation: how consistent are patterns in species richness and nestedness?

PubMed

Hill, Jane K; Gray, Michael A; Khen, Chey Vun; Benedick, Suzan; Tawatao, Noel; Hamer, Keith C

2011-11-27

Large areas of tropical forest now exist as remnants scattered across agricultural landscapes, and so understanding the impacts of forest fragmentation is important for biodiversity conservation. We examined species richness and nestedness among tropical forest remnants in birds (meta-analysis of published studies) and insects (field data for fruit-feeding Lepidoptera (butterflies and moths) and ants). Species-area relationships were evident in all four taxa, and avian and insect assemblages in remnants typically were nested subsets of those in larger areas. Avian carnivores and nectarivores and predatory ants were more nested than other guilds, implying that the sequential loss of species was more predictable in these groups, and that fragmentation alters the trophic organization of communities. For butterflies, the ordering of fragments to achieve maximum nestedness was by fragment area, suggesting that differences among fragments were driven mainly by extinction. In contrast for moths, maximum nestedness was achieved by ordering species by wing length; species with longer wings (implying better dispersal) were more likely to occur at all sites, including low diversity sites, suggesting that differences among fragments were driven more strongly by colonization. Although all four taxa exhibited high levels of nestedness, patterns of species turnover were also idiosyncratic, and thus even species-poor sites contributed to landscape-scale biodiversity, particularly for insects.

Ecological impacts of tropical forest fragmentation: how consistent are patterns in species richness and nestedness?

PubMed Central

Hill, Jane K.; Gray, Michael A.; Khen, Chey Vun; Benedick, Suzan; Tawatao, Noel; Hamer, Keith C.

2011-01-01

Large areas of tropical forest now exist as remnants scattered across agricultural landscapes, and so understanding the impacts of forest fragmentation is important for biodiversity conservation. We examined species richness and nestedness among tropical forest remnants in birds (meta-analysis of published studies) and insects (field data for fruit-feeding Lepidoptera (butterflies and moths) and ants). Species–area relationships were evident in all four taxa, and avian and insect assemblages in remnants typically were nested subsets of those in larger areas. Avian carnivores and nectarivores and predatory ants were more nested than other guilds, implying that the sequential loss of species was more predictable in these groups, and that fragmentation alters the trophic organization of communities. For butterflies, the ordering of fragments to achieve maximum nestedness was by fragment area, suggesting that differences among fragments were driven mainly by extinction. In contrast for moths, maximum nestedness was achieved by ordering species by wing length; species with longer wings (implying better dispersal) were more likely to occur at all sites, including low diversity sites, suggesting that differences among fragments were driven more strongly by colonization. Although all four taxa exhibited high levels of nestedness, patterns of species turnover were also idiosyncratic, and thus even species-poor sites contributed to landscape-scale biodiversity, particularly for insects. PMID:22006967

Budget Allocation in a Competitive Communication Spectrum Economy

NASA Astrophysics Data System (ADS)

Lin, Ming-Hua; Tsai, Jung-Fa; Ye, Yinyu

2009-12-01

This study discusses how to adjust "monetary budget" to meet each user's physical power demand, or balance all individual utilities in a competitive "spectrum market" of a communication system. In the market, multiple users share a common frequency or tone band and each of them uses the budget to purchase its own transmit power spectra (taking others as given) in maximizing its Shannon utility or pay-off function that includes the effect of interferences. A market equilibrium is a budget allocation, price spectrum, and tone power distribution that independently and simultaneously maximizes each user's utility. The equilibrium conditions of the market are formulated and analyzed, and the existence of an equilibrium is proved. Computational results and comparisons between the competitive equilibrium and Nash equilibrium solutions are also presented, which show that the competitive market equilibrium solution often provides more efficient power distribution.

Solvent system selectivities in countercurrent chromatography using Salicornia gaudichaudiana metabolites as practical example with off-line electrospray mass-spectrometry injection profiling.

PubMed

Costa, Fernanda das Neves; Jerz, Gerold; Figueiredo, Fabiana de Souza; Winterhalter, Peter; Leitão, Gilda Guimarães

2015-03-13

For the development of an efficient two-stage isolation process for high-speed countercurrent chromatography (HSCCC) with focus on principal metabolites from the ethyl acetate extract of the halophyte plant Salicornia gaudichaudiana, separation selectivities of two different biphasic solvent systems with similar polarities were evaluated using the elution and extrusion approach. Efficiency in isolation of target compounds is determined by the solvent system selectivity and their chronological use in multiple separation steps. The system n-hexane-ethyl acetate-methanol-water (0.5:6:0.5:6, v/v/v/v) resulted in a comprehensive separation of polyphenolic glycosides. The system n-hexane-n-butanol-water (1:1:2, v/v/v) was less universal but was highly efficient in the fractionation of positional isomers such as di-substituted cinnamic acid quinic acid derivatives. Multiple metabolite detection performed on recovered HSCCC tube fractions was done with rapid mass-spectrometry profiling by sequential off-line injections to electrospray mass-spectrometry (ESI-MS/MS). Selective ion traces of metabolites delivered reconstituted preparative HSCCC runs. Molecular weight distribution of target compounds in single HSCCC tube fractions and MS/MS fragment data were available. Chromatographic areas with strong co-elution effects and fractions of pure recoverable compounds were visualized. In total 11 metabolites have been identified and monitored. Result of this approach was a fast isolation protocol for S. gaudichaudiana metabolites using two solvent systems in a strategic sequence. The process could easily be scaled-up to larger lab-scale or industrial recovery. Copyright © 2015 Elsevier B.V. All rights reserved.

Descriptive study of the Socratic method: evidence for verbal shaping.

PubMed

Calero-Elvira, Ana; Froján-Parga, María Xesús; Ruiz-Sancho, Elena María; Alpañés-Freitag, Manuel

2013-12-01

In this study we analyzed 65 fragments of session recordings in which a cognitive behavioral therapist employed the Socratic method with her patients. Specialized coding instruments were used to categorize the verbal behavior of the psychologist and the patients. First the fragments were classified as more or less successful depending on the overall degree of concordance between the patient's verbal behavior and the therapeutic objectives. Then the fragments were submitted to sequential analysis so as to discover regularities linking the patient's verbal behavior and the therapist's responses to it. Important differences between the more and the less successful fragments involved the therapist's approval or disapproval of verbalizations that approximated therapeutic goals. These approvals and disapprovals were associated with increases and decreases, respectively, in the patient's behavior. These results are consistent with the existence, in this particular case, of a process of shaping through which the therapist modifies the patient's verbal behavior in the overall direction of his or her chosen therapeutic objectives. © 2013.

2D FT-ICR MS of Calmodulin: A Top-Down and Bottom-Up Approach.

PubMed

Floris, Federico; van Agthoven, Maria; Chiron, Lionel; Soulby, Andrew J; Wootton, Christopher A; Lam, Yuko P Y; Barrow, Mark P; Delsuc, Marc-André; O'Connor, Peter B

2016-09-01

Two-dimensional Fourier transform ion cyclotron resonance mass spectrometry (2D FT-ICR MS) allows data-independent fragmentation of all ions in a sample and correlation of fragment ions to their precursors through the modulation of precursor ion cyclotron radii prior to fragmentation. Previous results show that implementation of 2D FT-ICR MS with infrared multi-photon dissociation (IRMPD) and electron capture dissociation (ECD) has turned this method into a useful analytical tool. In this work, IRMPD tandem mass spectrometry of calmodulin (CaM) has been performed both in one-dimensional and two-dimensional FT-ICR MS using a top-down and bottom-up approach. 2D IRMPD FT-ICR MS is used to achieve extensive inter-residue bond cleavage and assignment for CaM, using its unique features for fragment identification in a less time- and sample-consuming experiment than doing the same thing using sequential MS/MS experiments. Graphical Abstract ᅟ.

Linkage and Anomeric Differentiation in Trisaccharides by Sequential Fragmentation and Variable-Wavelength Infrared Photodissociation

NASA Astrophysics Data System (ADS)

Tan, Yanglan; Polfer, Nicolas C.

2015-02-01

Carbohydrates and their derivatives play important roles in biological systems, but their isomeric heterogeneity also presents a considerable challenge for analytical techniques. Here, a stepwise approach using infrared multiple-photon dissociation (IRMPD) via a tunable CO2 laser (9.2-10.7 μm) was employed to characterize isomeric variants of glucose-based trisaccharides. After the deprotonated trisaccharides were trapped and fragmented to disaccharide C2 fragments in a Fourier transform ion cyclotron resonance (FTICR) cell, a further variable-wavelength infrared irradiation of the C2 ion produced wavelength-dependent dissociation patterns that are represented as heat maps. The photodissociation patterns of these C2 fragments are shown to be strikingly similar to the photodissociation patterns of disaccharides with identical glycosidic bonds. Conversely, the photodissociation patterns of different glycosidic linkages exhibit considerable differences. On the basis of these results, the linkage position and anomericity of glycosidic bonds of disaccharide units in trisaccharides can be systematically differentiated and identified, providing a promising approach to characterize the structures of isomeric oligosaccharides.

Convergent solid-phase synthesis of hirudin.

PubMed

Goulas, Spyros; Gatos, Dimitrios; Barlos, Kleomenis

2006-02-01

Hirudin variant 1 (HV1), a small protein consisting of 65 amino acids and three disulfide bonds, was synthesized by using Fmoc-based convergent methods on 2-chlorotrityl resin (CLTR). The linear sequence was assembled by the sequential condensation of 7 protected fragments, on the resin-bound 55-65 fragment. The conditions of fragment assembly were carefully studied to determine the most efficient synthetic protocol. Crude reduced [Cys(16, 28)(Acm)]-HV1 thus obtained was easily purified to homogeneity by RP-HPLC. Disulfide bridges were successfully formed by a two-step procedure, involving an oxidative folding step to form Cys(6)-Cys(14) and Cys(22)-Cys(39) linkages, followed by iodine oxidation to form the Cys(16)-Cys(28) bond. The correct disulfide bond alignment was established by peptide mapping using Staphylococcus aureus V8 protease at pH 4.5.

Terrane accretion: Insights from numerical modelling

NASA Astrophysics Data System (ADS)

Vogt, Katharina; Gerya, Taras

2016-04-01

The oceanic crust is not homogenous, but contains significantly thicker crust than norm, i.e. extinct arcs, spreading ridges, detached continental fragments, volcanic piles or oceanic swells. These (crustal) fragments may collide with continental crust and form accretionary complexes, contributing to its growth. We analyse this process using a thermo-mechanical computer model (i2vis) of an ocean-continent subduction zone. In this model the oceanic plate can bend spontaneously under the control of visco-plastic rheologies. It moreover incorporates effects such as mineralogical phase changes, fluid release and consumption, partial melting and melt extraction. Based on our 2-D experiments we suggest that the lithospheric buoyancy of the downgoing slab and the rheological strength of crustal material may result in a variety of accretionary processes. In addition to terrane subduction, we are able to identify three distinct modes of terrane accretion: frontal accretion, basal accretion and underplating plateaus. We show that crustal fragments may dock onto continental crust and cease subduction, be scrapped off the downgoing plate, or subduct to greater depth prior to slab break off and subsequent exhumation. Direct consequences of these processes include slab break off, subduction zone transference, structural reworking, formation of high-pressure terranes, partial melting and crustal growth.

Dynamics of fragment formation in neutron-rich matter

NASA Astrophysics Data System (ADS)

Alcain, P. N.; Dorso, C. O.

2018-01-01

Background: Neutron stars are astronomical systems with nucleons subjected to extreme conditions. Due to the longer range Coulomb repulsion between protons, the system has structural inhomogeneities. Several interactions tailored to reproduce nuclear matter plus a screened Coulomb term reproduce these inhomogeneities known as nuclear pasta. These structural inhomogeneities, located in the crusts of neutron stars, can also arise in expanding systems depending on the thermodynamic conditions (temperature, proton fraction, etc.) and the expansion velocity. Purpose: We aim to find the dynamics of the fragment formation for expanding systems simulated according to the little big bang model. This expansion resembles the evolution of merging neutron stars. Method: We study the dynamics of the nucleons with semiclassical molecular dynamics models. Starting with an equilibrium configuration, we expand the system homogeneously until we arrive at an asymptotic configuration (i.e., very low final densities). We study, with four different cluster recognition algorithms, the fragment distribution throughout this expansion and the dynamics of the cluster formation. Results: Studying the topology of the equilibrium states, before the expansion, we reproduced the known pasta phases plus a novel phase we called pregnocchi, consisting of proton aggregates embedded in a neutron sea. We have identified different fragmentation regimes, depending on the initial temperature and fragment velocity. In particular, for the already mentioned pregnocchi, a neutron cloud surrounds the clusters during the early stages of the expansion, resulting in systems that give rise to configurations compatible with the emergence of the r process. Conclusions: We showed that a proper identification of the cluster distribution is highly dependent on the cluster recognition algorithm chosen, and found that the early cluster recognition algorithm (ECRA) was the most stable one. This approach allowed us to identify the dynamics of the fragment formation. These calculations pave the way to a comparison between Earth experiments and neutron star studies.

The sensitivity of tokamak magnetohydrodynamics stability on the edge equilibrium

NASA Astrophysics Data System (ADS)

Zheng, L. J.; Kotschenreuther, M. T.; Valanju, P.

2017-10-01

Due to the X-point singularity, the safety factor tends to infinity as approaching to the last closed flux surface. The numerical treatments of the near X-point behavior become challenging both for equilibrium and stability. The usual solution is to cut off a small fraction of edge region for system stability evaluation or simply use an up-down symmetric equilibrium without X-point as an approximation. In this work, we assess the sensitivity of this type of equilibrium treatments on the stability calculation. It is found that the system stability can depend strongly on the safety factor value (qa) at the edge after the cutting-off. When the edge safety factor value falls in the vicinity of a rational mode number (referred to as the resonant gap), the system becomes quite unstable due to the excitation of the peeling type modes. Instead, when the edge safety factor is outside the resonant gaps, the system is much more stable and the predominant modes become the usual external kink (or ballooning and infernal) type. It is also found that the resonant gaps become smaller and smaller as qa increases. The ideal magnetohydrodynamic peeling ballooning stability diagram is widely used to explain the experimental observations, and the current results indicate that the conventional peeling ballooning stability diagram based on the simplified equilibrium needs to be reexamined.

Population annealing simulations of a binary hard-sphere mixture

NASA Astrophysics Data System (ADS)

Callaham, Jared; Machta, Jonathan

2017-06-01

Population annealing is a sequential Monte Carlo scheme well suited to simulating equilibrium states of systems with rough free energy landscapes. Here we use population annealing to study a binary mixture of hard spheres. Population annealing is a parallel version of simulated annealing with an extra resampling step that ensures that a population of replicas of the system represents the equilibrium ensemble at every packing fraction in an annealing schedule. The algorithm and its equilibration properties are described, and results are presented for a glass-forming fluid composed of a 50/50 mixture of hard spheres with diameter ratio of 1.4:1. For this system, we obtain precise results for the equation of state in the glassy regime up to packing fractions φ ≈0.60 and study deviations from the Boublik-Mansoori-Carnahan-Starling-Leland equation of state. For higher packing fractions, the algorithm falls out of equilibrium and a free volume fit predicts jamming at packing fraction φ ≈0.667 . We conclude that population annealing is an effective tool for studying equilibrium glassy fluids and the jamming transition.

Intermittent many-body dynamics at equilibrium

NASA Astrophysics Data System (ADS)

Danieli, C.; Campbell, D. K.; Flach, S.

2017-06-01

The equilibrium value of an observable defines a manifold in the phase space of an ergodic and equipartitioned many-body system. A typical trajectory pierces that manifold infinitely often as time goes to infinity. We use these piercings to measure both the relaxation time of the lowest frequency eigenmode of the Fermi-Pasta-Ulam chain, as well as the fluctuations of the subsequent dynamics in equilibrium. The dynamics in equilibrium is characterized by a power-law distribution of excursion times far off equilibrium, with diverging variance. Long excursions arise from sticky dynamics close to q -breathers localized in normal mode space. Measuring the exponent allows one to predict the transition into nonergodic dynamics. We generalize our method to Klein-Gordon lattices where the sticky dynamics is due to discrete breathers localized in real space.

Criticality in a non-equilibrium, driven system: charged colloidal rods (fd-viruses) in electric fields.

PubMed

Kang, K; Dhont, J K G

2009-11-01

Experiments on suspensions of charged colloidal rods (fd-virus particles) in external electric fields are performed, which show that a non-equilibrium critical point can be identified. Several transition lines of field-induced phases and states meet at this point and it is shown that there is a length- and time-scale which diverge at the non-equilibrium critical point. The off-critical and critical behavior is characterized, with both power law and logarithmic divergencies. These experiments show that analogous features of the classical, critical divergence of correlation lengths and relaxation times in equilibrium systems are also exhibited by driven systems that are far out of equilibrium, related to phases/states that do not exist in the absence of the external field.

Design and objectives of FTM-West model

Treesearch

Peter J. Ince; Henry Spelter

2006-01-01

The FTM-West (“fuel treatment market” model for U.S. West) is a dynamic partial market equilibrium model of regional softwood timber and wood product markets, designed to project future market impacts of expanded fuel treatment programs that remove trees to reduce fire hazard on forestlands in the U.S. West. The model solves sequentially the annual equilibria in wood...

Periodate and hypobromite modification of Southern pine wood to improve sorption of copper ion

Treesearch

James D. McSweeny; Roger M. Rowell; George C. Chen; Thomas L. Eberhardt; Min Soo-Hong

2008-01-01

Milled southern pine wood was modified with sequential treatments of sodium periodate and sodium hypobromite for the purpose of improving copper ion (Cu2+) sorption capacity of the wood when tested in 24-h equilibrium batch tests. The modified wood provided additional carboxyl groups to those in the native wood and substantially increased Cu2+ uptake over that of...

Neutron production in coincidence with fragments from the 4Ca+H reactions at Elab=357 and 565 A MeV

NASA Astrophysics Data System (ADS)

Tuvà, C.; Albergo, S.; Boemi, D.; Caccia, Z.; Chen, C.-X.; Costa, S.; Crawford, H. J.; Cronqvist, M.; Engelage, J.; Greiner, L.; Guzik, T. G.; Insolia, A.; Knott, C. N.; Lindstrom, P. J.; Mitchell, J. W.; Potenza, R.; Russo, G. V.; Soutoul, A.; Testard, O.; Tricomi, A.; Tull, C. E.; Waddington, C. J.; Webber, W. R.; Wefel, J. P.

2000-04-01

In the frame of the Transport Collaboration neutrons in coincidence with charged fragments produced in the 40Ca+H reaction at Elab=357 and 565 A MeV have been measured at the Heavy Ion Spectrometer System (HISS) facility of the Lawrence Berkeley National Laboratory, using the multifunctional neutron spectrometer MUFFINS. The detector covered a narrow angular range about the beam in the forward direction (0°-3.2°). In this contribution we report absolute neutron production cross sections in coincidence with charged fragments (10⩽Z⩽20). The neutron multiplicities have been estimated from the comparison between the neutron cross sections, in coincidence with the fragments, and the elemental cross sections. We have found evidence for a pre-equilibrium emission of prompt neutrons in superposition to a `slower' deexcitation of the equilibrated remnant by emission of nucleons and fragments, as already seen in the inclusive rapidity distributions.

Movement of particles using sequentially activated dielectrophoretic particle trapping

DOEpatents

Miles, Robin R.

2004-02-03

Manipulation of DNA and cells/spores using dielectrophoretic (DEP) forces to perform sample preparation protocols for polymerized chain reaction (PCR) based assays for various applications. This is accomplished by movement of particles using sequentially activated dielectrophoretic particle trapping. DEP forces induce a dipole in particles, and these particles can be trapped in non-uniform fields. The particles can be trapped in the high field strength region of one set of electrodes. By switching off this field and switching on an adjacent electrodes, particles can be moved down a channel with little or no flow.

Essentials of Conservation Biotechnology: A mini review

NASA Astrophysics Data System (ADS)

Merlyn Keziah, S.; Subathra Devi, C.

2017-11-01

Equilibrium of biodiversity is essential for the maintenance of the ecosystem as they are interdependent on each other. The decline in biodiversity is a global problem and an inevitable threat to the mankind. Major threats include unsustainable exploitation, habitat destruction, fragmentation, transformation, genetic pollution, invasive exotic species and degradation. This review covers the management strategies of biotechnology which include sin situ, ex situ conservation, computerized taxonomic analysis through construction of phylogenetic trees, calculating genetic distance, prioritizing the group for conservation, digital preservation of biodiversities within the coding and decoding keys, molecular approaches to asses biodiversity like polymerase chain reaction, real time, randomly amplified polymorphic DNA, restriction fragment length polymorphism, amplified fragment length polymorphism, single sequence repeats, DNA finger printing, single nucleotide polymorphism, cryopreservation and vitrification.

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

Tuve, C.; Albergo, S.; Boemi, D.

In the frame of the Transport Collaboration neutrons in coincidence with charged fragments produced in the {sup 40}Ca + H reaction at E{sub lab} = 357 and 565 AMeV have been measured at the Heavy Ion Spectrometer System (HISS) facility of the Lawrence Berkeley National Laboratory, using the multifunctional neutron spectrometer MUFFINS. The detector covered a narrow angular range about the beam in the forward direction (0? - 3.2?). In this contribution we report absolute neutron production cross sections in coincidence with charged fragments (10 {<=} Z {<=} 20). The neutron multiplicities have been estimated from the comparison between themore » neutron cross sections, in coincidence with the fragments, and the elemental cross sections. We have found evidence for a pre-equilibrium emission of prompt neutrons in superposition to a 'slower' deexcitation of the equilibrated remnant by emission of nucleons and fragments, as already seen in the inclusive rapidity distributions.« less

Redistribution of flexibility in stabilizing antibody fragment mutants follows Le Châtelier's principle.

PubMed

Li, Tong; Tracka, Malgorzata B; Uddin, Shahid; Casas-Finet, Jose; Jacobs, Donald J; Livesay, Dennis R

2014-01-01

Le Châtelier's principle is the cornerstone of our understanding of chemical equilibria. When a system at equilibrium undergoes a change in concentration or thermodynamic state (i.e., temperature, pressure, etc.), La Châtelier's principle states that an equilibrium shift will occur to offset the perturbation and a new equilibrium is established. We demonstrate that the effects of stabilizing mutations on the rigidity ⇔ flexibility equilibrium within the native state ensemble manifest themselves through enthalpy-entropy compensation as the protein structure adjusts to restore the global balance between the two. Specifically, we characterize the effects of mutation to single chain fragments of the anti-lymphotoxin-β receptor antibody using a computational Distance Constraint Model. Statistically significant changes in the distribution of both rigidity and flexibility within the molecular structure is typically observed, where the local perturbations often lead to distal shifts in flexibility and rigidity profiles. Nevertheless, the net gain or loss in flexibility of individual mutants can be skewed. Despite all mutants being exclusively stabilizing in this dataset, increased flexibility is slightly more common than increased rigidity. Mechanistically the redistribution of flexibility is largely controlled by changes in the H-bond network. For example, a stabilizing mutation can induce an increase in rigidity locally due to the formation of new H-bonds, and simultaneously break H-bonds elsewhere leading to increased flexibility distant from the mutation site via Le Châtelier. Increased flexibility within the VH β4/β5 loop is a noteworthy illustration of this long-range effect.

Redistribution of Flexibility in Stabilizing Antibody Fragment Mutants Follows Le Châtelier’s Principle

PubMed Central

Li, Tong; Tracka, Malgorzata B.; Uddin, Shahid; Casas-Finet, Jose; Jacobs, Donald J.; Livesay, Dennis R.

2014-01-01

Le Châtelier’s principle is the cornerstone of our understanding of chemical equilibria. When a system at equilibrium undergoes a change in concentration or thermodynamic state (i.e., temperature, pressure, etc.), La Châtelier’s principle states that an equilibrium shift will occur to offset the perturbation and a new equilibrium is established. We demonstrate that the effects of stabilizing mutations on the rigidity ⇔ flexibility equilibrium within the native state ensemble manifest themselves through enthalpy-entropy compensation as the protein structure adjusts to restore the global balance between the two. Specifically, we characterize the effects of mutation to single chain fragments of the anti-lymphotoxin-β receptor antibody using a computational Distance Constraint Model. Statistically significant changes in the distribution of both rigidity and flexibility within the molecular structure is typically observed, where the local perturbations often lead to distal shifts in flexibility and rigidity profiles. Nevertheless, the net gain or loss in flexibility of individual mutants can be skewed. Despite all mutants being exclusively stabilizing in this dataset, increased flexibility is slightly more common than increased rigidity. Mechanistically the redistribution of flexibility is largely controlled by changes in the H-bond network. For example, a stabilizing mutation can induce an increase in rigidity locally due to the formation of new H-bonds, and simultaneously break H-bonds elsewhere leading to increased flexibility distant from the mutation site via Le Châtelier. Increased flexibility within the VH β4/β5 loop is a noteworthy illustration of this long-range effect. PMID:24671209

Plasma shaping effects on tokamak scrape-off layer turbulence

NASA Astrophysics Data System (ADS)

Riva, Fabio; Lanti, Emmanuel; Jolliet, Sébastien; Ricci, Paolo

2017-03-01

The impact of plasma shaping on tokamak scrape-off layer (SOL) turbulence is investigated. The drift-reduced Braginskii equations are written for arbitrary magnetic geometries, and an analytical equilibrium model is used to introduce the dependence of turbulence equations on tokamak inverse aspect ratio (ε ), Shafranov’s shift (Δ), elongation (κ), and triangularity (δ). A linear study of plasma shaping effects on the growth rate of resistive ballooning modes (RBMs) and resistive drift waves (RDWs) reveals that RBMs are strongly stabilized by elongation and negative triangularity, while RDWs are only slightly stabilized in non-circular magnetic geometries. Assuming that the linear instabilities saturate due to nonlinear local flattening of the plasma gradient, the equilibrium gradient pressure length {L}p=-{p}e/{{\

Folding mechanism of an extremely thermostable (βα)(8)-barrel enzyme: a high kinetic barrier protects the protein from denaturation.

PubMed

Carstensen, Linn; Zoldák, Gabriel; Schmid, Franz-Xaver; Sterner, Reinhard

2012-04-24

HisF, the cyclase subunit of imidazole glycerol phosphate synthase (ImGPS) from Thermotoga maritima, is an extremely thermostable (βα)(8)-barrel protein. We elucidated the unfolding and refolding mechanism of HisF. Its unfolding transition is reversible and adequately described by the two-state model, but 6 weeks is necessary to reach equilibrium (at 25 °C). During refolding, initially a burst-phase off-pathway intermediate is formed. The subsequent productive folding occurs in two kinetic phases with time constants of ~3 and ~20 s. They reflect a sequential process via an on-pathway intermediate, as revealed by stopped-flow double-mixing experiments. The final step leads to native HisF, which associates with the glutaminase subunit HisH to form the functional ImGPS complex. The conversion of the on-pathway intermediate to the native protein results in a 10(6)-fold increase of the time constant for unfolding from 89 ms to 35 h (at 4.0 M GdmCl) and thus establishes a high energy barrier to denaturation. We conclude that the extra stability of HisF is used for kinetic protection against unfolding. In its refolding mechanism, HisF resembles other (βα)(8)-barrel proteins.

A method to calculate fission-fragment yields Y(Z,N) versus proton and neutron number in the Brownian shape-motion model

DOE PAGES

Moller, Peter; Ichikawa, Takatoshi

2015-12-23

In this study, we propose a method to calculate the two-dimensional (2D) fission-fragment yield Y(Z,N) versus both proton and neutron number, with inclusion of odd-even staggering effects in both variables. The approach is to use the Brownian shape-motion on a macroscopic-microscopic potential-energy surface which, for a particular compound system is calculated versus four shape variables: elongation (quadrupole moment Q 2), neck d, left nascent fragment spheroidal deformation ϵ f1, right nascent fragment deformation ϵ f2 and two asymmetry variables, namely proton and neutron numbers in each of the two fragments. The extension of previous models 1) introduces a method tomore » calculate this generalized potential-energy function and 2) allows the correlated transfer of nucleon pairs in one step, in addition to sequential transfer. In the previous version the potential energy was calculated as a function of Z and N of the compound system and its shape, including the asymmetry of the shape. We outline here how to generalize the model from the “compound-system” model to a model where the emerging fragment proton and neutron numbers also enter, over and above the compound system composition.« less

Tapering off long-term opioid therapy in chronic non-cancer pain patients: a randomized clinical trial.

PubMed

Kurita, Geana Paula; Højsted, Jette; Sjøgren, Per

2018-05-13

The indications for initiating long-term opioid treatment (L-TOT) for chronic non-cancer pain (CNCP) are often unclear and associated with problematic use. This study aimed at evaluating the efficacy of stabilizing opioid therapy followed by a sequential opioid tapering off program in CNCP patients. A randomized clinical trial with a medications stabilization period (Phase 1) followed by a opioid tapering off program (Phase 2). In Phase 2, patients were randomized to Control Group (stable treatment) or Taper off Group (sequential opioid dose reduction) and assessed at baseline, after stabilization and up to six months. Primary outcomes: measures of cognitive function; secondary outcomes: pain, sleep, rest, quality of life, depression, anxiety, opioid misuse, and opioid withdrawal symptoms. Two hundred seventy-four patients were screened; 75 were included, out of which 40 dropped out before Phase 2. Those who succeeded Phase 1 (n=35) had weak/moderate improvements of psychomotor function (p=0.020), sleeping hours (p=0.031), opioid withdrawal symptoms (p=0.019), measures of quality of life (p≤0.043) and opioid misuse scores (p=0.003). In Phase 2, patients in Taper off Group (n=15) experienced stable pain intensity and felt significantly more rested at third assessment than the Control Group (n=20). The opioid tapering off program was not successful due to the vast number of dropouts. Phase 1 was associated with weak to moderate improvements on psychomotor function, sleeping, opioid withdrawal symptoms, quality of life, and reduced risk of opioid misuse. In the intervention group of Phase 2, pain intensity was stable and patients felt more rested. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Object formation in visual working memory: Evidence from object-based attention.

PubMed

Zhou, Jifan; Zhang, Haihang; Ding, Xiaowei; Shui, Rende; Shen, Mowei

2016-09-01

We report on how visual working memory (VWM) forms intact perceptual representations of visual objects using sub-object elements. Specifically, when objects were divided into fragments and sequentially encoded into VWM, the fragments were involuntarily integrated into objects in VWM, as evidenced by the occurrence of both positive and negative object-based attention effects: In Experiment 1, when subjects' attention was cued to a location occupied by the VWM object, the target presented at the location of that object was perceived as occurring earlier than that presented at the location of a different object. In Experiment 2, responses to a target were significantly slower when a distractor was presented at the same location as the cued object (Experiment 2). These results suggest that object fragments can be integrated into objects within VWM in a manner similar to that of visual perception. Copyright © 2016 Elsevier B.V. All rights reserved.

Correlations between emission timescale of fragments and isospin dynamics in 124Sn+64Ni and 112Sn+58Ni reactions at 35A MeV

NASA Astrophysics Data System (ADS)

De Filippo, E.; Pagano, A.; Russotto, P.; Amorini, F.; Anzalone, A.; Auditore, L.; Baran, V.; Berceanu, I.; Borderie, B.; Bougault, R.; Bruno, M.; Cap, T.; Cardella, G.; Cavallaro, S.; Chatterjee, M. B.; Chbihi, A.; Colonna, M.; D'Agostino, M.; Dayras, R.; Di Toro, M.; Frankland, J.; Galichet, E.; Gawlikowicz, W.; Geraci, E.; Grzeszczuk, A.; Guazzoni, P.; Kowalski, S.; La Guidara, E.; Lanzalone, G.; Lanzanò, G.; Le Neindre, N.; Lombardo, I.; Maiolino, C.; Papa, M.; Piasecki, E.; Pirrone, S.; Płaneta, R.; Politi, G.; Pop, A.; Porto, F.; Rivet, M. F.; Rizzo, F.; Rosato, E.; Schmidt, K.; Siwek-Wilczyńska, K.; Skwira-Chalot, I.; Trifirò, A.; Trimarchi, M.; Verde, G.; Vigilante, M.; Wieleczko, J. P.; Wilczyński, J.; Zetta, L.; Zipper, W.

2012-07-01

We present a new experimental method to correlate the isotopic composition of intermediate mass fragments (IMF) emitted at midrapidity in semiperipheral collisions with the emission timescale: IMFs emitted in the early stage of the reaction show larger values of isospin asymmetry, stronger angular anisotropies, and reduced odd-even staggering effects in neutron to proton ratio distributions than those produced in sequential statistical emission. All these effects support the concept of isospin “migration”, that is sensitive to the density gradient between participant and quasispectator nuclear matter, in the so called neck fragmentation mechanism. By comparing the data to a stochastic mean field (SMF) simulation we show that this method gives valuable constraints on the symmetry energy term of nuclear equation of state at subsaturation densities. An indication emerges for a linear density dependence of the symmetry energy.

Monitoring lipase/esterase activity by stopped flow in a sequential injection analysis system using p-nitrophenyl butyrate.

PubMed

Pliego, Jorge; Mateos, Juan Carlos; Rodriguez, Jorge; Valero, Francisco; Baeza, Mireia; Femat, Ricardo; Camacho, Rosa; Sandoval, Georgina; Herrera-López, Enrique J

2015-01-27

Lipases and esterases are biocatalysts used at the laboratory and industrial level. To obtain the maximum yield in a bioprocess, it is important to measure key variables, such as enzymatic activity. The conventional method for monitoring hydrolytic activity is to take out a sample from the bioreactor to be analyzed off-line at the laboratory. The disadvantage of this approach is the long time required to recover the information from the process, hindering the possibility to develop control systems. New strategies to monitor lipase/esterase activity are necessary. In this context and in the first approach, we proposed a lab-made sequential injection analysis system to analyze off-line samples from shake flasks. Lipase/esterase activity was determined using p-nitrophenyl butyrate as the substrate. The sequential injection analysis allowed us to measure the hydrolytic activity from a sample without dilution in a linear range from 0.05-1.60 U/mL, with the capability to reach sample dilutions up to 1000 times, a sampling frequency of five samples/h, with a kinetic reaction of 5 min and a relative standard deviation of 8.75%. The results are promising to monitor lipase/esterase activity in real time, in which optimization and control strategies can be designed.

Monitoring Lipase/Esterase Activity by Stopped Flow in a Sequential Injection Analysis System Using p-Nitrophenyl Butyrate

PubMed Central

Pliego, Jorge; Mateos, Juan Carlos; Rodriguez, Jorge; Valero, Francisco; Baeza, Mireia; Femat, Ricardo; Camacho, Rosa; Sandoval, Georgina; Herrera-López, Enrique J.

2015-01-01

Lipases and esterases are biocatalysts used at the laboratory and industrial level. To obtain the maximum yield in a bioprocess, it is important to measure key variables, such as enzymatic activity. The conventional method for monitoring hydrolytic activity is to take out a sample from the bioreactor to be analyzed off-line at the laboratory. The disadvantage of this approach is the long time required to recover the information from the process, hindering the possibility to develop control systems. New strategies to monitor lipase/esterase activity are necessary. In this context and in the first approach, we proposed a lab-made sequential injection analysis system to analyze off-line samples from shake flasks. Lipase/esterase activity was determined using p-nitrophenyl butyrate as the substrate. The sequential injection analysis allowed us to measure the hydrolytic activity from a sample without dilution in a linear range from 0.05–1.60 U/mL, with the capability to reach sample dilutions up to 1000 times, a sampling frequency of five samples/h, with a kinetic reaction of 5 min and a relative standard deviation of 8.75%. The results are promising to monitor lipase/esterase activity in real time, in which optimization and control strategies can be designed. PMID:25633600

Fission Fragment Studies by Gamma-Ray Spectrometry with the Mass Separator Lohengrin

NASA Astrophysics Data System (ADS)

Materna, T.; Amouroux, C.; Bail, A.; Bideau, A.; Chabod, S.; Faust, H.; Capellan, N.; Kessedjian, G.; Köster, U.; Letourneau, A.; Litaize, O.; Martin, F.; Mathieu, L.; Méplan, O.; Panebianco, S.; Régis, J.-M.; Rudigier, M.; Sage, C.; Serot, O.; Urban, W.

2014-09-01

A gamma spectrometric technique was implemented at the exit of the fission fragment separator of the ILL. It allows a precise measurement of isotopic yields of most important actinides in the heavy fragment region by an unambiguous identification of the nuclear charge of the fragments selected by the mass spectrometer. The status of the project and last results are reviewed. A spin-off of this activity is the identification of unknown nanosecond isomers in exotic nuclei through the observation of a disturbed ionic charge distribution. This technique has been improved to provide an estimation of the lifetime of the isomeric state.

Totally endoscopic sequential arterial coronary artery bypass grafting on the beating heart

PubMed Central

Ak, Koray; Wimmer-Greinecker, Gerhard; Dzemali, Omer; Moritz, Anton; Dogan, Selami

2007-01-01

A 50-year-old man was referred to the Department of Thoracic and Cardiovascular Surgery at the Johann Wolfgang-Goethe University (Frankfurt, Germany) with angina on exertion. An evaluation revealed critical stenosis involving the proximal portion of the left anterior descending artery and the first diagonal branch. The patient underwent successful sequential grafting of the left internal mammary artery to the left anterior descending artery and the diagonal branch using a totally endoscopic coronary artery bypass grafting technique on the beating heart with a new version of the da Vinci Surgical System (Intuitive Surgical, USA). To the authors’ knowledge, this is the first report in literature to describe sequential arterial off-pump grafting of two anterior wall target vessels using a totally endoscopic technique on the beating heart. PMID:17440646

Conformational and stereoelectronic investigation in 1,2-difluoropropane: The gauche effect

NASA Astrophysics Data System (ADS)

Bitencourt, Michelle; Freitas, Matheus P.; Rittner, Roberto

2007-09-01

The effect of attaching an additional fluorine atom at C-2 in 1-fluoropropane (FP), giving 1,2-difluoropropane (DFP), on its conformational equilibrium, is theoretically evaluated. This substitution causes critical implications on the conformer stabilities of DFP (TG, GT and GG conformations) and the steric and electrostatic interactions should favor the conformer with fluorine atoms trans. However, the gauche effect plays a major role in describing the energies balance in DFP, shifting the equilibrium towards the conformation in which the two fluorine atoms are gauche. The origin of this effect is discussed through an NBO analysis, which allows the evaluation of both classical and non-classical (hyperconjugation and bent bonds) interactions as the prevailing factors governing the conformational equilibrium of molecules containing the 1,2-difluoroethane fragment.

Free energy change of off-eutectic binary alloys on solidification

NASA Technical Reports Server (NTRS)

Ohsaka, K.; Trinh, E. H.; Lin, J.-C.; Perepezko, J. H.

1991-01-01

A formula for the free energy difference between the undercooled liquid phase and the stable solid phase is derived for off-eutectic binary alloys in which the equilibrium solid/liquid transition takes place over a certain temperature range. The free energy change is then evaluated numerically for a Bi-25 at. pct Cd alloy modeled as a sub-subregular solution.

Equilibrium properties of blackbody radiation with an ultraviolet energy cut-off

NASA Astrophysics Data System (ADS)

Mishra, Dheeraj Kumar; Chandra, Nitin; Vaibhav, Vinay

2017-10-01

We study various equilibrium thermodynamic properties of blackbody radiation (i.e. a photon gas) with an ultraviolet energy cut-off. We find that the energy density, specific heat etc. follow usual acoustic phonon dynamics as have been well studied by Debye. Other thermodynamic quantities like pressure, entropy etc. have also been calculated. The usual Stefan-Boltzmann law gets modified. We observe that the values of the thermodynamic quantities with the energy cut-off is lower than the corresponding values in the theory without any such scale. The phase-space measure is also expected to get modified for an exotic spacetime appearing at Planck scale, which in turn leads to the modification of Planck energy density distribution and the Wien's displacement law. We found that the non-perturbative nature of the thermodynamic quantities in the SR limit (for both unmodified and modified cases), due to nonanalyticity of the leading term, is a general feature of the theory accompanied with an ultraviolet energy cut-off. We have also discussed the possible modification in the case of Big Bang and the Stellar objects and have suggested a table top experiment for verification in effective low energy case.

Development of an air knife to remove seed coat fragments during lint cleaning

USDA-ARS?s Scientific Manuscript database

An air knife is a tool commonly used to blow off debris in a manufacturing line. The knife may also be used to break the attachment force between a lint cleaner saw and a seed coat fragment (SCF) with attached fiber, and remove them. Work continued on evaluating an auxiliary air knife mounted on t...

Particle connectedness and cluster formation in sequential depositions of particles: integral-equation theory.

PubMed

Danwanichakul, Panu; Glandt, Eduardo D

2004-11-15

We applied the integral-equation theory to the connectedness problem. The method originally applied to the study of continuum percolation in various equilibrium systems was modified for our sequential quenching model, a particular limit of an irreversible adsorption. The development of the theory based on the (quenched-annealed) binary-mixture approximation includes the Ornstein-Zernike equation, the Percus-Yevick closure, and an additional term involving the three-body connectedness function. This function is simplified by introducing a Kirkwood-like superposition approximation. We studied the three-dimensional (3D) system of randomly placed spheres and 2D systems of square-well particles, both with a narrow and with a wide well. The results from our integral-equation theory are in good accordance with simulation results within a certain range of densities.

Particle connectedness and cluster formation in sequential depositions of particles: Integral-equation theory

NASA Astrophysics Data System (ADS)

Danwanichakul, Panu; Glandt, Eduardo D.

2004-11-01

We applied the integral-equation theory to the connectedness problem. The method originally applied to the study of continuum percolation in various equilibrium systems was modified for our sequential quenching model, a particular limit of an irreversible adsorption. The development of the theory based on the (quenched-annealed) binary-mixture approximation includes the Ornstein-Zernike equation, the Percus-Yevick closure, and an additional term involving the three-body connectedness function. This function is simplified by introducing a Kirkwood-like superposition approximation. We studied the three-dimensional (3D) system of randomly placed spheres and 2D systems of square-well particles, both with a narrow and with a wide well. The results from our integral-equation theory are in good accordance with simulation results within a certain range of densities.

Coulomb Fission in Multiply-Charged Ammonia Clusters: Accurate Measurements of the Rayleigh Instability Limit from Fragmentation Patterns.

PubMed

Harris, Christopher; Stace, Anthony J

2018-03-15

A series of experiments have been undertaken on the fragmentation of multiply charged ammonia clusters, (NH 3 ) n z+ , where z ≤ 8 and n ≤ 850, to establish Rayleigh instability limits, whereby clusters at certain critical sizes become unstable due to Coulomb repulsion between the resident charges. Experimental results on size-selected clusters are found to be in excellent agreement with theoretical predictions of Rayleigh instability limits at all values of the charge. Electrostatic theory has been used to help identify fragmentation patterns on the assumption that the clusters separate into two dielectric spheres, and the predicted Coulomb repulsion energies used to establish pathways and the sizes of cluster fragments. The results show that fragmentation is very asymmetric in terms of both the numbers of molecules involved and the amount of charge each fragment accommodates. For clusters carrying a charge ≤+4, the results show that fragmentation proceeds via the loss of small, singly charged clusters. When clusters carry a charge of +5 or more, the experimental observations suggest a marked switch in behavior. Although the laboratory measurements equate to fragmentation via the loss of a large dication cluster, electrostatic theory supports an interpretation that involves the sequential loss of two smaller, singly charged clusters possibly accompanied by the extensive evaporation of neutral molecules. It is suggested that this change in fragmentation pattern is driven by the channelling of Coulomb repulsion energy into intermolecular modes within these larger clusters. Overall, the results appear to support the ion evaporation model that is frequently used to interpret electrospray experiments.

Computer-mediated instructional video: a randomised controlled trial comparing a sequential and a segmented instructional video in surgical hand wash.

PubMed

Schittek Janda, M; Tani Botticelli, A; Mattheos, N; Nebel, D; Wagner, A; Nattestad, A; Attström, R

2005-05-01

Video-based instructions for clinical procedures have been used frequently during the preceding decades. To investigate in a randomised controlled trial the learning effectiveness of fragmented videos vs. the complete sequential video and to analyse the attitudes of the user towards video as a learning aid. An instructional video on surgical hand wash was produced. The video was available in two different forms in two separate web pages: one as a sequential video and one fragmented into eight short clips. Twenty-eight dental students in the second semester were randomised into an experimental (n = 15) and a control group (n = 13). The experimental group used the fragmented form of the video and the control group watched the complete one. The use of the videos was logged and the students were video taped whilst undertaking a test hand wash. The videos were analysed systematically and blindly by two independent clinicians. The students also performed a written test concerning learning outcome from the videos as well as they answered an attitude questionnaire. The students in the experimental group watched the video significantly longer than the control group. There were no significant differences between the groups with regard to the ratings and scores when performing the hand wash. The experimental group had significantly better results in the written test compared with those of the control group. There was no significant difference between the groups with regard to attitudes towards the use of video for learning, as measured by the Visual Analogue Scales. Most students in both groups expressed satisfaction with the use of video for learning. The students demonstrated positive attitudes and acceptable learning outcome from viewing CAL videos as a part of their pre-clinical training. Videos that are part of computer-based learning settings would ideally be presented to the students both as a segmented and as a whole video to give the students the option to choose the form of video which suits the individual student's learning style.

Thermodynamically balanced inside-out (TBIO) PCR-based gene synthesis: a novel method of primer design for high-fidelity assembly of longer gene sequences

PubMed Central

Gao, Xinxin; Yo, Peggy; Keith, Andrew; Ragan, Timothy J.; Harris, Thomas K.

2003-01-01

A novel thermodynamically-balanced inside-out (TBIO) method of primer design was developed and compared with a thermodynamically-balanced conventional (TBC) method of primer design for PCR-based gene synthesis of codon-optimized gene sequences for the human protein kinase B-2 (PKB2; 1494 bp), p70 ribosomal S6 subunit protein kinase-1 (S6K1; 1622 bp) and phosphoinositide-dependent protein kinase-1 (PDK1; 1712 bp). Each of the 60mer TBIO primers coded for identical nucleotide regions that the 60mer TBC primers covered, except that half of the TBIO primers were reverse complement sequences. In addition, the TBIO and TBC primers contained identical regions of temperature- optimized primer overlaps. The TBC method was optimized to generate sequential overlapping fragments (∼0.4–0.5 kb) for each of the gene sequences, and simultaneous and sequential combinations of overlapping fragments were tested for their ability to be assembled under an array of PCR conditions. However, no fully synthesized gene sequences could be obtained by this approach. In contrast, the TBIO method generated an initial central fragment (∼0.4–0.5 kb), which could be gel purified and used for further inside-out bidirectional elongation by additional increments of 0.4–0.5 kb. By using the newly developed TBIO method of PCR-based gene synthesis, error-free synthetic genes for the human protein kinases PKB2, S6K1 and PDK1 were obtained with little or no corrective mutagenesis. PMID:14602936

Dissociative Photoionization of Diethyl Ether.

PubMed

Voronova, Krisztina; Mozaffari Easter, Chrissa M; Covert, Kyle J; Bodi, Andras; Hemberger, Patrick; Sztáray, Bálint

2015-10-29

The dissociative photoionization of internal energy selected diethyl ether ions was investigated by imaging photoelectron photoion coincidence spectroscopy. In a large, 5 eV energy range Et2O(+) cations decay by two parallel and three sequential dissociative photoionization channels, which can be modeled well using statistical theory. The 0 K appearance energies of the CH3CHOCH2CH3(+) (H-loss, m/z = 73) and CH3CH2O═CH2(+) (methyl-loss, m/z = 59) fragment ions were determined to be 10.419 ± 0.015 and 10.484 ± 0.008 eV, respectively. The reemergence of the hydrogen-loss ion above 11 eV is attributed to transition-state (TS) switching, in which the second, outer TS is rate-determining at high internal energies. At 11.81 ± 0.05 eV, a secondary fragment of the CH3CHOCH2CH3(+) (m/z = 73) ion, protonated acetaldehyde, CH3CH═OH(+) (m/z = 45) appears. On the basis of the known thermochemical onset of this fragment, a reverse barrier of 325 meV was found. Two more sequential dissociation reactions were examined, namely, ethylene and formaldehyde losses from the methyl-loss daughter ion. The 0 K appearance energies of 11.85 ± 0.07 and 12.20 ± 0.08 eV, respectively, indicate no reverse barrier in these processes. The statistical model of the dissociative photoionization can also be used to predict the fractional ion abundances in threshold photoionization at large temperatures, which could be of use in, for example, combustion diagnostics.

The application of "double isolation" in Fourier transform ion cyclotron resonance sustained off-resonance irradiation collisionally-induced dissociation tandem mass spectrometry to remove labile isobaric impurities.

PubMed

Gates, Paul J; Lopes, Norberto P; Pinto, Emani; Colepicolo, Pio; Cardozo, Karina H M

2011-01-01

This study reports the application of "double isolation" in sustained off-resonance irradiation collisionally-induced dissociation tandem mass spectrometry (SORI-CID-MS/MS) to remove radio- frequency (RF) fragment ions of very close mass isobaric ions (0.02 m/z apart). Analyses were performed with a fraction of a biological extract isolated from a macroalgae containing the mycosporine-like amino acid asterina-330. Direct isolation of the precursor ion by narrowing the isolation window proved ineffective as it impinged upon the required ion thus substantially reducing its intensity. By increasing the correlated sweep time, ejection efficiency of the isolation was improved, but caused the unwanted side-effect of RF fragmentation of labile ions. Finally, by skipping the ion activation step and performing a second isolation (in the MS(3) module) the RF fragments from the first isolation were removed leaving a very pure isolation of the required precursor ion and allowed a very clean CID fragmentation. We demonstrated that the m/z 272.1351 ion is derived from the loss of NH(3) from m/z 289.1620 isobaric impurity and is not related to asterina-330. This application represents a powerful tool to remove unwanted ions in the MS/MS spectrum that result from fragmentation of isobaric ions.

Invasion versus isolation: Trade-offs in managing native salmonids with barriers to upstream movement

Treesearch

Kurt D. Fausch; Bruce E. Rieman; Jason B. Dunham; Michael K. Young; Douglas P. Peterson

2009-01-01

Conservation biologists often face the trade-off that increasing connectivity in fragmented landscapes to reduce extinction risk of native species can foster invasion by non-native species that enter via the corridors created, which can then increase extinction risk. This dilemma is acute for stream fishes, especially native salmonids, because their populations are...

The erosion of carbonate stone by acid rain: Laboratory and field investigations

USGS Publications Warehouse

Baedecker, P.A.; Reddy, M.M.

1993-01-01

One of the goals of research on the effects of acidic deposition on carbonate stone surfaces is to define the incremental impact of acidic deposition relative to natural weathering processes on the rate of carbonate stone erosion. If rain that impacts carbonate stone surfaces is resident on the surface long enough to approach chemical equilibrium, the incremental effect of hydrogen ion is expected to be small (i.e., 6% for a rain of pH 4.0). Under nonequilibrium (i.e., high flow rate) conditions, kinetic considerations suggest that the incremental effect of hydrogen ion deposition could be quite significant. Field run-off experiments involving the chemical analysis of rain collected from inclined stone slabs have been used to evaluate stone dissolution processes under ambient conditions of wet and dry deposition of acidic species. The stoichiometry of the reaction of stone with hydrogen ion is difficult to define from the field data due to scatter in the data attributed to hydrodynamic effects. Laboratory run-off experiments show that the stoichiometry is best defined by a reaction with H+ in which CO2 is released from the system. The baseline effect caused by water in equilibrium with atmospheric CO2 is identical in the field and in laboratory simulation. The experiments show that the solutions are close enough to equilibrium for the incremental effect of hydrogen ion to be minor (i.e., 24% for marble for a rain of pH 4.0) relative to dissolution due to water and carbonic acid reactions. Stone erosion rates based on physical measurement are approximately double the recession rates that are due to dissolution (estimated from the observed calcium content of the run-off solutions). The difference may reflect the loss of granular material not included in recession estimates based on the run-off data. Neither the field nor the laboratory run-off experiments indicate a pH dependence for the grain-removal process.

Shift in the equilibrium between on and off states of the allosteric switch in Ras-GppNHp affected by small molecules and bulk solvent composition.

PubMed

Holzapfel, Genevieve; Buhrman, Greg; Mattos, Carla

2012-08-07

Ras GTPase cycles between its active GTP-bound form promoted by GEFs and its inactive GDP-bound form promoted by GAPs to affect the control of various cellular functions. It is becoming increasingly apparent that subtle regulation of the GTP-bound active state may occur through promotion of substates mediated by an allosteric switch mechanism that induces a disorder to order transition in switch II upon ligand binding at an allosteric site. We show with high-resolution structures that calcium acetate and either dithioerythritol (DTE) or dithiothreitol (DTT) soaked into H-Ras-GppNHp crystals in the presence of a moderate amount of poly(ethylene glycol) (PEG) can selectively shift the equilibrium to the "on" state, where the active site appears to be poised for catalysis (calcium acetate), or to what we call the "ordered off" state, which is associated with an anticatalytic conformation (DTE or DTT). We also show that the equilibrium is reversible in our crystals and dependent on the nature of the small molecule present. Calcium acetate binding in the allosteric site stabilizes the conformation observed in the H-Ras-GppNHp/NOR1A complex, and PEG, DTE, and DTT stabilize the anticatalytic conformation observed in the complex between the Ras homologue Ran and Importin-β. The small molecules are therefore selecting biologically relevant conformations in the crystal that are sampled by the disordered switch II in the uncomplexed GTP-bound form of H-Ras. In the presence of a large amount of PEG, the ordered off conformation predominates, whereas in solution, in the absence of PEG, switch regions appear to remain disordered in what we call the off state, unable to bind DTE.

Shift in the Equilibrium between On and Off States of the Allosteric Switch in Ras-GppNHp Affected by Small Molecules and Bulk Solvent Composition

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

Holzapfel, Genevieve; Buhrman, Greg; Mattos, Carla

2012-08-31

Ras GTPase cycles between its active GTP-bound form promoted by GEFs and its inactive GDP-bound form promoted by GAPs to affect the control of various cellular functions. It is becoming increasingly apparent that subtle regulation of the GTP-bound active state may occur through promotion of substates mediated by an allosteric switch mechanism that induces a disorder to order transition in switch II upon ligand binding at an allosteric site. We show with high-resolution structures that calcium acetate and either dithioerythritol (DTE) or dithiothreitol (DTT) soaked into H-Ras-GppNHp crystals in the presence of a moderate amount of poly(ethylene glycol) (PEG) canmore » selectively shift the equilibrium to the 'on' state, where the active site appears to be poised for catalysis (calcium acetate), or to what we call the 'ordered off' state, which is associated with an anticatalytic conformation (DTE or DTT). We also show that the equilibrium is reversible in our crystals and dependent on the nature of the small molecule present. Calcium acetate binding in the allosteric site stabilizes the conformation observed in the H-Ras-GppNHp/NOR1A complex, and PEG, DTE, and DTT stabilize the anticatalytic conformation observed in the complex between the Ras homologue Ran and Importin-{beta}. The small molecules are therefore selecting biologically relevant conformations in the crystal that are sampled by the disordered switch II in the uncomplexed GTP-bound form of H-Ras. In the presence of a large amount of PEG, the ordered off conformation predominates, whereas in solution, in the absence of PEG, switch regions appear to remain disordered in what we call the off state, unable to bind DTE.« less

Intermittent Fermi-Pasta-Ulam Dynamics at Equilibrium

NASA Astrophysics Data System (ADS)

Campbell, David; Danieli, Carlo; Flach, Sergej

The equilibrium value of an observable defines a manifold in the phase space of an ergodic and equipartitioned many-body syste. A typical trajectory pierces that manifold infinitely often as time goes to infinity. We use these piercings to measure both the relaxation time of the lowest frequency eigenmode of the Fermi-Pasta-Ulam chain, as well as the fluctuations of the subsequent dynamics in equilibrium. We show that previously obtained scaling laws for equipartition times are modified at low energy density due to an unexpected slowing down of the relaxation. The dynamics in equilibrium is characterized by a power-law distribution of excursion times far off equilibrium, with diverging variance. The long excursions arise from sticky dynamics close to regular orbits in the phase space. Our method is generalizable to large classes of many-body systems. The authors acknowledge financial support from IBS (Project Code IBS-R024-D1).

Asteroid Shapes Are Always Close To Fluid Equilibrium

NASA Astrophysics Data System (ADS)

Tanga, Paolo; Comito, C.; Hestroffer, D.; Richardson, D. C.

2010-10-01

The simple evidence that asteroid are composed by solid rocks suggests that their shape can be rather far from the theoretical equilibrium for rotating fluid bodies. The possible fragmented ("rubble-pile") nature of most of them has suggested interpretations based on elasto-plastic models (such as the Mohr-Coulomb theory) that take into account the static behavior of a granular structure. However, these approaches did not incorporate explicitly the possible evolution of shapes in time due to external factors such as crater forming impacts or tidal deformations. We revisited the theory of equilibrium shapes for fluids, quantitatively evaluating - by appropriate metrics - the distance of the observed shapes from fluid equilibrium. This distance turns out to be much smaller than previously expected. On the basis of this evidence, we simulated numerically the evolution of gravitational aggregates having a small degree of internal friction, consistent with the theoretical findings. Our results offer a global scenario for the evolution of asteroid shapes under the action of gradual stresses due to minor impacts, tidal forces and seismic shaking. We show that actual asteroid shapes are consistent with the evolution of aggregates tending towards minimum free energy states. We are able to explain the samples of observed shapes obtained by different techniques. Our findings strongly support a highly porous and fragmented nature for most asteroids, at least in an external layer. Reference: Tanga et al. 2009: ApJ Letters, 706, 1, L197-L202 Acknowledgments: PT and CC have been supported by the "Programme Nationale de Planetologie" of France; DCR acknowledges support by the NASA (grant no. NNX08AM39G issued through the Office of Space Science) and by the NSF (grant no. AST0708110).

Sedimentation equilibrium analysis of protein interactions with global implicit mass conservation constraints and systematic noise decomposition.

PubMed

Vistica, Jennifer; Dam, Julie; Balbo, Andrea; Yikilmaz, Emine; Mariuzza, Roy A; Rouault, Tracey A; Schuck, Peter

2004-03-15

Sedimentation equilibrium is a powerful tool for the characterization of protein self-association and heterogeneous protein interactions. Frequently, it is applied in a configuration with relatively long solution columns and with equilibrium profiles being acquired sequentially at several rotor speeds. The present study proposes computational tools, implemented in the software SEDPHAT, for the global analysis of equilibrium data at multiple rotor speeds with multiple concentrations and multiple optical detection methods. The detailed global modeling of such equilibrium data can be a nontrivial computational problem. It was shown previously that mass conservation constraints can significantly improve and extend the analysis of heterogeneous protein interactions. Here, a method for using conservation of mass constraints for the macromolecular redistribution is proposed in which the effective loading concentrations are calculated from the sedimentation equilibrium profiles. The approach is similar to that described by Roark (Biophys. Chem. 5 (1976) 185-196), but its utility is extended by determining the bottom position of the solution columns from the macromolecular redistribution. For analyzing heterogeneous associations at multiple protein concentrations, additional constraints that relate the effective loading concentrations of the different components or their molar ratio in the global analysis are introduced. Equilibrium profiles at multiple rotor speeds also permit the algebraic determination of radial-dependent baseline profiles, which can govern interference optical ultracentrifugation data, but usually also occur, to a smaller extent, in absorbance optical data. Finally, the global analysis of equilibrium profiles at multiple rotor speeds with implicit mass conservation and computation of the bottom of the solution column provides an unbiased scale for determining molar mass distributions of noninteracting species. The properties of these tools are studied with theoretical and experimental data sets.

OSCILLATING FILAMENTS. I. OSCILLATION AND GEOMETRICAL FRAGMENTATION

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

Gritschneder, Matthias; Heigl, Stefan; Burkert, Andreas, E-mail: gritschm@usm.uni-muenchen.de

2017-01-10

We study the stability of filaments in equilibrium between gravity and internal as well as external pressure using the grid-based AMR code RAMSES. A homogeneous, straight cylinder below a critical line mass is marginally stable. However, if the cylinder is bent, such as with a slight sinusoidal perturbation, an otherwise stable configuration starts to oscillate, is triggered into fragmentation, and collapses. This previously unstudied behavior allows a filament to fragment at any given scale, as long as it has slight bends. We call this process “geometrical fragmentation.” In our realization, the spacing between the cores matches the wavelength of the sinusoidalmore » perturbation, whereas up to now, filaments were thought to be only fragmenting on the characteristic scale set by the mass-to-line ratio. Using first principles, we derive the oscillation period as well as the collapse timescale analytically. To enable a direct comparison with observations, we study the line-of-sight velocity for different inclinations. We show that the overall oscillation pattern can hide the infall signature of cores.« less

The interaction of E. coli integration host factor and lambda cos DNA: multiple complex formation and protein-induced bending.

PubMed Central

Kosturko, L D; Daub, E; Murialdo, H

1989-01-01

The interaction of E. coli's integration Host Factor (IHF) with fragments of lambda DNA containing the cos site has been studied by gel-mobility retardation and electron microscopy. The cos fragment used in the mobility assays is 398 bp and spans a region from 48,298 to 194 on the lambda chromosome. Several different complexes of IHF with this fragment can be distinguished by their differential mobility on polyacrylamide gels. Relative band intensities indicate that the formation of a complex between IHF and this DNA fragment has an equilibrium binding constant of the same magnitude as DNA fragments containing lambda's attP site. Gel-mobility retardation and electron microscopy have been employed to show that IHF sharply bends DNA near cos and to map the bending site. The protein-induced bend is near an intrinsic bend due to DNA sequence. The position of the bend suggests that IHF's role in lambda DNA packaging may be the enhancement of terminase binding/cos cutting by manipulating DNA structure. Images PMID:2521383

How Networks of Informal Trails Cause Landscape Level Damage to Vegetation.

PubMed

Barros, Agustina; Marina Pickering, Catherine

2017-07-01

When visitors are not constrained to remain on formal trails, informal trail networks can develop and damage plant communities in protected areas. These networks can form in areas with low growing vegetation, where formal trails are limited, where there is limited regulation and where vegetation is slow to recover once disturbed. To demonstrate the extent of impacts from unregulated recreational use, we assessed damage to alpine vegetation by hikers and pack animals in the highest protected area in the southern Hemisphere: Aconcagua Park, in the Andes. Within the 237 ha area surveyed in the Horcones Valley, over 19 km of trails were found, nearly all of which (94%) were informal. This network of trails resulted in the direct loss of 11.5 ha of vegetation and extensive fragmentation of alpine meadows (21 fragments) and steppe vegetation (68 fragments). When levels of disturbance off these trails were quantified using rapid visual assessments, 81% of 102 randomly located plots showed evidence of disturbance, with the severity of disturbance greatest close to trails. As a result, vegetation in 90% of the Valley has been damaged by visitor use, nearly all of it from unregulated use. These results highlight the extent to which informal trails and trampling off-trail can cause landscape damage to areas of high conservation value, and hence the importance of better regulation of visitor use. The methodology used for off-trail impact assessment can be easily applied or adapted for other popular protected areas where trampling off-trail is also an issue.

Cluster formation in nuclear reactions from mean-field inhomogeneities

NASA Astrophysics Data System (ADS)

Napolitani, Paolo; Colonna, Maria; Mancini-Terracciano, Carlo

2018-05-01

Perturbing fluids of neutrons and protons (nuclear matter) may lead, as the most catastrophic effect, to the rearrangement of the fluid into clusters of nucleons. A similar process may occur in a single atomic nucleus undergoing a violent perturbation, like in heavy-ion collisions tracked in particle accelerators at around 30 to 50 MeV per nucleon: in this conditions, after the initial collision shock, the nucleus expands and then clusterises into several smaller nuclear fragments. Microscopically, when violent perturbation are applied to nuclear matter, a process of clusterisation arises from the combination of several fluctuation modes of large-amplitude where neutrons and protons may oscillate in phase or out of phase. The imposed perturbation leads to conditions of instability, the wavelengths which are the most amplified have sizes comparable to small atomic nuclei. We found that these conditions, explored in heavy-ion collisions, correspond to the splitting of a nucleus into fragments ranging from Oxygen to Neon in a time interval shorter than one zeptosecond (10 ‑ 21s). From the out-of-phase oscillations of neutrons and protons another property arises, the smaller fragments belonging to a more volatile phase get more neutron enriched: in the heavy-ion collision case this process, called distillation, reflects in the isotopic distributions of the fragments. The resulting dynamical description of heavy-ion collisions is an improvement with respect to more usual statistical approaches, based on the equilibrium assumption. It allows in fact to characterise also the very fast early stages of the collision process which are out of equilibrium. Such dynamical description is the core of the Boltzmann-Langevin One Body (BLOB) model, which in its latest development unifies in a common approach the description of fluctuations in nuclear matter, and a predictive description of the disintegration of nuclei into nuclear fragments. After a theoretical introduction, a few practical examples will be illustrated. This paper resumes the extended analysis of fluctuations in nuclear matter of ref. [2] and briefly reviews applications to heavy-ion collisions.

Does avian species richness in natural patch mosaics follow the forest fragmentation paradigm?

USGS Publications Warehouse

Pavlacky, D.C.; Anderson, S.H.

2007-01-01

As one approaches the north-eastern limit of pinyon (Pinus spp.) juniper (Juniperus spp.) vegetation on the Colorado Plateau, USA, woodland patches become increasingly disjunct, grading into sagebrush (Artemisia spp.)-dominated landscapes. Patterns of avian species richness in naturally heterogeneous forests may or may not respond to patch discontinuity in the same manner as bird assemblages in fragmented agricultural systems. We used observational data from naturally patchy woodlands and predictions derived from studies of human-modified agricultural forests to estimate the effects of patch area, shape, isolation and distance to contiguous woodland on avian species richness. We predicted that patterns of species richness in naturally patchy juniper woodlands would differ from those observed in fragmented agricultural systems. Our objectives were to (1) estimate the effect of naturally occurring patch structure on avian species richness with respect to habitat affinity and migratory strategy and (2) assess the concordance of the effects to predictions from agricultural forest systems. We used the analogy between populations and communities to estimate species richness, where species are treated as individuals in the application of traditional capture-recapture theory. Information-theoretic model selection showed that overall species richness was explained primarily by the species area relationship. There was some support for a model with greater complexity than the equilibrium theory of island biogeography where the isolation of large patches resulted in greater species richness. Species richness of woodland-dwelling birds was best explained by the equilibrium hypothesis with partial landscape complementation by open-country species in isolated patches. Species richness within specific migratory strategies showed concomitant increases and no shifts in species composition along the patch area gradient. Our results indicate that many patterns of species richness considered to be fragmentation effects may be general consequences of patch discontinuity and are ubiquitous in naturally heterogeneous systems. There was no evidence for the effects of patch shape and distance to contiguous woodland in juniper woodland, suggesting edge effects and dependence upon regional species pools are characteristics of fragmented agricultural systems. Natural patch mosaics may provide benchmarks for evaluating fragmentation effects and managing forests by mimicking natural landscape patterns. ?? 2007 The Zoological Society of London.

Descartes Mountains and Cayley Plains - Composition and provenance

NASA Technical Reports Server (NTRS)

Drake, M. J.; Taylor, G. J.; Goles, G. G.

1974-01-01

Trace element compositions of petrographically characterized 2-4 mm lithic fragments from Apollo 16 soil samples are used to calculate initial REE concentrations in liquids in equilibrium with lunar anorthosites and to discuss the provenance of the Cayley Formation. Lithic fragments may be subdivided into four groups: (1) ANT rocks, (2) K- and SiO2-rich mesostasis-bearing rocks, (3) poikiloblastic rocks, and (4) (spinel) troctolites. Model liquids in equilibrium with essentially monominerallic anorthosites have initial REE concentrations 5-8 times those of chondrites. The REE contents of K- and SiO2-rich mesostasis-bearing rocks and poikiloblastic rocks are dominated by the mesostasis phases. ANT rocks appear to be more abundant in the Descartes Mountains, while poikiloblastic rocks appear to be more abundant in the Cayley Plains. Poikiloblastic rocks have intermediate to high LIL-element concentrations yet the low gamma-ray activity of Mare Orientale implies low LIL-element concentrations. Consequently, it is unlikely that the Cayley Formation is Orientale ejecta. A local origin as ejecta from smaller impacts is a more plausible model for the deposition of the Cayley Formation.

Time of day affects implicit memory for unattended stimuli.

PubMed

Rothen, Nicolas; Meier, Beat

2016-11-01

We investigated whether circadian arousal affects perceptual priming as a function of whether stimuli were attended or ignored during learning. We tested 160 participants on- and off-peak with regards to their circadian arousal. In the study phase, they were presented with two superimposed pictures in different colours. They had to name the pictures of one colour while ignoring the others. In the test phase, they were presented with the same and randomly intermixed new pictures. Each picture was presented in black colour in a fragment completion task. Priming was measured as the difference in fragmentation level at which the pictures from the study phase were named compared to the new pictures. Priming was stronger for attended than ignored pictures. Time of day affected priming only for ignored pictures, with stronger priming effects off-peak than on-peak. Thus, circadian arousal seems to favour the encoding of unattended materials specifically at off-peak. Copyright © 2016 Elsevier Inc. All rights reserved.

Two-dimensional heteroclinic attractor in the generalized Lotka-Volterra system

NASA Astrophysics Data System (ADS)

Afraimovich, Valentin S.; Moses, Gregory; Young, Todd

2016-05-01

We study a simple dynamical model exhibiting sequential dynamics. We show that in this model there exist sets of parameter values for which a cyclic chain of saddle equilibria, O k , k=1,\\ldots,p , have two-dimensional unstable manifolds that contain orbits connecting each O k to the next two equilibrium points O k+1 and O k+2 in the chain ({{O}p+1}={{O}1} ). We show that the union of these equilibria and their unstable manifolds form a two-dimensional surface with a boundary that is homeomorphic to a cylinder if p is even and a Möbius strip if p is odd. If, further, each equilibrium in the chain satisfies a condition called ‘dissipativity’, then this surface is asymptotically stable.

Population Annealing Monte Carlo for Frustrated Systems

NASA Astrophysics Data System (ADS)

Amey, Christopher; Machta, Jonathan

Population annealing is a sequential Monte Carlo algorithm that efficiently simulates equilibrium systems with rough free energy landscapes such as spin glasses and glassy fluids. A large population of configurations is initially thermalized at high temperature and then cooled to low temperature according to an annealing schedule. The population is kept in thermal equilibrium at every annealing step via resampling configurations according to their Boltzmann weights. Population annealing is comparable to parallel tempering in terms of efficiency, but has several distinct and useful features. In this talk I will give an introduction to population annealing and present recent progress in understanding its equilibration properties and optimizing it for spin glasses. Results from large-scale population annealing simulations for the Ising spin glass in 3D and 4D will be presented. NSF Grant DMR-1507506.

Simultaneous bilateral stereotactic procedure for deep brain stimulation implants: a significant step for reducing operation time.

PubMed

Fonoff, Erich Talamoni; Azevedo, Angelo; Angelos, Jairo Silva Dos; Martinez, Raquel Chacon Ruiz; Navarro, Jessie; Reis, Paul Rodrigo; Sepulveda, Miguel Ernesto San Martin; Cury, Rubens Gisbert; Ghilardi, Maria Gabriela Dos Santos; Teixeira, Manoel Jacobsen; Lopez, William Omar Contreras

2016-07-01

OBJECT Currently, bilateral procedures involve 2 sequential implants in each of the hemispheres. The present report demonstrates the feasibility of simultaneous bilateral procedures during the implantation of deep brain stimulation (DBS) leads. METHODS Fifty-seven patients with movement disorders underwent bilateral DBS implantation in the same study period. The authors compared the time required for the surgical implantation of deep brain electrodes in 2 randomly assigned groups. One group of 28 patients underwent traditional sequential electrode implantation, and the other 29 patients underwent simultaneous bilateral implantation. Clinical outcomes of the patients with Parkinson's disease (PD) who had undergone DBS implantation of the subthalamic nucleus using either of the 2 techniques were compared. RESULTS Overall, a reduction of 38.51% in total operating time for the simultaneous bilateral group (136.4 ± 20.93 minutes) as compared with that for the traditional consecutive approach (220.3 ± 27.58 minutes) was observed. Regarding clinical outcomes in the PD patients who underwent subthalamic nucleus DBS implantation, comparing the preoperative off-medication condition with the off-medication/on-stimulation condition 1 year after the surgery in both procedure groups, there was a mean 47.8% ± 9.5% improvement in the Unified Parkinson's Disease Rating Scale Part III (UPDRS-III) score in the simultaneous group, while the sequential group experienced 47.5% ± 15.8% improvement (p = 0.96). Moreover, a marked reduction in the levodopa-equivalent dose from preoperatively to postoperatively was similar in these 2 groups. The simultaneous bilateral procedure presented major advantages over the traditional sequential approach, with a shorter total operating time. CONCLUSIONS A simultaneous stereotactic approach significantly reduces the operation time in bilateral DBS procedures, resulting in decreased microrecording time, contributing to the optimization of functional stereotactic procedures.

Mechanistic studies on a sequential PDT protocol

NASA Astrophysics Data System (ADS)

Kessel, David

2016-03-01

A low (~LD15) PDT dose resulting in selective lysosomal photodamage can markedly promote photokilling by subsequent photodamage targeted to mitochondria. Experimental data are consistent with the proposal that cleavage of the autophagyassociated protein ATG5 to a pro-apoptotic fragment is responsible for this effect. This process is known to be dependent on the proteolytic activity of calpain. We have proposed that Ca2+ released from photodamaged lysosomes is the trigger for ATG5 cleavage. We can now document the conversion of ATG5 to the truncated form after lysosomal photodamage. Photofrin, a photosensitizer that targets both mitochondria and lysosomes, can be used for either phase of the sequential PDT process. The ability of Photofrin to target both loci may explain the well-documented efficacy of this agent.

Sequential and direct ionic excitation in the strong-field ionization of 1-butene molecules.

PubMed

Schell, Felix; Boguslavskiy, Andrey E; Schulz, Claus Peter; Patchkovskii, Serguei; Vrakking, Marc J J; Stolow, Albert; Mikosch, Jochen

2018-05-18

We study the Strong-Field Ionization (SFI) of the hydrocarbon 1-butene as a function of wavelength using photoion-photoelectron covariance and coincidence spectroscopy. We observe a striking transition in the fragment-associated photoelectron spectra: from a single Above Threshold Ionization (ATI) progression for photon energies less than the cation D0-D1 gap to two ATI progressions for a photon energy greater than this gap. For the first case, electronically excited cations are created by SFI populating the ground cationic state D0, followed by sequential post-ionization excitation. For the second case, direct sub-cycle SFI to the D1 excited cation state contributes significantly. Our experiments access ionization dynamics in a regime where strong-field and resonance-enhanced processes can interplay.

Synthesis of Aromatic Aza-metallapentalenes from Metallabenzene via Sequential Ring Contraction/Annulation

NASA Astrophysics Data System (ADS)

Wang, Tongdao; Han, Feifei; Huang, Haiping; Li, Jinhua; Zhang, Hong; Zhu, Jun; Lin, Zhenyang; Xia, Haiping

2015-04-01

The concept of aromaticity has long played an important role in chemistry and continues to fascinate both experimentalists and theoreticians. Among the archetypal aromatic compounds, heteroaromatics are particularly attractive. Recently, substitution of a transition-metal fragment for a carbon atom in the anti-aromatic hydrocarbon pentalene has led to the new heteroaromatic osmapentalenes. However, construction of the aza-homolog of osmapentalenes cannot be accomplished by a similar synthetic manipulation. Here, we report the synthesis of aza-osmapentalenes by sequential ring contraction/annulation reactions of osmabenzenes via osmapentafulvenes. Nuclear magnetic resonance spectra, X-ray crystallographic analysis, and DFT calculations all suggest that these aza-osmapentalenes exhibit aromatic character. Thus, the stepwise transformation of metallabenzenes to metallapentafulvenes and then aza-metallapentalenes provides an efficient and facile synthetic route to these bicyclic heteroaromatics.

A theoretical and mass spectrometry study of the fragmentation of mycosporine-like amino acids

NASA Astrophysics Data System (ADS)

Cardozo, Karina H. M.; Vessecchi, Ricardo; Carvalho, Valdemir M.; Pinto, Ernani; Gates, Paul J.; Colepicolo, Pio; Galembeck, Sérgio E.; Lopes, Norberto P.

2008-06-01

In the present study, the mycosporine-like amino acids (MAAs) were isolated from the marine red alga Gracilaria tenuistipitata and analysed by high-resolution accurate-mass sequential mass spectrometry (MSn). In addition to the proposed fragmentation mechanism based on the MSn analysis, it is clearly demonstrated that the elimination of mass 15 is a radical processes taking place at the methoxyl substituent of the double bond. This characteristic loss of a methyl radical was studied by theoretical calculations and the homolytic cleavage of the OC bond is suggested to be dependent on the bond weakening. The protonation site of the MAAs was indicated by analysis of the Fukui functions and the relative Gibbs energies of the several possible protonated forms.

Effect of isospin diffusion on the production of neutron-rich nuclei in multinucleon transfer reactions

NASA Astrophysics Data System (ADS)

Niu, Fei; Chen, Peng-Hui; Guo, Ya-Fei; Ma, Chun-Wang; Feng, Zhao-Qing

2018-03-01

The isospin dissipation dynamics in multinucleon transfer reactions has been investigated within the dinuclear system model. Production cross sections of neutron-rich isotopes around projectile-like and target-like fragments are estimated in collisions of Ni,6458+208Pb and 78.86,91Kr +198Pt near Coulomb barrier energies. The isospin diffusion in the nucleon transfer process is coupled to the dissipation of relative motion energy and angular momentum of colliding system. The available data of projectile-like fragments via multinucleon transfer reactions are nicely reproduced. It is found that the light projectile-like fragments are produced in the neutron-rich region because of the isospin equilibrium in two colliding nuclei. However, the heavy target-like fragments tend to be formed on the neutron-poor side above the β -stability line. The neutron-rich projectiles move the maximal yields of heavy nuclei to the neutron-rich domain and are available for producing the heavy exotic isotopes, in particular around the neutron shell closure of N =126 .

Influence of the C-terminus of the glycophorin A transmembrane fragment on the dimerization process.

PubMed Central

Orzáez, M.; Pérez-Payá, E.; Mingarro, I.

2000-01-01

The monomer-dimer equilibrium of the glycophorin A (GpA) transmembrane (TM) fragment has been used as a model system to investigate the amino acid sequence requirements that permit an appropriate helix-helix packing in a membrane-mimetic environment. In particular, we have focused on a region of the helix where no crucial residues for packing have been yet reported. Various deletion and replacement mutants in the C-terminal region of the TM fragment showed that the distance between the dimerization motif and the flanking charged residues from the cytoplasmic side of the protein is important for helix packing. Furthermore, selected GpA mutants have been used to illustrate the rearrangement of TM fragments that takes place when leucine repeats are introduced in such protein segments. We also show that secondary structure of GpA derivatives was independent from dimerization, in agreement with the two-stage model for membrane protein folding and oligomerization. PMID:10892817

Soil erosion and effluent particle size distribution under different initial conditions and rock fragment coverage

NASA Astrophysics Data System (ADS)

Jomaa, S.; Barry, D. A.; Brovelli, A.; Heng, B. C. P.; Sander, G. C.; Parlange, J.-Y.

2012-04-01

It is well known that the presence of rock fragments on the soil surface and the soil's initial characteristics (moisture content, surface roughness, bulk density, etc.) are key factors influencing soil erosion dynamics and sediment delivery. In addition, the interaction of these factors increases the complexity of soil erosion patterns and makes predictions more difficult. The aim of this study was (i) to investigate the effect of soil initial conditions and rock fragment coverage on soil erosion yields and effluent particle size distribution and (ii) to evaluate to what extent the rock fragment coverage controls this relationship. Three laboratory flume experiments with constant precipitation rate of 74 mm/h on a loamy soil parcel with a 2% slope were performed. Experiments with duration of 2 h were conducted using the 6-m × 2-m EPFL erosion flume. During each experiment two conditions were considered, a bare soil and a rock fragment-protected (with 40% coverage) soil. The initial soil surface state was varied between the three experiments, from a freshly re-ploughed and almost dry condition to a compacted soil with a well-developed shield layer and high moisture content. Experiments were designed so that rain splash was the primary driver of soil erosion. Results showed that the amount of eroded mass was highly controlled by the initial soil conditions and whether the steady-state equilibrium was un-, partially- or fully- developed during the previous event. Additionally, results revealed that sediment yields and particle size composition in the initial part of an erosion event are more sensitive to the erosion history than the long-time behaviour. This latter appears to be mainly controlled by rainfall intensity. If steady-state was achieved for a previous event, then the next event consistently produced concentrations for each size class that peaked rapidly, and then declined gradually to steady-state equilibrium. If steady state was not obtained, then different and more complex behaviour was observed in the next event, with large differences found between fine, medium and coarse size classes. The presence of rock fragments on the topsoil reduced the time needed to reach steady state compared with the bare soil. This was attributed to the reduction of rain splash erosion caused by the rapid development of the overland flow, as a result of rock fragments reducing the flow cross-sectional area.

Body movements during the off-ice execution of back spins in figure skating.

PubMed

Mapelli, Andrea; Rodano, Renato; Fiorentini, Angelo; Giustolisi, Andrea; Sidequersky, Fernanda V; Sforza, Chiarella

2013-10-01

Using an optoelectronic motion capture system, we quantitatively assessed the arrangement of body segments and the displacement of the horizontal projection of the center of mass (CM) in seven skaters performing off-ice back spins on a rotating device (spinner). The position of the CM at the beginning of the spins was not a determining factor, but its rapid stabilization towards the center of the spinner, together with the achievement of a stable arrangement of trunk and limbs, was crucial to get the dynamic equilibrium, necessary for a lasting performance. At full spinning, however, there was an indicative variety of individual body postures. A final deceleration, associable with the loss of body equilibrium, was detected in the last spin of most of skaters. In conclusion, the current investigation demonstrated that the off-ice execution of back spin, a critical movement of ice skating, can be measured in laboratory, thus providing quantitative information to both the skaters and the coaches. The analysis is not invasive, and it may be proposed also for longitudinal evaluations of skating and postural training. Copyright © 2013 Elsevier Ltd. All rights reserved.

MaPLE: A MapReduce Pipeline for Lattice-based Evaluation and Its Application to SNOMED CT

PubMed Central

Zhang, Guo-Qiang; Zhu, Wei; Sun, Mengmeng; Tao, Shiqiang; Bodenreider, Olivier; Cui, Licong

2015-01-01

Non-lattice fragments are often indicative of structural anomalies in ontological systems and, as such, represent possible areas of focus for subsequent quality assurance work. However, extracting the non-lattice fragments in large ontological systems is computationally expensive if not prohibitive, using a traditional sequential approach. In this paper we present a general MapReduce pipeline, called MaPLE (MapReduce Pipeline for Lattice-based Evaluation), for extracting non-lattice fragments in large partially ordered sets and demonstrate its applicability in ontology quality assurance. Using MaPLE in a 30-node Hadoop local cloud, we systematically extracted non-lattice fragments in 8 SNOMED CT versions from 2009 to 2014 (each containing over 300k concepts), with an average total computing time of less than 3 hours per version. With dramatically reduced time, MaPLE makes it feasible not only to perform exhaustive structural analysis of large ontological hierarchies, but also to systematically track structural changes between versions. Our change analysis showed that the average change rates on the non-lattice pairs are up to 38.6 times higher than the change rates of the background structure (concept nodes). This demonstrates that fragments around non-lattice pairs exhibit significantly higher rates of change in the process of ontological evolution. PMID:25705725

MaPLE: A MapReduce Pipeline for Lattice-based Evaluation and Its Application to SNOMED CT.

PubMed

Zhang, Guo-Qiang; Zhu, Wei; Sun, Mengmeng; Tao, Shiqiang; Bodenreider, Olivier; Cui, Licong

2014-10-01

Non-lattice fragments are often indicative of structural anomalies in ontological systems and, as such, represent possible areas of focus for subsequent quality assurance work. However, extracting the non-lattice fragments in large ontological systems is computationally expensive if not prohibitive, using a traditional sequential approach. In this paper we present a general MapReduce pipeline, called MaPLE (MapReduce Pipeline for Lattice-based Evaluation), for extracting non-lattice fragments in large partially ordered sets and demonstrate its applicability in ontology quality assurance. Using MaPLE in a 30-node Hadoop local cloud, we systematically extracted non-lattice fragments in 8 SNOMED CT versions from 2009 to 2014 (each containing over 300k concepts), with an average total computing time of less than 3 hours per version. With dramatically reduced time, MaPLE makes it feasible not only to perform exhaustive structural analysis of large ontological hierarchies, but also to systematically track structural changes between versions. Our change analysis showed that the average change rates on the non-lattice pairs are up to 38.6 times higher than the change rates of the background structure (concept nodes). This demonstrates that fragments around non-lattice pairs exhibit significantly higher rates of change in the process of ontological evolution.

Algorithmic mechanisms for reliable crowdsourcing computation under collusion.

PubMed

Fernández Anta, Antonio; Georgiou, Chryssis; Mosteiro, Miguel A; Pareja, Daniel

2015-01-01

We consider a computing system where a master processor assigns a task for execution to worker processors that may collude. We model the workers' decision of whether to comply (compute the task) or not (return a bogus result to save the computation cost) as a game among workers. That is, we assume that workers are rational in a game-theoretic sense. We identify analytically the parameter conditions for a unique Nash Equilibrium where the master obtains the correct result. We also evaluate experimentally mixed equilibria aiming to attain better reliability-profit trade-offs. For a wide range of parameter values that may be used in practice, our simulations show that, in fact, both master and workers are better off using a pure equilibrium where no worker cheats, even under collusion, and even for colluding behaviors that involve deviating from the game.

Algorithmic Mechanisms for Reliable Crowdsourcing Computation under Collusion

PubMed Central

Fernández Anta, Antonio; Georgiou, Chryssis; Mosteiro, Miguel A.; Pareja, Daniel

2015-01-01

We consider a computing system where a master processor assigns a task for execution to worker processors that may collude. We model the workers’ decision of whether to comply (compute the task) or not (return a bogus result to save the computation cost) as a game among workers. That is, we assume that workers are rational in a game-theoretic sense. We identify analytically the parameter conditions for a unique Nash Equilibrium where the master obtains the correct result. We also evaluate experimentally mixed equilibria aiming to attain better reliability-profit trade-offs. For a wide range of parameter values that may be used in practice, our simulations show that, in fact, both master and workers are better off using a pure equilibrium where no worker cheats, even under collusion, and even for colluding behaviors that involve deviating from the game. PMID:25793524

Off-equilibrium infrared structure of self-interacting scalar fields: Universal scaling, vortex-antivortex superfluid dynamics, and Bose-Einstein condensation

NASA Astrophysics Data System (ADS)

Deng, Jian; Schlichting, Soeren; Venugopalan, Raju; Wang, Qun

2018-05-01

We map the infrared dynamics of a relativistic single-component (N =1 ) interacting scalar field theory to that of nonrelativistic complex scalar fields. The Gross-Pitaevskii (GP) equation, describing the real-time dynamics of single-component ultracold Bose gases, is obtained at first nontrivial order in an expansion proportional to the powers of λ ϕ2/m2 where λ , ϕ , and m are the coupling constant, the scalar field, and the particle mass respectively. Our analytical studies are corroborated by numerical simulations of the spatial and momentum structure of overoccupied scalar fields in (2+1)-dimensions. Universal scaling of infrared modes, vortex-antivortex superfluid dynamics, and the off-equilibrium formation of a Bose-Einstein condensate are observed. Our results for the universal scaling exponents are in agreement with those extracted in the numerical simulations of the GP equation. As in these simulations, we observe coarsening phase kinetics in the Bose superfluid with strongly anomalous scaling exponents relative to that of vertex resummed kinetic theory. Our relativistic field theory framework further allows one to study more closely the coupling between superfluid and normal fluid modes, specifically the turbulent momentum and spatial structure of the coupling between a quasiparticle cascade to the infrared and an energy cascade to the ultraviolet. We outline possible applications of the formalism to the dynamics of vortex-antivortex formation and to the off-equilibrium dynamics of the strongly interacting matter formed in heavy-ion collisions.

Sequential capillary electrophoresis analysis using optically gated sample injection and UV/vis detection.

PubMed

Liu, Xiaoxia; Tian, Miaomiao; Camara, Mohamed Amara; Guo, Liping; Yang, Li

2015-10-01

We present sequential CE analysis of amino acids and L-asparaginase-catalyzed enzyme reaction, by combing the on-line derivatization, optically gated (OG) injection and commercial-available UV-Vis detection. Various experimental conditions for sequential OG-UV/vis CE analysis were investigated and optimized by analyzing a standard mixture of amino acids. High reproducibility of the sequential CE analysis was demonstrated with RSD values (n = 20) of 2.23, 2.57, and 0.70% for peak heights, peak areas, and migration times, respectively, and the LOD of 5.0 μM (for asparagine) and 2.0 μM (for aspartic acid) were obtained. With the application of the OG-UV/vis CE analysis, sequential online CE enzyme assay of L-asparaginase-catalyzed enzyme reaction was carried out by automatically and continuously monitoring the substrate consumption and the product formation every 12 s from the beginning to the end of the reaction. The Michaelis constants for the reaction were obtained and were found to be in good agreement with the results of traditional off-line enzyme assays. The study demonstrated the feasibility and reliability of integrating the OG injection with UV/vis detection for sequential online CE analysis, which could be of potential value for online monitoring various chemical reaction and bioprocesses. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Who's Afraid of Old Mother Hubbard?

ERIC Educational Resources Information Center

Ohanian, Susan

1990-01-01

Refutes the sequential, building-block theory of cultural literacy which advocates mastery of a prescribed body of cultural knowledge. Argues that teachers must help students find joyful encounters with words which will knock their socks off and inspire them both to search for understanding and to reach for another book. (SR)

The IP vs. VDE competition as a key factor determining the stability of the MgBX 5 (X = F, Cl) compounds

NASA Astrophysics Data System (ADS)

Sikorska, Celina; Skurski, Piotr

2010-11-01

The explanation of the MgBX 5 (X = F, Cl) systems existence and stability is provided on the basis of theoretical considerations supported by ab initio calculations. The equilibrium structures and most probable fragmentation processes of 26 (including isomers) MgBX 5 molecules and six OBX 5 compounds (for comparison) were examined and discussed. The competition between the ionization potential (IP) of the MgX subunit and the electron binding energy (VDE) of the BX 4 fragment was found to be the key factor determining the ability to form a stable compound of MgBX 5 type.

Incorporation of charge transfer into the explicit polarization fragment method by grand canonical density functional theory.

PubMed

Isegawa, Miho; Gao, Jiali; Truhlar, Donald G

2011-08-28

Molecular fragmentation algorithms provide a powerful approach to extending electronic structure methods to very large systems. Here we present a method for including charge transfer between molecular fragments in the explicit polarization (X-Pol) fragment method for calculating potential energy surfaces. In the conventional X-Pol method, the total charge of each fragment is preserved, and charge transfer between fragments is not allowed. The description of charge transfer is made possible by treating each fragment as an open system with respect to the number of electrons. To achieve this, we applied Mermin's finite temperature method to the X-Pol wave function. In the application of this method to X-Pol, the fragments are open systems that partially equilibrate their number of electrons through a quasithermodynamics electron reservoir. The number of electrons in a given fragment can take a fractional value, and the electrons of each fragment obey the Fermi-Dirac distribution. The equilibrium state for the electrons is determined by electronegativity equalization with conservation of the total number of electrons. The amount of charge transfer is controlled by re-interpreting the temperature parameter in the Fermi-Dirac distribution function as a coupling strength parameter. We determined this coupling parameter so as to reproduce the charge transfer energy obtained by block localized energy decomposition analysis. We apply the new method to ten systems, and we show that it can yield reasonable approximations to potential energy profiles, to charge transfer stabilization energies, and to the direction and amount of charge transferred. © 2011 American Institute of Physics

Incorporation of charge transfer into the explicit polarization fragment method by grand canonical density functional theory

PubMed Central

Isegawa, Miho; Gao, Jiali; Truhlar, Donald G.

2011-01-01

Molecular fragmentation algorithms provide a powerful approach to extending electronic structure methods to very large systems. Here we present a method for including charge transfer between molecular fragments in the explicit polarization (X-Pol) fragment method for calculating potential energy surfaces. In the conventional X-Pol method, the total charge of each fragment is preserved, and charge transfer between fragments is not allowed. The description of charge transfer is made possible by treating each fragment as an open system with respect to the number of electrons. To achieve this, we applied Mermin's finite temperature method to the X-Pol wave function. In the application of this method to X-Pol, the fragments are open systems that partially equilibrate their number of electrons through a quasithermodynamics electron reservoir. The number of electrons in a given fragment can take a fractional value, and the electrons of each fragment obey the Fermi–Dirac distribution. The equilibrium state for the electrons is determined by electronegativity equalization with conservation of the total number of electrons. The amount of charge transfer is controlled by re-interpreting the temperature parameter in the Fermi–Dirac distribution function as a coupling strength parameter. We determined this coupling parameter so as to reproduce the charge transfer energy obtained by block localized energy decomposition analysis. We apply the new method to ten systems, and we show that it can yield reasonable approximations to potential energy profiles, to charge transfer stabilization energies, and to the direction and amount of charge transferred. PMID:21895159

Dendrites fragmentation induced by oscillating cavitation bubbles in ultrasound field.

PubMed

Wang, S; Kang, J; Zhang, X; Guo, Z

2018-02-01

The fragmentation of the dendrites of succinonitrile (SCN)-2-wt.% acetone organic transparent alloy caused by ultrasound-induced cavitation bubbles was studied by using ultra-high-speed digital camera with a rate of 40,000fps. Real-time imaging reveals that the vibrating cavitation bubbles can fragment not only secondary arms but also the primary ones under high ultrasound power. The secondary arms always broke at their roots as a result of stress concentration induced by oscillated cavitation bubble and then ripped off from their primary arms. Generally the fragment process takes tens of milliseconds from bending to breaking, while the break always occurs immediately in less than 25μs. Copyright © 2017. Published by Elsevier B.V.

Comparison of different strategies in prenatal screening for Down's syndrome: cost effectiveness analysis of computer simulation.

PubMed

Gekas, Jean; Gagné, Geneviève; Bujold, Emmanuel; Douillard, Daniel; Forest, Jean-Claude; Reinharz, Daniel; Rousseau, François

2009-02-13

To assess and compare the cost effectiveness of three different strategies for prenatal screening for Down's syndrome (integrated test, sequential screening, and contingent screenings) and to determine the most useful cut-off values for risk. Computer simulations to study integrated, sequential, and contingent screening strategies with various cut-offs leading to 19 potential screening algorithms. The computer simulation was populated with data from the Serum Urine and Ultrasound Screening Study (SURUSS), real unit costs for healthcare interventions, and a population of 110 948 pregnancies from the province of Québec for the year 2001. Cost effectiveness ratios, incremental cost effectiveness ratios, and screening options' outcomes. The contingent screening strategy dominated all other screening options: it had the best cost effectiveness ratio ($C26,833 per case of Down's syndrome) with fewer procedure related euploid miscarriages and unnecessary terminations (respectively, 6 and 16 per 100,000 pregnancies). It also outperformed serum screening at the second trimester. In terms of the incremental cost effectiveness ratio, contingent screening was still dominant: compared with screening based on maternal age alone, the savings were $C30,963 per additional birth with Down's syndrome averted. Contingent screening was the only screening strategy that offered early reassurance to the majority of women (77.81%) in first trimester and minimised costs by limiting retesting during the second trimester (21.05%). For the contingent and sequential screening strategies, the choice of cut-off value for risk in the first trimester test significantly affected the cost effectiveness ratios (respectively, from $C26,833 to $C37,260 and from $C35,215 to $C45,314 per case of Down's syndrome), the number of procedure related euploid miscarriages (from 6 to 46 and from 6 to 45 per 100,000 pregnancies), and the number of unnecessary terminations (from 16 to 26 and from 16 to 25 per 100,000 pregnancies). Contingent screening, with a first trimester cut-off value for high risk of 1 in 9, is the preferred option for prenatal screening of women for pregnancies affected by Down's syndrome.

Loss of heterozygosity at D8S262: an early genetic event of hepatocarcinogenesis.

PubMed

Zhu, Qiao; Gong, Li; Liu, Xiaoyan; Wang, Jun; Ren, Pin; Zhang, Wendong; Yao, Li; Han, Xiujuan; Zhu, Shaojun; Lan, Miao; Li, Yanhong; Zhang, Wei

2015-06-16

Hepatocellular carcinoma (HCC) is a multi-factor, multi-step, multi-gene and complicated process resulting from the accumulation of sequential genetic and epigenetic alterations. An important change among them is from precancerous lesions to HCC. However, only few studies have been reported about the sequential genetic changes during hepatocarcinogenesis. We observed firstly molecular karyotypes of 10 matched HCC using Affymetrix single-nucleotide polymorphism (SNP) 6.0 arrays, and found chromosomal fragments with high incidence (more than 70%) of loss of heterozygosity (LOH). Then, we selected 28 microsatellite markers at some gene spanning these chromosomal fragments, and examined the frequency of LOH of 128 matched HCC and 43 matched precancerous lesions-dysplastic nodules (DN) by a PCR-based analysis. Finally, we investigated the expression of proteins encoded by these genes in HCC, DN and the surrounding hepatic tissues. The result of Affymetrix SNP6.0 arrays demonstrated that more than 70% (7/10) cases had chromosomal fragment deletion on 4q13.3-35.1, 8p23.2-21.2, 16q11.2-24.3, and 17p13.3-12. Among 28 microsatellite markers selected, LOH frequencies at D8S262 for DN and HCC were found to be the highest, 51.2% and 72.7%, respectively. Immunohistochemically, the positive rate of its adjacent gene CSMD1 in HCC, DN, and the surrounding hepatic tissues were 27.3% (35/128), 75% (33/44), and 82% (105/128), respectively. LOH at D8S262 may be associated with an early genetic event of hepatocarcinogenesis, and a predictor for the monitor and prevention of HCC. The virtual slides for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1557074981159099 .

Isobaric yield ratio difference between the 140 A MeV 58Ni + 9Be and 64Ni +9Be reactions studied by the antisymmetric molecular dynamics model

NASA Astrophysics Data System (ADS)

Qiao, C. Y.; Wei, H. L.; Ma, C. W.; Zhang, Y. L.; Wang, S. S.

2015-07-01

Background: The isobaric yield ratio difference (IBD) method is found to be sensitive to the density difference of neutron-rich nucleus induced reaction around the Fermi energy. Purpose: An investigation is performed to study the IBD results in the transport model. Methods: The antisymmetric molecular dynamics (AMD) model plus the sequential decay model gemini are adopted to simulate the 140 A MeV 58 ,64Ni +9Be reactions. A relative small coalescence radius Rc= 2.5 fm is used for the phase space at t = 500 fm/c to form the hot fragment. Two limitations on the impact parameter (b 1 =0 -2 fm and b 2 =0 -9 fm) are used to study the effect of central collisions in IBD. Results: The isobaric yield ratios (IYRs) for the large-A fragments are found to be suppressed in the symmetric reaction. The IBD results for fragments with neutron excess I = 0 and 1 are obtained. A small difference is found in the IBDs with the b 1 and b 2 limitations in the AMD simulated reactions. The IBD with b 1 and b 2 are quite similar in the AMD + GEMINI simulated reactions. Conclusions: The IBDs for the I =0 and 1 chains are mainly determined by the central collisions, which reflects the nuclear density in the core region of the reaction system. The increasing part of the IBD distribution is found due to the difference between the densities in the peripheral collisions of the reactions. The sequential decay process influences the IBD results. The AMD + GEMINI simulation can better reproduce the experimental IBDs than the AMD simulation.

Fragmenting networks by targeting collective influencers at a mesoscopic level.

PubMed

Kobayashi, Teruyoshi; Masuda, Naoki

2016-11-25

A practical approach to protecting networks against epidemic processes such as spreading of infectious diseases, malware, and harmful viral information is to remove some influential nodes beforehand to fragment the network into small components. Because determining the optimal order to remove nodes is a computationally hard problem, various approximate algorithms have been proposed to efficiently fragment networks by sequential node removal. Morone and Makse proposed an algorithm employing the non-backtracking matrix of given networks, which outperforms various existing algorithms. In fact, many empirical networks have community structure, compromising the assumption of local tree-like structure on which the original algorithm is based. We develop an immunization algorithm by synergistically combining the Morone-Makse algorithm and coarse graining of the network in which we regard a community as a supernode. In this way, we aim to identify nodes that connect different communities at a reasonable computational cost. The proposed algorithm works more efficiently than the Morone-Makse and other algorithms on networks with community structure.

Fragmenting networks by targeting collective influencers at a mesoscopic level

NASA Astrophysics Data System (ADS)

Kobayashi, Teruyoshi; Masuda, Naoki

2016-11-01

A practical approach to protecting networks against epidemic processes such as spreading of infectious diseases, malware, and harmful viral information is to remove some influential nodes beforehand to fragment the network into small components. Because determining the optimal order to remove nodes is a computationally hard problem, various approximate algorithms have been proposed to efficiently fragment networks by sequential node removal. Morone and Makse proposed an algorithm employing the non-backtracking matrix of given networks, which outperforms various existing algorithms. In fact, many empirical networks have community structure, compromising the assumption of local tree-like structure on which the original algorithm is based. We develop an immunization algorithm by synergistically combining the Morone-Makse algorithm and coarse graining of the network in which we regard a community as a supernode. In this way, we aim to identify nodes that connect different communities at a reasonable computational cost. The proposed algorithm works more efficiently than the Morone-Makse and other algorithms on networks with community structure.

Fragmenting networks by targeting collective influencers at a mesoscopic level

PubMed Central

Kobayashi, Teruyoshi; Masuda, Naoki

2016-01-01

A practical approach to protecting networks against epidemic processes such as spreading of infectious diseases, malware, and harmful viral information is to remove some influential nodes beforehand to fragment the network into small components. Because determining the optimal order to remove nodes is a computationally hard problem, various approximate algorithms have been proposed to efficiently fragment networks by sequential node removal. Morone and Makse proposed an algorithm employing the non-backtracking matrix of given networks, which outperforms various existing algorithms. In fact, many empirical networks have community structure, compromising the assumption of local tree-like structure on which the original algorithm is based. We develop an immunization algorithm by synergistically combining the Morone-Makse algorithm and coarse graining of the network in which we regard a community as a supernode. In this way, we aim to identify nodes that connect different communities at a reasonable computational cost. The proposed algorithm works more efficiently than the Morone-Makse and other algorithms on networks with community structure. PMID:27886251

The carry-over of Campylobacter isolates between sequential poultry flocks.

PubMed

Shreeve, J E; Toszeghy, M; Ridley, A; Newell, D G

2002-01-01

The carry-over of Campylobacter strains from one flock to a subsequent flock in the same broiler house has been studied using molecular epidemiological techniques. In all, 524 Campylobacter strains, isolated from two sequential broiler flocks from 60 broiler houses, were typed by restriction fragment polymorphism of the polymerase chain reaction (PCR) product of the flaA and flaB genes (fla typing). Selected strains were also typed using pulsed field gel electrophoresis (PFGE). By fla typing, 15 (21%) of the 60 houses with Campylobacter-positive sequential flocks had identical genotypes. In 10 (16% overall) of these houses the strains were also identical by PFGE. The difference in PFGE patterns in the strains from the three remaining houses may be indicative of genetic instability. Overall, these results suggest that carry-over from one flock to a subsequent flock in the same house is a relatively infrequent event and, therefore, that routine broiler house cleansing and/or disinfection is largely adequate to eliminate Campylobacter contamination. An alternative explanation of the low level carry-over is a persistent source or reservoir, external to the environment of the broiler houses.

TRIGGERED STAR FORMATION SURROUNDING WOLF-RAYET STAR HD 211853

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

Liu Tie; Wu Yuefang; Zhang Huawei

The environment surrounding Wolf-Rayet (W-R) star HD 211853 is studied in molecular, infrared, as well as radio, and H I emission. The molecular ring consists of well-separated cores, which have a volume density of 10{sup 3} cm{sup -3} and kinematic temperature {approx}20 K. Most of the cores are under gravitational collapse due to external pressure from the surrounding ionized gas. From the spectral energy distribution modeling toward the young stellar objects, the sequential star formation is revealed on a large scale in space spreading from the W-R star to the molecular ring. A small-scale sequential star formation is revealed towardmore » core 'A', which harbors a very young star cluster. Triggered star formations are thus suggested. The presence of the photodissociation region, the fragmentation of the molecular ring, the collapse of the cores, and the large-scale sequential star formation indicate that the 'collect and collapse' process functions in this region. The star-forming activities in core 'A' seem to be affected by the 'radiation-driven implosion' process.« less

Pathways of proton transfer in the light-driven pump bacteriorhodopsin

NASA Technical Reports Server (NTRS)

Lanyi, J. K.

1993-01-01

The mechanism of proton transport in the light-driven pump bacteriorhodopsin is beginning to be understood. Light causes the all-trans to 13-cis isomerization of the retinal chromophore. This sets off a sequential and directed series of transient decreases in the pKa's of a) the retinal Schiff base, b) an extracellular proton release complex which includes asp-85, and c) a cytoplasmic proton uptake complex which includes asp-96. The timing of these pKa changes during the photoreaction cycle causes sequential proton transfers which result in the net movement of a proton across the protein, from the cytoplasmic to the extracellular surface.

Evidence for a Shared Mechanism in the Formation of Urea-Induced Kinetic and Equilibrium Intermediates of Horse Apomyoglobin from Ultrarapid Mixing Experiments.

PubMed

Mizukami, Takuya; Abe, Yukiko; Maki, Kosuke

2015-01-01

In this study, the equivalence of the kinetic mechanisms of the formation of urea-induced kinetic folding intermediates and non-native equilibrium states was investigated in apomyoglobin. Despite having similar structural properties, equilibrium and kinetic intermediates accumulate under different conditions and via different mechanisms, and it remains unknown whether their formation involves shared or distinct kinetic mechanisms. To investigate the potential mechanisms of formation, the refolding and unfolding kinetics of horse apomyoglobin were measured by continuous- and stopped-flow fluorescence over a time range from approximately 100 μs to 10 s, along with equilibrium unfolding transitions, as a function of urea concentration at pH 6.0 and 8°C. The formation of a kinetic intermediate was observed over a wider range of urea concentrations (0-2.2 M) than the formation of the native state (0-1.6 M). Additionally, the kinetic intermediate remained populated as the predominant equilibrium state under conditions where the native and unfolded states were unstable (at ~0.7-2 M urea). A continuous shift from the kinetic to the equilibrium intermediate was observed as urea concentrations increased from 0 M to ~2 M, which indicates that these states share a common kinetic folding mechanism. This finding supports the conclusion that these intermediates are equivalent. Our results in turn suggest that the regions of the protein that resist denaturant perturbations form during the earlier stages of folding, which further supports the structural equivalence of transient and equilibrium intermediates. An additional folding intermediate accumulated within ~140 μs of refolding and an unfolding intermediate accumulated in <1 ms of unfolding. Finally, by using quantitative modeling, we showed that a five-state sequential scheme appropriately describes the folding mechanism of horse apomyoglobin.

Rationalizing fragment based drug discovery for BACE1: insights from FB-QSAR, FB-QSSR, multi objective (MO-QSPR) and MIF studies

NASA Astrophysics Data System (ADS)

Manoharan, Prabu; Vijayan, R. S. K.; Ghoshal, Nanda

2010-10-01

The ability to identify fragments that interact with a biological target is a key step in FBDD. To date, the concept of fragment based drug design (FBDD) is increasingly driven by bio-physical methods. To expand the boundaries of QSAR paradigm, and to rationalize FBDD using In silico approach, we propose a fragment based QSAR methodology referred here in as FB-QSAR. The FB-QSAR methodology was validated on a dataset consisting of 52 Hydroxy ethylamine (HEA) inhibitors, disclosed by GlaxoSmithKline Pharmaceuticals as potential anti-Alzheimer agents. To address the issue of target selectivity, a major confounding factor in the development of selective BACE1 inhibitors, FB-QSSR models were developed using the reported off target activity values. A heat map constructed, based on the activity and selectivity profile of the individual R-group fragments, and was in turn used to identify superior R-group fragments. Further, simultaneous optimization of multiple properties, an issue encountered in real-world drug discovery scenario, and often overlooked in QSAR approaches, was addressed using a Multi Objective (MO-QSPR) method that balances properties, based on the defined objectives. MO-QSPR was implemented using Derringer and Suich desirability algorithm to identify the optimal level of independent variables ( X) that could confer a trade-off between selectivity and activity. The results obtained from FB-QSAR were further substantiated using MIF (Molecular Interaction Fields) studies. To exemplify the potentials of FB-QSAR and MO-QSPR in a pragmatic fashion, the insights gleaned from the MO-QSPR study was reverse engineered using Inverse-QSAR in a combinatorial fashion to enumerate some prospective novel, potent and selective BACE1 inhibitors.

Rationalizing fragment based drug discovery for BACE1: insights from FB-QSAR, FB-QSSR, multi objective (MO-QSPR) and MIF studies.

PubMed

Manoharan, Prabu; Vijayan, R S K; Ghoshal, Nanda

2010-10-01

The ability to identify fragments that interact with a biological target is a key step in FBDD. To date, the concept of fragment based drug design (FBDD) is increasingly driven by bio-physical methods. To expand the boundaries of QSAR paradigm, and to rationalize FBDD using In silico approach, we propose a fragment based QSAR methodology referred here in as FB-QSAR. The FB-QSAR methodology was validated on a dataset consisting of 52 Hydroxy ethylamine (HEA) inhibitors, disclosed by GlaxoSmithKline Pharmaceuticals as potential anti-Alzheimer agents. To address the issue of target selectivity, a major confounding factor in the development of selective BACE1 inhibitors, FB-QSSR models were developed using the reported off target activity values. A heat map constructed, based on the activity and selectivity profile of the individual R-group fragments, and was in turn used to identify superior R-group fragments. Further, simultaneous optimization of multiple properties, an issue encountered in real-world drug discovery scenario, and often overlooked in QSAR approaches, was addressed using a Multi Objective (MO-QSPR) method that balances properties, based on the defined objectives. MO-QSPR was implemented using Derringer and Suich desirability algorithm to identify the optimal level of independent variables (X) that could confer a trade-off between selectivity and activity. The results obtained from FB-QSAR were further substantiated using MIF (Molecular Interaction Fields) studies. To exemplify the potentials of FB-QSAR and MO-QSPR in a pragmatic fashion, the insights gleaned from the MO-QSPR study was reverse engineered using Inverse-QSAR in a combinatorial fashion to enumerate some prospective novel, potent and selective BACE1 inhibitors.

Phonon cross-plane transport and thermal boundary resistance: effect of heat source size and thermal boundary resistance on phonon characteristics

NASA Astrophysics Data System (ADS)

Ali, H.; Yilbas, B. S.

2016-09-01

Phonon cross-plane transport across silicon and diamond thin films pair is considered, and thermal boundary resistance across the films pair interface is examined incorporating the cut-off mismatch and diffusive mismatch models. In the cut-off mismatch model, phonon frequency mismatch for each acoustic branch is incorporated across the interface of the silicon and diamond films pair in line with the dispersion relations of both films. The frequency-dependent and transient solution of the Boltzmann transport equation is presented, and the equilibrium phonon intensity ratios at the silicon and diamond film edges are predicted across the interface for each phonon acoustic branch. Temperature disturbance across the edges of the films pair is incorporated to assess the phonon transport characteristics due to cut-off and diffusive mismatch models across the interface. The effect of heat source size, which is allocated at high-temperature (301 K) edge of the silicon film, on the phonon transport characteristics at the films pair interface is also investigated. It is found that cut-off mismatch model predicts higher values of the thermal boundary resistance across the films pair interface as compared to that of the diffusive mismatch model. The ratio of equilibrium phonon intensity due to the cut-off mismatch over the diffusive mismatch models remains >1 at the silicon edge, while it becomes <1 at the diamond edge for all acoustic branches.

Filetype Identification Using Long, Summarized N-Grams

DTIC Science & Technology

2011-03-01

compressed or encrypted data . If the algorithm used to compress or encrypt the data can be determined, then it is frequently possible to uncom- press...fragments. His implementation utilized the bzip2 library to compress the file fragments. The bzip2 library is based off the Lempel - Ziv -Markov chain... algorithm that uses a dictionary compression scheme to remove repeating data patterns within a set of data . The removed patterns are listed within the

Competition and equilibria in electricity markets based on two-settlement system: A conjectural variation approach

NASA Astrophysics Data System (ADS)

Watts, David

This dissertation studies electricity markets based on two-settlement systems and applies the concept of conjectural variation (CV) as a tool for representing different levels of competitiveness in the market. Some recent theoretical works are addressed to support the use of CV as a solution concept. A notion of consistency is introduced to make the level of competitiveness of the market endogenous, and allows finding consistent CV equilibria and the corresponding conditions for existence of equilibria. First, a case is studied in which firms hold exogenous levels of forward commitments. Then, backward induction and sub-game perfection are used to solve sequentially for the spot and forward market equilibrium. This allows analyzing how firms take positions in the forward market, based on considering their later impact on the spot market. It is concluded that positions taken in the forward market depend largely on firms expectations about the competitiveness of both the spot and the forward market. Forward markets are welfare enhancing even if they are not as competitive as the associated spot market as long as they are not too oligopolistie. The above formulation is used to model a dynamic scenario to analyze market stability, linking this research to Dr. Alvarado's earlier research on market stability. This brings about interesting trade offs between market power and market stability.

Factorization of the association rate coefficient in ligand rebinding to heme proteins

NASA Astrophysics Data System (ADS)

Young, Robert D.

1984-01-01

A stochastic theory of ligand migration in biomolecules is used to analyze the recombination of small ligands to heme proteins after flash photolysis. The stochastic theory is based on a generalized sequential barrier model in which a ligand binds by overcoming a series of barriers formed by the solvent protein interface, the protein matrix, and the heme distal histidine system. The stochastic theory shows that the association rate coefficient λon factorizes into three terms λon =γ12Nout, where γ12 is the rate coefficient from the heme pocket to the heme binding site, is the equilibrium pocket occupation factor, and Nout is the fraction of heme proteins which do not undergo geminate recombination of a flashed-off ligand. The factorization of λon holds for any number of barriers and with no assumptions regarding the various rate coefficients so long as the exponential solvent process occurs. Transitions of a single ligand are allowed between any two sites with two crucial exceptions: (i) the heme binding site acts as a trap so that thermal dissociation of a bound ligand does not occur within the time of the measurement; (ii) the final step in the rebinding process always has a ligand in the heme pocket from where the ligand binds to the heme iron.

Picking up the pieces: conserving remnant natural areas in the post-industrial landscape of the Calumet Region

USGS Publications Warehouse

Labus, Paul; Whitman, Richard L.; Nevers, Meredith Becker

1999-01-01

The Calumet Region was shaped by geologic forces, succession, and interacting biomes converging on a unique natural landscape. Over the past 4500 years, a strand plain has formed to the north of a geologic area called Toleston Beach. Sequential and differential primary succession of dune and swale communities in this region allowed species from different biomes to interact freely. In the mid-nineteenth century, commerce and settlement drastically changed the area, and natural areas were fragmented, manipulated, and degraded by cultural intrusions and industrialization. Despite the near obliteration of dune and swale habitat, small fragments of natural land escaped destruction. These native fragments maintained some semblance of the landscape that once covered the region. Currently, these native fragments are threatened by the lingering intrusion of historic contamination and the continuing presence of industry and commerce. Restoration and conservation of these remnants will need to be a process of integrating biological diversity goals into the landscape of the industrialized region through planning and design. We outline here the natural history of the region, the philosophical rationale for conservation, and possible approaches for integrating and maintaining these valuable remnant resources and processes.

Hitting the target: fragment screening with acoustic in situ co-crystallization of proteins plus fragment libraries on pin-mounted data-collection micromeshes.

PubMed

Yin, Xingyu; Scalia, Alexander; Leroy, Ludmila; Cuttitta, Christina M; Polizzo, Gina M; Ericson, Daniel L; Roessler, Christian G; Campos, Olven; Ma, Millie Y; Agarwal, Rakhi; Jackimowicz, Rick; Allaire, Marc; Orville, Allen M; Sweet, Robert M; Soares, Alexei S

2014-05-01

Acoustic droplet ejection (ADE) is a powerful technology that supports crystallographic applications such as growing, improving and manipulating protein crystals. A fragment-screening strategy is described that uses ADE to co-crystallize proteins with fragment libraries directly on MiTeGen MicroMeshes. Co-crystallization trials can be prepared rapidly and economically. The high speed of specimen preparation and the low consumption of fragment and protein allow the use of individual rather than pooled fragments. The Echo 550 liquid-handling instrument (Labcyte Inc., Sunnyvale, California, USA) generates droplets with accurate trajectories, which allows multiple co-crystallization experiments to be discretely positioned on a single data-collection micromesh. This accuracy also allows all components to be transferred through small apertures. Consequently, the crystallization tray is in equilibrium with the reservoir before, during and after the transfer of protein, precipitant and fragment to the micromesh on which crystallization will occur. This strict control of the specimen environment means that the crystallography experiments remain identical as the working volumes are decreased from the few microlitres level to the few nanolitres level. Using this system, lysozyme, thermolysin, trypsin and stachydrine demethylase crystals were co-crystallized with a small 33-compound mini-library to search for fragment hits. This technology pushes towards a much faster, more automated and more flexible strategy for structure-based drug discovery using as little as 2.5 nl of each major component.

Hitting the target: fragment screening with acoustic in situ co-crystallization of proteins plus fragment libraries on pin-mounted data-collection micromeshes

PubMed Central

Yin, Xingyu; Scalia, Alexander; Leroy, Ludmila; Cuttitta, Christina M.; Polizzo, Gina M.; Ericson, Daniel L.; Roessler, Christian G.; Campos, Olven; Ma, Millie Y.; Agarwal, Rakhi; Jackimowicz, Rick; Allaire, Marc; Orville, Allen M.; Sweet, Robert M.; Soares, Alexei S.

2014-01-01

Acoustic droplet ejection (ADE) is a powerful technology that supports crystallographic applications such as growing, improving and manipulating protein crystals. A fragment-screening strategy is described that uses ADE to co-crystallize proteins with fragment libraries directly on MiTeGen MicroMeshes. Co-crystallization trials can be prepared rapidly and economically. The high speed of specimen preparation and the low consumption of fragment and protein allow the use of individual rather than pooled fragments. The Echo 550 liquid-handling instrument (Labcyte Inc., Sunnyvale, California, USA) generates droplets with accurate trajectories, which allows multiple co-crystallization experiments to be discretely positioned on a single data-collection micromesh. This accuracy also allows all components to be transferred through small apertures. Consequently, the crystallization tray is in equilibrium with the reservoir before, during and after the transfer of protein, precipitant and fragment to the micromesh on which crystallization will occur. This strict control of the specimen environment means that the crystallography experiments remain identical as the working volumes are decreased from the few microlitres level to the few nanolitres level. Using this system, lysozyme, thermolysin, trypsin and stachydrine demethylase crystals were co-crystallized with a small 33-compound mini-library to search for fragment hits. This technology pushes towards a much faster, more automated and more flexible strategy for structure-based drug discovery using as little as 2.5 nl of each major component. PMID:24816088

Kolkata Paise Restaurant Problem and the Cyclically Fair Norm

NASA Astrophysics Data System (ADS)

Banerjee, Priyodorshi; Mitra, Manipushpak; Mukherjee, Conan

In this paper we revisit the Kolkata Paise Restaurant problem by allowing for a more general (but common) preference of the n customers defined over the set of n restaurants. This generalization allows for the possibility that each pure strategy Nash equilibrium differs from the Pareto efficient allocation. By assuming that n is small and by allowing for mutual interaction across all customers we design strategies to sustain cyclically fair norm as a sub-game perfect equilibrium of the Kolkata Paise Restaurant problem. We have a cyclically fair norm if n strategically different Pareto efficient strategies are sequentially sustained in a way such that each customer gets serviced in all the n restaurants exactly once between periods 1 and n and then again the same process is repeated between periods (n+1) and 2n and so on.

Off-normal deposition of PTFE thin films during 157-nm irradiation

NASA Astrophysics Data System (ADS)

George, Sharon R.; Langford, Stephen C.; Dickinson, J. Thomas

2010-03-01

Polytetrafluoroethylene (PTFE) is valued for its chemical stability, low surface energy, and insulating properties. The ablation of PTFE by F2 excimer lasers (157 nm photons) involves photochemical scission of C-C bonds along the polymer chain. Depending on the fluence, the fragment masses can range from 50 to 2000 amu. Gaussian beam profiles allow for the production of spatially non-uniform distributions of fragment masses, with the lighter fragments concentrated in the center of the laser spot. The resulting trajectories for the light fragments can be strongly forward directed, while the heavy fragments are directed more to the side, well away from the surface normal. We present experimental evidence for these angular distributions, and numerically simulate this behavior with a simple, two-component hydrodynamic model. Under the conditions of our work, most of the ablated mass appears as heavier fragments and can be collected on substrates mounted to the sides or above and below the laser spot. This geometry may have advantages in some applications of pulsed laser deposition.

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

PubMed

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

2008-04-01

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

40 CFR 63.1574 - What notifications must I submit and when?

Code of Federal Regulations, 2013 CFR

2013-07-01

... catalyst regenerator. (iv) Procedures and analytical methods you will use to determine the equilibrium... of the sorbent material (but not less frequent than once every 4 hours during coke burn-off). If the...

40 CFR 63.1574 - What notifications must I submit and when?

Code of Federal Regulations, 2014 CFR

2014-07-01

... catalyst regenerator. (iv) Procedures and analytical methods you will use to determine the equilibrium... of the sorbent material (but not less frequent than once every 4 hours during coke burn-off). If the...

40 CFR 63.1574 - What notifications must I submit and when?

Code of Federal Regulations, 2012 CFR

2012-07-01

... catalyst regenerator. (iv) Procedures and analytical methods you will use to determine the equilibrium... of the sorbent material (but not less frequent than once every 4 hours during coke burn-off). If the...

Equilibrium evolution in oscillating-field current-drive experiments

NASA Astrophysics Data System (ADS)

McCollam, K. J.; Anderson, J. K.; Blair, A. P.; Craig, D.; Den Hartog, D. J.; Ebrahimi, F.; O'Connell, R.; Reusch, J. A.; Sarff, J. S.; Stephens, H. D.; Stone, D. R.; Brower, D. L.; Deng, B. H.; Ding, W. X.

2010-08-01

Oscillating-field current drive (OFCD) is a proposed method of steady-state toroidal plasma sustainment in which ac poloidal and toroidal loop voltages are applied to produce a dc plasma current. OFCD is added to standard, inductively sustained reversed-field pinch plasmas in the Madison Symmetric Torus [R. N. Dexter et al., Fusion Technol. 19, 131 (1991)]. Equilibrium profiles and fluctuations during a single cycle are measured and analyzed for different relative phases between the two OFCD voltages and for OFCD off. For OFCD phases leading to the most added plasma current, the measured energy confinement is slightly better than that for OFCD off. By contrast, the phase of the maximum OFCD helicity-injection rate also has the maximum decay rate, which is ascribed to transport losses during discrete magnetic-fluctuation events induced by OFCD. Resistive-magnetohydrodynamic simulations of the experiments reproduce the observed phase dependence of the added current.

Multisegment nanowire sensors for the detection of DNA molecules.

PubMed

Wang, Xu; Ozkan, Cengiz S

2008-02-01

We describe a novel application for detecting specific single strand DNA sequences using multisegment nanowires via a straightforward surface functionalization method. Nanowires comprising CdTe-Au-CdTe segments are fabricated using electrochemical deposition, and electrical characterization indicates a p-type behavior for the multisegment nanostructures, in a back-to-back Schottky diode configuration. Such nanostructures modified with thiol-terminated probe DNA fragments could function as high fidelity sensors for biomolecules at very low concentration. The gold segment is utilized for functionalization and binding of single strand DNA (ssDNA) fragments while the CdTe segments at both ends serve to modulate the equilibrium Fermi level of the heterojunction device upon hybridization of the complementary DNA fragments (cDNA) to the ssDNA over the Au segment. Employing such multisegment nanowires could lead to the fabrication more sophisticated and high multispecificity biosensors via selective functionalization of individual segments for biowarfare sensing and medical diagnostics applications.

Direct Self-Sustained Fragmentation Cascade of Reactive Droplets

NASA Astrophysics Data System (ADS)

Inoue, Chihiro; Izato, Yu-ichiro; Miyake, Atsumi; Villermaux, Emmanuel

2017-02-01

A traditional hand-held firework generates light streaks similar to branched pine needles, with ever smaller ramifications. These streaks are the trajectories of incandescent reactive liquid droplets bursting from a melted powder. We have uncovered the detailed sequence of events, which involve a chemical reaction with the oxygen of air, thermal decomposition of metastable compounds in the melt, gas bubble nucleation and bursting, liquid ligaments and droplets formation, all occurring in a sequential fashion. We have also evidenced a rare instance in nature of a spontaneous fragmentation process involving a direct cascade from big to smaller droplets. Here, the self-sustained direct cascade is shown to proceed over up to eight generations, with well-defined time and length scales, thus answering a century old question, and enriching, with a new example, the phenomenology of comminution.

76 FR 45705 - Approval and Promulgation of Air Quality Implementation Plans; Pennsylvania; Diesel-Powered Motor...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-01

... following methods: A. http://www.regulations.gov . Follow the on-line instructions for submitting comments... the equipment is in good working order, if necessary as part of the inspection; (6) idling of a... off school property during queuing for the sequential discharge or pickup of students where the...

School-Based Mutual Support Groups for Parents: An Intervention Guidebook.

ERIC Educational Resources Information Center

Simoni, Jane M.

This handbook focuses on steps and tasks related to establishing mutual support groups for parents in a school setting. A sequential approach is described that involves: working within the school to get started; recruiting members; training parents how to run their own meetings; and offering off-site consultation as requested. The first section…

A simple fluorescent probe for the fast sequential detection of copper and biothiols based on a benzothiazole derivative

NASA Astrophysics Data System (ADS)

Shen, Youming; Zhang, Xiangyang; Zhang, Chunxiang; Zhang, Youyu; Jin, Junling; Li, Haitao

2018-02-01

A simple benzothiazole fluorescent chemosensor was developed for the fast sequential detection of Cu2 + and biothiols through modulating the excited-state intramolecular proton transfer (ESIPT) process. The compound 1 exhibits highly selective and sensitive fluorescence ;on-off; recognition to Cu2 + with a 1:1 binding stoichiometry by ESIPT hinder. The in situ generated 1-Cu2 + complex can serve as an ;on-off; fluorescent probe for high selectivity toward biothiols via Cu2 + displacement approach, which exerts ESIPT recovery. It is worth pointing out that the 1-Cu2 + complex shows faster for cysteins (within 1 min) than other biothiols such as homocysteine (25 min) and glutathione (25 min). Moreover, the compound 1 displays 160 nm Stoke-shift for reversibly monitoring Cu2 + and biothiols. In addition, the probe is successfully used for fluorescent cellular imaging. This strategy via modulation the ESIPT state has been used for determination of Cu2 + and Cys with satisfactory results, which further demonstrates its value of practical applications.

Characterization of Hypervelocity Metal Fragments for Explosive Initiation

NASA Astrophysics Data System (ADS)

Yeager, John; Bowden, Patrick; Guildenbecher, Daniel; Olles, Joseph

2017-06-01

The off-normal detonation behavior of two plastic-bonded explosive (PBX) formulations was studied using explosively-driven aluminum fragments moving at hypersonic velocity. Witness plate materials, including copper and polycarbonate, were used to characterize the distribution of particles, finding that the aluminum did not fragment homogeneously but rather with larger particles in a ring surrounding finer particles. Digital holography experiments were conducted to measure three-dimensional shape and size of the fastest-moving fragments, which ranged between 100 and 700 microns and traveled between 2 and 3.5 km/s. Crucially, these experiments showed variability in the fragmentation in terms of the number of fragments at the leading edge of the fragment field, indicating that both single and multiple shock impacts could be imparted to the target material. Lower density PBX 9407 (RDX-based) was initiable at up to 4.5 inches, while higher density PBX 9501 (HMX-based) was only initiable at up to 0.25 inches. This type of data is critical for safety experiments and hydrocode simulations to quantify shock-to-detonation transition mechanisms and the associated risk-margins for these materials.

Coordination and interpretation of vocal and visible resources: 'trail-off' conjunctions.

PubMed

Walker, Gareth

2012-03-01

The empirical focus of this paper is a conversational turn-taking phenomenon in which conjunctions produced immediately after a point of possible syntactic and pragmatic completion are treated by co-participants as points of possible completion and transition relevance. The data for this study are audio-video recordings of 5 unscripted face-to-face interactions involving native speakers of US English, yielding 28 'trail-off' conjunctions. Detailed sequential analysis of talk is combined with analysis of visible features (including gaze, posture, gesture and involvement with material objects) and technical phonetic analysis. A range of phonetic and visible features are shown to regularly co-occur in the production of 'trail-off' conjunctions. These features distinguish them from other conjunctions followed by the cessation of talk.

General mechanism of two-state protein folding kinetics.

PubMed

Rollins, Geoffrey C; Dill, Ken A

2014-08-13

We describe here a general model of the kinetic mechanism of protein folding. In the Foldon Funnel Model, proteins fold in units of secondary structures, which form sequentially along the folding pathway, stabilized by tertiary interactions. The model predicts that the free energy landscape has a volcano shape, rather than a simple funnel, that folding is two-state (single-exponential) when secondary structures are intrinsically unstable, and that each structure along the folding path is a transition state for the previous structure. It shows how sequential pathways are consistent with multiple stochastic routes on funnel landscapes, and it gives good agreement with the 9 order of magnitude dependence of folding rates on protein size for a set of 93 proteins, at the same time it is consistent with the near independence of folding equilibrium constant on size. This model gives estimates of folding rates of proteomes, leading to a median folding time in Escherichia coli of about 5 s.

Man versus Rivers: the lost equilibrium of the Tisza River due to engineering works

NASA Astrophysics Data System (ADS)

Kiss, Timea; Fiala, Károly

2016-04-01

The direct and indirect human impacts alter the catchment and the channel characteristics, which will result in further hydro-morphological alterations of rivers. The modified fluvial environment will create new hydrological hazards for the society, so for the successful and sustainable hazard and risk management it is important to evaluate the equilibrium and sensitivity of rivers. The aim of the paper is to evaluate the hydrological and morphological effects of engineering works along the Tisza River, Hungary. Based on the trends of the different fluvial processes the equilibrium of the river will be evaluated to ground further engineering works. The Tisza River, was one of the first systematically regulated rivers in Europe. In the late 19th century artificial cut-offs were made, shortening the river by ca. 30%. The hydrology and the morphology of the Tisza adapted to this, as the channel became temporarily wider and deeper (by 20-25%). The cut-offs had an effect on the channel for ca. 60-70 years. Simultaneously, artificial levees were built, thus the overbank floodplain aggradation became more intensive (from 0.02-0.07 cm/y to 0.3-0.8 mm/y). The floodplain aggradation became higher by 2-4 times since 1970's, as the vegetation became denser. However, in the 21st c. the floodplain vegetation became so uncontrollably dense, that the pattern and rate of accumulation changed again, and now it is limited just to the banks. So the levee could be considered as continuous disturbing factor, besides, the unmanaged floodplain vegetation appeared as a new disturbing force accelerating the processes. In the 20th century revetments were constructed to stop the lateral migration of the channel. This resulted in channel distortion, as it became sharper and the cross-sectional area decreased by 28%. As revetments were constructed along ca. 51% of the channel, the meandering channel forms became replaced features characteristic in incising rivers, for example point-bars disappeared and mass movements became common, especially in the 21st c. As the channel becomes too narrow and confined, the landslides erode the revetments too, thus a natural channel-widening will took place. Thus, the Tisza aligned to the new hydro-morphology after the artificial cut-offs within few decades, and within the given energy and slope conditions the river reached an equilibrium state. However in the 21st c. there are several evidences on the non-equilibrium state: the height and frequency of floods increase, their discharge decreases; the slope of the river declines; and the specific stream power increases. Morphological sign of the lost equilibrium is the vertical and horizontal distortion of the channel (caused by revetments!) and the decreasing flood conductivity of the floodplain (caused by dense, unmanaged floodplain vegetation). The rate of these processes refers to accelerating equilibrium loss. Thus the state of the Tisza could be referred as "non-equilibrium" or "pseudo-equilibrium". Therefore, if further engineering works will be planned, it must be considered that the river might give unexpected hydro-morphological responses on any disturbance.

Sequential Auctions with Partially Substitutable Goods

NASA Astrophysics Data System (ADS)

Vetsikas, Ioannis A.; Jennings, Nicholas R.

In this paper, we examine a setting in which a number of partially substitutable goods are sold in sequential single unit auctions. Each bidder needs to buy exactly one of these goods. In previous work, this setting has been simplified by assuming that bidders do not know their valuations for all items a priori, but rather are informed of their true valuation for each item right before the corresponding auction takes place. This assumption simplifies the strategies of bidders, as the expected revenue from future auctions is the same for all bidders due to the complete lack of private information. In our analysis we don't make this assumption. This complicates the computation of the equilibrium strategies significantly. We examine this setting both for first and second-price auction variants, initially when the closing prices are not announced, for which we prove that sequential first and second-price auctions are revenue equivalent. Then we assume that the prices are announced; because of the asymmetry in the announced prices between the two auction variants, revenue equivalence does not hold in this case. We finish the paper, by giving some initial results about the case when free disposal is allowed, and therefore a bidder can purchase more than one item.

Laser lithotripsy of gallstones: alexandrite and rhodamine-6G versus coumarin dye laser: fragmentation and fiber burn-off in vitro

NASA Astrophysics Data System (ADS)

Hochberger, Juergen; Bredt, Marion; Mueller, Gudrun; Hahn, Eckhart G.; Ell, Christian

1993-05-01

In the following study three different pulsed laser lithotripsy systems were compared for the fine fragmentation of identical sets of natural and synthetic gallstones `in vitro.' Using a pulsed coumarin dye laser (504 nm), a pulsed rhodamine 6G dye laser (595 nm), and a pulsed Alexandrite laser (755 nm) a total of 184 concrements of known chemical composition, size, and weight were disintegrated to a fragment size of

Diffusion-model analysis of pPb and PbPb collisions at LHC energies

NASA Astrophysics Data System (ADS)

Schulz, P.; Wolschin, G.

2018-06-01

We present an analysis of centrality-dependent pseudorapidity distributions of produced charged hadrons in pPb and PbPb collisions at the Large Hadron Collider (LHC) energy of s NN = 5.02 TeV, and of minimum-bias pPb collisions at 8.16 TeV within the non-equilibrium-statistical relativistic diffusion model (RDM). In a three-source approach, the role of the fragmentation sources is emphasized. Together with the Jacobian transformation from rapidity to pseudorapidity and the limiting fragmentation conjecture, these are essential for modeling the centrality dependence. For central PbPb collisions, a prediction at the projected FCC energy of s NN = 39 TeV is made.

Coagulation-Fragmentation Model for Animal Group-Size Statistics

NASA Astrophysics Data System (ADS)

Degond, Pierre; Liu, Jian-Guo; Pego, Robert L.

2017-04-01

We study coagulation-fragmentation equations inspired by a simple model proposed in fisheries science to explain data for the size distribution of schools of pelagic fish. Although the equations lack detailed balance and admit no H-theorem, we are able to develop a rather complete description of equilibrium profiles and large-time behavior, based on recent developments in complex function theory for Bernstein and Pick functions. In the large-population continuum limit, a scaling-invariant regime is reached in which all equilibria are determined by a single scaling profile. This universal profile exhibits power-law behavior crossing over from exponent -2/3 for small size to -3/2 for large size, with an exponential cutoff.

A C. elegans Hox gene switches on, off, on and off again to regulate proliferation, differentiation and morphogenesis.

PubMed

Salser, S J; Kenyon, C

1996-05-01

Hox genes establish body pattern throughout the animal kingdom, but the role these genes play at the cellular level to modify and shape parts of the body remains a mystery. We find that the C. elegans Antennapedia homolog, mab-5, sequentially programs many independent events within individual cell lineages. In one body region, mab-5 first switches ON in a lineage to stimulate proliferation, then OFF to specify epidermal structures, then ON in just one branch of the lineage to promote neuroblast formation, and finally OFF to permit proper sense organ morphology. In a neighboring lineage, continuous mab-5 expression leads to a different pattern of development. Thus, this Hox gene achieves much of its power to diversify the anteroposterior axis through fine spatiotemporal differences in expression coupled with a changing pattern of cellular response.

Ripple gate drive circuit for fast operation of series connected IGBTs

DOEpatents

Rockot, Joseph H.; Murray, Thomas W.; Bass, Kevin C.

2005-09-20

A ripple gate drive circuit includes a plurality of transistors having their power terminals connected in series across an electrical potential. A plurality of control circuits, each associated with one of the transistors, is provided. Each control circuit is responsive to a control signal and an optical signal received from at least one other control circuit for controlling the conduction of electrical current through the power terminals of the associated transistor. The control circuits are responsive to a first state of the control circuit for causing each transistor in series to turn on sequentially and responsive to a second state of the control signal for causing each transistor in series to turn off sequentially.

Impact of Aging on the Dynamics of Memory Retrieval: A Time-Course Analysis

ERIC Educational Resources Information Center

Oztekin, Ilke; Gungor, Nur Zeynep; Badre, David

2012-01-01

The response-signal speed-accuracy trade-off (SAT) procedure was used to provide an in-depth investigation of the impact of aging on the dynamics of short-term memory retrieval. Young and older adults studied sequentially presented 3-item lists, immediately followed by a recognition probe. Analyses of composite list and serial position SAT…

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

Serin, E.; Codel, G.; Mabhouti, H.

Purpose: In small field geometries, the electronic equilibrium can be lost, making it challenging for the dose-calculation algorithm to accurately predict the dose, especially in the presence of tissue heterogeneities. In this study, dosimetric accuracy of Monte Carlo (MC) advanced dose calculation and sequential algorithms of Multiplan treatment planning system were investigated for small radiation fields incident on homogeneous and heterogeneous geometries. Methods: Small open fields of fixed cones of Cyberknife M6 unit 100 to 500 mm2 were used for this study. The fields were incident on in house phantom containing lung, air, and bone inhomogeneities and also homogeneous phantom.more » Using the same film batch, the net OD to dose calibration curve was obtained using CK with the 60 mm fixed cone by delivering 0- 800 cGy. Films were scanned 48 hours after irradiation using an Epson 1000XL flatbed scanner. The dosimetric accuracy of MC and sequential algorithms in the presence of the inhomogeneities was compared against EBT3 film dosimetry Results: Open field tests in a homogeneous phantom showed good agreement between two algorithms and film measurement For MC algorithm, the minimum gamma analysis passing rates between measured and calculated dose distributions were 99.7% and 98.3% for homogeneous and inhomogeneous fields in the case of lung and bone respectively. For sequential algorithm, the minimum gamma analysis passing rates were 98.9% and 92.5% for for homogeneous and inhomogeneous fields respectively for used all cone sizes. In the case of the air heterogeneity, the differences were larger for both calculation algorithms. Overall, when compared to measurement, the MC had better agreement than sequential algorithm. Conclusion: The Monte Carlo calculation algorithm in the Multiplan treatment planning system is an improvement over the existing sequential algorithm. Dose discrepancies were observed for in the presence of air inhomogeneities.« less

LETTER TO THE EDITOR: Phase transition in a random fragmentation problem with applications to computer science

NASA Astrophysics Data System (ADS)

Dean, David S.; Majumdar, Satya N.

2002-08-01

We study a fragmentation problem where an initial object of size x is broken into m random pieces provided x > x0 where x0 is an atomic cut-off. Subsequently, the fragmentation process continues for each of those daughter pieces whose sizes are bigger than x0. The process stops when all the fragments have sizes smaller than x0. We show that the fluctuation of the total number of splitting events, characterized by the variance, generically undergoes a nontrivial phase transition as one tunes the branching number m through a critical value m = mc. For m < mc, the fluctuations are Gaussian where as for m > mc they are anomalously large and non-Gaussian. We apply this general result to analyse two different search algorithms in computer science.

Infrared Stark and Zeeman spectroscopy of OH–CO: The entrance channel complex along the OH + CO → trans-HOCO reaction pathway

DOE PAGES

Brice, Joseph T.; Liang, Tao; Raston, Paul L.; ...

2016-09-27

Here, sequential capture of OH and CO by superfluid helium droplets leads exclusively to the formation of the linear, entrance-channel complex, OH-CO. This species is characterized by infrared laser Stark and Zeeman spectroscopy via measurements of the fundamental OH stretching vibration. Experimental dipole moments are in disagreement with ab initio calculations at the equilibrium geometry, indicating large-amplitude motion on the ground state potential energy surface. Vibrational averaging along the hydroxyl bending coordinate recovers 80% of the observed deviation from the equilibrium dipole moment. Inhomogeneous line broadening in the zero-field spectrum is modeled with an effective Hamiltonian approach that aims tomore » account for the anisotropic molecule-helium interaction potential that arises as the OH-CO complex is displaced from the center of the droplet.« less

Mechanisms of Phosphorus Removal by Recycled Crushed Concrete.

PubMed

Deng, Yihuan; Wheatley, Andrew

2018-02-17

Due to urbanisation, there are large amounts of waste concrete, particularly in rapidly industrialising countries. Currently, demolished concrete is mainly recycled as aggregate for reconstruction. This study has shown that larger sizes (2-5 mm) of recycled concrete aggregate (RCA) removed more than 90% of P from effluent when at pH 5. Analysis of the data, using equilibrium models, indicated a best fit with the Langmuir which predicated an adsorption capacity of 6.88 mg/g. Kinetic analysis indicated the equilibrium adsorption time was 12 h, with pseudo second-order as the best fit. The thermal dynamic tests showed that the adsorption was spontaneous and, together with the evidence from the sequential extraction and desorption experiments, indicated the initial mechanism was physical attraction to the surface followed by chemical reactions which prevented re-release. These results suggested that RCA could be used for both wastewater treatment and P recovery.

Mechanisms of Phosphorus Removal by Recycled Crushed Concrete

PubMed Central

Wheatley, Andrew

2018-01-01

Due to urbanisation, there are large amounts of waste concrete, particularly in rapidly industrialising countries. Currently, demolished concrete is mainly recycled as aggregate for reconstruction. This study has shown that larger sizes (2–5 mm) of recycled concrete aggregate (RCA) removed more than 90% of P from effluent when at pH 5. Analysis of the data, using equilibrium models, indicated a best fit with the Langmuir which predicated an adsorption capacity of 6.88 mg/g. Kinetic analysis indicated the equilibrium adsorption time was 12 h, with pseudo second-order as the best fit. The thermal dynamic tests showed that the adsorption was spontaneous and, together with the evidence from the sequential extraction and desorption experiments, indicated the initial mechanism was physical attraction to the surface followed by chemical reactions which prevented re-release. These results suggested that RCA could be used for both wastewater treatment and P recovery. PMID:29462987

Comprehensive proteomic analysis of Penicillium verrucosum.

PubMed

Nöbauer, Katharina; Hummel, Karin; Mayrhofer, Corina; Ahrens, Maike; Setyabudi, Francis M C; Schmidt-Heydt, Markus; Eisenacher, Martin; Razzazi-Fazeli, Ebrahim

2017-05-01

Mass spectrometric identification of proteins in species lacking validated sequence information is a major problem in veterinary science. In the present study, we used ochratoxin A producing Penicillium verrucosum to identify and quantitatively analyze proteins of an organism with yet no protein information available. The work presented here aimed to provide a comprehensive protein identification of P. verrucosum using shotgun proteomics. We were able to identify 3631 proteins in an "ab initio" translated database from DNA sequences of P. verrucosum. Additionally, a sequential window acquisition of all theoretical fragment-ion spectra analysis was done to find differentially regulated proteins at two different time points of the growth curve. We compared the proteins at the beginning (day 3) and at the end of the log phase (day 12). © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

First Observation of Three-Neutron Sequential Emission from 25O

NASA Astrophysics Data System (ADS)

Sword, C.; Brett, J.; Deyoung, P. A.; Frank, N.; Karrick, H.; Kuchera, A. N.; MoNA Collaboration

2017-09-01

An active area of nuclear physics research is to evaluate models of the nuclear force by studying the structure of neutron-rich isotopes. In this experiment, a 101.3 MeV/u 27Ne beam from the National Superconducting Cyclotron Laboratory collided with a liquid deuterium target. The collision resulted in two-proton removal from the 27Ne beam which created excited 25O that decayed into three neutrons and an 22O fragment. The neutrons were detected by arrays of scintillating plastic bars, while a 4-Tesla dipole magnet placed directly after the target redirected charged fragments to a series of charged-particle detectors. From measured velocities of the neutrons and 22O fragments, the decay energy of 25O was calculated on an event-by-event basis with invariant mass spectroscopy. Using GEANT4, we simulated the decay of all nuclei that could have been created by the beam collision. By successfully fitting simulated decay processes to experimental data, we determined the decay processes present in the experiment. This work is supported by the National Science Foundation under Grants No. PHY-1306074 and No. PHY-1613188.

A Rapid, One-Pot Synthesis of β-Siloxy-α-Haloaldehydes

PubMed Central

Saadi, Jakub; Akakura, Matsujiro

2011-01-01

The Mukaiyama cross aldol reaction of α-fluoro-, α-chloro-, and α-bromoacetaldehyde-derived (Z)-tris(trimethylsilyl)- silyl enol ethers furnishing anti-β-siloxy-α-haloaldehydes is described. A highly diastereoselective, one-pot, sequential double aldol process, affording novel β,δ-bissiloxy-α,γ-bishaloaldehydes is developed. Reactions are catalyzed by C6F5CHTf2 and C6F5CTf2AlMe2 (0.5–1.5 mol%) and provide access to halogenated polyketide fragments. PMID:21815682

The application of PIT tags to measure transport of detrital coral fragments on a fringing reef: Majuro Atoll, Marshall Islands

NASA Astrophysics Data System (ADS)

Ford, Murray R.

2014-06-01

Passive integrated transponder (PIT) tags are a radio-frequency identification device widely used as a machine-readable identification tool in fisheries research. PIT tags have also been employed, to a lesser extent, to track the movement of gravel-sized clasts within fluvial and coastal systems. In this study, PIT tags were inserted into detrital coral fragments and used to establish source-sink transport pathways on a fringing reef on Majuro Atoll in the Marshall Islands. Results suggest the transport of gravel-sized material on the inter-tidal reef flat is exclusively across-reef towards the lagoon. Considerable variation in the distance travelled by fragments was observed. Fragments were largely intact and visually recognisable after almost 5 months on the reef flat. However, the branches of some recovered fragments had broken off and corallite abrasion was observed in recovered fragments. This study indicates that PIT tags are an inexpensive and powerful new addition to the suite of sediment transport and taphonomic tools for researchers working within coral reef systems.

Electrochemical Transfer of S Between Molten Steel and Molten Slag

NASA Astrophysics Data System (ADS)

Kim, Dong-Hyun; Kim, Wook; Kang, Youn-Bae

2018-06-01

S transfer between molten steel and molten slag was investigated in view of the electrochemical character of S transfer. C-saturated molten steel containing S was allowed to react with CaO-SiO2-Al2O3-MgO slag at 1673 K (1400 °C) until the two phases arrive at a chemical equilibrium. The application of an electric field of constant current through graphite electrodes lowered the S content in the molten steel below its chemical equilibrium level, and the system arrived at a new equilibrium level (electrochemical equilibrium). However, subsequent shutting off of the electric field did not lead to the system reverting to the original chemical equilibrium: reversion of S was observed but to a limited extent. The application of an electric field of opposite direction or flowing of CO gas allowed significant reversion of S. Side reactions (decomposition of oxide components) were observed, and these were considered to be coupled to the transfer of S. An electrochemical reaction mechanism was proposed based on the experimental observations found in the present study.

Parallel theoretical study of the two components of the prompt fission neutrons: Dynamically released at scission and evaporated from fully accelerated fragments

NASA Astrophysics Data System (ADS)

Carjan, Nicolae; Rizea, Margarit; Talou, Patrick

2017-09-01

Prompt fission neutrons (PFN) angular and energy distributions for the reaction 235U(nth,f) are calculated as a function of the mass asymmetry of the fission fragments using two extreme assumptions: 1) PFN are released during the neck rupture due to the diabatic coupling between the neutron degree of freedom and the rapidly changing neutron-nucleus potential. These unbound neutrons are faster than the separation of the nascent fragments and most of them leave the fissioning system in few 10-21 sec. i.e., at the begining of the acceleration phase. Surrounding the fissioning nucleus by a sphere one can calculate the radial component of the neutron current density. Its time integral gives the angular distribution with respect to the fission axis. The average energy of each emitted neutron is also calculated using the unbound part of each neutron wave packet. The distribution of these average energies gives the general trends of the PFN spectrum: the slope, the range and the average value. 2) PFN are evaporated from fully accelerated, fully equilibrated fission fragments. To follow the de-excitation of these fragments via neutron and γ-ray sequential emissions, a Monte Carlo sampling of the initial conditions and a Hauser-Feshbach statistical approach is used. Recording at each step the emission probability, the energy and the angle of each evaporated neutron one can construct the PFN energy and the PFN angular distribution in the laboratory system. The predictions of these two methods are finally compared with recent experimental results obtained for a given fragment mass ratio.

In vitro cariostatic effect of whitening toothpastes in human dental enamel-microhardness evaluation.

PubMed

Watanabe, Melina Mayumi; Rodrigues, José Augusto; Marchi, Giselle Maria; Ambrosano, Gláucia Maria Bovi

2005-06-01

The aim of this study was to evaluate, in vitro, the cariostatic effect of whitening toothpastes. Ninety-five dental fragments were obtained from nonerupted third molars. The fragments were embedded in polystyrene resin and sequentially polished with abrasive papers (400-, 600-, and 1,000-grit) and diamond pastes of 6, 3, and 1 microm. The fragments were assigned in five groups according to toothpaste treatment: G1 = Rembrandt Plus with Peroxide; G2 = Crest Dual Action Whitening; G3 = Aquafresh Whitening Triple Protection; and the control groups: G4 = Sensodyne Original (without fluoride); G5 = Sensodyne Sodium Bicarbonated (with fluoride). The initial enamel microhardness evaluations were done. For 2 weeks the fragments were submitted daily to a de-remineralization cycle followed by a 10-minute toothpaste slurry. After that, the final microhardness tests were done. The percentage of mineral loss of enamel was determined for statistical analysis. Analysis of variance and the Tukey test were applied. The results did not show statistically significant differences in mineral loss among groups G1, G2, G3, and G5, which statistically differ from G4 (toothpaste without fluoride). G4 showed the highest mineral loss (P < or = .05). The whitening toothpastes evaluated showed a cariostatic effect similar to regular, nonwhitening toothpaste.

Petrological and geochemical Highlights in the floating fragments of the October 2011 submarine eruption offshore El Hierro (Canary Islands): Relevance of submarine hydrothermal processes

NASA Astrophysics Data System (ADS)

Rodriguez-Losada, Jose A.; Eff-Darwich, Antonio; Hernandez, Luis E.; Viñas, Ronaldo; Pérez, Nemesio; Hernandez, Pedro; Melián, Gladys; Martinez-Frías, Jesús; Romero-Ruiz, M. Carmen; Coello-Bravo, Juan Jesús

2015-02-01

This paper describes the main physical, petrological and geochemical features of the floating fragments that were emitted in the initial stages of the 2011-2012 submarine eruption off the coast of the Canarian island of El Hierro, located 380 km from the Northwest African Coast. It attempts to assess the potential of radiometric analyses to discern the intriguing origin of the floating fragments and the differences between their constituent parts. In this regard, the material that conforms the core of the fragments contains the largest concentration of uranium (U) ever found in volcanic rocks of the Canary Islands. This enrichment in U is not found in the content of thorium (Th), hence the floating fragments have an unusual U/Th ratio, namely equal to or larger than 3. Although the origin of this material is under discussion, it is proposed that the enrichment in U is the result of hydrothermal processes.

The Tephra Layer From the Plinian Eruption in ™r‘faj”kull 1362, Southeast Iceland

NASA Astrophysics Data System (ADS)

Selbekk, R. S.

2002-12-01

Pyroclastic fallout from the 1362 eruption of ™r‘faj”kull forms one of the volcanic marker horizons of the North Atlantic. This contribution reports the mineralogical and geochemical characteristics of the ™r‘faj”kull 1362 fallout and its grain-size distribution. A non-rifting 120 km long volcanic lineament some 50 km east of the Eastern Rift-Zone of Iceland is defined by transitional and alkalic volcanic rocks resting unconformably on late Tertiary strata. ™r‘faj”kull which forms the southern termination of this off-rift liniment is an ice-covered stratovolcano (2200 masl) composed mostly of subglacially formed hyaloclastite ranging from basalts to rhyolites. The two historical (1100 yrs) eruptions of ™r‘faj”kull include a small explosive eruption in 1727 and a large devastating Plinian eruption associated with major lahars and a caldera collapse in 1362. Between 1 and 2 km3 dense rock equivalent or 5-10 km3 of rhyolitic pumice was erupted and the fallout was mainly towards ESE. Tentative modelling of the PT-conditions of the magma formation, based on glass/mineral equilibria, indicates that the source was a near-eutectic melt in equilibrium with fayalite, hedenbergite, oligoclase and hematite at some 0.2 GPa pressure. A profile through the fallout was sampled at elevation of about 1100 masl on the SE flank of the volcano. A deposit of 1.8 m thickness was collected in 14 units for examination of composition, mineralogy and grain-size distribution during the eruption. In the profile the fallout is fine grained vesicular glass (1-3% minerals, 3% lithic fragments) with bubble wall thickness in the low micron range. The high and even vesiculation of the glass indicates fast magma ascent and explains the extreme mechanical fragmentation within the eruptive column, yielding between 50 and 80 wt% of less than 0.25 mm grain size. A reconstruction of the Plinian phase, based on grain-size analysis and abundance of lithic fragments, reveals that the eruption proceeded in three successive phases. An initial explosion produced phreatomagmatic debris associated with up to 35% of lithic fragments. In distal facies of the fallout, the initial phase is recognised as pale brownish base of the otherwise white glassy layer. The material ejection proceeded in two largely similar phases. These phases are separated only by a transition in grain size distribution indicating a temporary lowering in the effusion rate.

A comparative study of the structures and electronic properties of graphene fragments: A DFT and MP2 survey

NASA Astrophysics Data System (ADS)

de Carvalho, E. F. V.; Lopez-Castillo, A.; Roberto-Neto, O.

2018-01-01

Graphene can be viewed as sheet of benzene rings fused together forming a variety of structures including the trioxotriangulenes (TOTs) which is a class of organic molecules with electro-active properties. In order to clarify such properties, structures and electronic properties of the graphene fragments phenalenyl, triangulene, 6-oxophenalenoxyl, and X3TOT (X = H, F, Cl) are computed. Validation of the methodologies are carried out using the density functionals B3LYP, M06-2X, B2PLYP-D, and the MP2 theory, giving equilibrium geometries of benzene, naphthalene, and anthracene with mean unsigned error (MUE) of only 0.003, 0.007, 0.004, and 0.007 Å, respectively in relation to experiment.

Issues in Coastal Zone Management.

ERIC Educational Resources Information Center

Davis, Derrin

1992-01-01

Addresses the following issues relevant to coastal zone management: overcrowding, resource exploitation, pollution, agriculture, fisheries, industrial, and other uses. Describes conflicts and trade-offs in management typified by fragmented agency decision making. Discusses implications of the greenhouse effect, sustainable development, and the…

A strategy for comprehensive identification of sequential constituents using ultra-high-performance liquid chromatography coupled with linear ion trap-Orbitrap mass spectrometer, application study on chlorogenic acids in Flos Lonicerae Japonicae.

PubMed

Zhang, Jia-yu; Wang, Zi-jian; Li, Yun; Liu, Ying; Cai, Wei; Li, Chen; Lu, Jian-qiu; Qiao, Yan-jiang

2016-01-15

The analytical methodologies for evaluation of multi-component system in traditional Chinese medicines (TCMs) have been inadequate or unacceptable. As a result, the unclarity of multi-component hinders the sufficient interpretation of their bioactivities. In this paper, an ultra-high-performance liquid chromatography coupled with linear ion trap-Orbitrap (UPLC-LTQ-Orbitrap)-based strategy focused on the comprehensive identification of TCM sequential constituents was developed. The strategy was characterized by molecular design, multiple ion monitoring (MIM), targeted database hits and mass spectral trees similarity filter (MTSF), and even more isomerism discrimination. It was successfully applied in the HRMS data-acquisition and processing of chlorogenic acids (CGAs) in Flos Lonicerae Japonicae (FLJ), and a total of 115 chromatographic peaks attributed to 18 categories were characterized, allowing a comprehensive revelation of CGAs in FLJ for the first time. This demonstrated that MIM based on molecular design could improve the efficiency to trigger MS/MS fragmentation reactions. Targeted database hits and MTSF searching greatly facilitated the processing of extremely large information data. Besides, the introduction of diagnostic product ions (DPIs) discrimination, ClogP analysis, and molecular simulation, raised the efficiency and accuracy to characterize sequential constituents especially position and geometric isomers. In conclusion, the results expanded our understanding on CGAs in FLJ, and the strategy could be exemplary for future research on the comprehensive identification of sequential constituents in TCMs. Meanwhile, it may propose a novel idea for analyzing sequential constituents, and is promising for quality control and evaluation of TCMs. Copyright © 2015 Elsevier B.V. All rights reserved.

Computer programs for axial flow compressor design

NASA Technical Reports Server (NTRS)

Carmody, R. H.; Creveling, H. F.

1969-01-01

Four computer programs examine effects of design parameters and indicate areas for research of multistage axial flow compressors. The programs provide information on velocity diagrams and stage-by-stage performance calculation, radial equilibrium of flow, radial distribution of total pressure, and off-design performance calculation.

Evidence for a Shared Mechanism in the Formation of Urea-Induced Kinetic and Equilibrium Intermediates of Horse Apomyoglobin from Ultrarapid Mixing Experiments

PubMed Central

Mizukami, Takuya; Abe, Yukiko; Maki, Kosuke

2015-01-01

In this study, the equivalence of the kinetic mechanisms of the formation of urea-induced kinetic folding intermediates and non-native equilibrium states was investigated in apomyoglobin. Despite having similar structural properties, equilibrium and kinetic intermediates accumulate under different conditions and via different mechanisms, and it remains unknown whether their formation involves shared or distinct kinetic mechanisms. To investigate the potential mechanisms of formation, the refolding and unfolding kinetics of horse apomyoglobin were measured by continuous- and stopped-flow fluorescence over a time range from approximately 100 μs to 10 s, along with equilibrium unfolding transitions, as a function of urea concentration at pH 6.0 and 8°C. The formation of a kinetic intermediate was observed over a wider range of urea concentrations (0–2.2 M) than the formation of the native state (0–1.6 M). Additionally, the kinetic intermediate remained populated as the predominant equilibrium state under conditions where the native and unfolded states were unstable (at ~0.7–2 M urea). A continuous shift from the kinetic to the equilibrium intermediate was observed as urea concentrations increased from 0 M to ~2 M, which indicates that these states share a common kinetic folding mechanism. This finding supports the conclusion that these intermediates are equivalent. Our results in turn suggest that the regions of the protein that resist denaturant perturbations form during the earlier stages of folding, which further supports the structural equivalence of transient and equilibrium intermediates. An additional folding intermediate accumulated within ~140 μs of refolding and an unfolding intermediate accumulated in <1 ms of unfolding. Finally, by using quantitative modeling, we showed that a five-state sequential scheme appropriately describes the folding mechanism of horse apomyoglobin. PMID:26244984

ANI-1, A data set of 20 million calculated off-equilibrium conformations for organic molecules

NASA Astrophysics Data System (ADS)

Smith, Justin S.; Isayev, Olexandr; Roitberg, Adrian E.

2017-12-01

One of the grand challenges in modern theoretical chemistry is designing and implementing approximations that expedite ab initio methods without loss of accuracy. Machine learning (ML) methods are emerging as a powerful approach to constructing various forms of transferable atomistic potentials. They have been successfully applied in a variety of applications in chemistry, biology, catalysis, and solid-state physics. However, these models are heavily dependent on the quality and quantity of data used in their fitting. Fitting highly flexible ML potentials, such as neural networks, comes at a cost: a vast amount of reference data is required to properly train these models. We address this need by providing access to a large computational DFT database, which consists of more than 20 M off equilibrium conformations for 57,462 small organic molecules. We believe it will become a new standard benchmark for comparison of current and future methods in the ML potential community.

Relationship between Measures of Working Memory Capacity and the Time Course of Short-Term Memory Retrieval and Interference Resolution

ERIC Educational Resources Information Center

Oztekin, Ilke; McElree, Brian

2010-01-01

The response-signal speed-accuracy trade-off (SAT) procedure was used to investigate the relationship between measures of working memory capacity and the time course of short-term item recognition. High- and low-span participants studied sequentially presented 6-item lists, immediately followed by a recognition probe. Analyses of composite list…

Quantum dot immunoassays in renewable surface column and 96-well plate formats for the fluorescence detection of Botulinum neurotoxin using high-affinity antibodies

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

Warner, Marvin G.; Grate, Jay W.; Tyler, Abby J.

2009-09-01

A fluorescence sandwich immunoassay using high affinity antibodies and quantum dot (QD) reporters has been developed for detection of botulinum toxin serotype A (BoNT/A). For the development of the assay, a nontoxic recombinant fragment of the holotoxin (BoNT/A-HC-fragment) has been used as a structurally valid simulant for the full toxin molecule. The antibodies used, AR4 and RAZ1, bind to nonoverlapping epitopes present on both the full toxin and on the recombinant fragment. In one format, the immunoassay is carried out in a 96-well plate with detection in a standard plate reader. Detection down to 31 pM of the BoNT/Hc-fragment wasmore » demonstrated with a total incubation time of 3 hours, using AR4 as the capture antibody and QD-coupled RAZ1 as the reporter. In a second format, the AR4 capture antibody was coupled to Sepharose beads, and the immunochemical reactions were carried out in microcentrifuge tubes with an incubation time of 1 hour. These beads were subsequently captured and concentrated in a rotating rod “renewable surface” flow cell as part of a sequential injection fluidic system. This flow cell was equipped with a fiber optic system for fluorescence measurements. In PBS buffer solution matrix, the BoNT/A-HC-fragment was detected to concentrations as low as 5 pM using the fluidic measurement approach.« less

The More the Merrier?. Entropy and Statistics of Asexual Reproduction in Freshwater Planarians

NASA Astrophysics Data System (ADS)

Quinodoz, Sofia; Thomas, Michael A.; Dunkel, Jörn; Schötz, Eva-Maria

2011-04-01

The trade-off between traits in life-history strategies has been widely studied for sexual and parthenogenetic organisms, but relatively little is known about the reproduction strategies of asexual animals. Here, we investigate clonal reproduction in the freshwater planarian Schmidtea mediterranea, an important model organism for regeneration and stem cell research. We find that these flatworms adopt a randomized reproduction strategy that comprises both asymmetric binary fission and fragmentation (generation of multiple offspring during a reproduction cycle). Fragmentation in planarians has primarily been regarded as an abnormal behavior in the past; using a large-scale experimental approach, we now show that about one third of the reproduction events in S. mediterranea are fragmentations, implying that fragmentation is part of their normal reproductive behavior. Our analysis further suggests that certain characteristic aspects of the reproduction statistics can be explained in terms of a maximum relative entropy principle.

Ingestion of marine debris plastic by the wedge-tailed shearwater Ardenna pacifica in the Great Barrier Reef, Australia.

PubMed

Verlis, K M; Campbell, M L; Wilson, S P

2013-07-15

We present the first evidence of ingestion of plastic by seabirds from the southern Great Barrier Reef (GBR), Australia. The occurrence of marine debris ingestion in the wedge-tailed shearwater, Ardenna pacifica, on Heron Island was the focus of this preliminary research. Our findings indicate that 21% of surveyed chicks are fed plastic fragments by their parents, having ingested 3.2 fragments on average. The most common colours of ingested plastic fragments were off/white (37.5%) and green (31.3%). Ingested fragments had a mean size of 10.17±4.55 mm and a mean weight of 0.056±0.051 g. Our results indicate that further research is critical to understanding the extent of ingestion, colour preferences, and what impacts ingestion may have on these and other seabird populations in the GBR. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

Yin, Xingyu; Stony Brook University, NY 11794-5215; Nanjing University, Nanjing, Jiangsu

A method is presented for screening fragment libraries using acoustic droplet ejection to co-crystallize proteins and chemicals directly on micromeshes with as little as 2.5 nl of each component. This method was used to identify previously unreported fragments that bind to lysozyme, thermolysin, and trypsin. Acoustic droplet ejection (ADE) is a powerful technology that supports crystallographic applications such as growing, improving and manipulating protein crystals. A fragment-screening strategy is described that uses ADE to co-crystallize proteins with fragment libraries directly on MiTeGen MicroMeshes. Co-crystallization trials can be prepared rapidly and economically. The high speed of specimen preparation and the lowmore » consumption of fragment and protein allow the use of individual rather than pooled fragments. The Echo 550 liquid-handling instrument (Labcyte Inc., Sunnyvale, California, USA) generates droplets with accurate trajectories, which allows multiple co-crystallization experiments to be discretely positioned on a single data-collection micromesh. This accuracy also allows all components to be transferred through small apertures. Consequently, the crystallization tray is in equilibrium with the reservoir before, during and after the transfer of protein, precipitant and fragment to the micromesh on which crystallization will occur. This strict control of the specimen environment means that the crystallography experiments remain identical as the working volumes are decreased from the few microlitres level to the few nanolitres level. Using this system, lysozyme, thermolysin, trypsin and stachydrine demethylase crystals were co-crystallized with a small 33-compound mini-library to search for fragment hits. This technology pushes towards a much faster, more automated and more flexible strategy for structure-based drug discovery using as little as 2.5 nl of each major component.« less

Confort 15 model of conduit dynamics: applications to Pantelleria Green Tuff and Etna 122 BC eruptions

NASA Astrophysics Data System (ADS)

Campagnola, S.; Romano, C.; Mastin, L. G.; Vona, A.

2016-06-01

Numerical simulations are useful tools to illustrate how flow parameters and physical processes may affect eruption dynamics of volcanoes. In this paper, we present an updated version of the Conflow model, an open-source numerical model for flow in eruptive conduits during steady-state pyroclastic eruptions (Mastin and Ghiorso in A numerical program for steady-state flow of magma-gas mixtures through vertical eruptive conduits. U.S. Geological Survey Open File Report 00-209, 2000). In the modified version, called Confort 15, the rheological constraints are improved, incorporating the most recent constitutive equations of both the liquid viscosity and crystal-bearing rheology. This allows all natural magma compositions, including the peralkaline melts excluded in the original version, to be investigated. The crystal-bearing rheology is improved by computing the effect of strain rate and crystal shape on the rheology of natural magmatic suspensions and expanding the crystal content range in which rheology can be modeled compared to the original version ( Conflow is applicable to magmatic mixtures with up to 30 vol% crystal content). Moreover, volcanological studies of the juvenile products (crystal and vesicle size distribution) of the investigated eruption are directly incorporated into the modeling procedure. Vesicle number densities derived from textural analyses are used to calculate, through Toramaru equations, maximum decompression rates experienced during ascent. Finally, both degassing under equilibrium and disequilibrium conditions are considered. This allows considerations on the effect of different fragmentation criteria on the conduit flow analyses, the maximum volume fraction criterion ("porosity criterion"), the brittle fragmentation criterion and the overpressure fragmentation criterion. Simulations of the pantelleritic and trachytic phases of the Green Tuff (Pantelleria) and of the Plinian Etna 122 BC eruptions are performed to test the upgrades in the Confort 15 modeling. Conflow and Confort 15 numerical results are compared analyzing the effect of viscosity, decompression rate, temperature, fragmentation criteria (critical strain rate, porosity and overpressure criteria) and equilibrium versus disequilibrium degassing in the magma flow along volcanic conduits. The equilibrium simulation results indicate that an increase in viscosity, a faster decompression rate, a decrease in temperature or the application of the porosity criterion in place of the strain rate one produces a deepening in fragmentation depth. Initial velocity and mass flux of the mixture are directly correlated with each other, inversely proportional to an increase in viscosity, except for the case in which a faster decompression rate is assumed. Taking into account up-to-date viscosity parameterization or input faster decompression rate, a much larger decrease in the average pressure along the conduit compared to previous studies is recorded, enhancing water exsolution and degassing. Disequilibrium degassing initiates only at very shallow conditions near the surface. Brittle fragmentation (i.e., depending on the strain rate criterion) in the pantelleritic Green Tuff eruption simulations is mainly a function of the initial temperature. In the case of the Etna 122 BC Plinian eruption, the viscosity strongly affects the magma ascent dynamics along the conduit. Using Confort 15, and therefore incorporating the most recent constitutive rheological parameterizations, we could calculate the mixture viscosity increase due to the presence of microlites. Results show that these seemingly low-viscosity magmas can explosively fragment in a brittle manner. Mass fluxes resulting from simulations which better represent the natural case (i.e., microlite-bearing) are consistent with values found in the literature for Plinian eruptions (~106 kg/s). The disequilibrium simulations, both for Green Tuff and Etna 122 BC eruptions, indicate that overpressure sufficient for fragmentation (if present) occurs only at very shallow conditions near the surface.

Superasymmetric fission of heavy nuclei induced by intermediate-energy protons

NASA Astrophysics Data System (ADS)

Deppman, A.; Andrade-II, E.; Guimarães, V.; Karapetyan, G. S.; Tavares, O. A. P.; Balabekyan, A. R.; Demekhina, N. A.; Adam, J.; Garcia, F.; Katovsky, K.

2013-12-01

In this work we present the results for the investigation of intermediate-mass fragment (IMF) production with the proton-induced reaction at 660 MeV on 238U and 237Np target. The data were obtained with the LNR Phasotron U-400M Cyclotron at Joint Institute for Nuclear Research (JINR), Dubna, Russia. A total of 93 isotopes, in the mass range of 30

Single center, single operator comparative study of the effectiveness of electrohydraulic and electromagnetic lithotripters in the management of 10- to 20-mm single upper urinary tract calculi.

PubMed

Jamshaid, Anila; Ather, M Hammad; Hussain, Ghazi; Khawaja, Karim B

2008-11-01

This study compared the efficacy and safety profile of electrohydraulic (EH) and electromagnetic (EM) lithotriptors in the treatment of 10- to 20-mm renal and proximal ureteric stones at a single center and by a single operator. Between January 2001 and December 2006, we sequentially treated patients meeting study inclusion criteria with MPL 9000 Dornier EH for the first 3 years, followed by the EM Siemens Modularis shockwave lithotripsy (SWL) unit. A single operator performed all SWL treatments under the supervision of an admitting urologist. We analyzed the demographic features and stone- and treatment-related parameters including complications for both groups. In each group, the stone-free rate and efficiency quotient was determined at 1-3 months. Of 274 patients, we sequentially treated 112 using the EH lithotriptor, and 162 the EM lithotriptor. The pre-SWL patients and stone-related parameters were similar in the two groups, except for diagnostic imaging modalities. The mean number of SWL sessions, need for ancillary procedure, retreatment rate, stone location, stone-free rate, and efficiency quotient were not significantly different between groups. The mean number of shockwaves required for complete fragmentation was 2977 and 6044 (P < .000) for the EH and EM groups, respectively. Single center, single operator experience with two types of lithotriptor indicated that both are equally efficacious, with similar safety profiles. The only significant difference was that the EH lithotriptor required fewer shockwaves for fragmentation.

Comparative solution equilibrium studies on pentamethylcyclopentadienyl rhodium complexes of 2,2'-bipyridine and ethylenediamine and their interaction with human serum albumin.

PubMed

Enyedy, Éva A; Mészáros, János P; Dömötör, Orsolya; Hackl, Carmen M; Roller, Alexander; Keppler, Bernhard K; Kandioller, Wolfgang

2015-11-01

Complex formation equilibrium processes of the (N,N) donor containing 2,2'-bipyridine (bpy) and ethylenediamine (en) with (η(5)-pentamethylcyclopentadienyl)rhodium(III) were investigated in aqueous solution via pH-potentiometry, (1)H NMR spectroscopy, and UV-vis spectrophotometry in the absence and presence of chloride ions. The structure of [RhCp*(en)Cl]ClO4 (Cp*, pentamethylcyclopentadienyl) was also studied by single-crystal X-ray diffraction. pKa values of 8.56 and 9.58 were determined for [RhCp*(bpy)(H2O)](2+) and [RhCp*(en)(H2O)](2+), respectively resulting in the formation of negligible amount of mixed hydroxido complexes at pH 7.4. Stability and the H2O/Cl(-) co-ligand exchange constants of bpy and en complexes considerably exceed those of the bidentate O-donor deferiprone. The strong affinity of the bpy and en complexes to chloride ions most probably contributes to their low antiproliferative effect. Interactions between human serum albumin (HSA) and [RhCp*(H2O)3](2+), its complexes formed with deferiprone, bpy and en were also monitored by (1)H NMR spectroscopy, ultrafiltration/UV-vis and spectrofluorometry. Numerous binding sites (≥ 8) are available for [RhCp*(H2O)3](2+); and the interaction takes place most probably via covalent bonds through the imidazole nitrogen of His. According to the various fluorescence studies [RhCp*(H2O)3](2+) binds on sites I and II, and coordination of surface side chain donor atoms of the protein is also feasible. The binding of the bpy and en complex is weaker and slower compared to that of [RhCp*(H2O)3](2+), and formation of ternary HSA-RhCp*-ligand adducts was proved. In the case of the deferiprone complex, the RhCp* fragment is cleaved off when HSA is loaded with low equivalents of the compound.

The application of intraoperative transit time flow measurement to accurately assess anastomotic quality in sequential vein grafting

PubMed Central

Yu, Yang; Zhang, Fan; Gao, Ming-Xin; Li, Hai-Tao; Li, Jing-Xing; Song, Wei; Huang, Xin-Sheng; Gu, Cheng-Xiong

2013-01-01

OBJECTIVES Intraoperative transit time flow measurement (TTFM) is widely used to assess anastomotic quality in coronary artery bypass grafting (CABG). However, in sequential vein grafting, the flow characteristics collected by the conventional TTFM method are usually associated with total graft flow and might not accurately indicate the quality of every distal anastomosis in a sequential graft. The purpose of our study was to examine a new TTFM method that could assess the quality of each distal anastomosis in a sequential graft more reliably than the conventional TTFM approach. METHODS Two TTFM methods were tested in 84 patients who underwent sequential saphenous off-pump CABG in Beijing An Zhen Hospital between April and August 2012. In the conventional TTFM method, normal blood flow in the sequential graft was maintained during the measurement, and the flow probe was placed a few centimetres above the anastomosis to be evaluated. In the new method, blood flow in the sequential graft was temporarily reduced during the measurement by placing an atraumatic bulldog clamp at the graft a few centimetres distal to the anastomosis to be evaluated, while the position of the flow probe remained the same as in the conventional method. This new TTFM method was named the flow reduction TTFM. Graft flow parameters measured by both methods were compared. RESULTS Compared with the conventional TTFM, the flow reduction TTFM resulted in significantly lower mean graft blood flow (P < 0.05); in contrast, yielded significantly higher pulsatility index (P < 0.05). Diastolic filling was not significantly different between the two methods and was >50% in both cases. Interestingly, the flow reduction TTFM identified two defective middle distal anastomoses that the conventional TTFM failed to detect. Graft flows near the defective distal anastomoses were improved substantially after revision. CONCLUSIONS In this study, we found that temporary reduction of graft flow during TTFM seemed to enhance the sensitivity of TTFM to less-than-critical anastomotic defects in a sequential graft and to improve the overall accuracy of the intraoperative assessment of anastomotic quality in sequential vein grafting. PMID:24000314

Dna Sequencing

DOEpatents

Tabor, Stanley; Richardson, Charles C.

1995-04-25

A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

General Mechanism of Two-State Protein Folding Kinetics

PubMed Central

Rollins, Geoffrey C.; Dill, Ken A.

2016-01-01

We describe here a general model of the kinetic mechanism of protein folding. In the Foldon Funnel Model, proteins fold in units of secondary structures, which form sequentially along the folding pathway, stabilized by tertiary interactions. The model predicts that the free energy landscape has a volcano shape, rather than a simple funnel, that folding is two-state (single-exponential) when secondary structures are intrinsically unstable, and that each structure along the folding path is a transition state for the previous structure. It shows how sequential pathways are consistent with multiple stochastic routes on funnel landscapes, and it gives good agreement with the 9 order of magnitude dependence of folding rates on protein size for a set of 93 proteins, at the same time it is consistent with the near independence of folding equilibrium constant on size. This model gives estimates of folding rates of proteomes, leading to a median folding time in Escherichia coli of about 5 s. PMID:25056406

Cortical Actomyosin Breakage Triggers Shape Oscillations in Cells and Cell Fragments

PubMed Central

Paluch, Ewa; Piel, Matthieu; Prost, Jacques; Bornens, Michel; Sykes, Cécile

2005-01-01

Cell shape and movements rely on complex biochemical pathways that regulate actin, microtubules, and substrate adhesions. Some of these pathways act through altering the cortex contractility. Here we examined cellular systems where contractility is enhanced by disassembly of the microtubules. We found that adherent cells, when detached from their substrate, developed a membrane bulge devoid of detectable actin and myosin. A constriction ring at the base of the bulge oscillated from one side of the cell to the other. The movement was accompanied by sequential redistribution of actin and myosin to the membrane. We observed this oscillatory behavior also in cell fragments of various sizes, providing a simplified, nucleus-free system for biophysical studies. Our observations suggest a mechanism based on active gel dynamics and inspired by symmetry breaking of actin gels growing around beads. The proposed mechanism for breakage of the actomyosin cortex may be used for cell polarization. PMID:15879479

Control of electron excitation and localization in the dissociation of H2(+) and its isotopes using two sequential ultrashort laser pulses.

PubMed

He, Feng; Ruiz, Camilo; Becker, Andreas

2007-08-24

We study the control of dissociation of the hydrogen molecular ion and its isotopes exposed to two ultrashort laser pulses by solving the time-dependent Schrödinger equation. While the first ultraviolet pulse is used to excite the electron wave packet on the dissociative 2psigma{u} state, a second time-delayed near-infrared pulse steers the electron between the nuclei. Our results show that by adjusting the time delay between the pulses and the carrier-envelope phase of the near-infrared pulse, a high degree of control over the electron localization on one of the dissociating nuclei can be achieved (in about 85% of all fragmentation events). The results demonstrate that current (sub-)femtosecond technology can provide a control over both electron excitation and localization in the fragmentation of molecules.

Differentiated planetesimal impacts into a terrestrial magma ocean: Fate of the iron core

NASA Astrophysics Data System (ADS)

Kendall, Jordan D.; Melosh, H. J.

2016-08-01

The abundance of moderately siderophile elements (;iron-loving;; e.g. Co, Ni) in the Earth's mantle is 10 to 100 times larger than predicted by chemical equilibrium between silicate melt and iron at low pressure, but it does match expectation for equilibrium at high pressure and temperature. Recent studies of differentiated planetesimal impacts assume that planetesimal cores survive the impact intact as concentrated masses that passively settle from a zero initial velocity and undergo turbulent entrainment in a global magma ocean; under these conditions, cores greater than 10 km in diameter do not fully mix without a sufficiently deep magma ocean. We have performed hydrocode simulations that revise this assumption and yield a clearer picture of the impact process for differentiated planetesimals possessing iron cores with radius = 100 km that impact into magma oceans. The impact process strips away the silicate mantle of the planetesimal and then stretches the iron core, dispersing the liquid iron into a much larger volume of the underlying liquid silicate mantle. Lagrangian tracer particles track the initially intact iron core as the impact stretches and disperses the core. The final displacement distance of initially closest tracer pairs gives a metric of core stretching. The statistics of stretching imply mixing that separates the iron core into sheets, ligaments, and smaller fragments, on a scale of 10 km or less. The impact dispersed core fragments undergo further mixing through turbulent entrainment as the molten iron fragments rain through the magma ocean and settle deeper into the planet. Our results thus support the idea that iron in the cores of even large differentiated planetesimals can chemically equilibrate deep in a terrestrial magma ocean.

Bilayer lift-off process for aluminum metallization

NASA Astrophysics Data System (ADS)

Wilson, Thomas E.; Korolev, Konstantin A.; Crow, Nathaniel A.

2015-01-01

Recently published reports in the literature for bilayer lift-off processes have described recipes for the patterning of metals that have recommended metal-ion-free developers, which do etch aluminum. We report the first measurement of the dissolution rate of a commercial lift-off resist (LOR) in a sodium-based buffered commercial developer that does not etch aluminum. We describe a reliable lift-off recipe that is safe for multiple process steps in patterning thin (<100 nm) and thick aluminum devices with micron-feature sizes. Our patterning recipe consists of an acid cleaning of the substrate, the bilayer (positive photoresist/LOR) deposition and development, the sputtering of the aluminum film along with a palladium capping layer and finally, the lift-off of the metal film by immersion in the LOR solvent. The insertion into the recipe of postexposure and sequential develop-bake-develop process steps are necessary for an acceptable undercut. Our recipe also eliminates any need for accompanying sonication during lift-off that could lead to delamination of the metal pattern from the substrate. Fine patterns were achieved for both 100-nm-thick granular aluminum/palladium bilayer bolometers and 500-nm-thick aluminum gratings with 6-μm lines and 4-μm spaces.

A sequential sampling account of response bias and speed-accuracy tradeoffs in a conflict detection task.

PubMed

Vuckovic, Anita; Kwantes, Peter J; Humphreys, Michael; Neal, Andrew

2014-03-01

Signal Detection Theory (SDT; Green & Swets, 1966) is a popular tool for understanding decision making. However, it does not account for the time taken to make a decision, nor why response bias might change over time. Sequential sampling models provide a way of accounting for speed-accuracy trade-offs and response bias shifts. In this study, we test the validity of a sequential sampling model of conflict detection in a simulated air traffic control task by assessing whether two of its key parameters respond to experimental manipulations in a theoretically consistent way. Through experimental instructions, we manipulated participants' response bias and the relative speed or accuracy of their responses. The sequential sampling model was able to replicate the trends in the conflict responses as well as response time across all conditions. Consistent with our predictions, manipulating response bias was associated primarily with changes in the model's Criterion parameter, whereas manipulating speed-accuracy instructions was associated with changes in the Threshold parameter. The success of the model in replicating the human data suggests we can use the parameters of the model to gain an insight into the underlying response bias and speed-accuracy preferences common to dynamic decision-making tasks. © 2013 American Psychological Association

Evading the strength–ductility trade-off dilemma in steel through gradient hierarchical nanotwins

PubMed Central

Wei, Yujie; Li, Yongqiang; Zhu, Lianchun; Liu, Yao; Lei, Xianqi; Wang, Gang; Wu, Yanxin; Mi, Zhenli; Liu, Jiabin; Wang, Hongtao; Gao, Huajian

2014-01-01

The strength–ductility trade-off has been a long-standing dilemma in materials science. This has limited the potential of many structural materials, steels in particular. Here we report a way of enhancing the strength of twinning-induced plasticity steel at no ductility trade-off. After applying torsion to cylindrical twinning-induced plasticity steel samples to generate a gradient nanotwinned structure along the radial direction, we find that the yielding strength of the material can be doubled at no reduction in ductility. It is shown that this evasion of strength–ductility trade-off is due to the formation of a gradient hierarchical nanotwinned structure during pre-torsion and subsequent tensile deformation. A series of finite element simulations based on crystal plasticity are performed to understand why the gradient twin structure can cause strengthening and ductility retention, and how sequential torsion and tension lead to the observed hierarchical nanotwinned structure through activation of different twinning systems. PMID:24686581

Composition of an avian guild in spatially structured habitats supports a competition–colonization trade-off

PubMed Central

Rodríguez, Alejandro; Jansson, Gunnar; Andrén, Henrik

2007-01-01

Assuming better colonization abilities of inferior competitors, the competition–colonization trade-off (CCTO) is one of the hypotheses that explains spatial variation of species composition in fragmented habitats. Whereas this mechanism may structure some plant and insect communities, ecologists have failed to document its operation in other natural systems, and its generality has been questioned. We combined fieldwork and published data to study the composition of a guild of passerines (Parus cristatus, Parus montanus, Parus ater and Regulus regulus) inhabiting 10 landscapes that differed in the amount of forest habitat. The species were ordered in a stable, well-defined competitive hierarchy, and the dispersal ability of each species was inversely correlated with its position in this hierarchy. In functionally continuous landscapes, superior competitors occupied most fragments and all guild members commonly occurred. The relative incidences of superior and inferior competitors were reversed, and differences amplified, in landscapes where patches were physically (distance) or functionally (matrix hardness) isolated. We found little support for two competing hypotheses, namely reduced habitat quality in isolated patches and lower abundance of a keystone predator (Glaucidium passerinum) in fragmented landscapes. We concluded that the CCTO offered the most probable explanation for variation in the composition of the Parus guild across landscapes. PMID:17389222

Composition of an avian guild in spatially structured habitats supports a competition-colonization trade-off.

PubMed

Rodríguez, Alejandro; Jansson, Gunnar; Andrén, Henrik

2007-06-07

Assuming better colonization abilities of inferior competitors, the competition-colonization trade-off (CCTO) is one of the hypotheses that explains spatial variation of species composition in fragmented habitats. Whereas this mechanism may structure some plant and insect communities, ecologists have failed to document its operation in other natural systems, and its generality has been questioned. We combined fieldwork and published data to study the composition of a guild of passerines (Parus cristatus, Parus montanus, Parus ater and Regulus regulus) inhabiting 10 landscapes that differed in the amount of forest habitat. The species were ordered in a stable, well-defined competitive hierarchy, and the dispersal ability of each species was inversely correlated with its position in this hierarchy. In functionally continuous landscapes, superior competitors occupied most fragments and all guild members commonly occurred. The relative incidences of superior and inferior competitors were reversed, and differences amplified, in landscapes where patches were physically (distance) or functionally (matrix hardness) isolated. We found little support for two competing hypotheses, namely reduced habitat quality in isolated patches and lower abundance of a keystone predator (Glaucidium passerinum) in fragmented landscapes. We concluded that the CCTO offered the most probable explanation for variation in the composition of the Parus guild across landscapes.

Cell Division and Evolution of Biological Tissues

NASA Astrophysics Data System (ADS)

Rivier, Nicolas; Arcenegui-Siemens, Xavier; Schliecker, Gudrun

A tissue is a geometrical, space-filling, random cellular network; it remains in this steady state while individual cells divide. Cell division (fragmentation) is a local, elementary topological transformation which establishes statistical equilibrium of the structure. Statistical equilibrium is characterized by observable relations (Lewis, Aboav) between cell shapes, sizes and those of their neighbours, obtained through maximum entropy and topological correlation extending to nearest neighbours only, i.e. maximal randomness. For a two-dimensional tissue (epithelium), the distribution of cell shapes and that of mother and daughter cells can be obtained from elementary geometrical and physical arguments, except for an exponential factor favouring division of larger cells, and exponential and combinatorial factors encouraging a most symmetric division. The resulting distributions are very narrow, and stationarity severely restricts the range of an adjustable structural parameter

Evolution of specialization under non-equilibrium population dynamics.

PubMed

Nurmi, Tuomas; Parvinen, Kalle

2013-03-21

We analyze the evolution of specialization in resource utilization in a mechanistically underpinned discrete-time model using the adaptive dynamics approach. We assume two nutritionally equivalent resources that in the absence of consumers grow sigmoidally towards a resource-specific carrying capacity. The consumers use resources according to the law of mass-action with rates involving trade-off. The resulting discrete-time model for the consumer population has over-compensatory dynamics. We illuminate the way non-equilibrium population dynamics affect the evolutionary dynamics of the resource consumption rates, and show that evolution to the trimorphic coexistence of a generalist and two specialists is possible due to asynchronous non-equilibrium population dynamics of the specialists. In addition, various forms of cyclic evolutionary dynamics are possible. Furthermore, evolutionary suicide may occur even without Allee effects and demographic stochasticity. Copyright © 2013 Elsevier Ltd. All rights reserved.

The causes and ecological correlates of head scale asymmetry and fragmentation in a tropical snake.

PubMed

Brown, Gregory P; Madsen, Thomas; Dubey, Sylvain; Shine, Rick

2017-09-12

The challenge of identifying the proximate causes and ecological consequences of phenotypic variation can be facilitated by studying traits that are usually but not always bilaterally symmetrical; deviations from symmetry likely reflect disrupted embryogenesis. Based on a 19-year mark-recapture study of >1300 slatey-grey snakes (Stegonotus cucullatus) in tropical Australia, and incubation of >700 eggs, we document developmental and ecological correlates of two morphological traits: asymmetry and fragmentation of head scales. Asymmetry was directional (more scales on the left side) and was higher in individuals with lower heterozygosity, but was not heritable. In contrast, fragmentation was heritable and was higher in females than males. Both scale asymmetry and fragmentation were increased by rapid embryogenesis but were not affected by hydric conditions during incubation. Snakes with asymmetry and fragmentation exhibited slightly lower survival and increased (sex-specific) movements, and females with more scale fragmentation produced smaller eggs. Counterintuitively, snakes with more asymmetry had higher growth rates (possibly reflecting trade-offs with other traits), and snakes with more fragmentation had fewer parasites (possibly due to lower feeding rates). Our data paint an unusually detailed picture of the complex genetic and environmental factors that, by disrupting early embryonic development, generate variations in morphology that have detectable correlations with ecological performance.

21 CFR 862.2270 - Thin-layer chromatography system for clinical use.

Code of Federal Regulations, 2011 CFR

2011-04-01

... a mixture. The mixture of compounds is absorbed onto a stationary phase or thin layer of inert material (e.g., cellulose, alumina, etc.) and eluted off by a moving solvent (moving phase) until equilibrium occurs between the two phases. (b) Classification. Class I (general controls). The device is...

Salt weathering on Mars

NASA Astrophysics Data System (ADS)

Jagoutz, E.

Large well rounded boulders and angular rock fragments characterizes the Martian landscape as seen on the recent excellent quality photos. Analyzing the different rock-shapes indicates a time sequence of emplacement, fragmentation and transport of different rocks on Mars, which might give interesting insight into transport and weathering processes. Larger commonly well rounded boulders were emplaced onto gravel plains. After emplacement, these rocks were fragmented and disassembled. Nests of angular rock fragments are marking the locations of preexisting larger rocks. Frequently it is possible to reconstruct larger rounded rocks from smaller angular fragments. In other cases transport after fragmentation obscured the relationship of the fragments. However, a strewn field of fragments is still reminiscent of the preexisting rock. Mechanical salt weathering could be a plausible explanation for the insitu fragmentation of larger rounded blocks into angular fragments. Impact or secondary air fall induced fragmentation produces very different patterns, as observed around impact crates on Earth. Salt weathering of rocks is a common process in terrestrial environments. Salt crystallization in capillaries causes fragmentation of rocks, irrespective of the process of salt transportation and concentration. On Earth significant salt weathering can be observed in different climatic environments: in the transition zone of alluvial aprons and salt playas in desserts and in dry valleys of Antarctica. In terrestrial semi-arid areas the salt is transported by salt solution, which is progressively concentrated by evaporation. In Antarctic dry valleys freeze-thaw cycles causes salt transportation and crystallization resulting in rock fragmentation. This salt induced process can lead to complete destruction of rocks and converts rocks to fine sand. The efficient breakdown of rocks is dominating the landscape in some dry valleys of the Earth but possibly also on Mars. (Malin, 1974). However, irrespectively of the climatic environment a liquid brine is a necessity for salt induced fragmentation of rocks. If salt weathering is responsible for the fragmented rocks on the Martian surface it implies a temporary present of liquid H_2O. However, due to the present dry atmosphere on Mars brines can only be present in restricted places without being in equilibrium with the atmosphere (Clark and van Hart 1980). M. C. Malin (1974) JGR Vol 79,26 p 3888-3894 B. C. Clark and D. C. vanHart (1980) ICARUS 45, 370-378

Phased array ghost elimination.

PubMed

Kellman, Peter; McVeigh, Elliot R

2006-05-01

Parallel imaging may be applied to cancel ghosts caused by a variety of distortion mechanisms, including distortions such as off-resonance or local flow, which are space variant. Phased array combining coefficients may be calculated that null ghost artifacts at known locations based on a constrained optimization, which optimizes SNR subject to the nulling constraint. The resultant phased array ghost elimination (PAGE) technique is similar to the method known as sensitivity encoding (SENSE) used for accelerated imaging; however, in this formulation is applied to full field-of-view (FOV) images. The phased array method for ghost elimination may result in greater flexibility in designing acquisition strategies. For example, in multi-shot EPI applications ghosts are typically mitigated by the use of an interleaved phase encode acquisition order. An alternative strategy is to use a sequential, non-interleaved phase encode order and cancel the resultant ghosts using PAGE parallel imaging. Cancellation of ghosts by means of phased array processing makes sequential, non-interleaved phase encode acquisition order practical, and permits a reduction in repetition time, TR, by eliminating the need for echo-shifting. Sequential, non-interleaved phase encode order has benefits of reduced distortion due to off-resonance, in-plane flow and EPI delay misalignment. Furthermore, the use of EPI with PAGE has inherent fat-water separation and has been used to provide off-resonance correction using a technique referred to as lipid elimination with an echo-shifting N/2-ghost acquisition (LEENA), and may further generalized using the multi-point Dixon method. Other applications of PAGE include cancelling ghosts which arise due to amplitude or phase variation during the approach to steady state. Parallel imaging requires estimates of the complex coil sensitivities. In vivo estimates may be derived by temporally varying the phase encode ordering to obtain a full k-space dataset in a scheme similar to the autocalibrating TSENSE method. This scheme is a generalization of the UNFOLD method used for removing aliasing in undersampled acquisitions. The more general scheme may be used to modulate each EPI ghost image to a separate temporal frequency as described in this paper. Copyright (c) 2006 John Wiley & Sons, Ltd.

Phased array ghost elimination

PubMed Central

Kellman, Peter; McVeigh, Elliot R.

2007-01-01

Parallel imaging may be applied to cancel ghosts caused by a variety of distortion mechanisms, including distortions such as off-resonance or local flow, which are space variant. Phased array combining coefficients may be calculated that null ghost artifacts at known locations based on a constrained optimization, which optimizes SNR subject to the nulling constraint. The resultant phased array ghost elimination (PAGE) technique is similar to the method known as sensitivity encoding (SENSE) used for accelerated imaging; however, in this formulation is applied to full field-of-view (FOV) images. The phased array method for ghost elimination may result in greater flexibility in designing acquisition strategies. For example, in multi-shot EPI applications ghosts are typically mitigated by the use of an interleaved phase encode acquisition order. An alternative strategy is to use a sequential, non-interleaved phase encode order and cancel the resultant ghosts using PAGE parallel imaging. Cancellation of ghosts by means of phased array processing makes sequential, non-interleaved phase encode acquisition order practical, and permits a reduction in repetition time, TR, by eliminating the need for echo-shifting. Sequential, non-interleaved phase encode order has benefits of reduced distortion due to off-resonance, in-plane flow and EPI delay misalignment. Furthermore, the use of EPI with PAGE has inherent fat-water separation and has been used to provide off-resonance correction using a technique referred to as lipid elimination with an echo-shifting N/2-ghost acquisition (LEENA), and may further generalized using the multi-point Dixon method. Other applications of PAGE include cancelling ghosts which arise due to amplitude or phase variation during the approach to steady state. Parallel imaging requires estimates of the complex coil sensitivities. In vivo estimates may be derived by temporally varying the phase encode ordering to obtain a full k-space dataset in a scheme similar to the autocalibrating TSENSE method. This scheme is a generalization of the UNFOLD method used for removing aliasing in undersampled acquisitions. The more general scheme may be used to modulate each EPI ghost image to a separate temporal frequency as described in this paper. PMID:16705636

Antibody engineering of a cytotoxic monoclonal antibody 84 against human embryonic stem cells: Investigating the effects of multivalency on cytotoxicity.

PubMed

Klement, Maximilian; Zheng, Jiyun; Liu, Chengcheng; Tan, Heng-Liang; Wong, Victor Vai Tak; Choo, Andre Boon-Hwa; Lee, Dong-Yup; Ow, Dave Siak-Wei

2017-02-10

Antibody fragments have shown targeted specificity to their antigens, but only modest tissue retention times in vivo and in vitro. Multimerization has been used as a protein engineering tool to increase the number of binding units and thereby enhance the efficacy and retention time of antibody fragments. In this work, we explored the effects of valency using a series of self-assembling polypeptides based on the GCN4 leucine zipper multimerization domain fused to a single-chain variable fragment via an antibody upper hinge sequence. Four engineered antibody fragments with a valency from one to four antigen-binding units of a cytotoxic monoclonal antibody 84 against human embryonic stem cells (hESC) were constructed. We hypothesized that higher cytotoxicity would be observed for fragments with increased valency. Flow cytometry analysis revealed that the trimeric and tetrameric engineered antibody fragments resulted in the highest degree of cytotoxicity to the undifferentiated hESC, while the engineered antibody fragments were observed to have improved tissue penetration into cell clusters. Thus, a trade off was made for the trimeric versus tetrameric fragment due to improved tissue penetration. These results have direct implications for antibody-mediated removal of undifferentiated hESC during regenerative medicine and cell therapy. Copyright © 2016 The Author(s). Published by Elsevier B.V. All rights reserved.

Molecular mechanism of DNA association with single-stranded DNA binding protein

PubMed Central

Maffeo, Christopher

2017-01-01

Abstract During DNA replication, the single-stranded DNA binding protein (SSB) wraps single-stranded DNA (ssDNA) with high affinity to protect it from degradation and prevent secondary structure formation. Although SSB binds ssDNA tightly, it can be repositioned along ssDNA to follow the advancement of the replication fork. Using all-atom molecular dynamics simulations, we characterized the molecular mechanism of ssDNA association with SSB. Placed in solution, ssDNA–SSB assemblies were observed to change their structure spontaneously; such structural changes were suppressed in the crystallographic environment. Repeat simulations of the SSB–ssDNA complex under mechanical tension revealed a multitude of possible pathways for ssDNA to come off SSB punctuated by prolonged arrests at reproducible sites at the SSB surface. Ensemble simulations of spontaneous association of short ssDNA fragments with SSB detailed a three-dimensional map of local affinity to DNA; the equilibrium amount of ssDNA bound to SSB was found to depend on the electrolyte concentration but not on the presence of the acidic tips of the SSB tails. Spontaneous formation of ssDNA bulges and their diffusive motion along SSB surface was directly observed in multiple 10-µs-long simulations. Such reptation-like motion was confined by DNA binding to high-affinity spots, suggesting a two-step mechanism for SSB diffusion. PMID:29059392

Development of position-sensitive time-of-flight spectrometer for fission fragment research

DOE PAGES

Arnold, C. W.; Tovesson, F.; Meierbachtol, K.; ...

2014-07-09

A position-sensitive, high-resolution time-of-flight detector for fission fragments has been developed. The SPectrometer for Ion DEtermination in fission Research (SPIDER) is a 2E–2v spectrometer designed to measure the mass of light fission fragments to a single mass unit. The time pick-off detector pairs to be used in SPIDER have been tested with α-particles from 229Th and its decay chain and α-particles and spontaneous fission fragments from 252Cf. Each detector module is comprised of thin electron conversion foil, electrostatic mirror, microchannel plates, and delay-line anodes. Particle trajectories on the order of 700 mm are determined accurately to within 0.7 mm. Flightmore » times were measured with 250 ps resolution FWHM. Computed particle velocities are accurate to within 0.06 mm/ns corresponding to a precision of 0.5%. As a result, an ionization chamber capable of 400 keV energy resolution coupled with the velocity measurements described here will pave the way for modestly efficient measurements of light fission fragments with unit mass resolution.« less

Sequential Modelling of Building Rooftops by Integrating Airborne LIDAR Data and Optical Imagery: Preliminary Results

NASA Astrophysics Data System (ADS)

Sohn, G.; Jung, J.; Jwa, Y.; Armenakis, C.

2013-05-01

This paper presents a sequential rooftop modelling method to refine initial rooftop models derived from airborne LiDAR data by integrating it with linear cues retrieved from single imagery. A cue integration between two datasets is facilitated by creating new topological features connecting between the initial model and image lines, with which new model hypotheses (variances to the initial model) are produced. We adopt Minimum Description Length (MDL) principle for competing the model candidates and selecting the optimal model by considering the balanced trade-off between the model closeness and the model complexity. Our preliminary results, combined with the Vaihingen data provided by ISPRS WGIII/4 demonstrate the image-driven modelling cues can compensate the limitations posed by LiDAR data in rooftop modelling.

Lithium formate ion clusters formation during electrospray ionization: Evidence of magic number clusters by mass spectrometry and ab initio calculations

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

Shukla, Anil; Bogdanov, Bogdan

2015-02-14

Small cationic and anionic clusters of lithium formate were generated by electrospray ionization and their fragmentations were studied by tandem mass spectrometry. Singly as well as multiply charged clusters were formed with the general formulae, (HCOOLi)nLi+, (HCOOLi)nLimm+, (HCOOLi)nHCOO- and (HCOOLi)n(HCOO)mm-. Several magic number cluster ions were observed in both the positive and negative ion modes although more predominant in the positive ion mode with (HCOOLi)3Li+ being the most abundant and stable cluster ions. Fragmentations of singly charged clusters proceed first by the loss of a dimer unit ((HCOOLi)2) followed by sequential loss of monomer units (HCOOLi). In the case ofmore » positive cluster ions, all fragmentations lead to the magic cluster (HCOOLi)3Li+ at higher collision energies which later fragments to dimer and monomer ions in lower abundance. Quantum mechanical calculations performed for smaller cluster ions showed that the trimer ion has a closed ring structure similar to the phenalenylium structure with three closed rings connected to the lithium ion. Further additions of monomer units result in similar symmetric structures for hexamer and nonamer cluster ions. Thermochemical calculations show that trimer cluster ion is relatively more stable than neighboring cluster ions, supporting the experimental observation of a magic number cluster with enhanced stability.« less

A fragment of alpha-actinin promotes monocyte/macrophage maturation in vitro.

PubMed

Luikart, S; Wahl, D; Hinkel, T; Masri, M; Oegema, T

1999-02-01

Conditioned media (CM) from cultures of HL-60 myeloid leukemia cells grown on extracellular bone marrow matrix contains a factor that induces macrophage-like maturation of HL-60 cells. This factor was purified from the CM of HL-60 cells grown on bone marrow stroma by ammonium sulfate precipitation, then sequential chromatography on DEAE, affi-gel blue affinity, gel exclusion, and wheat germ affinity columns, followed by C-4 reverse phase HPLC, and SDS-PAGE. The maturation promoting activity of the CM was identified in a single 31 kD protein. Amino acid sequence analysis of four internal tryptic peptides of this protein confirmed significant homology with amino acid residues 48-60, 138-147, 215-220, and 221-236 of human cytoskeletal alpha-actinin. An immunoaffinity purified rabbit polyclonal anti-chicken alpha-actinin inhibited the activity of HL-60 conditioned media. A 27 kD amino-terminal fragment of alpha-actinin produced by thermolysin digestion of chicken gizzard alpha-actinin, but not intact alpha-actinin, had maturation promoting activity on several cell types, including blood monocytes, as measured by lysozyme secretion and tartrate-resistant acid phosphatase staining. We conclude that an extracellular alpha-actinin fragment can promote monocyte/macrophage maturation. This represents the first example of a fragment of a cytoskeletal component, which may be released during tissue remodeling and repair, playing a role in phagocyte maturation.

Integrated Ceramic Membrane System for Hydrogen Production

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

Schwartz, Joseph; Lim, Hankwon; Drnevich, Raymond

2010-08-05

Phase I was a technoeconomic feasibility study that defined the process scheme for the integrated ceramic membrane system for hydrogen production and determined the plan for Phase II. The hydrogen production system is comprised of an oxygen transport membrane (OTM) and a hydrogen transport membrane (HTM). Two process options were evaluated: 1) Integrated OTM-HTM reactor – in this configuration, the HTM was a ceramic proton conductor operating at temperatures up to 900°C, and 2) Sequential OTM and HTM reactors – in this configuration, the HTM was assumed to be a Pd alloy operating at less than 600°C. The analysis suggestedmore » that there are no technical issues related to either system that cannot be managed. The process with the sequential reactors was found to be more efficient, less expensive, and more likely to be commercialized in a shorter time than the single reactor. Therefore, Phase II focused on the sequential reactor system, specifically, the second stage, or the HTM portion. Work on the OTM portion was conducted in a separate program. Phase IIA began in February 2003. Candidate substrate materials and alloys were identified and porous ceramic tubes were produced and coated with Pd. Much effort was made to develop porous substrates with reasonable pore sizes suitable for Pd alloy coating. The second generation of tubes showed some improvement in pore size control, but this was not enough to get a viable membrane. Further improvements were made to the porous ceramic tube manufacturing process. When a support tube was successfully coated, the membrane was tested to determine the hydrogen flux. The results from all these tests were used to update the technoeconomic analysis from Phase I to confirm that the sequential membrane reactor system can potentially be a low-cost hydrogen supply option when using an existing membrane on a larger scale. Phase IIB began in October 2004 and focused on demonstrating an integrated HTM/water gas shift (WGS) reactor to increase CO conversion and produce more hydrogen than a standard water gas shift reactor would. Substantial improvements in substrate and membrane performance were achieved in another DOE project (DE-FC26-07NT43054). These improved membranes were used for testing in a water gas shift environment in this program. The amount of net H2 generated (defined as the difference of hydrogen produced and fed) was greater than would be produced at equilibrium using conventional water gas shift reactors up to 75 psig because of the shift in equilibrium caused by continuous hydrogen removal. However, methanation happened at higher pressures, 100 and 125 psig, and resulted in less net H2 generated than would be expected by equilibrium conversion alone. An effort to avoid methanation by testing in more oxidizing conditions (by increasing CO2/CO ratio in a feed gas) was successful and net H2 generated was higher (40-60%) than a conventional reactor at equilibrium at all pressures tested (up to 125 psig). A model was developed to predict reactor performance in both cases with and without methanation. The required membrane area depends on conditions, but the required membrane area is about 10 ft2 to produce about 2000 scfh of hydrogen. The maximum amount of hydrogen that can be produced in a membrane reactor decreased significantly due to methanation from about 2600 scfh to about 2400 scfh. Therefore, it is critical to eliminate methanation to fully benefit from the use of a membrane in the reaction. Other modeling work showed that operating a membrane reactor at higher temperature provides an opportunity to make the reactor smaller and potentially provides a significant capital cost savings compared to a shift reactor/PSA combination.« less

Pinch-off syndrome: transection of implantable central venous access device.

PubMed

Sugimoto, Takuya; Nagata, Hiroshi; Hayashi, Ken; Kano, Nobuyasu

2012-11-30

As the population of people with cancer increases so does the number of patients who take chemotherapy. Majority of them are administered parentally continuously. Implantable central venous catheter device is a good choice for those patients; however, severe complication would occur concerning the devices. Pinch-off syndrome is one of the most severe complications. The authors report a severe case of pinch-off syndrome. The patient with the implantable central venous device could not take chemotherapy because the device occluded. Further examination revealed the transection of the catheter. The transected fragment of the catheter in the heart was successfully removed by using a loop snare placed through the right femoral vein.

Optimal trajectories of aircraft and spacecraft

NASA Technical Reports Server (NTRS)

Miele, A.

1990-01-01

Work done on algorithms for the numerical solutions of optimal control problems and their application to the computation of optimal flight trajectories of aircraft and spacecraft is summarized. General considerations on calculus of variations, optimal control, numerical algorithms, and applications of these algorithms to real-world problems are presented. The sequential gradient-restoration algorithm (SGRA) is examined for the numerical solution of optimal control problems of the Bolza type. Both the primal formulation and the dual formulation are discussed. Aircraft trajectories, in particular, the application of the dual sequential gradient-restoration algorithm (DSGRA) to the determination of optimal flight trajectories in the presence of windshear are described. Both take-off trajectories and abort landing trajectories are discussed. Take-off trajectories are optimized by minimizing the peak deviation of the absolute path inclination from a reference value. Abort landing trajectories are optimized by minimizing the peak drop of altitude from a reference value. Abort landing trajectories are optimized by minimizing the peak drop of altitude from a reference value. The survival capability of an aircraft in a severe windshear is discussed, and the optimal trajectories are found to be superior to both constant pitch trajectories and maximum angle of attack trajectories. Spacecraft trajectories, in particular, the application of the primal sequential gradient-restoration algorithm (PSGRA) to the determination of optimal flight trajectories for aeroassisted orbital transfer are examined. Both the coplanar case and the noncoplanar case are discussed within the frame of three problems: minimization of the total characteristic velocity; minimization of the time integral of the square of the path inclination; and minimization of the peak heating rate. The solution of the second problem is called nearly-grazing solution, and its merits are pointed out as a useful engineering compromise between energy requirements and aerodynamics heating requirements.

Concomitant or sequential administration of live attenuated japanese encephalitis chimeric virus vaccine and yellow fever 17D vaccine

PubMed Central

Nasveld, Peter E; Marjason, Joanne; Bennett, Sonya; Aaskov, John; Elliott, Suzanne; McCarthy, Karen; Kanesa-thasan, Niranjan; Feroldi, Emmanuel

2010-01-01

A randomized, double-blind, study was conducted to evaluate the safety, tolerability and immunogenicity of a live attenuated Japanese encephalitis chimeric virus vaccine (JE-CV) co-administered with live attenuated yellow fever (YF) vaccine (YF-17D strain; Stamaril®, Sanofi Pasteur) or administered sequentially. Participants (n = 108) were randomized to receive: YF followed by JE-CV 30 days later, JE followed by YF 30 days later, or the co-administration of JE and YF followed or preceded by placebo 30 days later or earlier. Placebo was used in a double-dummy fashion to ensure masking. Neutralizing antibody titers against JE-CV, YF-17D and selected wild-type JE virus strains was determined using a 50% serum-dilution plaque reduction neutralization test (PRNT50). Seroconversion was defined as the appearance of a neutralizing antibody titer above the assay cut-off post-immunization when not present pre-injection at day 0, or a least a four-fold rise in neutralizing antibody titer measured before the pre-injection day 0 and later post vaccination samples. There were no serious adverse events. Most adverse events (AEs) after JE vaccination were mild to moderate in intensity, and similar to those reported following YF vaccination. Seroconversion to JE-CV was 100% and 91% in the JE/YF and YF/JE sequential vaccination groups, respectively, compared with 96% in the co-administration group. All participants seroconverted to YF vaccine and retained neutralizing titers above the assay cut-off at month six. Neutralizing antibodies against JE vaccine were detected in 82–100% of participants at month six. These results suggest that both vaccines may be successfully co-administered simultaneously or 30 days apart. PMID:20864814

Adsorption Equilibrium and Modeling of Water Vapor on Reduced and Unreduced Silver-Exchanged Mordenite

DOE PAGES

Nan, Yue; Lin, Ronghong; Liu, Jiuxu; ...

2017-06-26

This work is related to the removal of tritiated water and radioactive iodine from off-gases released during spent nuclear fuel reprocessing. Specifically, it is focused on the adsorption equilibrium of water on reduced silver mordenite (Ag 0Z), which is the state-of-art solid adsorbent for iodine retention in the off-gas treatment. As the off-gases contain different gas species, including iodine and water, Ag 0Z would take up iodine and water simultaneously during the adsorption process. Therefore, understanding the adsorption of water on Ag 0Z is important and necessary for studying the performance of Ag 0Z in off-gas treatment processes. The isothermsmore » of water (nonradioactive water) on Ag 0Z were obtained at temperatures of 25, 40, 60, 100, 150, and 200 °C with a continuous-flow adsorption system. The data were analyzed using the Heterogeneous Langmuir and generalized statistical thermodynamic adsorption (GSTA) models, and thermodynamic parameters of the isotherms were obtained from both models. Both models were found capable of describing the isotherms. Isotherms of water on the unreduced silver mordenite (AgZ) were also obtained at 25, 40, and 60 °C and parametrized by the GSTA model. Through the comparison of the isotherms of Ag 0Z and AgZ, it was found that Ag 0Z had a higher water adsorption capacity than AgZ. The comparison of their thermodynamic parameters suggested that the interaction of water molecules with the H + in Ag 0Z was stronger than that with the Ag + in AgZ.« less

Adsorption Equilibrium and Modeling of Water Vapor on Reduced and Unreduced Silver-Exchanged Mordenite

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

Nan, Yue; Lin, Ronghong; Liu, Jiuxu

This work is related to the removal of tritiated water and radioactive iodine from off-gases released during spent nuclear fuel reprocessing. Specifically, it is focused on the adsorption equilibrium of water on reduced silver mordenite (Ag 0Z), which is the state-of-art solid adsorbent for iodine retention in the off-gas treatment. As the off-gases contain different gas species, including iodine and water, Ag 0Z would take up iodine and water simultaneously during the adsorption process. Therefore, understanding the adsorption of water on Ag 0Z is important and necessary for studying the performance of Ag 0Z in off-gas treatment processes. The isothermsmore » of water (nonradioactive water) on Ag 0Z were obtained at temperatures of 25, 40, 60, 100, 150, and 200 °C with a continuous-flow adsorption system. The data were analyzed using the Heterogeneous Langmuir and generalized statistical thermodynamic adsorption (GSTA) models, and thermodynamic parameters of the isotherms were obtained from both models. Both models were found capable of describing the isotherms. Isotherms of water on the unreduced silver mordenite (AgZ) were also obtained at 25, 40, and 60 °C and parametrized by the GSTA model. Through the comparison of the isotherms of Ag 0Z and AgZ, it was found that Ag 0Z had a higher water adsorption capacity than AgZ. The comparison of their thermodynamic parameters suggested that the interaction of water molecules with the H + in Ag 0Z was stronger than that with the Ag + in AgZ.« less

Evaluation of mineral-aqueous chemical equilibria of felsic reservoirs with low-medium temperature: A comparative study in Yangbajing geothermal field and Guangdong geothermal fields

NASA Astrophysics Data System (ADS)

Li, Jiexiang; Sagoe, Gideon; Yang, Guang; Lu, Guoping

2018-02-01

Classical geothermometers are useful tools for estimating reservoir temperatures of geothermal systems. However, their application to low-medium temperature reservoirs is limited because large variations of temperatures calculated by different classical geothermometers are usually observed. In order to help choose the most appropriate classical geothermometer for calculating the temperatures of low-medium temperature reservoirs, this study evaluated the mineral-aqueous equilibria of typical low-medium temperature felsic reservoirs in the Yangbajing geothermal field and Guangdong geothermal fields. The findings of this study support that reservoirs in the Guangdong geothermal fields have no direct magma influence. Also, natural reservoirs may represent the intermediate steady state before reaching full equilibrium, which rarely occurs. For the low-medium temperature geothermal systems without the influence of magma, even with seawater intrusion, the process of minerals reaching mineral-aqueous equilibrium is sequential: chlorite and chalcedony are the first, then followed by K-feldspar, kaolinite and K-mica. Chlorite may reach equilibrium at varying activity values, and the equilibrium between K-feldspar and kaolinite or K-feldspar and K-mica can fix the contents of K and Al in the solutions. Although the SiO2 and Al attain equilibrium state, albite and laumontite remain unsaturated and thus may affect low-medium temperature calculations. In this study, the chalcedony geothermometer was found to be the most suitable geothermometer for low-medium temperature reservoirs. The results of K-Mg geothermometer may be useful to complement that of the chalcedony geothermometer in low-medium temperature reservoir systems. Na-K geothermometer will give unreliable results at low-medium temperatures; and Na-K-Ca will also be unsuitable to calculate reservoir temperatures lower than 180 °C, probably caused by the chemical imbalance of laumontite.

Variable Gene Dispersal Conditions and Spatial Deforestation Patterns Can Interact to Affect Tropical Tree Conservation Outcomes

PubMed Central

Kashimshetty, Yamini; Pelikan, Stephan; Rogstad, Steven H.

2015-01-01

Tropical lowland rain forest (TLRF) biodiversity is under threat from anthropogenic factors including deforestation which creates forest fragments of different sizes that can further undergo various internal patterns of logging. Such interventions can modify previous equilibrium abundance and spatial distribution patterns of offspring recruitment and/or pollen dispersal. Little is known about how these aspects of deforestation and fragmentation might synergistically affect TLRF tree recovery demographics and population genetics in newly formed forest fragments. To investigate these TLRF anthropogenic disturbance processes we used the computer program NEWGARDEN (NG), which models spatially-explicit, individual-based plant populations, to simulate 10% deforestation in six different spatial logging patterns for the plant functional type of a long-lived TLRF canopy tree species. Further, each logging pattern was analyzed under nine varying patterns of offspring versus pollen dispersal distances that could have arisen post-fragmentation. Results indicated that gene dispersal condition (especially via offspring) had a greater effect on population growth and genetic diversity retention (explaining 98.5% and 88.8% of the variance respectively) than spatial logging pattern (0.2% and 4.7% respectively), with ‘Near’ distance dispersal maximizing population growth and genetic diversity relative to distant dispersal. Within logged regions of the fragment, deforestation patterns closer to fragment borders more often exhibited lower population recovery rates and founding genetic diversity retention relative to more centrally located logging. These results suggest newly isolated fragments have populations that are more sensitive to the way in which their offspring and pollen dispersers are affected than the spatial pattern in which subsequent logging occurs, and that large variation in the recovery rates of different TLRF tree species attributable to altered gene dispersal regimens will be a likely outcome of fragmentation. Conservation implications include possible manual interventions (manual manipulations of offspring dispersers and/or pollinators) in forest fragments to increase population recovery and genetic diversity retention. PMID:26000951

Variable gene dispersal conditions and spatial deforestation patterns can interact to affect tropical tree conservation outcomes.

PubMed

Kashimshetty, Yamini; Pelikan, Stephan; Rogstad, Steven H

2015-01-01

Tropical lowland rain forest (TLRF) biodiversity is under threat from anthropogenic factors including deforestation which creates forest fragments of different sizes that can further undergo various internal patterns of logging. Such interventions can modify previous equilibrium abundance and spatial distribution patterns of offspring recruitment and/or pollen dispersal. Little is known about how these aspects of deforestation and fragmentation might synergistically affect TLRF tree recovery demographics and population genetics in newly formed forest fragments. To investigate these TLRF anthropogenic disturbance processes we used the computer program NEWGARDEN (NG), which models spatially-explicit, individual-based plant populations, to simulate 10% deforestation in six different spatial logging patterns for the plant functional type of a long-lived TLRF canopy tree species. Further, each logging pattern was analyzed under nine varying patterns of offspring versus pollen dispersal distances that could have arisen post-fragmentation. Results indicated that gene dispersal condition (especially via offspring) had a greater effect on population growth and genetic diversity retention (explaining 98.5% and 88.8% of the variance respectively) than spatial logging pattern (0.2% and 4.7% respectively), with 'Near' distance dispersal maximizing population growth and genetic diversity relative to distant dispersal. Within logged regions of the fragment, deforestation patterns closer to fragment borders more often exhibited lower population recovery rates and founding genetic diversity retention relative to more centrally located logging. These results suggest newly isolated fragments have populations that are more sensitive to the way in which their offspring and pollen dispersers are affected than the spatial pattern in which subsequent logging occurs, and that large variation in the recovery rates of different TLRF tree species attributable to altered gene dispersal regimens will be a likely outcome of fragmentation. Conservation implications include possible manual interventions (manual manipulations of offspring dispersers and/or pollinators) in forest fragments to increase population recovery and genetic diversity retention.

Biosynthesis and NMR-studies of a double transmembrane domain from the Y4 receptor, a human GPCR.

PubMed

Zou, Chao; Naider, Fred; Zerbe, Oliver

2008-12-01

The human Y4 receptor, a class A G-protein coupled receptor (GPCR) primarily targeted by the pancreatic polypeptide (PP), is involved in a large number of physiologically important functions. This paper investigates a Y4 receptor fragment (N-TM1-TM2) comprising the N-terminal domain, the first two transmembrane (TM) helices and the first extracellular loop followed by a (His)(6) tag, and addresses synthetic problems encountered when recombinantly producing such fragments from GPCRs in Escherichia coli. Rigorous purification and usage of the optimized detergent mixture 28 mM dodecylphosphocholine (DPC)/118 mM% 1-palmitoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)] (LPPG) resulted in high quality TROSY spectra indicating protein conformational homogeneity. Almost complete assignment of the backbone, including all TM residue resonances was obtained. Data on internal backbone dynamics revealed a high secondary structure content for N-TM1-TM2. Secondary chemical shifts and sequential amide proton nuclear Overhauser effects defined the TM helices. Interestingly, the properties of the N-terminal domain of this large fragment are highly similar to those determined on the isolated N-terminal domain in the presence of DPC micelles.

Fragmentation pathways of tungsten hexacarbonyl clusters upon electron ionization.

PubMed

Neustetter, M; Jabbour Al Maalouf, E; Limão-Vieira, P; Denifl, S

2016-08-07

Electron ionization of neat tungsten hexacarbonyl (W(CO)6) clusters has been investigated in a crossed electron-molecular beam experiment coupled with a mass spectrometer system. The molecule is used for nanofabrication processes through electron beam induced deposition and ion beam induced deposition techniques. Positive ion mass spectra of W(CO)6 clusters formed by electron ionization at 70 eV contain the ion series of the type W(CO)n (+) (0 ≤ n ≤ 6) and W2(CO)n (+) (0 ≤ n ≤ 12). In addition, a series of peaks are observed and have been assigned to WC(CO)n (+) (0 ≤ n ≤ 3) and W2C(CO)n (+) (0 ≤ n ≤ 10). A distinct change of relative fragment ion intensity can be observed for clusters compared to the single molecule. The characteristic fragmentation pattern obtained in the mass spectra can be explained by a sequential decay of the ionized organometallic, which is also supported by the study of the clusters when embedded in helium nanodroplets. In addition, appearance energies for the dissociative ionization channels for singly charged ions have been estimated from experimental ion efficiency curves.

Critical reappraisal of embryo quality as a predictive parameter for pregnancy outcome: a pilot study.

PubMed

Campo, R; Binda, M M; Van Kerkhoven, G; Frederickx, V; Serneels, A; Roziers, P; Lopes, A S; Gordts, S; Puttemans, P; Gordts, S

2010-01-01

Pilot study to analyse the efficacy and embryo morphology using a new human embryo culture medium (GM501) versus the conventional used medium (ISM1). Over a four-month period, all patients at the Leuven Institute of Fertility and Embryology (LIFE) were -randomly allocated to have their embryos cultured in either the standard sequential culture medium ISM1 (control) or in a new universal medium (GM501) (study group). Primary outcome parameters were clinical pregnancy and live birth rate. The secondary outcome parameter was the correlation of embryo fragmentation rate with pregnancy outcome. We did not observe any differences between the ISM1 control group and GM501 study group with regard to fertilization, pregnancy, implantation rates, ongoing pregnancy, and babies born. The number of embryos with a minimal fragmentation rate (less than 30%) was significantly higher in the GM501 study group. Although a significant higher embryo fragmentation rate was seen in In vitro culture of embryos in GM501, pregnancy outcome results were comparable to those of embryos cultured in ISM1. According to our results the value of embryo morphological criteria as a parameter for pregnancy outcome should be examined and discussed again.

Polarization imaging of comets at geocentric distances smaller than 0.5 au: Comet 73P/Schwassmann-Wachmann 3

NASA Astrophysics Data System (ADS)

Hadamcik, E.; Levasseur-Regourd, A.-C.

2014-07-01

Remote observations of sunlight scattered by solid particles provide information on the particle properties for a large variety of comets. When comets approach the Sun, solid particles and gases are released from the surface or from the inner layers [1,2]. If the comet is close enough to the Earth, the inner coma may be studied. Different coma regions are observed corresponding to different dust properties, e.g., in jets or fresh ejected dust around the coma. Narrow-band continuum filters or broader-band filters in less contaminated spectral domains (red or near infrared) are currently used to avoid or reduce the contributions from gaseous emission. Comet 73P/Schwassmann-Wachmann 3 is a fascinating fragmenting comet. Different observations in 1995 revealed an increase of activity and at least four fragments of the nucleus. In its 2011 apparition, the fragments were well separated and appeared like small individual comets. In 2006, its apparition was very favorable and allowed high- spatial resolution imaging by different complementary techniques. We observed three fragments of comet 73P/Schwassmann-Wachmann 3 from April 27 to May 3, 2006, by imaging polarimetry with the 80-cm telescope at Observatoire de Haute-Provence. The distance to the Earth was smaller than 0.2 au. Fragment C resembles a classical active comet. Regions of high and lower polarization were observed in the inner coma, appearing to change almost periodically. The variation of polarization in the inner coma was important from one night to the next one, the whole coma polarization being about constant for nucleus distances greater than 2000 km and increasing with the phase angle. Fragment B continued its (sequential) fragmentation, with a region of secondary fragments progressively moving away from the main nucleus in the antisolar direction. The chemical composition has been reported as being similar in all the fragments [3], but differences were observed between them in polarization underlining differences in, e.g., structure or size distribution of the particles during their ejection and fragmentation. The variation of polarization in the coma and around the fragments will be presented. Finally, a comparison to other comets, including split comets observed at small geocentric distances, will be provided.

Basic functional trade-offs in cognition: An integrative framework.

PubMed

Del Giudice, Marco; Crespi, Bernard J

2018-06-14

Trade-offs between advantageous but conflicting properties (e.g., speed vs. accuracy) are ubiquitous in cognition, but the relevant literature is conceptually fragmented, scattered across disciplines, and has not been organized in a coherent framework. This paper takes an initial step toward a general theory of cognitive trade-offs by examining four key properties of goal-directed systems: performance, efficiency, robustness, and flexibility. These properties define a number of basic functional trade-offs that can be used to map the abstract "design space" of natural and artificial cognitive systems. Basic functional trade-offs provide a shared vocabulary to describe a variety of specific trade-offs including speed vs. accuracy, generalist vs. specialist, exploration vs. exploitation, and many others. By linking specific features of cognitive functioning to general properties such as robustness and efficiency, it becomes possible to harness some powerful insights from systems engineering and systems biology to suggest useful generalizations, point to under-explored but potentially important trade-offs, and prompt novel hypotheses and connections between disparate areas of research. Copyright © 2018 Elsevier B.V. All rights reserved.

Optimal Linear Responses for Markov Chains and Stochastically Perturbed Dynamical Systems

NASA Astrophysics Data System (ADS)

Antown, Fadi; Dragičević, Davor; Froyland, Gary

2018-03-01

The linear response of a dynamical system refers to changes to properties of the system when small external perturbations are applied. We consider the little-studied question of selecting an optimal perturbation so as to (i) maximise the linear response of the equilibrium distribution of the system, (ii) maximise the linear response of the expectation of a specified observable, and (iii) maximise the linear response of the rate of convergence of the system to the equilibrium distribution. We also consider the inhomogeneous, sequential, or time-dependent situation where the governing dynamics is not stationary and one wishes to select a sequence of small perturbations so as to maximise the overall linear response at some terminal time. We develop the theory for finite-state Markov chains, provide explicit solutions for some illustrative examples, and numerically apply our theory to stochastically perturbed dynamical systems, where the Markov chain is replaced by a matrix representation of an approximate annealed transfer operator for the random dynamical system.

Visualizing non-equilibrium lithiation of spinel oxide via in situ transmission electron microscopy

PubMed Central

He, Kai; Zhang, Sen; Li, Jing; Yu, Xiqian; Meng, Qingping; Zhu, Yizhou; Hu, Enyuan; Sun, Ke; Yun, Hongseok; Yang, Xiao-Qing; Zhu, Yimei; Gan, Hong; Mo, Yifei; Stach, Eric A.; Murray, Christopher B.; Su, Dong

2016-01-01

Spinel transition metal oxides are important electrode materials for lithium-ion batteries, whose lithiation undergoes a two-step reaction, whereby intercalation and conversion occur in a sequential manner. These two reactions are known to have distinct reaction dynamics, but it is unclear how their kinetics affects the overall electrochemical response. Here we explore the lithiation of nanosized magnetite by employing a strain-sensitive, bright-field scanning transmission electron microscopy approach. This method allows direct, real-time, high-resolution visualization of how lithiation proceeds along specific reaction pathways. We find that the initial intercalation process follows a two-phase reaction sequence, whereas further lithiation leads to the coexistence of three distinct phases within single nanoparticles, which has not been previously reported to the best of our knowledge. We use phase-field theory to model and describe these non-equilibrium reaction pathways, and to directly correlate the observed phase evolution with the battery's discharge performance. PMID:27157119

De-vitrification of nanoscale phase-separated amorphous thin films in the immiscible copper-niobium system

NASA Astrophysics Data System (ADS)

Puthucode, A.; Devaraj, A.; Nag, S.; Bose, S.; Ayyub, P.; Kaufman, M. J.; Banerjee, R.

2014-05-01

Copper and niobium are mutually immiscible in the solid state and exhibit a large positive enthalpy of mixing in the liquid state. Using vapour quenching via magnetron co-sputter deposition, far-from equilibrium amorphous Cu-Nb films have been deposited which exhibit a nanoscale phase separation. Annealing these amorphous films at low temperatures (~200 °C) initiates crystallization via the nucleation and growth of primary nanocrystals of a face-centred cubic Cu-rich phase separated by the amorphous matrix. Interestingly, subsequent annealing at a higher temperature (>300 °C) leads to the polymorphic nucleation and growth of large spherulitic grains of a body-centred cubic Nb-rich phase within the retained amorphous matrix of the partially crystallized film. This sequential two-stage crystallization process has been investigated in detail by combining transmission electron microscopy [TEM] (including high-resolution TEM) and atom probe tomography studies. These results provide new insights into the crystallization behaviour of such unusual far-from equilibrium phase-separated metallic glasses in immiscible systems.

Universal Off-Equilibrium Scaling of Critical Cumulants in the QCD Phase Diagram

DOE PAGES

Mukherjee, Swagato; Venugopalan, Raju; Yin, Yi

2016-11-23

Exploiting the universality between the QCD critical point and the three-dimensional Ising model, closed form expressions derived for nonequilibrium critical cumulants on the crossover side of the critical point reveal that they can differ in both magnitude and sign from equilibrium expectations. Here, we demonstrate here that key elements of the Kibble-Zurek framework of nonequilibrium phase transitions can be employed to describe the dynamics of these critical cumulants. Lastly, our results suggest that observables sensitive to critical dynamics in heavy-ion collisions should be expressible as universal scaling functions, thereby providing powerful model-independent guidance in searches for the QCD critical point.

Localization to delocalization crossover in a driven nonlinear cavity array

NASA Astrophysics Data System (ADS)

Brown, Oliver T.; Hartmann, Michael J.

2018-05-01

We study nonlinear cavity arrays where the particle relaxation rate in each cavity increases with the excitation number. We show that coherent parametric inputs can drive such arrays into states with commensurate filling that form non-equilibrium analogs of Mott insulating states. We explore the boundaries of the Mott insulating phase and the crossover to a delocalized phase with spontaneous first order coherence. While sharing many similarities with the Mott insulator to superfluid transition in equilibrium, the phase diagrams we find also show marked differences. Particularly the off diagonal order does not become long range since the influence of dephasing processes increases with increasing tunneling rates.

Rational Design of Potent Antagonists to the Human Growth Hormone Receptor

NASA Astrophysics Data System (ADS)

Fuh, Germaine; Cunningham, Brian C.; Fukunaga, Rikiro; Nagata, Shigekazu; Goeddel, David V.; Wells, James A.

1992-06-01

A hybrid receptor was constructed that contained the extracellular binding domain of the human growth hormone (hGH) receptor linked to the transmembrane and intracellular domains of the murine granulocyte colony-stimulating factor receptor. Addition of hGH to a myeloid leukemia cell line (FDC-P1) that expressed the hybrid receptor caused proliferation of these cells. The mechanism for signal transduction of the hybrid receptor required dimerization because monoclonal antibodies to the hGH receptor were agonists whereas their monovalent fragments were not. Receptor dimerization occurs sequentially-a receptor binds to site 1 on hGH, and then a second receptor molecule binds to site 2 on hGH. On the basis of this sequential mechanism, which may occur in many other cytokine receptors, inactive hGH analogs were designed that were potent antagonists to hGH-induced cell proliferation. Such antagonists could be useful for treating clinical conditions of hGH excess, such as acromegaly.

Nuclear interference in the Coulomb explosion of H2+ in short vuv laser fields.

PubMed

Førre, Morten; Barmaki, Samira; Bachau, Henri

2009-03-27

We report ab initio calculations of H2+ three-photon ionization by vuv/fs 10(12) W/cm(2) laser pulses including electronic and vibrational degrees of freedom in the Born-Oppenheimer approximation. The initial nuclear wave packet of H2+(1ssigma(g)) is assumed to be equal to the H2 vibrational ground state. For pulse durations longer than 10 fs, we find an unexpected modulation in the kinetic energy spectra of the correlated fragments (H++H+). It is shown that the structures in the spectra originate from the interference between a direct and a sequential dissociation channel. While the first channel is open even for relatively short pulses, the sequential one only opens for pulse durations longer than 10 fs. In the latter case we show that interference between the two components results in a modulated kinetic energy release spectrum in the dissociation channel 3dsigma(g), which is reflected in the ionization spectrum.

Formation of Stone-Wales edge: Multistep reconstruction and growth mechanisms of zigzag nanographene.

PubMed

Dang, Jing-Shuang; Wang, Wei-Wei; Zheng, Jia-Jia; Nagase, Shigeru; Zhao, Xiang

2017-10-05

Although the existence of Stone-Wales (5-7) defect at graphene edge has been clarified experimentally, theoretical study on the formation mechanism is still imperfect. In particular, the regioselectivity of multistep reactions at edge (self-reconstruction and growth with foreign carbon feedstock) is essential to understand the kinetic behavior of reactive boundaries but investigations are still lacking. Herein, by using finite-sized models, multistep reconstructions and carbon dimer additions of a bared zigzag edge are introduced using density functional theory calculations. The zigzag to 5-7 transformation is proved as a site-selective process to generate alternating 5-7 pairs sequentially and the first step with largest barrier is suggested as the rate-determining step. Conversely, successive C 2 insertions on the active edge are calculated to elucidate the formation of 5-7 edge during graphene growth. A metastable intermediate with a triple sequentially fused pentagon fragment is proved as the key structure for 5-7 edge formation. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Isolation and characterization of a new zinc-binding protein from albacore tuna plasma

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

Dyke, B.; Hegenauer, J.; Saltman, P.

1987-06-02

The protein responsible for sequestering high levels of zinc in the plasma of the albacore tuna (Thunnus alalunga) has been isolated by sequential chromatography. The glycoprotein has a molecular weight of 66,000. Approximately 8.2% of its amino acid residues are histidines. Equilibrium dialysis experiments show it to bind 3 mol of zinc/mol of protein. The stoichiometric constant for the association of zinc with a binding site containing three histidines was determined to be 10/sup 9.4/. This protein is different from albumin and represents a previously uncharacterized zinc transport protein.

Polycondensation of Asparagine-comprising Dipeptides in Aqueous Media-A Simulation of Polypeptide Formation in Primordial Earth Hydrosphere

NASA Astrophysics Data System (ADS)

Munegumi, Toratane; Tanikawa, Naoya

2017-09-01

Asparagine and aspartic acid might have mutually transformed in the primordial hydrosphere of the earth, if ammonia and aspartic acid had existed in equilibrium. These amino acids seem to contribute to polypeptides, while the simple amino acids glycine and alanine easily form cyclic dipeptides and do not achieve long peptide chains. Asparagine-comprising dipeptides contribute some kinds of activation forms of dipeptides because these can polymerize faster than asparagine only. The new finding of polypeptide formation suggests a pathway of sequential polypeptides to evolve a diversity of polypeptides.

Polycondensation of Asparagine-comprising Dipeptides in Aqueous Media-A Simulation of Polypeptide Formation in Primordial Earth Hydrosphere.

PubMed

Munegumi, Toratane; Tanikawa, Naoya

2017-09-01

Asparagine and aspartic acid might have mutually transformed in the primordial hydrosphere of the earth, if ammonia and aspartic acid had existed in equilibrium. These amino acids seem to contribute to polypeptides, while the simple amino acids glycine and alanine easily form cyclic dipeptides and do not achieve long peptide chains. Asparagine-comprising dipeptides contribute some kinds of activation forms of dipeptides because these can polymerize faster than asparagine only. The new finding of polypeptide formation suggests a pathway of sequential polypeptides to evolve a diversity of polypeptides.

Off-Policy Integral Reinforcement Learning Method to Solve Nonlinear Continuous-Time Multiplayer Nonzero-Sum Games.

PubMed

Song, Ruizhuo; Lewis, Frank L; Wei, Qinglai

2017-03-01

This paper establishes an off-policy integral reinforcement learning (IRL) method to solve nonlinear continuous-time (CT) nonzero-sum (NZS) games with unknown system dynamics. The IRL algorithm is presented to obtain the iterative control and off-policy learning is used to allow the dynamics to be completely unknown. Off-policy IRL is designed to do policy evaluation and policy improvement in the policy iteration algorithm. Critic and action networks are used to obtain the performance index and control for each player. The gradient descent algorithm makes the update of critic and action weights simultaneously. The convergence analysis of the weights is given. The asymptotic stability of the closed-loop system and the existence of Nash equilibrium are proved. The simulation study demonstrates the effectiveness of the developed method for nonlinear CT NZS games with unknown system dynamics.

Effect of Sequential Treatment with Bisphosphonates After Teriparatide in Ovariectomized Rats: A Direct Comparison Between Risedronate and Alendronate.

PubMed

Yano, Tetsuo; Yamada, Mei; Inoue, Daisuke

2017-07-01

Teriparatide (TPTD), a recombinant human parathyroid hormone N-terminal fragment (1-34), is a widely used bone anabolic drug for osteoporosis. Sequential treatment with antiresorptives such as bisphosphonates after TPTD discontinuation is generally recommended. However, relative effects of bisphosphonates have not been determined. In the present study, we directly compared effects of risedronate (RIS) and alendronate (ALN) on bone mineral density (BMD), bone turnover, structural property and strength in ovariectomized (OVX) rats, when administered after TPTD. Female Sprague Dawley rats were divided into one sham-operated and eight ovariectomized groups. TPTD, RIS, and ALN were given subcutaneously twice per week for 4 or 8 weeks after 4 week treatment with TPTD. TPTD significantly increased BMD (+9.6%) in OVX rats after 4 weeks of treatment. 8 weeks after TPTD withdrawal, vehicle-treated group showed a blunted BMD increase of +8.4% from the baseline. In contrast, 8 weeks of treatment with RIS and ALN significantly increased BMD to 17.4 and 21.8%, respectively. While ALN caused a consistently larger increase in BMD, sequential treatment with RIS resulted in lower Tb.Sp compared to ALN in the fourth lumbar vertebra as well as in greater stiffness in compression test. In conclusion, the present study demonstrated that sequential therapy with ALN and RIS after TPTD both improved bone mass and structure. Our results further suggest that RIS may have a greater effect on improving bone quality and stiffness than ALN despite less prominent effect on BMD. Further studies are necessary to determine clinical relevance of these findings to fracture rate.

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

Sengupta, M.; Ganesh, R.

The dynamics of cylindrically trapped electron plasma has been investigated using a newly developed 2D Electrostatic PIC code that uses unapproximated, mass-included equations of motion for simulation. Exhaustive simulations, covering the entire range of Brillouin ratio, were performed for uniformly filled circular profiles in rigid rotor equilibrium. The same profiles were then loaded away from equilibrium with an initial value of rigid rotation frequency different from that required for radial force balance. Both these sets of simulations were performed for an initial zero-temperature or cold load of the plasma with no spread in either angular velocity or radial velocity. Themore » evolution of the off-equilibrium initial conditions to a steady state involve radial breathing of the profile that scales in amplitude and algebraic growth with Brillouin fraction. For higher Brillouin fractions, the growth of the breathing mode is followed by complex dynamics of spontaneous hollow density structures, excitation of poloidal modes, leading to a monotonically falling density profile.« less

Stuttering Min oscillations within E. coli bacteria: a stochastic polymerization model

NASA Astrophysics Data System (ADS)

Sengupta, Supratim; Derr, Julien; Sain, Anirban; Rutenberg, Andrew D.

2012-10-01

We have developed a 3D off-lattice stochastic polymerization model to study the subcellular oscillation of Min proteins in the bacteria Escherichia coli, and used it to investigate the experimental phenomenon of Min oscillation stuttering. Stuttering was affected by the rate of immediate rebinding of MinE released from depolymerizing filament tips (processivity), protection of depolymerizing filament tips from MinD binding and fragmentation of MinD filaments due to MinE. Processivity, protection and fragmentation each reduce stuttering, speed oscillations and MinD filament lengths. Neither processivity nor tip protection were, on their own, sufficient to produce fast stutter-free oscillations. While filament fragmentation could, on its own, lead to fast oscillations with infrequent stuttering; high levels of fragmentation degraded oscillations. The infrequent stuttering observed in standard Min oscillations is consistent with short filaments of MinD, while we expect that mutants that exhibit higher stuttering frequencies will exhibit longer MinD filaments. Increased stuttering rate may be a useful diagnostic to find observable MinD polymerization under experimental conditions.

Punctuations and Agendas: A New Look at Local Government Budget Expenditures

ERIC Educational Resources Information Center

Jordan, Meagan M.

2003-01-01

Punctuated equilibrium theory (PET) is an agenda-based theory that offers a theoretical foundation for large budget shifts. PET emphasizes that the static, incremental nature of agendas is occasionally interrupted by punctuations. These punctuations indicate shifts in priority among the agenda items, and with those agenda shifts come trade-offs.…

LWIR HgCdTe: Innovative detectors in an incumbent technology

NASA Technical Reports Server (NTRS)

Tennant, William E.

1990-01-01

HgCdTe is the current material of choice for high performance imagers operating at relatively high temperatures. Its lack of technological maturity compared with silicon and wide-band gap III-V compounds is more than offset by its outstanding IR sensitivity and by the relatively benign effect of its materials defects. This latter property has allowed non-equilibrium growth techniques, metal oxide chemical vapor deposition (MOCVD) and molecular beam epitaxy (MBE), to produce device quality long wavelength infrared (LWIR) HgCdTe even on common substrates like GaAs and GaAs/Si. Detector performance in these exotic materials structures is comparable in many ways with devices in equilibrium-grown material. Lifetimes are similar. RoA values at 77K as high as several hundred have been seen in HgCdTe/GaAs/Si with 9.5 micron cut-off wavelength. HgCdTe/GaAs layers with approx. 15 micron cut-off wavelengths have given average 77K RoAs of greater than 2. Hybrid focal plane arrays have been evaluated with excellent operability.

Steady bipartite coherence induced by non-equilibrium environment

NASA Astrophysics Data System (ADS)

Huangfu, Yong; Jing, Jun

2018-01-01

We study the steady state of two coupled two-level atoms interacting with a non-equilibrium environment that consists of two heat baths at different temperatures. Specifically, we analyze four cases with respect to the configuration about the interactions between atoms and heat baths. Using secular approximation, the conventional master equation usually neglects steady-state coherence, even when the system is coupled with a non-equilibrium environment. When employing the master equation with no secular approximation, we find that the system coherence in our model, denoted by the off-diagonal terms in the reduced density matrix spanned by the eigenvectors of the system Hamiltonian, would survive after a long-time decoherence evolution. The absolute value of residual coherence in the system relies on different configurations of interaction channels between the system and the heat baths. We find that a large steady quantum coherence term can be achieved when the two atoms are resonant. The absolute value of quantum coherence decreases in the presence of additional atom-bath interaction channels. Our work sheds new light on the mechanism of steady-state coherence in microscopic quantum systems in non-equilibrium environments.

Insurance choice and tax-preferred health savings accounts.

PubMed

Cardon, James H; Showalter, Mark H

2007-03-01

We develop an infinite horizon utility maximization model of the interaction between insurance choice and tax-preferred health savings accounts. The model can be used to examine a wide range of policy options, including flexible spending accounts, health savings accounts, and health reimbursement accounts. We also develop a 2-period model to simulate various implications of the model. Key results from the simulation analysis include the following: (1) with no adverse selection, use of unrestricted health savings accounts leads to modest welfare gains, after accounting for the tax revenue loss; (2) with adverse selection and an initial pooling equilibrium comprised of "sick" and "healthy" consumers, introducing HSAs can, but does not necessarily, lead to a new pooling equilibrium. The new equilibrium results in a higher coinsurance rate, an increase in expected utility for healthy consumers, and a decrease in expected utility for sick consumers; (3) with adverse selection and a separating equilibrium, both sick and healthy consumers are better off with a health savings account; (4) efficiency gains are possible when insurance contracts are explicitly linked to tax-preferred health savings accounts.

Sequential quantum secret sharing in a noisy environment aided with weak measurements

NASA Astrophysics Data System (ADS)

Ray, Maharshi; Chatterjee, Sourav; Chakrabarty, Indranil

2016-05-01

In this work we give a (n,n)-threshold protocol for sequential secret sharing of quantum information for the first time. By sequential secret sharing we refer to a situation where the dealer is not having all the secrets at the same time, at the beginning of the protocol; however if the dealer wishes to share secrets at subsequent phases she/he can realize it with the help of our protocol. First of all we present our protocol for three parties and later we generalize it for the situation where we have more (n> 3) parties. Interestingly, we show that our protocol of sequential secret sharing requires less amount of quantum as well as classical resource as compared to the situation wherein existing protocols are repeatedly used. Further in a much more realistic situation, we consider the sharing of qubits through two kinds of noisy channels, namely the phase damping channel (PDC) and the amplitude damping channel (ADC). When we carry out the sequential secret sharing in the presence of noise we observe that the fidelity of secret sharing at the kth iteration is independent of the effect of noise at the (k - 1)th iteration. In case of ADC we have seen that the average fidelity of secret sharing drops down to ½ which is equivalent to a random guess of the quantum secret. Interestingly, we find that by applying weak measurements one can enhance the average fidelity. This increase of the average fidelity can be achieved with certain trade off with the success probability of the weak measurements.

Hierarchical Bayesian analysis of outcome- and process-based social preferences and beliefs in Dictator Games and sequential Prisoner's Dilemmas.

PubMed

Aksoy, Ozan; Weesie, Jeroen

2014-05-01

In this paper, using a within-subjects design, we estimate the utility weights that subjects attach to the outcome of their interaction partners in four decision situations: (1) binary Dictator Games (DG), second player's role in the sequential Prisoner's Dilemma (PD) after the first player (2) cooperated and (3) defected, and (4) first player's role in the sequential Prisoner's Dilemma game. We find that the average weights in these four decision situations have the following order: (1)>(2)>(4)>(3). Moreover, the average weight is positive in (1) but negative in (2), (3), and (4). Our findings indicate the existence of strong negative and small positive reciprocity for the average subject, but there is also high interpersonal variation in the weights in these four nodes. We conclude that the PD frame makes subjects more competitive than the DG frame. Using hierarchical Bayesian modeling, we simultaneously analyze beliefs of subjects about others' utility weights in the same four decision situations. We compare several alternative theoretical models on beliefs, e.g., rational beliefs (Bayesian-Nash equilibrium) and a consensus model. Our results on beliefs strongly support the consensus effect and refute rational beliefs: there is a strong relationship between own preferences and beliefs and this relationship is relatively stable across the four decision situations. Copyright © 2014 Elsevier Inc. All rights reserved.

Expanding Lipidome Coverage Using LC-MS/MS Data-Dependent Acquisition with Automated Exclusion List Generation

NASA Astrophysics Data System (ADS)

Koelmel, Jeremy P.; Kroeger, Nicholas M.; Gill, Emily L.; Ulmer, Candice Z.; Bowden, John A.; Patterson, Rainey E.; Yost, Richard A.; Garrett, Timothy J.

2017-05-01

Untargeted omics analyses aim to comprehensively characterize biomolecules within a biological system. Changes in the presence or quantity of these biomolecules can indicate important biological perturbations, such as those caused by disease. With current technological advancements, the entire genome can now be sequenced; however, in the burgeoning fields of lipidomics, only a subset of lipids can be identified. The recent emergence of high resolution tandem mass spectrometry (HR-MS/MS), in combination with ultra-high performance liquid chromatography, has resulted in an increased coverage of the lipidome. Nevertheless, identifications from MS/MS are generally limited by the number of precursors that can be selected for fragmentation during chromatographic elution. Therefore, we developed the software IE-Omics to automate iterative exclusion (IE), where selected precursors using data-dependent topN analyses are excluded in sequential injections. In each sequential injection, unique precursors are fragmented until HR-MS/MS spectra of all ions above a user-defined intensity threshold are acquired. IE-Omics was applied to lipidomic analyses in Red Cross plasma and substantia nigra tissue. Coverage of the lipidome was drastically improved using IE. When applying IE-Omics to Red Cross plasma and substantia nigra lipid extracts in positive ion mode, 69% and 40% more molecular identifications were obtained, respectively. In addition, applying IE-Omics to a lipidomics workflow increased the coverage of trace species, including odd-chained and short-chained diacylglycerides and oxidized lipid species. By increasing the coverage of the lipidome, applying IE to a lipidomics workflow increases the probability of finding biomarkers and provides additional information for determining etiology of disease.

Translations of Eastern Europe, Political, Sociological, and Military Affairs. Number 1398.

DTIC Science & Technology

1977-06-09

concentrated realism . Finally, "Tanase Scatiu," a film based on fragments of Duiliu Zamfirescu’s works and put together in a screenplay by MLhnea Gheorgiu...trans- position but rather recreated an actual and psychological universe, the world of the original novels of a century ago, with penetrating realism ...acquire, as well as the atmosphere of an era. A judicious equilibrium is established between the crude realism of the framework and the figurative

Stacked-unstacked equilibrium at the nick site of DNA.

PubMed

Protozanova, Ekaterina; Yakovchuk, Peter; Frank-Kamenetskii, Maxim D

2004-09-17

Stability of duplex DNA with respect to separation of complementary strands is crucial for DNA executing its major functions in the cell and it also plays a central role in major biotechnology applications of DNA: DNA sequencing, polymerase chain reaction, and DNA microarrays. Two types of interaction are well known to contribute to DNA stability: stacking between adjacent base-pairs and pairing between complementary bases. However, their contribution into the duplex stability is yet to be determined. Now we fill this fundamental gap in our knowledge of the DNA double helix. We have prepared a series of 32, 300 bp-long DNA fragments with solitary nicks in the same position differing only in base-pairs flanking the nick. Electrophoretic mobility of these fragments in the gel has been studied. Assuming the equilibrium between stacked and unstacked conformations at the nick site, all 32 stacking free energy parameters have been obtained. Only ten of them are essential and they govern the stacking interactions between adjacent base-pairs in intact DNA double helix. A full set of DNA stacking parameters has been determined for the first time. From these data and from a well-known dependence of DNA melting temperature on G.C content, the contribution of base-pairing into duplex stability has been estimated. The obtained energy parameters of the DNA double helix are of paramount importance for understanding sequence-dependent DNA flexibility and for numerous biotechnology applications.

The impact of slice-reduced computed tomography on histogram-based densitometry assessment of lung fibrosis in patients with systemic sclerosis.

PubMed

Nguyen-Kim, Thi Dan Linh; Maurer, Britta; Suliman, Yossra A; Morsbach, Fabian; Distler, Oliver; Frauenfelder, Thomas

2018-04-01

To evaluate usability of slice-reduced sequential computed tomography (CT) compared to standard high-resolution CT (HRCT) in patients with systemic sclerosis (SSc) for qualitative and quantitative assessment of interstitial lung disease (ILD) with respect to (I) detection of lung parenchymal abnormalities, (II) qualitative and semiquantitative visual assessment, (III) quantification of ILD by histograms and (IV) accuracy for the 20%-cut off discrimination. From standard chest HRCT of 60 SSc patients sequential 9-slice-computed tomography (reduced HRCT) was retrospectively reconstructed. ILD was assessed by visual scoring and quantitative histogram parameters. Results from standard and reduced HRCT were compared using non-parametric tests and analysed by univariate linear regression analyses. With respect to the detection of parenchymal abnormalities, only the detection of intrapulmonary bronchiectasis was significantly lower in reduced HRCT compared to standard HRCT (P=0.039). No differences were found comparing visual scores for fibrosis severity and extension from standard and reduced HRCT (P=0.051-0.073). All scores correlated significantly (P<0.001) to histogram parameters derived from both, standard and reduced HRCT. Significant higher values of kurtosis and skewness for reduced HRCT were found (both P<0.001). In contrast to standard HRCT histogram parameters from reduced HRCT showed significant discrimination at cut-off 20% fibrosis (sensitivity 88% kurtosis and skewness; specificity 81% kurtosis and 86% skewness; cut-off kurtosis ≤26, cut-off skewness ≤4; both P<0.001). Reduced HRCT is a robust method to assess lung fibrosis in SSc with minimal radiation dose with no difference in scoring assessment of lung fibrosis severity and extension in comparison to standard HRCT. In contrast to standard HRCT histogram parameters derived from the approach of reduced HRCT could discriminate at a threshold of 20% lung fibrosis with high sensitivity and specificity. Hence it might be used to detect early disease progression of lung fibrosis in context of monitoring and treatment of SSc patients.

N-terminal galanin-(1-16) fragment is an agonist at the hippocampal galanin receptor

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

Fisone, G.; Berthold, M.; Bedecs, K.

1989-12-01

The galanin N-terminal fragment (galanin-(1-16)) has been prepared by solid-phase synthesis and by enzymic cleavage of galanin by endoproteinase Asp-N. This peptide fragment displaced {sup 125}I-labeled galanin in receptor autoradiography experiments on rat forebrain and spinal cord and in equilibrium binding experiments from high-affinity binding sites in the ventral hippocampus with an IC50 of approximately 3 nM. In tissue slices of the same brain area, galanin-(1-16), similarly to galanin, inhibited the muscarinic agonist-stimulated breakdown of inositol phospholipids. Upon intracerebroventricular administration, galanin-(1-16) (10 micrograms/15 microliters) also inhibited the scopolamine (0.3 mg/kg, s.c.)-evoked release of acetylcholine, as studied in vivo by microdialysis.more » Substitution of (L-Trp2) for (D-Trp2) resulted in a 500-fold loss in affinity as compared with galanin-(1-16). It is concluded that, in the ventral hippocampus, the N-terminal galanin fragment (galanin-(1-16)) is recognized by the galanin receptors controlling acetylcholine release and muscarinic agonist-stimulated inositol phospholipid breakdown as a high-affinity agonist and that amino acid residue (Trp2) plays an important role in the receptor-ligand interactions.« less

Insights into the Impact of Linker Flexibility and Fragment Ionization on the Design of CK2 Allosteric Inhibitors: Comparative Molecular Dynamics Simulation Studies.

PubMed

Zhou, Yue; Zhang, Na; Qi, Xiaoqian; Tang, Shan; Sun, Guohui; Zhao, Lijiao; Zhong, Rugang; Peng, Yongzhen

2018-01-01

Protein kinase is a novel therapeutic target for human diseases. The off-target and side effects of ATP-competitive inhibitors preclude them from the clinically relevant drugs. The compounds targeting the druggable allosteric sites outside the highly conversed ATP binding pocket have been identified as promising alternatives to overcome current barriers of ATP-competitive inhibitors. By simultaneously interacting with the αD region (new allosteric site) and sub-ATP binding pocket, the attractive compound CAM4066 was named as allosteric inhibitor of CK2α. It has been demonstrated that the rigid linker and non-ionizable substituted fragment resulted in significant decreased inhibitory activities of compounds. The molecular dynamics simulations and energy analysis revealed that the appropriate coupling between the linker and pharmacophore fragments were essential for binding of CAM4066 with CK2α. The lower flexible linker of compound 21 lost the capability of coupling fragments A and B to αD region and positive area, respectively, whereas the methyl benzoate of fragment B induced the re-orientated Pre-CAM4066 with the inappropriate polar interactions. Most importantly, the match between the optimized linker and pharmacophore fragments is the challenging work of fragment-linking based drug design. These results provide rational clues to further structural modification and development of highly potent allosteric inhibitors of CK2.

Insights into the Impact of Linker Flexibility and Fragment Ionization on the Design of CK2 Allosteric Inhibitors: Comparative Molecular Dynamics Simulation Studies

PubMed Central

Zhou, Yue; Zhang, Na; Qi, Xiaoqian; Tang, Shan; Zhao, Lijiao; Zhong, Rugang; Peng, Yongzhen

2018-01-01

Protein kinase is a novel therapeutic target for human diseases. The off-target and side effects of ATP-competitive inhibitors preclude them from the clinically relevant drugs. The compounds targeting the druggable allosteric sites outside the highly conversed ATP binding pocket have been identified as promising alternatives to overcome current barriers of ATP-competitive inhibitors. By simultaneously interacting with the αD region (new allosteric site) and sub-ATP binding pocket, the attractive compound CAM4066 was named as allosteric inhibitor of CK2α. It has been demonstrated that the rigid linker and non-ionizable substituted fragment resulted in significant decreased inhibitory activities of compounds. The molecular dynamics simulations and energy analysis revealed that the appropriate coupling between the linker and pharmacophore fragments were essential for binding of CAM4066 with CK2α. The lower flexible linker of compound 21 lost the capability of coupling fragments A and B to αD region and positive area, respectively, whereas the methyl benzoate of fragment B induced the re-orientated Pre-CAM4066 with the inappropriate polar interactions. Most importantly, the match between the optimized linker and pharmacophore fragments is the challenging work of fragment-linking based drug design. These results provide rational clues to further structural modification and development of highly potent allosteric inhibitors of CK2. PMID:29301250

Identification of human antibody fragment clones specific for tetanus toxoid in a bacteriophage. lambda. immunoexpression library

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

Mullinax, R.L.; Gross, E.A.; Amberg, J.R.

1990-10-01

The authors have applied a molecular biology approach to the identification of human monoclonal antibodies. Human peripheral blood lymphocyte mRNA was converted to cDNA and a select subset was amplified by the polymerase chain reaction. These products, containing coding sequences for numerous immunoglobulin heavy- and {kappa} light-chain variable and constant region domains, were inserted into modified bacteriophase {lambda} expression vectors and introduced into Escherichia coli by infection to yield a combinatorial immunoexpression library. Clones with binding activity to tetanus toxoid were identified by filter hybridization with radiolabeled antigen and appeared at a frequency of 0.2{percent} in the library. These humanmore » antigen binding fragments, consisting of a heavy-chain fragment covalently linked to a light chain, displayed high affinity of binding to tetanus toxoid with equilibrium constants in the nanomolar range but did not cross-react with other proteins tested. They estimate that this human immunoexpression library contains 20,000 clones with high affinity and specificity to our chosen antigen.« less

Origin and history of chondrite regolith, fragmental and impact-melt breccias from Spain

NASA Technical Reports Server (NTRS)

Casanova, I.; Keil, K.; Wieler, R.; San Miguel, A.; King, E. A.

1990-01-01

Six ordinary chondrite breccias from the Museo Nacional de Ciencias Naturales, Madrid (Spain), are described and classified as follows: the solar gas-rich regolith breccia Oviedo (H5); the premetamorphic fragmental breccias Cabezo de Mayo (type 6, L-LL), and Sevilla (LL4); the fragmental breccias Canellas (H4) and Gerona (H5); and the impact melt breccia, Madrid (L6). It is confirmed that chondrites with typical light-dark structures and petrographic properties typical of regolith breccias may (Oviedo) or may not (Canellas) be solar gas-rich. Cabezo de Mayo and Sevilla show convincing evidence that they were assembled prior to peak metamorphism and were equilibrated during subsequent reheating. Compositions of olivine and low-Ca pyroxene in host chondrite and breccia clasts in Cabezo de Mayo are transitional between groups L and LL. It is suggested, based on mineralogic and oxygen isotopic compositions of host and clasts, that the rock formed on the L parent body by mixing, prior to peak metamorphism. This was followed by partial equilibrium of two different materials: the indigenous L chondrite host and exotic LL melt rock clasts.

Origin and history of chondrite regolith, fragmental and impact-melt breccias from Spain

NASA Astrophysics Data System (ADS)

Casanova, I.; Keil, K.; Wieler, R.; San Miguel, A.; King, E. A.

1990-06-01

Six ordinary chondrite breccias from the Museo Nacional de Ciencias Naturales, Madrid (Spain), are described and classified as follows: the solar gas-rich regolith breccia Oviedo (H5); the premetamorphic fragmental breccias Cabezo de Mayo (type 6, L-LL), and Sevilla (LL4); the fragmental breccias Canellas (H4) and Gerona (H5); and the impact melt breccia, Madrid (L6). It is confirmed that chondrites with typical light-dark structures and petrographic properties typical of regolith breccias may (Oviedo) or may not (Canellas) be solar gas-rich. Cabezo de Mayo and Sevilla show convincing evidence that they were assembled prior to peak metamorphism and were equilibrated during subsequent reheating. Compositions of olivine and low-Ca pyroxene in host chondrite and breccia clasts in Cabezo de Mayo are transitional between groups L and LL. It is suggested, based on mineralogic and oxygen isotopic compositions of host and clasts, that the rock formed on the L parent body by mixing, prior to peak metamorphism. This was followed by partial equilibrium of two different materials: the indigenous L chondrite host and exotic LL melt rock clasts.

Role of filament annealing in the kinetics and thermodynamics of nucleated polymerization.

PubMed

Michaels, Thomas C T; Knowles, Tuomas P J

2014-06-07

The formation of nanoscale protein filaments from soluble precursor molecules through nucleated polymerization is a common form of supra-molecular assembly phenomenon. This process underlies the generation of a range of both functional and pathological structures in nature. Filament breakage has emerged as a key process controlling the kinetics of the growth reaction since it increases the number of filament ends in the system that can act as growth sites. In order to ensure microscopic reversibility, however, the inverse process of fragmentation, end-to-end annealing of filaments, is a necessary component of a consistent description of such systems. Here, we combine Smoluchowski kinetics with nucleated polymerization models to generate a master equation description of protein fibrillization, where filamentous structures can undergo end-to-end association, in addition to elongation, fragmentation, and nucleation processes. We obtain self-consistent closed-form expressions for the growth kinetics and discuss the key physics that emerges from considering filament fusion relative to current fragmentation only models. Furthermore, we study the key time scales that describe relaxation to equilibrium.

Towards simultaneous Talbot bands based optical coherence tomography and scanning laser ophthalmoscopy imaging.

PubMed

Marques, Manuel J; Bradu, Adrian; Podoleanu, Adrian Gh

2014-05-01

We report a Talbot bands-based optical coherence tomography (OCT) system capable of producing longitudinal B-scan OCT images and en-face scanning laser ophthalmoscopy (SLO) images of the human retina in-vivo. The OCT channel employs a broadband optical source and a spectrometer. A gap is created between the sample and reference beams while on their way towards the spectrometer's dispersive element to create Talbot bands. The spatial separation of the two beams facilitates collection by an SLO channel of optical power originating exclusively from the retina, deprived from any contribution from the reference beam. Three different modes of operation are presented, constrained by the minimum integration time of the camera used in the spectrometer and by the galvo-scanners' scanning rate: (i) a simultaneous acquisition mode over the two channels, useful for small size imaging, that conserves the pixel-to-pixel correspondence between them; (ii) a hybrid sequential mode, where the system switches itself between the two regimes and (iii) a sequential "on-demand" mode, where the system can be used in either OCT or SLO regimes for as long as required. The two sequential modes present varying degrees of trade-off between pixel-to-pixel correspondence and independent full control of parameters within each channel. Images of the optic nerve and fovea regions obtained in the simultaneous (i) and in the hybrid sequential mode (ii) are presented.

Towards simultaneous Talbot bands based optical coherence tomography and scanning laser ophthalmoscopy imaging

PubMed Central

Marques, Manuel J.; Bradu, Adrian; Podoleanu, Adrian Gh.

2014-01-01

We report a Talbot bands-based optical coherence tomography (OCT) system capable of producing longitudinal B-scan OCT images and en-face scanning laser ophthalmoscopy (SLO) images of the human retina in-vivo. The OCT channel employs a broadband optical source and a spectrometer. A gap is created between the sample and reference beams while on their way towards the spectrometer’s dispersive element to create Talbot bands. The spatial separation of the two beams facilitates collection by an SLO channel of optical power originating exclusively from the retina, deprived from any contribution from the reference beam. Three different modes of operation are presented, constrained by the minimum integration time of the camera used in the spectrometer and by the galvo-scanners’ scanning rate: (i) a simultaneous acquisition mode over the two channels, useful for small size imaging, that conserves the pixel-to-pixel correspondence between them; (ii) a hybrid sequential mode, where the system switches itself between the two regimes and (iii) a sequential “on-demand” mode, where the system can be used in either OCT or SLO regimes for as long as required. The two sequential modes present varying degrees of trade-off between pixel-to-pixel correspondence and independent full control of parameters within each channel. Images of the optic nerve and fovea regions obtained in the simultaneous (i) and in the hybrid sequential mode (ii) are presented. PMID:24877006

Fragmentation Cross Sections of 290 and 400 MeV/nucleon 12C Beamson Elemental Targets

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

Zeitlin, C.; Guetersloh, S.; Heilbronn, L.

Charge-changing and fragment production cross sections at 0circ have been obtained for interactions of 290 MeV/nucleon and 400MeV/nucleon carbon beams with C, CH2, Al, Cu, Sn, and Pb targets. Thesebeams are relevant to cancer therapy, space radiation, and the productionof radioactive beams. We compare to previously published results using Cand CH2 targets at similar beam energies. Due to ambiguities arising fromthe presence of multiple fragments on many events, previous publicationshave reported only cross sections for B and Be fragments. In this work wehave extracted cross sections for all fragment species, using dataobtained at three distinct values of angular acceptance, supplementedmore » bydata taken with the detector stack placed off the beam axis. A simulationof the experiment with the PHITS Monte Carlo code shows fair agreementwith the data obtained with the large acceptance detectors, but agreementis poor at small acceptance. The measured cross sections are alsocompared to the predictions of the one-dimensional cross section modelsEPAX2 and NUCFRG2; the latter is presently used in NASA's space radiationtransport calculations. Though PHITS and NUCFRG2 reproduce thecharge-changing cross sections with reasonable accuracy, none of themodels is able to accurately predict the fragment cross sections for allfragment species and target materials.« less

Evolution of Holocene tidal systems along the Dutch coast: effects of rivers, coastal boundary conditions, eco-engineering species, inherited relief and human interference

NASA Astrophysics Data System (ADS)

Haas, T. D.; Pierik, H. J.; van der Spek, A.; Cohen, K.; van Maanen, B.; Kleinhans, M. G.

2016-12-01

Estuaries and tidal basins are partly enclosed coastal bodies of water with a free connection to the open sea at their tidal inlet and with no to marginal riverine input (tidal basins) or substantial riverine input (estuaries). Their tidal inlets can only remain open over Holocene timescales when (1) the formation of accommodation space exceeds infilling or (2) the inlet system is in dynamic equilibrium (sediment input equals output). Physical and numerical modelling suggest that estuaries and tidal basins develop toward a dynamic equilibrium under constant boundary conditions and remain open over long timescales, whereas many natural estuaries and tidal basins have filled up and were closed off or became deltas during the Holocene. This raises the question if and how tidal inlets can remain open over long timescales? And what is the effect of river inflow and sediment supply thereon? Here we compare the Holocene evolution of tidal systems along the Dutch coast to empirically identify the most important factors that control their long-term evolution. Along the coast of the Netherlands estuaries and tidal basins were formed during the middle Holocene driven by rapid relative sea-level rise and during the late Holocene driven by natural and human-induced subsidence in coastal plain peatlands. During the Holocene tidal inlets connected to rivers (estuaries) were able to persist and attain dynamic equilibrium while tidal basins without or with a very marginal riverine inflow were unstable and closed off under abundant sediment supply. There are many examples of long-lived tidal inlets that rapidly closed off after upstream river avulsion leading to a decrease and finally loss of riverine input. Long-term net import of sediment from the sea into Dutch tidal basins is favoured by strong, flood-dominated, tidal asymmetry along the Dutch coast, the shallow sand-rich floor of the North Sea and the abundance of mud in the coastal area supplied by the Rhine and Meuse rivers. While sandy tidal basins may obtain dynamic equilibrium and remain open over long timescales, we hypothesize that an abundance of mud and eco-engineering species often culminates in continuous basin filling with fine sediment and the growth of intertidal and supratidal areas, eventually resulting in closure of the basin.

Statistical analysis of experimental multifragmentation events in 64Zn+112Sn at 40 MeV/nucleon

NASA Astrophysics Data System (ADS)

Lin, W.; Zheng, H.; Ren, P.; Liu, X.; Huang, M.; Wada, R.; Chen, Z.; Wang, J.; Xiao, G. Q.; Qu, G.

2018-04-01

A statistical multifragmentation model (SMM) is applied to the experimentally observed multifragmentation events in an intermediate heavy-ion reaction. Using the temperature and symmetry energy extracted from the isobaric yield ratio (IYR) method based on the modified Fisher model (MFM), SMM is applied to the reaction 64Zn+112Sn at 40 MeV/nucleon. The experimental isotope distribution and mass distribution of the primary reconstructed fragments are compared without afterburner and they are well reproduced. The extracted temperature T and symmetry energy coefficient asym from SMM simulated events, using the IYR method, are also consistent with those from the experiment. These results strongly suggest that in the multifragmentation process there is a freezeout volume, in which the thermal and chemical equilibrium is established before or at the time of the intermediate-mass fragments emission.

Trade-off between information and disturbance in qubit thermometry

NASA Astrophysics Data System (ADS)

Seveso, Luigi; Paris, Matteo G. A.

2018-03-01

We address the trade-off between information and disturbance in qubit thermometry from the perspective of quantum estimation theory. Given a quantum measurement, we quantify information via the Fisher information of the measurement and disturbance via four different figures of merit, which capture different aspects (statistical, thermodynamical, geometrical) of the trade-off. For each disturbance measure, the efficient measurements, i.e., the measurements that introduce a disturbance not greater than any other measurement extracting the same amount of information, are determined explicitly. The family of efficient measurements varies with the choice of the disturbance measure. On the other hand, commutativity between the elements of the probability operator-valued measure (POVM) and the equilibrium state of the thermometer is a necessary condition for efficiency with respect to any figure of disturbance.

Hepatic sinusoid is not well-stirred: estimation of the degree of axial mixing by analysis of lobular concentration gradients formed during uptake of thyroxine by the perfused rat liver

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

Weisiger, R.A.; Mendel, C.M.; Cavalieri, R.R.

1986-03-01

Two general models have been proposed for predicting the effects of metabolism, protein binding, and plasma flow on the removal of drugs by the liver. These models differ in the degree of plasma mixing assumed to exist within each hepatic sinusoid. The venous equilibrium model treats the sinusoid as a single well-stirred compartment, whereas the sinusoidal model effectively breaks up the sinusoid into a large number of sequentially perfused compartments which do not exchange their contents except through plasma flow. As a consequence, the sinusoidal model, but not the venous equilibrium model, predicts that the concentration of highly extracted drugsmore » will decline as the plasma flows through the hepatic lobule. To determine which of these alternative models best describes the hepatic uptake process, we looked for evidence that concentration gradients are formed during the uptake of (/sup 125/I)thyroxine by the perfused rat liver. Autoradiography of tissue slices after perfusion of the portal vein at physiologic flow rates with protein-free buffer containing (/sup 125/I)thyroxine demonstrated a rapid exponential fall in grain density with distance from the portal venule, declining by half for each 8% of the mean length of the sinusoid. Reversing the direction of perfusate flow reversed the direction of the autoradiographic gradients, indicating that they primarily reflect differences in the concentration of thyroxine within the hepatic sinusoids rather than differences in the uptake capacity of portal and central hepatocytes. Analysis of the data using models in which each sinusoid was represented by different numbers of sequentially perfused compartments (1-20) indicated that at least eight compartments were necessary to account for the magnitude of the gradients seen.« less

Modeling free energy availability from Hadean hydrothermal systems to the first metabolism.

PubMed

Simoncini, E; Russell, M J; Kleidon, A

2011-12-01

Off-axis Hydrothermal Systems (HSs) are seen as the possible setting for the emergence of life. As the availability of free energy is a general requirement to drive any form of metabolism, we ask here under which conditions free energy generation by geologic processes is greatest and relate these to the conditions found at off-axis HSs. To do so, we present a conceptual model in which we explicitly capture the energetics of fluid motion and its interaction with exothermic reactions to maintain a state of chemical disequilibrium. Central to the interaction is the temperature at which the exothermic reactions take place. This temperature not only sets the equilibrium constant of the chemical reactions and thereby the distance of the actual state to chemical equilibrium, but these reactions also shape the temperature gradient that drives convection and thereby the advection of reactants to the reaction sites and the removal of the products that relate to geochemical free energy generation. What this conceptual model shows is that the positive feedback between convection and the chemical kinetics that is found at HSs favors a greater rate of free energy generation than in the absence of convection. Because of the lower temperatures and because the temperature of reactions is determined more strongly by these dynamics rather than an external heat flux, the conditions found at off-axis HSs should result in the greatest rates of geochemical free energy generation. Hence, we hypothesize from these thermodynamic considerations that off-axis HSs seem most conducive for the emergence of protometabolic pathways as these provide the greatest, abiotic generation rates of chemical free energy.

Fragment-based screening in tandem with phenotypic screening provides novel antiparasitic hits.

PubMed

Blaazer, Antoni R; Orrling, Kristina M; Shanmugham, Anitha; Jansen, Chimed; Maes, Louis; Edink, Ewald; Sterk, Geert Jan; Siderius, Marco; England, Paul; Bailey, David; de Esch, Iwan J P; Leurs, Rob

2015-01-01

Methods to discover biologically active small molecules include target-based and phenotypic screening approaches. One of the main difficulties in drug discovery is elucidating and exploiting the relationship between drug activity at the protein target and disease modification, a phenotypic endpoint. Fragment-based drug discovery is a target-based approach that typically involves the screening of a relatively small number of fragment-like (molecular weight <300) molecules that efficiently cover chemical space. Here, we report a fragment screening on TbrPDEB1, an essential cyclic nucleotide phosphodiesterase (PDE) from Trypanosoma brucei, and human PDE4D, an off-target, in a workflow in which fragment hits and a series of close analogs are subsequently screened for antiparasitic activity in a phenotypic panel. The phenotypic panel contained T. brucei, Trypanosoma cruzi, Leishmania infantum, and Plasmodium falciparum, the causative agents of human African trypanosomiasis (sleeping sickness), Chagas disease, leishmaniasis, and malaria, respectively, as well as MRC-5 human lung cells. This hybrid screening workflow has resulted in the discovery of various benzhydryl ethers with antiprotozoal activity and low toxicity, representing interesting starting points for further antiparasitic optimization. © 2014 Society for Laboratory Automation and Screening.

Developments in SPR Fragment Screening.

PubMed

Chavanieu, Alain; Pugnière, Martine

2016-01-01

Fragment-based approaches have played an increasing role alongside high-throughput screening in drug discovery for 15 years. The label-free biosensor technology based on surface plasmon resonance (SPR) is now sensitive and informative enough to serve during primary screens and validation steps. In this review, the authors discuss the role of SPR in fragment screening. After a brief description of the underlying principles of the technique and main device developments, they evaluate the advantages and adaptations of SPR for fragment-based drug discovery. SPR can also be applied to challenging targets such as membrane receptors and enzymes. The high-level of immobilization of the protein target and its stability are key points for a relevant screening that can be optimized using oriented immobilized proteins and regenerable sensors. Furthermore, to decrease the rate of false negatives, a selectivity test may be performed in parallel on the main target bearing the binding site mutated or blocked with a low-off-rate ligand. Fragment-based drug design, integrated in a rational workflow led by SPR, will thus have a predominant role for the next wave of drug discovery which could be greatly enhanced by new improvements in SPR devices.

Sequential Adaptive Multi-Modality Target Detection and Classification Using Physics Based Models

DTIC Science & Technology

2006-09-01

estimation," R. Raghuram, R. Raich and A.O. Hero, IEEE Intl. Conf. on Acoustics, Speech , and Signal Processing, Toulouse France, June 2006, <http...can then be solved using off-the-shelf classifiers such as radial basis functions, SVM, or kNN classifier structures. When applied to mine detection we...stage waveform selection for adaptive resource constrained state estimation," 2006 IEEE Intl. Conf. on Acoustics, Speech , and Signal Processing

Multi-period equilibrium/near-equilibrium in electricity markets based on locational marginal prices

NASA Astrophysics Data System (ADS)

Garcia Bertrand, Raquel

In this dissertation we propose an equilibrium procedure that coordinates the point of view of every market agent resulting in an equilibrium that simultaneously maximizes the independent objective of every market agent and satisfies network constraints. Therefore, the activities of the generating companies, consumers and an independent system operator are modeled: (1) The generating companies seek to maximize profits by specifying hourly step functions of productions and minimum selling prices, and bounds on productions. (2) The goals of the consumers are to maximize their economic utilities by specifying hourly step functions of demands and maximum buying prices, and bounds on demands. (3) The independent system operator then clears the market taking into account consistency conditions as well as capacity and line losses so as to achieve maximum social welfare. Then, we approach this equilibrium problem using complementarity theory in order to have the capability of imposing constraints on dual variables, i.e., on prices, such as minimum profit conditions for the generating units or maximum cost conditions for the consumers. In this way, given the form of the individual optimization problems, the Karush-Kuhn-Tucker conditions for the generating companies, the consumers and the independent system operator are both necessary and sufficient. The simultaneous solution to all these conditions constitutes a mixed linear complementarity problem. We include minimum profit constraints imposed by the units in the market equilibrium model. These constraints are added as additional constraints to the equivalent quadratic programming problem of the mixed linear complementarity problem previously described. For the sake of clarity, the proposed equilibrium or near-equilibrium is first developed for the particular case considering only one time period. Afterwards, we consider an equilibrium or near-equilibrium applied to a multi-period framework. This model embodies binary decisions, i.e., on/off status for the units, and therefore optimality conditions cannot be directly applied. To avoid limitations provoked by binary variables, while retaining the advantages of using optimality conditions, we define the multi-period market equilibrium using Benders decomposition, which allows computing binary variables through the master problem and continuous variables through the subproblem. Finally, we illustrate these market equilibrium concepts through several case studies.

Production and characterization of anti-(mucin MUC1) single-domain antibody in tobacco (Nicotiana tabacum cultivar Xanthi).

PubMed

Ismaili, Ahmad; Jalali-Javaran, Mokhtar; Rasaee, Mohammad J; Rahbarizadeh, Fatemeh; Forouzandeh-Moghadam, Mehdi; Memari, Hamid Rajabi

2007-05-01

Members of the Camelidae (camels, dromedaries, llamas, alpacas, guanacos and vicunas) are known to produce Igs (immunoglobulins) devoid of light chains and CH1s (constant heavy-chain domains). The antigen-specific binding fragments of these heavy-chain antibodies therefore comprise one single domain (the so-called 'VHH') and are of great importance in biotechnological applications. To evaluate the expression and biological activity of sdAbs (single-domain antibodies) in plants, which, on account of their small size and antigen-recognition properties, would have a major impact on antibody-engineering strategies, we constructed a pBI121-VHH gene encoding the recombinant sdAb fragments with specificity for a cancer-associated mucin, MUC1. Analysis of transgenic tobacco (Nicotiana tabacum cultivar Xanthi) plants by PCR and Western blotting demonstrated the expression of sdAb, while ELISA results with various MUC1 antigens and immunocytochemistry with cancerous cell lines confirmed that the activity of these molecules compared favourably with that of the parent recombinant antibodies. Protein purification was achieved by using sequential (NH4)2SO4 precipitation, gel filtration and immunoaffinity chromatography. Analysis of the purified VHH by ELISA indicated that the purified antibody fragments were able to react successfully with a MUC1-related peptide. These results reaffirm that the tobacco plant is a suitable host for the production of correctly folded VHH antibody fragments with diagnostic and therapeutic applications.

Integrated quantification and identification of aldehydes and ketones in biological samples.

PubMed

Siegel, David; Meinema, Anne C; Permentier, Hjalmar; Hopfgartner, Gérard; Bischoff, Rainer

2014-05-20

The identification of unknown compounds remains to be a bottleneck of mass spectrometry (MS)-based metabolomics screening experiments. Here, we present a novel approach which facilitates the identification and quantification of analytes containing aldehyde and ketone groups in biological samples by adding chemical information to MS data. Our strategy is based on rapid autosampler-in-needle-derivatization with p-toluenesulfonylhydrazine (TSH). The resulting TSH-hydrazones are separated by ultrahigh-performance liquid chromatography (UHPLC) and detected by electrospray ionization-quadrupole-time-of-flight (ESI-QqTOF) mass spectrometry using a SWATH (Sequential Window Acquisition of all Theoretical Fragment-Ion Spectra) data-independent high-resolution mass spectrometry (HR-MS) approach. Derivatization makes small, poorly ionizable or retained analytes amenable to reversed phase chromatography and electrospray ionization in both polarities. Negatively charged TSH-hydrazone ions furthermore show a simple and predictable fragmentation pattern upon collision induced dissociation, which enables the chemo-selective screening for unknown aldehydes and ketones via a signature fragment ion (m/z 155.0172). By means of SWATH, targeted and nontargeted application scenarios of the suggested derivatization route are enabled in the frame of a single UHPLC-ESI-QqTOF-HR-MS workflow. The method's ability to simultaneously quantify and identify molecules containing aldehyde and ketone groups is demonstrated using 61 target analytes from various compound classes and a (13)C labeled yeast matrix. The identification of unknowns in biological samples is detailed using the example of indole-3-acetaldehyde.

Fuel accumulations in Piedmont loblolly pine plantations

Treesearch

Ernst V. Brender; W. Henry McNab; Shelton Williams

1976-01-01

Weight of minor vegetation under unthinned loblolly pine (Pinus taeda L.) plantations was closely related to stand age and basal area stocking. Weight of this vegetation peaked 3 years after clearcutting and planting, then diminished as the pine canopy became denser. Forest floor weight increased steadily through age 23, when it began to level off. Equilibrium forest...

Forest product trade impacts of an invasive species: modeling structure and intervention trade-offs

Treesearch

Jeffrey Prestemon; Shushuai Zhu; James A. Turner; Joseph Buongiorno; Ruhong Li

2006-01-01

Asian gypsy and nun moth introductions into the United States, possibly arriving on imported Siberian coniferous logs, threaten domestic forests and product markers and could have global market consequences. We simulate, using the Global Forest Products Model (a spatial equilibrium model of the world forest sector), the consequences under current policies of a...

Numerical simulation of transport and sequential biodegradation of chlorinated aliphatic hydrocarbons using CHAIN_2D

NASA Astrophysics Data System (ADS)

Schaerlaekens, J.; Mallants, D.; Imûnek, J.; van Genuchten, M. Th.; Feyen, J.

1999-12-01

Microbiological degradation of perchloroethylene (PCE) under anaerobic conditions follows a series of chain reactions, in which, sequentially, trichloroethylene (TCE), cis-dichloroethylene (c-DCE), vinylchloride (VC) and ethene are generated. First-order degradation rate constants, partitioning coefficients and mass exchange rates for PCE, TCE, c-DCE and VC were compiled from the literature. The parameters were used in a case study of pump-and-treat remediation of a PCE-contaminated site near Tilburg, The Netherlands. Transport, non-equilibrium sorption and biodegradation chain processes at the site were simulated using the CHAIN_2D code without further calibration. The modelled PCE compared reasonably well with observed PCE concentrations in the pumped water. We also performed a scenario analysis by applying several increased reductive dechlorination rates, reflecting different degradation conditions (e.g. addition of yeast extract and citrate). The scenario analysis predicted considerably higher concentrations of the degradation products as a result of enhanced reductive dechlorination of PCE. The predicted levels of the very toxic compound VC were now an order of magnitude above the maximum permissible concentration levels.

Comparison of Cf-252 thin-film sources prepared by evaporation or self-transfer

DOE PAGES

Algutifan, Noor J.; Sherman, Steven R.; Alexander, Charles W.

2014-11-29

Californium-252 (Z = 98) is valued as a potent neutron source due to its spontaneous fission decay path. Thin film sources containing Cf-252 were prepared by two techniques: evaporation and self-transfer. The sources were analyzed by alpha and gamma spectroscopy. Results indicate that self-transfer sources exhibit less alpha energy straggling and energy loss than evaporative sources. Fission fragments may also self-transfer, and sources made by self-transfer may need some decay time to reach radioactive equilibrium.

Properties of true quaternary fission of nuclei with allowance for its multistep and sequential character

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

Kadmensky, S. G., E-mail: kadmensky@phys.vsu.ru; Titova, L. V.; Bulychev, A. O.

An analysis of basicmechanisms of binary and ternary fission of nuclei led to the conclusion that true ternary and quaternary fission of nuclei has a sequential two-step (three-step) character, where, at the first step, a fissile nucleus emits a third light particle (third and fourth light particles) under shakeup effects associated with a nonadiabatic character of its collective deformation motion, whereupon the residual nucleus undergoes fission to two fission fragments. Owing to this, the formulas derived earlier for the widths with respect to sequential two- and three-step decays of nuclei in constructing the theory of two-step twoproton decays and multistepmore » decays in chains of genetically related nuclei could be used to describe the relative yields and angular and energy distributions of third and fourth light particles emitted in (α, α), (t, t), and (α, t) pairs upon the true quaternary spontaneous fission of {sup 252}Cf and thermal-neutron-induced fission of {sup 235}U and {sup 233}U target nuclei. Mechanisms that explain a sharp decrease in the yield of particles appearing second in time and entering into the composition of light-particle pairs that originate from true quaternary fission of nuclei in relation to the yields of analogous particles in true ternary fission of nuclei are proposed.« less

A multicenter study benchmarks software tools for label-free proteome quantification.

PubMed

Navarro, Pedro; Kuharev, Jörg; Gillet, Ludovic C; Bernhardt, Oliver M; MacLean, Brendan; Röst, Hannes L; Tate, Stephen A; Tsou, Chih-Chiang; Reiter, Lukas; Distler, Ute; Rosenberger, George; Perez-Riverol, Yasset; Nesvizhskii, Alexey I; Aebersold, Ruedi; Tenzer, Stefan

2016-11-01

Consistent and accurate quantification of proteins by mass spectrometry (MS)-based proteomics depends on the performance of instruments, acquisition methods and data analysis software. In collaboration with the software developers, we evaluated OpenSWATH, SWATH 2.0, Skyline, Spectronaut and DIA-Umpire, five of the most widely used software methods for processing data from sequential window acquisition of all theoretical fragment-ion spectra (SWATH)-MS, which uses data-independent acquisition (DIA) for label-free protein quantification. We analyzed high-complexity test data sets from hybrid proteome samples of defined quantitative composition acquired on two different MS instruments using different SWATH isolation-window setups. For consistent evaluation, we developed LFQbench, an R package, to calculate metrics of precision and accuracy in label-free quantitative MS and report the identification performance, robustness and specificity of each software tool. Our reference data sets enabled developers to improve their software tools. After optimization, all tools provided highly convergent identification and reliable quantification performance, underscoring their robustness for label-free quantitative proteomics.

Identification of substance P precursor forms in human brain tissue.

PubMed Central

Nyberg, F; le Grevés, P; Terenius, L

1985-01-01

Substance P prohormones were identified in the caudate nucleus, hypothalamus, and substantia nigra of human brain. A polypeptide fraction of acidic brain extracts was fractionated on Sephadex G-50. The lyophilized fractions were sequentially treated with trypsin and a substance P-degrading enzyme with strong preference toward the Phe7-Phe8 and Phe8-Gly9 bonds. The released substance P(1-7) fragment was isolated by ion-exchange chromatography and quantitated by a specific radioimmunoassay. Confirmation of the structure of the isolated radioimmunoassay-active fragment was achieved by electrophoresis and HPLC. By using this enzymatic/radioimmunoassay procedure, two polypeptide fractions of apparent Mr 5000 and 15,000, respectively, were identified. The latter component was the major one of the two but was estimated to account for only about 5% of total substance P radioimmunoassay activity. Because it is of the size predicted from the nucleotide sequences of cDNA for substance P prohormones in bovine brain, the Mr 15,000 component may represent the full-length prohormone. PMID:2408270

Complete structural characterization of ceramides as [M – H]− ions by multiple-stage linear ion trap mass spectrometry

PubMed Central

Hsu, Fong-Fu

2016-01-01

Ceramide is a huge lipid family consisting of diversified structures including various modifications in the fatty acyl chain and the long chain base (LCB). In this contribution, negative-ion ESI linear ion-trap multiple-stage mass spectrometric method (LIT MSn) towards complete structural determination of ceramides in ten major families characterized as the [M – H]− ions is described. Multiple sets of fragment ions reflecting the fatty acyl chain and LCB were observed in the CID MS2 spectrum, while the sequential MS3 and MS4 spectra contain structural information for locating the double bond and the functional groups, permitting realization of the fragmentation processes. Thereby, differentiation of ceramide molecules varied by chain length, the LCB (sphingosine, phytosphigosine, 6-hydroxy-sphingosine), and by the modification (α-hydroxy-, β-hydroxy-, ω-hydroxy-FA) can be achieved; and many isomeric structures in the biological specimen can be revealed in detail. PMID:27523779

Infrared laser dissociation of single megadalton polymer ions in a gated electrostatic ion trap: the added value of statistical analysis of individual events.

PubMed

Halim, Mohammad A; Clavier, Christian; Dagany, Xavier; Kerleroux, Michel; Dugourd, Philippe; Dunbar, Robert C; Antoine, Rodolphe

2018-05-07

In this study, we report the unimolecular dissociation mechanism of megadalton SO 3 -containing poly(2-acrylamido-2-methyl-1-propanesulfonic acid) (PAMPS) polymer cations and anions with the aid of infrared multiphoton dissociation coupled to charge detection ion trap mass spectrometry. A gated electrostatic ion trap ("Benner trap") is used to store and detect single gaseous polymer ions generated by positive and negative polarity in an electrospray ionization source. The trapped ions are then fragmented due to the sequential absorption of multiple infrared photons produced from a continuous-wave CO 2 laser. Several fragmentation pathways having distinct signatures are observed. Highly charged parent ions characteristically adopt a distinctive "stair-case" pattern (assigned to the "fission" process) whereas low charge species take on a "funnel like" shape (assigned to the "evaporation" process). Also, the log-log plot of the dissociation rate constants as a function of laser intensity between PAMPS positive and negative ions is significantly different.

Impact of power index, hydroureteronephrosis, stone size, and composition on the efficacy of in situ boosted ESWL for primary proximal ureteral calculi.

PubMed

Singh, I; Gupta, N P; Hemal, A K; Dogra, P N; Ansari, M S; Seth, A; Aron, M

2001-07-01

The efficacy, safety, feasibility, and outcome of in situ treatment applied to select proximal ureteral calculi was assessed and analyzed with a view to avoiding auxiliary interventions and providing high clearance rates in the shortest possible time. We studied the impact of several clinically important variables, including power index, degree of hydroureteronephrosis (HDUN), stone size, and composition on the efficacy of sequential in situ boosted extracorporeal shock wave lithotripsy (ESWL) in a select group. The power index requirement for the in situ boosted protocol and the impact of the stone size/composition, degree of HDUN, and clearance rates were also analyzed. An in situ (no instrumentation) boosted protocol was applied to 130 primary unimpacted proximal ureteral calculi with no prior intervention. A typical session with the Siemens Lithostar Plus comprised 3000 shock waves, in installments of 500, deployed at a power setting of 1 to 4 kV with a gradual stepwise escalation. Sequential boosted additional sessions of ESWL were administered on days 2, 7, and 14, tailored to the degree of fragmentation, clearance status, and amount of residual stone bulk. Several parameters (shock waves, kilovolts used, fluoroscopy time, number of sessions, stone size, composition, fragmentation, clearance, and HDUN) were recorded and the results analyzed statistically. The results were excellent in 83.8%, with a mean duration to complete clearance of 11.3 days. In situ ESWL failed in 7.69%, and the auxiliary intervention rate was 10.7%. Pre-ESWL HDUN was present in 78.3%, the mean power index was 184.6/session/case, and the average stone burden was 8.9 mm(2). Calcium oxalate monohydrate was the most common stone (56%). Renal colic was the most common side effect observed. The power index, fragmentation at the first session, and stone size were found to be the most favorable significant variables affecting stone clearance. The degree of HDUN, number of sessions, and stone composition did not significantly impact the clearance rates. In situ boosted ESWL should be the first-line therapeutic modality in select unimpacted primary proximal ureteral stones.

Combustion diagnosis for analysis of solid propellant rocket abort hazards: Role of spectroscopy

NASA Astrophysics Data System (ADS)

Gill, W.; Cruz-Cabrera, A. A.; Donaldson, A. B.; Lim, J.; Sivathanu, Y.; Bystrom, E.; Haug, A.; Sharp, L.; Surmick, D. M.

2014-11-01

Solid rocket propellant plume temperatures have been measured using spectroscopic methods as part of an ongoing effort to specify the thermal-chemical-physical environment in and around a burning fragment of an exploded solid rocket at atmospheric pressures. Such specification is needed for launch safety studies where hazardous payloads become involved with large fragments of burning propellant. The propellant burns in an off-design condition producing a hot gas flame loaded with burning metal droplets. Each component of the flame (soot, droplets and gas) has a characteristic temperature, and it is only through the use of spectroscopy that their temperature can be independently identified.

Sequential cancer immunotherapy: targeted activity of dimeric TNF and IL-8

PubMed Central

Adrian, Nicole; Siebenborn, Uta; Fadle, Natalie; Plesko, Margarita; Fischer, Eliane; Wüest, Thomas; Stenner, Frank; Mertens, Joachim C.; Knuth, Alexander; Ritter, Gerd; Old, Lloyd J.; Renner, Christoph

2009-01-01

Polymorphonuclear neutrophils (PMNs) are potent effectors of inflammation and their attempts to respond to cancer are suggested by their systemic, regional and intratumoral activation. We previously reported on the recruitment of CD11b+ leukocytes due to tumor site-specific enrichment of TNF activity after intravenous administration of a dimeric TNF immunokine with specificity for fibroblast activation protein (FAP). However, TNF-induced chemo-attraction and extravasation of PMNs from blood into the tumor is a multistep process essentially mediated by interleukin 8. With the aim to amplify the TNF-induced and IL-8-mediated chemotactic response, we generated immunocytokines by N-terminal fusion of a human anti-FAP scFv fragment with human IL-8 (IL-872) and its N-terminally truncated form IL-83-72. Due to the dramatic difference in chemotaxis induction in vitro, we favored the mature chemokine fused to the anti-FAP scFv for further investigation in vivo. BALB/c nu/nu mice were simultaneously xenografted with FAP-positive or -negative tumors and extended chemo-attraction of PMNs was only detectable in FAP-expressing tissue after intravenous administration of the anti-FAP scFv-IL-872 construct. As TNF-activated PMNs are likewise producers and primary targets for IL-8, we investigated the therapeutic efficacy of co-administration of both effectors: Sequential application of scFv-IL-872 and dimeric IgG1-TNF fusion proteins significantly enhanced anti-tumor activity when compared either to a single effector treatment regimen or sequential application of non-targeted cytokines, indicating that the tumor-restricted sequential application of IL-872 and TNF is a promising approach for cancer therapy. PMID:19267427

Effects of subtle differences in ligand constitution and conformation in metallo-supramolecular self-assembled polygons.

PubMed

Brusilowskij, Boris; Dzyuba, Egor V; Troff, Ralf W; Schalley, Christoph A

2011-12-07

3,3'-Bis(pyridin-[n]-ylethynyl)biphenyl (n = 3, 4) and the corresponding 2,2'-bipyridines assemble with (dppp)Pt(II) triflate into metallo-supramolecular polygons. Depending on the position of the terminal pyridine N atoms, the assembly reaction leads to different equilibrium products. With the slow ligand exchange on Pt(II) complexes, the equilibrium is reached on a many-hour time-scale. During the assembly process, larger polygons form under kinetic control. This was confirmed by time-dependent (1)H and (31)P NMR spectroscopy in line with complementary ESI mass spectrometric experiments. The constitutional difference in the pyridine N-atom position is reflected in the tandem mass spectra of the complex ions. In addition, a highly specific fragmentation process of mass-selected M(3)L(3) ions was observed, which proceeds through a ring contraction yielding smaller M(2)L(2) ions.

The nature of the continuous non-equilibrium phase transition of Axelrod's model

NASA Astrophysics Data System (ADS)

Peres, Lucas R.; Fontanari, José F.

2015-09-01

Axelrod's model in the square lattice with nearest-neighbors interactions exhibits culturally homogeneous as well as culturally fragmented absorbing configurations. In the case in which the agents are characterized by F = 2 cultural features and each feature assumes k states drawn from a Poisson distribution of parameter q, these regimes are separated by a continuous transition at qc = 3.10 +/- 0.02 . Using Monte Carlo simulations and finite-size scaling we show that the mean density of cultural domains μ is an order parameter of the model that vanishes as μ ∼ (q - q_c)^β with β = 0.67 +/- 0.01 at the critical point. In addition, for the correlation length critical exponent we find ν = 1.63 +/- 0.04 and for Fisher's exponent, τ = 1.76 +/- 0.01 . This set of critical exponents places the continuous phase transition of Axelrod's model apart from the known universality classes of non-equilibrium lattice models.

Defying the activity-stability trade-off in enzymes: taking advantage of entropy to enhance activity and thermostability.

PubMed

Siddiqui, Khawar Sohail

2017-05-01

The biotechnological applications of enzymes are limited due to the activity-stability trade-off, which implies that an increase in activity is accompanied by a concomitant decrease in protein stability. This premise is based on thermally adapted homologous enzymes where cold-adapted enzymes show high intrinsic activity linked to enhanced thermolability. In contrast, thermophilic enzymes show low activity around ambient temperatures. Nevertheless, genetically and chemically modified enzymes are beginning to show that the activity-stability trade-off can be overcome. In this review, the origin of the activity-stability trade-off, the thermodynamic basis for enhanced activity and stability, and various approaches for escaping the activity-stability trade-off are discussed. The role of entropy in enhancing both the activity and the stability of enzymes is highlighted with a special emphasis placed on the involvement of solvent water molecules. This review is concluded with suggestions for further research, which underscores the implications of these findings in the context of productivity curves, the Daniel-Danson equilibrium model, catalytic antibodies, and life on cold planets.

The Dynamics of Massive Starless Cores with ALMA

NASA Astrophysics Data System (ADS)

Tan, Jonathan C.; Kong, Shuo; Butler, Michael J.; Caselli, Paola; Fontani, Francesco

2013-12-01

How do stars that are more massive than the Sun form, and thus how is the stellar initial mass function (IMF) established? Such intermediate- and high-mass stars may be born from relatively massive pre-stellar gas cores, which are more massive than the thermal Jeans mass. The turbulent core accretion model invokes such cores as being in approximate virial equilibrium and in approximate pressure equilibrium with their surrounding clump medium. Their internal pressure is provided by a combination of turbulence and magnetic fields. Alternatively, the competitive accretion model requires strongly sub-virial initial conditions that then lead to extensive fragmentation to the thermal Jeans scale, with intermediate- and high-mass stars later forming by competitive Bondi-Hoyle accretion. To test these models, we have identified four prime examples of massive (~100 M ⊙) clumps from mid-infrared extinction mapping of infrared dark clouds. Fontani et al. found high deuteration fractions of N2H+ in these objects, which are consistent with them being starless. Here we present ALMA observations of these four clumps that probe the N2D+ (3-2) line at 2.''3 resolution. We find six N2D+ cores and determine their dynamical state. Their observed velocity dispersions and sizes are broadly consistent with the predictions of the turbulent core model of self-gravitating, magnetized (with Alfvén Mach number mA ~ 1) and virialized cores that are bounded by the high pressures of their surrounding clumps. However, in the most massive cores, with masses up to ~60 M ⊙, our results suggest that moderately enhanced magnetic fields (so that mA ~= 0.3) may be needed for the structures to be in virial and pressure equilibrium. Magnetically regulated core formation may thus be important in controlling the formation of massive cores, inhibiting their fragmentation, and thus helping to establish the stellar IMF.

Development of Potent Antiviral Drugs Inspired by Viral Hexameric DNA-Packaging Motors with Revolving Mechanism

PubMed Central

Pi, Fengmei; Zhao, Zhengyi; Chelikani, Venkata; Yoder, Kristine; Kvaratskhelia, Mamuka

2016-01-01

The intracellular parasitic nature of viruses and the emergence of antiviral drug resistance necessitate the development of new potent antiviral drugs. Recently, a method for developing potent inhibitory drugs by targeting biological machines with high stoichiometry and a sequential-action mechanism was described. Inspired by this finding, we reviewed the development of antiviral drugs targeting viral DNA-packaging motors. Inhibiting multisubunit targets with sequential actions resembles breaking one bulb in a series of Christmas lights, which turns off the entire string. Indeed, studies on viral DNA packaging might lead to the development of new antiviral drugs. Recent elucidation of the mechanism of the viral double-stranded DNA (dsDNA)-packaging motor with sequential one-way revolving motion will promote the development of potent antiviral drugs with high specificity and efficiency. Traditionally, biomotors have been classified into two categories: linear and rotation motors. Recently discovered was a third type of biomotor, including the viral DNA-packaging motor, beside the bacterial DNA translocases, that uses a revolving mechanism without rotation. By analogy, rotation resembles the Earth's rotation on its own axis, while revolving resembles the Earth's revolving around the Sun (see animations at http://rnanano.osu.edu/movie.html). Herein, we review the structures of viral dsDNA-packaging motors, the stoichiometries of motor components, and the motion mechanisms of the motors. All viral dsDNA-packaging motors, including those of dsDNA/dsRNA bacteriophages, adenoviruses, poxviruses, herpesviruses, mimiviruses, megaviruses, pandoraviruses, and pithoviruses, contain a high-stoichiometry machine composed of multiple components that work cooperatively and sequentially. Thus, it is an ideal target for potent drug development based on the power function of the stoichiometries of target complexes that work sequentially. PMID:27356896

Fragmentation pathways of tungsten hexacarbonyl clusters upon electron ionization

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

Neustetter, M.; Jabbour Al Maalouf, E.; Denifl, S., E-mail: Stephan.Denifl@uibk.ac.at, E-mail: plimaovieira@fct.unl.pt

2016-08-07

Electron ionization of neat tungsten hexacarbonyl (W(CO){sub 6}) clusters has been investigated in a crossed electron-molecular beam experiment coupled with a mass spectrometer system. The molecule is used for nanofabrication processes through electron beam induced deposition and ion beam induced deposition techniques. Positive ion mass spectra of W(CO){sub 6} clusters formed by electron ionization at 70 eV contain the ion series of the type W(CO){sub n}{sup +} (0 ≤ n ≤ 6) and W{sub 2}(CO){sub n}{sup +} (0 ≤ n ≤ 12). In addition, a series of peaks are observed and have been assigned to WC(CO){sub n}{sup +} (0 ≤more » n ≤ 3) and W{sub 2}C(CO){sub n}{sup +} (0 ≤ n ≤ 10). A distinct change of relative fragment ion intensity can be observed for clusters compared to the single molecule. The characteristic fragmentation pattern obtained in the mass spectra can be explained by a sequential decay of the ionized organometallic, which is also supported by the study of the clusters when embedded in helium nanodroplets. In addition, appearance energies for the dissociative ionization channels for singly charged ions have been estimated from experimental ion efficiency curves.« less

Critical reappraisal of embryo quality as a predictive parameter for pregnancy outcome: a pilot study

PubMed Central

Campo, R.; Binda, M.M.; Van Kerkhoven, G.; Frederickx, V.; Serneels, A.; Roziers, P.; Lopes, A.S.; Gordts, S.; Puttemans, P.; Gordts, S.

2010-01-01

Aim of the study: Pilot study to analyse the efficacy and embryo morphology using a new human embryo culture medium (GM501) versus the conventional used medium (ISM1). Methods: Over a four-month period, all patients at the Leuven Institute of Fertility and Embryology (LIFE) were randomly allocated to have their embryos cultured in either the standard sequential culture medium ISM1 (control) or in a new universal medium (GM501) (study group). Primary outcome parameters were clinical pregnancy and live birth rate. The secondary outcome parameter was the correlation of embryo fragmentation rate with pregnancy outcome. Results: We did not observe any differences between the ISM1 control group and GM501 study group with regard to fertilization, pregnancy, implantation rates, ongoing pregnancy, and babies born. The number of embryos with a minimal fragmentation rate (less than 30%) was significantly higher in the GM501 study group. Conclusion: Although a significant higher embryo fragmentation rate was seen in In vitro culture of embryos in GM501, pregnancy outcome results were comparable to those of embryos cultured in ISM1. According to our results the value of embryo morphological criteria as a parameter for pregnancy outcome should be examined and discussed again. PMID:25009716

Visualizing non-equilibrium lithiation of spinel oxide via in situ transmission electron microscopy

DOE PAGES

He, Kai; Zhang, Sen; Li, Jing; ...

2016-05-09

In this study, spinel transition metal oxides are an important class of materials that are being considered as electrodes for lithium-ion batteries, due to their low cost and high theoretical capacity. The lithiation of these compounds is known to undergo a two-step reaction, whereby intercalation and conversion occur in a sequential fashion. These two reactions are known to have distinct reaction dynamics, but it is unclear how the kinetics of these processes affect the overall electrochemical response. Here, we explore the lithiation of nanosized magnetite (F e3O 4) by employing a new strain-sensitive, bright-field scanning transmission electron microscopy approach.

A Fragment-Cloud Model for Breakup of Asteroids with Varied Internal Structures

NASA Technical Reports Server (NTRS)

Wheeler, Lorien; Mathias, Donovan; Stokan, Ed; Brown, Peter

2016-01-01

As an asteroid descends toward Earth, it deposits energy in the atmosphere through aerodynamic drag and ablation. Asteroid impact risk assessments rely on energy deposition estimates to predict blast overpressures and ground damage that may result from an airburst, such as the one that occurred over Chelyabinsk, Russia in 2013. The rates and altitudes at which energy is deposited along the entry trajectory depend upon how the bolide fragments, which in turn depends upon its internal structure and composition. In this work, we have developed an analytic asteroid fragmentation model to assess the atmospheric energy deposition of asteroids with a range of structures and compositions. The modeling approach combines successive fragmentation of larger independent pieces with aggregate debris clouds released with each fragmentation event. The model can vary the number and masses of fragments produced, the amount of mass released as debris clouds, the size-strength scaling used to increase the robustness of smaller fragments, and other parameters. The initial asteroid body can be seeded with a distribution of independent fragment sizes amid a remaining debris mass to represent loose rubble pile conglomerations, can be given an outer regolith later, or can be defined as a coherent or fractured monolith. This approach enables the model to represent a range of breakup behaviors and reproduce detailed energy deposition features such as multiple flares due to successive burst events, high-altitude regolith blow-off, or initial disruption of rubble piles followed by more energetic breakup of the constituent boulders. These capabilities provide a means to investigate sensitivities of ground damage to potential variations in asteroid structure.

A Fragment-Cloud Approach for Modeling Atmospheric Breakup of Asteroids with Varied Internal Structures

NASA Astrophysics Data System (ADS)

Wheeler, Lorien; Mathias, Donovan; NASA Engineering Risk Assessment Team, NASA Asteroid Threat Assessment Project

2016-10-01

As an asteroid descends toward Earth, it deposits energy in the atmosphere through aerodynamic drag and ablation. Asteroid impact risk assessments rely on energy deposition estimates to predict blast overpressures and ground damage that may result from an airburst, such as the one that occurred over Chelyabinsk, Russia in 2013. The rates and altitudes at which energy is deposited along the entry trajectory depend upon how the bolide fragments, which in turn depends upon its internal structure and composition. In this work, an analytic asteroid fragmentation model has been developed to model the atmospheric breakup and resulting energy deposition of asteroids with a range of internal structures. The modeling approach combines successive fragmentation of larger independent pieces with aggregate debris clouds released with each fragmentation event. The model can vary the number and masses of fragments produced, the amount of mass released as debris clouds, and the size-strength scaling used to increase the robustness of smaller fragments. The initial asteroid body can be seeded with a distribution of independent fragment sizes amid a remaining debris mass to represent loose rubble pile conglomerations, or can be defined as a monolith with an outer regolith layer. This approach enables the model to represent a range of breakup behaviors and reproduce detailed energy deposition features such as multiple flares due to successive burst events, high-altitude regolith blow-off, or initial disruption of rubble piles followed by more energetic breakup of the constituent boulders. These capabilities provide a means to investigate sensitivities of ground damage to potential variations in asteroid structure.

Structure investigation of codeine drug using mass spectrometry, thermal analyses and semi-emperical molecular orbital (MO) calculations

NASA Astrophysics Data System (ADS)

Zayed, M. A.; Hawash, M. F.; Fahmey, M. A.

2006-05-01

Codeine is an analgesic with uses similar to morphine, but it has a mild sedative effect. It is preferable used as phosphate form and it is often administrated by mouth with aspirin or paracetamol. Therefore, it is important to investigate its structure to know the active groups and weak bonds responsible for its medical activity. Consequently in the present work, codeine was investigated by mass spectrometry and thermal analyses (TG, DTG and DTA) and confirming by semi-empirical MO-calculation (PM3 method) in the neutral and positively charged forms of the drug. Some results of studying the d-block element complexes of codeine were used to declare the relationship between drug structure and its chemical reactivity in vitro system. The mass spectra and thermal analyses fragmentation pathways were proposed and compared to each other to select the most suitable scheme representing the correct fragmentation of this drug. From EI mass spectra, the main primary cleavage site of the charged drug molecule is that due to β-cleavage to nitrogen atom in its skeleton. It occurs in two parallel mechanisms with the same possibility, i.e. no difference in appearance activation energy between them. In the neutral drug form the primary site cleavage is that occurs in the ether ring. Thermal analyses of the neutral form of the drug revealed the high response of the drug to the temperature variation with very fast rate. It decomposed in several sequential steps in the temperature range 200-600 °C. The initial thermal fragments are very similar to that obtained by mass spectrometric fragmentation. Therefore, comparison between mass and thermal helps in selection of the proper pathway representing the fragmentation of this drug. This comparison successfully confirmed by MOC. These calculations give the bond order, charge distribution, heat of formation and possible hybridization of some atoms in different position of the drug skeleton. This helps the successful choice of the weakest bond at which both mass and thermal fragmentation occurs. Therefore, the best fragmentation pathway of this drug is correctly selected. The effect of such fragmentation on the drug behavior in the human body can be expected as a result of comparing these data with that obtained on studying codeine metal complexes using mass and thermal fragmentation techniques.

[Revascularization of left anterior descending artery area using a skeletonized left internal mammary artery: a comparison between sequential and separate grafting].

PubMed

Shen, J Q; Ji, Q; Ding, W J; Xia, L M; Wei, L; Wang, C S

2018-03-13

Objective: To evaluate in-hospital and mid-term outcomes of sequential versus separate grafting of in situ skeletonized left internal mammary artery (LIMA) to the left coronary system in a single-center, propensity-matched study. Methods: After propensity score matching, 120 pairs of patients undergoing first, scheduled, isolated coronary artery bypass grafting (CABG) with in situ skeletonized LIMA grafting to the left anterior descending artery (LAD) territory were entered into a sequential group (sequential grafting of LIMA to the diagonal artery and then to the LAD) or a control group (separate grafting of LIMA to the LAD). The in-hospital and follow-up clinical outcomes and follow-up LIMA graft patency were compared. Results: The two propensity score-matched groups had similar in-hospital and follow-up clinical outcomes. The number of bypass conduits ranged from 3 to 6 (with a mean of 3.5), and 91.3%(219/240)of the included patients received off-pump CABG surgery. No significant differences were found between the two propensity score-matched groups in the in-hospital outcomes, including in-hospital death and the incidence of complications associated with CABG (prolonged ventilation, peroperative stroke, re-operation before discharge, and deep sternal wound infection). During follow-up, 9 patients (4 patients from the sequential group and 5 patients from the control group) died, and the all-cause mortality rate was 3.9%. No significant difference was found in the all-cause mortality rate between the 2 groups[3.4% (4/116) vs 4.3% (5/115), P =0.748]. During follow-up period, 99.1% (115/116) patency for the diagonal site and 98.3% (114/116) for the LAD site were determined by coronary computed tomographic angiography after sequential LIMA grafting, both of which were similar with graft patency of separate grafting of in situ skeletonized LIMA to the LAD. Conclusions: Revascularization of the left coronary system using a skeletonized LIMA resulted in excellent in-hospital and mid-term clinical outcomes and graft patency using sequential grafting.

Air conditioning impact on the dynamics of radon and its daughters concentration.

PubMed

Kozak, Krzysztof; Grządziel, Dominik; Połednik, Bernard; Mazur, Jadwiga; Dudzińska, Marzenna R; Mroczek, Mariusz

2014-12-01

Radon and its decay products are harmful pollutants present in indoor air and are responsible for the majority of the effective dose due to ionising radiation that people are naturally exposed to. The paper presents the results of the series of measurements of radon and its progeny (in unattached and attached fractions) as well as indoor air parameters: temperature, relative humidity, number and mass concentrations of fine aerosol particles. The measurements were carried out in the auditorium (lecture hall), which is an indoor air quality laboratory, in controlled conditions during two periods of time: when air conditioning (AC) was switched off (unoccupied auditorium) and when it was switched on (auditorium in normal use). The significant influence of AC and of students' presence on the dynamics of radon and its progeny was confirmed. A decrease in the mean value of radon and its attached progeny was found when AC was working. The mean value of radon equilibrium factor F was also lower when AC was working (0.49) than when it was off (0.61). The linear correlations were found between attached radon progeny concentration and particle number and mass concentration only when the AC was switched off. This research is being conducted with the aim to study the variability of radon equilibrium factor F which is essential to determine the effective dose due to radon and its progeny inhalation. © The Author 2013. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Near Earth asteroid orbit perturbation and fragmentation

NASA Technical Reports Server (NTRS)

Ahrens, Thomas J.; Harris, Alan W.

1992-01-01

Collisions by near earth asteroids or the nuclei of comets pose varying levels of threat to man. A relatively small object, approximately 100 meter diameter, which might be found on an impact trajectory with a populated region of the Earth, could potentially be diverted from an Earth impacting trajectory by mass driver rocket systems. For larger bodies, such systems would appear to be beyond current technology. For any size object, nuclear explosions appear to be more efficient, using either the prompt blow-off from neutron radiation, the impulse from ejecta of near-surface explosion for deflection, or as a fragmenting charge. Practical deflections of bodies with diameters of 0.1, 1, and 10 km require interception, years to decades prior to earth encounter, with explosions a few kilotons, megatons, or gigatons, respectively, of equivalent TNT energy to achieve orbital velocity changes or destruction to a level where fragments are dispersed to harmless spatial densities.

Fluorescent hydroxylamine derived from the fragmentation of PAMAM dendrimers for intracellular hypochlorite recognition.

PubMed

Wu, Te-Haw; Liu, Ching-Ping; Chien, Chih-Te; Lin, Shu-Yi

2013-08-26

Herein, a promising sensing approach based on the structure fragmentation of poly(amidoamine) (PAMAM) dendrimers for the selective detection of intracellular hypochlorite (OCl(-)) is reported. PAMAM dendrimers were easily disrupted by a cascade of oxidations in the tertiary amines of the dendritic core to produce an unsaturated hydroxylamine with blue fluorescence. Specially, the novel fluorophore was only sensitive to OCl(-), one of reactive oxygen species (ROS), resulting in an irreversible fluorescence turn-off. The fluorescent hydroxylamine was selectively oxidised by OCl(-) to form a labile oxoammonium cation that underwent further degradation. Without using any troublesomely synthetic steps, the novel sensing platform based on the fragmentation of PAMAM dendrimers, can be applied to detect OCl(-) in macrophage cells. The results suggest that the sensing approach may be useful for the detection of intracellular OCl(-) with minimal interference from biological matrixes. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

DETECTORS AND EXPERIMENTAL METHODS: Equivalent properties of single event burnout induced by different sources

NASA Astrophysics Data System (ADS)

Yang, Shi-Yu; Cao, Zhou; Da, Dao-An; Xue, Yu-Xiong

2009-05-01

The experimental results of single event burnout induced by heavy ions and 252Cf fission fragments in power MOSFET devices have been investigated. It is concluded that the characteristics of single event burnout induced by 252Cf fission fragments is consistent to that in heavy ions. The power MOSFET in the “turn-off" state is more susceptible to single event burnout than it is in the “turn-on" state. The thresholds of the drain-source voltage for single event burnout induced by 173 MeV bromine ions and 252Cf fission fragments are close to each other, and the burnout cross section is sensitive to variation of the drain-source voltage above the threshold of single event burnout. In addition, the current waveforms of single event burnouts induced by different sources are similar. Different power MOSFET devices may have different probabilities for the occurrence of single event burnout.

Azimuthal correlation and collective behavior in nucleus-nucleus collisions

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

Mali, P.; Mukhopadhyay, A., E-mail: amitabha-62@rediffmail.com; Sarkar, S.

2015-03-15

Various flow effects of nuclear and hadronic origin are investigated in nucleus-nucleus collisions. Nuclear emulsion data collected from {sup 84}Kr + Ag/Br interaction at an incident energy of 1.52 GeV per nucleon and from {sup 28}Si + Ag/Br interaction at an incident energy of 14.5 GeV per nucleon are used in the investigation. The transverse momentum distribution and the flow angle analysis show that collective behavior, like a bounce-off effect of the projectile spectators and a sidesplash effect of the target spectators, are present in our event samples. From an azimuthal angle analysis of the data we also see amore » direct flow of the projectile fragments and of the produced charged particles. On the other hand, for both data samples the target fragments exhibit a reverse flow, while the projectile fragments exhibit an elliptic flow. Relevant flow parameters are measured.« less

Small scale thermal violence experiments for combined insensitive high explosive and booster materials

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

Rae, Philip J; Bauer, Clare L; Stennett, C

A small scale cook-off experiment has been designed to provide a violence metric for both booster and IHE materials, singly and in combination. The experiment has a simple, axisymmetric geometry provided by a 10 mm internal diameter cylindrical steel confinement up to 80 mm in length. Heating is applied from one end of the sample length creating pseudo 1-D heating profile and a thermal gradient across the sample(s). At the opposite end of the confinement to the heating block, a machined groove provides a point of rupture that generates a cylindrical fragment. The displacement of the external face of themore » fragment is detected by Heterodyne Velocimetry. Proof of concept experiments are reported focusing on HMX and TATB formulations, and are described in relation to confinement, ullage and heating profile. The development of a violence metric, based upon fragment velocity records is discussed.« less

Unmelted Meteoritic Debris Collected from Eltanin Ejecta in Polarstern Cores from Expedition ANT XII/4

NASA Technical Reports Server (NTRS)

Kyte, Frank T.

2002-01-01

A total of 1.7g of unmelted meteorite particles have been recovered from FS Polarstern piston cores collected on expedition ANT XII/4 that contain ejecta from the Eltanin impact event. Most of the mass (1.2 g) is a large, single specimen that is a polymict breccia, similar in mineralogy and chemistry to howardites or the silicate fraction of mesosiderites. Most of the remaining mass is in several large individual pieces (20-75mg each) that are polymict breccias, fragments dominated by pyroxene, and an igneous rock fragment. The latter has highly fractionated REE, similar to those reported in mafic clasts from mesosiderites. Other types of specimens identified include fragments dominated by maskelynite or olivine. These pieces of the projectile probably survived impact by being blown off the back surface of the Eltanin asteroid during its impact into the Bellingshausen Sea.

Study of protein folding under native conditions by rapidly switching the hydrostatic pressure inside an NMR sample cell

PubMed Central

Charlier, Cyril; Alderson, T. Reid; Courtney, Joseph M.; Ying, Jinfa; Anfinrud, Philip

2018-01-01

In general, small proteins rapidly fold on the timescale of milliseconds or less. For proteins with a substantial volume difference between the folded and unfolded states, their thermodynamic equilibrium can be altered by varying the hydrostatic pressure. Using a pressure-sensitized mutant of ubiquitin, we demonstrate that rapidly switching the pressure within an NMR sample cell enables study of the unfolded protein under native conditions and, vice versa, study of the native protein under denaturing conditions. This approach makes it possible to record 2D and 3D NMR spectra of the unfolded protein at atmospheric pressure, providing residue-specific information on the folding process. 15N and 13C chemical shifts measured immediately after dropping the pressure from 2.5 kbar (favoring unfolding) to 1 bar (native) are close to the random-coil chemical shifts observed for a large, disordered peptide fragment of the protein. However, 15N relaxation data show evidence for rapid exchange, on a ∼100-μs timescale, between the unfolded state and unstable, structured states that can be considered as failed folding events. The NMR data also provide direct evidence for parallel folding pathways, with approximately one-half of the protein molecules efficiently folding through an on-pathway kinetic intermediate, whereas the other half fold in a single step. At protein concentrations above ∼300 μM, oligomeric off-pathway intermediates compete with folding of the native state. PMID:29666248

Nonvolatile reconfigurable sequential logic in a HfO2 resistive random access memory array.

PubMed

Zhou, Ya-Xiong; Li, Yi; Su, Yu-Ting; Wang, Zhuo-Rui; Shih, Ling-Yi; Chang, Ting-Chang; Chang, Kuan-Chang; Long, Shi-Bing; Sze, Simon M; Miao, Xiang-Shui

2017-05-25

Resistive random access memory (RRAM) based reconfigurable logic provides a temporal programmable dimension to realize Boolean logic functions and is regarded as a promising route to build non-von Neumann computing architecture. In this work, a reconfigurable operation method is proposed to perform nonvolatile sequential logic in a HfO 2 -based RRAM array. Eight kinds of Boolean logic functions can be implemented within the same hardware fabrics. During the logic computing processes, the RRAM devices in an array are flexibly configured in a bipolar or complementary structure. The validity was demonstrated by experimentally implemented NAND and XOR logic functions and a theoretically designed 1-bit full adder. With the trade-off between temporal and spatial computing complexity, our method makes better use of limited computing resources, thus provides an attractive scheme for the construction of logic-in-memory systems.

New data on the mobility of Pt emitted from catalytic converters.

PubMed

Fliegel, Daniel; Berner, Zsolt; Eckhardt, Detlef; Stüben, Doris

2004-05-01

The mobility and speciation of Pt was investigated in dust deposited in highway tunnels and in gully sediments. For this, a sequential extraction technique was used in combination with a microwave digestion procedure, followed by detection of Pt with high resolution ICP-MS. A digestion procedure using HNO(3)/HCl/H(2)O(2) was developed and its efficiency tested for environmental materials. Total Pt contents ranged from approximately 100 to 300 microg/kg. The high share of chemically mobile Pt in the tunnel dust (up to about 40%) indicates that Pt is predominantly emitted in a mobile form from the converter. The absence of a mobile fraction in the gully sediment is explained by the elution of Pt by run-off. Except for the mobile and easily mobilised fractions none of the other fractions of the sequential extraction contains Pt, neither in the dust samples nor in the gully sediment.

Sequential webcam monitoring and modeling of marine debris abundance.

PubMed

Kako, Shin'ichiro; Isobe, Atsuhiko; Kataoka, Tomoya; Yufu, Kei; Sugizono, Shuto; Plybon, Charlie; Murphy, Thomas A

2018-05-14

The amount of marine debris washed ashore on a beach in Newport, Oregon, USA was observed automatically and sequentially using a webcam system. To investigate potential causes of the temporal variability of marine debris abundance, its time series was compared with those of satellite-derived wind speeds and sea surface height off the Oregon coast. Shoreward flow induced by downwelling-favorable southerly winds increases marine debris washed ashore on the beach in winter. We also found that local sea-level rise caused by westerly winds, especially at spring tide, moved the high-tide line toward the land, so that marine debris littered on the beach was likely to re-drift into the ocean. Seasonal and sub-monthly fluctuations of debris abundance were well reproduced using a simple numerical model driven by satellite-derived wind data, with significant correlation at 95% confidence level. Copyright © 2018 Elsevier Ltd. All rights reserved.

Small satellites

NASA Technical Reports Server (NTRS)

Thomas, P.; Veverka, J.; Dermott, S.

1986-01-01

Satellites smaller than Mimas (r = 195 km) are distinguished by irregular overall shapes and by rough limb topography. Material properties and impact cratering dominate the shaping of these objects. Long fragmentation histories can produce a variety of internal structures, but so far there is no direct evidence that any small satellite is an equilibrium ellipsoid made up of noncohesive gravitationally bound rubble. One many bodies that orbit close to their primary the tidal and rotational components of surface gravity strongly affect the directions of local g and thereby affect the redistribution of regolith by mass wasting. Downslope movement of regolith is extensive on Deimos, and is probably effective on many other small satellites. It is shown that in some cases observed patterns of downslope mass wasting cold produce useful constraints on the satellite's mean density. The diversity of features seen in the few high-resolution images of small satellites currently available suggests that these objects have undergone complex histories of cratering, fragmentation, and regolith evolution.

Neutron-induced fission: properties of prompt neutron and γ rays as a function of incident energy

NASA Astrophysics Data System (ADS)

Stetcu, I.; Talou, P.; Kawano, T.

2016-06-01

We have applied the Hauser-Feshbach statistical theory, in a Monte-Carlo implementation, to the de-excitation of fission fragments, obtaining a reasonable description of the characteristics of neutrons and gamma rays emitted before beta decays toward stability. Originally implemented for the spontaneous fission of 252Cf and the neutroninduced fission of 235U and 239Pu at thermal neutron energy, in this contribution we discuss the extension of the formalism to incident neutron energies up to 20 MeV. For the emission of pre-fission neutrons, at incident energies beyond second-chance fission, we take into account both the pre-equilibrium and statistical pre-fission components. Phenomenological parameterizations of mass, charge and TKE yields are used to obtain the initial conditions for the fission fragments that subsequently decay via neutron and emissions. We illustrate this approach for 239Pu(n,f).

Thermodynamic approach to the stability of multi-phase systems. Application to the Y 2O 3–Fe system

DOE PAGES

Samolyuk, German D.; Osetskiy, Yury N.

2015-07-07

Oxide-metal systems (OMSs) are important in many practical applications, and therefore, are under extensive studies using a wide range of techniques. The most accurate theoretical approaches are based on density functional theory (DFT), which are limited to ~10 2 atoms. Multi-scale approaches, e.g., DFT+Monte Carlo, are often used to model OMSs at the atomic level. These approaches can describe qualitatively the kinetics of some processes but not the overall stability of OMSs. In this paper, we propose a thermodynamic approach to study equilibrium in multiphase systems, which can be sequentially enhanced by considering different defects and microstructures. We estimate themore » thermodynamic equilibrium by minimization the free energy of the whole multiphase system using a limited set of defects and microstructural objects for which the properties are calculated by DFT. As an example, we consider Y 2O 3+bcc Fe with vacancies in both the Y 2O 3 and bcc Fe phases, Y substitutions and O interstitials in Fe, Fe impurities and antisite defects in Y 2O 3. The output of these calculations is the thermal equilibrium concentration of all the defects for a particular temperature and composition. The results obtained confirmed the high temperature stability of yttria in iron. As a result, model development towards more accurate calculations is discussed.« less

Formation and fragmentation of quadruply charged molecular ions by intense femtosecond laser pulses.

PubMed

Yatsuhashi, Tomoyuki; Nakashima, Nobuaki

2010-07-22

We investigated the formation and fragmentation of multiply charged molecular ions of several aromatic molecules by intense nonresonant femtosecond laser pulses of 1.4 mum with a 130 fs pulse duration (up to 2 x 10(14) W cm(-2)). Quadruply charged states were produced for 2,3-benzofluorene and triphenylene molecular ion in large abundance, whereas naphthalene and 1,1'-binaphthyl resulted only in up to triply charged molecular ions. The laser wavelength was nonresonant with regard to the electronic transitions of the neutral molecules, and the degree of fragmentation was strongly correlated with the absorption of the singly charged cation radical. Little fragmentation was observed for naphthalene (off-resonant with cation), whereas heavy fragmentation was observed in the case of 1,1'-binaphthyl (resonant with cation). The degree of H(2) (2H) and 2H(2) (4H) elimination from molecular ions increased as the charge states increased in all the molecules examined. A striking difference was found between triply and quadruply charged 2,3-benzofluorene: significant suppression of molecular ions with loss of odd number of hydrogen was observed in the quadruply charged ions. The Coulomb explosion of protons in the quadruply charged state and succeeding fragmentation resulted in the formation of triply charged molecular ions with an odd number of hydrogens. The hydrogen elimination mechanism in the highly charged state is discussed.

Basketball lay-up - foot loading characteristics and the number of trials necessary to obtain stable plantar pressure variables.

PubMed

Chua, YaoHui K; Quek, Raymond K K; Kong, Pui W

2017-03-01

This study aimed (1) to profile the plantar loading characteristics when performing the basketball lay-up in a realistic setting and (2) to determine the number of trials necessary to establish a stable mean for plantar loading variables during the lay-up. Thirteen university male basketball players [age: 23.0 (1.4) years, height: 1.75 (0.05) m, mass: 68.4 (8.6) kg] performed ten successful basketball lay-ups from a stationary position. Plantar loading variables were recorded using the Novel Pedar-X in-shoe system. Loading variables including peak force, peak pressure, and pressure-time integral were extracted from eight foot regions. Performance stability of plantar loading variables during the take-off and landing steps were assessed using the sequential averaging technique and intra-class correlation coefficient (ICC). High plantar loadings were experienced at the heel during the take-off steps, and both the heel and forefoot regions upon landing. The sequential estimation technique revealed a five-eight trial range to achieve a stable mean across all plantar loading variables, whereas ICC analysis was insensitive to inter-trial differences of repeated lay-up performances. Future studies and performance evaluation protocols on plantar loading during basketball lay-ups should include at least eight trials to ensure that the measurements obtained are sufficiently stable.

Quantitative experimental modelling of fragmentation during explosive volcanism

NASA Astrophysics Data System (ADS)

Thordén Haug, Ø.; Galland, O.; Gisler, G.

2012-04-01

Phreatomagmatic eruptions results from the violent interaction between magma and an external source of water, such as ground water or a lake. This interaction causes fragmentation of the magma and/or the host rock, resulting in coarse-grained (lapilli) to very fine-grained (ash) material. The products of phreatomagmatic explosions are classically described by their fragment size distribution, which commonly follows power laws of exponent D. Such descriptive approach, however, considers the final products only and do not provide information on the dynamics of fragmentation. The aim of this contribution is thus to address the following fundamental questions. What are the physics that govern fragmentation processes? How fragmentation occurs through time? What are the mechanisms that produce power law fragment size distributions? And what are the scaling laws that control the exponent D? To address these questions, we performed a quantitative experimental study. The setup consists of a Hele-Shaw cell filled with a layer of cohesive silica flour, at the base of which a pulse of pressurized air is injected, leading to fragmentation of the layer of flour. The fragmentation process is monitored through time using a high-speed camera. By varying systematically the air pressure (P) and the thickness of the flour layer (h) we observed two morphologies of fragmentation: "lift off" where the silica flour above the injection inlet is ejected upwards, and "channeling" where the air pierces through the layer along sub-vertical conduit. By building a phase diagram, we show that the morphology is controlled by P/dgh, where d is the density of the flour and g is the gravitational acceleration. To quantify the fragmentation process, we developed a Matlab image analysis program, which calculates the number and sizes of the fragments, and so the fragment size distribution, during the experiments. The fragment size distributions are in general described by power law distributions of exponents D. This procedure allows, for the first time, to determine the scaling laws that govern the number of fragments (N), the average size of the fragments (A) and D. We show that (1) N scales with P^(1/2), (2) A scales with P^(-2/3), (3) D scales with P^(1/5). Our experimental procedure thus appears as a unique tool to unravel the complex physics of fragmentation during phreatomagmatic explosions.

Changes in fibrinolysis and severity of organ failure in sepsis: a prospective observational study using point-of-care test--ROTEM.

PubMed

Prakash, Shivesh; Verghese, Santosh; Roxby, David; Dixon, Dani; Bihari, Shailesh; Bersten, Andrew

2015-04-01

We hypothesized that the thromboelastometry (ROTEM; Pentapharm GmbH, Munich, Germany) fibrinolysis parameter "maximum lysis" (ML) would have an independent inverse association with the severity of organ failure in sepsis. Selected adult patients with sepsis (n = 77) were recruited within 24 hours of antibiotic commencement. Patients with Sequential Organ Failure Assessment score higher than 1 (n = 57) were followed for 72 hours. Prothrombin fragments 1 + 2, plasminogen activator inhibitor-1 (aPAI-1), ROTEM, and routine coagulation tests were measured daily along with Sequential Organ Failure Assessment scores. The activity of functional aPAI-1 increased with increasing severity of organ failure (P = .01) and was higher as compared with healthy controls (95% confidence interval, -65.4 to -29.9; P < .001). There was a decreasing trend in ML with increased organ failure (P = .001); however, there was no trend in d-dimer. Among all tests, only the lower ML (ß = -0.38, P < .001) and higher international normalized ratio (INR; ß = 0.32, P = .002) values significantly contributed to greater severity of organ failure (R(2) = 0.35, F2,73 = 19.29, P < .001). Despite an increase in INR, the prothrombin fragment remained unchanged (P = .89). Strong correlations were observed between early (24 hours) increase in fibrinolysis and recovery of organ failures for 48 hours (ML: r = 0.679, P = .001; aPAI-1: r = 0.694, P < .001). Lower ML and higher INR values predicted greater severity of organ failure at presentation. Further studies are required, as ROTEM could aid selection of patients and guide interventions aimed at fibrinolysis in severe sepsis. Copyright © 2014 Elsevier Inc. All rights reserved.

Proton-decaying, light nuclei accessed via the invariant-mass method

NASA Astrophysics Data System (ADS)

Brown, Kyle

2017-01-01

Two-nucleon decay is the most recently discovered nuclear decay mode. For proton-rich nuclei, the majority of multi-proton decays occur via sequential steps of one-proton emission. Direct two-proton (2p) decay was believed to occur only in even-Z nuclei beyond the proton drip line where one-proton decay is energy forbidden. This has been observed for the ground states of around a dozen nuclei including 6Be, the lightest case, and 54Zn, the heaviest case. Direct 2p decay has also recently been observed for isobaric analog states where all possible 1p intermediates are either isospin allowed and energy forbidden, or energy-allowed and isospin forbidden. For light proton emitters, the lifetimes are short enough that the invariant-mass technique is ideal for measuring the decay energy, intrinsic width and, for multi-proton decays, the momentum correlations between the fragments. I will describe recent measurements of proton emitters using the invariant-mass technique with the High Resolution Array (HiRA). I will present a new, high-statistics measurement on the sequential 2p decay of excited states in 17Ne. Measuring the momentum correlations between the decay fragments allow us to determine the 1p intermediate state through which the decay proceeds. I will present data on the isobaric-analog pair 8C and 8BIAS, which highlight the two known types of direct 2p decay. I will also present the first observation of 17Na, which is unbound with respect to three-proton emission. Finally I will present a new measurement on the width of the first-excited state of 9C and compare to recent theoretical calculations.

Sequential Superresolution Imaging of Multiple Targets Using a Single Fluorophore

PubMed Central

Lidke, Diane S.; Lidke, Keith A.

2015-01-01

Fluorescence superresolution (SR) microscopy, or fluorescence nanoscopy, provides nanometer scale detail of cellular structures and allows for imaging of biological processes at the molecular level. Specific SR imaging methods, such as localization-based imaging, rely on stochastic transitions between on (fluorescent) and off (dark) states of fluorophores. Imaging multiple cellular structures using multi-color imaging is complicated and limited by the differing properties of various organic dyes including their fluorescent state duty cycle, photons per switching event, number of fluorescent cycles before irreversible photobleaching, and overall sensitivity to buffer conditions. In addition, multiple color imaging requires consideration of multiple optical paths or chromatic aberration that can lead to differential aberrations that are important at the nanometer scale. Here, we report a method for sequential labeling and imaging that allows for SR imaging of multiple targets using a single fluorophore with negligible cross-talk between images. Using brightfield image correlation to register and overlay multiple image acquisitions with ~10 nm overlay precision in the x-y imaging plane, we have exploited the optimal properties of AlexaFluor647 for dSTORM to image four distinct cellular proteins. We also visualize the changes in co-localization of the epidermal growth factor (EGF) receptor and clathrin upon EGF addition that are consistent with clathrin-mediated endocytosis. These results are the first to demonstrate sequential SR (s-SR) imaging using direct stochastic reconstruction microscopy (dSTORM), and this method for sequential imaging can be applied to any superresolution technique. PMID:25860558

[Molecular dynamics of immune complex of photoadduct-containing DNA with Fab-Anti-DNA antibody fragment].

PubMed

Akberova, N I; Zhmurov, A A; Nevzorova, T A; Litvinov, R I

2016-01-01

Antibodies to DNA play an important role in the pathogenesis of autoimmune diseases. The elucidation of structural mechanisms of both the antigen recognition and the interaction of anti-DNA antibodies with DNA will help to understand the role of DNA-containing immune complexes in various pathologies and can provide a basis for new treatment modalities. Moreover, the DNA-antibody complex is an analog of specific intracellular DNA-protein interactions. In this work, we used in silico molecular dynamic simulations of bimolecular complexes of the dsDNA segment containing the Fab fragment of an anti-DNA antibody to obtain the detailed thermodynamic and structural characteristics of dynamic intermolecular interactions. Using computationally modified crystal structure of the Fab-DNA complex (PDB ID: 3VW3), we studied the equilibrium molecular dynamics of the 64M-5 antibody Fab fragment associated with the dsDNA fragment containing the thymine dimer, the product of DNA photodamage. Amino acid residues that constitute paratopes and the complementary nucleotide epitopes for the Fab-DNA construct were identified. Stacking and electrostatic interactions were found to play the main role in mediating the most specific antibody-dsDNA contacts, while hydrogen bonds were less significant. These findings may shed light on the formation and properties of pathogenic anti-DNA antibodies in autoimmune diseases, such as systemic lupus erythematosus associated with skin photosensitivity and DNA photodamage.

Ionization balance of impurities in turbulent scrape-off layer plasmas I: local ionization-recombination equilibrium

NASA Astrophysics Data System (ADS)

Guzman, F.; Marandet, Y.; Tamain, P.; Bufferand, H.; Ciraolo, G.; Ghendrih, Ph; Guirlet, R.; Rosato, J.; Valentinuzzi, M.

2015-12-01

In magnetized fusion devices, cross field impurity transport is often dominated by turbulence, in particular in the scrape-off layer. In these outer regions of the plasma, fluctuations of plasma parameters can be comparable to mean values, and the way ionization and recombination sources are treated in transport codes becomes questionnable. In fact, sources are calculated using the mean density and temperature values, with no account of fluctuations. In this work we investigate the modeling uncertainties introduced by this approximation, both qualitatively and quantitatively for the local ionization equilibrium. As a first step transport effects are neglected, and their role will be discussed in a companion paper. We show that temperature fluctuations shift the ionization balance towards lower temperatures, essentially because of the very steep temperature dependence of the ionization rate coefficients near the threshold. To reach this conclusion, a thorough analysis of the time scales involved is carried out, in order to devise a proper way of averaging over fluctuations. The effects are found to be substantial only for fairly large relative fluctuation levels for temperature, that is of the order of a few tens of percents.

Binding equilibrium and kinetics of membrane-anchored receptors and ligands in cell adhesion: Insights from computational model systems and theory.

PubMed

Weikl, Thomas R; Hu, Jinglei; Xu, Guang-Kui; Lipowsky, Reinhard

2016-09-02

The adhesion of cell membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. In this article, we review recent results from simulations and theory that lead to novel insights on how the binding equilibrium and kinetics of these proteins is affected by the membranes and by the membrane anchoring and molecular properties of the proteins. Simulations and theory both indicate that the binding equilibrium constant [Formula: see text] and the on- and off-rate constants of anchored receptors and ligands in their 2-dimensional (2D) membrane environment strongly depend on the membrane roughness from thermally excited shape fluctuations on nanoscales. Recent theory corroborated by simulations provides a general relation between [Formula: see text] and the binding constant [Formula: see text] of soluble variants of the receptors and ligands that lack the membrane anchors and are free to diffuse in 3 dimensions (3D).

Binding equilibrium and kinetics of membrane-anchored receptors and ligands in cell adhesion: Insights from computational model systems and theory

PubMed Central

Weikl, Thomas R.; Hu, Jinglei; Xu, Guang-Kui; Lipowsky, Reinhard

2016-01-01

ABSTRACT The adhesion of cell membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. In this article, we review recent results from simulations and theory that lead to novel insights on how the binding equilibrium and kinetics of these proteins is affected by the membranes and by the membrane anchoring and molecular properties of the proteins. Simulations and theory both indicate that the binding equilibrium constant K2D and the on- and off-rate constants of anchored receptors and ligands in their 2-dimensional (2D) membrane environment strongly depend on the membrane roughness from thermally excited shape fluctuations on nanoscales. Recent theory corroborated by simulations provides a general relation between K2D and the binding constant K3D of soluble variants of the receptors and ligands that lack the membrane anchors and are free to diffuse in 3 dimensions (3D). PMID:27294442

Solutions for Reacting and Nonreacting Viscous Shock Layers with Multicomponent Diffusion and Mass Injection. Ph.D. Thesis - Virginia Polytechnic Inst. and State Univ.

NASA Technical Reports Server (NTRS)

Moss, J. N.

1971-01-01

Numerical solutions are presented for the viscous shocklayer equations where the chemistry is treated as being either frozen, equilibrium, or nonequilibrium. Also the effects of the diffusion model, surface catalyticity, and mass injection on surface transport and flow parameters are considered. The equilibrium calculations for air species using multicomponent: diffusion provide solutions previously unavailable. The viscous shock-layer equations are solved by using an implicit finite-difference scheme. The flow is treated as a mixture of inert and thermally perfect species. Also the flow is assumed to be in vibrational equilibrium. All calculations are for a 45 deg hyperboloid. The flight conditions are those for various altitudes and velocities in the earth's atmosphere. Data are presented showing the effects of the chemical models; diffusion models; surface catalyticity; and mass injection of air, water, and ablation products on heat transfer; skin friction; shock stand-off distance; wall pressure distribution; and tangential velocity, temperature, and species profiles.

On Nash Equilibrium and Evolutionarily Stable States That Are Not Characterised by the Folk Theorem

PubMed Central

Li, Jiawei; Kendall, Graham

2015-01-01

In evolutionary game theory, evolutionarily stable states are characterised by the folk theorem because exact solutions to the replicator equation are difficult to obtain. It is generally assumed that the folk theorem, which is the fundamental theory for non-cooperative games, defines all Nash equilibria in infinitely repeated games. Here, we prove that Nash equilibria that are not characterised by the folk theorem do exist. By adopting specific reactive strategies, a group of players can be better off by coordinating their actions in repeated games. We call it a type-k equilibrium when a group of k players coordinate their actions and they have no incentive to deviate from their strategies simultaneously. The existence and stability of the type-k equilibrium in general games is discussed. This study shows that the sets of Nash equilibria and evolutionarily stable states have greater cardinality than classic game theory has predicted in many repeated games. PMID:26288088

Method for treating a nuclear process off-gas stream

DOEpatents

Pence, Dallas T.; Chou, Chun-Chao

1984-01-01

Disclosed is a method for selectively removing and recovering the noble gas and other gaseous components typically emitted during nuclear process operations. The method is adaptable and useful for treating dissolver off-gas effluents released during reprocessing of spent nuclear fuels whereby to permit radioactive contaminant recovery prior to releasing the remaining off-gases to the atmosphere. Briefly, the method sequentially comprises treating the off-gas stream to preliminarily remove NO.sub.x, hydrogen and carbon-containing organic compounds, and semivolatile fission product metal oxide components therefrom; adsorbing iodine components on silver-exchanged mordenite; removing water vapor carried by said stream by means of a molecular sieve; selectively removing the carbon dioxide components of said off-gas stream by means of a molecular sieve; selectively removing xenon in gas phase by passing said stream through a molecular sieve comprising silver-exchanged mordenite; selectively separating krypton from oxygen by means of a molecular sieve comprising silver-exchanged mordenite; selectively separating krypton from the bulk nitrogen stream using a molecular sieve comprising silver-exchanged mordenite cooled to about -140.degree. to -160.degree. C.; concentrating the desorbed krypton upon a molecular sieve comprising silver-exchange mordenite cooled to about -140.degree. to -160.degree. C.; and further cryogenically concentrating, and the recovering for storage, the desorbed krypton.

From Vulcanian explosions to sustained explosive eruptions: The role of diffusive mass transfer in conduit flow dynamics

NASA Astrophysics Data System (ADS)

Mason, R. M.; Starostin, A. B.; Melnik, O. E.; Sparks, R. S. J.

2006-05-01

Magmatic explosive eruptions are influenced by mass transfer processes of gas diffusion into bubbles caused by decompression. Melnik and Sparks [Melnik, O.E., Sparks, R.S.J. 2002, Modelling of conduit flow dynamic during explosive activity at Soufriere Hills Volcano, Montserrat. In: Druitt, T.H., Kokelaar, B.P. (eds). The Eruption of Soufriere Hills Volcano, Montserrat, from 1995 to 1999. Geological Society, London, Memoirs, 21, 307-317] proposed two end member cases corresponding to complete equilibrium and complete disequilibrium. In the first case, diffusion is fast enough to maintain the system near equilibrium and a long-lived explosive eruption develops. In the latter case, pre-existing bubbles expand under conditions of explosive eruption and decompression, but diffusive gas transfer is negligible. This leads to a much shorter eruption. Here we develop this model to consider the role of mass transfer by investigating transient flows at the start of an explosive eruption triggered by a sudden decompression. The simulations reveal a spectrum of behaviours from sustained to short-lived highly non-equilibrium Vulcanian-style explosions lasting a few tens of seconds, through longer lasting eruptions that can be sustained for tens of minutes and finally to eruptions that can last hours or even days. Behaviour is controlled by a mass-transfer parameter, ω, which equals n*2/3D, where n* is the bubble number density and D is the diffusivity. The parameter ω is expected to vary between 10 - 5 and 1 s - 1 in nature and reflects a time-scale for efficient diffusion. The spectrum of model behaviours is consistent with variations in styles of explosive eruptions of silicic volcanoes. In the initial stages peak discharges occur over 10-20 s and then decline to low discharges. If a critical bubble overpressure is assumed to be the criterion for fragmentation then fragmentation may stop and start several times in the declining period causing several pulses of high-intensity discharge. For the cases of strong disequilibria, the fluxes can decrease to negligible values where other processes, such as gas escape through permeable magma, prevents explosive conditions becoming re-established so that explosive activity stops and dome growth can start. For cases closer to the equilibrium the eruption can evolve towards a quasi-steady sustained flow, never declining sufficiently for gas escape to become dominant.

Accelerated Combinatorial High Throughput Star Polymer Synthesis via a Rapid One-Pot Sequential Aqueous RAFT (rosa-RAFT) Polymerization Scheme.

PubMed

Cosson, Steffen; Danial, Maarten; Saint-Amans, Julien Rosselgong; Cooper-White, Justin J

2017-04-01

Advanced polymerization methodologies, such as reversible addition-fragmentation transfer (RAFT), allow unprecedented control over star polymer composition, topology, and functionality. However, using RAFT to produce high throughput (HTP) combinatorial star polymer libraries remains, to date, impracticable due to several technical limitations. Herein, the methodology "rapid one-pot sequential aqueous RAFT" or "rosa-RAFT," in which well-defined homo-, copolymer, and mikto-arm star polymers can be prepared in very low to medium reaction volumes (50 µL to 2 mL) via an "arm-first" approach in air within minutes, is reported. Due to the high conversion of a variety of acrylamide/acrylate monomers achieved during each successive short reaction step (each taking 3 min), the requirement for intermediary purification is avoided, drastically facilitating and accelerating the star synthesis process. The presented methodology enables RAFT to be applied to HTP polymeric bio/nanomaterials discovery pipelines, in which hundreds of complex polymeric formulations can be rapidly produced, screened, and scaled up for assessment in a wide range of applications. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The costs of avoiding environmental impacts from shale-gas surface infrastructure.

PubMed

Milt, Austin W; Gagnolet, Tamara D; Armsworth, Paul R

2016-12-01

Growing energy demand has increased the need to manage conflicts between energy production and the environment. As an example, shale-gas extraction requires substantial surface infrastructure, which fragments habitats, erodes soils, degrades freshwater systems, and displaces rare species. Strategic planning of shale-gas infrastructure can reduce trade-offs between economic and environmental objectives, but the specific nature of these trade-offs is not known. We estimated the cost of avoiding impacts from land-use change on forests, wetlands, rare species, and streams from shale-energy development within leaseholds. We created software for optimally siting shale-gas surface infrastructure to minimize its environmental impacts at reasonable construction cost. We visually assessed sites before infrastructure optimization to test whether such inspection could be used to predict whether impacts could be avoided at the site. On average, up to 38% of aggregate environmental impacts of infrastructure could be avoided for 20% greater development costs by spatially optimizing infrastructure. However, we found trade-offs between environmental impacts and costs among sites. In visual inspections, we often distinguished between sites that could be developed to avoid impacts at relatively low cost (29%) and those that could not (20%). Reductions in a metric of aggregate environmental impact could be largely attributed to potential displacement of rare species, sedimentation, and forest fragmentation. Planners and regulators can estimate and use heterogeneous trade-offs among development sites to create industry-wide improvements in environmental performance and do so at reasonable costs by, for example, leveraging low-cost avoidance of impacts at some sites to offset others. This could require substantial effort, but the results and software we provide can facilitate the process. © 2016 Society for Conservation Biology.

Trading efficiency for effectiveness in similarity-based indexing for image databases

NASA Astrophysics Data System (ADS)

Barros, Julio E.; French, James C.; Martin, Worthy N.; Kelly, Patrick M.

1995-11-01

Image databases typically manage feature data that can be viewed as points in a feature space. Some features, however, can be better expressed as a collection of points or described by a probability distribution function (PDF) rather than as a single point. In earlier work we introduced a similarity measure and a method for indexing and searching the PDF descriptions of these items that guarantees an answer equivalent to sequential search. Unfortunately, certain properties of the data can restrict the efficiency of that method. In this paper we extend that work and examine trade-offs between efficiency and answer quality or effectiveness. These trade-offs reduce the amount of work required during a search by reducing the number of undesired items fetched without excluding an excessive number of the desired ones.

Comparison between natural Rain drop size distributions and corresponding models near equilibrium state during warm rain

NASA Astrophysics Data System (ADS)

Barthes, Laurent; Mallet, Cécile

2010-05-01

Keywords: Rain Drop Size Distribution, Breakup, coalescence, disdrometer The study of the vertical evolution of raindrop size distributions (DSDs) during rainfall, from the freezing level isotherm to ground level, is a key to improving our understanding of the microphysics of rain. In numerous domains such as remote sensing, telecommunications, soil erosion, and the study of the rain's efficiency in 'washing' the atmosphere, the DSD plays an important role. Among the different processes affecting the evolution of DSD, breakup and coalescence are two of the most significant. Models of coalescence and breakup lead to equilibrium of the raindrop size distribution (DSD) after a fall through sufficient vertical height. At equilibrium, the DSD no longer evolves, and its shape is unique whatever the rain rate or LWC. This implies that the DSD is known, to within a multiplication constant. These models based on experimental measurements have been developed over the past 40 years. The Low and List (1982a,b) parameterization (hereinafter LL82) and the Greg M. McFarquhar (2004) model are both based on the same laboratory experiments, which lead to an equilibrium drop size distribution (EDSD) with two or three peaks, and an exponential tail with a slope of approximately Λ=65 cm-1. Numerous measurements using disdrometer collected in different climatic areas: Paris, France (Mars to October 2000), Iowa-City (April to October 2002), and Djougou (Benin June to September 2006) corresponding to 537 hours of rain period have shown that for high rain rates, close to a state of equilibrium, this slope lies between Λ=20 - 22 cm-1. This latter value is corroborated by others measurements found in the literature (Hu & Srivastava, 1995). Hu & Srivastava suggested that the Low and List parameterization may overestimate the effects of the breakup process. This hypothesis is in adequation with recent laboratory experiments (A.P. Barros 2008) in which the authors conclude that the number of fragments droplets produced when small drops and large drops collide is overestimate. As new parameterization of LL82 is not possible due to the lack of new sufficient large experimental dataset, we have simply tried in the present study to 'compensate' the problem previously mentioned by replacing the coalescence/breakup model proposed in LL82 by another one in which the breakup process is less dominant. In order to evaluate the relevance of this modification, some of the DSD parameters such as slope, mean volume diameter, and relation between moments are calculated, and comparisons with experimental DSD are made. Simulations at equilibrium lead to a DSD tail with a slope of 23 cm-1 and a mean volume diameter equal to 2.5 mm. These values are in good agreements with experimental data. Similarly, the linear relationship between No* and the rainfall rate is also in good agreement. In the last part, the modified parameterization is then used to study the evolution of an initially gamma-like DSD in a 1D vertical rain shaft. References Barros, A. P., O. P. Prat, P. Shrestha, F. Y. Testik, and L. F. Bliven, 2008. Revisiting Low and List (1982): evaluation of raindrop collision using laboratory observations and modeling. Journal of the Atmospheric Sciences. Vol. 65(9), pp. 2983-2993. Hu, Z., and R. C. Srivastava: 1995: Evolution of raindrop size distribution by coalescence, breakup, and evaporation: Theory and observations. J. Atmos. Sci., 52, 1761-1783. Low, T. B. and R. List, 1982a: Collision, coalescence, and breakup of raindrops. Part I: Experimentally established coalescence efficiencies and fragment size distributions in breakup. J. Atmos. Sci., 39, 1591-1606. ___ 1982b: Collision, coalescence, and breakup of raindrops. Part II: Parameterization of fragment size distributions. J. Atmos. Sci., 39, 1607-1618. McFarquhar, G. M, 2004: A new representation of collision-induced breakup of raindrops and its implications for the shapes of raindrop size distributions, J. Atmos. Sci., 61(7), 777-794.

Mechanism of 1,4,5,8-naphthalene tetracarboxylic acid dianhydride hydrolysis and formation in aqueous solution.

PubMed

Barros, T C; Cuccovia, I M; Farah, J P S; Masini, J C; Chaimovich, H; Politi, M J

2006-01-07

The study of highly conjugated, carbonyl-containing molecules such as 1,4,5,8-naphthalene tetracarboxylic dianhydride, III, is of interest since reactivity differences and transmission of electronic effects through the conjugated framework can be evidenced. The kinetics of hydrolysis of III in aqueous solution were determined from 5 M acid to pH 10. In basic solution hydrolysis of III yields, sequentially, 1,4,5,8-naphthalene diacid monoanhydride, II, and 1,4,5,8-naphthalene tetracarboxylic acid, I. The second order rate constant for alkaline hydrolysis is 200 fold higher for the first ring opening. The water-catalyzed hydrolysis of III yields a pH-dependent mixture of ionic forms of I and II. The rate constant for water-catalyzed hydrolysis of III is 25 fold higher than that for II. In concentrated acid the rates for reaching equilibrium (I, II and III) increase and III is the major product. The pK(a)s of I (3.24, 5.13 and 6.25) and II (3.05, 5.90) were determined by potentiometric, fluorescence and UV spectroscopy titrations and by quantitative fit of the kinetic and equilibrium data. The apparent, pH-dependent, equilibrium constants, K(EqII), for anhydride formation between I and II were obtained from the UV spectra. The quantitative fit of kinetic and equilibrium data are consistent with the assumption that anhydride formation only proceeds with the fully protonated species for both I and II and permitted the estimation of the equilibrium constants for anhydride formation, K(EqII). The value of K(EqII) (I <==> II) between pH 1 and 6 was ca. 5. Geometry optimization calculations in the gas phase of the reactions of III in alkaline, neutral and acid conditions, at the DFT level of theory, gave electronic distributions that were qualitatively consistent with the experimental results.

Slow Photoelectron Spectroscopy and State-Selected Unimolecular Decomposition of Ionized DNA Bases Analogues

NASA Astrophysics Data System (ADS)

Mahjoub, Ahmed; Hochlaf, Majdi; Poisson, Lionel; Garcia, Gustavo A.; Nahon, Laurent

2013-06-01

We studied the single-photon ionization of gas-phase 2-Piperidone (DNA basis analogue) and of its dimer using vacuum-ultraviolet (VUV) synchrotron radiation coupled to a velocity map imaging electron/ion coincidence spectrometer The slow photoelectron spectrum (SPES) of the monomer is dominated by the vibrational transitions to the ground state. These spectra are assigned with the help of theoretical calculations dealing with the equilibrium geometries, electronic-state patterns and evolutions, harmonic and anharmonic wavenumbers. After its formation, dimer is subject of intramolecular isomerization, H transfer and then unimolecular fragmentation processes. The near threshold photofragmentation pattern of the cationic 2-Piperidone cation and its dimer has been recorded. The experimental method yields the fragment intensity as a function of the internal energy deposited into the parent cation. In parallel, ab initio studies on ionic and neutral fragmentation products have been performed with the aim of determining the isomers of the ionic products observed experimentally as well as of their neutral counterparts. L. Nahon, N. De Oliveria,J. F. Gil,B. Pilette,O. Marcouillé, B. La garde and F. Polack Journal of Synchrotron Radiation {19}(4), 508-520; 2012

Recognition of Y Fragment Deletion by Genotyping Graphs after Amplified by PowerPlex® 21 Detection Kit.

PubMed

Wang, S C; Ding, M M; Wei, X L; Zhang, T; Yao, F

2016-06-01

To recognize the possibility of Y fragment deletion of Amelogenin gene intuitively and simply according to the genotyping graphs. By calculating the ratio of total peak height of genotyping graphs, the statistics of equilibrium distribution between Amelogenin and D3S1358 loci, Amelogenin X-gene and Amelogenin Y-gene, and different alleles of D3S1358 loci from 1 968 individuals was analyzed after amplified by PowerPlex ® 21 detection kit. Sum of peak height of Amelogenin X allele was not less than 60% that of D3S1358 loci alleles in 90.8% female samples, and sum of peak height of Amelogenin X allele was not higher than 70% that of D3S1358 loci alleles in 94.9% male samples. The result of genotyping after amplified by PowerPlex ® 21 detection kit shows that the possibility of Y fragment deletion should be considered when only Amelogenin X-gene of Amelogenin is detected and the peak height of Amelogenin X-gene is not higher than 70% of the total peak height of D3S1358 loci. Copyright© by the Editorial Department of Journal of Forensic Medicine

Modelling fragmentations of aminoacids after resonant electron attachment: quantum evidence of possible direct -OH detachment

NASA Astrophysics Data System (ADS)

Panosetti, C.; Baccarelli, I.; Sebastianelli, F.; Gianturco, F. A.

2010-10-01

We investigate some aspects of the radiation damage mechanisms in biomolecules, focusing on the modelling of resonant fragmentation caused by the attachment of low-energy electrons (LEEs) initially ejected by biological tissues when exposed to ionizing radiation. Scattering equations are formulated within a symmetry-adapted, single-center expansion of both continuum and bound electrons, and the interaction forces are obtained from a combination of ab initio calculations and a nonempirical model of exchange and correlation effects developped in our group. We present total elastic scattering cross-sections and resonance features obtained for the equilibrium geometries of glycine, alanine, proline and valine. Our results at those geometries of the target molecules are briefly shown to qualitatively explain some of the fragmentation patterns obtained in experiments. We further carry out a one-dimensional (1D) modeling for the dynamics of intramolecular energy transfers mediated by the vibrational activation of selected bonds: our calculations indicate that resonant electron attachment to glycine can trigger direct, dissociative evolution of the complex into (Gly-OH)- and -OH losses, while they also find that the same process does not occur via a direct, 1D dissociative path in the larger aminoacids of the present study.

Silicon nanowire sensor for DNA detection and sequencing: an ab initio simulation

NASA Astrophysics Data System (ADS)

Lu, Wenchang; Li, Yan; Hodak, Miroslav; Xiao, Zhongcan; Bernholc, Jerry

Electrical sensors able to detect DNA replication and determine its sequence would enable fast and relatively cheap diagnosis of gene-related vulnerabilities and cancers. At present, it is already possible to electrically monitor DNA replication events using a Klenow fragment of polymerase I attached to a carbon nanotube. Since devices based on Si nanowires would be much easier to produce in quantity, we examine theoretically the sensitivity of a Si nanowire/Klenow fragment for electrical detection of nucleotide addition. A highly parallel real-space multigrid code is used for DFT-based non-equilibrium Green's function calculations involving up to 16,000 atoms, employing highly-accurate variationally-optimized localized orbitals. We find that the open and closed Klenow fragment configurations, prior and during nucleotide addition, respectively, screen the Si nanowire differently and result in a detectable current difference. The sensitivity is the largest in the subthreshold regime while the absolute current difference is maximized in the turn-on state. The sensitivity decreases with an increase of the nanowire size, as expected, but the current difference between different enzymatic states is nearly independent on the nanowire size up to 800 Å2 cross section.

Continuous approximation for interaction energy of adamantane encapsulated inside carbon nanotubes

NASA Astrophysics Data System (ADS)

Baowan, Duangkamon; Hill, James M.; Bacsa, Wolfgang

2018-02-01

The interaction energy for two adjacent adamantane molecules and that of adamantane molecules encapsulated inside carbon nanotubes are investigated considering only dipole-dipole induced interaction. The Lennard-Jones potential and the continuous approximation are utilised to derive analytical expressions for these interaction energies. The equilibrium distance 3.281 Å between two adamantane molecules is determined. The smallest carbon nanotube radius b0 that can encapsulate the adamantane molecule and the radius of the tube bmax that gives the maximum suction energy, linearly depend on the adamantane radius, are calculated. For larger diameter tubes, the off axis position has been calculated, and equilibrium distance between molecule and tube wall is found to be close to the interlayer spacing in graphene.

[Hypothesis on the equilibrium point and variability of amplitude, speed and time of single-joint movement].

PubMed

Latash, M; Gottleib, G

1990-01-01

Problems of single-joint movement variability are analysed in the framework of the equilibrium-point hypothesis (the lambda-model). Control of the movements is described with three parameters related to movement amplitude speed, and time. Three strategies emerge from this description. Only one of them is likely to lead to a Fitts' type speed-accuracy trade-off. Experiments were performed to test one of the predictions of the model. Subjects performed identical sets of single-joint fast movements with open or closed eyes and some-what different instructions. Movements performed with closed eyes were characterized with higher peak speeds and unchanged variability in seeming violation of the Fitt's law and in a good correspondence to the model.

Mechanisms of DNA disentangling by type II topoisomerases. Comment on "Disentangling DNA molecules" by Alexander Vologodskii

NASA Astrophysics Data System (ADS)

Yan, Jie

2016-09-01

In this article [1] Dr. Vologodskii presents a comprehensive discussion on the mechanisms by which the type II topoisomerases unknot/disentangle DNA molecules. It is motivated by a mysterious capability of the nanometer-size enzymes to keep the steady-state probability of DNA entanglement/knot almost two orders of magnitude below that expected from thermal equilibrium [2-5]. In spite of obvious functional advantages of the enzymes, it raises a question regarding how such high efficiency could be achieved. The off-equilibrium steady state distribution of DNA topology is powered by ATP consumption. However, it remains unclear how this energy is utilized to bias the distribution toward disentangled/unknotted topological states of DNA.

Trade-offs in the social-ecological values associated with different land-uses in the eastern Amazon

EPA Science Inventory

Current trajectories of rural development across much of the tropics are not sustainable. Forests continue to be cleared at a rate of c. 50,000 km2 p.a. and much of the remaining forests are severely degraded from the effects of fragmentation, over-exploitation, fire and climate ...

Using chromium stable isotope ratios to quantify Cr(VI) reduction: Lack of sorption effects

USGS Publications Warehouse

Ellis, A.S.; Johnson, T.M.; Bullen, T.D.

2004-01-01

Chromium stable isotope values can be effectively used to monitor reduction of Cr(VI) in natural waters. We investigate effects of sorption during transport of Cr(VI) which may also shift Cr isotopes values, complicating efforts to quantify reduction. This study shows that Cr stable isotope fractionation caused by sorption is negligible. Equilibrium fractionation of Cr stable isotopes between dissolved Cr-(VI) and Cr(VI) adsorbed onto ??-Al2O3 and goethite is less than 0.04???. (53Cr/52Cr) under environmentally relevant pH conditions. Batch experiments at pH 4.0 and pH 6.0 were conducted in series to sequentially magnify small isotope fractionations. A simple transport model suggests that adsorption may cause amplification of a small isotope fractionation along extreme fringes of a plume, leading to shifts in 53Cr/52Cr values. We therefore suggest that isotope values at extreme fringes of Cr plumes be critically evaluated for sorption effects. A kinetic effect was observed in experiments with goethite at pH 4 where apparently lighter isotopes diffuse into goethite clumps at a faster rate before eventually reaching equilibrium. This observed kinetic effect may be important in a natural system that has not attained equilibrium and is in need of further study. Cr isotope fractionation caused by speciation of Cr(VI) between HCrO4- and CrO42- was also examined, and we conclude that it is not measurable. In the absence of isotope fractionation caused by equilibrium speciation and sorption, most of the variation in ??53 Cr values may be attributed to reduction, and reliable estimates of Cr reduction can be made.

Probing the Non-Native H Helix Translocation in Apomyoglobin Folding Intermediates

PubMed Central

2015-01-01

Apomyoglobin folds via sequential helical intermediates that are formed by rapid collapse of the A, B, G, and H helix regions. An equilibrium molten globule with a similar structure is formed near pH 4. Previous studies suggested that the folding intermediates are kinetically trapped states in which folding is impeded by non-native packing of the G and H helices. Fluorescence spectra of mutant proteins in which cysteine residues were introduced at several positions in the G and H helices show differential quenching of W14 fluorescence, providing direct evidence of translocation of the H helix relative to helices A and G in both the kinetic and equilibrium intermediates. Förster resonance energy transfer measurements show that a 5-({2-[(acetyl)amino]ethyl}amino)naphthalene-1-sulfonic acid acceptor coupled to K140C (helix H) is closer to Trp14 (helix A) in the equilibrium molten globule than in the native state, by a distance that is consistent with sliding of the H helix in an N-terminal direction by approximately one helical turn. Formation of an S108C–L135C disulfide prevents H helix translocation in the equilibrium molten globule by locking the G and H helices into their native register. By enforcing nativelike packing of the A, G, and H helices, the disulfide resolves local energetic frustration and facilitates transient docking of the E helix region onto the hydrophobic core but has only a small effect on the refolding rate. The apomyoglobin folding landscape is highly rugged, with several energetic bottlenecks that frustrate folding; relief of any one of the major identified bottlenecks is insufficient to speed progression to the transition state. PMID:24857522

Impact analysis of off-road-vehicle use on vegetation in the Grand Mere dune environment. [Lake Michigan

NASA Technical Reports Server (NTRS)

Schultink, G. (Principal Investigator)

1977-01-01

The author has identified the following significant results. A linear regression between percent nonvegetative land and the time variable was completed for the two sample areas. Sample area no. 1 showed an average vegetation loss of 1.901% per year, while the loss for sample area no. 2 amounted to 5.889% per year. Two basic reasons for the difference were assumed to play a role: the difference in access potential and the amount of already fragmented vegetation complexes in existence during the first year of the comparative analysis - 1970. Sample area no. 2 was located closer to potential access points and was more fragmented initially.

Implementation of dipolar direct current (DDC) collision-induced dissociation in storage and transmission modes on a quadrupole/time-of-flight tandem mass spectrometer.

PubMed

Webb, Ian K; Londry, Frank A; McLuckey, Scott A

2011-09-15

Means for effecting dipolar direct current collision-induced dissociation (DDC CID) on a quadrupole/time-of-flight in a mass spectrometer have been implemented for the broadband dissociation of a wide range of analyte ions. The DDC fragmentation method in electrodynamic storage and transmission devices provides a means for inducing fragmentation of ions over a large mass-to-charge range simultaneously. It can be effected within an ion storage step in a quadrupole collision cell that is operated as a linear ion trap or as ions are continuously transmitted through the collision cell. A DDC potential is applied across one pair of rods in the quadrupole collision cell of a QqTOF hybrid mass spectrometer to effect fragmentation. In this study, ions derived from a small drug molecule, a model peptide, a small protein, and an oligonucleotide were subjected to the DDC CID method in either an ion trapping or an ion transmission mode (or both). Several key experimental parameters that affect DDC CID results, such as time, voltage, low mass cutoff, and bath gas pressure, are illustrated with protonated leucine enkephalin. The DDC CID dissociation method gives a readily tunable, broadband tool for probing the primary structures of a wide range of analyte ions. The method provides an alternative to the narrow resonance conditions of conventional ion trap CID and it can access more extensive sequential fragmentation, depending upon conditions. The DDC CID approach constitutes a collision analog to infrared multiphoton dissociation (IRMPD). Copyright © 2011 John Wiley & Sons, Ltd.

Characterization and Modeling of the Collision Induced Dissociation Patterns of Deprotonated Glycosphingolipids: Cleavage of the Glycosidic Bond

NASA Astrophysics Data System (ADS)

Rožman, Marko

2016-01-01

Glycosphingolipid fragmentation behavior was investigated by combining results from analysis of a series of negative ion tandem mass spectra and molecular modeling. Fragmentation patterns extracted from 75 tandem mass spectra of mainly acidic glycosphingolipid species (gangliosides) suggest prominent cleavage of the glycosidic bonds with retention of the glycosidic oxygen atom by the species formed from the reducing end (B and Y ion formation). Dominant product ions arise from dissociation of sialic acids glycosidic bonds whereas product ions resulting from cleavage of other glycosidic bonds are less abundant. Potential energy surfaces and unimolecular reaction rates of several low-energy fragmentation pathways leading to cleavage of glycosidic bonds were estimated in order to explain observed dissociation patterns. Glycosidic bond cleavage in both neutral (unsubstituted glycosyl group) and acidic glycosphingolipids was the outcome of the charge-directed intramolecular nucleophilic substitution (SN2) mechanism. According to the suggested mechanism, the nucleophile in a form of carboxylate or oxyanion attacks the carbon at position one of the sugar ring, simultaneously breaking the glycosidic bond and yielding an epoxide. For gangliosides, unimolecular reaction rates suggest that dominant product ions related to the cleavage of sialic acid glycosidic bonds are formed via direct dissociation channels. On the other hand, low abundant product ions related to the dissociation of other glycosidic bonds are more likely to be the result of sequential dissociation. Although results from this study mainly contribute to the understanding of glycosphingolipid fragmentation chemistry, some mechanistic findings regarding cleavage of the glycosidic bond may be applicable to other glycoconjugates.

Instabilities of Current Carrying Torus

NASA Astrophysics Data System (ADS)

Liu, Wenjuan; Qiu, J.

2010-05-01

We investigate the initial equilibrium and stability conditions for an uniform current-carrying plasma ring with a non-trivial toroidal magnetic field Bt. Realistic parameters comparable to observations are used to describe the magnetic field inside and outside the torus. The external poloidal magnetic field is assumed to fall off as a power function with decay index n (n = - d log (Bex) /d log(h)). The parameter space is explored to find all initial equilibrium solutions, at which perturbation is introduced. It is shown that with non-trivial toroidal field, the current ring attains equilibrium with a weaker external field. It is also shown that the torus attains equilibrium at higher altitude when the external field decays more rapidly (greater n) or the ratio of the toroidal flux in the torus to the external field increases. We further study stabilities of the torus at equilibrium by defining a critical decay index ncr (Kliem and Török 2006). A sufficiently strong toroidal field can completely suppress the torus instability due to the current hoop force. With a weak toroidal field, similar to the case of Bt=0, the instability occurs when the external magnetic field declines rapidly with height when the field decay index n>ncr. For realistic sets of parameters, the equilibrium height is within 10 solar radii, and the effective ncr is in the range of 1.0-1.6. The critical decay index increases when the ratio of the toroidal flux to the external field decreases. This work is supported by NSF CAREER grant ATM-0748428.

U.S. Army Research Office Workshop on Smart Materials, Structures and Mathematical Issues Held in Blacksburg, Virginia on 15-16 September 1988

DTIC Science & Technology

1989-01-01

prestrained Nitinol (an alloy of nickel and titanium) wires are embedded in an off-axis position in the graphite fiber reinforced epoxy composite beam... Nitinol ) alloy. Shape memory alloys have been applied to a number of items including connectors and heat engines, but have usually found application in... nitinol wire; the design includes prevention from ancillary jams. Miwa (1985) discusses the use of SMA actuator to sequential robotic control of multiple

Operation and maintenance cost data for residential photovoltaic modules/panels

NASA Technical Reports Server (NTRS)

Oster, J. R., Jr.; Zaremski, D. R., Jr.; Albert, E. M.; Hawkins, S. L.

1980-01-01

Costs associated with the operation and maintenance of residential photovoltaic modules and arrays are studied. Six basic topics related to operation and maintenance to photovoltaic arrays are investigated: maintenance; cleaning; panel replacement; gasket repair/replacement; wiring repair/replacement; and termination repair/replacement. The effects of the mounting types (rack mount, stand off mount, direct mount and integral mount) and the installation/replacement type (sequential, partial interruption and independent) are identified and described. Methods of reducing maintenance costs are suggested.

Mojibake - The rehearsal of word fragments in verbal recall.

PubMed

Lange-Küttner, Christiane; Sykorova, Eva

2015-01-01

Theories of verbal rehearsal usually assume that whole words are being rehearsed. However, words consist of letter sequences, or syllables, or word onset-vowel-coda, amongst many other conceptualizations of word structure. A more general term is the 'grain size' of word units (Ziegler and Goswami, 2005). In the current study, a new method measured the quantitative percentage of correctly remembered word structure. The amount of letters in the correct letter sequence as per cent of word length was calculated, disregarding missing or added letters. A forced rehearsal was tested by repeating each memory list four times. We tested low frequency (LF) English words versus geographical (UK) town names to control for content. We also tested unfamiliar international (INT) non-words and names of international (INT) European towns to control for familiarity. An immediate versus distributed repetition was tested with a between-subject design. Participants responded with word fragments in their written recall especially when they had to remember unfamiliar words. While memory of whole words was sensitive to content, presentation distribution and individual sex and language differences, recall of word fragments was not. There was no trade-off between memory of word fragments with whole word recall during the repetition, instead also word fragments significantly increased. Moreover, while whole word responses correlated with each other during repetition, and word fragment responses correlated with each other during repetition, these two types of word recall responses were not correlated with each other. Thus there may be a lower layer consisting of free, sparse word fragments and an upper layer that consists of language-specific, orthographically and semantically constrained words.

Effects of herbivory and patch size on tree seedling survivorship in a fog-dependent coastal rainforest in semiarid Chile.

PubMed

del-Val, Ek; Armesto, Juan J; Barbosa, Olga; Marquet, Pablo A

2007-09-01

The landscape (matrix) surrounding habitat fragments critically affects the biodiversity of those fragments due to biotic interchange and physical effects. However, to date, there have been only a limited number of studies on plant-animal interactions in fragmented landscapes, particularly on how tree seedling herbivory is affected by fragmentation. We have examined this question in a fog-dependent mosaic of rainforest fragments located on coastal mountaintops of semiarid Chile (30 degrees S), where the effects of the surrounding semiarid matrix and forest patch size (0.1-22 ha) on tree seedling survival were simultaneously addressed. The rainforest is strongly dominated by the endemic evergreen tree species Aextoxicon punctatum (Olivillo, approx. 80% of basal area). To assess the magnitudes and causes of Olivillo seedling mortality, we set up a field experiment where 512 tree seedlings of known age were transplanted into four forest fragments of different sizes in four 1.5 x 3-m plots per patch; one-half of each plot was fenced off with chicken wire to exclude small mammals. The plots were monitored for 22 months. Overall, 50% of the plants died during the experiment. The exclusion of small mammals from the plots increased seedling survival by 25%, with the effect being greater in smaller patches where matrix-dwelling herbivores are more abundant. This experiment highlights the important role of the surrounding matrix in affecting the persistence of trees in forest fragments. Because herbivores from the matrix cause greater tree seedling mortality in small patches, their effects must be taken into account in forest conservation-restoration plans.

Balancing "hands-on" with "hands-off" physical therapy interventions for the treatment of central sensitization pain in osteoarthritis.

PubMed

Lluch Girbés, E; Meeus, M; Baert, I; Nijs, J

2015-04-01

Traditional understanding of osteoarthritis-related pain has recently been challenged in light of evidence supporting a key role of central sensitization in a subgroup of this population. This fact may erroneously lead musculoskeletal therapists to conclude that hands-on interventions have no place in OA management, and that hands-off interventions must be applied exclusively. The aim of this paper is to encourage clinicians in finding an equilibrium between hands-on and hands-off interventions in patients with osteoarthritis-related pain dominated by central sensitization. The theoretical rationale for simultaneous application of manual therapy and pain neuroscience education is presented. Practical problems when combining these interventions are also addressed. Future studies should explore the combined effects of these treatment strategies to examine whether they increase therapeutic outcomes against current approaches for chronic osteoarthritis-related pain. Copyright © 2014 Elsevier Ltd. All rights reserved.

"Cut-off" effect of antioxidants and/or probes of variable lipophilicity in microheterogeneous media.

PubMed

Aliaga, Carolina; López de Arbina, Amaia; Rezende, Marcos Caroli

2016-09-01

The activities of two hydrophilic (ascorbic acid and Trolox) and two hydrophobic (α-tocopherol and BHT) antioxidants were measured by reaction with a series of 4-alkanoyloxyTEMPO radical probes 1 in buffered (pH 7), aqueous, micellar solutions of reduced Triton-X 100. In all cases, a cut-off effect was observed, in line with previous observations of the same effect for the partitioning of probe series 1 in this medium. These results support an interpretation of the cut-off effect in food emulsions, based on the "amphiphobic" nature of either the antioxidants or probes: competition between two molecular moieties, for the micellar hydrophobic core, tends to expose a reacting fragment differently to a more hydrophilic microenvironment, as the probe or antioxidant hydrophobicity increases. Copyright © 2016 Elsevier Ltd. All rights reserved.

The impact of slice-reduced computed tomography on histogram-based densitometry assessment of lung fibrosis in patients with systemic sclerosis

PubMed Central

Maurer, Britta; Suliman, Yossra A.; Morsbach, Fabian; Distler, Oliver; Frauenfelder, Thomas

2018-01-01

Background To evaluate usability of slice-reduced sequential computed tomography (CT) compared to standard high-resolution CT (HRCT) in patients with systemic sclerosis (SSc) for qualitative and quantitative assessment of interstitial lung disease (ILD) with respect to (I) detection of lung parenchymal abnormalities, (II) qualitative and semiquantitative visual assessment, (III) quantification of ILD by histograms and (IV) accuracy for the 20%-cut off discrimination. Methods From standard chest HRCT of 60 SSc patients sequential 9-slice-computed tomography (reduced HRCT) was retrospectively reconstructed. ILD was assessed by visual scoring and quantitative histogram parameters. Results from standard and reduced HRCT were compared using non-parametric tests and analysed by univariate linear regression analyses. Results With respect to the detection of parenchymal abnormalities, only the detection of intrapulmonary bronchiectasis was significantly lower in reduced HRCT compared to standard HRCT (P=0.039). No differences were found comparing visual scores for fibrosis severity and extension from standard and reduced HRCT (P=0.051–0.073). All scores correlated significantly (P<0.001) to histogram parameters derived from both, standard and reduced HRCT. Significant higher values of kurtosis and skewness for reduced HRCT were found (both P<0.001). In contrast to standard HRCT histogram parameters from reduced HRCT showed significant discrimination at cut-off 20% fibrosis (sensitivity 88% kurtosis and skewness; specificity 81% kurtosis and 86% skewness; cut-off kurtosis ≤26, cut-off skewness ≤4; both P<0.001). Conclusions Reduced HRCT is a robust method to assess lung fibrosis in SSc with minimal radiation dose with no difference in scoring assessment of lung fibrosis severity and extension in comparison to standard HRCT. In contrast to standard HRCT histogram parameters derived from the approach of reduced HRCT could discriminate at a threshold of 20% lung fibrosis with high sensitivity and specificity. Hence it might be used to detect early disease progression of lung fibrosis in context of monitoring and treatment of SSc patients. PMID:29850118

Sequential character of low-energy ternary and quaternary nuclear fission

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

Kadmensky, S. G., E-mail: kadmensky@phys.vsu.ru; Bulychev, A. O.

2016-09-15

An analysis of low-energy true ternary (quaternary) nuclear fission leads to the conclusion that these fission modes have a sequential two-step (three-step) character such that the emission of a third particle (third and fourth particles) and the separation of fission fragments occur at distinctly different instants, in contrast to the simultaneous emergence of all fission products in the case of onestep ternary (quaternary) fission. This conclusion relies on the following arguments. First, the emission of a third particle (third and fourth particles) from a fissile nucleus is due to a nonevaporative mechanism associated with a nonadiabatic character of the collectivemore » deformation motion of this nucleus at the stages preceding its scission. Second, the axial symmetry of the deformed fissile compound nucleus and the direction of its symmetry axis both remain unchanged at all stages of ternary (quaternary) fission. This circumstancemakes it possible to explain themechanism of the appearance of observed anisotropies and T — odd asymmeries in the angular distributions of products of ternary (quaternary) nuclear fission. Third, the T —odd asymmetry discovered experimentally in ternary nuclear fission induced by cold polarized neutrons obeys the T —invariance condition only in the case of a sequential two-step (three-step) character of true ternary (quaternary) nuclear fission. At the same time, this asymmetry is not a T —invariant quantity in the case of the simultaneous emission of products of true ternary (quaternary) nuclear fission from the fissile compound nucleus.« less

Remotely Adjustable Hydraulic Pump

NASA Technical Reports Server (NTRS)

Kouns, H. H.; Gardner, L. D.

1987-01-01

Outlet pressure adjusted to match varying loads. Electrohydraulic servo has positioned sleeve in leftmost position, adjusting outlet pressure to maximum value. Sleeve in equilibrium position, with control land covering control port. For lowest pressure setting, sleeve shifted toward right by increased pressure on sleeve shoulder from servovalve. Pump used in aircraft and robots, where hydraulic actuators repeatedly turned on and off, changing pump load frequently and over wide range.

Predicting coexistence of plants subject to a tolerance-competition trade-off.

PubMed

Haegeman, Bart; Sari, Tewfik; Etienne, Rampal S

2014-06-01

Ecological trade-offs between species are often invoked to explain species coexistence in ecological communities. However, few mathematical models have been proposed for which coexistence conditions can be characterized explicitly in terms of a trade-off. Here we present a model of a plant community which allows such a characterization. In the model plant species compete for sites where each site has a fixed stress condition. Species differ both in stress tolerance and competitive ability. Stress tolerance is quantified as the fraction of sites with stress conditions low enough to allow establishment. Competitive ability is quantified as the propensity to win the competition for empty sites. We derive the deterministic, discrete-time dynamical system for the species abundances. We prove the conditions under which plant species can coexist in a stable equilibrium. We show that the coexistence conditions can be characterized graphically, clearly illustrating the trade-off between stress tolerance and competitive ability. We compare our model with a recently proposed, continuous-time dynamical system for a tolerance-fecundity trade-off in plant communities, and we show that this model is a special case of the continuous-time version of our model.

Salt Effects on Surface Structures of Polyelectrolyte Multilayers (PEMs) Investigated by Vibrational Sum Frequency Generation (SFG) Spectroscopy.

PubMed

Ge, Aimin; Matsusaki, Michiya; Qiao, Lin; Akashi, Mitsuru; Ye, Shen

2016-04-26

Sum frequency generation (SFG) vibrational spectroscopy was employed to investigate the surface structures of polyelectrolyte multilayers (PEMs) constructed by sequentially alternating adsorption of poly(diallyldimethylammonium chloride) (PDDA) and poly(styrenesulfonate) (PSS). It was found that the surface structures and surface charge density of the as-deposited PEMs of PDDA/PSS significantly depend on the concentration of sodium chloride (NaCl) present in the polyelectrolyte solutions. Furthermore, it was found that the surface structure of the as-deposited PEMs is in a metastable state and will reach the equilibrium state by diffusion of the polyelectrolyte chain after an aging process, resulting in a polyelectrolyte mixture on the PEM surfaces.

Aging of clean foams

NASA Astrophysics Data System (ADS)

Weon, Byung Mook; Stewart, Peter S.

2014-11-01

Aging is an inevitable process in living systems. Here we show how clean foams age with time through sequential coalescence events: in particular, foam aging resembles biological aging. We measure population dynamics of bubbles in clean foams through numerical simulations with a bubble network model. We demonstrate that death rates of individual bubbles increase exponentially with time, independent on initial conditions, which is consistent with the Gompertz mortality law as usually found in biological aging. This consistency suggests that clean foams as far-from-equilibrium dissipative systems are useful to explore biological aging. This work (NRF-2013R1A22A04008115) was supported by Mid-career Researcher Program through NRF grant funded by the MEST.

Multi-objective design optimization of antenna structures using sequential domain patching with automated patch size determination

NASA Astrophysics Data System (ADS)

Koziel, Slawomir; Bekasiewicz, Adrian

2018-02-01

In this article, a simple yet efficient and reliable technique for fully automated multi-objective design optimization of antenna structures using sequential domain patching (SDP) is discussed. The optimization procedure according to SDP is a two-step process: (i) obtaining the initial set of Pareto-optimal designs representing the best possible trade-offs between considered conflicting objectives, and (ii) Pareto set refinement for yielding the optimal designs at the high-fidelity electromagnetic (EM) simulation model level. For the sake of computational efficiency, the first step is realized at the level of a low-fidelity (coarse-discretization) EM model by sequential construction and relocation of small design space segments (patches) in order to create a path connecting the extreme Pareto front designs obtained beforehand. The second stage involves response correction techniques and local response surface approximation models constructed by reusing EM simulation data acquired in the first step. A major contribution of this work is an automated procedure for determining the patch dimensions. It allows for appropriate selection of the number of patches for each geometry variable so as to ensure reliability of the optimization process while maintaining its low cost. The importance of this procedure is demonstrated by comparing it with uniform patch dimensions.

A Longitudinal Study in Children With Sequential Bilateral Cochlear Implants: Time Course for the Second Implanted Ear and Bilateral Performance.

PubMed

Reeder, Ruth M; Firszt, Jill B; Cadieux, Jamie H; Strube, Michael J

2017-01-01

Whether, and if so when, a second-ear cochlear implant should be provided to older, unilaterally implanted children is an ongoing clinical question. This study evaluated rate of speech recognition progress for the second implanted ear and with bilateral cochlear implants in older sequentially implanted children and evaluated localization abilities. A prospective longitudinal study included 24 bilaterally implanted children (mean ear surgeries at 5.11 and 14.25 years). Test intervals were every 3-6 months through 24 months postbilateral. Test conditions were each ear and bilaterally for speech recognition and localization. Overall, the rate of progress for the second implanted ear was gradual. Improvements in quiet continued through the second year of bilateral use. Improvements in noise were more modest and leveled off during the second year. On all measures, results from the second ear were poorer than the first. Bilateral scores were better than either ear alone for all measures except sentences in quiet and localization. Older sequentially implanted children with several years between surgeries may obtain speech understanding in the second implanted ear; however, performance may be limited and rate of progress gradual. Continued contralateral ear hearing aid use and reduced time between surgeries may enhance outcomes.

Sequential assessment via daphnia and zebrafish for systematic toxicity screening of heterogeneous substances.

PubMed

Jang, Gun Hyuk; Park, Chang-Beom; Kang, Benedict J; Kim, Young Jun; Lee, Kwan Hyi

2016-09-01

Environment and organisms are persistently exposed by a mixture of various substances. However, the current evaluation method is mostly based on an individual substance's toxicity. A systematic toxicity evaluation of heterogeneous substances needs to be established. To demonstrate toxicity assessment of mixture, we chose a group of three typical ingredients in cosmetic sunscreen products that frequently enters ecosystems: benzophenone-3 (BP-3), ethylhexyl methoxycinnamate (EHMC), and titanium dioxide nanoparticle (TiO2 NP). We first determined a range of nominal toxic concentration of each ingredient or substance using Daphnia magna, and then for the subsequent organismal level phenotypic assessment, chose the wild-type zebrafish embryos. Any phenotype change, such as body deformation, led to further examinations on the specific organs of transgenic zebrafish embryos. Based on the systematic toxicity assessments of the heterogeneous substances, we offer a sequential environmental toxicity assessment protocol that starts off by utilizing Daphnia magna to determine a nominal concentration range of each substance and finishes by utilizing the zebrafish embryos to detect defects on the embryos caused by the heterogeneous substances. The protocol showed additive toxic effects of the mixtures. We propose a sequential environmental toxicity assessment protocol for the systematic toxicity screening of heterogeneous substances from Daphnia magna to zebrafish embryo in-vivo models. Copyright © 2016 Elsevier Ltd. All rights reserved.

Implementation of Temperature Sequential Controller on Variable Speed Drive

NASA Astrophysics Data System (ADS)

Cheong, Z. X.; Barsoum, N. N.

2008-10-01

There are many pump and motor installations with quite extensive speed variation, such as Sago conveyor, heating, ventilation and air conditioning (HVAC) and water pumping system. A common solution for these applications is to run several fixed speed motors in parallel, with flow control accomplish by turning the motors on and off. This type of control method causes high in-rush current, and adds a risk of damage caused by pressure transients. This paper explains the design and implementation of a temperature speed control system for use in industrial and commercial sectors. Advanced temperature speed control can be achieved by using ABB ACS800 variable speed drive-direct torque sequential control macro, programmable logic controller and temperature transmitter. The principle of direct torque sequential control macro (DTC-SC) is based on the control of torque and flux utilizing the stator flux field orientation over seven preset constant speed. As a result of continuous comparison of ambient temperature to the references temperatures; electromagnetic torque response is particularly fast to the motor state and it is able maintain constant speeds. Experimental tests have been carried out by using ABB ACS800-U1-0003-2, to validate the effectiveness and dynamic respond of ABB ACS800 against temperature variation, loads, and mechanical shocks.

Microsynthesis and electron ionization mass spectral studies of O(S)-alkyl N,N-dimethyl alkylphosphono(thiolo)thionoamidates for Chemical Weapons Convention verification.

PubMed

Saeidian, Hamdollah; Babri, Mehran; Abdoli, Morteza; Sarabadani, Mansour; Ashrafi, Davood; Naseri, Mohammad Taghi

2012-12-15

The availability of mass spectra and interpretation skills are essential for unambiguous identification of the Chemical Weapons Convention (CWC)-related chemicals. The O(S)-alkyl N,N-dimethyl alkylphosphono(thiolo)thionoamidates are included in the list of scheduled CWC-related compounds, but there are very few spectra from these compounds in the literature. This paper examines these spectra and their mass spectral fragmentation routes. The title chemicals were prepared through microsynthetic protocols and were analyzed using electron ionization mass spectrometry with gas chromatography as a MS-inlet system. Structures of fragments were confirmed using analysis of fragment ions of deuterated analogs, tandem mass spectrometry and density functional theory (DFT) calculations. Mass spectrometric studies revealed some interesting fragmentation pathways during the ionization process, such as alkene and amine elimination and McLafferty-type rearrangements. The most important fragmentation route of the chemicals is the thiono-thiolo rearrangement. DFT calculations are used to support MS results and to reveal relative preference formation of fragment ions. The retention indices (RIs) of all the studied compounds are also reported. Mass spectra of the synthesized compounds were investigated with the aim to enrich the Organization for the Prohibition of Chemical Weapons (OPCW) Central Analytical Database (OCAD) which may be used for detection and identification of CWC-related chemicals during on-site inspection and/or off-site analysis such as OPCW proficiency tests. Copyright © 2012 John Wiley & Sons, Ltd.

Multimodeling Framework for Predicting Water Quality in Fragmented Agriculture-Forest Ecosystems

NASA Astrophysics Data System (ADS)

Rose, J. B.; Guber, A.; Porter, W. F.; Williams, D.; Tamrakar, S.; Dechen Quinn, A.

2012-12-01

Both livestock and wildlife are major contributors of nonpoint pollution of surface water bodies. The interactions among them can substantially increase the chance of contamination especially in fragmented agriculture-forest landscapes, where wildlife (e.g. white tailed deer) can transmit diseases between remote farms. Unfortunately, models currently available for predicting fate and transport of microorganisms in these ecosystems do not account for such interactions. The objectives of this study are to develop and test a multimodeling framework that assesses the risk of microbial contamination of surface water caused by wildlife-livestock interactions in fragmented agriculture-forest ecosystems. The framework consists of a modified Soil Water Assessment Tool (SWAT), KINematic Runoff and EROSion model (KINEROS2) with the add-on module STWIR (Microorganism Transport with Infiltration and Runoff), RAMAS GIS, SIR compartmental model and Quantitative Microbial Risk Assessment model (QMRA). The watershed-scale model SWAT simulates plant biomass growth, wash-off of microorganisms from foliage and soil, overland and in-stream microbial transport, microbial growth, and die-off in foliage and soil. RAMAS GIS model predicts the most probable habitat and subsequent population of white-tailed deer based on land use and crop biomass. KINEROS-STWIR simulates overland transport of microorganisms released from soil, surface applied manure, and fecal deposits during runoff events at high temporal and special resolutions. KINEROS-STWIR and RAMAS GIS provide input for an SIR compartmental model which simulates disease transmission within and between deer groups. This information is used in SWAT model to account for transmission and deposition of pathogens by white tailed deer in stream water, foliage and soil. The QMRA approach extends to microorganisms inactivated in forage and water consumed by deer. Probabilities of deer infections and numbers of infected animals are computed based on a dose-response approach, including Beta Poisson and Maximum Risk models, which take into account pathogen variation in infectivity. An example of the Multimodeling framework performance for a fragmented agriculture-forest ecosystem will be shown in the presentation.

A sequential-move game for enhancing safety and security cooperation within chemical clusters.

PubMed

Pavlova, Yulia; Reniers, Genserik

2011-02-15

The present paper provides a game theoretic analysis of strategic cooperation on safety and security among chemical companies within a chemical industrial cluster. We suggest a two-stage sequential move game between adjacent chemical plants and the so-called Multi-Plant Council (MPC). The MPC is considered in the game as a leader player who makes the first move, and the individual chemical companies are the followers. The MPC's objective is to achieve full cooperation among players through establishing a subsidy system at minimum expense. The rest of the players rationally react to the subsidies proposed by the MPC and play Nash equilibrium. We show that such a case of conflict between safety and security, and social cooperation, belongs to the 'coordination with assurance' class of games, and we explore the role of cluster governance (fulfilled by the MPC) in achieving a full cooperative outcome in domino effects prevention negotiations. The paper proposes an algorithm that can be used by the MPC to develop the subsidy system. Furthermore, a stepwise plan to improve cross-company safety and security management in a chemical industrial cluster is suggested and an illustrative example is provided. Copyright © 2010 Elsevier B.V. All rights reserved.

Determination of yeast assimilable nitrogen content in wine fermentations by sequential injection analysis with spectrophotometric detetection.

PubMed

Muik, Barbara; Edelmann, Andrea; Lendl, Bernhard; Ayora-Cañada, María José

2002-09-01

An automated method for measuring the primary amino acid concentration in wine fermentations by sequential injection analysis with spectrophotometric detection was developed. Isoindole-derivatives from the primary amino acid were formed by reaction with o-phthaldialdehyde and N-acetyl- L-cysteine and measured at 334 nm with respect to a baseline point at 700 nm to compensate the observed Schlieren effect. As the reaction kinetic was strongly matrix dependent the analytical readout at the final reaction equilibrium has been evaluated. Therefore four parallel reaction coils were included in the flow system to be capable of processing four samples simultaneously. Using isoleucine as the representative primary amino acid in wine fermentations a linear calibration curve from 2 to 10 mM isoleucine, corresponding to 28 to 140 mg nitrogen/L (N/L) was obtained. The coefficient of variation of the method was 1.5% at a throughput of 12 samples per hour. The developed method was successfully used to monitor two wine fermentations during alcoholic fermentation. The results were in agreement with an external reference method based on high performance liquid chromatography. A mean-t-test showed no significant differences between the two methods at a confidence level of 95%.

Ensemble Sampling vs. Time Sampling in Molecular Dynamics Simulations of Thermal Conductivity

DOE PAGES

Gordiz, Kiarash; Singh, David J.; Henry, Asegun

2015-01-29

In this report we compare time sampling and ensemble averaging as two different methods available for phase space sampling. For the comparison, we calculate thermal conductivities of solid argon and silicon structures, using equilibrium molecular dynamics. We introduce two different schemes for the ensemble averaging approach, and show that both can reduce the total simulation time as compared to time averaging. It is also found that velocity rescaling is an efficient mechanism for phase space exploration. Although our methodology is tested using classical molecular dynamics, the ensemble generation approaches may find their greatest utility in computationally expensive simulations such asmore » first principles molecular dynamics. For such simulations, where each time step is costly, time sampling can require long simulation times because each time step must be evaluated sequentially and therefore phase space averaging is achieved through sequential operations. On the other hand, with ensemble averaging, phase space sampling can be achieved through parallel operations, since each ensemble is independent. For this reason, particularly when using massively parallel architectures, ensemble sampling can result in much shorter simulation times and exhibits similar overall computational effort.« less

Cowbird Distribution at Different Scales of Fragmentation: Trade-offs Between Breeding and Feeding Opportunities

Treesearch

Therese M. Donovan; Frank r. Thompson III; John R. Faaborg

2000-01-01

The distribution of Brown-headed Cowbirds should reflect the distribution of their feeding (agricultural or grassy areas) and breeding (host) resources. Because an increase in one resource (e.g., agricultural areas) is often at the expense of the second resource (forest hosts), relationships between cowbird abundance, forest area, and number of hosts may reflect this...

Structural Feature Ions for Distinguishing N- and O-Linked Glycan Isomers by LC-ESI-IT MS/MS

NASA Astrophysics Data System (ADS)

Everest-Dass, Arun V.; Abrahams, Jodie L.; Kolarich, Daniel; Packer, Nicolle H.; Campbell, Matthew P.

2013-06-01

Glycomics is the comprehensive study of glycan expression in an organism, cell, or tissue that relies on effective analytical technologies to understand glycan structure-function relationships. Owing to the macro- and micro-heterogeneity of oligosaccharides, detailed structure characterization has required an orthogonal approach, such as a combination of specific exoglycosidase digestions, LC-MS/MS, and the development of bioinformatic resources to comprehensively profile a complex biological sample. Liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS/MS) has emerged as a key tool in the structural analysis of oligosaccharides because of its high sensitivity, resolution, and robustness. Here, we present a strategy that uses LC-ESI-MS/MS to characterize over 200 N- and O-glycans from human saliva glycoproteins, complemented by sequential exoglycosidase treatment, to further verify the annotated glycan structures. Fragment-specific substructure diagnostic ions were collated from an extensive screen of the literature available on the detailed structural characterization of oligosaccharides and, together with other specific glycan structure feature ions derived from cross-ring and glycosidic-linkage fragmentation, were used to characterize the glycans and differentiate isomers. The availability of such annotated mass spectrometric fragmentation spectral libraries of glycan structures, together with such substructure diagnostic ions, will be key inputs for the future development of the automated elucidation of oligosaccharide structures from MS/MS data.

Dynamic fractionation of trace metals in soil and sediment samples using rotating coiled column extraction and sequential injection microcolumn extraction: a comparative study.

PubMed

Rosende, Maria; Savonina, Elena Yu; Fedotov, Petr S; Miró, Manuel; Cerdà, Víctor; Wennrich, Rainer

2009-09-15

Dynamic fractionation has been recognized as an appealing alternative to conventional equilibrium-based sequential extraction procedures (SEPs) for partitioning of trace elements (TE) in environmental solid samples. This paper reports the first attempt for harmonization of flow-through dynamic fractionation using two novel methods, the so-called sequential injection microcolumn (SIMC) extraction and rotating coiled column (RCC) extraction. In SIMC extraction, a column packed with the solid sample is clustered in a sequential injection system, while in RCC, the particulate matter is retained under the action of centrifugal forces. In both methods, the leachants are continuously pumped through the solid substrates by the use of either peristaltic or syringe pumps. A five-step SEP was selected for partitioning of Cu, Pb and Zn in water soluble/exchangeable, acid-soluble, easily reducible, easily oxidizable and moderately reducible fractions from 0.2 to 0.5 g samples at an extractant flow rate of 1.0 mL min(-1) prior to leachate analysis by inductively coupled plasma-atomic emission spectrometry. Similarities and discrepancies between both dynamic approaches were ascertained by fractionation of TE in certified reference materials, namely, SRM 2711 Montana Soil and GBW 07311 sediment, and two real soil samples as well. Notwithstanding the different extraction conditions set by both methods, similar trends of metal distribution were in generally found. The most critical parameters for reliable assessment of mobilizable pools of TE in worse-case scenarios are the size-distribution of sample particles, the density of particles, the content of organic matter and the concentration of major elements. For reference materials and a soil rich in organic matter, the extraction in RCC results in slightly higher recoveries of environmentally relevant fractions of TE, whereas SIMC leaching is more effective for calcareous soils.

Cation disorder and gas phase equilibrium in an YBa 2Cu 3O 7- x superconducting thin film

NASA Astrophysics Data System (ADS)

Shin, Dong Chan; Ki Park, Yong; Park, Jong-Chul; Kang, Suk-Joong L.; Yong Yoon, Duk

1997-02-01

YBa 2Cu 3O 7- x superconducting thin films have been grown by in situ off-axis rf sputtering with varying oxygen pressure, Ba/Y ratio in a target, and deposition temperature. With decreasing oxygen pressure, increasing Ba/Y ratio, increasing deposition temperature, the critical temperature of the thin films decreased and the c-axis length increased. The property change of films with the variation of deposition variables has been explained by a gas phase equilibrium of the oxidation reaction of Ba and Y. Applying Le Chatelier's principle to the oxidation reaction, we were able to predict the relation of deposition variables and the resultant properties of thin films; the prediction was in good agreement with the experimental results. From the relation between the three deposition variables and gas phase equilibrium, a 3-dimensional processing diagram was introduced. This diagram has shown that the optimum deposition condition of YBa 2Cu 3O 7- x thin films is not a fixed point but can be varied. The gas phase equilibrium can also be applied to the explanation of previous results that good quality films were obtained at low deposition temperature using active species, such as O, O 3, and O 2+.

Droplet spreading and capillary imbibition in a porous medium: A coupled IB-VOF method based numerical study

NASA Astrophysics Data System (ADS)

Das, Saurish; Patel, H. V.; Milacic, E.; Deen, N. G.; Kuipers, J. A. M.

2018-01-01

We investigate the dynamics of a liquid droplet in contact with a surface of a porous structure by means of the pore-scale level, fully resolved numerical simulations. The geometrical details of the solid porous matrix are resolved by a sharp interface immersed boundary method on a Cartesian computational grid, whereas the motion of the gas-liquid interface is tracked by a mass conservative volume of fluid method. The numerical simulations are performed considering a model porous structure that is approximated by a 3D cubical scaffold with cylindrical struts. The effect of the porosity and the equilibrium contact angle (between the gas-liquid interface and the solid struts) on the spreading behavior, liquid imbibition, and apparent contact angle (between the gas-liquid interface and the porous base) are studied. We also perform several simulations for droplet spreading on a flat surface as a reference case. Gas-liquid systems of the Laplace number, La = 45 and La = 144 × 103 are considered neglecting the effect of gravity. We report the time exponent (n) and pre-factor (C) of the power law describing the evolution of the spreading diameter (S = Ctn) for different equilibrium contact angles and porosity. Our simulations reveal that the apparent or macroscopic contact angle varies linearly with the equilibrium contact angle and increases with porosity. Not necessarily for all the wetting porous structures, a continuous capillary drainage occurs, and we find that the rate of the capillary drainage very much depends on the fluid inertia. At La = 144 × 103, numerically we capture the capillary wave induced pinch-off and daughter droplet ejection. We observe that on the porous structure the pinch-off is weak compared to that on a flat plate.

Callipeltosides A, B and C: Total Syntheses and Structural Confirmation

PubMed Central

Frost, James R; Pearson, Colin M; Snaddon, Thomas N; Booth, Richard A; Turner, Richard M; Gold, Johan; Shaw, David M; Gaunt, Matthew J; Ley, Steven V

2015-01-01

Since their isolation almost 20 years ago, the callipeltosides have been of long standing interest to the synthetic community owing to their unique structural features and inherent biological activity. Herein we present our full research effort that has led to the synthesis of these molecules. Key aspects of our final strategy include 1) synthesis of the C1–C9 pyran core (5) using an AuCl3-catalysed cyclisation; 2) formation of C10–C22 vinyl iodide (55) by sequential bidirectional Stille reactions and 3) diastereoselective union of these advanced fragments by means of an alkenylzinc addition (d.r.=91:9 at C9). The common callipeltoside aglycon (4) was completed in a further five steps. Following this, all three sugar fragments were appended to provide the entire callipeltoside family. In addition to this, D-configured callipeltose B was synthesised and appended to the callipeltoside aglycon. The 1H NMR spectrum of this molecule was found to be significantly different to the natural isolate, further supporting our assignment of callipeltoside B (2). PMID:26230615

Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody

PubMed Central

Kwong, Peter D.; Wyatt, Richard; Robinson, James; Sweet, Raymond W.; Sodroski, Joseph; Hendrickson, Wayne A.

2017-01-01

The entry of human immunodeficiency virus (HIV) into cells requires the sequential interaction of the viral exterior envelope glycoprotein, gp120, with the CD4 glycoprotein and a chemokine receptor on the cell surface. These interactions initiate a fusion of the viral and cellular membranes. Although gpl20 can elicit virus-neutralizing antibodies, HIV eludes the immune system. We have solved the X-ray crystal structure at 2.5 Å resolution of an HIV-1 gp120 core complexed with a two-domain fragment of human CD4 and an antigen-binding fragment of a neutralizing antibody that blocks chemokine-receptor binding. The structure reveals a cavity-laden CD4-gp120 interface, a conserved binding site for the chemokine receptor, evidence for a conformational change upon CD4 binding, the nature of a CD4-induced antibody epitope, and specific mechanisms for immune evasion. Our results provide a framework for understanding the complex biology of HIV entry into cells and should guide efforts to intervene. PMID:9641677

Biochemical analyses indicate that binding and cleavage specificities define the ordered processing of human Okazaki fragments by Dna2 and FEN1.

PubMed

Gloor, Jason W; Balakrishnan, Lata; Campbell, Judith L; Bambara, Robert A

2012-08-01

In eukaryotic Okazaki fragment processing, the RNA primer is displaced into a single-stranded flap prior to removal. Evidence suggests that some flaps become long before they are cleaved, and that this cleavage involves the sequential action of two nucleases. Strand displacement characteristics of the polymerase show that a short gap precedes the flap during synthesis. Using biochemical techniques, binding and cleavage assays presented here indicate that when the flap is ∼ 30 nt long the nuclease Dna2 can bind with high affinity to the flap and downstream double strand and begin cleavage. When the polymerase idles or dissociates the Dna2 can reorient for additional contacts with the upstream primer region, allowing the nuclease to remain stably bound as the flap is further shortened. The DNA can then equilibrate to a double flap that can bind Dna2 and flap endonuclease (FEN1) simultaneously. When Dna2 shortens the flap even more, FEN1 can displace the Dna2 and cleave at the flap base to make a nick for ligation.

Protein Folding—How and Why: By Hydrogen Exchange, Fragment Separation, and Mass Spectrometry

PubMed Central

Englander, S. Walter; Mayne, Leland; Kan, Zhong-Yuan; Hu, Wenbing

2017-01-01

Advanced hydrogen exchange (HX) methodology can now determine the structure of protein folding intermediates and their progression in folding pathways. Key developments over time include the HX pulse labeling method with nuclear magnetic resonance analysis, development of the fragment separation method, the addition to it of mass spectrometric (MS) analysis, and recent improvements in the HX MS technique and data analysis. Also, the discovery of protein foldons and their role supplies an essential interpretive link. Recent work using HX pulse labeling with HX MS analysis finds that a number of proteins fold by stepping through a reproducible sequence of native-like intermediates in an ordered pathway. The stepwise nature of the pathway is dictated by the cooperative foldon unit construction of the protein. The pathway order is determined by a sequential stabilization principle; prior native-like structure guides the formation of adjacent native-like structure. This view does not match the funneled energy landscape paradigm of a very large number of folding tracks, which was framed before foldons were known. PMID:27145881

PGLa-H tandem-repeat peptides active against multidrug resistant clinical bacterial isolates.

PubMed

Rončević, Tomislav; Gajski, Goran; Ilić, Nada; Goić-Barišić, Ivana; Tonkić, Marija; Zoranić, Larisa; Simunić, Juraj; Benincasa, Monica; Mijaković, Marijana; Tossi, Alessandro; Juretić, Davor

2017-02-01

Antimicrobial peptides (AMPs) are promising candidates for new antibiotic classes but often display an unacceptably high toxicity towards human cells. A naturally produced C-terminal fragment of PGLa, named PGLa-H, has been reported to have a very low haemolytic activity while maintaining a moderate antibacterial activity. A sequential tandem repeat of this fragment, diPGLa-H, was designed, as well as an analogue with a Val to Gly substitution at a key position. These peptides showed markedly improved in vitro bacteriostatic and bactericidal activity against both reference strains and multidrug resistant clinical isolates of Gram-negative and Gram-positive pathogens, with generally low toxicity for human cells as assessed by haemolysis, cell viability, and DNA damage assays. The glycine substitution analogue, kiadin, had a slightly better antibacterial activity and reduced haemolytic activity, which may correlate with an increased flexibility of its helical structure, as deduced using molecular dynamics simulations. These peptides may serve as useful lead compounds for developing anti-infective agents against resistant Gram-negative and Gram-positive species. Copyright © 2016 Elsevier B.V. All rights reserved.

Dissecting the dynamic conformations of the metamorphic protein lymphotactin.

PubMed

Harvey, Sophie R; Porrini, Massimiliano; Konijnenberg, Albert; Clarke, David J; Tyler, Robert C; Langridge-Smith, Patrick R R; MacPhee, Cait E; Volkman, Brian F; Barran, Perdita E

2014-10-30

A mass spectrometer provides an ideal laboratory to probe the structure and stability of isolated protein ions. Interrogation of each discrete mass/charge-separated species enables the determination of the intrinsic stability of a protein fold, gaining snapshots of unfolding pathways. In solution, the metamorphic protein lymphotactin (Ltn) exists in equilibrium between two distinct conformations, a monomeric (Ltn10) and a dimeric (Ltn40) fold. Here, we use electron capture dissociation (ECD) and drift tube ion mobility-mass spectrometry (DT IM-MS) to analyze both forms and use molecular dynamics (MD) to consider how the solution fold alters in a solvent-free environment. DT IM-MS reveals significant conformational flexibility for the monomer, while the dimer appears more conformationally restricted. These findings are supported by MD calculations, which reveal how salt bridges stabilize the conformers in vacuo. Following ECD experiments, a distinctive fragmentation pattern is obtained for both the monomer and dimer. Monomer fragmentation becomes more pronounced with increasing charge state especially in the disordered regions and C-terminal α-helix in the solution fold. Lower levels of fragmentation are seen in the β-sheet regions and in regions that contain salt bridges, identified by MD simulations. The lowest charge state of the dimer for which we obtain ECD data ([D+9H](9+)) exhibits extensive fragmentation with no relationship to the solution fold and has a smaller collision cross section (CCS) than charge states 10-13+, suggesting a "collapsed" encounter complex. Other charge states of the dimer, as for the monomer, are resistant to fragmentation in regions of β-sheets in the solution fold. This study provides evidence for preservation and loss of global fold and secondary structural elements, providing a tantalizing glimpse into the power of the emerging field of native top-down mass spectrometry.

Non local-thermodynamical-equilibrium effects in the simulation of laser-produced plasmas

NASA Astrophysics Data System (ADS)

Klapisch, M.; Bar-Shalom, A.; Oreg, J.; Colombant, D.

1998-05-01

Local thermodynamic equilibrium (LTE) breaks down in directly or indirectly driven laser plasmas because of sharp gradients, energy deposition, etc. For modeling non-LTE effects in hydrodynamical simulations, Busquet's model [Phys. Fluids B 5, 4191 (1993)] is very convenient and efficient. It uses off-line generated LTE opacities and equation of states via an effective, radiation-dependent ionization temperature Tz. An overview of the model is given. The results are compared with an elaborate collisional radiative model based on superconfigurations. The agreements for average charge Z* and opacities are surprisingly good, even more so when the plasma is immersed in a radiation field. Some remaining discrepancy at low density is attributed to dielectronic recombination. Improvement appears possible, especially for emissivities, because the concept of ionization temperature seems to be validated.

Current Saturation Avoidance with Real-Time Control using DPCS

NASA Astrophysics Data System (ADS)

Ferrara, M.; Hutchinson, I.; Wolfe, S.; Stillerman, J.; Fredian, T.

2008-11-01

Tokamak ohmic-transformer and equilibrium-field coils need to be able to operate near their maximum current capabilities. However if they reach their upper limit during high-performance discharges or in the presence of a strong off-normal event, shape control is compromised, and instability, even plasma disruptions can result. On Alcator C-Mod we designed and tested an anti-saturation routine which detects the impending saturation of OH and EF currents and interpolates to a neighboring safe equilibrium in real-time. The routine was implemented with a multi-processor, multi-time-scale control scheme, which is based on a master process and multiple asynchronous slave processes. The scheme is general and can be used for any computationally-intensive algorithm. USDoE award DE- FC02-99ER545512.

The Navy/NASA Engine Program (NNEP89): Interfacing the program for the calculation of complex Chemical Equilibrium Compositions (CEC)

NASA Technical Reports Server (NTRS)

Gordon, Sanford

1991-01-01

The NNEP is a general computer program for calculating aircraft engine performance. NNEP has been used extensively to calculate the design and off-design (matched) performance of a broad range of turbine engines, ranging from subsonic turboprops to variable cycle engines for supersonic transports. Recently, however, there has been increased interest in applications for which NNEP is not capable of simulating, such as the use of alternate fuels including cryogenic fuels and the inclusion of chemical dissociation effects at high temperatures. To overcome these limitations, NNEP was extended by including a general chemical equilibrium method. This permits consideration of any propellant system and the calculation of performance with dissociation effects. The new extended program is referred to as NNEP89.

On the fragmentation of filaments in a molecular cloud simulation

NASA Astrophysics Data System (ADS)

Chira, R.-A.; Kainulainen, J.; Ibáñez-Mejía, J. C.; Henning, Th.; Mac Low, M.-M.

2018-03-01

Context. The fragmentation of filaments in molecular clouds has attracted a lot of attention recently as there seems to be a close relation between the evolution of filaments and star formation. The study of the fragmentation process has been motivated by simple analytical models. However, only a few comprehensive studies have analysed the evolution of filaments using numerical simulations where the filaments form self-consistently as part of large-scale molecular cloud evolution. Aim. We address the early evolution of parsec-scale filaments that form within individual clouds. In particular, we focus on three questions: How do the line masses of filaments evolve? How and when do the filaments fragment? How does the fragmentation relate to the line masses of the filaments? Methods: We examine three simulated molecular clouds formed in kiloparsec-scale numerical simulations performed with the FLASH adaptive mesh refinement magnetohydrodynamic code. The simulations model a self-gravitating, magnetised, stratified, supernova-driven interstellar medium, including photoelectric heating and radiative cooling. We follow the evolution of the clouds for 6 Myr from the time self-gravity starts to act. We identify filaments using the DisPerSe algorithm, and compare the results to other filament-finding algorithms. We determine the properties of the identified filaments and compare them with the predictions of analytic filament stability models. Results: The average line masses of the identified filaments, as well as the fraction of mass in filamentary structures, increases fairly continuously after the onset of self-gravity. The filaments show fragmentation starting relatively early: the first fragments appear when the line masses lie well below the critical line mass of Ostriker's isolated hydrostatic equilibrium solution ( 16 M⊙ pc-1), commonly used as a fragmentation criterion. The average line masses of filaments identified in three-dimensional volume density cubes increases far more quickly than those identified in two-dimensional column density maps. Conclusions: Our results suggest that hydrostatic or dynamic compression from the surrounding cloud has a significant impact on the early dynamical evolution of filaments. A simple model of an isolated, isothermal cylinder may not provide a good approach for fragmentation analysis. Caution must be exercised in interpreting distributions of properties of filaments identified in column density maps, especially in the case of low-mass filaments. Comparing or combining results from studies that use different filament finding techniques is strongly discouraged.

Maintaining equilibrium in professional role identity: a grounded theory study of health visitors' perceptions of their changing professional practice context.

PubMed

Machin, Alison I; Machin, Tony; Pearson, Pauline

2012-07-01

This article reports the study of a group of United Kingdom health visitors' interactions with their changing practice context, focusing on role identity and influences on its stability. United Kingdom policies have urged health visitors to refocus their role as key public health nurses. Reduced role identity clarity precipitated the emergence of different models of health visiting public health work. An inconsistent role standard can lead to role identity fragmentation and conflict across a group. It may precipitate individual role crisis, affecting optimum role performance. Seventeen health visitors in two United Kingdom community healthcare organizations participated in a grounded theory study, incorporating constant comparative analysis. Direct observations and individual interviews were undertaken between 2002 and 2008. Four interlinked categories emerged: professional role identity (core category); professional role in action; interprofessional working; and local micro-systems for practice; each influencing participants' sense of identity and self-worth. The Role Identity Equilibrium Process explains interactive processes occurring at different levels of participants' practice. Re-establishing equilibrium and consistency in health visiting identity is a priority. This study's findings have significance for other nurses and health professionals working in complex systems, affected by role change and challenges to role identity. © 2011 Blackwell Publishing Ltd.

Steering the azido-tetrazole equilibrium of 4-azidopyrimidines via substituent variation - implications for drug design and azide-alkyne cycloadditions.

PubMed

Thomann, A; Zapp, J; Hutter, M; Empting, M; Hartmann, R W

2015-11-21

This paper focuses on an interesting constitutional isomerism called azido-tetrazole equilibrium which is observed in azido-substituted N-heterocycles. We present a systematic investigation of substituent effects on the isomer ratio within a 2-substituted 4-azidopyrimidine model scaffold. NMR- and IR-spectroscopy as well as X-ray crystallography were employed for thorough analysis and characterization of synthesized derivatives. On the basis of this data, we demonstrate the possibility to steer this valence tautomerism towards the isomer of choice by means of substituent variation. We show that the tetrazole form can act as an efficient disguise for the corresponding azido group masking its well known reactivity in azide-alkyne cycloadditions (ACCs). In copper(I)-catalyzed AAC reactions, substituent-stabilized tetrazoles displayed a highly decreased or even abolished reactivity whereas azides and compounds in the equilibrium were directly converted. By use of an acid sensitive derivative, we provide, to our knowledge, the first experimental basis for a possible exploitation of this dynamic isomerism as a pH-dependent azide-protecting motif for selective SPAAC conjugations in aqueous media. Finally, we demonstrate the applicability and efficiency of stabilized tetrazolo[1,5-c]pyrimidines for Fragment-Based Drug Design (FBDD) in the field of quorum sensing inhibitors.

Off-line simulation inspires insight: A neurodynamics approach to efficient robot task learning.

PubMed

Sousa, Emanuel; Erlhagen, Wolfram; Ferreira, Flora; Bicho, Estela

2015-12-01

There is currently an increasing demand for robots able to acquire the sequential organization of tasks from social learning interactions with ordinary people. Interactive learning-by-demonstration and communication is a promising research topic in current robotics research. However, the efficient acquisition of generalized task representations that allow the robot to adapt to different users and contexts is a major challenge. In this paper, we present a dynamic neural field (DNF) model that is inspired by the hypothesis that the nervous system uses the off-line re-activation of initial memory traces to incrementally incorporate new information into structured knowledge. To achieve this, the model combines fast activation-based learning to robustly represent sequential information from single task demonstrations with slower, weight-based learning during internal simulations to establish longer-term associations between neural populations representing individual subtasks. The efficiency of the learning process is tested in an assembly paradigm in which the humanoid robot ARoS learns to construct a toy vehicle from its parts. User demonstrations with different serial orders together with the correction of initial prediction errors allow the robot to acquire generalized task knowledge about possible serial orders and the longer term dependencies between subgoals in very few social learning interactions. This success is shown in a joint action scenario in which ARoS uses the newly acquired assembly plan to construct the toy together with a human partner. Copyright © 2015 Elsevier Ltd. All rights reserved.

Sequence learning in Parkinson's disease: Focusing on action dynamics and the role of dopaminergic medication.

PubMed

Ruitenberg, Marit F L; Duthoo, Wout; Santens, Patrick; Seidler, Rachael D; Notebaert, Wim; Abrahamse, Elger L

2016-12-01

Previous studies on movement sequence learning in Parkinson's disease (PD) have produced mixed results. A possible explanation for the inconsistent findings is that some studies have taken dopaminergic medication into account while others have not. Additionally, in previous studies the response modalities did not allow for an investigation of the action dynamics of sequential movements as they unfold over time. In the current study we investigated sequence learning in PD by specifically considering the role of medication status in a sequence learning task where mouse movements were performed. The focus on mouse movements allowed us to examine the action dynamics of sequential movement in terms of initiation time, movement time, movement accuracy, and velocity. PD patients performed the sequence learning task once on their regular medication, and once after overnight withdrawal from their medication. Results showed that sequence learning as reflected in initiation times was impaired when PD patients performed the task ON medication compared to OFF medication. In contrast, sequence learning as reflected in the accuracy of movement trajectories was enhanced when performing the task ON compared to OFF medication. Our findings suggest that while medication enhances execution processes of movement sequence learning, it may at the same time impair planning processes that precede actual execution. Overall, the current study extends earlier findings on movement sequence learning in PD by differentiating between various components of performance, and further refines previous dopamine overdose effects in sequence learning. Copyright © 2016 Elsevier Ltd. All rights reserved.

Complexation induced aggregation and deaggregation of acridine orange with sulfobutylether-β-cyclodextrin.

PubMed

Sayed, Mhejabeen; Jha, Shruti; Pal, Haridas

2017-09-13

The present study reports a contrasting interaction behaviour of a biologically important dye, acridine orange (AOH + ), with a highly water soluble anionic host, based on a β-cyclodextrin (βCD) scaffold, i.e. sulfobutylether-β-cyclodextrin (SBEβCD), in comparison to native βCD. AOH + shows striking modulation in its photophysical properties, representing sequential changes in the modes of interaction with increasing SBEβCD concentration. At lower SBEβCD concentrations, AOH + preferentially binds in dimeric forms at the negatively charged SBEβCD portals, leading to strong fluorescence quenching. At higher SBEβCD concentrations, the dimeric dyes convert to monomeric forms and subsequently undergo both inclusion and exo complex formation with 1 : 1 stoichiometry, resulting in a large fluorescence enhancement. The intriguing observation of sequential fluorescence switch off and switch on for an AOH + -SBEβCD system is clearly facilitated by the presence of butylether chains with SO 3 - end groups at the portals of SBEβCD, providing an additional ion-ion interaction and much enhanced hydrophobic interaction for cationic AOH + compared to the native βCD host. To the best of our knowledge, such fluorescence off/on switching through multistep host-guest binding has not been reported so far in the literature. The present study not only provides a detailed insight into the unique binding interactions of AOH + with the SBEβCD host, but the findings of this study are also expected to be useful in designing supramolecular based drug formulations, drug delivery systems, sensors, and so on.

Lower limb joint kinetics and ankle joint stiffness in the sprint start push-off.

PubMed

Charalambous, Laura; Irwin, Gareth; Bezodis, Ian N; Kerwin, David

2012-01-01

Sprint push-off technique is fundamental to sprint performance and joint stiffness has been identified as a performance-related variable during dynamic movements. However, joint stiffness for the push-off and its relationship with performance (times and velocities) has not been reported. The aim of this study was to quantify and explain lower limb net joint moments and mechanical powers, and ankle stiffness during the first stance phase of the push-off. One elite sprinter performed 10 maximal sprint starts. An automatic motion analysis system (CODA, 200 Hz) with synchronized force plates (Kistler, 1000 Hz) collected kinematic profiles at the hip, knee, and ankle and ground reaction forces, providing input for inverse dynamics analyses. The lower-limb joints predominately extended and revealed a proximal-to-distal sequential pattern of maximal extensor angular velocity and positive power production. Pearson correlations revealed relationships (P < 0.05) between ankle stiffness (5.93 ± 0.75 N x m x deg(-1)) and selected performance variables. Relationships between negative power phase ankle stiffness and horizontal (r = -0.79) and vertical (r = 0.74) centre of mass velocities were opposite in direction to the positive power phase ankle stiffness (horizontal: r = 0.85; vertical: r = -0.54). Thus ankle stiffness may affect the goals of the sprint push-off in different ways, depending on the phase of stance considered.

Synthesis of a novel magnetic Fe3O4/γ-Al2O3 hybrid composite using electrode-alternation technique for the removal of an azo dye

NASA Astrophysics Data System (ADS)

Jung, Kyung-Won; Choi, Brian Hyun; Ahn, Kyu-Hong; Lee, Sang-Hyup

2017-11-01

A novel magnetic adsorbent of Fe3O4/γ-Al2O3 hybrid composite (denoted as M-Fe/Al-H) was developed electrochemically via a sequential application of iron and aluminum electrodes in a one-pot fashion, which called here as electrode-alternation technique, followed by pyrolysis. Physical and chemical properties of the prepared adsorbents were characterized and their feasibility towards the removal of di-anionic azo dye Acid Black 1 (AB1) was assessed. Textural and structural characterization revealed that the prepared M-Fe/Al-H possesses superior properties than those of M-Fe (sole usage of iron electrode), which may improve the adsorption capacity. Kinetics revealed that the adsorption equilibrium was reached within 12 h with approximately 90% of the equilibrium adsorption capacity within the first 3 h. Comprehensive analysis using the pseudo-second order and intraparticle diffusion models indicated that the dominant mechanism of the reaction is film diffusion with intraparticle diffusion being the rate determining step. The adsorption equilibrium isotherm data were best represented by the Sips isotherm model, which found to be approximately 1501, 1786, and 1959 mg/g at 283, 293, and 303 K, respectively. The exceptional performance as well as its ease of separation allows M-Fe/Al-H to be a promising candidate as an effective for azo dye removal from various aqueous medium.

One-Dimensional Transport with Equilibrium Chemistry (OTEQ) - A Reactive Transport Model for Streams and Rivers

USGS Publications Warehouse

Runkel, Robert L.

2010-01-01

OTEQ is a mathematical simulation model used to characterize the fate and transport of waterborne solutes in streams and rivers. The model is formed by coupling a solute transport model with a chemical equilibrium submodel. The solute transport model is based on OTIS, a model that considers the physical processes of advection, dispersion, lateral inflow, and transient storage. The equilibrium submodel is based on MINTEQ, a model that considers the speciation and complexation of aqueous species, acid-base reactions, precipitation/dissolution, and sorption. Within OTEQ, reactions in the water column may result in the formation of solid phases (precipitates and sorbed species) that are subject to downstream transport and settling processes. Solid phases on the streambed may also interact with the water column through dissolution and sorption/desorption reactions. Consideration of both mobile (waterborne) and immobile (streambed) solid phases requires a unique set of governing differential equations and solution techniques that are developed herein. The partial differential equations describing physical transport and the algebraic equations describing chemical equilibria are coupled using the sequential iteration approach. The model's ability to simulate pH, precipitation/dissolution, and pH-dependent sorption provides a means of evaluating the complex interactions between instream chemistry and hydrologic transport at the field scale. This report details the development and application of OTEQ. Sections of the report describe model theory, input/output specifications, model applications, and installation instructions. OTEQ may be obtained over the Internet at http://water.usgs.gov/software/OTEQ.

Etching of moldavities under natural conditions

NASA Technical Reports Server (NTRS)

Knobloch, V.; Knoblochova, Z.; Urbanec, Z.

1983-01-01

The hypothesis that a part of the lechatellierites which originated by etching from a basic moldavite mass became broken off after deposition of moldavite in the sedimentation layer is advanced. Those found close to the original moldavite were measured for statistical averaging of length. The average length of lechatelierite fibers per cubic mm of moldavite mass volume was determined by measurement under a microscope in toluene. The data were used to calculate the depth of the moldavite layer that had to be etched to produce the corresponding amount of lechatelierite fragments. The calculations from five "fields" of moldavite surface, where layers of fixed lechatelierite fragments were preserved, produced values of 2.0, 3.1, 3.5, 3.9 and 4.5. Due to inadvertent loss of some fragments the determined values are somewhat lower than those found in references. The difference may be explained by the fact that the depth of the layer is only that caused by etching after moldavite deposition.

Fragmentation of Newtonian and viscoelastic liquids during rotary atomization

NASA Astrophysics Data System (ADS)

Keshavarz, Bavand; Moore, John; Houze, Eric; Koerner, Michael; McKinley, Gareth; MIT Collaboration; Axalta Coating Systems Collaboration

2015-11-01

Animals drying their wet fur by rapidly shaking their body and rotary atomization in paint coating are just a few examples in which centripetal acceleration is used to disintegrate liquid films into smaller fragments. Narrower size distributions and well-defined geometrical fluid pathlines (similar to the involute of a circle) are the main advantages of this type of atomization as compared to air-assisted atomization. Despite these inherent advantages there is a paucity of fundamental knowledge about the roles of fluid rheology in this process. We study the effects of viscosity by performing rotary atomization tests on silicone oils with a wide range of viscosities (1-1000 mPa.s). Viscoelastic effects are also probed by spraying solutions of polyethylene oxide (PEO) dissolved in water at different concentrations. Our results show that understanding the effects of liquid properties on the instabilities that control rotary atomization (primarily Rayleigh-Taylor instability during the ligament formation followed by Rayleigh-Plateau instability during droplet pinch-off) can help us understand the resulting fragment size distributions.

Monitoring variations of dimethyl sulfide and dimethylsulfoniopropionate in seawater and the atmosphere based on sequential vapor generation and ion molecule reaction mass spectrometry.

PubMed

Iyadomi, Satoshi; Ezoe, Kentaro; Ohira, Shin-Ichi; Toda, Kei

2016-04-01

To monitor the fluctuations of dimethyl sulfur compounds at the seawater/atmosphere interface, an automated system was developed based on sequential injection analysis coupled with vapor generation-ion molecule reaction mass spectrometry (SIA-VG-IMRMS). Using this analytical system, dissolved dimethyl sulfide (DMS(aq)) and dimethylsulfoniopropionate (DMSP), a precursor to DMS in seawater, were monitored together sequentially with atmospheric dimethyl sulfide (DMS(g)). A shift from the equilibrium point between DMS(aq) and DMS(g) results in the emission of DMS to the atmosphere. Atmospheric DMS emitted from seawater plays an important role as a source of cloud condensation nuclei, which influences the oceanic climate. Water samples were taken periodically and dissolved DMS(aq) was vaporized for analysis by IMRMS. After that, DMSP was hydrolyzed to DMS and acrylic acid, and analyzed in the same manner as DMS(aq). The vaporization behavior and hydrolysis of DMSP to DMS were investigated to optimize these conditions. Frequent (every 30 min) determination of the three components, DMS(aq)/DMSP (nanomolar) and DMS(g) (ppbv), was carried out by SIA-VG-IMRMS. Field analysis of the dimethyl sulfur compounds was undertaken at a coastal station, which succeeded in showing detailed variations of the compounds in a natural setting. Observed concentrations of the dimethyl sulfur compounds both in the atmosphere and seawater largely changed with time and similar variations were repeatedly observed over several days, suggesting diurnal variations in the DMS flux at the seawater/atmosphere interface.

Population structure and genetic diversity of black redhorse (Moxostoma duquesnei) in a highly fragmented watershed

USGS Publications Warehouse

Reid, S.M.; Wilson, C.C.; Mandrak, N.E.; Carl, L.M.

2008-01-01

Dams have the potential to affect population size and connectivity, reduce genetic diversity, and increase genetic differences among isolated riverine fish populations. Previous research has reported adverse effects on the distribution and demographics of black redhorse (Moxostoma duquesnei), a threatened fish species in Canada. However, effects on genetic diversity and population structure are unknown. We used microsatellite DNA markers to assess the number of genetic populations in the Grand River (Ontario) and to test whether dams have resulted in a loss of genetic diversity and increased genetic differentiation among populations. Three hundred and seventy-seven individuals from eight Grand River sites were genotyped at eight microsatellite loci. Measures of genetic diversity were moderately high and not significantly different among populations; strong evidence of recent population bottlenecks was not detected. Pairwise FST and exact tests identified weak (global FST = 0.011) but statistically significant population structure, although little population structuring was detected using either genetic distances or an individual-based clustering method. Neither geographic distance nor the number of intervening dams were correlated with pairwise differences among populations. Tests for regional equilibrium indicate that Grand River populations were either in equilibrium between gene flow and genetic drift or that gene flow is more influential than drift. While studies on other species have identified strong dam-related effects on genetic diversity and population structure, this study suggests that barrier permeability, river fragment length and the ecological characteristics of affected species can counterbalance dam-related effects. ?? 2007 Springer Science+Business Media B.V.

Phenomenological Partial Specific Volumes for G-Quadruplex DNAs

PubMed Central

Hellman, Lance M.; Rodgers, David W.; Fried, Michael G.

2009-01-01

Accurate partial specific volume (ν̄) values are required for sedimentation velocity and sedimentation equilibrium analyses. For nucleic acids, the estimation of these values is complicated by the fact that ν̄ depends on base composition, secondary structure, solvation and the concentrations and identities of ions in the surrounding buffer. Here we describe sedimentation equilibrium measurements of the apparent isopotential partial specific volume φ′ for two G-quadruplex DNAs and a single-stranded DNA of similar molecular weight and base composition. The G-quadruplex DNAs are a 22 nucleotide fragment of the human telomere consensus sequence and a 27 nucleotide fragment from the human c-myc promoter. The single-stranded DNA is 26 nucleotides long and is designed to have low propensity to form secondary structures. Parallel measurements were made in buffers containing NaCl and in buffers containing KCl, spanning the range 0.09M ≤ [salt] ≤ 2.3M. Limiting values of φ′, extrapolated to [salt] = 0M, were: 22-mer (NaCl-form), 0.525 ± 0.004 mL/g; 22-mer (KCl-form), 0.531 ± 0.006 mL/g; 27-mer (NaCl-form), 0.548 ± 0.005 mL/g; 27-mer (KCl-form), 0.557 ± 0.006 mL/g; 26-mer (NaCl-form), 0.555 ± 0.004 mL/g; 26-mer (KCl-form), 0.564 ± 0.006 mL/g. Small changes in φ′ with [salt] suggest that large changes in counterion association or hydration are unlikely to take place over these concentration ranges. PMID:19238377

From psychosocial equilibrium to catastrophic breakdown: Cyprus 1955-1974.

PubMed

Galatariotou, Catia

2008-08-01

The recent history of Cyprus presents an example of a society in which a centuries-long peaceful coexistence of diverse populations gave way to violence and murderous hate, with devastating end results. This paper tries to understand and describe the process by which Cypriot society slid from a position of psychosocial equilibrium and integration towards one of disintegration, fragmentation and catastrophic breakdown. This paper draws from work by social anthropologists, sociologists, historians and others, and from my own personal experience. To these I applied insights afforded by psychoanalysis to identify and explore the psychic processes and states of mind that characterized a psychosocial disintegrative process. I came to see external political events and internal psychological processes as inseparably intertwined and dynamically interdependent, each emanating from and catalysing the other. The factual details of the process described are of course unique in their local specificity, but the psychic phenomena that characterized it are not: at both the individual and group levels they are replicated in other societies undergoing similar processes of self-destruction.

Conformation-driven quantum interference effects mediated by through-space conjugation in self-assembled monolayers

NASA Astrophysics Data System (ADS)

Carlotti, Marco; Kovalchuk, Andrii; Wächter, Tobias; Qiu, Xinkai; Zharnikov, Michael; Chiechi, Ryan C.

2016-12-01

Tunnelling currents through tunnelling junctions comprising molecules with cross-conjugation are markedly lower than for their linearly conjugated analogues. This effect has been shown experimentally and theoretically to arise from destructive quantum interference, which is understood to be an intrinsic, electronic property of molecules. Here we show experimental evidence of conformation-driven interference effects by examining through-space conjugation in which π-conjugated fragments are arranged face-on or edge-on in sufficiently close proximity to interact through space. Observing these effects in the latter requires trapping molecules in a non-equilibrium conformation closely resembling the X-ray crystal structure, which we accomplish using self-assembled monolayers to construct bottom-up, large-area tunnelling junctions. In contrast, interference effects are completely absent in zero-bias simulations on the equilibrium, gas-phase conformation, establishing through-space conjugation as both of fundamental interest and as a potential tool for tuning tunnelling charge-transport in large-area, solid-state molecular-electronic devices.

Black Hole Firewalls and Lorentzian Relativity

NASA Astrophysics Data System (ADS)

Winterberg, Friedwardt

2013-04-01

In a paper published (Z. f. Naturforsch. 56a, 889, 2001) I had shown that the pre-Einstein theory of relativity by Lorentz and Poincare, extended to the general theory of relativity and quantum mechanics, predicts the disintegration of matter by passing through the event horizon. The zero point vacuum energy is there cut-off at the Planck energy, but Lorentz-invariant all the way up to this energy. The cut-off creates a distinguished reference system in which this energy is at rest. For non-relativistic velocities relative to this reference system, the special and general relativity remain a good approximations, with matter held together in a stable equilibrium by electrostatic forces (or forces acting like them) as a solution of an elliptic partial differential equation derived from Maxwell's equation. But in approaching and crossing the velocity of light in the distinguished reference system, which is equivalent in approaching and crossing of the event horizon, the elliptic differential equation goes over into a hyperbolic differential equation (as in fluid dynamics from subsonic to supersonic flow), and there is no such equilibrium. According to Schwarzschild's interior solution, the event horizon of a collapsing mass appears first as a point in its center, thereafter moving radially outwards, thereby converting all the mass into energy, explaining the observed gamma ray bursters.

Equilibrium configuration of a stratus floating above accretion disks: Full-disk calculation

NASA Astrophysics Data System (ADS)

Itanishi, Yusuke; Fukue, Jun

2017-06-01

We examine floating strati above a luminous accretion disk, supported by the radiative force from the entire disk, and calculate the equilibrium locus, which depends on the disk luminosity and the optical depth of the stratus. Due to the radiative transfer effect (albedo effect), the floating height of the stratus with a finite optical depth generally becomes high, compared with the particle case. In contrast to the case of the near-disk approximation, moreover, the floating height becomes yet higher in the present full-disk calculation, since the intense radiation from the inner disk is taken into account. As a result, when the disk luminosity normalized by the Eddington luminosity is ˜0.3 and the stratus optical depth is around unity, the stable configuration disappears at around r ˜ 50 rg, rg being the Schwarzschild radius, and the stratus would be blown off as a cloudy wind consisting of many strati with appropriate conditions. This luminosity is sufficiently smaller than the Eddington one, and the present results suggest that the radiation-driven cloudy wind can be easily blown off from the sub-Eddington disk, and this can explain various outflows observed in ultra-fast outflow objects as well as in broad-absorption-line quasars.

Influence of surface tension on the instabilities and bifurcations of a particle in a drop under shear

NASA Astrophysics Data System (ADS)

Gallaire, Francois; Zhu, Lailai

2016-11-01

While the deformation regimes under flow of anuclear cells, like red blood cells, have been widely analyzed, the dynamics of nuclear cells are less explored. The objective of this work is to investigate the interplay between the stiff nucleus, modeled here as a rigid spherical particle and the surrounding deformable cell membrane, modeled for simplicity as an immiscible droplet, subjected to an external unbounded plane shear flow. A three-dimensional boundary integral implementation is developed to describe the interface-structure interaction characterized by two dimensionless numbers: the capillary number Ca , defined as the ratio of shear to capillary forces and and the particle-droplet size ratio. For large Ca , i.e. very deformable droplets, the particle has a stable equilibrium position at the center of the droplet. However, for smaller Ca , both the plane symmetry and the time invariance are broken and the particle migrates to a closed orbit located off the symmetry plane, reaching a limit cycle. For even smaller capillary numbers, the time invariance is restored and the particle reaches a steady equilibrium position off the symmetry plane. This series of bifurcations is analyzed and possible physical mechanisms from which they originate are discussed. Financial support by ERC Grant SimCoMiCs 280117 is gratefully acknowledged.

Fragmentation pathways and structural characterization of organophosphorus compounds related to the Chemical Weapons Convention by electron ionization and electrospray ionization tandem mass spectrometry.

PubMed

Hosseini, Seyed Esmaeil; Saeidian, Hamid; Amozadeh, Ali; Naseri, Mohammad Taghi; Babri, Mehran

2016-12-30

For unambiguous identification of Chemical Weapons Convention (CWC)-related chemicals in environmental samples, the availability of mass spectra, interpretation skills and rapid microsynthesis of suspected chemicals are essential requirements. For the first time, the electron ionization single quadrupole and electrospray ionization tandem mass spectra of a series of O-alkyl N-[bis(dimethylamino)methylidene]-P-methylphosphonamidates (Scheme 1, cpd 4) were studied for CWC verification purposes. O-Alkyl N-[bis(dimethylamino)methylidene]-P-methylphosphonamidates were prepared through a microsynthetic method and were analyzed using electron ionization and electrospray ionization mass spectrometry with gas and liquid chromatography, respectively, as MS-inlet systems. General EI and ESI fragmentation pathways were proposed and discussed, and collision-induced dissociation studies of the protonated derivatives of these compounds were performed to confirm proposed fragment ion structures by analyzing mass spectra of deuterated analogs. Mass spectrometric studies revealed some interesting fragmentation pathways during the ionization process, such as McLafferty rearrangement, hydrogen rearrangement and a previously unknown intramolecular electrophilic aromatic substitution reaction. The EI and ESI fragmentation routes of the synthesized compounds 4 were investigated with the aim of detecting and identifying CWC-related chemicals during on-site inspection and/or off-site analysis and toxic chemical destruction monitoring. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Sedimentology of the Shangoluwe breccias and timing of the Cu mineralisation (Katanga Supergroup, D. R. of Congo)

NASA Astrophysics Data System (ADS)

Mambwe, Pascal; Kipata, Louis; Chabu, Mumba; Muchez, Philippe; Lubala, Toto; Jébrak, Michel; Delvaux, Damien

2017-08-01

The origin of breccias in the Neoproterozoic Katanga Supergroup in D.R of Congo is still a matter of debate. At the Shangoluwe Cu deposit located in the Kambove mining district (central part of the Lufilian arc), the sedimentary breccias bearing Cu mineralisation have been investigated for lithological and sedimentological study, quantitative analysis of the breccias fragments and fault kinematic analysis in order to understand the origin of the breccias, their lithostratigraphic position and the timing of mineralisation. At Shangoluwe, three sedimentary breccias sequentially deposited within the Kundelungu rocks can be identified on the basis of the nature of the matrix and fragments; from bottom to the top, the Ferruginous Breccias, the Dolomitic Breccias and the Siliceous Breccias. These breccias were deposited as lenses. The presence of debris and grain flows, a finely laminated matrix, pseudo-stratification, normal and reverse graded-bedding, and the presence of interbedded siltstone, sandy shale, dolomitic shale, shale and dolomite, are considered as evidence of a sedimentary origin of the breccias. The log normal distribution of the fragments indicates that gravity flow was the main deposition mechanism. The Ferruginous and Dolomitic Breccias are regarded as contemporaneous with the Kundelungu Group. They were deposited as lenses interbedded in the Kanianga and Mongwe formations, both affected by the Lufilian orogeny (D1 - Kolwezian and D2 - Monwezian phases). The Siliceous Breccias are post-orogenic as shown by the presence of an erosional and angular unconformity respectively on the Dolomitic Breccias and the Kundelungu formations. Therefore, the Siliceous Breccias are attributed to the Lower Palaeozoic Biano Subgroup and the lithostratigraphy of the Biano Subgroup is proposed for revision accordingly. Copper mineralisation post-dates the deposition of the breccias, the dissolution of dolomite fragments and in-situ fragmentation. This mineralisation occurred during late- to post-orogenic extension of the Lufilian orogeny, and was remobilised during the Cenozoic.

Growth Dynamics of the Threatened Caribbean Staghorn Coral Acropora cervicornis: Influence of Host Genotype, Symbiont Identity, Colony Size, and Environmental Setting

PubMed Central

Lirman, Diego; Schopmeyer, Stephanie; Galvan, Victor; Drury, Crawford; Baker, Andrew C.; Baums, Iliana B.

2014-01-01

Background The drastic decline in the abundance of Caribbean acroporid corals (Acropora cervicornis, A. palmata) has prompted the listing of this genus as threatened as well as the development of a regional propagation and restoration program. Using in situ underwater nurseries, we documented the influence of coral genotype and symbiont identity, colony size, and propagation method on the growth and branching patterns of staghorn corals in Florida and the Dominican Republic. Methodology/Principal Findings Individual tracking of> 1700 nursery-grown staghorn fragments and colonies from 37 distinct genotypes (identified using microsatellites) in Florida and the Dominican Republic revealed a significant positive relationship between size and growth, but a decreasing rate of productivity with increasing size. Pruning vigor (enhanced growth after fragmentation) was documented even in colonies that lost 95% of their coral tissue/skeleton, indicating that high productivity can be maintained within nurseries by sequentially fragmenting corals. A significant effect of coral genotype was documented for corals grown in a common-garden setting, with fast-growing genotypes growing up to an order of magnitude faster than slow-growing genotypes. Algal-symbiont identity established using qPCR techniques showed that clade A (likely Symbiodinium A3) was the dominant symbiont type for all coral genotypes, except for one coral genotype in the DR and two in Florida that were dominated by clade C, with A- and C-dominated genotypes having similar growth rates. Conclusion/Significance The threatened Caribbean staghorn coral is capable of extremely fast growth, with annual productivity rates exceeding 5 cm of new coral produced for every cm of existing coral. This species benefits from high fragment survivorship coupled by the pruning vigor experienced by the parent colonies after fragmentation. These life-history characteristics make A. cervicornis a successful candidate nursery species and provide optimism for the potential role that active propagation can play in the recovery of this keystone species. PMID:25268812

True ternary fission, the collinear cluster tripartition (CCT) of {sup 252}Cf

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

Oertzen, W. von; Pyatkov, Y. V.; Kamanin, D.

2012-10-20

In systematic work over the last decade (see Pyatkov et al. [12] and refs therein), the ternary fission decay of heavy nuclei, in {sup 235}U(n,fff) and {sup 252}Cf(sf) has been studied in a collinear geometry. The name used for this process is (CCT), with three fragments of similar size in a collinear decay, it is the true ternary fission. This decay has been observed in spontaneous fission as well as in a neutron induced reaction. The measurements are based on different experimental set-ups, with binary coincidences containing TOF and energy determinations. With two detector telescopes placed at 180 Degree-Sign ,more » the measurements of masses and energies of each of the registered two fragments, give complete kinematic solutions. Thus the missing mass events in binary coincidences can be determined, these events are obtained by blocking one of the lighter fragments on a structure in front of the detectors. The relatively high yield of CCT (more than 10{sup -3} per binary fission) is explained. It is due to the favourable Q-values (more positive than for binary) and the large phase space of the ternary CCT-decay, dominated by three (magic) clusters: e.g. isotopes of Sn, Ca and Ni, {sup 132}Sn+{sup 50}Ca+{sup 70}Ni. It is shown that the collinear (prolate) geometry has the favoured potential energy relative to the oblate shapes. The ternary fission is considered to be a sequential process. With this assumption the kinetic energies of the fragments have been calculated by Vijay et al.. The third fragments have very low kinetic energies (below 20 MeV) and have thus escaped their detection in previous work on 'ternary fission', where in addition an oblate shape and a triangle for the momentum vectors have been assumed.« less

Lithium formate ion clusters formation during electrospray ionization: Evidence of magic number clusters by mass spectrometry and ab initio calculations

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

Shukla, Anil, E-mail: Anil.Shukla@pnnl.gov; Bogdanov, Bogdan

2015-02-14

Small cationic and anionic clusters of lithium formate were generated by electrospray ionization and their fragmentations were studied by tandem mass spectrometry (collision-induced dissociation with N{sub 2}). Singly as well as multiply charged clusters were formed in both positive and negative ion modes with the general formulae, (HCOOLi){sub n}Li{sup +}, (HCOOLi){sub n}Li{sub m}{sup m+}, (HCOOLi){sub n}HCOO{sup −}, and (HCOOLi){sub n}(HCOO){sub m}{sup m−}. Several magic number cluster (MNC) ions were observed in both the positive and negative ion modes although more predominant in the positive ion mode with (HCOOLi){sub 3}Li{sup +} being the most abundant and stable cluster ion. Fragmentations ofmore » singly charged positive clusters proceed first by the loss of a dimer unit ((HCOOLi){sub 2}) followed by the loss of monomer units (HCOOLi) although the former remains the dominant dissociation process. In the case of positive cluster ions, all fragmentations lead to the magic cluster (HCOOLi){sub 3}Li{sup +} as the most abundant fragment ion at higher collision energies which then fragments further to dimer and monomer ions at lower abundances. In the negative ion mode, however, singly charged clusters dissociated via sequential loss of monomer units. Multiply charged clusters in both positive and negative ion modes dissociated mainly via Coulomb repulsion. Quantum chemical calculations performed for smaller cluster ions showed that the trimer ion has a closed ring structure similar to the phenalenylium structure with three closed rings connected to the central lithium ion. Further additions of monomer units result in similar symmetric structures for hexamer and nonamer cluster ions. Thermochemical calculations show that trimer cluster ion is relatively more stable than neighboring cluster ions, supporting the experimental observation of a magic number cluster with enhanced stability.« less

Adaptive Multi-Agent Systems for Constrained Optimization

NASA Technical Reports Server (NTRS)

Macready, William; Bieniawski, Stefan; Wolpert, David H.

2004-01-01

Product Distribution (PD) theory is a new framework for analyzing and controlling distributed systems. Here we demonstrate its use for distributed stochastic optimization. First we review one motivation of PD theory, as the information-theoretic extension of conventional full-rationality game theory to the case of bounded rational agents. In this extension the equilibrium of the game is the optimizer of a Lagrangian of the (probability distribution of) the joint state of the agents. When the game in question is a team game with constraints, that equilibrium optimizes the expected value of the team game utility, subject to those constraints. The updating of the Lagrange parameters in the Lagrangian can be viewed as a form of automated annealing, that focuses the MAS more and more on the optimal pure strategy. This provides a simple way to map the solution of any constrained optimization problem onto the equilibrium of a Multi-Agent System (MAS). We present computer experiments involving both the Queen s problem and K-SAT validating the predictions of PD theory and its use for off-the-shelf distributed adaptive optimization.

System-state and operating condition sensitive control method and apparatus for electric power delivery systems

NASA Technical Reports Server (NTRS)

Burns, III, William Wesley (Inventor); Wilson, Thomas George (Inventor)

1978-01-01

This invention provides a method and apparatus for determining a precise switching sequence for the power switching elements of electric power delivery systems of the on-off switching type and which enables extremely fast transient response, precise regulation and highly stable operation. The control utilizes the values of the power delivery system power handling network components, a desired output characteristic, a system timing parameter, and the externally imposed operating conditions to determine where steady state operations should be in order to yield desired output characteristics for the given system specifications. The actual state of the power delivery system is continuously monitored and compared to a state-space boundary which is derived from the desired equilibrium condition, and from the information obtained from this comparison, the system is moved to the desired equilibrium condition in one cycle of switching control. Since the controller continuously monitors the power delivery system's externally imposed operating conditions, a change in the conditions is immediately sensed and a new equilibrium condition is determined and achieved, again in a single cycle of switching control.

Punishment in a complementarity game

NASA Astrophysics Data System (ADS)

Li, W.; Cai, X.; Wang, Q. A.

2006-05-01

We study the effects arisen from the punishment in an evolutionary complementarity game. Each round one member of population “buyers” deals with a randomly chosen member of population “sellers”. When the buyer's offer is greater than the seller's, a deal is done and both players are rewarded by gaining some points. Otherwise the transaction is not successful and both will lose certain points as punishment. Our simulations indicate that the resulting equilibrium of the game with punishment embedded is remarkably time-delayed compared to the counterpart of the non-punishment game. However, the median fee and the success rate of deals at the equilibrium remain nearly unchanged in various cases of games with different degrees of punishment, whether severe or not. Symmetry, between the two populations, and the equilibrium value can still be maintained when the members of both of them are punished fairly in any failed transaction. If they are done in a different manner, namely, the members of one population are subject to very severe punishment whereas their opponents receive less or no punishment at all, the latter in most cases will be better off.

The use of autologous adult, allogenic juvenile, and combined juvenile-adult cartilage fragments for the repair of chondral defects.

PubMed

Bonasia, Davide Edoardo; Martin, James A; Marmotti, Antonio; Kurriger, Gail L; Lehman, Abigail D; Rossi, Roberto; Amendola, Annunziato

2016-12-01

The goal of the study was to evaluate the repair of chondral lesions treated with combined autologous adult/allogenic juvenile cartilage fragments, compared with isolated adult and isolated juvenile cartilage fragments. Fifty-eight adult (>16 week old) and five juvenile (<6 week old) New Zealand White female rabbits were used. A large osteochondral defect was created in the center of the femoral trochlea of adult rabbits. The rabbits were divided in four groups: Group 1 = untreated defects (controls); Group 2 = adult cartilage fragments; Group 3 = juvenile cartilage fragments; and Group 4 = adult + juvenile cartilage fragments. Killings were performed at 3 and 6 months. The defects were evaluated with ICRS macroscopic score, modified O'Driscoll score, and Collagen type II immunostaining. At 3 months, Group 4 performed better than Group 1, in terms of modified O'Driscoll score (p = 0.001) and Collagen type II immunostaining (p = 0.015). At 6 months, Group 4 showed higher modified O'Driscoll score (p = 0.003) and Collagen type II immunostaining score (p < 0.001) than Group 1. Histologically, also Group 3 performed better than Group 1 (p = 0.03), and Group 4 performed better than Group 2 (p = 0.004). Mixing adult and juvenile cartilage fragments improved cartilage repair in a rabbit model. In the clinical setting, a new "one-stage" procedure combining the two cartilage sources can be hypothesized, with the advantages of improved chondral repair and large defect coverage, because of the use of an off-the-shelf juvenile allograft. Further studies on larger animals and clinical trials are required to confirm these results.

Dimerized plasmin fragment D as a potential biomarker to predict successful catheter-directed thrombolysis therapy in acute deep vein thrombosis.

PubMed

Luo, Chien-Ming; Wu, I-Hui; Chan, Chih-Yang; Chen, Yih-Sharng; Yang, Wei-Shiung; Wang, Shoei-Shen

2015-10-01

The value of dimerized plasmin fragment D in the clinical monitoring during the catheter-directed thrombolysis in patients with acute deep vein thrombosis is not known. Dimerized plasmin fragment D levels in 24 patients with acute deep vein thrombosis undergoing catheter-directed thrombolysis were prospectively evaluated. The plasma dimerized plasmin fragment D level was measured serially before and at every 12 h during catheter-directed thrombolysis for 24 h. Technical success was defined as restoration of patency and flow with less than 50% residual thrombus by surveillance rotational venography. Technical success was achieved in 79.2% (19 of 24) of the treated limbs after catheter-directed thrombolysis. In univariate analysis, there was significant elevation of the dimerized plasmin fragment D at 12th h after starting the catheter-directed thrombolysis (P < 0.05) in patients with less than 50% residual thrombus stenosis. The optimal cut-off value of dimerized plasmin fragment D to predict successful catheter-directed thrombolysis was determined as 18.4 µg/ml at the 12th h after starting the catheter-directed thrombolysis with sensitivity 0.8 and specificity 0.8 (P = 0.03). It was further validated in multivariate logistic regression analysis (odds ratio: 14.38; 95% CI: 1.22-169.20; P = 0.03). Catheter-directed thrombolysis is safe and effective for restoration of blood flow in patients with acute deep vein thrombosis. Dimerized plasmin fragment D value greater than 18.4 µg/ml at the 12th h after starting catheter-directed thrombolysis had a high predictive rate of greater than 50% lysis at the end of catheter-directed thrombolysis. © The Author(s) 2014.

An endogenously produced fragment of cardiac myosin-binding protein C is pathogenic and can lead to heart failure.

PubMed

Razzaque, Md Abdur; Gupta, Manish; Osinska, Hanna; Gulick, James; Blaxall, Burns C; Robbins, Jeffrey

2013-08-16

A stable 40-kDa fragment is produced from cardiac myosin-binding protein C when the heart is stressed using a stimulus, such as ischemia-reperfusion injury. Elevated levels of the fragment can be detected in the diseased mouse and human heart, but its ability to interfere with normal cardiac function in the intact animal is unexplored. To understand the potential pathogenicity of the 40-kDa fragment in vivo and to investigate the molecular pathways that could be targeted for potential therapeutic intervention. We generated cardiac myocyte-specific transgenic mice using a Tet-Off inducible system to permit controlled expression of the 40-kDa fragment in cardiomyocytes. When expression of the 40-kDa protein is induced by crossing the responder animals with tetracycline transactivator mice under conditions in which substantial quantities approximating those observed in diseased hearts are reached, the double-transgenic mice subsequently experience development of sarcomere dysgenesis and altered cardiac geometry, and the heart fails between 12 and 17 weeks of age. The induced double-transgenic mice had development of cardiac hypertrophy with myofibrillar disarray and fibrosis, in addition to activation of pathogenic MEK-ERK pathways. Inhibition of MEK-ERK signaling was achieved by injection of the mitogen-activated protein kinase (MAPK)/ERK inhibitor U0126. The drug effectively improved cardiac function, normalized heart size, and increased probability of survival. These results suggest that the 40-kDa cardiac myosin-binding protein C fragment, which is produced at elevated levels during human cardiac disease, is a pathogenic fragment that is sufficient to cause hypertrophic cardiomyopathy and heart failure.

Mojibake – The rehearsal of word fragments in verbal recall

PubMed Central

Lange-Küttner, Christiane; Sykorova, Eva

2015-01-01

Theories of verbal rehearsal usually assume that whole words are being rehearsed. However, words consist of letter sequences, or syllables, or word onset-vowel-coda, amongst many other conceptualizations of word structure. A more general term is the ‘grain size’ of word units (Ziegler and Goswami, 2005). In the current study, a new method measured the quantitative percentage of correctly remembered word structure. The amount of letters in the correct letter sequence as per cent of word length was calculated, disregarding missing or added letters. A forced rehearsal was tested by repeating each memory list four times. We tested low frequency (LF) English words versus geographical (UK) town names to control for content. We also tested unfamiliar international (INT) non-words and names of international (INT) European towns to control for familiarity. An immediate versus distributed repetition was tested with a between-subject design. Participants responded with word fragments in their written recall especially when they had to remember unfamiliar words. While memory of whole words was sensitive to content, presentation distribution and individual sex and language differences, recall of word fragments was not. There was no trade-off between memory of word fragments with whole word recall during the repetition, instead also word fragments significantly increased. Moreover, while whole word responses correlated with each other during repetition, and word fragment responses correlated with each other during repetition, these two types of word recall responses were not correlated with each other. Thus there may be a lower layer consisting of free, sparse word fragments and an upper layer that consists of language-specific, orthographically and semantically constrained words. PMID:25941500

Durable complete responses off all treatment in patients with metastatic malignant melanoma after sequential immunotherapy followed by a finite course of BRAF inhibitor therapy

PubMed Central

Wyluda, Edward J; Cheng, Jihua; Schell, Todd D; Haley, Jeremy S; Mallon, Carol; Neves, Rogerio I; Robertson, Gavin; Sivik, Jeffrey; Mackley, Heath; Talamo, Giampaolo; Drabick, Joseph J

2015-01-01

We report 3 cases of durable complete response (CR) in patients with BRAF-mutated metastatic melanoma who were initially treated unsuccessfully with sequential immunotherapies (high dose interleukin 2 followed by ipilimumab with or without concurrent radiation therapy). After progression during or post immunotherapy, these patients were given BRAF inhibitor therapy and developed rapid CRs. Based on the concomitant presence of autoimmune manifestations (including vitiligo and hypophysitis), we postulated that there was a synergistic effect between the prior immune therapy and the BRAF targeting agents. Accordingly, the inhibitors were gradually weaned off beginning at 3 months and were stopped completely at 9–12 months. The three patients remain well and in CR off of all therapy at up to 15 months radiographic follow-up. The institution of the BRAF therapy was associated with development of severe rheumatoid-like arthritis in 2 patients which persisted for months after discontinuation of therapy, suggesting it was not merely a known toxicity of BRAF inhibitors (arthralgias). On immunologic analysis, these patients had high levels of non-T-regulatory, CD4 positive effector phenotype T-cells, which persisted after completion of therapy. Of note, we had previously reported a similar phenomenon in patients with metastatic melanoma who failed high dose interleukin-2 and were then placed on a finite course of temozolomide with rapid complete responses that have remained durable for many years after discontinuation of temozolomide. We postulate that a finite course of cytotoxic or targeted therapy specific for melanoma given after apparent failure of prior immunotherapy can result in complete and durable remissions that may persist long after the specific cytotoxic or targeted agents have been discontinued suggesting the existence of sequence specific synergism between immunotherapy and these agents. Here, we discuss these cases in the context of the literature on synergy between conventional or targeted cytotoxic therapy and immunotherapy in cancer treatment. PMID:25806780

Durable complete responses off all treatment in patients with metastatic malignant melanoma after sequential immunotherapy followed by a finite course of BRAF inhibitor therapy.

PubMed

Wyluda, Edward J; Cheng, Jihua; Schell, Todd D; Haley, Jeremy S; Mallon, Carol; Neves, Rogerio I; Robertson, Gavin; Sivik, Jeffrey; Mackley, Heath; Talamo, Giampaolo; Drabick, Joseph J

2015-01-01

We report 3 cases of durable complete response (CR) in patients with BRAF-mutated metastatic melanoma who were initially treated unsuccessfully with sequential immunotherapies (high dose interleukin 2 followed by ipilimumab with or without concurrent radiation therapy). After progression during or post immunotherapy, these patients were given BRAF inhibitor therapy and developed rapid CRs. Based on the concomitant presence of autoimmune manifestations (including vitiligo and hypophysitis), we postulated that there was a synergistic effect between the prior immune therapy and the BRAF targeting agents. Accordingly, the inhibitors were gradually weaned off beginning at 3 months and were stopped completely at 9-12 months. The three patients remain well and in CR off of all therapy at up to 15 months radiographic follow-up. The institution of the BRAF therapy was associated with development of severe rheumatoid-like arthritis in 2 patients which persisted for months after discontinuation of therapy, suggesting it was not merely a known toxicity of BRAF inhibitors (arthralgias). On immunologic analysis, these patients had high levels of non-T-regulatory, CD4 positive effector phenotype T-cells, which persisted after completion of therapy. Of note, we had previously reported a similar phenomenon in patients with metastatic melanoma who failed high dose interleukin-2 and were then placed on a finite course of temozolomide with rapid complete responses that have remained durable for many years after discontinuation of temozolomide. We postulate that a finite course of cytotoxic or targeted therapy specific for melanoma given after apparent failure of prior immunotherapy can result in complete and durable remissions that may persist long after the specific cytotoxic or targeted agents have been discontinued suggesting the existence of sequence specific synergism between immunotherapy and these agents. Here, we discuss these cases in the context of the literature on synergy between conventional or targeted cytotoxic therapy and immunotherapy in cancer treatment.

Gel-based supramolecular ON-OFF switch from aryl-triazolyl peptides with excellent chiro-optical, thixotropic, and self-healing characteristics.

PubMed

Srivastava, Bhartendu K; Muraleedharan, Kannoth M

2018-02-28

Systematic structure-property optimization of an achiral gelator (aryl-triazolyl homo dipeptide, 1.0) through a fragment replacement approach led to the identification of a new chiral system (aryl-triazolyl dipeptide 1.4 having leucine as the C-terminal residue) which exhibits consistent and perfectly reversible chiro-optical responses on sol-gel transition that can work like an ON-OFF switch. The gelator 1.4 could also direct the assembly of 1.0 in a sergeant-soldier mode to give similar CD responses. In addition, its gels are mouldable, self-healing and highly thixotropic, making it important from an application standpoint.

Feasibility of bioengineered two-stages sequential batch reactor and filtration-adsorption process for complex agrochemical effluent.

PubMed

Manekar, Pravin; Biswas, Rima; Urewar, Chaitali; Pal, Sukdeb; Nandy, Tapas

2013-11-01

In the present study, the feasibility of a bioengineered two-stages sequential batch reactor (BTSSBR) followed by filtration-adsorption process was investigated to treat the agrochemical effluent by overcoming factor affecting process stability such as microbial imbalance and substrate sensitivity. An air stripper stripped 90% of toxic ammonia, and combined with other streams for bio-oxidation and filtration-adsorption. The BTSSBR system achieved bio-oxidation at 6 days hydraulic retention time by fending off microbial imbalance and substrate sensitivity. The maximum reduction in COD and BOD by heterotrophic bacteria in the first reactor was 87% and 90%, respectively. Removal of toxic ammoniacal-nitrogen by autotrophic bacteria in a post-second stage bio-oxidation was 97%. The optimum filtration and adsorption of pollutants were achieved at a filtration rate of 10 and 9 m(3)m(-2)h(-1), respectively. The treatment scheme comprising air stripper, BTSSBR and filtration-adsorption process showed a great promise for treating the agrochemical effluent. Copyright © 2013 Elsevier Ltd. All rights reserved.

Controlled fragmentation of multimaterial fibres and films via polymer cold-drawing.

PubMed

Shabahang, Soroush; Tao, Guangming; Kaufman, Joshua J; Qiao, Yangyang; Wei, Lei; Bouchenot, Thomas; Gordon, Ali P; Fink, Yoel; Bai, Yuanli; Hoy, Robert S; Abouraddy, Ayman F

2016-06-23

Polymer cold-drawing is a process in which tensile stress reduces the diameter of a drawn fibre (or thickness of a drawn film) and orients the polymeric chains. Cold-drawing has long been used in industrial applications, including the production of flexible fibres with high tensile strength such as polyester and nylon. However, cold-drawing of a composite structure has been less studied. Here we show that in a multimaterial fibre composed of a brittle core embedded in a ductile polymer cladding, cold-drawing results in a surprising phenomenon: controllable and sequential fragmentation of the core to produce uniformly sized rods along metres of fibre, rather than the expected random or chaotic fragmentation. These embedded structures arise from mechanical-geometric instabilities associated with 'neck' propagation. Embedded, structured multimaterial threads with complex transverse geometry are thus fragmented into a periodic train of rods held stationary in the polymer cladding. These rods can then be easily extracted via selective dissolution of the cladding, or can self-heal by thermal restoration to re-form the brittle thread. Our method is also applicable to composites with flat rather than cylindrical geometries, in which case cold-drawing leads to the break-up of an embedded or coated brittle film into narrow parallel strips that are aligned normally to the drawing axis. A range of materials was explored to establish the universality of this effect, including silicon, germanium, gold, glasses, silk, polystyrene, biodegradable polymers and ice. We observe, and verify through nonlinear finite-element simulations, a linear relationship between the smallest transverse scale and the longitudinal break-up period. These results may lead to the development of dynamical and thermoreversible camouflaging via a nanoscale Venetian-blind effect, and the fabrication of large-area structured surfaces that facilitate high-sensitivity bio-detection.

From Flashes to Edges to Objects: Recovery of Local Edge Fragments Initiates Spatiotemporal Boundary Formation

PubMed Central

Erlikhman, Gennady; Kellman, Philip J.

2016-01-01

Spatiotemporal boundary formation (SBF) is the perception of illusory boundaries, global form, and global motion from spatially and temporally sparse transformations of texture elements (Shipley and Kellman, 1993a, 1994; Erlikhman and Kellman, 2015). It has been theorized that the visual system uses positions and times of element transformations to extract local oriented edge fragments, which then connect by known interpolation processes to produce larger contours and shapes in SBF. To test this theory, we created a novel display consisting of a sawtooth arrangement of elements that disappeared and reappeared sequentially. Although apparent motion along the sawtooth would be expected, with appropriate spacing and timing, the resulting percept was of a larger, moving, illusory bar. This display approximates the minimal conditions for visual perception of an oriented edge fragment from spatiotemporal information and confirms that such events may be initiating conditions in SBF. Using converging objective and subjective methods, experiments showed that edge formation in these displays was subject to a temporal integration constraint of ~80 ms between element disappearances. The experiments provide clear support for models of SBF that begin with extraction of local edge fragments, and they identify minimal conditions required for this process. We conjecture that these results reveal a link between spatiotemporal object perception and basic visual filtering. Motion energy filters have usually been studied with orientation given spatially by luminance contrast. When orientation is not given in static frames, these same motion energy filters serve as spatiotemporal edge filters, yielding local orientation from discrete element transformations over time. As numerous filters of different characteristic orientations and scales may respond to any simple SBF stimulus, we discuss the aperture and ambiguity problems that accompany this conjecture and how they might be resolved by the visual system. PMID:27445886

Controlled fragmentation of multimaterial fibres and films via polymer cold-drawing

NASA Astrophysics Data System (ADS)

Shabahang, Soroush; Tao, Guangming; Kaufman, Joshua J.; Qiao, Yangyang; Wei, Lei; Bouchenot, Thomas; Gordon, Ali P.; Fink, Yoel; Bai, Yuanli; Hoy, Robert S.; Abouraddy, Ayman F.

2016-06-01

Polymer cold-drawing is a process in which tensile stress reduces the diameter of a drawn fibre (or thickness of a drawn film) and orients the polymeric chains. Cold-drawing has long been used in industrial applications, including the production of flexible fibres with high tensile strength such as polyester and nylon. However, cold-drawing of a composite structure has been less studied. Here we show that in a multimaterial fibre composed of a brittle core embedded in a ductile polymer cladding, cold-drawing results in a surprising phenomenon: controllable and sequential fragmentation of the core to produce uniformly sized rods along metres of fibre, rather than the expected random or chaotic fragmentation. These embedded structures arise from mechanical-geometric instabilities associated with ‘neck’ propagation. Embedded, structured multimaterial threads with complex transverse geometry are thus fragmented into a periodic train of rods held stationary in the polymer cladding. These rods can then be easily extracted via selective dissolution of the cladding, or can self-heal by thermal restoration to re-form the brittle thread. Our method is also applicable to composites with flat rather than cylindrical geometries, in which case cold-drawing leads to the break-up of an embedded or coated brittle film into narrow parallel strips that are aligned normally to the drawing axis. A range of materials was explored to establish the universality of this effect, including silicon, germanium, gold, glasses, silk, polystyrene, biodegradable polymers and ice. We observe, and verify through nonlinear finite-element simulations, a linear relationship between the smallest transverse scale and the longitudinal break-up period. These results may lead to the development of dynamical and thermoreversible camouflaging via a nanoscale Venetian-blind effect, and the fabrication of large-area structured surfaces that facilitate high-sensitivity bio-detection.

Comparison of the Nanopulse Lithotripter to the Holmium Laser: Stone Fragmentation Efficiency and Impact on Flexible Ureteroscope Deflection and Flow.

PubMed

Kaplan, Adam G; Chen, Tony T; Sankin, Georgy; Yang, Chen; Dale, Joanne A; Simmons, W Neal; Zhong, Pei; Preminger, Glenn M; Lipkin, Michael Eric

2016-11-01

The Nanopulse Lithotripter (NPL; Lithotech Medical, Israel) is a novel intracorporeal device that uses a nanosecond duration electrical discharge through a reusable flexible coaxial probe to endoscopically fragment urinary stones. This device was compared with a holmium laser lithotripsy (HoL) with regard to stone fragmentation efficiency (SFE) and its impact on flexible ureteroscope (URS) deflection and flow of irrigation. Using a custom bench model, a 6 mm BegoStone cylindrical phantom (mixture 5:2) was confined under 0.9% saline atop sequential mesh sieves. The SFE of two NPL probe sizes (2.0F, 3.6F) and two HoL fibers (200, 365 μm) was evaluated using concordant settings of 1 J and 5 Hz. URS deflection and irrigation flow with NPL probes in the working channel were tested in five new fourth generation flexible URS and compared with other adjunct endourologic instruments. The 2.0F NPL showed improved SFE compared with the 200 μm laser (86 mg/min vs 52 mg/min, p = 0.014) as did the 3.6F NPL vs the 365 μm laser (173 mg/min vs 80 mg/min, p = 0.05). The NPL created more 1 to 2 mm fragments; the laser created more dust. URS deflection reduced by 3.75° with the 2.0 NPL probe. URS irrigation flow reduced from 36.5 to 6.3 mL/min with the 2.0F NPL probe. NPL shows improved SFE compared with HoL. Flow with the 2.0F probe is akin to a stone basket. NPL offers an effective alternative to HoL.

Mass spectrometric comparison of swift heavy ion-induced and anaerobic thermal degradation of polymers

NASA Astrophysics Data System (ADS)

Lima, V.; Hossain, U. H.; Walbert, T.; Seidl, T.; Ensinger, W.

2018-03-01

The study of polymers irradiated by highly energetic ions and the resulting radiation-induced degradation is of major importance for space and particle accelerator applications. The mechanism of ion-induced molecular fragmentation of polyethylene, polyethyleneimine and polyamide was investigated by means of mass spectrometry and infrared spectroscopy. The results show that the introduction of nitrogen and oxygen into the polymer influences the stability rendering aliphatic polymers with heteroatoms less stable. A comparison to thermal decomposition data from literature reveals that ion-induced degradation is different in its bond fracture mechanism. While thermal degradation starts at the weakest bond, which is usually the carbon-heteroatom bond, energetic ion irradiation leads in the first step to scission of all types of bonds creating smaller molecular fragments. This is due to the localized extreme energy input under non-equilibrium conditions when the ions transfer kinetic energy onto electrons. These findings are of relevance for the choice of polymers for long-term application in both space and accelerator facilities.

cgDNAweb: a web interface to the cgDNA sequence-dependent coarse-grain model of double-stranded DNA.

PubMed

De Bruin, Lennart; Maddocks, John H

2018-06-14

The sequence-dependent statistical mechanical properties of fragments of double-stranded DNA is believed to be pertinent to its biological function at length scales from a few base pairs (or bp) to a few hundreds of bp, e.g. indirect read-out protein binding sites, nucleosome positioning sequences, phased A-tracts, etc. In turn, the equilibrium statistical mechanics behaviour of DNA depends upon its ground state configuration, or minimum free energy shape, as well as on its fluctuations as governed by its stiffness (in an appropriate sense). We here present cgDNAweb, which provides browser-based interactive visualization of the sequence-dependent ground states of double-stranded DNA molecules, as predicted by the underlying cgDNA coarse-grain rigid-base model of fragments with arbitrary sequence. The cgDNAweb interface is specifically designed to facilitate comparison between ground state shapes of different sequences. The server is freely available at cgDNAweb.epfl.ch with no login requirement.

A recombinant dromedary antibody fragment (VHH or nanobody) directed against human Duffy antigen receptor for chemokines.

PubMed

Smolarek, Dorota; Hattab, Claude; Hassanzadeh-Ghassabeh, Gholamreza; Cochet, Sylvie; Gutiérrez, Carlos; de Brevern, Alexandre G; Udomsangpetch, Rachanee; Picot, Julien; Grodecka, Magdalena; Wasniowska, Kazimiera; Muyldermans, Serge; Colin, Yves; Le Van Kim, Caroline; Czerwinski, Marcin; Bertrand, Olivier

2010-10-01

Fy blood group antigens are carried by the Duffy antigen receptor for chemokines (DARC), a red cells receptor for Plasmodium vivax broadly implicated in human health and diseases. Recombinant VHHs, or nanobodies, the smallest intact antigen binding fragment derivative from the heavy chain-only antibodies present in camelids, were prepared from a dromedary immunized against DARC N-terminal extracellular domain and selected for DARC binding. A described VHH, CA52, does recognize native DARC on cells. It inhibits P. vivax invasion of erythrocytes and displaces interleukin-8 bound to DARC. The targeted epitope overlaps the well-defined DARC Fy6 epitope. K (D) of CA52-DARC equilibrium is sub-nanomolar, hence ideal to develop diagnostic or therapeutic compounds. Immunocapture by immobilized CA52 yielded highly purified DARC from engineered K562 cells. This first report on a VHH with specificity for a red blood cell protein exemplifies VHHs' potentialities to target, to purify, and to modulate the function of cellular markers.

Acanthamoeba castellanii contains a ribosomal RNA enhancer binding protein which stimulates TIF-IB binding and transcription under stringent conditions.

PubMed

Yang, Q; Radebaugh, C A; Kubaska, W; Geiss, G K; Paule, M R

1995-11-11

The intergenic spacer (IGS) of Acanthamoeba castellanii rRNA genes contains repeated elements which are weak enhancers for transcription by RNA polymerase I. A protein, EBF, was identified and partially purified which binds to the enhancers and to several other sequences within the IGS, but not to other DNA fragments, including the rRNA core promoter. No consensus binding sequence could be discerned in these fragments and bound factor is in rapid equilibrium with unbound. EBF has functional characteristics similar to vertebrate upstream binding factors (UBF). Not only does it bind to the enhancer and other IGS elements, but it also stimulates binding of TIF-IB, the fundamental transcription initiation factor, to the core promoter and stimulates transcription from the promoter. Attempts to identify polypeptides with epitopes similar to rat or Xenopus laevis UBF suggest that structurally the protein from A.castellanii is not closely related to vertebrate UBF.

Acanthamoeba castellanii contains a ribosomal RNA enhancer binding protein which stimulates TIF-IB binding and transcription under stringent conditions.

PubMed Central

Yang, Q; Radebaugh, C A; Kubaska, W; Geiss, G K; Paule, M R

1995-01-01

The intergenic spacer (IGS) of Acanthamoeba castellanii rRNA genes contains repeated elements which are weak enhancers for transcription by RNA polymerase I. A protein, EBF, was identified and partially purified which binds to the enhancers and to several other sequences within the IGS, but not to other DNA fragments, including the rRNA core promoter. No consensus binding sequence could be discerned in these fragments and bound factor is in rapid equilibrium with unbound. EBF has functional characteristics similar to vertebrate upstream binding factors (UBF). Not only does it bind to the enhancer and other IGS elements, but it also stimulates binding of TIF-IB, the fundamental transcription initiation factor, to the core promoter and stimulates transcription from the promoter. Attempts to identify polypeptides with epitopes similar to rat or Xenopus laevis UBF suggest that structurally the protein from A.castellanii is not closely related to vertebrate UBF. Images PMID:7501455

First assembly times and equilibration in stochastic coagulation-fragmentation

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

D’Orsogna, Maria R.; Department of Mathematics, CSUN, Los Angeles, California 91330-8313; Lei, Qi

2015-07-07

We develop a fully stochastic theory for coagulation and fragmentation (CF) in a finite system with a maximum cluster size constraint. The process is modeled using a high-dimensional master equation for the probabilities of cluster configurations. For certain realizations of total mass and maximum cluster sizes, we find exact analytical results for the expected equilibrium cluster distributions. If coagulation is fast relative to fragmentation and if the total system mass is indivisible by the mass of the largest allowed cluster, we find a mean cluster-size distribution that is strikingly broader than that predicted by the corresponding mass-action equations. Combinations ofmore » total mass and maximum cluster size under which equilibration is accelerated, eluding late-stage coarsening, are also delineated. Finally, we compute the mean time it takes particles to first assemble into a maximum-sized cluster. Through careful state-space enumeration, the scaling of mean assembly times is derived for all combinations of total mass and maximum cluster size. We find that CF accelerates assembly relative to monomer kinetic only in special cases. All of our results hold in the infinite system limit and can be only derived from a high-dimensional discrete stochastic model, highlighting how classical mass-action models of self-assembly can fail.« less

Increased Antibody Affinity Confers Broad In Vitro Protection against Escape Mutants of Severe Acute Respiratory Syndrome Coronavirus

PubMed Central

Rani, Mridula; Bolles, Meagan; Donaldson, Eric F.; Van Blarcom, Thomas; Baric, Ralph; Iverson, Brent

2012-01-01

Even though the effect of antibody affinity on neutralization potency is well documented, surprisingly, its impact on neutralization breadth and escape has not been systematically determined. Here, random mutagenesis and DNA shuffling of the single-chain variable fragment of the neutralizing antibody 80R followed by bacterial display screening using anchored periplasmic expression (APEx) were used to generate a number of higher-affinity variants of the severe acute respiratory syndrome coronavirus (SARS-CoV)-neutralizing antibody 80R with equilibrium dissociation constants (KD) as low as 37 pM, a >270-fold improvement relative to that of the parental 80R single-chain variable fragment (scFv). As expected, antigen affinity was shown to correlate directly with neutralization potency toward the icUrbani strain of SARS-CoV. Additionally, the highest-affinity antibody fragment displayed 10-fold-increased broad neutralization in vitro and completely protected against several SARS-CoV strains containing substitutions associated with antibody escape. Importantly, higher affinity also led to the suppression of viral escape mutants in vitro. Escape from the highest-affinity variant required reduced selective pressure and multiple substitutions in the binding epitope. Collectively, these results support the hypothesis that engineered antibodies with picomolar dissociation constants for a neutralizing epitope can confer escape-resistant protection. PMID:22696652

Diverse Metals and Sulfides in Polymict Ureilites EET 83309 and EET 87720

NASA Technical Reports Server (NTRS)

Herrin, J. S.; Mittlefehldt, D. W.; Downes, H.; Humayun, M.

2007-01-01

Ureilites are a group of carbon-bearing ultramafic achondrites. The majority of samples are monomict with major and trace element compositions consistent with a restitic origin after extensive loss of basaltic melts and significant loss of their metallic component during anatexis. Monomict ureilites are thought to represent largely intact samples of the ureilite parent body (UPB) mantle. Polymict ureilites, by contrast, are fragmental breccias consisting of welded lithic clasts and isolated mineral fragments thought to be regolith that assembled after major disruption fragmented large portions of the UPB mantle. In most polymict ureilites, the majority of clasts consist of material similar to monomict ureilites gardened from the UPB mantle but other materials, both endogenic and xenogenic to the UPB are also found in polymict ureilites, including clasts texturally and compositionally similar to known chondrite types as well as feldspathic melt rocks and clasts of Ca-Al-Ti-rich assemblages. In this study, we demonstrate that polymict ureilites also contain a variety of metal and sulfide compositions of diverse origins. They offer insight into the final equilibrium conditions of disrupted portions of the UPB mantle and the diversity of materials locally available for regolith formation, and provide evidence for only limited post-regolith formation thermal metamorphism.